From a4f48bb24e4b0bd379a89914aa9e5c560a7274af Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Tue, 29 Aug 2023 09:55:08 +0200 Subject: [PATCH 001/107] Add CI Added static linting, type checking for each commit as well as pytest testing for each master push. Add linting and static analysis CI Use deprecated pipeline key for server woodpecker version Format black Install poetry environment before pyright Add pytest CI Update dependencies, Fix black Ensure tests run on master branch --- .woodpecker/lint.yml | 16 +++++ .woodpecker/static_analysis.yml | 9 +++ .woodpecker/test.yml | 10 +++ README.md | 21 +++++- papis_extract/extractor.py | 14 ++-- poetry.lock | 111 ++++++++++++++++++++++++-------- pyproject.toml | 4 ++ tests/test_annotation.py | 7 ++ 8 files changed, 157 insertions(+), 35 deletions(-) create mode 100644 .woodpecker/lint.yml create mode 100644 .woodpecker/static_analysis.yml create mode 100644 .woodpecker/test.yml create mode 100644 tests/test_annotation.py diff --git a/.woodpecker/lint.yml b/.woodpecker/lint.yml new file mode 100644 index 0000000..eb67dbe --- /dev/null +++ b/.woodpecker/lint.yml @@ -0,0 +1,16 @@ +pipeline: + lint_ruff: + image: python + commands: + - pip install ruff + - python --version && poetry --version && ruff --version + - echo "----------------- running ruff lint ------------------" + - ruff check . + + lint_black: + image: python + commands: + - pip install black + - python --version && poetry --version && black --version + - echo "----------------- running black lint ----------------" + - black --check . diff --git a/.woodpecker/static_analysis.yml b/.woodpecker/static_analysis.yml new file mode 100644 index 0000000..3506c5c --- /dev/null +++ b/.woodpecker/static_analysis.yml @@ -0,0 +1,9 @@ +pipeline: + pyright: + image: ghcr.io/withlogicco/poetry:1.5.1 + commands: + - pip install pyright + - poetry install + - python --version && poetry --version && pyright --version + - echo "------------- running pyright typecheck -------------" + - poetry run pyright diff --git a/.woodpecker/test.yml b/.woodpecker/test.yml new file mode 100644 index 0000000..44e264d --- /dev/null +++ b/.woodpecker/test.yml @@ -0,0 +1,10 @@ +branches: master + +pipeline: + pytest: + image: ghcr.io/withlogicco/poetry:1.5.1 + commands: + - poetry install + - python --version && poetry --version + - echo "------------- running pytest -------------" + - poetry run pytest diff --git a/README.md b/README.md index b403962..8aa6b5b 100644 --- a/README.md +++ b/README.md @@ -173,12 +173,22 @@ Known issues to be fixed: - [x] if both content and text are empty, do not extract an annotation - [x] Speed? - should be fine, on my machine (old i5 laptop) it takes around 90s for ~1000 documents with ~4000 annotations -- [ ] ensure all cmdline options do what they should +- [x] ensure all cmdline options do what they should +- [ ] annotations carry over color object from fitz, should just be Color object or simple tuple with rgb vals +- [ ] docstrings, docstrings! +- [ ] testing testing testing!! + - [ ] refactor into some better abstractions (e.g. Exporter Protocol -> stdout/markdown implementations; Extractor Protocol -> PDF implementation) features to be implemented: +- [ ] CICD + - [x] static analysis (lint, typecheck etc) on pushes + - [ ] test pipeline on master pushes + - [ ] release pipeline to pypi on tags - [ ] on_add hook to extract annotations as files are added + - needs upstream help, 'on_add' hook, and pass-through of affected documents - [ ] add page number if available + - exists in Annotation, just need to place in output - [ ] show overall amount of extractions at the end - [ ] custom formatting decided by user - [ ] improved default exporters @@ -186,7 +196,14 @@ features to be implemented: - pretty display on stdout (rich?) - csv/tsv to stdout - table fmt stdout? -- [ ] arbitrary color -> name settings not dependent on color name existing +- [ ] allow custom colors -> tag name settings not dependent on color name existing (e.g. {"important": (1.0,0.0,0.0)}) +- [ ] `--overwrite` mode where existing annotations are not dropped but overwritten on same line of note +- [ ] `--force` mode where we simply do not drop anything + +upstream changes: + +- [ ] need a hook for adding a document/file +- [ ] need hooks to actually pass through information on the thing they worked on (i.e. their document) ## Issues diff --git a/papis_extract/extractor.py b/papis_extract/extractor.py index 9467231..88ff012 100644 --- a/papis_extract/extractor.py +++ b/papis_extract/extractor.py @@ -42,7 +42,7 @@ def start(filename: Path) -> list[Annotation]: def _tag_from_colorname(colorname: str) -> str: - color_mapping: dict[str,str] = getdict("tags", "plugins.extract") + color_mapping: dict[str, str] = getdict("tags", "plugins.extract") if not color_mapping: return "" @@ -82,6 +82,7 @@ def _retrieve_annotation_content( # just a highlight without any text return (None, None) + # mimics the functions in papis.config.{getlist,getint,getfloat} etc. def getdict(key: str, section: Optional[str] = None) -> dict[str, str]: """Dict getter @@ -97,13 +98,14 @@ def getdict(key: str, section: Optional[str] = None) -> dict[str, str]: rawvalue = eval(rawvalue) except Exception: raise SyntaxError( - "The key '{}' must be a valid Python object: {}" - .format(key, rawvalue)) + "The key '{}' must be a valid Python object: {}".format(key, rawvalue) + ) else: if not isinstance(rawvalue, dict): raise SyntaxError( - "The key '{}' must be a valid Python dict. Got: {} (type {!r})" - .format(key, rawvalue, type(rawvalue).__name__)) + "The key '{}' must be a valid Python dict. Got: {} (type {!r})".format( + key, rawvalue, type(rawvalue).__name__ + ) + ) return rawvalue - diff --git a/poetry.lock b/poetry.lock index e225e20..8d6734d 100644 --- a/poetry.lock +++ b/poetry.lock @@ -224,6 +224,17 @@ files = [ {file = "idna-3.4.tar.gz", hash = "sha256:814f528e8dead7d329833b91c5faa87d60bf71824cd12a7530b5526063d02cb4"}, ] +[[package]] +name = "iniconfig" +version = "2.0.0" +description = "brain-dead simple config-ini parsing" +optional = false +python-versions = ">=3.7" +files = [ + {file = "iniconfig-2.0.0-py3-none-any.whl", hash = "sha256:b6a85871a79d2e3b22d2d1b94ac2824226a63c6b741c88f7ae975f18b6778374"}, + {file = "iniconfig-2.0.0.tar.gz", hash = "sha256:2d91e135bf72d31a410b17c16da610a82cb55f6b0477d1a902134b24a455b8b3"}, +] + [[package]] name = "isbnlib" version = "3.10.14" @@ -456,6 +467,17 @@ html5 = ["html5lib"] htmlsoup = ["BeautifulSoup4"] source = ["Cython (>=0.29.35)"] +[[package]] +name = "packaging" +version = "23.1" +description = "Core utilities for Python packages" +optional = false +python-versions = ">=3.7" +files = [ + {file = "packaging-23.1-py3-none-any.whl", hash = "sha256:994793af429502c4ea2ebf6bf664629d07c1a9fe974af92966e4b8d2df7edc61"}, + {file = "packaging-23.1.tar.gz", hash = "sha256:a392980d2b6cffa644431898be54b0045151319d1e7ec34f0cfed48767dd334f"}, +] + [[package]] name = "papis" version = "0.13" @@ -504,6 +526,21 @@ files = [ {file = "pbr-5.11.1.tar.gz", hash = "sha256:aefc51675b0b533d56bb5fd1c8c6c0522fe31896679882e1c4c63d5e4a0fccb3"}, ] +[[package]] +name = "pluggy" +version = "1.3.0" +description = "plugin and hook calling mechanisms for python" +optional = false +python-versions = ">=3.8" +files = [ + {file = "pluggy-1.3.0-py3-none-any.whl", hash = "sha256:d89c696a773f8bd377d18e5ecda92b7a3793cbe66c87060a6fb58c7b6e1061f7"}, + {file = "pluggy-1.3.0.tar.gz", hash = "sha256:cf61ae8f126ac6f7c451172cf30e3e43d3ca77615509771b3a984a0730651e12"}, +] + +[package.extras] +dev = ["pre-commit", "tox"] +testing = ["pytest", 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"sha256:b4bf8c45bd59934ed84001ad51e11b4ee40d40a1229d2c79f9c592b0a3f6bd8a"}, +] + +[package.dependencies] +colorama = {version = "*", markers = "sys_platform == \"win32\""} +iniconfig = "*" +packaging = "*" +pluggy = ">=0.12,<2.0" + +[package.extras] +testing = ["argcomplete", "attrs (>=19.2.0)", "hypothesis (>=3.56)", "mock", "nose", "pygments (>=2.7.2)", "requests", "setuptools", "xmlschema"] + [[package]] name = "python-doi" version = "0.2.0" @@ -923,4 +980,4 @@ files = [ [metadata] lock-version = "2.0" python-versions = "^3.11" -content-hash = "2e158747df6100e105c98494d8b5f4b23b7076ae76295ce7a28facf02488ebd5" +content-hash = "d519605837788792d06ffc7bca7a92b315612ca6052227c53c558ec49dffec9f" diff --git a/pyproject.toml b/pyproject.toml index 8ee3741..4ca3257 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -18,6 +18,10 @@ python-magic = "^0.4.27" [tool.poetry.plugins."papis.command"] extract = "papis_extract:main" + +[tool.poetry.group.dev.dependencies] +pytest = "^7.4.0" + [build-system] requires = ["poetry-core"] build-backend = "poetry.core.masonry.api" diff --git a/tests/test_annotation.py b/tests/test_annotation.py new file mode 100644 index 0000000..72c7a75 --- /dev/null +++ b/tests/test_annotation.py @@ -0,0 +1,7 @@ +from papis_extract.annotation_data import Annotation + + +def test_matches_colorname_exact(): + sut = Annotation("testfile", colors={"stroke": (1.0, 0.0, 0.0)}) + c_name = sut.colorname + assert c_name == "red" From 85f3d9595ddc5b5080ba51cf7cb71bfccf6db8f2 Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Tue, 29 Aug 2023 11:07:53 +0200 Subject: [PATCH 002/107] Update documentation for CI and release info --- README.md | 21 +++++++++++++-------- 1 file changed, 13 insertions(+), 8 deletions(-) diff --git a/README.md b/README.md index 8aa6b5b..d2d1574 100644 --- a/README.md +++ b/README.md @@ -1,8 +1,8 @@ # papis-extract - Quickly extract annotations from your pdf files with the help of the [papis](https://github.com/papis/papis) bibliography manager.\ @@ -11,11 +11,14 @@ Easily organize all your highlights and thoughts next to your documents and refe ## Installation: -You can install from pypi with `pip install git+`. +You can install from pypi with `pip install git+https://git.martyoeh.me/Marty/papis-extract.git`. That's it! If you have papis and papis-extract installed in the same environment (whether virtual or global), everything should now be set up. +I am currently working towards the first release for pypi, see the below roadmap; +when that is done you will also be able to install in the usual pypi way. + To check if everything is working you should now see the `extract` command listed when running `papis --help`. You will be set up with the default options but if you want to change anything, read on in configuration below. @@ -166,7 +169,7 @@ The option should generally not take too much tuning, but it is there if you nee This should generally be an alright default but is here to be changed for example if you work with a lot of different annotation colors (where dark purple and light purple may different meanings) and get false positives in automatic tag recognition, or no tags are recognized at all. -## Roadmap +## Roadmap to first release Known issues to be fixed: @@ -183,14 +186,13 @@ features to be implemented: - [ ] CICD - [x] static analysis (lint, typecheck etc) on pushes - - [ ] test pipeline on master pushes + - [x] test pipeline on master pushes - [ ] release pipeline to pypi on tags -- [ ] on_add hook to extract annotations as files are added - - needs upstream help, 'on_add' hook, and pass-through of affected documents - [ ] add page number if available - exists in Annotation, just need to place in output - [ ] show overall amount of extractions at the end - [ ] custom formatting decided by user + - in config as { "myformatter": ">{tag}\n{quote}\n{note}\n{page} etc"} - [ ] improved default exporters - markdown into notes - pretty display on stdout (rich?) @@ -199,6 +201,9 @@ features to be implemented: - [ ] allow custom colors -> tag name settings not dependent on color name existing (e.g. {"important": (1.0,0.0,0.0)}) - [ ] `--overwrite` mode where existing annotations are not dropped but overwritten on same line of note - [ ] `--force` mode where we simply do not drop anything +- [ ] `--format` option to choose from default or set up a custom formatter +- [ ] on_add hook to extract annotations as files are added + - needs upstream help, 'on_add' hook, and pass-through of affected documents upstream changes: From eff29a574b7358278d09e0c080cf8aeab864bbb5 Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Tue, 29 Aug 2023 11:40:19 +0200 Subject: [PATCH 003/107] Switch to node image for pyright --- .woodpecker/static_analysis.yml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/.woodpecker/static_analysis.yml b/.woodpecker/static_analysis.yml index 3506c5c..248f0f4 100644 --- a/.woodpecker/static_analysis.yml +++ b/.woodpecker/static_analysis.yml @@ -1,8 +1,9 @@ pipeline: pyright: - image: ghcr.io/withlogicco/poetry:1.5.1 + image: node commands: - - pip install pyright + - apt-get update && apt-get --yes install python3-poetry + - npm install --global pyright - poetry install - python --version && poetry --version && pyright --version - echo "------------- running pyright typecheck -------------" From 3f6bae260d08b307da9f1565cc0443ae92c5601b Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Tue, 29 Aug 2023 12:07:45 +0200 Subject: [PATCH 004/107] Switch to node-python image --- .woodpecker/static_analysis.yml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/.woodpecker/static_analysis.yml b/.woodpecker/static_analysis.yml index 248f0f4..786af22 100644 --- a/.woodpecker/static_analysis.yml +++ b/.woodpecker/static_analysis.yml @@ -1,8 +1,7 @@ pipeline: pyright: - image: node + image: nikolaik/python-nodejs commands: - - apt-get update && apt-get --yes install python3-poetry - npm install --global pyright - poetry install - python --version && poetry --version && pyright --version From b564ab479237a6fecc9a4859b2c69161fc524fae Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Tue, 29 Aug 2023 12:15:10 +0200 Subject: [PATCH 005/107] Add continuous integration pipeline Added static analysis (lint, type checking) to be done on each push, and testing to be done on each master branch commit. --- .woodpecker/lint.yml | 16 +++++ .woodpecker/static_analysis.yml | 9 +++ .woodpecker/test.yml | 10 +++ README.md | 38 ++++++++--- papis_extract/extractor.py | 14 ++-- poetry.lock | 111 ++++++++++++++++++++++++-------- pyproject.toml | 4 ++ tests/test_annotation.py | 7 ++ 8 files changed, 168 insertions(+), 41 deletions(-) create mode 100644 .woodpecker/lint.yml create mode 100644 .woodpecker/static_analysis.yml create mode 100644 .woodpecker/test.yml create mode 100644 tests/test_annotation.py diff --git a/.woodpecker/lint.yml b/.woodpecker/lint.yml new file mode 100644 index 0000000..eb67dbe --- /dev/null +++ b/.woodpecker/lint.yml @@ -0,0 +1,16 @@ +pipeline: + lint_ruff: + image: python + commands: + - pip install ruff + - python --version && poetry --version && ruff --version + - echo "----------------- running ruff lint ------------------" + - ruff check . + + lint_black: + image: python + commands: + - pip install black + - python --version && poetry --version && black --version + - echo "----------------- running black lint ----------------" + - black --check . diff --git a/.woodpecker/static_analysis.yml b/.woodpecker/static_analysis.yml new file mode 100644 index 0000000..786af22 --- /dev/null +++ b/.woodpecker/static_analysis.yml @@ -0,0 +1,9 @@ +pipeline: + pyright: + image: nikolaik/python-nodejs + commands: + - npm install --global pyright + - poetry install + - python --version && poetry --version && pyright --version + - echo "------------- running pyright typecheck -------------" + - poetry run pyright diff --git a/.woodpecker/test.yml b/.woodpecker/test.yml new file mode 100644 index 0000000..44e264d --- /dev/null +++ b/.woodpecker/test.yml @@ -0,0 +1,10 @@ +branches: master + +pipeline: + pytest: + image: ghcr.io/withlogicco/poetry:1.5.1 + commands: + - poetry install + - python --version && poetry --version + - echo "------------- running pytest -------------" + - poetry run pytest diff --git a/README.md b/README.md index b403962..d2d1574 100644 --- a/README.md +++ b/README.md @@ -1,8 +1,8 @@ # papis-extract - Quickly extract annotations from your pdf files with the help of the [papis](https://github.com/papis/papis) bibliography manager.\ @@ -11,11 +11,14 @@ Easily organize all your highlights and thoughts next to your documents and refe ## Installation: -You can install from pypi with `pip install git+`. +You can install from pypi with `pip install git+https://git.martyoeh.me/Marty/papis-extract.git`. That's it! If you have papis and papis-extract installed in the same environment (whether virtual or global), everything should now be set up. +I am currently working towards the first release for pypi, see the below roadmap; +when that is done you will also be able to install in the usual pypi way. + To check if everything is working you should now see the `extract` command listed when running `papis --help`. You will be set up with the default options but if you want to change anything, read on in configuration below. @@ -166,27 +169,46 @@ The option should generally not take too much tuning, but it is there if you nee This should generally be an alright default but is here to be changed for example if you work with a lot of different annotation colors (where dark purple and light purple may different meanings) and get false positives in automatic tag recognition, or no tags are recognized at all. -## Roadmap +## Roadmap to first release Known issues to be fixed: - [x] if both content and text are empty, do not extract an annotation - [x] Speed? - should be fine, on my machine (old i5 laptop) it takes around 90s for ~1000 documents with ~4000 annotations -- [ ] ensure all cmdline options do what they should +- [x] ensure all cmdline options do what they should +- [ ] annotations carry over color object from fitz, should just be Color object or simple tuple with rgb vals +- [ ] docstrings, docstrings! +- [ ] testing testing testing!! + - [ ] refactor into some better abstractions (e.g. Exporter Protocol -> stdout/markdown implementations; Extractor Protocol -> PDF implementation) features to be implemented: -- [ ] on_add hook to extract annotations as files are added +- [ ] CICD + - [x] static analysis (lint, typecheck etc) on pushes + - [x] test pipeline on master pushes + - [ ] release pipeline to pypi on tags - [ ] add page number if available + - exists in Annotation, just need to place in output - [ ] show overall amount of extractions at the end - [ ] custom formatting decided by user + - in config as { "myformatter": ">{tag}\n{quote}\n{note}\n{page} etc"} - [ ] improved default exporters - markdown into notes - pretty display on stdout (rich?) - csv/tsv to stdout - table fmt stdout? -- [ ] arbitrary color -> name settings not dependent on color name existing +- [ ] allow custom colors -> tag name settings not dependent on color name existing (e.g. {"important": (1.0,0.0,0.0)}) +- [ ] `--overwrite` mode where existing annotations are not dropped but overwritten on same line of note +- [ ] `--force` mode where we simply do not drop anything +- [ ] `--format` option to choose from default or set up a custom formatter +- [ ] on_add hook to extract annotations as files are added + - needs upstream help, 'on_add' hook, and pass-through of affected documents + +upstream changes: + +- [ ] need a hook for adding a document/file +- [ ] need hooks to actually pass through information on the thing they worked on (i.e. their document) ## Issues diff --git a/papis_extract/extractor.py b/papis_extract/extractor.py index 9467231..88ff012 100644 --- a/papis_extract/extractor.py +++ b/papis_extract/extractor.py @@ -42,7 +42,7 @@ def start(filename: Path) -> list[Annotation]: def _tag_from_colorname(colorname: str) -> str: - color_mapping: dict[str,str] = getdict("tags", "plugins.extract") + color_mapping: dict[str, str] = getdict("tags", "plugins.extract") if not color_mapping: return "" @@ -82,6 +82,7 @@ def _retrieve_annotation_content( # just a highlight without any text return (None, None) + # mimics the functions in papis.config.{getlist,getint,getfloat} etc. def getdict(key: str, section: Optional[str] = None) -> dict[str, str]: """Dict getter @@ -97,13 +98,14 @@ def getdict(key: str, section: Optional[str] = None) -> dict[str, str]: rawvalue = eval(rawvalue) except Exception: raise SyntaxError( - "The key '{}' must be a valid Python object: {}" - .format(key, rawvalue)) + "The key '{}' must be a valid Python object: {}".format(key, rawvalue) + ) else: if not isinstance(rawvalue, dict): raise SyntaxError( - "The key '{}' must be a valid Python dict. Got: {} (type {!r})" - .format(key, rawvalue, type(rawvalue).__name__)) + "The key '{}' must be a valid Python dict. Got: {} (type {!r})".format( + key, rawvalue, type(rawvalue).__name__ + ) + ) return rawvalue - diff --git a/poetry.lock b/poetry.lock index e225e20..8d6734d 100644 --- a/poetry.lock +++ b/poetry.lock @@ -224,6 +224,17 @@ files = [ {file = "idna-3.4.tar.gz", hash = "sha256:814f528e8dead7d329833b91c5faa87d60bf71824cd12a7530b5526063d02cb4"}, ] +[[package]] +name = "iniconfig" +version = "2.0.0" +description = "brain-dead simple config-ini parsing" +optional = false +python-versions = ">=3.7" +files = [ + {file = "iniconfig-2.0.0-py3-none-any.whl", hash = "sha256:b6a85871a79d2e3b22d2d1b94ac2824226a63c6b741c88f7ae975f18b6778374"}, + {file = "iniconfig-2.0.0.tar.gz", hash = "sha256:2d91e135bf72d31a410b17c16da610a82cb55f6b0477d1a902134b24a455b8b3"}, +] + [[package]] name = "isbnlib" version = "3.10.14" @@ -456,6 +467,17 @@ html5 = ["html5lib"] htmlsoup = ["BeautifulSoup4"] source = ["Cython (>=0.29.35)"] +[[package]] +name = "packaging" +version = "23.1" +description = "Core utilities for Python packages" +optional = false +python-versions = ">=3.7" +files = [ + {file = "packaging-23.1-py3-none-any.whl", hash = "sha256:994793af429502c4ea2ebf6bf664629d07c1a9fe974af92966e4b8d2df7edc61"}, + {file = "packaging-23.1.tar.gz", hash = "sha256:a392980d2b6cffa644431898be54b0045151319d1e7ec34f0cfed48767dd334f"}, +] + [[package]] name = "papis" version = "0.13" @@ -504,6 +526,21 @@ files = [ {file = "pbr-5.11.1.tar.gz", hash = "sha256:aefc51675b0b533d56bb5fd1c8c6c0522fe31896679882e1c4c63d5e4a0fccb3"}, ] +[[package]] +name = "pluggy" +version = "1.3.0" +description = "plugin and hook calling mechanisms for python" +optional = false +python-versions = ">=3.8" +files = [ + {file = "pluggy-1.3.0-py3-none-any.whl", hash = "sha256:d89c696a773f8bd377d18e5ecda92b7a3793cbe66c87060a6fb58c7b6e1061f7"}, + {file = "pluggy-1.3.0.tar.gz", hash = "sha256:cf61ae8f126ac6f7c451172cf30e3e43d3ca77615509771b3a984a0730651e12"}, +] + +[package.extras] +dev = ["pre-commit", "tox"] +testing = ["pytest", 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"sha256:b4bf8c45bd59934ed84001ad51e11b4ee40d40a1229d2c79f9c592b0a3f6bd8a"}, +] + +[package.dependencies] +colorama = {version = "*", markers = "sys_platform == \"win32\""} +iniconfig = "*" +packaging = "*" +pluggy = ">=0.12,<2.0" + +[package.extras] +testing = ["argcomplete", "attrs (>=19.2.0)", "hypothesis (>=3.56)", "mock", "nose", "pygments (>=2.7.2)", "requests", "setuptools", "xmlschema"] + [[package]] name = "python-doi" version = "0.2.0" @@ -923,4 +980,4 @@ files = [ [metadata] lock-version = "2.0" python-versions = "^3.11" -content-hash = "2e158747df6100e105c98494d8b5f4b23b7076ae76295ce7a28facf02488ebd5" +content-hash = "d519605837788792d06ffc7bca7a92b315612ca6052227c53c558ec49dffec9f" diff --git a/pyproject.toml b/pyproject.toml index 8ee3741..4ca3257 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -18,6 +18,10 @@ python-magic = "^0.4.27" [tool.poetry.plugins."papis.command"] extract = "papis_extract:main" + +[tool.poetry.group.dev.dependencies] +pytest = "^7.4.0" + [build-system] requires = ["poetry-core"] build-backend = "poetry.core.masonry.api" diff --git a/tests/test_annotation.py b/tests/test_annotation.py new file mode 100644 index 0000000..72c7a75 --- /dev/null +++ b/tests/test_annotation.py @@ -0,0 +1,7 @@ +from papis_extract.annotation_data import Annotation + + +def test_matches_colorname_exact(): + sut = Annotation("testfile", colors={"stroke": (1.0, 0.0, 0.0)}) + c_name = sut.colorname + assert c_name == "red" From e325b89c9b2699e7d9e1333ce5a7f7a926c3b168 Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Tue, 29 Aug 2023 12:40:36 +0200 Subject: [PATCH 006/107] Move all extraction logic into extractor module The publically accessible default interface only contains the command line command interface and a single run function. --- papis_extract/__init__.py | 64 +++++++++----------------------------- papis_extract/extractor.py | 52 +++++++++++++++++++++++++++++-- 2 files changed, 64 insertions(+), 52 deletions(-) diff --git a/papis_extract/__init__.py b/papis_extract/__init__.py index 0b44c48..af3a834 100644 --- a/papis_extract/__init__.py +++ b/papis_extract/__init__.py @@ -1,19 +1,14 @@ -from pathlib import Path -import re - import click -import fitz_new as fitz -import magic import papis.cli import papis.config import papis.document -from papis.document import Document import papis.logging import papis.notes import papis.strings +from papis.document import Document from papis_extract import extractor, exporter -from papis_extract.annotation_data import Annotation, AnnotatedDocument +from papis_extract.annotation_data import AnnotatedDocument logger = papis.logging.get_logger(__name__) @@ -76,50 +71,19 @@ def main( logger.warning(papis.strings.no_documents_retrieved_message) return - doc_annotations: list[AnnotatedDocument] = _get_annotations_for_documents(documents) + run(documents, edit=manual, write=write, git=git) + + +def run( + documents: list[Document], + edit: bool = False, + write: bool = False, + git: bool = False, +) -> None: + + doc_annotations: list[AnnotatedDocument] = extractor.start(documents) if write: - exporter.to_notes(doc_annotations, edit=manual, git=git) + exporter.to_notes(doc_annotations, edit=edit, git=git) else: exporter.to_stdout(doc_annotations) - - # note_file: Path = Path(papis.notes.notes_path_ensured(documents[0])) - - -def is_pdf(fname: Path) -> bool: - return magic.from_file(fname, mime=True) == "application/pdf" - - -def _get_annotations_for_documents( - documents: list[Document], -) -> list[AnnotatedDocument]: - output: list[AnnotatedDocument] = [] - for doc in documents: - annotations: list[Annotation] = [] - found_pdf: bool = False - for file in doc.get_files(): - fname = Path(file) - if not _is_file_processable(fname): - break - found_pdf = True - - try: - annotations.extend(extractor.start(fname)) - except fitz.FileDataError as e: - print(f"File structure errors for {file}.\n{e}") - - if not found_pdf: - # have to remove curlys or papis logger gets upset - desc = re.sub("[{}]", "", papis.document.describe(doc)) - logger.warning("Did not find suitable PDF file for document: " f"{desc}") - output.append(AnnotatedDocument(doc, annotations)) - return output - - -def _is_file_processable(fname: Path) -> bool: - if not fname.is_file(): - logger.error(f"File {str(fname)} not readable.") - return False - if not is_pdf(fname): - return False - return True diff --git a/papis_extract/extractor.py b/papis_extract/extractor.py index 88ff012..51d6ade 100644 --- a/papis_extract/extractor.py +++ b/papis_extract/extractor.py @@ -1,17 +1,51 @@ +import re from pathlib import Path from typing import Any, Optional import Levenshtein +import magic import fitz_new as fitz import papis.logging import papis.config +import papis.document +from papis.document import Document -from papis_extract.annotation_data import Annotation +from papis_extract.annotation_data import Annotation, AnnotatedDocument logger = papis.logging.get_logger(__name__) +def start( + documents: list[Document], +) -> list[AnnotatedDocument]: + """Extract all annotations from passed documents. -def start(filename: Path) -> list[Annotation]: + Returns all annotations contained in the papis + documents passed in. + """ + + output: list[AnnotatedDocument] = [] + for doc in documents: + annotations: list[Annotation] = [] + found_pdf: bool = False + for file in doc.get_files(): + fname = Path(file) + if not _is_file_processable(fname): + break + found_pdf = True + + try: + annotations.extend(extract(fname)) + except fitz.FileDataError as e: + print(f"File structure errors for {file}.\n{e}") + + if not found_pdf: + # have to remove curlys or papis logger gets upset + desc = re.sub("[{}]", "", papis.document.describe(doc)) + logger.warning("Did not find suitable PDF file for document: " f"{desc}") + output.append(AnnotatedDocument(doc, annotations)) + return output + +def extract(filename: Path) -> list[Annotation]: """Extract annotations from a file. Returns all readable annotations contained in the file @@ -41,6 +75,20 @@ def start(filename: Path) -> list[Annotation]: return annotations +def is_pdf(fname: Path) -> bool: + return magic.from_file(fname, mime=True) == "application/pdf" + + + + +def _is_file_processable(fname: Path) -> bool: + if not fname.is_file(): + logger.error(f"File {str(fname)} not readable.") + return False + if not is_pdf(fname): + return False + return True + def _tag_from_colorname(colorname: str) -> str: color_mapping: dict[str, str] = getdict("tags", "plugins.extract") if not color_mapping: From 256117d45175ded87c3887ec5ae74c05442f8780 Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Tue, 29 Aug 2023 13:49:22 +0200 Subject: [PATCH 007/107] Add mustache templating Added mustache templating engine to be able to provide custom formatting strings. --- papis_extract/annotation_data.py | 42 +++++++++++----------------- poetry.lock | 13 ++++++++- pyproject.toml | 1 + tests/test_annotation.py | 48 ++++++++++++++++++++++++++++++-- 4 files changed, 75 insertions(+), 29 deletions(-) diff --git a/papis_extract/annotation_data.py b/papis_extract/annotation_data.py index 298f964..26e63cd 100644 --- a/papis_extract/annotation_data.py +++ b/papis_extract/annotation_data.py @@ -1,9 +1,9 @@ -import re import math from dataclasses import dataclass, field import papis.config from papis.document import Document +import chevron TEXT_SIMILARITY_MINIMUM = 0.75 COLOR_SIMILARITY_MINIMUM = 0.833 @@ -23,12 +23,13 @@ class Annotation: """A PDF annotation object""" file: str - type: str = "Highlight" - text: str = "" - content: str = "" - page: int = 1 colors: dict = field(default_factory=lambda: {"stroke": (0.0, 0.0, 0.0)}) + content: str = "" + page: int = 0 tag: str = "" + text: str = "" + type: str = "Highlight" + minimum_similarity_color: float = 1.0 def format(self, formatting): """Return a formatted string of the annotation. @@ -37,27 +38,15 @@ class Annotation: formatted with the correct marker replacements and removals, ready for display or writing. """ - output = formatting - replacements = { - r"{quote}": self.text, - r"{note}": self.content, - r"{page}": str(self.page), - r"{newline}": "\n", - r"{tag}": self.tag, + data = { + "file": self.file, + "quote": self.text, + "note": self.content, + "page": self.page, + "tag": self.tag, + "type": self.type, } - pattern = re.compile( - "|".join( - [re.escape(k) for k in sorted(replacements, key=len, reverse=True)] - ), - flags=re.DOTALL, - ) - patt_quote_container = re.compile(r"{%quote_container(.*?)%}") - patt_note_container = re.compile(r"{%note_container(.*?)%}") - patt_tag_container = re.compile(r"{%tag_container(.*?)%}") - output = patt_quote_container.sub(r"\1" if self.text else "", output) - output = patt_note_container.sub(r"\1" if self.content else "", output) - output = patt_tag_container.sub(r"\1" if self.tag else "", output) - return pattern.sub(lambda x: replacements[x.group(0)], output) + return chevron.render(formatting, data) @property def colorname(self): @@ -73,9 +62,10 @@ class Annotation: minimum_similarity = ( papis.config.getfloat("minimum_similarity_color", "plugins.extract") or 1.0 ) + minimum_similarity = self.minimum_similarity_color for name, values in COLORS.items(): similarity_ratio = self._color_similarity_ratio(values, annot_colors) - if similarity_ratio > minimum_similarity: + if similarity_ratio >= minimum_similarity: minimum_similarity = similarity_ratio nearest = name return nearest diff --git a/poetry.lock b/poetry.lock index 8d6734d..1336bfc 100644 --- a/poetry.lock +++ b/poetry.lock @@ -147,6 +147,17 @@ files = [ {file = "charset_normalizer-3.2.0-py3-none-any.whl", hash = "sha256:8e098148dd37b4ce3baca71fb394c81dc5d9c7728c95df695d2dca218edf40e6"}, ] +[[package]] +name = "chevron" +version = "0.14.0" +description = "Mustache templating language renderer" +optional = false +python-versions = "*" +files = [ + {file = "chevron-0.14.0-py3-none-any.whl", hash = "sha256:fbf996a709f8da2e745ef763f482ce2d311aa817d287593a5b990d6d6e4f0443"}, + {file = "chevron-0.14.0.tar.gz", hash = "sha256:87613aafdf6d77b6a90ff073165a61ae5086e21ad49057aa0e53681601800ebf"}, +] + [[package]] name = "click" version = "8.1.7" @@ -980,4 +991,4 @@ files = [ [metadata] lock-version = "2.0" python-versions = "^3.11" -content-hash = "d519605837788792d06ffc7bca7a92b315612ca6052227c53c558ec49dffec9f" +content-hash = "a3af36ed2941235df158c20ba9b66bdf5a0af0554235fd004ec77c3e88def3c3" diff --git a/pyproject.toml b/pyproject.toml index 4ca3257..8ee68a7 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -14,6 +14,7 @@ papis = "^0.13" click = "^8.1.7" whoosh = "^2.7.4" python-magic = "^0.4.27" +chevron = "^0.14.0" [tool.poetry.plugins."papis.command"] extract = "papis_extract:main" diff --git a/tests/test_annotation.py b/tests/test_annotation.py index 72c7a75..d9f6188 100644 --- a/tests/test_annotation.py +++ b/tests/test_annotation.py @@ -1,7 +1,51 @@ +import pytest from papis_extract.annotation_data import Annotation -def test_matches_colorname_exact(): - sut = Annotation("testfile", colors={"stroke": (1.0, 0.0, 0.0)}) +@pytest.mark.parametrize( + "fmt_string,expected", + [ + ("{{quote}}", "I am the text value"), + ( + "> {{quote}}\n{{#note}}Note: {{note}}{{/note}}", + "> I am the text value\nNote: Whereas I represent the note", + ), + ( + "{{#note}}Note: {{note}}{{/note}}{{#page}}, p. {{page}}{{/page}}", + "Note: Whereas I represent the note", + ), + ], +) +def test_formatting(fmt_string, expected): + sut = Annotation( + "myfile", + text="I am the text value", + content="Whereas I represent the note", + ) + + assert sut.format(fmt_string) == expected + +def test_colorname_matches_exact(): + sut = Annotation( + "testfile", colors={"stroke": (1.0,0.0,0.0)}, minimum_similarity_color=1.0 + ) + c_name = sut.colorname + assert c_name == "red" + +# TODO inject closeness value instead of relying on default +@pytest.mark.parametrize( + "color_value", + [ + (1.0, 0.0, 0.0), + (0.9, 0.0, 0.0), + (0.8, 0.0, 0.0), + (0.7, 0.0, 0.0), + (0.51, 0.0, 0.0), + ], +) +def test_matches_inexact_colorname(color_value): + sut = Annotation( + "testfile", colors={"stroke": color_value}, minimum_similarity_color=0.833 + ) c_name = sut.colorname assert c_name == "red" From 20873e6ef88184c60a25b2fd5d2f2294fad35650 Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Tue, 29 Aug 2023 22:23:52 +0200 Subject: [PATCH 008/107] Change annotation color to simple rgb tuple --- papis_extract/annotation_data.py | 4 ++-- papis_extract/extractor.py | 14 ++++++++++---- tests/test_annotation.py | 4 ++-- 3 files changed, 14 insertions(+), 8 deletions(-) diff --git a/papis_extract/annotation_data.py b/papis_extract/annotation_data.py index 26e63cd..fa06e0d 100644 --- a/papis_extract/annotation_data.py +++ b/papis_extract/annotation_data.py @@ -23,7 +23,7 @@ class Annotation: """A PDF annotation object""" file: str - colors: dict = field(default_factory=lambda: {"stroke": (0.0, 0.0, 0.0)}) + colors: tuple[float, float, float] = field(default_factory=lambda: (0.0, 0.0, 0.0)) content: str = "" page: int = 0 tag: str = "" @@ -56,7 +56,7 @@ class Annotation: using euclidian distance between the two color vectors. """ annot_colors = ( - self.colors.get("stroke") or self.colors.get("fill") or (0.0, 0.0, 0.0) + self.colors or (0.0, 0.0, 0.0) ) nearest = None minimum_similarity = ( diff --git a/papis_extract/extractor.py b/papis_extract/extractor.py index 51d6ade..a4bc536 100644 --- a/papis_extract/extractor.py +++ b/papis_extract/extractor.py @@ -14,12 +14,13 @@ from papis_extract.annotation_data import Annotation, AnnotatedDocument logger = papis.logging.get_logger(__name__) + def start( documents: list[Document], ) -> list[AnnotatedDocument]: """Extract all annotations from passed documents. - Returns all annotations contained in the papis + Returns all annotations contained in the papis documents passed in. """ @@ -45,6 +46,7 @@ def start( output.append(AnnotatedDocument(doc, annotations)) return output + def extract(filename: Path) -> list[Annotation]: """Extract annotations from a file. @@ -58,11 +60,16 @@ def extract(filename: Path) -> list[Annotation]: quote, note = _retrieve_annotation_content(page, annot) if not quote and not note: continue + col = ( + annot.colors.get("fill") + or annot.colors.get("stroke") + or (0.0, 0.0, 0.0) + ) a = Annotation( file=str(filename), text=quote or "", content=note or "", - colors=annot.colors, + colors=col, type=annot.type[1], page=(page.number or 0) + 1, ) @@ -79,8 +86,6 @@ def is_pdf(fname: Path) -> bool: return magic.from_file(fname, mime=True) == "application/pdf" - - def _is_file_processable(fname: Path) -> bool: if not fname.is_file(): logger.error(f"File {str(fname)} not readable.") @@ -89,6 +94,7 @@ def _is_file_processable(fname: Path) -> bool: return False return True + def _tag_from_colorname(colorname: str) -> str: color_mapping: dict[str, str] = getdict("tags", "plugins.extract") if not color_mapping: diff --git a/tests/test_annotation.py b/tests/test_annotation.py index d9f6188..542c3a8 100644 --- a/tests/test_annotation.py +++ b/tests/test_annotation.py @@ -27,7 +27,7 @@ def test_formatting(fmt_string, expected): def test_colorname_matches_exact(): sut = Annotation( - "testfile", colors={"stroke": (1.0,0.0,0.0)}, minimum_similarity_color=1.0 + "testfile", colors=(1.0,0.0,0.0), minimum_similarity_color=1.0 ) c_name = sut.colorname assert c_name == "red" @@ -45,7 +45,7 @@ def test_colorname_matches_exact(): ) def test_matches_inexact_colorname(color_value): sut = Annotation( - "testfile", colors={"stroke": color_value}, minimum_similarity_color=0.833 + "testfile", colors=color_value, minimum_similarity_color=0.833 ) c_name = sut.colorname assert c_name == "red" From e56f0141369df0a630015ad8bb2d7a23f2cee689 Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Thu, 31 Aug 2023 21:32:24 +0200 Subject: [PATCH 009/107] Add formatting style Markdown --- papis_extract/__init__.py | 6 +++--- papis_extract/annotation_data.py | 19 ++++++++++++++++--- papis_extract/exporter.py | 20 +++++++++----------- tests/test_formatting.py | 14 ++++++++++++++ 4 files changed, 42 insertions(+), 17 deletions(-) create mode 100644 tests/test_formatting.py diff --git a/papis_extract/__init__.py b/papis_extract/__init__.py index af3a834..e396962 100644 --- a/papis_extract/__init__.py +++ b/papis_extract/__init__.py @@ -8,7 +8,7 @@ import papis.strings from papis.document import Document from papis_extract import extractor, exporter -from papis_extract.annotation_data import AnnotatedDocument +from papis_extract.annotation_data import AnnotatedDocument, Markdown logger = papis.logging.get_logger(__name__) @@ -84,6 +84,6 @@ def run( doc_annotations: list[AnnotatedDocument] = extractor.start(documents) if write: - exporter.to_notes(doc_annotations, edit=edit, git=git) + exporter.to_notes(doc_annotations, Markdown(), edit=edit, git=git) else: - exporter.to_stdout(doc_annotations) + exporter.to_stdout(doc_annotations, Markdown()) diff --git a/papis_extract/annotation_data.py b/papis_extract/annotation_data.py index fa06e0d..486c397 100644 --- a/papis_extract/annotation_data.py +++ b/papis_extract/annotation_data.py @@ -1,5 +1,6 @@ import math from dataclasses import dataclass, field +from typing import Protocol import papis.config from papis.document import Document @@ -55,9 +56,7 @@ class Annotation: Finds the closest named color to the annotation and returns it, using euclidian distance between the two color vectors. """ - annot_colors = ( - self.colors or (0.0, 0.0, 0.0) - ) + annot_colors = self.colors or (0.0, 0.0, 0.0) nearest = None minimum_similarity = ( papis.config.getfloat("minimum_similarity_color", "plugins.extract") or 1.0 @@ -85,3 +84,17 @@ class Annotation: class AnnotatedDocument: document: Document annotations: list[Annotation] + + +@dataclass +class Templating(Protocol): + string: str + + +@dataclass +class Markdown: + string: str = ( + "{{#tag}}#{{tag}}\n{{/tag}}" + "{{#quote}}> {{quote}}{{/quote}} {{#page}}[p. {{page}}]{{/page}}\n" + "{{#note}} NOTE: {{note}}{{/note}}" + ) diff --git a/papis_extract/exporter.py b/papis_extract/exporter.py index b1220d0..08bcfbb 100644 --- a/papis_extract/exporter.py +++ b/papis_extract/exporter.py @@ -7,17 +7,12 @@ import papis.git import papis.config import Levenshtein -from papis_extract.annotation_data import AnnotatedDocument, Annotation +from papis_extract.annotation_data import AnnotatedDocument, Annotation, Templating logger = papis.logging.get_logger(__name__) -def _format_annotation(annotation: Annotation) -> str: - note = f"NOTE: {annotation.content}" if annotation.content else "" - return f"> {annotation.text}\n {note}" - - -def to_stdout(annots: list[AnnotatedDocument]) -> None: +def to_stdout(annots: list[AnnotatedDocument], template: Templating) -> None: """Pretty print annotations to stdout. Gives a nice human-readable representations of @@ -27,6 +22,7 @@ def to_stdout(annots: list[AnnotatedDocument]) -> None: if not annots: return + last = annots[-1] for entry in annots: if not entry.annotations: continue @@ -39,13 +35,15 @@ def to_stdout(annots: list[AnnotatedDocument]) -> None: f"{title_decoration}\n{papis.document.describe(entry.document)}\n{title_decoration}\n" ) for a in entry.annotations: - print(_format_annotation(a)) + print(a.format(template.string)) - if entry != annots[-1]: + if entry != last: print("\n") -def to_notes(annots: list[AnnotatedDocument], edit: bool, git: bool) -> None: +def to_notes( + annots: list[AnnotatedDocument], template: Templating, edit: bool, git: bool +) -> None: """Write annotations into document notes. Permanently writes the given annotations into notes @@ -61,7 +59,7 @@ def to_notes(annots: list[AnnotatedDocument], edit: bool, git: bool) -> None: formatted_annotations: list[str] = [] for a in entry.annotations: - formatted_annotations.append(_format_annotation(a)) + formatted_annotations.append(a.format(template.string)) _add_annots_to_note(entry.document, formatted_annotations) diff --git a/tests/test_formatting.py b/tests/test_formatting.py new file mode 100644 index 0000000..07f1092 --- /dev/null +++ b/tests/test_formatting.py @@ -0,0 +1,14 @@ +import chevron + +from papis_extract.annotation_data import Markdown + +def test_markdown_default(): + fmt = Markdown() + assert chevron.render(fmt.string, { + "file": "somefile/somewhere.pdf", + "quote": "I am quote", + "note": "and including note.", + "page": 46, + "tag": "important", + "type": "highlight", + }) == "#important\n> I am quote [p. 46]\n NOTE: and including note." From 5450776eb2604da52de14f751effdcfc46d8572f Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Thu, 31 Aug 2023 21:40:38 +0200 Subject: [PATCH 010/107] refactor: Extract templating to model module --- papis_extract/__init__.py | 3 ++- papis_extract/annotation_data.py | 13 ------------- papis_extract/exporter.py | 3 ++- papis_extract/model/templating.py | 16 ++++++++++++++++ 4 files changed, 20 insertions(+), 15 deletions(-) create mode 100644 papis_extract/model/templating.py diff --git a/papis_extract/__init__.py b/papis_extract/__init__.py index e396962..b9b5451 100644 --- a/papis_extract/__init__.py +++ b/papis_extract/__init__.py @@ -8,7 +8,8 @@ import papis.strings from papis.document import Document from papis_extract import extractor, exporter -from papis_extract.annotation_data import AnnotatedDocument, Markdown +from papis_extract.annotation_data import AnnotatedDocument +from papis_extract.model.templating import Markdown logger = papis.logging.get_logger(__name__) diff --git a/papis_extract/annotation_data.py b/papis_extract/annotation_data.py index 486c397..6b641c4 100644 --- a/papis_extract/annotation_data.py +++ b/papis_extract/annotation_data.py @@ -85,16 +85,3 @@ class AnnotatedDocument: document: Document annotations: list[Annotation] - -@dataclass -class Templating(Protocol): - string: str - - -@dataclass -class Markdown: - string: str = ( - "{{#tag}}#{{tag}}\n{{/tag}}" - "{{#quote}}> {{quote}}{{/quote}} {{#page}}[p. {{page}}]{{/page}}\n" - "{{#note}} NOTE: {{note}}{{/note}}" - ) diff --git a/papis_extract/exporter.py b/papis_extract/exporter.py index 08bcfbb..2b0d4fd 100644 --- a/papis_extract/exporter.py +++ b/papis_extract/exporter.py @@ -7,7 +7,8 @@ import papis.git import papis.config import Levenshtein -from papis_extract.annotation_data import AnnotatedDocument, Annotation, Templating +from papis_extract.annotation_data import AnnotatedDocument +from papis_extract.model.templating import Templating logger = papis.logging.get_logger(__name__) diff --git a/papis_extract/model/templating.py b/papis_extract/model/templating.py new file mode 100644 index 0000000..f1ebb92 --- /dev/null +++ b/papis_extract/model/templating.py @@ -0,0 +1,16 @@ +from dataclasses import dataclass +from typing import Protocol + + +@dataclass +class Templating(Protocol): + string: str + + +@dataclass +class Markdown: + string: str = ( + "{{#tag}}#{{tag}}\n{{/tag}}" + "{{#quote}}> {{quote}}{{/quote}} {{#page}}[p. {{page}}]{{/page}}\n" + "{{#note}} NOTE: {{note}}{{/note}}" + ) From e633c0335e8a0c61a9b72868cac345424d6db716 Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Tue, 19 Sep 2023 17:34:33 +0200 Subject: [PATCH 011/107] chore: Make whoosh database optional dependency --- pyproject.toml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 8ee68a7..8f52f48 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -12,17 +12,19 @@ pymupdf = "^1.23.1" levenshtein = "^0.21.1" papis = "^0.13" click = "^8.1.7" -whoosh = "^2.7.4" +whoosh = { version = "^2.7.4", optional = true } python-magic = "^0.4.27" chevron = "^0.14.0" -[tool.poetry.plugins."papis.command"] -extract = "papis_extract:main" - +[tool.poetry.extras] +whoosh = ["whoosh"] [tool.poetry.group.dev.dependencies] pytest = "^7.4.0" +[tool.poetry.plugins."papis.command"] +extract = "papis_extract:main" + [build-system] requires = ["poetry-core"] build-backend = "poetry.core.masonry.api" From 4eb983d9e38e957f2044df62fa829b364be4842e Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Tue, 19 Sep 2023 17:35:39 +0200 Subject: [PATCH 012/107] refactor: Move templating to separate file --- papis_extract/__init__.py | 2 +- papis_extract/annotation_data.py | 7 ++-- papis_extract/exporter.py | 6 ++-- papis_extract/model/templating.py | 16 ---------- papis_extract/templating.py | 35 ++++++++++++++++++++ tests/test_annotation.py | 19 +++++------ tests/test_formatting.py | 53 +++++++++++++++++++++++++------ 7 files changed, 97 insertions(+), 41 deletions(-) delete mode 100644 papis_extract/model/templating.py create mode 100644 papis_extract/templating.py diff --git a/papis_extract/__init__.py b/papis_extract/__init__.py index b9b5451..c23ae39 100644 --- a/papis_extract/__init__.py +++ b/papis_extract/__init__.py @@ -9,7 +9,7 @@ from papis.document import Document from papis_extract import extractor, exporter from papis_extract.annotation_data import AnnotatedDocument -from papis_extract.model.templating import Markdown +from papis_extract.templating import Markdown logger = papis.logging.get_logger(__name__) diff --git a/papis_extract/annotation_data.py b/papis_extract/annotation_data.py index 6b641c4..c94244f 100644 --- a/papis_extract/annotation_data.py +++ b/papis_extract/annotation_data.py @@ -1,11 +1,12 @@ import math from dataclasses import dataclass, field -from typing import Protocol import papis.config from papis.document import Document import chevron +from papis_extract.templating import Templating + TEXT_SIMILARITY_MINIMUM = 0.75 COLOR_SIMILARITY_MINIMUM = 0.833 @@ -32,7 +33,7 @@ class Annotation: type: str = "Highlight" minimum_similarity_color: float = 1.0 - def format(self, formatting): + def format(self, template: Templating): """Return a formatted string of the annotation. Given a provided formatting pattern, this method returns the annotation @@ -47,7 +48,7 @@ class Annotation: "tag": self.tag, "type": self.type, } - return chevron.render(formatting, data) + return chevron.render(template.string, data) @property def colorname(self): diff --git a/papis_extract/exporter.py b/papis_extract/exporter.py index 2b0d4fd..0fca9d7 100644 --- a/papis_extract/exporter.py +++ b/papis_extract/exporter.py @@ -8,7 +8,7 @@ import papis.config import Levenshtein from papis_extract.annotation_data import AnnotatedDocument -from papis_extract.model.templating import Templating +from papis_extract.templating import Templating logger = papis.logging.get_logger(__name__) @@ -36,7 +36,7 @@ def to_stdout(annots: list[AnnotatedDocument], template: Templating) -> None: f"{title_decoration}\n{papis.document.describe(entry.document)}\n{title_decoration}\n" ) for a in entry.annotations: - print(a.format(template.string)) + print(a.format(template)) if entry != last: print("\n") @@ -60,7 +60,7 @@ def to_notes( formatted_annotations: list[str] = [] for a in entry.annotations: - formatted_annotations.append(a.format(template.string)) + formatted_annotations.append(a.format(template)) _add_annots_to_note(entry.document, formatted_annotations) diff --git a/papis_extract/model/templating.py b/papis_extract/model/templating.py deleted file mode 100644 index f1ebb92..0000000 --- a/papis_extract/model/templating.py +++ /dev/null @@ -1,16 +0,0 @@ -from dataclasses import dataclass -from typing import Protocol - - -@dataclass -class Templating(Protocol): - string: str - - -@dataclass -class Markdown: - string: str = ( - "{{#tag}}#{{tag}}\n{{/tag}}" - "{{#quote}}> {{quote}}{{/quote}} {{#page}}[p. {{page}}]{{/page}}\n" - "{{#note}} NOTE: {{note}}{{/note}}" - ) diff --git a/papis_extract/templating.py b/papis_extract/templating.py new file mode 100644 index 0000000..c8abf7f --- /dev/null +++ b/papis_extract/templating.py @@ -0,0 +1,35 @@ +from dataclasses import dataclass +from typing import Protocol + + +@dataclass +class Templating(Protocol): + header: str + string: str + footer: str + + +@dataclass +class Markdown: + header: str = "" + string: str = ( + "{{#tag}}#{{tag}}\n{{/tag}}" + "{{#quote}}> {{quote}}{{/quote}} {{#page}}[p. {{page}}]{{/page}}\n" + "{{#note}} NOTE: {{note}}{{/note}}" + ) + footer: str = "" + + +@dataclass +class Csv: + header: str = "type, tag, page, quote, note, file" + string: str = "{{type}}, {{tag}}, {{page}}, {{quote}}, {{note}}, {{file}}" + footer: str = "" + + +@dataclass +class Custom: + def __init__(self, header: str = "", string: str = "", footer: str = "") -> None: + self.header = header + self.string = string + self.footer = footer diff --git a/tests/test_annotation.py b/tests/test_annotation.py index 542c3a8..60b35ed 100644 --- a/tests/test_annotation.py +++ b/tests/test_annotation.py @@ -1,17 +1,20 @@ import pytest from papis_extract.annotation_data import Annotation +from papis_extract.templating import Custom @pytest.mark.parametrize( "fmt_string,expected", [ - ("{{quote}}", "I am the text value"), + (Custom(string="{{quote}}"), "I am the text value"), ( - "> {{quote}}\n{{#note}}Note: {{note}}{{/note}}", + Custom(string="> {{quote}}\n{{#note}}Note: {{note}}{{/note}}"), "> I am the text value\nNote: Whereas I represent the note", ), ( - "{{#note}}Note: {{note}}{{/note}}{{#page}}, p. {{page}}{{/page}}", + Custom( + string="{{#note}}Note: {{note}}{{/note}}{{#page}}, p. {{page}}{{/page}}" + ), "Note: Whereas I represent the note", ), ], @@ -25,13 +28,13 @@ def test_formatting(fmt_string, expected): assert sut.format(fmt_string) == expected + def test_colorname_matches_exact(): - sut = Annotation( - "testfile", colors=(1.0,0.0,0.0), minimum_similarity_color=1.0 - ) + sut = Annotation("testfile", colors=(1.0, 0.0, 0.0), minimum_similarity_color=1.0) c_name = sut.colorname assert c_name == "red" + # TODO inject closeness value instead of relying on default @pytest.mark.parametrize( "color_value", @@ -44,8 +47,6 @@ def test_colorname_matches_exact(): ], ) def test_matches_inexact_colorname(color_value): - sut = Annotation( - "testfile", colors=color_value, minimum_similarity_color=0.833 - ) + sut = Annotation("testfile", colors=color_value, minimum_similarity_color=0.833) c_name = sut.colorname assert c_name == "red" diff --git a/tests/test_formatting.py b/tests/test_formatting.py index 07f1092..5ab53c2 100644 --- a/tests/test_formatting.py +++ b/tests/test_formatting.py @@ -1,14 +1,49 @@ import chevron -from papis_extract.annotation_data import Markdown +from papis_extract.templating import Markdown, Csv + + +def test_template_markers(): + ... + def test_markdown_default(): fmt = Markdown() - assert chevron.render(fmt.string, { - "file": "somefile/somewhere.pdf", - "quote": "I am quote", - "note": "and including note.", - "page": 46, - "tag": "important", - "type": "highlight", - }) == "#important\n> I am quote [p. 46]\n NOTE: and including note." + assert ( + chevron.render( + fmt.string, + { + "file": "somefile/somewhere.pdf", + "quote": "I am quote", + "note": "and including note.", + "page": 46, + "tag": "important", + "type": "highlight", + }, + ) + == "#important\n> I am quote [p. 46]\n NOTE: and including note." + ) + + +def test_csv_string(): + fmt = Csv() + assert ( + chevron.render( + fmt.string, + { + "file": "somefile/somewhere.pdf", + "quote": "I am quote", + "note": "and including note.", + "page": 46, + "tag": "important", + "type": "highlight", + }, + ) + == "highlight, important, 46, " + "I am quote, and including note., somefile/somewhere.pdf" + ) + + +def test_csv_header(): + fmt = Csv() + assert chevron.render(fmt.header, {}) == "type, tag, page, quote, note, file" From 07d4de9a4663af692a51ddd87483291e6f3c059b Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Tue, 19 Sep 2023 17:52:45 +0200 Subject: [PATCH 013/107] docs: Add docstrings --- papis_extract/annotation_data.py | 9 ++++++++- papis_extract/exporter.py | 8 ++++++++ papis_extract/extractor.py | 1 + 3 files changed, 17 insertions(+), 1 deletion(-) diff --git a/papis_extract/annotation_data.py b/papis_extract/annotation_data.py index c94244f..5fd5546 100644 --- a/papis_extract/annotation_data.py +++ b/papis_extract/annotation_data.py @@ -22,7 +22,10 @@ COLORS = { @dataclass class Annotation: - """A PDF annotation object""" + """A PDF annotation object. + + Contains all information necessary for the annotation itself, content and metadata. + """ file: str colors: tuple[float, float, float] = field(default_factory=lambda: (0.0, 0.0, 0.0)) @@ -83,6 +86,10 @@ class Annotation: @dataclass class AnnotatedDocument: + """Contains all annotations belonging to a single papis document. + + Combines a document with a list of annotations which belong to it.""" document: Document annotations: list[Annotation] + # TODO could implement a from_doc() static method to generate annotation list? diff --git a/papis_extract/exporter.py b/papis_extract/exporter.py index 0fca9d7..8e05c6c 100644 --- a/papis_extract/exporter.py +++ b/papis_extract/exporter.py @@ -115,6 +115,14 @@ def _add_annots_to_note( def _drop_existing_annotations( formatted_annotations: list[str], file_lines: list[str] ) -> list[str]: + """Returns the input annotations dropping any existing. + + Takes a list of formatted annotations and a list of strings + (most probably existing lines in a file). If anny annotations + match an existing line closely enough, they will be dropped. + + Returns list of annotations without duplicates. + """ minimum_similarity = ( papis.config.getfloat("minimum_similarity", "plugins.extract") or 1.0 ) diff --git a/papis_extract/extractor.py b/papis_extract/extractor.py index a4bc536..f6802f0 100644 --- a/papis_extract/extractor.py +++ b/papis_extract/extractor.py @@ -83,6 +83,7 @@ def extract(filename: Path) -> list[Annotation]: def is_pdf(fname: Path) -> bool: + """Check if file is a pdf, using mime type.""" return magic.from_file(fname, mime=True) == "application/pdf" From 9674592a9f63b9a9680b542955f1a7a0e288af2c Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Tue, 19 Sep 2023 17:55:30 +0200 Subject: [PATCH 014/107] docs: Add developer notes to README --- README.md | 40 ++++++++++++++++++++++++++++++---------- 1 file changed, 30 insertions(+), 10 deletions(-) diff --git a/README.md b/README.md index d2d1574..61a6f47 100644 --- a/README.md +++ b/README.md @@ -96,7 +96,7 @@ in fact you can use the plugin without having to set up any of it if you are hap The full default settings look as follows: -```yaml +```conf [plugins.extract] on_import: False tags = {"important": "red", "toread": "blue"} @@ -107,7 +107,7 @@ minimum_similarity_color = 0.833 # for matching tag to color ### Automatic extraction -```yaml +```conf [plugins.extract] on_import: True ``` @@ -119,7 +119,7 @@ if `False` extraction only happens when you explicitly invoke it. Extraction will *not* happen automatically when you add new annotations to an existing document, regardless of this setting. -#### Automatic tagging +### Automatic tagging By supplying the tags option with a valid python dictionary of the form `{"tag": "color", "tag2": "color2"}`, you can enable automatic tagging for your annotations. @@ -128,7 +128,7 @@ You thus ascribe specific meanings to the colors you use in highlighting. For example, if you always highlight the most essential arguments and findings in red and always highlight things you have to follow up on in blue, you can assign the meanings 'important' and 'todo' to them respectively as follows: -```yaml +```conf [plugins.extract] tags = {"red": "important", "blue": "toread"} ``` @@ -140,7 +140,7 @@ no defaults are set here. ### Advanced configuration -```yaml +```conf [plugins.extract] minimum_similarity: 0.75, # for checking against existing annotations minimum_similarity_content: 0.9, # for checking if highlight or note @@ -219,12 +219,32 @@ This plugin makes an effort to find the right combination and extract the writte as well as any additional notes made - but things *will* slip through or extract weirdly every now and again. -The easiest extraction is provided if your program writes the selection itself into the highlight -content, because then we can just use that. It is harder to parse if it does not and will sometimes -get additional words in front or behind (especially if the highlight ends in the middle of a line) -or even cut a few off. +Secondly, a note on the pages: I use the page number that the mupdf library gives me when it +extracts anything from the pdf file. Sometimes that number will be correct for the document, +sometimes it will however be the number of the *pdf document* internally. This can happen if +e.g. an article or a book has frontmatter without numbering scheme or with a different one. +Sometimes the correct pages will still be embedded in the pdf and everything will work, +others it won't. So always double check your page numbers! -I am not sure if there is much I can do about this. +I am not sure if there is much I can do about these issues for now. + +## For developers + +and for myself whenever I forget. The basic building blocks currently in here are three: + +- extractors +: extract data from a source file attached to a papis document. + +- exporters +: put the extracted data somewhere like stdout or into your notes. + +- templates +: make sure the exporter saves the data according to your preferred layout, +such as a markdown syntax or csv-structure. + +Splitting it into those three building blocks makes it easier to recombine them in any way, +should someone want to save highlights as csv data in their notes, +or should we ever include more extractors than the one for PDFs. --- From cbe2e7cb03f5c40abf7d1b25bed497366026ae22 Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Tue, 19 Sep 2023 18:30:18 +0200 Subject: [PATCH 015/107] feat: Allow cli option for template choice --- papis_extract/__init__.py | 44 ++++++++++++++++++++++++++------------- 1 file changed, 29 insertions(+), 15 deletions(-) diff --git a/papis_extract/__init__.py b/papis_extract/__init__.py index c23ae39..6379b27 100644 --- a/papis_extract/__init__.py +++ b/papis_extract/__init__.py @@ -9,7 +9,7 @@ from papis.document import Document from papis_extract import extractor, exporter from papis_extract.annotation_data import AnnotatedDocument -from papis_extract.templating import Markdown +from papis_extract.templating import Csv, Markdown, Templating logger = papis.logging.get_logger(__name__) @@ -29,17 +29,24 @@ papis.config.register_default_settings(DEFAULT_OPTIONS) @click.help_option("-h", "--help") @papis.cli.query_argument() @papis.cli.doc_folder_option() -@papis.cli.git_option(help="Add changes made to the notes files") +@papis.cli.git_option(help="Commit changes made to the notes files.") @papis.cli.all_option() -@click.option( - "--manual/--no-manual", - "-m", - help="Open each note in editor for manual editing after extracting its annotations", -) @click.option( "--write/--no-write", "-w", - help="Do not write annotations to notes only print results to stdout", + help="Do not write annotations to notes only print results to stdout.", +) +@click.option( + "--manual/--no-manual", + "-m", + help= + "Open each note in editor for manual editing after extracting its annotations.", +) +@click.option( + "--template", + "-t", + type=click.Choice(["markdown", "csv"], case_sensitive=False), + help="Choose an output template to format annotations with.", ) def main( query: str, @@ -53,17 +60,19 @@ def main( doc_folder: str, manual: bool, write: bool, + template: str, git: bool, ) -> None: - """Extract annotations from any pdf document + """Extract annotations from any pdf document. The extract plugin allows manual or automatic extraction of all annotations - contained in the pdf documents belonging to entries of the pubs library. + contained in the pdf documents belonging to entries of the papis library. It can write those changes to stdout or directly create and update notes for papis documents. It adds a `papis extract` subcommand through which it is invoked, but can - optionally run whenever a new document is imported for a pubs entry. + optionally run whenever a new document is imported for a papis entry, + if set in the plugin configuration. """ documents = papis.cli.handle_doc_folder_query_all_sort( query, doc_folder, sort_field=None, sort_reverse=False, _all=_all @@ -72,7 +81,12 @@ def main( logger.warning(papis.strings.no_documents_retrieved_message) return - run(documents, edit=manual, write=write, git=git) + if template == "csv": + template_type = Csv() + else: + template_type = Markdown() + + run(documents, edit=manual, write=write, git=git, template=template_type) def run( @@ -80,11 +94,11 @@ def run( edit: bool = False, write: bool = False, git: bool = False, + template: Templating = Markdown(), ) -> None: - doc_annotations: list[AnnotatedDocument] = extractor.start(documents) if write: - exporter.to_notes(doc_annotations, Markdown(), edit=edit, git=git) + exporter.to_notes(doc_annotations, template, edit=edit, git=git) else: - exporter.to_stdout(doc_annotations, Markdown()) + exporter.to_stdout(doc_annotations, template) From 66f937e2a84dc1826396660a6b5a027eff01ba96 Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Tue, 19 Sep 2023 18:31:12 +0200 Subject: [PATCH 016/107] test: Add local papis settings for testing --- .papis.config | 7 +++++++ 1 file changed, 7 insertions(+) create mode 100644 .papis.config diff --git a/.papis.config b/.papis.config new file mode 100644 index 0000000..5e61770 --- /dev/null +++ b/.papis.config @@ -0,0 +1,7 @@ +[settings] +default-library = main +picktool = papis +formater = python + +[main] +dir = temp/lib From 5a6d672c76f7ccb058d894f95550c5236f6067a6 Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Tue, 19 Sep 2023 21:43:19 +0200 Subject: [PATCH 017/107] refactor: Move formatting logic to formatters Formatters (previously templates) were pure data containers before, continating the 'template' for how things should be formatted using mustache. The formatting would be done a) in the exporters and b) in the annotations. This spread of formatting has now been consolidated into the Formatter, which fixes the overall spread of formatting code and now can coherently format a whole output instead of just individual annotations. A formatter contains references to all documents and contained annotations and will format everything at once by default, but the formatting function can be invoked with reference to a specific annotated document to only format that. This commit should put more separation into the concerns of exporter and formatter and made formatting a concern purely of the formatters and annotation objects. --- README.md | 20 ++++--- papis_extract/__init__.py | 22 +++---- papis_extract/annotation_data.py | 8 +-- papis_extract/exporter.py | 54 +++++------------ papis_extract/formatter.py | 100 +++++++++++++++++++++++++++++++ papis_extract/templating.py | 35 ----------- 6 files changed, 138 insertions(+), 101 deletions(-) create mode 100644 papis_extract/formatter.py delete mode 100644 papis_extract/templating.py diff --git a/README.md b/README.md index 61a6f47..89052bf 100644 --- a/README.md +++ b/README.md @@ -177,8 +177,8 @@ Known issues to be fixed: - [x] Speed? - should be fine, on my machine (old i5 laptop) it takes around 90s for ~1000 documents with ~4000 annotations - [x] ensure all cmdline options do what they should -- [ ] annotations carry over color object from fitz, should just be Color object or simple tuple with rgb vals -- [ ] docstrings, docstrings! +- [x] annotations carry over color object from fitz, should just be Color object or simple tuple with rgb vals +- [x] docstrings, docstrings! - [ ] testing testing testing!! - [ ] refactor into some better abstractions (e.g. Exporter Protocol -> stdout/markdown implementations; Extractor Protocol -> PDF implementation) @@ -188,7 +188,7 @@ features to be implemented: - [x] static analysis (lint, typecheck etc) on pushes - [x] test pipeline on master pushes - [ ] release pipeline to pypi on tags -- [ ] add page number if available +- [x] add page number if available - exists in Annotation, just need to place in output - [ ] show overall amount of extractions at the end - [ ] custom formatting decided by user @@ -233,14 +233,18 @@ I am not sure if there is much I can do about these issues for now. and for myself whenever I forget. The basic building blocks currently in here are three: - extractors -: extract data from a source file attached to a papis document. +: Extract data from a source file attached to a papis document. + +- annotations +: The actual extracted blocks of text, containing some metadata + info as well, such as their color, type, page. - exporters -: put the extracted data somewhere like stdout or into your notes. +: Put the extracted data somewhere. For now stdout or into your notes. -- templates -: make sure the exporter saves the data according to your preferred layout, -such as a markdown syntax or csv-structure. +- formatters +: Make sure the exporter saves the data according to your preferred layout, + such as a markdown syntax or csv-structure. Splitting it into those three building blocks makes it easier to recombine them in any way, should someone want to save highlights as csv data in their notes, diff --git a/papis_extract/__init__.py b/papis_extract/__init__.py index 6379b27..026e613 100644 --- a/papis_extract/__init__.py +++ b/papis_extract/__init__.py @@ -8,8 +8,7 @@ import papis.strings from papis.document import Document from papis_extract import extractor, exporter -from papis_extract.annotation_data import AnnotatedDocument -from papis_extract.templating import Csv, Markdown, Templating +from papis_extract.formatter import MarkdownFormatter, Formatter logger = papis.logging.get_logger(__name__) @@ -39,8 +38,7 @@ papis.config.register_default_settings(DEFAULT_OPTIONS) @click.option( "--manual/--no-manual", "-m", - help= - "Open each note in editor for manual editing after extracting its annotations.", + help="Open note in editor for manual editing after annotation extraction.", ) @click.option( "--template", @@ -82,23 +80,19 @@ def main( return if template == "csv": - template_type = Csv() - else: - template_type = Markdown() - - run(documents, edit=manual, write=write, git=git, template=template_type) + raise NotImplementedError + run(documents, edit=manual, write=write, git=git, template=MarkdownFormatter()) def run( documents: list[Document], + template: Formatter, edit: bool = False, write: bool = False, git: bool = False, - template: Templating = Markdown(), ) -> None: - doc_annotations: list[AnnotatedDocument] = extractor.start(documents) - + template.annotated_docs = extractor.start(documents) if write: - exporter.to_notes(doc_annotations, template, edit=edit, git=git) + exporter.to_notes(template, edit=edit, git=git) else: - exporter.to_stdout(doc_annotations, template) + exporter.to_stdout(template) diff --git a/papis_extract/annotation_data.py b/papis_extract/annotation_data.py index 5fd5546..f0bad88 100644 --- a/papis_extract/annotation_data.py +++ b/papis_extract/annotation_data.py @@ -5,8 +5,6 @@ import papis.config from papis.document import Document import chevron -from papis_extract.templating import Templating - TEXT_SIMILARITY_MINIMUM = 0.75 COLOR_SIMILARITY_MINIMUM = 0.833 @@ -36,7 +34,7 @@ class Annotation: type: str = "Highlight" minimum_similarity_color: float = 1.0 - def format(self, template: Templating): + def format(self, template: str, doc: Document = Document()): """Return a formatted string of the annotation. Given a provided formatting pattern, this method returns the annotation @@ -50,8 +48,9 @@ class Annotation: "page": self.page, "tag": self.tag, "type": self.type, + "doc": doc, } - return chevron.render(template.string, data) + return chevron.render(template, data) @property def colorname(self): @@ -89,6 +88,7 @@ class AnnotatedDocument: """Contains all annotations belonging to a single papis document. Combines a document with a list of annotations which belong to it.""" + document: Document annotations: list[Annotation] diff --git a/papis_extract/exporter.py b/papis_extract/exporter.py index 8e05c6c..14ee617 100644 --- a/papis_extract/exporter.py +++ b/papis_extract/exporter.py @@ -7,62 +7,34 @@ import papis.git import papis.config import Levenshtein -from papis_extract.annotation_data import AnnotatedDocument -from papis_extract.templating import Templating +from papis_extract.formatter import Formatter logger = papis.logging.get_logger(__name__) -def to_stdout(annots: list[AnnotatedDocument], template: Templating) -> None: +def to_stdout(template: Formatter) -> None: """Pretty print annotations to stdout. Gives a nice human-readable representations of the annotations in somewhat of a list form. Not intended for machine-readability. """ - if not annots: - return - - last = annots[-1] - for entry in annots: - if not entry.annotations: - continue - - title_decoration = ( - f"{'=' * len(entry.document.get('title', ''))} " - f"{'-' * len(entry.document.get('author', ''))}" - ) - print( - f"{title_decoration}\n{papis.document.describe(entry.document)}\n{title_decoration}\n" - ) - for a in entry.annotations: - print(a.format(template)) - - if entry != last: - print("\n") + output:str = template.execute() + print(output.rstrip('\n')) -def to_notes( - annots: list[AnnotatedDocument], template: Templating, edit: bool, git: bool -) -> None: +def to_notes(template: Formatter, edit: bool, git: bool) -> None: """Write annotations into document notes. Permanently writes the given annotations into notes belonging to papis documents. Creates new notes for documents missing a note field or appends to existing. """ - if not annots: - return - - for entry in annots: - if not entry.annotations: - continue - - formatted_annotations: list[str] = [] - for a in entry.annotations: - formatted_annotations.append(a.format(template)) - - _add_annots_to_note(entry.document, formatted_annotations) + annotated_docs = template.annotated_docs + for entry in annotated_docs: + formatted_annotations = template.execute(entry).split("\n") + if formatted_annotations: + _add_annots_to_note(entry.document, formatted_annotations) if edit: papis.commands.edit.edit_notes(entry.document, git=git) @@ -117,7 +89,7 @@ def _drop_existing_annotations( ) -> list[str]: """Returns the input annotations dropping any existing. - Takes a list of formatted annotations and a list of strings + Takes a list of formatted annotations and a list of strings (most probably existing lines in a file). If anny annotations match an existing line closely enough, they will be dropped. @@ -130,7 +102,9 @@ def _drop_existing_annotations( remaining: list[str] = [] for an in formatted_annotations: an_split = an.splitlines() - if not _test_similarity(an_split[0], file_lines, minimum_similarity): + if an_split and not _test_similarity( + an_split[0], file_lines, minimum_similarity + ): remaining.append(an) return remaining diff --git a/papis_extract/formatter.py b/papis_extract/formatter.py new file mode 100644 index 0000000..3b921dc --- /dev/null +++ b/papis_extract/formatter.py @@ -0,0 +1,100 @@ +from dataclasses import dataclass, field +from typing import Protocol + +from papis_extract.annotation_data import AnnotatedDocument + + +@dataclass +class Formatter(Protocol): + annotated_docs: list[AnnotatedDocument] + header: str + string: str + footer: str + + def execute(self, doc: AnnotatedDocument | None = None) -> str: + raise NotImplementedError + + +@dataclass +class MarkdownFormatter: + annotated_docs: list[AnnotatedDocument] = field(default_factory=lambda: list()) + header: str = "" + string: str = ( + "{{#tag}}#{{tag}}\n{{/tag}}" + "{{#quote}}> {{quote}}{{/quote}} {{#page}}[p. {{page}}]{{/page}}\n" + "{{#note}} NOTE: {{note}}{{/note}}" + ) + footer: str = "" + + def execute(self, doc: AnnotatedDocument | None = None) -> str: + output = "" + documents = self.annotated_docs if doc is None else [doc] + last = documents[-1] + for entry in documents: + if not entry.annotations: + continue + + title_decoration = ( + f"{'=' * len(entry.document.get('title', ''))} " + f"{'-' * len(entry.document.get('author', ''))}" + ) + output += ( + f"{title_decoration}\n" + f"{entry.document['title']} - {entry.document['author']}\n" + f"{title_decoration}\n\n" + ) + for a in entry.annotations: + output += a.format(self.string) + + if entry != last: + print(f"entry: {entry}, last: {last}") + output += "\n\n\n" + + return output + +@dataclass +class CountFormatter: + annotated_docs: list[AnnotatedDocument] = field(default_factory=lambda: list()) + header: str = "" + string: str = "" + footer: str = "" + + def execute(self, doc: AnnotatedDocument | None = None) -> str: + output = "" + documents = self.annotated_docs if doc is None else [doc] + last = documents[-1] + for entry in documents: + if not entry.annotations: + continue + + title_decoration = ( + f"{'=' * len(entry.document.get('title', ''))} " + f"{'-' * len(entry.document.get('author', ''))}" + ) + output += ( + f"{title_decoration}\n" + f"{entry.document['title']} - {entry.document['author']}\n" + f"{title_decoration}\n\n" + ) + for a in entry.annotations: + output += a.format(self.string) + + if entry != last: + print(f"entry: {entry}, last: {last}") + output += "\n\n\n" + + return output + +@dataclass +class CsvFormatter: + header: str = "type, tag, page, quote, note, file" + string: str = "{{type}}, {{tag}}, {{page}}, {{quote}}, {{note}}, {{file}}" + footer: str = "" + + +@dataclass +class CustomFormatter: + def __init__(self, header: str = "", string: str = "", footer: str = "") -> None: + self.header = header + self.string = string + self.footer = footer diff --git a/papis_extract/templating.py b/papis_extract/templating.py deleted file mode 100644 index c8abf7f..0000000 --- a/papis_extract/templating.py +++ /dev/null @@ -1,35 +0,0 @@ -from dataclasses import dataclass -from typing import Protocol - - -@dataclass -class Templating(Protocol): - header: str - string: str - footer: str - - -@dataclass -class Markdown: - header: str = "" - string: str = ( - "{{#tag}}#{{tag}}\n{{/tag}}" - "{{#quote}}> {{quote}}{{/quote}} {{#page}}[p. {{page}}]{{/page}}\n" - "{{#note}} NOTE: {{note}}{{/note}}" - ) - footer: str = "" - - -@dataclass -class Csv: - header: str = "type, tag, page, quote, note, file" - string: str = "{{type}}, {{tag}}, {{page}}, {{quote}}, {{note}}, {{file}}" - footer: str = "" - - -@dataclass -class Custom: - def __init__(self, header: str = "", string: str = "", footer: str = "") -> None: - self.header = header - self.string = string - self.footer = footer From 5f0bc2ffad4c0da067b90395b23e2030298c2c85 Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Wed, 20 Sep 2023 08:38:06 +0200 Subject: [PATCH 018/107] feat: Add count formatter Added formatter which counts and outputs the number of annotations in each document. --- papis_extract/__init__.py | 11 ++++++++--- papis_extract/formatter.py | 30 +++++++++++++----------------- 2 files changed, 21 insertions(+), 20 deletions(-) diff --git a/papis_extract/__init__.py b/papis_extract/__init__.py index 026e613..e09b99d 100644 --- a/papis_extract/__init__.py +++ b/papis_extract/__init__.py @@ -8,7 +8,7 @@ import papis.strings from papis.document import Document from papis_extract import extractor, exporter -from papis_extract.formatter import MarkdownFormatter, Formatter +from papis_extract.formatter import CountFormatter, MarkdownFormatter, Formatter logger = papis.logging.get_logger(__name__) @@ -43,7 +43,7 @@ papis.config.register_default_settings(DEFAULT_OPTIONS) @click.option( "--template", "-t", - type=click.Choice(["markdown", "csv"], case_sensitive=False), + type=click.Choice(["markdown", "count", "csv"], case_sensitive=False), help="Choose an output template to format annotations with.", ) def main( @@ -81,7 +81,12 @@ def main( if template == "csv": raise NotImplementedError - run(documents, edit=manual, write=write, git=git, template=MarkdownFormatter()) + elif template == "count": + formatter = CountFormatter() + else: + formatter = MarkdownFormatter() + + run(documents, edit=manual, write=write, git=git, template=formatter) def run( diff --git a/papis_extract/formatter.py b/papis_extract/formatter.py index 3b921dc..6602a31 100644 --- a/papis_extract/formatter.py +++ b/papis_extract/formatter.py @@ -47,11 +47,11 @@ class MarkdownFormatter: output += a.format(self.string) if entry != last: - print(f"entry: {entry}, last: {last}") output += "\n\n\n" return output + @dataclass class CountFormatter: annotated_docs: list[AnnotatedDocument] = field(default_factory=lambda: list()) @@ -60,31 +60,27 @@ class CountFormatter: footer: str = "" def execute(self, doc: AnnotatedDocument | None = None) -> str: - output = "" documents = self.annotated_docs if doc is None else [doc] - last = documents[-1] + output = "" for entry in documents: if not entry.annotations: continue - title_decoration = ( - f"{'=' * len(entry.document.get('title', ''))} " - f"{'-' * len(entry.document.get('author', ''))}" - ) - output += ( - f"{title_decoration}\n" - f"{entry.document['title']} - {entry.document['author']}\n" - f"{title_decoration}\n\n" - ) - for a in entry.annotations: - output += a.format(self.string) + count = 0 + for _ in entry.annotations: + count += 1 - if entry != last: - print(f"entry: {entry}, last: {last}") - output += "\n\n\n" + d = entry.document + output += ( + f"{d['author'] if 'author' in d else ''}" + f"{' - ' if 'author' in d else ''}" # only put separator if author + f"{entry.document['title'] if 'title' in d else ''}: " + f"{count}\n" + ) return output + @dataclass class CsvFormatter: header: str = "type, tag, page, quote, note, file" From e511ffa48d8c59e9e8b01a343a3b8d2e97832af6 Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Wed, 20 Sep 2023 08:49:55 +0200 Subject: [PATCH 019/107] feat: Add CSV formatter Added formatter for csv-compatible syntax. The formatting is quite basic with no escaping happening should that be necessary. However, for an initial csv output it suffices for me. --- papis_extract/__init__.py | 19 ++++++++++++------- papis_extract/annotation_data.py | 4 ++-- papis_extract/exporter.py | 10 +++++----- papis_extract/formatter.py | 24 +++++++++++++++++++++--- 4 files changed, 40 insertions(+), 17 deletions(-) diff --git a/papis_extract/__init__.py b/papis_extract/__init__.py index e09b99d..6b38f9a 100644 --- a/papis_extract/__init__.py +++ b/papis_extract/__init__.py @@ -8,7 +8,12 @@ import papis.strings from papis.document import Document from papis_extract import extractor, exporter -from papis_extract.formatter import CountFormatter, MarkdownFormatter, Formatter +from papis_extract.formatter import ( + CountFormatter, + CsvFormatter, + MarkdownFormatter, + Formatter, +) logger = papis.logging.get_logger(__name__) @@ -80,24 +85,24 @@ def main( return if template == "csv": - raise NotImplementedError + formatter = CsvFormatter() elif template == "count": formatter = CountFormatter() else: formatter = MarkdownFormatter() - run(documents, edit=manual, write=write, git=git, template=formatter) + run(documents, edit=manual, write=write, git=git, formatter=formatter) def run( documents: list[Document], - template: Formatter, + formatter: Formatter, edit: bool = False, write: bool = False, git: bool = False, ) -> None: - template.annotated_docs = extractor.start(documents) + formatter.annotated_docs = extractor.start(documents) if write: - exporter.to_notes(template, edit=edit, git=git) + exporter.to_notes(formatter, edit=edit, git=git) else: - exporter.to_stdout(template) + exporter.to_stdout(formatter) diff --git a/papis_extract/annotation_data.py b/papis_extract/annotation_data.py index f0bad88..138b755 100644 --- a/papis_extract/annotation_data.py +++ b/papis_extract/annotation_data.py @@ -34,7 +34,7 @@ class Annotation: type: str = "Highlight" minimum_similarity_color: float = 1.0 - def format(self, template: str, doc: Document = Document()): + def format(self, formatting: str, doc: Document = Document()): """Return a formatted string of the annotation. Given a provided formatting pattern, this method returns the annotation @@ -50,7 +50,7 @@ class Annotation: "type": self.type, "doc": doc, } - return chevron.render(template, data) + return chevron.render(formatting, data) @property def colorname(self): diff --git a/papis_extract/exporter.py b/papis_extract/exporter.py index 14ee617..8f03ebd 100644 --- a/papis_extract/exporter.py +++ b/papis_extract/exporter.py @@ -12,27 +12,27 @@ from papis_extract.formatter import Formatter logger = papis.logging.get_logger(__name__) -def to_stdout(template: Formatter) -> None: +def to_stdout(formatter: Formatter) -> None: """Pretty print annotations to stdout. Gives a nice human-readable representations of the annotations in somewhat of a list form. Not intended for machine-readability. """ - output:str = template.execute() + output:str = formatter.execute() print(output.rstrip('\n')) -def to_notes(template: Formatter, edit: bool, git: bool) -> None: +def to_notes(formatter: Formatter, edit: bool, git: bool) -> None: """Write annotations into document notes. Permanently writes the given annotations into notes belonging to papis documents. Creates new notes for documents missing a note field or appends to existing. """ - annotated_docs = template.annotated_docs + annotated_docs = formatter.annotated_docs for entry in annotated_docs: - formatted_annotations = template.execute(entry).split("\n") + formatted_annotations = formatter.execute(entry).split("\n") if formatted_annotations: _add_annots_to_note(entry.document, formatted_annotations) diff --git a/papis_extract/formatter.py b/papis_extract/formatter.py index 6602a31..d687607 100644 --- a/papis_extract/formatter.py +++ b/papis_extract/formatter.py @@ -73,7 +73,7 @@ class CountFormatter: d = entry.document output += ( f"{d['author'] if 'author' in d else ''}" - f"{' - ' if 'author' in d else ''}" # only put separator if author + f"{' - ' if 'author' in d else ''}" # only put separator if author f"{entry.document['title'] if 'title' in d else ''}: " f"{count}\n" ) @@ -83,10 +83,28 @@ class CountFormatter: @dataclass class CsvFormatter: - header: str = "type, tag, page, quote, note, file" - string: str = "{{type}}, {{tag}}, {{page}}, {{quote}}, {{note}}, {{file}}" + annotated_docs: list[AnnotatedDocument] = field(default_factory=lambda: list()) + header: str = "type,tag,page,quote,note,author,title,ref,file" + string: str = ( + '{{type}},{{tag}},{{page}},"{{quote}}","{{note}}",' + '"{{doc.author}}","{{doc.title}}","{{doc.ref}}","{{file}}"' + ) footer: str = "" + def execute(self, doc: AnnotatedDocument | None = None) -> str: + documents = self.annotated_docs if doc is None else [doc] + output = f"{self.header}\n" + for entry in documents: + if not entry.annotations: + continue + + d = entry.document + for a in entry.annotations: + output += a.format(self.string, doc=d) + output += "\n" + + return output + @dataclass class CustomFormatter: From 3670f70319c8d9aa6c14be5982c4ac6572afe09a Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Wed, 20 Sep 2023 09:03:08 +0200 Subject: [PATCH 020/107] docs: Add formatting documentation Added documentation on using output templates and that they will invalidate the 'existing' annotation search. --- README.md | 28 +++++++++++++++++++++++++++- papis_extract/__init__.py | 3 --- 2 files changed, 27 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index 89052bf..95ec9ce 100644 --- a/README.md +++ b/README.md @@ -11,7 +11,7 @@ Easily organize all your highlights and thoughts next to your documents and refe ## Installation: -You can install from pypi with `pip install git+https://git.martyoeh.me/Marty/papis-extract.git`. +You can install through pip with `pip install git+https://git.martyoeh.me/Marty/papis-extract.git`. That's it! If you have papis and papis-extract installed in the same environment (whether virtual or global), everything should now be set up. @@ -87,6 +87,30 @@ On my current laptop, extracting ~4000 annotations from ~1000 library documents though this will vary with the length and size of the PDFs you have. For smaller workloads the process should be almost instant. +You can change the format that you want your annotations in with the `--template` option. +To output annotations in a markdown-compatible syntax (the default), do: + +```bash +papis extract --template markdown +``` + +To instead see them in a csv syntax simply invoke: + +```bash +papis extract --template csv +``` + +And if you only want to know how many annotations exist in the documents, you can invoke: + +```bash +papis extract --template count +``` + +For now, these are the only formatters the plugin knows about. + +Be aware that if you write to your notes using a different template the plugin will *not* detect old annotations and drop them, +so you will be doubling up your annotations. + ## Configuration ### Basic configuration @@ -181,6 +205,8 @@ Known issues to be fixed: - [x] docstrings, docstrings! - [ ] testing testing testing!! - [ ] refactor into some better abstractions (e.g. Exporter Protocol -> stdout/markdown implementations; Extractor Protocol -> PDF implementation) +- [ ] dependency injection for extractor/exporter/formatter/annotation modules + - [ ] any call to papis.config should start from init and be injected? features to be implemented: diff --git a/papis_extract/__init__.py b/papis_extract/__init__.py index 6b38f9a..f8f6941 100644 --- a/papis_extract/__init__.py +++ b/papis_extract/__init__.py @@ -53,12 +53,9 @@ papis.config.register_default_settings(DEFAULT_OPTIONS) ) def main( query: str, - # info: bool, # _papis_id: bool, # _file: bool, - # notes: bool, # _dir: bool, - # _format: str, _all: bool, doc_folder: str, manual: bool, From 31b878c9eb9dac75d9fc860a08d8084c8461bdce Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Wed, 20 Sep 2023 17:22:29 +0200 Subject: [PATCH 021/107] refactor: Move Annotations into annotation module --- papis_extract/{annotation_data.py => annotation.py} | 0 papis_extract/extractor.py | 2 +- papis_extract/formatter.py | 2 +- 3 files changed, 2 insertions(+), 2 deletions(-) rename papis_extract/{annotation_data.py => annotation.py} (100%) diff --git a/papis_extract/annotation_data.py b/papis_extract/annotation.py similarity index 100% rename from papis_extract/annotation_data.py rename to papis_extract/annotation.py diff --git a/papis_extract/extractor.py b/papis_extract/extractor.py index f6802f0..bdb8780 100644 --- a/papis_extract/extractor.py +++ b/papis_extract/extractor.py @@ -10,7 +10,7 @@ import papis.config import papis.document from papis.document import Document -from papis_extract.annotation_data import Annotation, AnnotatedDocument +from papis_extract.annotation import Annotation, AnnotatedDocument logger = papis.logging.get_logger(__name__) diff --git a/papis_extract/formatter.py b/papis_extract/formatter.py index d687607..4ba782d 100644 --- a/papis_extract/formatter.py +++ b/papis_extract/formatter.py @@ -1,7 +1,7 @@ from dataclasses import dataclass, field from typing import Protocol -from papis_extract.annotation_data import AnnotatedDocument +from papis_extract.annotation import AnnotatedDocument @dataclass From 929e70d7ac42337220ae7e5b998b5e22eb7002c5 Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Thu, 21 Sep 2023 19:36:00 +0200 Subject: [PATCH 022/107] chore: Update poetry.lock --- poetry.lock | 305 ++++++++++++++++++++++++++++------------------------ 1 file changed, 162 insertions(+), 143 deletions(-) diff --git a/poetry.lock b/poetry.lock index 1336bfc..963b69b 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand. 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[[package]] @@ -939,13 +955,13 @@ telegram = ["requests"] [[package]] name = "typing-extensions" -version = "4.7.1" -description = "Backported and Experimental Type Hints for Python 3.7+" +version = "4.8.0" +description = "Backported and Experimental Type Hints for Python 3.8+" optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" files = [ - {file = "typing_extensions-4.7.1-py3-none-any.whl", hash = "sha256:440d5dd3af93b060174bf433bccd69b0babc3b15b1a8dca43789fd7f61514b36"}, - {file = "typing_extensions-4.7.1.tar.gz", hash = "sha256:b75ddc264f0ba5615db7ba217daeb99701ad295353c45f9e95963337ceeeffb2"}, + {file = "typing_extensions-4.8.0-py3-none-any.whl", hash = "sha256:8f92fc8806f9a6b641eaa5318da32b44d401efaac0f6678c9bc448ba3605faa0"}, + {file = "typing_extensions-4.8.0.tar.gz", hash = "sha256:df8e4339e9cb77357558cbdbceca33c303714cf861d1eef15e1070055ae8b7ef"}, ] [[package]] @@ -980,7 +996,7 @@ files = [ name = "whoosh" version = "2.7.4" description = "Fast, pure-Python full text indexing, search, and spell checking library." -optional = false +optional = true python-versions = "*" files = [ {file = "Whoosh-2.7.4-py2.py3-none-any.whl", hash = "sha256:aa39c3c3426e3fd107dcb4bde64ca1e276a65a889d9085a6e4b54ba82420a852"}, @@ -988,7 +1004,10 @@ files = [ {file = "Whoosh-2.7.4.zip", hash = "sha256:e0857375f63e9041e03fedd5b7541f97cf78917ac1b6b06c1fcc9b45375dda69"}, ] +[extras] +whoosh = ["whoosh"] + [metadata] lock-version = "2.0" python-versions = "^3.11" -content-hash = "a3af36ed2941235df158c20ba9b66bdf5a0af0554235fd004ec77c3e88def3c3" +content-hash = "9eda99eff02c403365445d0e75fcc21ed7649a59407d358d0cd429a034cbc6c9" From 7ee8d4911e0ee2e323e29218dd4d30dad238ce97 Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Thu, 21 Sep 2023 21:54:24 +0200 Subject: [PATCH 023/107] refactor: Make formatters functions Formatters have been classes so far which contained some data (the tamplate to use for formatting and the annotations and documents to format) and the actual formatting logic (an execute function). However, we can inject the annotations to be formatted and the templates so far are static only, so they can be simple variables (we can think about how to inject them at another point should it come up, no bikeshedding now). This way, we can simply pass around one function per formatter, which should make the code much lighter, easier to add to and especially less stateful which means less areas of broken interactions to worry about. --- papis_extract/__init__.py | 21 +++--- papis_extract/exporter.py | 17 +++-- papis_extract/formatter.py | 142 +++++++++++++------------------------ 3 files changed, 70 insertions(+), 110 deletions(-) diff --git a/papis_extract/__init__.py b/papis_extract/__init__.py index f8f6941..9f9ad17 100644 --- a/papis_extract/__init__.py +++ b/papis_extract/__init__.py @@ -8,12 +8,7 @@ import papis.strings from papis.document import Document from papis_extract import extractor, exporter -from papis_extract.formatter import ( - CountFormatter, - CsvFormatter, - MarkdownFormatter, - Formatter, -) +from papis_extract.formatter import Formatter, format_count, format_csv, format_markdown logger = papis.logging.get_logger(__name__) @@ -82,11 +77,11 @@ def main( return if template == "csv": - formatter = CsvFormatter() + formatter = format_csv elif template == "count": - formatter = CountFormatter() + formatter = format_count else: - formatter = MarkdownFormatter() + formatter = format_markdown run(documents, edit=manual, write=write, git=git, formatter=formatter) @@ -98,8 +93,10 @@ def run( write: bool = False, git: bool = False, ) -> None: - formatter.annotated_docs = extractor.start(documents) + annotated_docs = extractor.start(documents) if write: - exporter.to_notes(formatter, edit=edit, git=git) + exporter.to_notes( + formatter=formatter, annotated_docs=annotated_docs, edit=edit, git=git + ) else: - exporter.to_stdout(formatter) + exporter.to_stdout(formatter=formatter, annotated_docs=annotated_docs) diff --git a/papis_extract/exporter.py b/papis_extract/exporter.py index 8f03ebd..5d22270 100644 --- a/papis_extract/exporter.py +++ b/papis_extract/exporter.py @@ -6,33 +6,35 @@ import papis.api import papis.git import papis.config import Levenshtein +from papis_extract.annotation import AnnotatedDocument from papis_extract.formatter import Formatter logger = papis.logging.get_logger(__name__) -def to_stdout(formatter: Formatter) -> None: +def to_stdout(formatter: Formatter, annotated_docs: list[AnnotatedDocument]) -> None: """Pretty print annotations to stdout. Gives a nice human-readable representations of the annotations in somewhat of a list form. Not intended for machine-readability. """ - output:str = formatter.execute() - print(output.rstrip('\n')) + output: str = formatter(annotated_docs) + print(output.rstrip("\n")) -def to_notes(formatter: Formatter, edit: bool, git: bool) -> None: +def to_notes( + formatter: Formatter, annotated_docs: list[AnnotatedDocument], edit: bool, git: bool +) -> None: """Write annotations into document notes. Permanently writes the given annotations into notes belonging to papis documents. Creates new notes for documents missing a note field or appends to existing. """ - annotated_docs = formatter.annotated_docs for entry in annotated_docs: - formatted_annotations = formatter.execute(entry).split("\n") + formatted_annotations = formatter([entry]).split("\n") if formatted_annotations: _add_annots_to_note(entry.document, formatted_annotations) @@ -67,7 +69,8 @@ def _add_annots_to_note( # add newline if theres no empty space at file end if len(existing) > 0 and existing[-1].strip() != "": f.write("\n") - f.write("\n".join(new_annotations)) + print(new_annotations) + f.write("\n\n".join(new_annotations)) f.write("\n") logger.info( f"Wrote {len(new_annotations)} " diff --git a/papis_extract/formatter.py b/papis_extract/formatter.py index 4ba782d..75056ea 100644 --- a/papis_extract/formatter.py +++ b/papis_extract/formatter.py @@ -1,114 +1,74 @@ -from dataclasses import dataclass, field -from typing import Protocol +from collections.abc import Callable from papis_extract.annotation import AnnotatedDocument - -@dataclass -class Formatter(Protocol): - annotated_docs: list[AnnotatedDocument] - header: str - string: str - footer: str - - def execute(self, doc: AnnotatedDocument | None = None) -> str: - raise NotImplementedError +Formatter = Callable[[list[AnnotatedDocument]], str] -@dataclass -class MarkdownFormatter: - annotated_docs: list[AnnotatedDocument] = field(default_factory=lambda: list()) - header: str = "" - string: str = ( +def format_markdown(docs: list[AnnotatedDocument] = []) -> str: + template = ( "{{#tag}}#{{tag}}\n{{/tag}}" - "{{#quote}}> {{quote}}{{/quote}} {{#page}}[p. {{page}}]{{/page}}\n" - "{{#note}} NOTE: {{note}}{{/note}}" + "{{#quote}}> {{quote}}{{/quote}} {{#page}}[p. {{page}}]{{/page}}" + "\n{{#note}} NOTE: {{note}}{{/note}}" ) - footer: str = "" + output = "" + for entry in docs: + if not entry.annotations: + continue - def execute(self, doc: AnnotatedDocument | None = None) -> str: - output = "" - documents = self.annotated_docs if doc is None else [doc] - last = documents[-1] - for entry in documents: - if not entry.annotations: - continue + title_decoration = ( + f"{'=' * len(entry.document.get('title', ''))} " + f"{'-' * len(entry.document.get('author', ''))}" + ) + output += ( + f"{title_decoration}\n" + f"{entry.document['title']} - {entry.document['author']}\n" + f"{title_decoration}\n\n" + ) + for a in entry.annotations: + output += a.format(template) + output += "\n" - title_decoration = ( - f"{'=' * len(entry.document.get('title', ''))} " - f"{'-' * len(entry.document.get('author', ''))}" - ) - output += ( - f"{title_decoration}\n" - f"{entry.document['title']} - {entry.document['author']}\n" - f"{title_decoration}\n\n" - ) - for a in entry.annotations: - output += a.format(self.string) + output += "\n\n\n" - if entry != last: - output += "\n\n\n" - - return output + return output -@dataclass -class CountFormatter: - annotated_docs: list[AnnotatedDocument] = field(default_factory=lambda: list()) - header: str = "" - string: str = "" - footer: str = "" +def format_count(docs: list[AnnotatedDocument] = []) -> str: + output = "" + for entry in docs: + if not entry.annotations: + continue - def execute(self, doc: AnnotatedDocument | None = None) -> str: - documents = self.annotated_docs if doc is None else [doc] - output = "" - for entry in documents: - if not entry.annotations: - continue + count = 0 + for _ in entry.annotations: + count += 1 - count = 0 - for _ in entry.annotations: - count += 1 + d = entry.document + output += ( + f"{d['author'] if 'author' in d else ''}" + f"{' - ' if 'author' in d else ''}" # only put separator if author + f"{entry.document['title'] if 'title' in d else ''}: " + f"{count}\n" + ) - d = entry.document - output += ( - f"{d['author'] if 'author' in d else ''}" - f"{' - ' if 'author' in d else ''}" # only put separator if author - f"{entry.document['title'] if 'title' in d else ''}: " - f"{count}\n" - ) - - return output + return output -@dataclass -class CsvFormatter: - annotated_docs: list[AnnotatedDocument] = field(default_factory=lambda: list()) +def format_csv(docs: list[AnnotatedDocument] = []) -> str: header: str = "type,tag,page,quote,note,author,title,ref,file" - string: str = ( + template: str = ( '{{type}},{{tag}},{{page}},"{{quote}}","{{note}}",' '"{{doc.author}}","{{doc.title}}","{{doc.ref}}","{{file}}"' ) - footer: str = "" + output = f"{header}\n" + for entry in docs: + if not entry.annotations: + continue - def execute(self, doc: AnnotatedDocument | None = None) -> str: - documents = self.annotated_docs if doc is None else [doc] - output = f"{self.header}\n" - for entry in documents: - if not entry.annotations: - continue + d = entry.document + for a in entry.annotations: + output += a.format(template, doc=d) + output += "\n" - d = entry.document - for a in entry.annotations: - output += a.format(self.string, doc=d) - output += "\n" - - return output - - -@dataclass -class CustomFormatter: - def __init__(self, header: str = "", string: str = "", footer: str = "") -> None: - self.header = header - self.string = string - self.footer = footer + return output From ee4690f52bc33f1ff9e7c13d5f3153abacd82219 Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Thu, 21 Sep 2023 22:01:51 +0200 Subject: [PATCH 024/107] feat: Add atx-style markdown Added markdown with atx style headers, can be chosen as alternative markdown template on the cli. The existing 'markdown' template will still default to setext-style headers. --- README.md | 6 +++++- papis_extract/__init__.py | 17 ++++++++-------- papis_extract/formatter.py | 40 ++++++++++++++++++++++++++++---------- 3 files changed, 44 insertions(+), 19 deletions(-) diff --git a/README.md b/README.md index 95ec9ce..b65623a 100644 --- a/README.md +++ b/README.md @@ -94,6 +94,9 @@ To output annotations in a markdown-compatible syntax (the default), do: papis extract --template markdown ``` +There are sub-variants of the formatter for atx-style headers, with `--template markdown-atx` (`# Headings`), +or setext-style with `--template markdown-setext` (the default style). + To instead see them in a csv syntax simply invoke: ```bash @@ -227,7 +230,8 @@ features to be implemented: - [ ] allow custom colors -> tag name settings not dependent on color name existing (e.g. {"important": (1.0,0.0,0.0)}) - [ ] `--overwrite` mode where existing annotations are not dropped but overwritten on same line of note - [ ] `--force` mode where we simply do not drop anything -- [ ] `--format` option to choose from default or set up a custom formatter +- [x] `--format` option to choose from default or set up a custom formatter + - called `--template` in current implementation - [ ] on_add hook to extract annotations as files are added - needs upstream help, 'on_add' hook, and pass-through of affected documents diff --git a/papis_extract/__init__.py b/papis_extract/__init__.py index 9f9ad17..e679e6a 100644 --- a/papis_extract/__init__.py +++ b/papis_extract/__init__.py @@ -8,7 +8,10 @@ import papis.strings from papis.document import Document from papis_extract import extractor, exporter -from papis_extract.formatter import Formatter, format_count, format_csv, format_markdown +from papis_extract.formatter import ( + Formatter, + formatters +) logger = papis.logging.get_logger(__name__) @@ -43,7 +46,10 @@ papis.config.register_default_settings(DEFAULT_OPTIONS) @click.option( "--template", "-t", - type=click.Choice(["markdown", "count", "csv"], case_sensitive=False), + type=click.Choice( + ["markdown", "markdown-setext", "markdown-atx", "count", "csv"], + case_sensitive=False, + ), help="Choose an output template to format annotations with.", ) def main( @@ -76,12 +82,7 @@ def main( logger.warning(papis.strings.no_documents_retrieved_message) return - if template == "csv": - formatter = format_csv - elif template == "count": - formatter = format_count - else: - formatter = format_markdown + formatter = formatters[template] run(documents, edit=manual, write=write, git=git, formatter=formatter) diff --git a/papis_extract/formatter.py b/papis_extract/formatter.py index 75056ea..b00a2ee 100644 --- a/papis_extract/formatter.py +++ b/papis_extract/formatter.py @@ -5,7 +5,9 @@ from papis_extract.annotation import AnnotatedDocument Formatter = Callable[[list[AnnotatedDocument]], str] -def format_markdown(docs: list[AnnotatedDocument] = []) -> str: +def format_markdown( + docs: list[AnnotatedDocument] = [], atx_headings: bool = False +) -> str: template = ( "{{#tag}}#{{tag}}\n{{/tag}}" "{{#quote}}> {{quote}}{{/quote}} {{#page}}[p. {{page}}]{{/page}}" @@ -16,15 +18,16 @@ def format_markdown(docs: list[AnnotatedDocument] = []) -> str: if not entry.annotations: continue - title_decoration = ( - f"{'=' * len(entry.document.get('title', ''))} " - f"{'-' * len(entry.document.get('author', ''))}" - ) - output += ( - f"{title_decoration}\n" - f"{entry.document['title']} - {entry.document['author']}\n" - f"{title_decoration}\n\n" - ) + heading = f"{entry.document['title']} - {entry.document['author']}\n" + if atx_headings: + output += f"# {heading}\n" + else: + title_decoration = ( + f"{'=' * len(entry.document.get('title', ''))} " + f"{'-' * len(entry.document.get('author', ''))}" + ) + output += f"{title_decoration}\n" f"{heading}" f"{title_decoration}\n\n" + for a in entry.annotations: output += a.format(template) output += "\n" @@ -34,6 +37,14 @@ def format_markdown(docs: list[AnnotatedDocument] = []) -> str: return output +def format_markdown_atx(docs: list[AnnotatedDocument] = []) -> str: + return format_markdown(docs, atx_headings=True) + + +def format_markdown_setext(docs: list[AnnotatedDocument] = []) -> str: + return format_markdown(docs, atx_headings=False) + + def format_count(docs: list[AnnotatedDocument] = []) -> str: output = "" for entry in docs: @@ -72,3 +83,12 @@ def format_csv(docs: list[AnnotatedDocument] = []) -> str: output += "\n" return output + + +formatters: dict[str, Formatter] = { + "count": format_count, + "csv": format_csv, + "markdown": format_markdown, + "markdown_atx": format_markdown_atx, + "markdown_setext": format_markdown_setext, +} From 1e29642cba6ca47333bcdf9372cfcb7d910355f7 Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Fri, 22 Sep 2023 20:04:39 +0200 Subject: [PATCH 025/107] test: Fix formatting and annotation tests --- papis_extract/formatter.py | 12 +++--- tests/test_annotation.py | 31 ++++++++++---- tests/test_formatting.py | 86 +++++++++++++++++++++----------------- 3 files changed, 77 insertions(+), 52 deletions(-) diff --git a/papis_extract/formatter.py b/papis_extract/formatter.py index b00a2ee..75ed556 100644 --- a/papis_extract/formatter.py +++ b/papis_extract/formatter.py @@ -10,8 +10,8 @@ def format_markdown( ) -> str: template = ( "{{#tag}}#{{tag}}\n{{/tag}}" - "{{#quote}}> {{quote}}{{/quote}} {{#page}}[p. {{page}}]{{/page}}" - "\n{{#note}} NOTE: {{note}}{{/note}}" + "{{#quote}}> {{quote}}{{/quote}}{{#page}} [p. {{page}}]{{/page}}" + "{{#note}}\n NOTE: {{note}}{{/note}}" ) output = "" for entry in docs: @@ -30,11 +30,11 @@ def format_markdown( for a in entry.annotations: output += a.format(template) - output += "\n" + output += "\n\n" output += "\n\n\n" - return output + return output.rstrip() def format_markdown_atx(docs: list[AnnotatedDocument] = []) -> str: @@ -63,7 +63,7 @@ def format_count(docs: list[AnnotatedDocument] = []) -> str: f"{count}\n" ) - return output + return output.rstrip() def format_csv(docs: list[AnnotatedDocument] = []) -> str: @@ -82,7 +82,7 @@ def format_csv(docs: list[AnnotatedDocument] = []) -> str: output += a.format(template, doc=d) output += "\n" - return output + return output.rstrip() formatters: dict[str, Formatter] = { diff --git a/tests/test_annotation.py b/tests/test_annotation.py index 60b35ed..c14ee93 100644 --- a/tests/test_annotation.py +++ b/tests/test_annotation.py @@ -1,25 +1,23 @@ +from papis.document import Document import pytest -from papis_extract.annotation_data import Annotation -from papis_extract.templating import Custom +from papis_extract.annotation import Annotation @pytest.mark.parametrize( "fmt_string,expected", [ - (Custom(string="{{quote}}"), "I am the text value"), + ("{{quote}}", "I am the text value"), ( - Custom(string="> {{quote}}\n{{#note}}Note: {{note}}{{/note}}"), + "> {{quote}}\n{{#note}}Note: {{note}}{{/note}}", "> I am the text value\nNote: Whereas I represent the note", ), ( - Custom( - string="{{#note}}Note: {{note}}{{/note}}{{#page}}, p. {{page}}{{/page}}" - ), + "{{#note}}Note: {{note}}{{/note}}{{#page}}, p. {{page}}{{/page}}", "Note: Whereas I represent the note", ), ], ) -def test_formatting(fmt_string, expected): +def test_formatting_replacements(fmt_string, expected): sut = Annotation( "myfile", text="I am the text value", @@ -28,6 +26,23 @@ def test_formatting(fmt_string, expected): assert sut.format(fmt_string) == expected +@pytest.mark.parametrize( + "fmt_string,expected", + [ + ("{{doc.title}}", "document-title"), + ("{{doc.title}}-{{doc.author}}", "document-title-document-author"), + ("{{quote}} ({{doc.author}})", "I am the text value (document-author)"), + ] +) +def test_formatting_document_access(fmt_string, expected): + sut = Annotation( + "myfile", + text="I am the text value", + content="Whereas I represent the note", + ) + doc = Document(data= {"title": "document-title", "author": "document-author"}) + + assert sut.format(fmt_string, doc=doc) == expected def test_colorname_matches_exact(): sut = Annotation("testfile", colors=(1.0, 0.0, 0.0), minimum_similarity_color=1.0) diff --git a/tests/test_formatting.py b/tests/test_formatting.py index 5ab53c2..5aaef70 100644 --- a/tests/test_formatting.py +++ b/tests/test_formatting.py @@ -1,49 +1,59 @@ -import chevron +from papis.document import Document +from papis_extract.annotation import AnnotatedDocument, Annotation -from papis_extract.templating import Markdown, Csv +from papis_extract.formatter import ( + format_count, + format_csv, + format_markdown, + format_markdown_atx, +) - -def test_template_markers(): - ... +an_doc: AnnotatedDocument = AnnotatedDocument( + Document(data={"author": "document-author", "title": "document-title"}), + [ + Annotation("myfile.pdf", text="my lovely text"), + Annotation("myfile.pdf", text="my second text", content="with note"), + ], +) def test_markdown_default(): - fmt = Markdown() - assert ( - chevron.render( - fmt.string, - { - "file": "somefile/somewhere.pdf", - "quote": "I am quote", - "note": "and including note.", - "page": 46, - "tag": "important", - "type": "highlight", - }, - ) - == "#important\n> I am quote [p. 46]\n NOTE: and including note." + fmt = format_markdown + assert fmt([an_doc]) == ( + """============== --------------- +document-title - document-author +============== --------------- + +> my lovely text + +> my second text + NOTE: with note""" ) -def test_csv_string(): - fmt = Csv() - assert ( - chevron.render( - fmt.string, - { - "file": "somefile/somewhere.pdf", - "quote": "I am quote", - "note": "and including note.", - "page": 46, - "tag": "important", - "type": "highlight", - }, - ) - == "highlight, important, 46, " - "I am quote, and including note., somefile/somewhere.pdf" +def test_markdown_atx(): + fmt = format_markdown_atx + assert fmt([an_doc]) == ( + """# document-title - document-author + +> my lovely text + +> my second text + NOTE: with note""" ) -def test_csv_header(): - fmt = Csv() - assert chevron.render(fmt.header, {}) == "type, tag, page, quote, note, file" +def test_count_default(): + fmt = format_count + assert fmt([an_doc]) == ("""document-author - document-title: 2""") + + +def test_csv_default(): + fmt = format_csv + assert fmt([an_doc]) == ( + "type,tag,page,quote,note,author,title,ref,file\n" + 'Highlight,,0,"my lovely text","","document-author",' + '"document-title","","myfile.pdf"\n' + 'Highlight,,0,"my second text","with note","document-author",' + '"document-title","","myfile.pdf"' + ) From 2700e4adc3b73b0ef00e0def87ecb47231092a6a Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Fri, 22 Sep 2023 21:53:55 +0200 Subject: [PATCH 026/107] test: Add code coverage dev dependency --- poetry.lock | 66 +++++++++++++++++++++++++++++++++++++++++++++++++- pyproject.toml | 1 + 2 files changed, 66 insertions(+), 1 deletion(-) diff --git a/poetry.lock b/poetry.lock index 963b69b..886f483 100644 --- 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"^3.11" -content-hash = "9eda99eff02c403365445d0e75fcc21ed7649a59407d358d0cd429a034cbc6c9" +content-hash = "dac37f6a903033ed95f65a69f7ca90a115aa390284835c2a8e82ea3fc0a196ab" diff --git a/pyproject.toml b/pyproject.toml index 8f52f48..8551182 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -21,6 +21,7 @@ whoosh = ["whoosh"] [tool.poetry.group.dev.dependencies] pytest = "^7.4.0" +coverage = "^7.3.1" [tool.poetry.plugins."papis.command"] extract = "papis_extract:main" From f67ac8cdb35e7256f8f0be3738fe9c1289de09ee Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Thu, 12 Oct 2023 19:26:41 +0200 Subject: [PATCH 027/107] chore: Fix markdown lint issues --- .markdownlint.yaml | 6 ++++++ README.md | 22 ++++++++++++---------- 2 files changed, 18 insertions(+), 10 deletions(-) create mode 100644 .markdownlint.yaml diff --git a/.markdownlint.yaml b/.markdownlint.yaml new file mode 100644 index 0000000..9e90f00 --- /dev/null +++ b/.markdownlint.yaml @@ -0,0 +1,6 @@ +MD013: false + +MD025: false + +MD007: + indent: 4 diff --git a/README.md b/README.md index b65623a..70d7afc 100644 --- a/README.md +++ b/README.md @@ -8,7 +8,7 @@ Quickly extract annotations from your pdf files with the help of the [papis](https://github.com/papis/papis) bibliography manager.\ Easily organize all your highlights and thoughts next to your documents and references.\ -## Installation: +## Installation You can install through pip with `pip install git+https://git.martyoeh.me/Marty/papis-extract.git`. @@ -24,7 +24,8 @@ You will be set up with the default options but if you want to change anything, > **Note** > This plugin is still in fairly early development. It does what I need it to do, but if you have a meticulously organized library *please* make backups before doing any operation which could affect your notes, or make use of the papis-included git options. -## Usage: + +## Usage `papis extract [OPTIONS] [QUERY]` @@ -117,6 +118,7 @@ so you will be doubling up your annotations. ## Configuration ### Basic configuration + Add `extract` plugin settings to your papis `config` file (usually `~/.config/papis/config`): You will rarely have to set everything explained in the next few paragraphs - in fact you can use the plugin without having to set up any of it if you are happy with the defaults. @@ -148,10 +150,10 @@ regardless of this setting. ### Automatic tagging -By supplying the tags option with a valid python dictionary of the form `{"tag": "color", "tag2": "color2"}`, +By supplying the tags option with a valid python dictionary of the form `{"tag": "color", "tag2": "color2"}`, you can enable automatic tagging for your annotations. -You thus ascribe specific meanings to the colors you use in highlighting. +You thus ascribe specific meanings to the colors you use in highlighting. For example, if you always highlight the most essential arguments and findings in red and always highlight things you have to follow up on in blue, you can assign the meanings 'important' and 'todo' to them respectively as follows: @@ -174,7 +176,7 @@ minimum_similarity_content: 0.9, # for checking if highlight or note minimum_similarity_color: 0.833, # for matching tag to color ``` -`minimum_similarity` sets the required similarity of an annotation with existing annotations in your notes to be dropped. +`minimum_similarity` sets the required similarity of an annotation with existing annotations in your notes to be dropped. Annotations you have in notes might change if you for example fix small spacing mistakes or a letter/punctuation that has been falsely recognized in the PDF or change similar things. Generally, this should be fine as it is but you should change this value if you either get new annotations dropped though they should be added (decrease the value) or annotations are added duplicating existing ones (increase the value). @@ -230,7 +232,7 @@ features to be implemented: - [ ] allow custom colors -> tag name settings not dependent on color name existing (e.g. {"important": (1.0,0.0,0.0)}) - [ ] `--overwrite` mode where existing annotations are not dropped but overwritten on same line of note - [ ] `--force` mode where we simply do not drop anything -- [x] `--format` option to choose from default or set up a custom formatter +- [x] `--format` option to choose from default or set up a custom formatter - called `--template` in current implementation - [ ] on_add hook to extract annotations as files are added - needs upstream help, 'on_add' hook, and pass-through of affected documents @@ -249,11 +251,11 @@ This plugin makes an effort to find the right combination and extract the writte as well as any additional notes made - but things *will* slip through or extract weirdly every now and again. -Secondly, a note on the pages: I use the page number that the mupdf library gives me when it +Secondly, a note on the pages: I use the page number that the mupdf library gives me when it extracts anything from the pdf file. Sometimes that number will be correct for the document, sometimes it will however be the number of the *pdf document* internally. This can happen if e.g. an article or a book has frontmatter without numbering scheme or with a different one. -Sometimes the correct pages will still be embedded in the pdf and everything will work, +Sometimes the correct pages will still be embedded in the pdf and everything will work, others it won't. So always double check your page numbers! I am not sure if there is much I can do about these issues for now. @@ -266,7 +268,7 @@ and for myself whenever I forget. The basic building blocks currently in here ar : Extract data from a source file attached to a papis document. - annotations -: The actual extracted blocks of text, containing some metadata +: The actual extracted blocks of text, containing some metadata info as well, such as their color, type, page. - exporters @@ -277,7 +279,7 @@ and for myself whenever I forget. The basic building blocks currently in here ar such as a markdown syntax or csv-structure. Splitting it into those three building blocks makes it easier to recombine them in any way, -should someone want to save highlights as csv data in their notes, +should someone want to save highlights as csv data in their notes, or should we ever include more extractors than the one for PDFs. --- From c9736a5f32734fe0b19333308f850455ec863dab Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Thu, 12 Oct 2023 19:27:16 +0200 Subject: [PATCH 028/107] test: Add tests for formatter sad paths --- tests/test_formatting.py | 35 ++++++++++++++++++++++++++++------- 1 file changed, 28 insertions(+), 7 deletions(-) diff --git a/tests/test_formatting.py b/tests/test_formatting.py index 5aaef70..d9a0d0f 100644 --- a/tests/test_formatting.py +++ b/tests/test_formatting.py @@ -6,6 +6,7 @@ from papis_extract.formatter import ( format_csv, format_markdown, format_markdown_atx, + format_markdown_setext, ) an_doc: AnnotatedDocument = AnnotatedDocument( @@ -15,12 +16,7 @@ an_doc: AnnotatedDocument = AnnotatedDocument( Annotation("myfile.pdf", text="my second text", content="with note"), ], ) - - -def test_markdown_default(): - fmt = format_markdown - assert fmt([an_doc]) == ( - """============== --------------- +md_default_output = """============== --------------- document-title - document-author ============== --------------- @@ -28,7 +24,11 @@ document-title - document-author > my second text NOTE: with note""" - ) + + +def test_markdown_default(): + fmt = format_markdown + assert fmt([an_doc]) == md_default_output def test_markdown_atx(): @@ -43,6 +43,11 @@ def test_markdown_atx(): ) +def test_markdown_setext(): + fmt = format_markdown_setext + assert fmt([an_doc]) == md_default_output + + def test_count_default(): fmt = format_count assert fmt([an_doc]) == ("""document-author - document-title: 2""") @@ -57,3 +62,19 @@ def test_csv_default(): 'Highlight,,0,"my second text","with note","document-author",' '"document-title","","myfile.pdf"' ) + + +# sadpath - no annotations contained for each format +def test_markdown_no_annotations(): + d: AnnotatedDocument = AnnotatedDocument(Document(data={}), []) + assert format_markdown([d]) == "" + + +def test_count_no_annotations(): + d: AnnotatedDocument = AnnotatedDocument(Document(data={}), []) + assert format_count([d]) == "" + + +def test_csv_no_annotations(): + d: AnnotatedDocument = AnnotatedDocument(Document(data={}), []) + assert format_csv([d]) == "type,tag,page,quote,note,author,title,ref,file" From 14f1b9e75c51372302b133de365c0ed1f06fa82a Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Tue, 17 Oct 2023 21:16:40 +0200 Subject: [PATCH 029/107] test: Add poetry-cov library --- poetry.lock | 20 +++++++++++++++++++- pyproject.toml | 1 + 2 files changed, 20 insertions(+), 1 deletion(-) diff --git a/poetry.lock b/poetry.lock index 886f483..c405f7c 100644 --- a/poetry.lock +++ b/poetry.lock @@ -730,6 +730,24 @@ pluggy = ">=0.12,<2.0" [package.extras] testing = ["argcomplete", "attrs (>=19.2.0)", "hypothesis (>=3.56)", "mock", "nose", "pygments (>=2.7.2)", "requests", "setuptools", "xmlschema"] +[[package]] +name = "pytest-cov" +version = "4.1.0" +description = "Pytest plugin for measuring coverage." +optional = false +python-versions = ">=3.7" +files = [ + {file = "pytest-cov-4.1.0.tar.gz", hash = "sha256:3904b13dfbfec47f003b8e77fd5b589cd11904a21ddf1ab38a64f204d6a10ef6"}, + {file = "pytest_cov-4.1.0-py3-none-any.whl", hash = "sha256:6ba70b9e97e69fcc3fb45bfeab2d0a138fb65c4d0d6a41ef33983ad114be8c3a"}, +] + +[package.dependencies] +coverage = {version = ">=5.2.1", extras = ["toml"]} +pytest = ">=4.6" + +[package.extras] +testing = ["fields", "hunter", "process-tests", "pytest-xdist", "six", "virtualenv"] + [[package]] name = "python-doi" version = "0.2.0" @@ -1074,4 +1092,4 @@ whoosh = ["whoosh"] [metadata] lock-version = "2.0" python-versions = "^3.11" -content-hash = "dac37f6a903033ed95f65a69f7ca90a115aa390284835c2a8e82ea3fc0a196ab" +content-hash = "02d5ac314a19f14103372c7ceccdaec080df3fdc2fdb1381f2f6343cd6d17db4" diff --git a/pyproject.toml b/pyproject.toml index 8551182..7e252fa 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -22,6 +22,7 @@ whoosh = ["whoosh"] [tool.poetry.group.dev.dependencies] pytest = "^7.4.0" coverage = "^7.3.1" +pytest-cov = "^4.1.0" [tool.poetry.plugins."papis.command"] extract = "papis_extract:main" From aeb18ae3585e51c08b758d9d31277df74d5dd988 Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Tue, 17 Oct 2023 22:01:41 +0200 Subject: [PATCH 030/107] feat: Add option to force-add annotations Will turn off looking for duplicate annotations and simply add all. --- papis_extract/__init__.py | 11 +++++++++-- papis_extract/exporter.py | 35 +++++++++++++++++++++++++++-------- 2 files changed, 36 insertions(+), 10 deletions(-) diff --git a/papis_extract/__init__.py b/papis_extract/__init__.py index e679e6a..686dcbb 100644 --- a/papis_extract/__init__.py +++ b/papis_extract/__init__.py @@ -52,6 +52,11 @@ papis.config.register_default_settings(DEFAULT_OPTIONS) ), help="Choose an output template to format annotations with.", ) +@click.option( + "--force/--no-force", + "-f", + help="Do not drop any annotations because they already exist.", +) def main( query: str, # _papis_id: bool, @@ -63,6 +68,7 @@ def main( write: bool, template: str, git: bool, + force: bool, ) -> None: """Extract annotations from any pdf document. @@ -84,7 +90,7 @@ def main( formatter = formatters[template] - run(documents, edit=manual, write=write, git=git, formatter=formatter) + run(documents, edit=manual, write=write, git=git, formatter=formatter, force=force) def run( @@ -93,11 +99,12 @@ def run( edit: bool = False, write: bool = False, git: bool = False, + force: bool = False, ) -> None: annotated_docs = extractor.start(documents) if write: exporter.to_notes( - formatter=formatter, annotated_docs=annotated_docs, edit=edit, git=git + formatter=formatter, annotated_docs=annotated_docs, edit=edit, git=git, force=force ) else: exporter.to_stdout(formatter=formatter, annotated_docs=annotated_docs) diff --git a/papis_extract/exporter.py b/papis_extract/exporter.py index 5d22270..af66b13 100644 --- a/papis_extract/exporter.py +++ b/papis_extract/exporter.py @@ -25,7 +25,11 @@ def to_stdout(formatter: Formatter, annotated_docs: list[AnnotatedDocument]) -> def to_notes( - formatter: Formatter, annotated_docs: list[AnnotatedDocument], edit: bool, git: bool + formatter: Formatter, + annotated_docs: list[AnnotatedDocument], + edit: bool, + git: bool, + force: bool, ) -> None: """Write annotations into document notes. @@ -36,7 +40,7 @@ def to_notes( for entry in annotated_docs: formatted_annotations = formatter([entry]).split("\n") if formatted_annotations: - _add_annots_to_note(entry.document, formatted_annotations) + _add_annots_to_note(entry.document, formatted_annotations, force=force) if edit: papis.commands.edit.edit_notes(entry.document, git=git) @@ -46,11 +50,26 @@ def _add_annots_to_note( document: papis.document.Document, formatted_annotations: list[str], git: bool = False, + force: bool = False, ) -> None: - """Append new annotations to the end of a note. + """ + Append new annotations to the end of a note. - Looks through note to determine any new annotations which should be - added and adds them to the end of the note file. + This function appends new annotations to the end of a note file. It takes in a + document object containing the note, a list of formatted annotations to be + added, and optional flags git and force. If git is True, the changes will be + committed to git. If force is True, the annotations will be added even if they + already exist in the note. + + :param document: The document object representing the note + :type document: class:`papis.document.Document` + :param formatted_annotations: A list of already formatted annotations to be added + :type formatted_annotations: list[str] + :param git: Flag indicating whether to commit changes to git, defaults to False. + :type git: bool, optional + :param force: Flag indicating whether to force adding annotations even if they + already exist, defaults to False. + :type force: bool, optional """ logger.debug("Adding annotations to note.") notes_path = papis.notes.notes_path_ensured(document) @@ -59,9 +78,9 @@ def _add_annots_to_note( with open(notes_path, "r") as file_read: existing = file_read.readlines() - new_annotations: list[str] = _drop_existing_annotations( - formatted_annotations, existing - ) + new_annotations: list[str] = [] + if not force: + new_annotations = _drop_existing_annotations(formatted_annotations, existing) if not new_annotations: return From 5cd5a05062ae3e010a2dc8424b5b1f78974783f9 Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Tue, 17 Oct 2023 22:03:35 +0200 Subject: [PATCH 031/107] chore: Fix black fmt --- papis_extract/__init__.py | 11 ++++++----- papis_extract/exporter.py | 2 +- tests/test_annotation.py | 6 ++++-- 3 files changed, 11 insertions(+), 8 deletions(-) diff --git a/papis_extract/__init__.py b/papis_extract/__init__.py index 686dcbb..31d720d 100644 --- a/papis_extract/__init__.py +++ b/papis_extract/__init__.py @@ -8,10 +8,7 @@ import papis.strings from papis.document import Document from papis_extract import extractor, exporter -from papis_extract.formatter import ( - Formatter, - formatters -) +from papis_extract.formatter import Formatter, formatters logger = papis.logging.get_logger(__name__) @@ -104,7 +101,11 @@ def run( annotated_docs = extractor.start(documents) if write: exporter.to_notes( - formatter=formatter, annotated_docs=annotated_docs, edit=edit, git=git, force=force + formatter=formatter, + annotated_docs=annotated_docs, + edit=edit, + git=git, + force=force, ) else: exporter.to_stdout(formatter=formatter, annotated_docs=annotated_docs) diff --git a/papis_extract/exporter.py b/papis_extract/exporter.py index af66b13..80adb8c 100644 --- a/papis_extract/exporter.py +++ b/papis_extract/exporter.py @@ -67,7 +67,7 @@ def _add_annots_to_note( :type formatted_annotations: list[str] :param git: Flag indicating whether to commit changes to git, defaults to False. :type git: bool, optional - :param force: Flag indicating whether to force adding annotations even if they + :param force: Flag indicating whether to force adding annotations even if they already exist, defaults to False. :type force: bool, optional """ diff --git a/tests/test_annotation.py b/tests/test_annotation.py index c14ee93..529a4c1 100644 --- a/tests/test_annotation.py +++ b/tests/test_annotation.py @@ -26,13 +26,14 @@ def test_formatting_replacements(fmt_string, expected): assert sut.format(fmt_string) == expected + @pytest.mark.parametrize( "fmt_string,expected", [ ("{{doc.title}}", "document-title"), ("{{doc.title}}-{{doc.author}}", "document-title-document-author"), ("{{quote}} ({{doc.author}})", "I am the text value (document-author)"), - ] + ], ) def test_formatting_document_access(fmt_string, expected): sut = Annotation( @@ -40,10 +41,11 @@ def test_formatting_document_access(fmt_string, expected): text="I am the text value", content="Whereas I represent the note", ) - doc = Document(data= {"title": "document-title", "author": "document-author"}) + doc = Document(data={"title": "document-title", "author": "document-author"}) assert sut.format(fmt_string, doc=doc) == expected + def test_colorname_matches_exact(): sut = Annotation("testfile", colors=(1.0, 0.0, 0.0), minimum_similarity_color=1.0) c_name = sut.colorname From 376282eaaab0600dd7344d0fb34c48c26042e24e Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Tue, 17 Oct 2023 22:09:54 +0200 Subject: [PATCH 032/107] test: Fix test running on main branch --- .woodpecker/test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.woodpecker/test.yml b/.woodpecker/test.yml index 44e264d..a23ae77 100644 --- a/.woodpecker/test.yml +++ b/.woodpecker/test.yml @@ -1,4 +1,4 @@ -branches: master +branches: main pipeline: pytest: From 1ef9a91e5540cbf183ab200a5e16b089c5207f38 Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Sat, 6 Jan 2024 11:11:30 +0100 Subject: [PATCH 033/107] test: Remove deprecated pipeline instruction --- .woodpecker/lint.yml | 2 +- .woodpecker/static_analysis.yml | 2 +- .woodpecker/test.yml | 5 +++-- 3 files changed, 5 insertions(+), 4 deletions(-) diff --git a/.woodpecker/lint.yml b/.woodpecker/lint.yml index eb67dbe..4400de4 100644 --- a/.woodpecker/lint.yml +++ b/.woodpecker/lint.yml @@ -1,4 +1,4 @@ -pipeline: +steps: lint_ruff: image: python commands: diff --git a/.woodpecker/static_analysis.yml b/.woodpecker/static_analysis.yml index 786af22..b817624 100644 --- a/.woodpecker/static_analysis.yml +++ b/.woodpecker/static_analysis.yml @@ -1,4 +1,4 @@ -pipeline: +steps: pyright: image: nikolaik/python-nodejs commands: diff --git a/.woodpecker/test.yml b/.woodpecker/test.yml index a23ae77..0dc8073 100644 --- a/.woodpecker/test.yml +++ b/.woodpecker/test.yml @@ -1,6 +1,7 @@ -branches: main +when: + branch: main -pipeline: +steps: pytest: image: ghcr.io/withlogicco/poetry:1.5.1 commands: From cd5f787220c925a4d653c2a36f08cc635e1eccf6 Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Thu, 18 Jan 2024 18:24:19 +0100 Subject: [PATCH 034/107] chore: Update dependencies to fix single-thread warning Fixed single-threaded warning provided from the fitz pymupdf library since the issue does not exist for this new version anymore. Bump version along the way. --- papis_extract/extractor.py | 2 +- poetry.lock | 812 ++++++++++++++++++------------------- pyproject.toml | 2 +- 3 files changed, 404 insertions(+), 412 deletions(-) diff --git a/papis_extract/extractor.py b/papis_extract/extractor.py index bdb8780..3ae1650 100644 --- a/papis_extract/extractor.py +++ b/papis_extract/extractor.py @@ -4,7 +4,7 @@ from typing import Any, Optional import Levenshtein import magic -import fitz_new as fitz +import fitz import papis.logging import papis.config import papis.document diff --git a/poetry.lock b/poetry.lock index c405f7c..14f75b0 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. [[package]] name = "arxiv2bib" @@ -12,30 +12,33 @@ files = [ [[package]] name = "beautifulsoup4" -version = "4.12.2" +version = "4.12.3" description = "Screen-scraping library" optional = false python-versions = ">=3.6.0" files = [ - {file = "beautifulsoup4-4.12.2-py3-none-any.whl", hash = "sha256:bd2520ca0d9d7d12694a53d44ac482d181b4ec1888909b035a3dbf40d0f57d4a"}, - {file = "beautifulsoup4-4.12.2.tar.gz", hash = "sha256:492bbc69dca35d12daac71c4db1bfff0c876c00ef4a2ffacce226d4638eb72da"}, + {file = "beautifulsoup4-4.12.3-py3-none-any.whl", hash = "sha256:b80878c9f40111313e55da8ba20bdba06d8fa3969fc68304167741bbf9e082ed"}, + {file = "beautifulsoup4-4.12.3.tar.gz", hash = "sha256:74e3d1928edc070d21748185c46e3fb33490f22f52a3addee9aee0f4f7781051"}, ] [package.dependencies] soupsieve = ">1.2" [package.extras] +cchardet = ["cchardet"] +chardet = ["chardet"] +charset-normalizer = ["charset-normalizer"] html5lib = ["html5lib"] lxml = ["lxml"] [[package]] name = "bibtexparser" -version = "1.4.0" +version = "1.4.1" description = "Bibtex parser for python 3" optional = false python-versions = "*" files = [ - {file = "bibtexparser-1.4.0.tar.gz", hash = "sha256:ca7ce2bc34e7c48a678dd49416429bb567441f26dbb13b3609082d8cd109ace6"}, + {file = "bibtexparser-1.4.1.tar.gz", hash = "sha256:e00e29e24676c4808e0b4333b37bb55cca9cbb7871a56f63058509281588d789"}, ] [package.dependencies] @@ -43,13 +46,13 @@ pyparsing = ">=2.0.3" [[package]] name = "certifi" -version = "2023.7.22" +version = "2023.11.17" description = "Python package for providing Mozilla's CA Bundle." optional = false python-versions = ">=3.6" files = [ - {file = "certifi-2023.7.22-py3-none-any.whl", hash = "sha256:92d6037539857d8206b8f6ae472e8b77db8058fec5937a1ef3f54304089edbb9"}, - {file = "certifi-2023.7.22.tar.gz", hash = "sha256:539cc1d13202e33ca466e88b2807e29f4c13049d6d87031a3c110744495cb082"}, + {file = "certifi-2023.11.17-py3-none-any.whl", hash = "sha256:e036ab49d5b79556f99cfc2d9320b34cfbe5be05c5871b51de9329f0603b0474"}, + {file = "certifi-2023.11.17.tar.gz", hash = "sha256:9b469f3a900bf28dc19b8cfbf8019bf47f7fdd1a65a1d4ffb98fc14166beb4d1"}, ] [[package]] @@ -65,86 +68,101 @@ files = [ [[package]] name = "charset-normalizer" -version = "3.2.0" +version = "3.3.2" description = "The Real First Universal Charset Detector. 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b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "papis-extract" -version = "0.1.0" +version = "0.2.0" description = "" authors = ["Marty Oehme "] readme = "README.md" From 765de505bbe8b7c4741cdf78264985273dea37f0 Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Sat, 20 Jan 2024 16:34:10 +0100 Subject: [PATCH 035/107] refactor: Remove AnnotatedDocument class The AnnotatedDocument class was, essentially, a simple tuple of a document and a list of annotations. While not bad in a vacuum, it is unwieldy and passing this around instead of a document, annotations, or both where necessary is more restrictive and frankly unnecessary. This commit removes the data class and any instances of its use. Instead, we now pass the individual components around to anything that needs them. This also frees us up to pass only annotations around for example. We also do not iterate through the selected papis documents to work on in each exporter anymore (since we only pass a single document), but in the main function itself. This leads to less duplication and makes the overall run function the overall single source of iteration through selected documents. Everything else only knows about a single document - the one it is operating on - which seems much neater. For now, it does not change much, but should make later work on extra exporters or extractors easier. --- papis_extract/__init__.py | 38 ++++++----- papis_extract/annotation.py | 12 ---- papis_extract/exporter.py | 27 ++++---- papis_extract/extractor.py | 42 ++++++------ papis_extract/formatter.py | 128 +++++++++++++++++++----------------- tests/test_formatting.py | 33 ++++------ 6 files changed, 142 insertions(+), 138 deletions(-) diff --git a/papis_extract/__init__.py b/papis_extract/__init__.py index 31d720d..8d7bf8a 100644 --- a/papis_extract/__init__.py +++ b/papis_extract/__init__.py @@ -7,7 +7,8 @@ import papis.notes import papis.strings from papis.document import Document -from papis_extract import extractor, exporter +from papis_extract import exporter, extractor +from papis_extract.annotation import Annotation from papis_extract.formatter import Formatter, formatters logger = papis.logging.get_logger(__name__) @@ -44,7 +45,7 @@ papis.config.register_default_settings(DEFAULT_OPTIONS) "--template", "-t", type=click.Choice( - ["markdown", "markdown-setext", "markdown-atx", "count", "csv"], + list(formatters.keys()), case_sensitive=False, ), help="Choose an output template to format annotations with.", @@ -85,27 +86,34 @@ def main( logger.warning(papis.strings.no_documents_retrieved_message) return - formatter = formatters[template] + formatter = formatters.get(template) run(documents, edit=manual, write=write, git=git, formatter=formatter, force=force) def run( documents: list[Document], - formatter: Formatter, + formatter: Formatter | None, edit: bool = False, write: bool = False, git: bool = False, force: bool = False, ) -> None: - annotated_docs = extractor.start(documents) - if write: - exporter.to_notes( - formatter=formatter, - annotated_docs=annotated_docs, - edit=edit, - git=git, - force=force, - ) - else: - exporter.to_stdout(formatter=formatter, annotated_docs=annotated_docs) + for doc in documents: + annotations: list[Annotation] = extractor.start(doc) + + if write: + exporter.to_notes( + formatter=formatter or formatters["markdown-atx"], + document=doc, + annotations=annotations, + edit=edit, + git=git, + force=force, + ) + else: + exporter.to_stdout( + formatter=formatter or formatters["markdown"], + document=doc, + annotations=annotations, + ) diff --git a/papis_extract/annotation.py b/papis_extract/annotation.py index 138b755..74342da 100644 --- a/papis_extract/annotation.py +++ b/papis_extract/annotation.py @@ -81,15 +81,3 @@ class Annotation: difference between full black and full white, as a float. """ return 1 - (abs(math.dist([*color_one], [*color_two])) / 3) - - -@dataclass -class AnnotatedDocument: - """Contains all annotations belonging to a single papis document. - - Combines a document with a list of annotations which belong to it.""" - - document: Document - annotations: list[Annotation] - - # TODO could implement a from_doc() static method to generate annotation list? diff --git a/papis_extract/exporter.py b/papis_extract/exporter.py index 80adb8c..120224e 100644 --- a/papis_extract/exporter.py +++ b/papis_extract/exporter.py @@ -6,27 +6,33 @@ import papis.api import papis.git import papis.config import Levenshtein -from papis_extract.annotation import AnnotatedDocument +from papis_extract.annotation import Annotation from papis_extract.formatter import Formatter logger = papis.logging.get_logger(__name__) -def to_stdout(formatter: Formatter, annotated_docs: list[AnnotatedDocument]) -> None: +def to_stdout( + formatter: Formatter, + document: papis.document.Document, + annotations: list[Annotation], +) -> None: """Pretty print annotations to stdout. Gives a nice human-readable representations of the annotations in somewhat of a list form. Not intended for machine-readability. """ - output: str = formatter(annotated_docs) - print(output.rstrip("\n")) + output: str = formatter(document, annotations) + if output: + print(output.rstrip("\n")) def to_notes( formatter: Formatter, - annotated_docs: list[AnnotatedDocument], + document: papis.document.Document, + annotations: list[Annotation], edit: bool, git: bool, force: bool, @@ -37,13 +43,12 @@ def to_notes( belonging to papis documents. Creates new notes for documents missing a note field or appends to existing. """ - for entry in annotated_docs: - formatted_annotations = formatter([entry]).split("\n") - if formatted_annotations: - _add_annots_to_note(entry.document, formatted_annotations, force=force) + formatted_annotations = formatter(document, annotations).split("\n") + if formatted_annotations: + _add_annots_to_note(document, formatted_annotations, force=force) - if edit: - papis.commands.edit.edit_notes(entry.document, git=git) + if edit: + papis.commands.edit.edit_notes(document, git=git) def _add_annots_to_note( diff --git a/papis_extract/extractor.py b/papis_extract/extractor.py index 3ae1650..180af25 100644 --- a/papis_extract/extractor.py +++ b/papis_extract/extractor.py @@ -10,41 +10,39 @@ import papis.config import papis.document from papis.document import Document -from papis_extract.annotation import Annotation, AnnotatedDocument +from papis_extract.annotation import Annotation logger = papis.logging.get_logger(__name__) def start( - documents: list[Document], -) -> list[AnnotatedDocument]: + document: Document, +) -> list[Annotation]: """Extract all annotations from passed documents. Returns all annotations contained in the papis documents passed in. """ - output: list[AnnotatedDocument] = [] - for doc in documents: - annotations: list[Annotation] = [] - found_pdf: bool = False - for file in doc.get_files(): - fname = Path(file) - if not _is_file_processable(fname): - break - found_pdf = True + annotations: list[Annotation] = [] + found_pdf: bool = False + for file in document.get_files(): + fname = Path(file) + if not _is_file_processable(fname): + break + found_pdf = True - try: - annotations.extend(extract(fname)) - except fitz.FileDataError as e: - print(f"File structure errors for {file}.\n{e}") + try: + annotations.extend(extract(fname)) + except fitz.FileDataError as e: + print(f"File structure errors for {file}.\n{e}") - if not found_pdf: - # have to remove curlys or papis logger gets upset - desc = re.sub("[{}]", "", papis.document.describe(doc)) - logger.warning("Did not find suitable PDF file for document: " f"{desc}") - output.append(AnnotatedDocument(doc, annotations)) - return output + if not found_pdf: + # have to remove curlys or papis logger gets upset + desc = re.sub("[{}]", "", papis.document.describe(document)) + logger.warning("Did not find suitable PDF file for document: " f"{desc}") + + return annotations def extract(filename: Path) -> list[Annotation]: diff --git a/papis_extract/formatter.py b/papis_extract/formatter.py index 75ed556..917e04c 100644 --- a/papis_extract/formatter.py +++ b/papis_extract/formatter.py @@ -1,86 +1,96 @@ from collections.abc import Callable -from papis_extract.annotation import AnnotatedDocument +from papis.document import Document -Formatter = Callable[[list[AnnotatedDocument]], str] +from papis_extract.annotation import Annotation + +Formatter = Callable[[Document, list[Annotation]], str] def format_markdown( - docs: list[AnnotatedDocument] = [], atx_headings: bool = False + document: Document = Document(), + annotations: list[Annotation] = [], + headings: str = "setext", # setext | atx | None ) -> str: + if not annotations: + return "" template = ( "{{#tag}}#{{tag}}\n{{/tag}}" "{{#quote}}> {{quote}}{{/quote}}{{#page}} [p. {{page}}]{{/page}}" "{{#note}}\n NOTE: {{note}}{{/note}}" ) output = "" - for entry in docs: - if not entry.annotations: - continue - heading = f"{entry.document['title']} - {entry.document['author']}\n" - if atx_headings: - output += f"# {heading}\n" - else: - title_decoration = ( - f"{'=' * len(entry.document.get('title', ''))} " - f"{'-' * len(entry.document.get('author', ''))}" - ) - output += f"{title_decoration}\n" f"{heading}" f"{title_decoration}\n\n" - - for a in entry.annotations: - output += a.format(template) - output += "\n\n" - - output += "\n\n\n" - - return output.rstrip() - - -def format_markdown_atx(docs: list[AnnotatedDocument] = []) -> str: - return format_markdown(docs, atx_headings=True) - - -def format_markdown_setext(docs: list[AnnotatedDocument] = []) -> str: - return format_markdown(docs, atx_headings=False) - - -def format_count(docs: list[AnnotatedDocument] = []) -> str: - output = "" - for entry in docs: - if not entry.annotations: - continue - - count = 0 - for _ in entry.annotations: - count += 1 - - d = entry.document - output += ( - f"{d['author'] if 'author' in d else ''}" - f"{' - ' if 'author' in d else ''}" # only put separator if author - f"{entry.document['title'] if 'title' in d else ''}: " - f"{count}\n" + heading = f"{document.get('title', '')} - {document.get('author', '')}" + if headings == "atx": + output = f"# {heading}\n\n" + elif headings == "setext": + title_decoration = ( + f"{'=' * len(document.get('title', ''))} " + f"{'-' * len(document.get('author', ''))}" ) + output = f"{title_decoration}\n{heading}\n{title_decoration}\n\n" + else: + output = "" + + for a in annotations: + output += a.format(template) + output += "\n\n" + + output += "\n\n\n" return output.rstrip() -def format_csv(docs: list[AnnotatedDocument] = []) -> str: +def format_markdown_atx( + document: Document = Document(), + annotations: list[Annotation] = [], +) -> str: + return format_markdown(document, annotations, headings="atx") + + +def format_markdown_setext( + document: Document = Document(), + annotations: list[Annotation] = [], +) -> str: + return format_markdown(document, annotations, headings="setext") + + +def format_count( + document: Document = Document(), + annotations: list[Annotation] = [], +) -> str: + if not annotations: + return "" + + count = 0 + for _ in annotations: + count += 1 + + return ( + f"{document.get('author', '')}" + f"{' - ' if 'author' in document else ''}" # only put separator if author + f"{document.get('title', '')}: " + f"{count}\n" + ).rstrip() + + +def format_csv( + document: Document = Document(), + annotations: list[Annotation] = [], +) -> str: header: str = "type,tag,page,quote,note,author,title,ref,file" template: str = ( '{{type}},{{tag}},{{page}},"{{quote}}","{{note}}",' '"{{doc.author}}","{{doc.title}}","{{doc.ref}}","{{file}}"' ) output = f"{header}\n" - for entry in docs: - if not entry.annotations: - continue + if not annotations: + return "" - d = entry.document - for a in entry.annotations: - output += a.format(template, doc=d) - output += "\n" + for a in annotations: + output += a.format(template, doc=document) + output += "\n" return output.rstrip() @@ -89,6 +99,6 @@ formatters: dict[str, Formatter] = { "count": format_count, "csv": format_csv, "markdown": format_markdown, - "markdown_atx": format_markdown_atx, - "markdown_setext": format_markdown_setext, + "markdown-atx": format_markdown_atx, + "markdown-setext": format_markdown_setext, } diff --git a/tests/test_formatting.py b/tests/test_formatting.py index d9a0d0f..244f4f8 100644 --- a/tests/test_formatting.py +++ b/tests/test_formatting.py @@ -1,5 +1,5 @@ from papis.document import Document -from papis_extract.annotation import AnnotatedDocument, Annotation +from papis_extract.annotation import Annotation from papis_extract.formatter import ( format_count, @@ -9,13 +9,11 @@ from papis_extract.formatter import ( format_markdown_setext, ) -an_doc: AnnotatedDocument = AnnotatedDocument( - Document(data={"author": "document-author", "title": "document-title"}), - [ - Annotation("myfile.pdf", text="my lovely text"), - Annotation("myfile.pdf", text="my second text", content="with note"), - ], -) +document = Document(data={"author": "document-author", "title": "document-title"}) +annotations = [ + Annotation("myfile.pdf", text="my lovely text"), + Annotation("myfile.pdf", text="my second text", content="with note"), +] md_default_output = """============== --------------- document-title - document-author ============== --------------- @@ -28,12 +26,12 @@ document-title - document-author def test_markdown_default(): fmt = format_markdown - assert fmt([an_doc]) == md_default_output + assert fmt(document, annotations) == md_default_output def test_markdown_atx(): fmt = format_markdown_atx - assert fmt([an_doc]) == ( + assert fmt(document, annotations) == ( """# document-title - document-author > my lovely text @@ -45,17 +43,17 @@ def test_markdown_atx(): def test_markdown_setext(): fmt = format_markdown_setext - assert fmt([an_doc]) == md_default_output + assert fmt(document, annotations) == md_default_output def test_count_default(): fmt = format_count - assert fmt([an_doc]) == ("""document-author - document-title: 2""") + assert fmt(document, annotations) == ("""document-author - document-title: 2""") def test_csv_default(): fmt = format_csv - assert fmt([an_doc]) == ( + assert fmt(document, annotations) == ( "type,tag,page,quote,note,author,title,ref,file\n" 'Highlight,,0,"my lovely text","","document-author",' '"document-title","","myfile.pdf"\n' @@ -66,15 +64,12 @@ def test_csv_default(): # sadpath - no annotations contained for each format def test_markdown_no_annotations(): - d: AnnotatedDocument = AnnotatedDocument(Document(data={}), []) - assert format_markdown([d]) == "" + assert format_markdown(document, []) == "" def test_count_no_annotations(): - d: AnnotatedDocument = AnnotatedDocument(Document(data={}), []) - assert format_count([d]) == "" + assert format_count(document, []) == "" def test_csv_no_annotations(): - d: AnnotatedDocument = AnnotatedDocument(Document(data={}), []) - assert format_csv([d]) == "type,tag,page,quote,note,author,title,ref,file" + assert format_csv(document, []) == "" From 3b4db7b6b8e035433abd94b19184cbcff41919c2 Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Sat, 20 Jan 2024 18:02:18 +0100 Subject: [PATCH 036/107] refactor: Extract PDF extractor into class Extractor is a general protocol with the PDF extraction routine now being one implementation of the protocol. Preparation for adding multiple extractors (epub,djvu, or specific progammes) in the future. --- papis_extract/extractor.py | 138 ++++---------------------------- papis_extract/extractors/pdf.py | 132 ++++++++++++++++++++++++++++++ 2 files changed, 147 insertions(+), 123 deletions(-) create mode 100644 papis_extract/extractors/pdf.py diff --git a/papis_extract/extractor.py b/papis_extract/extractor.py index 180af25..d88d365 100644 --- a/papis_extract/extractor.py +++ b/papis_extract/extractor.py @@ -1,20 +1,27 @@ import re from pathlib import Path -from typing import Any, Optional +from typing import Protocol -import Levenshtein -import magic import fitz -import papis.logging import papis.config import papis.document +import papis.logging from papis.document import Document from papis_extract.annotation import Annotation +from papis_extract.extractors.pdf import PdfExtractor logger = papis.logging.get_logger(__name__) +class Extractor(Protocol): + def can_process(self, filename: Path) -> bool: + ... + + def run(self, filename: Path) -> list[Annotation]: + ... + + def start( document: Document, ) -> list[Annotation]: @@ -24,16 +31,18 @@ def start( documents passed in. """ + pdf_extractor: Extractor = PdfExtractor() + annotations: list[Annotation] = [] found_pdf: bool = False for file in document.get_files(): fname = Path(file) - if not _is_file_processable(fname): + if not pdf_extractor.can_process(fname): break found_pdf = True try: - annotations.extend(extract(fname)) + annotations.extend(pdf_extractor.run(fname)) except fitz.FileDataError as e: print(f"File structure errors for {file}.\n{e}") @@ -45,120 +54,3 @@ def start( return annotations -def extract(filename: Path) -> list[Annotation]: - """Extract annotations from a file. - - Returns all readable annotations contained in the file - passed in. Only returns Highlight or Text annotations. - """ - annotations = [] - with fitz.Document(filename) as doc: - for page in doc: - for annot in page.annots(): - quote, note = _retrieve_annotation_content(page, annot) - if not quote and not note: - continue - col = ( - annot.colors.get("fill") - or annot.colors.get("stroke") - or (0.0, 0.0, 0.0) - ) - a = Annotation( - file=str(filename), - text=quote or "", - content=note or "", - colors=col, - type=annot.type[1], - page=(page.number or 0) + 1, - ) - a.tag = _tag_from_colorname(a.colorname or "") - annotations.append(a) - logger.debug( - f"Found {len(annotations)} " - f"{'annotation' if len(annotations) == 1 else 'annotations'} for {filename}." - ) - return annotations - - -def is_pdf(fname: Path) -> bool: - """Check if file is a pdf, using mime type.""" - return magic.from_file(fname, mime=True) == "application/pdf" - - -def _is_file_processable(fname: Path) -> bool: - if not fname.is_file(): - logger.error(f"File {str(fname)} not readable.") - return False - if not is_pdf(fname): - return False - return True - - -def _tag_from_colorname(colorname: str) -> str: - color_mapping: dict[str, str] = getdict("tags", "plugins.extract") - if not color_mapping: - return "" - - return color_mapping.get(colorname, "") - - -def _retrieve_annotation_content( - page: fitz.Page, annotation: fitz.Annot -) -> tuple[str | None, str | None]: - """Gets the text content of an annotation. - - Returns the actual content of an annotation. Sometimes - that is only the written words, sometimes that is only - annotation notes, sometimes it is both. Runs a similarity - comparison between strings to find out whether they - should both be included or are the same, using - Levenshtein distance. - """ - content = annotation.info["content"].replace("\n", " ") - written = page.get_textbox(annotation.rect).replace("\n", " ") - - # highlight with selection in note - minimum_similarity = ( - papis.config.getfloat("minimum_similarity_content", "plugins.extract") or 1.0 - ) - if Levenshtein.ratio(content, written) > minimum_similarity: - return (content, None) - # both a highlight and a note - elif content and written: - return (written, content) - # an independent note, not a highlight - elif content: - return (None, content) - # highlight with selection not in note - elif written: - return (written, None) - # just a highlight without any text - return (None, None) - - -# mimics the functions in papis.config.{getlist,getint,getfloat} etc. -def getdict(key: str, section: Optional[str] = None) -> dict[str, str]: - """Dict getter - - :returns: A python dict - :raises SyntaxError: Whenever the parsed syntax is either not a valid - python object or a valid python dict. - """ - rawvalue: Any = papis.config.general_get(key, section=section) - if isinstance(rawvalue, dict): - return rawvalue - try: - rawvalue = eval(rawvalue) - except Exception: - raise SyntaxError( - "The key '{}' must be a valid Python object: {}".format(key, rawvalue) - ) - else: - if not isinstance(rawvalue, dict): - raise SyntaxError( - "The key '{}' must be a valid Python dict. Got: {} (type {!r})".format( - key, rawvalue, type(rawvalue).__name__ - ) - ) - - return rawvalue diff --git a/papis_extract/extractors/pdf.py b/papis_extract/extractors/pdf.py new file mode 100644 index 0000000..ac39184 --- /dev/null +++ b/papis_extract/extractors/pdf.py @@ -0,0 +1,132 @@ +from pathlib import Path +from typing import Any, Optional + +import fitz +import Levenshtein +import magic +import papis.config +import papis.logging + +from papis_extract.annotation import Annotation + +logger = papis.logging.get_logger(__name__) + + +class PdfExtractor: + def can_process(self, filename: Path) -> bool: + if not filename.is_file(): + logger.error(f"File {str(filename)} not readable.") + return False + if not self._is_pdf(filename): + return False + return True + + def run(self, filename: Path) -> list[Annotation]: + """Extract annotations from a file. + + Returns all readable annotations contained in the file + passed in. Only returns Highlight or Text annotations. + """ + annotations = [] + with fitz.Document(filename) as doc: + for page in doc: + for annot in page.annots(): + quote, note = self._retrieve_annotation_content(page, annot) + if not quote and not note: + continue + col = ( + annot.colors.get("fill") + or annot.colors.get("stroke") + or (0.0, 0.0, 0.0) + ) + a = Annotation( + file=str(filename), + text=quote or "", + content=note or "", + colors=col, + type=annot.type[1], + page=(page.number or 0) + 1, + ) + a.tag = self._tag_from_colorname(a.colorname or "") + annotations.append(a) + logger.debug( + f"Found {len(annotations)} " + f"{'annotation' if len(annotations) == 1 else 'annotations'} for {filename}." + ) + return annotations + + + def _is_pdf(self, fname: Path) -> bool: + """Check if file is a pdf, using mime type.""" + return magic.from_file(fname, mime=True) == "application/pdf" + + + + def _tag_from_colorname(self, colorname: str) -> str: + color_mapping: dict[str, str] = self._getdict("tags", "plugins.extract") + if not color_mapping: + return "" + + return color_mapping.get(colorname, "") + + + def _retrieve_annotation_content(self, + page: fitz.Page, annotation: fitz.Annot + ) -> tuple[str | None, str | None]: + """Gets the text content of an annotation. + + Returns the actual content of an annotation. Sometimes + that is only the written words, sometimes that is only + annotation notes, sometimes it is both. Runs a similarity + comparison between strings to find out whether they + should both be included or are the same, using + Levenshtein distance. + """ + content = annotation.info["content"].replace("\n", " ") + written = page.get_textbox(annotation.rect).replace("\n", " ") + + # highlight with selection in note + minimum_similarity = ( + papis.config.getfloat("minimum_similarity_content", "plugins.extract") or 1.0 + ) + if Levenshtein.ratio(content, written) > minimum_similarity: + return (content, None) + # both a highlight and a note + elif content and written: + return (written, content) + # an independent note, not a highlight + elif content: + return (None, content) + # highlight with selection not in note + elif written: + return (written, None) + # just a highlight without any text + return (None, None) + + +# mimics the functions in papis.config.{getlist,getint,getfloat} etc. + def _getdict(self, key: str, section: Optional[str] = None) -> dict[str, str]: + """Dict getter + + :returns: A python dict + :raises SyntaxError: Whenever the parsed syntax is either not a valid + python object or a valid python dict. + """ + rawvalue: Any = papis.config.general_get(key, section=section) + if isinstance(rawvalue, dict): + return rawvalue + try: + rawvalue = eval(rawvalue) + except Exception: + raise SyntaxError( + "The key '{}' must be a valid Python object: {}".format(key, rawvalue) + ) + else: + if not isinstance(rawvalue, dict): + raise SyntaxError( + "The key '{}' must be a valid Python dict. Got: {} (type {!r})".format( + key, rawvalue, type(rawvalue).__name__ + ) + ) + + return rawvalue From f477deea7cd8366874208985c0da322f284b1864 Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Tue, 23 Jan 2024 08:58:32 +0100 Subject: [PATCH 037/107] feat: Add extractor cli choice Can only choose pdf for the time being, but allows additional extractors to be added in the future. --- papis_extract/__init__.py | 14 ++++++++++++++ papis_extract/extractor.py | 13 ++++++++----- 2 files changed, 22 insertions(+), 5 deletions(-) diff --git a/papis_extract/__init__.py b/papis_extract/__init__.py index 8d7bf8a..6239533 100644 --- a/papis_extract/__init__.py +++ b/papis_extract/__init__.py @@ -50,6 +50,18 @@ papis.config.register_default_settings(DEFAULT_OPTIONS) ), help="Choose an output template to format annotations with.", ) +@click.option( + "--extractor", + "-e", + "extractors", + type=click.Choice( + list(extractor.extractors.keys()), + case_sensitive=False, + ), + default=list(extractor.extractors.keys()), + multiple=True, + help="Choose an extractor to apply to the selected documents.", +) @click.option( "--force/--no-force", "-f", @@ -64,6 +76,7 @@ def main( doc_folder: str, manual: bool, write: bool, + extractors: str, template: str, git: bool, force: bool, @@ -86,6 +99,7 @@ def main( logger.warning(papis.strings.no_documents_retrieved_message) return + print(extractors) formatter = formatters.get(template) run(documents, edit=manual, write=write, git=git, formatter=formatter, force=force) diff --git a/papis_extract/extractor.py b/papis_extract/extractor.py index d88d365..b0aa3cf 100644 --- a/papis_extract/extractor.py +++ b/papis_extract/extractor.py @@ -34,23 +34,26 @@ def start( pdf_extractor: Extractor = PdfExtractor() annotations: list[Annotation] = [] - found_pdf: bool = False + file_available: bool = False for file in document.get_files(): fname = Path(file) if not pdf_extractor.can_process(fname): - break - found_pdf = True + continue + file_available = True try: annotations.extend(pdf_extractor.run(fname)) except fitz.FileDataError as e: print(f"File structure errors for {file}.\n{e}") - if not found_pdf: + if not file_available: # have to remove curlys or papis logger gets upset desc = re.sub("[{}]", "", papis.document.describe(document)) - logger.warning("Did not find suitable PDF file for document: " f"{desc}") + logger.warning("Did not find suitable file for document: " f"{desc}") return annotations +extractors: dict[str, Extractor] = { + "pdf": PdfExtractor(), +} From 629932a5e89b722ce99235f36f2755264ceb7dce Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Tue, 23 Jan 2024 09:10:42 +0100 Subject: [PATCH 038/107] feat: Loop through all chosen extractors --- papis_extract/__init__.py | 55 +++++++++++-------- papis_extract/{extractor.py => extraction.py} | 9 ++- 2 files changed, 37 insertions(+), 27 deletions(-) rename papis_extract/{extractor.py => extraction.py} (89%) diff --git a/papis_extract/__init__.py b/papis_extract/__init__.py index 6239533..47cd5d9 100644 --- a/papis_extract/__init__.py +++ b/papis_extract/__init__.py @@ -7,7 +7,7 @@ import papis.notes import papis.strings from papis.document import Document -from papis_extract import exporter, extractor +from papis_extract import exporter, extraction from papis_extract.annotation import Annotation from papis_extract.formatter import Formatter, formatters @@ -55,10 +55,10 @@ papis.config.register_default_settings(DEFAULT_OPTIONS) "-e", "extractors", type=click.Choice( - list(extractor.extractors.keys()), + list(extraction.extractors.keys()), case_sensitive=False, ), - default=list(extractor.extractors.keys()), + default=list(extraction.extractors.keys()), multiple=True, help="Choose an extractor to apply to the selected documents.", ) @@ -76,7 +76,7 @@ def main( doc_folder: str, manual: bool, write: bool, - extractors: str, + extractors: list[str], template: str, git: bool, force: bool, @@ -99,35 +99,46 @@ def main( logger.warning(papis.strings.no_documents_retrieved_message) return - print(extractors) formatter = formatters.get(template) - run(documents, edit=manual, write=write, git=git, formatter=formatter, force=force) + run( + documents, + edit=manual, + write=write, + git=git, + formatter=formatter, + extractors=[extraction.extractors.get(e) for e in extractors], + force=force, + ) def run( documents: list[Document], formatter: Formatter | None, + extractors: list[extraction.Extractor | None], edit: bool = False, write: bool = False, git: bool = False, force: bool = False, ) -> None: for doc in documents: - annotations: list[Annotation] = extractor.start(doc) + for ext in extractors: + if not ext: + continue - if write: - exporter.to_notes( - formatter=formatter or formatters["markdown-atx"], - document=doc, - annotations=annotations, - edit=edit, - git=git, - force=force, - ) - else: - exporter.to_stdout( - formatter=formatter or formatters["markdown"], - document=doc, - annotations=annotations, - ) + annotations: list[Annotation] = extraction.start(ext, doc) + if write: + exporter.to_notes( + formatter=formatter or formatters["markdown-atx"], + document=doc, + annotations=annotations, + edit=edit, + git=git, + force=force, + ) + else: + exporter.to_stdout( + formatter=formatter or formatters["markdown"], + document=doc, + annotations=annotations, + ) diff --git a/papis_extract/extractor.py b/papis_extract/extraction.py similarity index 89% rename from papis_extract/extractor.py rename to papis_extract/extraction.py index b0aa3cf..86f876c 100644 --- a/papis_extract/extractor.py +++ b/papis_extract/extraction.py @@ -23,6 +23,7 @@ class Extractor(Protocol): def start( + extractor: Extractor, document: Document, ) -> list[Annotation]: """Extract all annotations from passed documents. @@ -30,19 +31,17 @@ def start( Returns all annotations contained in the papis documents passed in. """ - - pdf_extractor: Extractor = PdfExtractor() - annotations: list[Annotation] = [] file_available: bool = False + for file in document.get_files(): fname = Path(file) - if not pdf_extractor.can_process(fname): + if not extractor.can_process(fname): continue file_available = True try: - annotations.extend(pdf_extractor.run(fname)) + annotations.extend(extractor.run(fname)) except fitz.FileDataError as e: print(f"File structure errors for {file}.\n{e}") From a51205954c2dcc76daf5a1dafe05e4efed2ac3b2 Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Tue, 23 Jan 2024 09:21:46 +0100 Subject: [PATCH 039/107] refactor: Extract extractor list to extractor module --- papis_extract/__init__.py | 7 ++++--- papis_extract/extraction.py | 6 ------ papis_extract/extractors/__init__.py | 6 ++++++ 3 files changed, 10 insertions(+), 9 deletions(-) create mode 100644 papis_extract/extractors/__init__.py diff --git a/papis_extract/__init__.py b/papis_extract/__init__.py index 47cd5d9..29b609a 100644 --- a/papis_extract/__init__.py +++ b/papis_extract/__init__.py @@ -8,6 +8,7 @@ import papis.strings from papis.document import Document from papis_extract import exporter, extraction +from papis_extract.extractors import all_extractors from papis_extract.annotation import Annotation from papis_extract.formatter import Formatter, formatters @@ -55,10 +56,10 @@ papis.config.register_default_settings(DEFAULT_OPTIONS) "-e", "extractors", type=click.Choice( - list(extraction.extractors.keys()), + list(all_extractors.keys()), case_sensitive=False, ), - default=list(extraction.extractors.keys()), + default=list(all_extractors.keys()), multiple=True, help="Choose an extractor to apply to the selected documents.", ) @@ -107,7 +108,7 @@ def main( write=write, git=git, formatter=formatter, - extractors=[extraction.extractors.get(e) for e in extractors], + extractors=[all_extractors.get(e) for e in extractors], force=force, ) diff --git a/papis_extract/extraction.py b/papis_extract/extraction.py index 86f876c..bf7391a 100644 --- a/papis_extract/extraction.py +++ b/papis_extract/extraction.py @@ -9,7 +9,6 @@ import papis.logging from papis.document import Document from papis_extract.annotation import Annotation -from papis_extract.extractors.pdf import PdfExtractor logger = papis.logging.get_logger(__name__) @@ -51,8 +50,3 @@ def start( logger.warning("Did not find suitable file for document: " f"{desc}") return annotations - - -extractors: dict[str, Extractor] = { - "pdf": PdfExtractor(), -} diff --git a/papis_extract/extractors/__init__.py b/papis_extract/extractors/__init__.py new file mode 100644 index 0000000..174b556 --- /dev/null +++ b/papis_extract/extractors/__init__.py @@ -0,0 +1,6 @@ +from papis_extract.extraction import Extractor +from papis_extract.extractors import pdf + +all_extractors: dict[str, Extractor] = { + "pdf": pdf.PdfExtractor(), +} From 2880c06f5348d6cd0b409d42454819f1b483b11f Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Tue, 23 Jan 2024 09:27:02 +0100 Subject: [PATCH 040/107] chore: Improve cli option help texts Fixed the write option text to be without wrong negation. Show default settings for flag options. --- papis_extract/__init__.py | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/papis_extract/__init__.py b/papis_extract/__init__.py index 29b609a..986ed99 100644 --- a/papis_extract/__init__.py +++ b/papis_extract/__init__.py @@ -35,12 +35,14 @@ papis.config.register_default_settings(DEFAULT_OPTIONS) @click.option( "--write/--no-write", "-w", - help="Do not write annotations to notes only print results to stdout.", + help="Write extracted annotations into papis notes.", + show_default=True, ) @click.option( "--manual/--no-manual", "-m", help="Open note in editor for manual editing after annotation extraction.", + show_default=True, ) @click.option( "--template", @@ -50,6 +52,7 @@ papis.config.register_default_settings(DEFAULT_OPTIONS) case_sensitive=False, ), help="Choose an output template to format annotations with.", + show_default=True, ) @click.option( "--extractor", @@ -61,12 +64,13 @@ papis.config.register_default_settings(DEFAULT_OPTIONS) ), default=list(all_extractors.keys()), multiple=True, - help="Choose an extractor to apply to the selected documents.", + help="Choose an extractor to apply to the selected documents. [default: all]", ) @click.option( "--force/--no-force", "-f", help="Do not drop any annotations because they already exist.", + show_default=True, ) def main( query: str, From 9169e1c98a6d4cdd50478ee20f06b167136222e7 Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Tue, 23 Jan 2024 09:49:31 +0100 Subject: [PATCH 041/107] chore: Improve stdout newline handling Always strip all newlines of the end of all entries, and then add a single newline back between entries. --- papis_extract/exporter.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/papis_extract/exporter.py b/papis_extract/exporter.py index 120224e..862a068 100644 --- a/papis_extract/exporter.py +++ b/papis_extract/exporter.py @@ -26,7 +26,7 @@ def to_stdout( """ output: str = formatter(document, annotations) if output: - print(output.rstrip("\n")) + print("{output}\n".format(output=output.rstrip("\n"))) def to_notes( From 11d570f9d8fbc873c6e0367088d912919e16d224 Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Tue, 23 Jan 2024 09:54:36 +0100 Subject: [PATCH 042/107] refactor: Rename annotation content variables Renamed the two variables describing an annotation's highlighted PDF-text and its appended note if any exists. Previously called 'text' (for the in-PDF highlighted content) and 'content' (for the additional supplied content). Now they are called 'content' for the IN PDF words, highlighted. and 'note' for the appended note given (or not) in an annotation. --- papis_extract/annotation.py | 6 +++--- papis_extract/extractors/pdf.py | 4 ++-- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/papis_extract/annotation.py b/papis_extract/annotation.py index 74342da..9c101e4 100644 --- a/papis_extract/annotation.py +++ b/papis_extract/annotation.py @@ -28,9 +28,9 @@ class Annotation: file: str colors: tuple[float, float, float] = field(default_factory=lambda: (0.0, 0.0, 0.0)) content: str = "" + note: str = "" page: int = 0 tag: str = "" - text: str = "" type: str = "Highlight" minimum_similarity_color: float = 1.0 @@ -43,8 +43,8 @@ class Annotation: """ data = { "file": self.file, - "quote": self.text, - "note": self.content, + "quote": self.content, + "note": self.note, "page": self.page, "tag": self.tag, "type": self.type, diff --git a/papis_extract/extractors/pdf.py b/papis_extract/extractors/pdf.py index ac39184..4bf1228 100644 --- a/papis_extract/extractors/pdf.py +++ b/papis_extract/extractors/pdf.py @@ -41,8 +41,8 @@ class PdfExtractor: ) a = Annotation( file=str(filename), - text=quote or "", - content=note or "", + content=quote or "", + note=note or "", colors=col, type=annot.type[1], page=(page.number or 0) + 1, From 3bd624788891adf1a5132ec56c3f8bed03741b89 Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Tue, 23 Jan 2024 10:12:41 +0100 Subject: [PATCH 043/107] chore: Add license and dev instructions --- COPYING | 674 +++++++++++++++++++++++++++++++++++++++++++++++++ README.md | 34 ++- pyproject.toml | 4 + 3 files changed, 706 insertions(+), 6 deletions(-) create mode 100644 COPYING diff --git a/COPYING b/COPYING new file mode 100644 index 0000000..f288702 --- /dev/null +++ b/COPYING @@ -0,0 +1,674 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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But first, please read +. diff --git a/README.md b/README.md index 70d7afc..1f5b6d0 100644 --- a/README.md +++ b/README.md @@ -198,7 +198,7 @@ The option should generally not take too much tuning, but it is there if you nee This should generally be an alright default but is here to be changed for example if you work with a lot of different annotation colors (where dark purple and light purple may different meanings) and get false positives in automatic tag recognition, or no tags are recognized at all. -## Roadmap to first release +## TODO: Roadmap to first release Known issues to be fixed: @@ -222,16 +222,18 @@ features to be implemented: - [x] add page number if available - exists in Annotation, just need to place in output - [ ] show overall amount of extractions at the end + - implemented for writing to notes (notes exporter) + - KNOWN ISSUE: currently returns number of annotation rows (may be multiple per annot) - [ ] custom formatting decided by user - in config as { "myformatter": ">{tag}\n{quote}\n{note}\n{page} etc"} - [ ] improved default exporters - - markdown into notes - - pretty display on stdout (rich?) - - csv/tsv to stdout - - table fmt stdout? + - [x] markdown into notes + - [ ] pretty display on stdout (rich?) + - [x] csv/tsv to stdout + - [ ] table fmt stdout? - [ ] allow custom colors -> tag name settings not dependent on color name existing (e.g. {"important": (1.0,0.0,0.0)}) - [ ] `--overwrite` mode where existing annotations are not dropped but overwritten on same line of note -- [ ] `--force` mode where we simply do not drop anything +- [x] `--force` mode where we simply do not drop anything - [x] `--format` option to choose from default or set up a custom formatter - called `--template` in current implementation - [ ] on_add hook to extract annotations as files are added @@ -282,6 +284,26 @@ Splitting it into those three building blocks makes it easier to recombine them should someone want to save highlights as csv data in their notes, or should we ever include more extractors than the one for PDFs. +To develop it together with an isolated `papis` instance you can simply inject papis into your +development environment, e.g. invoking the poetry environment shell and then manually installing: + +```bash +poetry shell +pip install papis +``` + +This will leave you with `papis` installed in the same virtual environment as your development. +However, what I do on my system instead to enable quick testing is inject it into a +system-wide (but isolated with `pipx`) papis setup: + +```bash +pipx install papis # create an isolated papis installation reachable form anywhere +pipx inject --editable papis . # inject this folder into the environment and keep up with any changes +``` + +This for me provides the ideal compromise of clean dev environment (papis is not directly part of it) +but quickly reachable installation to test my changes. + --- If you spot a bug or have an idea feel free to open an issue.\ diff --git a/pyproject.toml b/pyproject.toml index 28312cd..526732c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -3,8 +3,12 @@ name = "papis-extract" version = "0.2.0" description = "" authors = ["Marty Oehme "] +license = "GPL-3.0-or-later" readme = "README.md" packages = [{include = "papis_extract"}] +homepage = "https://git.martyoeh.me/Marty/papis-extract" +repository = "https://github.com/marty-oehme/papis-extract" +keywords = ["papis", "pdf", "biblatex", "bibtex", "bibliography", "reference manager", "research", "science"] [tool.poetry.dependencies] python = "^3.11" From ddb34fca7bd0232a8c412b57a9d946abf000e1bb Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Tue, 23 Jan 2024 23:45:49 +0100 Subject: [PATCH 044/107] refactor: Move tagging by color to Annotation --- papis_extract/annotation.py | 55 ++++++++++++++++++++++++++++++--- papis_extract/extractors/pdf.py | 36 --------------------- 2 files changed, 51 insertions(+), 40 deletions(-) diff --git a/papis_extract/annotation.py b/papis_extract/annotation.py index 9c101e4..26bec9d 100644 --- a/papis_extract/annotation.py +++ b/papis_extract/annotation.py @@ -1,9 +1,10 @@ import math from dataclasses import dataclass, field +from typing import Any, Optional +import chevron import papis.config from papis.document import Document -import chevron TEXT_SIMILARITY_MINIMUM = 0.75 COLOR_SIMILARITY_MINIMUM = 0.833 @@ -17,7 +18,6 @@ COLORS = { "orange": (1, 0.65, 0), } - @dataclass class Annotation: """A PDF annotation object. @@ -26,7 +26,7 @@ class Annotation: """ file: str - colors: tuple[float, float, float] = field(default_factory=lambda: (0.0, 0.0, 0.0)) + color: tuple[float, float, float] content: str = "" note: str = "" page: int = 0 @@ -34,6 +34,10 @@ class Annotation: type: str = "Highlight" minimum_similarity_color: float = 1.0 + def __post_init__(self): + self._color = self.color or field(default_factory=lambda: (0.0, 0.0, 0.0)) + self.tag = self.tag or self._tag_from_colorname(self.colorname or "") + def format(self, formatting: str, doc: Document = Document()): """Return a formatted string of the annotation. @@ -52,6 +56,15 @@ class Annotation: } return chevron.render(formatting, data) + @property + def color(self): + return self._color + + @color.setter + def color(self, value: tuple[float, float, float]): + self._color = value + self.tag = self._tag_from_colorname(self.colorname or "") + @property def colorname(self): """Return the stringified version of the annotation color. @@ -59,7 +72,7 @@ class Annotation: Finds the closest named color to the annotation and returns it, using euclidian distance between the two color vectors. """ - annot_colors = self.colors or (0.0, 0.0, 0.0) + annot_colors = self.color or (0.0, 0.0, 0.0) nearest = None minimum_similarity = ( papis.config.getfloat("minimum_similarity_color", "plugins.extract") or 1.0 @@ -81,3 +94,37 @@ class Annotation: difference between full black and full white, as a float. """ return 1 - (abs(math.dist([*color_one], [*color_two])) / 3) + + def _tag_from_colorname(self, colorname: str) -> str: + color_mapping: dict[str, str] = self._getdict("tags", "plugins.extract") + if not color_mapping: + return "" + + return color_mapping.get(colorname, "") + + # mimics the functions in papis.config.{getlist,getint,getfloat} etc. + def _getdict(self, key: str, section: Optional[str] = None) -> dict[str, str]: + """Dict getter + + :returns: A python dict + :raises SyntaxError: Whenever the parsed syntax is either not a valid + python object or a valid python dict. + """ + rawvalue: Any = papis.config.general_get(key, section=section) + if isinstance(rawvalue, dict): + return rawvalue + try: + rawvalue = eval(rawvalue) + except Exception: + raise SyntaxError( + "The key '{}' must be a valid Python object: {}".format(key, rawvalue) + ) + else: + if not isinstance(rawvalue, dict): + raise SyntaxError( + "The key '{}' must be a valid Python dict. Got: {} (type {!r})".format( + key, rawvalue, type(rawvalue).__name__ + ) + ) + + return rawvalue diff --git a/papis_extract/extractors/pdf.py b/papis_extract/extractors/pdf.py index 4bf1228..b38ed50 100644 --- a/papis_extract/extractors/pdf.py +++ b/papis_extract/extractors/pdf.py @@ -47,7 +47,6 @@ class PdfExtractor: type=annot.type[1], page=(page.number or 0) + 1, ) - a.tag = self._tag_from_colorname(a.colorname or "") annotations.append(a) logger.debug( f"Found {len(annotations)} " @@ -61,15 +60,6 @@ class PdfExtractor: return magic.from_file(fname, mime=True) == "application/pdf" - - def _tag_from_colorname(self, colorname: str) -> str: - color_mapping: dict[str, str] = self._getdict("tags", "plugins.extract") - if not color_mapping: - return "" - - return color_mapping.get(colorname, "") - - def _retrieve_annotation_content(self, page: fitz.Page, annotation: fitz.Annot ) -> tuple[str | None, str | None]: @@ -104,29 +94,3 @@ class PdfExtractor: return (None, None) -# mimics the functions in papis.config.{getlist,getint,getfloat} etc. - def _getdict(self, key: str, section: Optional[str] = None) -> dict[str, str]: - """Dict getter - - :returns: A python dict - :raises SyntaxError: Whenever the parsed syntax is either not a valid - python object or a valid python dict. - """ - rawvalue: Any = papis.config.general_get(key, section=section) - if isinstance(rawvalue, dict): - return rawvalue - try: - rawvalue = eval(rawvalue) - except Exception: - raise SyntaxError( - "The key '{}' must be a valid Python object: {}".format(key, rawvalue) - ) - else: - if not isinstance(rawvalue, dict): - raise SyntaxError( - "The key '{}' must be a valid Python dict. Got: {} (type {!r})".format( - key, rawvalue, type(rawvalue).__name__ - ) - ) - - return rawvalue From c53cd563b787fceffbfd72ab5a576a29f6fde08a Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Wed, 24 Jan 2024 08:55:43 +0100 Subject: [PATCH 045/107] feat: Add pocketbook extraction --- papis_extract/annotation.py | 10 +++-- papis_extract/exporter.py | 2 +- papis_extract/extraction.py | 2 +- papis_extract/extractors/__init__.py | 2 + papis_extract/extractors/pdf.py | 14 +++--- papis_extract/extractors/pocketbook.py | 60 ++++++++++++++++++++++++++ pyproject.toml | 2 + 7 files changed, 78 insertions(+), 14 deletions(-) create mode 100644 papis_extract/extractors/pocketbook.py diff --git a/papis_extract/annotation.py b/papis_extract/annotation.py index 26bec9d..0955e47 100644 --- a/papis_extract/annotation.py +++ b/papis_extract/annotation.py @@ -9,15 +9,19 @@ from papis.document import Document TEXT_SIMILARITY_MINIMUM = 0.75 COLOR_SIMILARITY_MINIMUM = 0.833 -COLORS = { - "red": (1, 0, 0), - "green": (0, 1, 0), +COLORS: dict[str, tuple[float, float, float]] = { "blue": (0, 0, 1), + "green": (0, 1, 0), + "red": (1, 0, 0), + "cyan": (0, 1, 1), "yellow": (1, 1, 0), + "magenta": (1, 0, 1), "purple": (0.5, 0, 0.5), + "pink": (1, 0.75, 0.8), "orange": (1, 0.65, 0), } + @dataclass class Annotation: """A PDF annotation object. diff --git a/papis_extract/exporter.py b/papis_extract/exporter.py index 862a068..11cb666 100644 --- a/papis_extract/exporter.py +++ b/papis_extract/exporter.py @@ -98,7 +98,7 @@ def _add_annots_to_note( f.write("\n") logger.info( f"Wrote {len(new_annotations)} " - f"{'annotation' if len(new_annotations) == 1 else 'annotations'} " + f"{'line' if len(new_annotations) == 1 else 'lines'} " f"to {papis.document.describe(document)}" ) diff --git a/papis_extract/extraction.py b/papis_extract/extraction.py index bf7391a..79c6d6a 100644 --- a/papis_extract/extraction.py +++ b/papis_extract/extraction.py @@ -47,6 +47,6 @@ def start( if not file_available: # have to remove curlys or papis logger gets upset desc = re.sub("[{}]", "", papis.document.describe(document)) - logger.warning("Did not find suitable file for document: " f"{desc}") + logger.info(f"No {type(extractor)} file for document: {desc}") return annotations diff --git a/papis_extract/extractors/__init__.py b/papis_extract/extractors/__init__.py index 174b556..ae9205a 100644 --- a/papis_extract/extractors/__init__.py +++ b/papis_extract/extractors/__init__.py @@ -1,6 +1,8 @@ from papis_extract.extraction import Extractor from papis_extract.extractors import pdf +from papis_extract.extractors.pocketbook import PocketBookExtractor all_extractors: dict[str, Extractor] = { "pdf": pdf.PdfExtractor(), + "pocketbook": PocketBookExtractor(), } diff --git a/papis_extract/extractors/pdf.py b/papis_extract/extractors/pdf.py index b38ed50..a5f8de4 100644 --- a/papis_extract/extractors/pdf.py +++ b/papis_extract/extractors/pdf.py @@ -1,5 +1,4 @@ from pathlib import Path -from typing import Any, Optional import fitz import Levenshtein @@ -43,7 +42,7 @@ class PdfExtractor: file=str(filename), content=quote or "", note=note or "", - colors=col, + color=col, type=annot.type[1], page=(page.number or 0) + 1, ) @@ -54,14 +53,12 @@ class PdfExtractor: ) return annotations - def _is_pdf(self, fname: Path) -> bool: """Check if file is a pdf, using mime type.""" return magic.from_file(fname, mime=True) == "application/pdf" - - def _retrieve_annotation_content(self, - page: fitz.Page, annotation: fitz.Annot + def _retrieve_annotation_content( + self, page: fitz.Page, annotation: fitz.Annot ) -> tuple[str | None, str | None]: """Gets the text content of an annotation. @@ -77,7 +74,8 @@ class PdfExtractor: # highlight with selection in note minimum_similarity = ( - papis.config.getfloat("minimum_similarity_content", "plugins.extract") or 1.0 + papis.config.getfloat("minimum_similarity_content", "plugins.extract") + or 1.0 ) if Levenshtein.ratio(content, written) > minimum_similarity: return (content, None) @@ -92,5 +90,3 @@ class PdfExtractor: return (written, None) # just a highlight without any text return (None, None) - - diff --git a/papis_extract/extractors/pocketbook.py b/papis_extract/extractors/pocketbook.py new file mode 100644 index 0000000..c7f2a9c --- /dev/null +++ b/papis_extract/extractors/pocketbook.py @@ -0,0 +1,60 @@ +from pathlib import Path + +import magic +import papis.config +import papis.logging +from bs4 import BeautifulSoup + +from papis_extract.annotation import COLORS, Annotation + +logger = papis.logging.get_logger(__name__) + + +class PocketBookExtractor: + def can_process(self, filename: Path) -> bool: + return magic.from_file(filename, mime=True) == "text/xml" + + def run(self, filename: Path) -> list[Annotation]: + """Extract annotations from pocketbook html file. + + Export annotations from pocketbook app and load add them + to a papis document as the exported html file. + + Returns all readable annotations contained in the file + passed in, with highlights, notes and pages if available. + """ + annotations: list[Annotation] = [] + try: + with open(filename) as f: + html = BeautifulSoup(f.read(), features="xml") + except FileNotFoundError: + logger.error(f"Could not open file {filename} for extraction.") + return [] + + for bm in html.select("div.bookmark"): + content = (bm.select_one("div.bm-text>p") or html.new_string("")).text + note = (bm.select_one("div.bm-note>p") or html.new_string("")).text + page = (bm.select_one("p.bm-page") or html.new_string("")).text + + el_classes = bm.attrs.get("class", "").split(" ") + color = (0, 0, 0) + for c in el_classes: + if "bm-color-" in c: + color = COLORS.get(c.removeprefix("bm-color-"), (0, 0, 0)) + break + + a = Annotation( + file=str(filename), + content=content or "", + note=note or "", + color=color, + type="Highlight", + page=int(page), + ) + annotations.append(a) + + logger.debug( + f"Found {len(annotations)} " + f"{'annotation' if len(annotations) == 1 else 'annotations'} for {filename}." + ) + return annotations diff --git a/pyproject.toml b/pyproject.toml index 526732c..0c793cd 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -19,9 +19,11 @@ click = "^8.1.7" whoosh = { version = "^2.7.4", optional = true } python-magic = "^0.4.27" chevron = "^0.14.0" +beautifulsoup4 = { version = "^4.12.3", optional = true } [tool.poetry.extras] whoosh = ["whoosh"] +pocketbook = ["beautifulsoup4"] [tool.poetry.group.dev.dependencies] pytest = "^7.4.0" From f4a26292a03402f4a87bf3b6eb6d5e2e5470156a Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Wed, 24 Jan 2024 11:13:35 +0100 Subject: [PATCH 046/107] fix: Remove debug print statement --- papis_extract/exporter.py | 1 - 1 file changed, 1 deletion(-) diff --git a/papis_extract/exporter.py b/papis_extract/exporter.py index 11cb666..144042c 100644 --- a/papis_extract/exporter.py +++ b/papis_extract/exporter.py @@ -93,7 +93,6 @@ def _add_annots_to_note( # add newline if theres no empty space at file end if len(existing) > 0 and existing[-1].strip() != "": f.write("\n") - print(new_annotations) f.write("\n\n".join(new_annotations)) f.write("\n") logger.info( From 67bfc303960707c858d8302ea29e7e02549c7454 Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Wed, 24 Jan 2024 11:13:49 +0100 Subject: [PATCH 047/107] refactor: Switch annotation away from dataclass To ease employing getters and setters, we switch the dataclass to a normal python undecorated class. --- papis_extract/annotation.py | 37 ++++++++++++++++++++++++------------- poetry.lock | 2 +- 2 files changed, 25 insertions(+), 14 deletions(-) diff --git a/papis_extract/annotation.py b/papis_extract/annotation.py index 0955e47..6371f28 100644 --- a/papis_extract/annotation.py +++ b/papis_extract/annotation.py @@ -29,18 +29,25 @@ class Annotation: Contains all information necessary for the annotation itself, content and metadata. """ - file: str - color: tuple[float, float, float] - content: str = "" - note: str = "" - page: int = 0 - tag: str = "" - type: str = "Highlight" - minimum_similarity_color: float = 1.0 - - def __post_init__(self): - self._color = self.color or field(default_factory=lambda: (0.0, 0.0, 0.0)) - self.tag = self.tag or self._tag_from_colorname(self.colorname or "") + def __init__( + self, + file: str, + color: tuple[float, float, float] = (0.0, 0.0, 0.0), + content: str = "", + note: str = "", + page: int = 0, + tag: str = "", + type: str = "Highlight", + minimum_similarity_color: float = 1.0, + ) -> None: + self.minimum_similarity_color = minimum_similarity_color + self.file = file + self.color = color + self.content = content + self.note = note + self.page = page + self.tag = tag + self.type = type def format(self, formatting: str, doc: Document = Document()): """Return a formatted string of the annotation. @@ -89,7 +96,11 @@ class Annotation: nearest = name return nearest - def _color_similarity_ratio(self, color_one, color_two): + def _color_similarity_ratio( + self, + color_one: tuple[float, float, float], + color_two: tuple[float, float, float], + ) -> float: """Return the similarity of two colors between 0 and 1. Takes two rgb color tuples made of floats between 0 and 1, diff --git a/poetry.lock b/poetry.lock index 14f75b0..644e1ab 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1084,4 +1084,4 @@ whoosh = ["whoosh"] [metadata] lock-version = "2.0" python-versions = "^3.11" -content-hash = "02d5ac314a19f14103372c7ceccdaec080df3fdc2fdb1381f2f6343cd6d17db4" +content-hash = "273c651cac44163ca183313ce3c7384577f090fd98fa6d28e6a3496cb28254ac" From 333bd279b9594a837ac63b275186bc3fdf516c80 Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Wed, 24 Jan 2024 11:14:45 +0100 Subject: [PATCH 048/107] fix: Fix test fixtures for new annotation structure --- tests/test_annotation.py | 15 ++++++++------- tests/test_formatting.py | 4 ++-- 2 files changed, 10 insertions(+), 9 deletions(-) diff --git a/tests/test_annotation.py b/tests/test_annotation.py index 529a4c1..98e7f31 100644 --- a/tests/test_annotation.py +++ b/tests/test_annotation.py @@ -1,5 +1,6 @@ -from papis.document import Document import pytest +from papis.document import Document + from papis_extract.annotation import Annotation @@ -20,8 +21,8 @@ from papis_extract.annotation import Annotation def test_formatting_replacements(fmt_string, expected): sut = Annotation( "myfile", - text="I am the text value", - content="Whereas I represent the note", + content="I am the text value", + note="Whereas I represent the note", ) assert sut.format(fmt_string) == expected @@ -38,8 +39,8 @@ def test_formatting_replacements(fmt_string, expected): def test_formatting_document_access(fmt_string, expected): sut = Annotation( "myfile", - text="I am the text value", - content="Whereas I represent the note", + content="I am the text value", + note="Whereas I represent the note", ) doc = Document(data={"title": "document-title", "author": "document-author"}) @@ -47,7 +48,7 @@ def test_formatting_document_access(fmt_string, expected): def test_colorname_matches_exact(): - sut = Annotation("testfile", colors=(1.0, 0.0, 0.0), minimum_similarity_color=1.0) + sut = Annotation("testfile", color=(1.0, 0.0, 0.0), minimum_similarity_color=1.0) c_name = sut.colorname assert c_name == "red" @@ -64,6 +65,6 @@ def test_colorname_matches_exact(): ], ) def test_matches_inexact_colorname(color_value): - sut = Annotation("testfile", colors=color_value, minimum_similarity_color=0.833) + sut = Annotation("testfile", color=color_value, minimum_similarity_color=0.833) c_name = sut.colorname assert c_name == "red" diff --git a/tests/test_formatting.py b/tests/test_formatting.py index 244f4f8..5b805a7 100644 --- a/tests/test_formatting.py +++ b/tests/test_formatting.py @@ -11,8 +11,8 @@ from papis_extract.formatter import ( document = Document(data={"author": "document-author", "title": "document-title"}) annotations = [ - Annotation("myfile.pdf", text="my lovely text"), - Annotation("myfile.pdf", text="my second text", content="with note"), + Annotation("myfile.pdf", content="my lovely text"), + Annotation("myfile.pdf", content="my second text", note="with note"), ] md_default_output = """============== --------------- document-title - document-author From f6c01895290c658bd37ccb3f3921820c4b9f7127 Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Wed, 24 Jan 2024 11:20:00 +0100 Subject: [PATCH 049/107] fix: Tag automation on tag creation Tagging by color only worked on manually invoking the `annotation.color = ()` setter. Now it works on initial instance creation. --- papis_extract/annotation.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/papis_extract/annotation.py b/papis_extract/annotation.py index 6371f28..65e4f01 100644 --- a/papis_extract/annotation.py +++ b/papis_extract/annotation.py @@ -42,11 +42,11 @@ class Annotation: ) -> None: self.minimum_similarity_color = minimum_similarity_color self.file = file - self.color = color + self._color = color self.content = content self.note = note self.page = page - self.tag = tag + self.tag = tag or self._tag_from_colorname(self.colorname or "") self.type = type def format(self, formatting: str, doc: Document = Document()): From e1e09b6011fa10089b14ea4246e91a80c5b46413 Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Wed, 24 Jan 2024 12:05:41 +0100 Subject: [PATCH 050/107] chore: Format pyproject --- pyproject.toml | 13 +++++++++++-- 1 file changed, 11 insertions(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 0c793cd..c712e4f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -5,10 +5,19 @@ description = "" authors = ["Marty Oehme "] license = "GPL-3.0-or-later" readme = "README.md" -packages = [{include = "papis_extract"}] +packages = [{ include = "papis_extract" }] homepage = "https://git.martyoeh.me/Marty/papis-extract" repository = "https://github.com/marty-oehme/papis-extract" -keywords = ["papis", "pdf", "biblatex", "bibtex", "bibliography", "reference manager", "research", "science"] +keywords = [ + "papis", + "pdf", + "biblatex", + "bibtex", + "bibliography", + "reference manager", + "research", + "science", +] [tool.poetry.dependencies] python = "^3.11" From e7e5258b3486eff9ebe07c070521184627a039fc Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Wed, 24 Jan 2024 12:07:04 +0100 Subject: [PATCH 051/107] feat: Only activate pocketbook extractor optionally Since we make the dependencies for pocketbook html extraction optional as an extra, this commit ensures the extractor (and cli option) only gets loaded when they exist. --- papis_extract/extractors/__init__.py | 13 ++++++++++++- 1 file changed, 12 insertions(+), 1 deletion(-) diff --git a/papis_extract/extractors/__init__.py b/papis_extract/extractors/__init__.py index ae9205a..3333c08 100644 --- a/papis_extract/extractors/__init__.py +++ b/papis_extract/extractors/__init__.py @@ -1,8 +1,19 @@ +import papis.logging + from papis_extract.extraction import Extractor from papis_extract.extractors import pdf from papis_extract.extractors.pocketbook import PocketBookExtractor +logger = papis.logging.get_logger(__name__) + all_extractors: dict[str, Extractor] = { "pdf": pdf.PdfExtractor(), - "pocketbook": PocketBookExtractor(), } + +try: + import bs4 + import magic + + all_extractors["pocketbook"] = PocketBookExtractor() +except ImportError: + logger.debug("pocketbook extractor not activated.") From 2f41906e6ac9924e8e1e87382faa55b6995cd22b Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Wed, 24 Jan 2024 12:21:51 +0100 Subject: [PATCH 052/107] docs: Add extractor and install info Added extractor info for the two currently existing extractors. Added install recommendation for pipx. --- README.md | 25 +++++++++++++++++++++---- 1 file changed, 21 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index 1f5b6d0..a25a304 100644 --- a/README.md +++ b/README.md @@ -19,6 +19,8 @@ everything should now be set up. I am currently working towards the first release for pypi, see the below roadmap; when that is done you will also be able to install in the usual pypi way. +If you manage your python environments with `pipx`, you can also `pipx inject --spec 'git+git+https://git.martyoeh.me/Marty/papis-extract.git` to add it to your specific papis environment. + To check if everything is working you should now see the `extract` command listed when running `papis --help`. You will be set up with the default options but if you want to change anything, read on in configuration below. @@ -198,6 +200,20 @@ The option should generally not take too much tuning, but it is there if you nee This should generally be an alright default but is here to be changed for example if you work with a lot of different annotation colors (where dark purple and light purple may different meanings) and get false positives in automatic tag recognition, or no tags are recognized at all. +## Extractors + +Currently, the program supports two annotation extractors: + +A **`pdf` extractor**, which takes highlights and annotations embedded in any PDF file. +It should work with most PDF styles, as long as annotations are marked as such +(does not work if e.g. highlights are baked onto text, or there is no text in the file). + +A `pocketbook` extractor, which takes bookmarks exported from the mobile [PocketBook](https://pocketbook.ch/en-ch/app) reader applications. +You can export bookmarks by opening a book, going to the notes list and selecting `Export notes...`. +Then import the resulting `.html` file into the library using `papis add` +(or `papis addto` to add it to existing documents). +You are then ready to use extract to get those annotations from the exported list into your notes. + ## TODO: Roadmap to first release Known issues to be fixed: @@ -267,7 +283,8 @@ I am not sure if there is much I can do about these issues for now. and for myself whenever I forget. The basic building blocks currently in here are three: - extractors -: Extract data from a source file attached to a papis document. +: Extract data from a source file attached to a papis document. + Crawls the actual files attached to documents to put them into annotation-friendly formats. - annotations : The actual extracted blocks of text, containing some metadata @@ -277,12 +294,12 @@ and for myself whenever I forget. The basic building blocks currently in here ar : Put the extracted data somewhere. For now stdout or into your notes. - formatters -: Make sure the exporter saves the data according to your preferred layout, +: Make sure the exporter saves the annotation data according to your preferred layout, such as a markdown syntax or csv-structure. -Splitting it into those three building blocks makes it easier to recombine them in any way, +Splitting it into those building blocks makes it easier to recombine them in any way, should someone want to save highlights as csv data in their notes, -or should we ever include more extractors than the one for PDFs. +or to include additional extractors or formatters. To develop it together with an isolated `papis` instance you can simply inject papis into your development environment, e.g. invoking the poetry environment shell and then manually installing: From c2a5190237949714fc6607b1afff6938ffd3a78e Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Wed, 24 Jan 2024 12:27:21 +0100 Subject: [PATCH 053/107] refactor: Improve module availability checks Followed ruff (Pyflakes) suggestion to use importlib utils directly instead of try and erroring with imports. --- papis_extract/extractors/__init__.py | 13 ++++++------- 1 file changed, 6 insertions(+), 7 deletions(-) diff --git a/papis_extract/extractors/__init__.py b/papis_extract/extractors/__init__.py index 3333c08..47ead33 100644 --- a/papis_extract/extractors/__init__.py +++ b/papis_extract/extractors/__init__.py @@ -1,3 +1,5 @@ +from importlib.util import find_spec + import papis.logging from papis_extract.extraction import Extractor @@ -6,14 +8,11 @@ from papis_extract.extractors.pocketbook import PocketBookExtractor logger = papis.logging.get_logger(__name__) -all_extractors: dict[str, Extractor] = { - "pdf": pdf.PdfExtractor(), -} +all_extractors: dict[str, Extractor] = {} -try: - import bs4 - import magic +all_extractors["pdf"] = pdf.PdfExtractor() +if find_spec("bs4") and find_spec("magic"): all_extractors["pocketbook"] = PocketBookExtractor() -except ImportError: +else: logger.debug("pocketbook extractor not activated.") From 86d53a19d4866b5ecc620b2f60dab4e21704e8f9 Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Wed, 24 Jan 2024 13:39:01 +0100 Subject: [PATCH 054/107] chore: Fix import lint error --- papis_extract/annotation.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/papis_extract/annotation.py b/papis_extract/annotation.py index 65e4f01..666c1bb 100644 --- a/papis_extract/annotation.py +++ b/papis_extract/annotation.py @@ -1,5 +1,5 @@ import math -from dataclasses import dataclass, field +from dataclasses import dataclass from typing import Any, Optional import chevron From 6a8f8a03bc27b4e002813302bebb7f9b930032f1 Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Wed, 24 Jan 2024 14:55:28 +0100 Subject: [PATCH 055/107] refactor: Extract pocketbook file opening method --- papis_extract/extractors/pocketbook.py | 20 ++++++++++++++------ 1 file changed, 14 insertions(+), 6 deletions(-) diff --git a/papis_extract/extractors/pocketbook.py b/papis_extract/extractors/pocketbook.py index c7f2a9c..942025f 100644 --- a/papis_extract/extractors/pocketbook.py +++ b/papis_extract/extractors/pocketbook.py @@ -23,14 +23,12 @@ class PocketBookExtractor: Returns all readable annotations contained in the file passed in, with highlights, notes and pages if available. """ - annotations: list[Annotation] = [] - try: - with open(filename) as f: - html = BeautifulSoup(f.read(), features="xml") - except FileNotFoundError: - logger.error(f"Could not open file {filename} for extraction.") + content = self._read_file(filename) + if not content: return [] + html = BeautifulSoup(content, features="xml") + annotations: list[Annotation] = [] for bm in html.select("div.bookmark"): content = (bm.select_one("div.bm-text>p") or html.new_string("")).text note = (bm.select_one("div.bm-note>p") or html.new_string("")).text @@ -58,3 +56,13 @@ class PocketBookExtractor: f"{'annotation' if len(annotations) == 1 else 'annotations'} for {filename}." ) return annotations + + def _read_file(self, filename: Path) -> str: + try: + with open(filename) as f: + return f.read() + except FileNotFoundError: + logger.error(f"Could not open file {filename} for extraction.") + return "" + + From c8e8453b681bf611fde7f237dfd6cda76e1a86ab Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Wed, 24 Jan 2024 14:56:30 +0100 Subject: [PATCH 056/107] feat: Add advanced pocketbook detection heuristic Added heuristic which checks for the existence of a specific meta tag written to the pocketbook XHTML file. --- papis_extract/extractors/pocketbook.py | 16 +++++++++++++--- 1 file changed, 13 insertions(+), 3 deletions(-) diff --git a/papis_extract/extractors/pocketbook.py b/papis_extract/extractors/pocketbook.py index 942025f..08b165d 100644 --- a/papis_extract/extractors/pocketbook.py +++ b/papis_extract/extractors/pocketbook.py @@ -12,7 +12,19 @@ logger = papis.logging.get_logger(__name__) class PocketBookExtractor: def can_process(self, filename: Path) -> bool: - return magic.from_file(filename, mime=True) == "text/xml" + content = self._read_file(filename) + if not content: + return False + + if not magic.from_buffer(content, mime=True) == "text/xml": + return False + + html = BeautifulSoup(content, features="xml") + if not html.find( + "meta", {"name": "generator", "content": "PocketBook Bookmarks Export"} + ): + return False + return True def run(self, filename: Path) -> list[Annotation]: """Extract annotations from pocketbook html file. @@ -64,5 +76,3 @@ class PocketBookExtractor: except FileNotFoundError: logger.error(f"Could not open file {filename} for extraction.") return "" - - From 72ddaaf1bc5dd7736fb74be744c1ad4e4997e069 Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Thu, 25 Jan 2024 21:34:40 +0100 Subject: [PATCH 057/107] refactor: Extract exporters to separate module --- papis_extract/__init__.py | 39 +++---- papis_extract/exporter.py | 160 ++++------------------------ papis_extract/exporters/__init__.py | 14 +++ papis_extract/exporters/notes.py | 131 +++++++++++++++++++++++ papis_extract/exporters/stdout.py | 26 +++++ 5 files changed, 213 insertions(+), 157 deletions(-) create mode 100644 papis_extract/exporters/__init__.py create mode 100644 papis_extract/exporters/notes.py create mode 100644 papis_extract/exporters/stdout.py diff --git a/papis_extract/__init__.py b/papis_extract/__init__.py index 986ed99..d0a6e45 100644 --- a/papis_extract/__init__.py +++ b/papis_extract/__init__.py @@ -7,9 +7,11 @@ import papis.notes import papis.strings from papis.document import Document -from papis_extract import exporter, extraction -from papis_extract.extractors import all_extractors from papis_extract.annotation import Annotation +from papis_extract import extraction +from papis_extract.exporter import Exporter +from papis_extract.extractors import all_extractors +from papis_extract.exporters import all_exporters from papis_extract.formatter import Formatter, formatters logger = papis.logging.get_logger(__name__) @@ -126,24 +128,25 @@ def run( git: bool = False, force: bool = False, ) -> None: + if write: + exporter: Exporter = all_exporters["notes"]( + formatter=formatter or formatters["markdown"], + edit=edit, + git=git, + force=force, + ) + else: + exporter: Exporter = all_exporters["stdout"]( + formatter=formatter or formatters["markdown"] + ) + + doc_annots: list[tuple[Document, list[Annotation]]] = [] for doc in documents: + annotations: list[Annotation] = [] for ext in extractors: if not ext: continue + annotations.extend(extraction.start(ext, doc)) + doc_annots.append((doc, annotations)) - annotations: list[Annotation] = extraction.start(ext, doc) - if write: - exporter.to_notes( - formatter=formatter or formatters["markdown-atx"], - document=doc, - annotations=annotations, - edit=edit, - git=git, - force=force, - ) - else: - exporter.to_stdout( - formatter=formatter or formatters["markdown"], - document=doc, - annotations=annotations, - ) + exporter.run(doc_annots) diff --git a/papis_extract/exporter.py b/papis_extract/exporter.py index 144042c..de1fe6c 100644 --- a/papis_extract/exporter.py +++ b/papis_extract/exporter.py @@ -1,146 +1,28 @@ -import papis.logging -import papis.document -import papis.notes -import papis.commands.edit -import papis.api -import papis.git -import papis.config -import Levenshtein -from papis_extract.annotation import Annotation +from dataclasses import dataclass +from typing import Protocol +import papis.api +import papis.commands.edit +import papis.config +import papis.document +import papis.git +import papis.logging +import papis.notes + +from papis_extract.annotation import Annotation from papis_extract.formatter import Formatter logger = papis.logging.get_logger(__name__) -def to_stdout( - formatter: Formatter, - document: papis.document.Document, - annotations: list[Annotation], -) -> None: - """Pretty print annotations to stdout. +@dataclass +class Exporter(Protocol): + formatter: Formatter + edit: bool = False + git: bool = False + force: bool = False - Gives a nice human-readable representations of - the annotations in somewhat of a list form. - Not intended for machine-readability. - """ - output: str = formatter(document, annotations) - if output: - print("{output}\n".format(output=output.rstrip("\n"))) - - -def to_notes( - formatter: Formatter, - document: papis.document.Document, - annotations: list[Annotation], - edit: bool, - git: bool, - force: bool, -) -> None: - """Write annotations into document notes. - - Permanently writes the given annotations into notes - belonging to papis documents. Creates new notes for - documents missing a note field or appends to existing. - """ - formatted_annotations = formatter(document, annotations).split("\n") - if formatted_annotations: - _add_annots_to_note(document, formatted_annotations, force=force) - - if edit: - papis.commands.edit.edit_notes(document, git=git) - - -def _add_annots_to_note( - document: papis.document.Document, - formatted_annotations: list[str], - git: bool = False, - force: bool = False, -) -> None: - """ - Append new annotations to the end of a note. - - This function appends new annotations to the end of a note file. It takes in a - document object containing the note, a list of formatted annotations to be - added, and optional flags git and force. If git is True, the changes will be - committed to git. If force is True, the annotations will be added even if they - already exist in the note. - - :param document: The document object representing the note - :type document: class:`papis.document.Document` - :param formatted_annotations: A list of already formatted annotations to be added - :type formatted_annotations: list[str] - :param git: Flag indicating whether to commit changes to git, defaults to False. - :type git: bool, optional - :param force: Flag indicating whether to force adding annotations even if they - already exist, defaults to False. - :type force: bool, optional - """ - logger.debug("Adding annotations to note.") - notes_path = papis.notes.notes_path_ensured(document) - - existing: list[str] = [] - with open(notes_path, "r") as file_read: - existing = file_read.readlines() - - new_annotations: list[str] = [] - if not force: - new_annotations = _drop_existing_annotations(formatted_annotations, existing) - if not new_annotations: - return - - with open(notes_path, "a") as f: - # add newline if theres no empty space at file end - if len(existing) > 0 and existing[-1].strip() != "": - f.write("\n") - f.write("\n\n".join(new_annotations)) - f.write("\n") - logger.info( - f"Wrote {len(new_annotations)} " - f"{'line' if len(new_annotations) == 1 else 'lines'} " - f"to {papis.document.describe(document)}" - ) - - if git: - msg = "Update notes for '{0}'".format(papis.document.describe(document)) - folder = document.get_main_folder() - if folder: - papis.git.add_and_commit_resources( - folder, [notes_path, document.get_info_file()], msg - ) - - -def _drop_existing_annotations( - formatted_annotations: list[str], file_lines: list[str] -) -> list[str]: - """Returns the input annotations dropping any existing. - - Takes a list of formatted annotations and a list of strings - (most probably existing lines in a file). If anny annotations - match an existing line closely enough, they will be dropped. - - Returns list of annotations without duplicates. - """ - minimum_similarity = ( - papis.config.getfloat("minimum_similarity", "plugins.extract") or 1.0 - ) - - remaining: list[str] = [] - for an in formatted_annotations: - an_split = an.splitlines() - if an_split and not _test_similarity( - an_split[0], file_lines, minimum_similarity - ): - remaining.append(an) - - return remaining - - -def _test_similarity( - string: str, lines: list[str], minimum_similarity: float = 1.0 -) -> bool: - for line in lines: - ratio = Levenshtein.ratio(string, line) - if ratio > minimum_similarity: - return True - return False + def run( + self, annot_docs: list[tuple[papis.document.Document, list[Annotation]]] + ) -> None: + ... diff --git a/papis_extract/exporters/__init__.py b/papis_extract/exporters/__init__.py new file mode 100644 index 0000000..6b5208b --- /dev/null +++ b/papis_extract/exporters/__init__.py @@ -0,0 +1,14 @@ + +import papis.logging + +from papis_extract.exporter import Exporter +from papis_extract.exporters.notes import NotesExporter +from papis_extract.exporters.stdout import StdoutExporter + + +logger = papis.logging.get_logger(__name__) + +all_exporters: dict[str, type[Exporter]] = {} + +all_exporters["stdout"] = StdoutExporter +all_exporters["notes"] = NotesExporter diff --git a/papis_extract/exporters/notes.py b/papis_extract/exporters/notes.py new file mode 100644 index 0000000..a218db7 --- /dev/null +++ b/papis_extract/exporters/notes.py @@ -0,0 +1,131 @@ +from dataclasses import dataclass +import Levenshtein +from papis.document import Document +from papis_extract.annotation import Annotation +from papis_extract.formatter import Formatter +from papis.logging import get_logger +import papis.notes +import papis.document +import papis.git +import papis.config +import papis.commands.edit + +logger = get_logger(__name__) + + +@dataclass +class NotesExporter: + formatter: Formatter + edit: bool = False + git: bool = False + force: bool = False + + def run(self, annot_docs: list[tuple[Document, list[Annotation]]]) -> None: + """Write annotations into document notes. + + Permanently writes the given annotations into notes + belonging to papis documents. Creates new notes for + documents missing a note field or appends to existing. + """ + for doc, annots in annot_docs: + formatted_annotations = self.formatter(doc, annots).split("\n") + if formatted_annotations: + self._add_annots_to_note(doc, formatted_annotations, force=self.force) + + if self.edit: + papis.commands.edit.edit_notes(doc, git=self.git) + + def _add_annots_to_note( + self, + document: Document, + formatted_annotations: list[str], + git: bool = False, + force: bool = False, + ) -> None: + """ + Append new annotations to the end of a note. + + This function appends new annotations to the end of a note file. It takes in a + document object containing the note, a list of formatted annotations to be + added, and optional flags git and force. If git is True, the changes will be + committed to git. If force is True, the annotations will be added even if they + already exist in the note. + + :param document: The document object representing the note + :type document: class:`papis.document.Document` + :param formatted_annotations: A list of already formatted annotations to be added + :type formatted_annotations: list[str] + :param git: Flag indicating whether to commit changes to git, defaults to False. + :type git: bool, optional + :param force: Flag indicating whether to force adding annotations even if they + already exist, defaults to False. + :type force: bool, optional + """ + logger.debug("Adding annotations to note.") + notes_path = papis.notes.notes_path_ensured(document) + + existing: list[str] = [] + with open(notes_path, "r") as file_read: + existing = file_read.readlines() + + new_annotations: list[str] = [] + if not force: + new_annotations = self._drop_existing_annotations( + formatted_annotations, existing + ) + if not new_annotations: + return + + with open(notes_path, "a") as f: + # add newline if theres no empty space at file end + if len(existing) > 0 and existing[-1].strip() != "": + f.write("\n") + f.write("\n\n".join(new_annotations)) + f.write("\n") + logger.info( + f"Wrote {len(new_annotations)} " + f"{'line' if len(new_annotations) == 1 else 'lines'} " + f"to {papis.document.describe(document)}" + ) + + if git: + msg = "Update notes for '{0}'".format(papis.document.describe(document)) + folder = document.get_main_folder() + if folder: + papis.git.add_and_commit_resources( + folder, [notes_path, document.get_info_file()], msg + ) + + def _drop_existing_annotations( + self, formatted_annotations: list[str], file_lines: list[str] + ) -> list[str]: + """Returns the input annotations dropping any existing. + + Takes a list of formatted annotations and a list of strings + (most probably existing lines in a file). If anny annotations + match an existing line closely enough, they will be dropped. + + Returns list of annotations without duplicates. + """ + minimum_similarity = ( + papis.config.getfloat("minimum_similarity", "plugins.extract") or 1.0 + ) + + remaining: list[str] = [] + for an in formatted_annotations: + an_split = an.splitlines() + if an_split and not self._test_similarity( + an_split[0], file_lines, minimum_similarity + ): + remaining.append(an) + + return remaining + + def _test_similarity( + self, string: str, lines: list[str], minimum_similarity: float = 1.0 + ) -> bool: + for line in lines: + ratio = Levenshtein.ratio(string, line) + if ratio > minimum_similarity: + return True + return False diff --git a/papis_extract/exporters/stdout.py b/papis_extract/exporters/stdout.py new file mode 100644 index 0000000..ed1cabf --- /dev/null +++ b/papis_extract/exporters/stdout.py @@ -0,0 +1,26 @@ +from dataclasses import dataclass + +from papis.document import Document + +from papis_extract.annotation import Annotation +from papis_extract.formatter import Formatter + + +@dataclass +class StdoutExporter: + formatter: Formatter + edit: bool = False + git: bool = False + force: bool = False + + def run(self, annot_docs: list[tuple[Document, list[Annotation]]]) -> None: + """Pretty print annotations to stdout. + + Gives a nice human-readable representations of + the annotations in somewhat of a list form. + Not intended for machine-readability. + """ + for doc, annots in annot_docs: + output: str = self.formatter(doc, annots) + if output: + print("{output}\n".format(output=output.rstrip("\n"))) From 163fd63038abe3eabd0a4b9562b8f11f651fa8d3 Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Thu, 25 Jan 2024 21:40:31 +0100 Subject: [PATCH 058/107] fix: Fixed pocketbook extractor trying to read all files The complete read routine would work before figuring out that it is a file of xml mimetype. This means that it would try to read to memory any file as the first thing, pdfs, even binaries. Of course doing so crashed the program. --- papis_extract/extractors/pocketbook.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/papis_extract/extractors/pocketbook.py b/papis_extract/extractors/pocketbook.py index 08b165d..56ab17c 100644 --- a/papis_extract/extractors/pocketbook.py +++ b/papis_extract/extractors/pocketbook.py @@ -12,11 +12,11 @@ logger = papis.logging.get_logger(__name__) class PocketBookExtractor: def can_process(self, filename: Path) -> bool: - content = self._read_file(filename) - if not content: + if not magic.from_file(filename, mime=True) == "text/xml": return False - if not magic.from_buffer(content, mime=True) == "text/xml": + content = self._read_file(filename) + if not content: return False html = BeautifulSoup(content, features="xml") From 905b20a79c527a2509c8b9738d5ca6ab3aade972 Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Thu, 25 Jan 2024 22:46:38 +0100 Subject: [PATCH 059/107] fix: Default markdown atx formatter for note exporter --- papis_extract/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/papis_extract/__init__.py b/papis_extract/__init__.py index d0a6e45..7944553 100644 --- a/papis_extract/__init__.py +++ b/papis_extract/__init__.py @@ -130,7 +130,7 @@ def run( ) -> None: if write: exporter: Exporter = all_exporters["notes"]( - formatter=formatter or formatters["markdown"], + formatter=formatter or formatters["markdown-atx"], edit=edit, git=git, force=force, From 5526b3d2c50efb7c20d802ad52da5cf7ab196cae Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Tue, 7 May 2024 10:54:11 +0200 Subject: [PATCH 060/107] docs: Update limitation information --- README.md | 17 +++++++++++++++-- 1 file changed, 15 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index a25a304..44d48b8 100644 --- a/README.md +++ b/README.md @@ -25,7 +25,9 @@ To check if everything is working you should now see the `extract` command liste You will be set up with the default options but if you want to change anything, read on in configuration below. > **Note** -> This plugin is still in fairly early development. It does what I need it to do, but if you have a meticulously organized library *please* make backups before doing any operation which could affect your notes, or make use of the papis-included git options. +> This plugin is still in fairly early development. +> It does what I need it to do, but if you have a meticulously organized library *please* make backups before doing any operation which could affect your notes, or make use of the papis-included git options. +> Take care to read the Issues section of this README if you intend to run it over a large collection. ## Usage @@ -114,8 +116,9 @@ papis extract --template count For now, these are the only formatters the plugin knows about. -Be aware that if you write to your notes using a different template the plugin will *not* detect old annotations and drop them, +Be aware that if you re-write to your notes using a completely different template than the original the plugin will *not* detect old annotations and drop them, so you will be doubling up your annotations. +See the `minimum_similarity_color` configuration option for more details. ## Configuration @@ -150,6 +153,9 @@ if `False` extraction only happens when you explicitly invoke it. Extraction will *not* happen automatically when you add new annotations to an existing document, regardless of this setting. +> **Note** +> This option does not work yet due to currently missing upstream features. + ### Automatic tagging By supplying the tags option with a valid python dictionary of the form `{"tag": "color", "tag2": "color2"}`, @@ -254,6 +260,7 @@ features to be implemented: - called `--template` in current implementation - [ ] on_add hook to extract annotations as files are added - needs upstream help, 'on_add' hook, and pass-through of affected documents +- [ ] target same minimum Python version as papis upstream (3.8 as of papis 0.13) upstream changes: @@ -262,6 +269,12 @@ upstream changes: ## Issues +First, a note in general: There is the functionality to run this plugin over your whole library in a single command and also in a way that makes permanent changes to that library. +This is intended and, in my view, an important aspect of what this plugin provides and the batch functionality of cli programs in general. +However, it can also lead to frustrating clean-up time if something messes up or, in the worst case, data loss. +The extractors attempt to ascertain what files they can operate on with certain heuristics but will not be fail-safe. +Take the note at the top of this README to heart and always have backups on hand before larger operations. + A note on the extraction: Highlights in pdfs can be somewhat difficult to parse (as are most things in them). Sometimes they contain the selected text that is written on the page, sometimes they contain the annotators thoughts as a note, sometimes they contain nothing. From c21ab4a76cd43ddae8840af0984fe0c41cb94e4a Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Tue, 7 May 2024 10:55:14 +0200 Subject: [PATCH 061/107] chore: Update dependencies Pin new versions of levenshtein and pymupdf to fix build process. This also means updating from importing fitz to importing pymupdf soon in the source. --- poetry.lock | 465 ++++++++++++++++++++++++------------------------- pyproject.toml | 4 +- 2 files changed, 229 insertions(+), 240 deletions(-) diff --git a/poetry.lock b/poetry.lock index 644e1ab..2d8d498 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand. 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papis_extract/__init__.py | 5 +++-- papis_extract/formatter.py | 6 ++---- 2 files changed, 5 insertions(+), 6 deletions(-) diff --git a/papis_extract/__init__.py b/papis_extract/__init__.py index 7944553..855d80f 100644 --- a/papis_extract/__init__.py +++ b/papis_extract/__init__.py @@ -88,10 +88,11 @@ def main( git: bool, force: bool, ) -> None: - """Extract annotations from any pdf document. + """Extract annotations from any documents. The extract plugin allows manual or automatic extraction of all annotations - contained in the pdf documents belonging to entries of the papis library. + contained in the documents belonging to entries of the papis library, + primarily targeting PDF documents currently. It can write those changes to stdout or directly create and update notes for papis documents. diff --git a/papis_extract/formatter.py b/papis_extract/formatter.py index 917e04c..76c977b 100644 --- a/papis_extract/formatter.py +++ b/papis_extract/formatter.py @@ -23,15 +23,13 @@ def format_markdown( heading = f"{document.get('title', '')} - {document.get('author', '')}" if headings == "atx": - output = f"# {heading}\n\n" + output += f"# {heading}\n\n" elif headings == "setext": title_decoration = ( f"{'=' * len(document.get('title', ''))} " f"{'-' * len(document.get('author', ''))}" ) - output = f"{title_decoration}\n{heading}\n{title_decoration}\n\n" - else: - output = "" + output += f"{title_decoration}\n{heading}\n{title_decoration}\n\n" for a in annotations: output += a.format(template) From b5c081fbf38909d8afbfd6fbd57a7d8bb8429baa Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Wed, 12 Jun 2024 11:06:27 +0200 Subject: [PATCH 063/107] feat: Change count display to lead with count The actual count is now the first item on each line, to make it easier to sort, strip, delete and compare afterwards. --- papis_extract/formatter.py | 6 +++--- tests/test_formatting.py | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/papis_extract/formatter.py b/papis_extract/formatter.py index 76c977b..986d691 100644 --- a/papis_extract/formatter.py +++ b/papis_extract/formatter.py @@ -66,10 +66,10 @@ def format_count( count += 1 return ( + f"{count} " f"{document.get('author', '')}" - f"{' - ' if 'author' in document else ''}" # only put separator if author - f"{document.get('title', '')}: " - f"{count}\n" + f"{': ' if 'author' in document else ''}" # only put separator if author + f"{document.get('title', '')}" ).rstrip() diff --git a/tests/test_formatting.py b/tests/test_formatting.py index 5b805a7..b018041 100644 --- a/tests/test_formatting.py +++ b/tests/test_formatting.py @@ -48,7 +48,7 @@ def test_markdown_setext(): def test_count_default(): fmt = format_count - assert fmt(document, annotations) == ("""document-author - document-title: 2""") + assert fmt(document, annotations) == ("""2 document-author: document-title""") def test_csv_default(): From 9eb7399536fec9792e2fa4ae0fabb441601ff88f Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Wed, 12 Jun 2024 11:16:32 +0200 Subject: [PATCH 064/107] chore: Set strict typing mode for pyright lsp --- pyproject.toml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/pyproject.toml b/pyproject.toml index 807df6a..c9257a5 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -45,3 +45,6 @@ extract = "papis_extract:main" [build-system] requires = ["poetry-core"] build-backend = "poetry.core.masonry.api" + +[tool.pyright] +typeCheckingMode = "strict" From c2aec7add605519769ea5d63be4a9615767946d9 Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Wed, 12 Jun 2024 11:45:35 +0200 Subject: [PATCH 065/107] feat: Notify formatters if formatting first entry This allows headers to be created by a formatter, which will *only* be added to the very first entry created and not to each entry. Currently for example this is used to create a csv header but not for each document in turn. --- papis_extract/exporters/notes.py | 7 +++++-- papis_extract/exporters/stdout.py | 4 +++- papis_extract/formatter.py | 26 ++++++++++++++++++++++---- tests/test_formatting.py | 9 +++++++++ 4 files changed, 39 insertions(+), 7 deletions(-) diff --git a/papis_extract/exporters/notes.py b/papis_extract/exporters/notes.py index a218db7..22b4ce0 100644 --- a/papis_extract/exporters/notes.py +++ b/papis_extract/exporters/notes.py @@ -28,7 +28,8 @@ class NotesExporter: documents missing a note field or appends to existing. """ for doc, annots in annot_docs: - formatted_annotations = self.formatter(doc, annots).split("\n") + # first always true since we write single doc per note + formatted_annotations: list[str] = self.formatter(doc, annots, first=True).split("\n") if formatted_annotations: self._add_annots_to_note(doc, formatted_annotations, force=self.force) @@ -80,7 +81,9 @@ class NotesExporter: # add newline if theres no empty space at file end if len(existing) > 0 and existing[-1].strip() != "": f.write("\n") - f.write("\n\n".join(new_annotations)) + # FIXME this either joins them too close or moves them too far apart + # We need a better algorithm which knows what a full 'annotation' is. + f.write("\n".join(new_annotations)) f.write("\n") logger.info( f"Wrote {len(new_annotations)} " diff --git a/papis_extract/exporters/stdout.py b/papis_extract/exporters/stdout.py index ed1cabf..f8a229f 100644 --- a/papis_extract/exporters/stdout.py +++ b/papis_extract/exporters/stdout.py @@ -20,7 +20,9 @@ class StdoutExporter: the annotations in somewhat of a list form. Not intended for machine-readability. """ + first_entry = True for doc, annots in annot_docs: - output: str = self.formatter(doc, annots) + output: str = self.formatter(doc, annots, first=first_entry) if output: print("{output}\n".format(output=output.rstrip("\n"))) + first_entry = False diff --git a/papis_extract/formatter.py b/papis_extract/formatter.py index 986d691..18e15b2 100644 --- a/papis_extract/formatter.py +++ b/papis_extract/formatter.py @@ -1,15 +1,29 @@ -from collections.abc import Callable - +from typing import Protocol from papis.document import Document from papis_extract.annotation import Annotation -Formatter = Callable[[Document, list[Annotation]], str] +class Formatter(Protocol): + """Basic formatter protocol. + + Every valid formatter must implement at least this protocol. + A formatter is a function which receives a document and a list + of annotations and spits them out in some formatted way. + + Formatters additionally must take the (often optional) passed + parameter 'first' which signals to the formatter that the current + document entry is the very first one to be printed in whatever + exporter is used, if multiple entries are printed. + This can be useful for adding a header if necessary for the format. + """ + def __call__(self, document: Document, annotations: list[Annotation], first: bool) -> str: + ... def format_markdown( document: Document = Document(), annotations: list[Annotation] = [], + first: bool = False, headings: str = "setext", # setext | atx | None ) -> str: if not annotations: @@ -43,6 +57,7 @@ def format_markdown( def format_markdown_atx( document: Document = Document(), annotations: list[Annotation] = [], + first: bool = False, ) -> str: return format_markdown(document, annotations, headings="atx") @@ -50,6 +65,7 @@ def format_markdown_atx( def format_markdown_setext( document: Document = Document(), annotations: list[Annotation] = [], + first: bool = False, ) -> str: return format_markdown(document, annotations, headings="setext") @@ -57,6 +73,7 @@ def format_markdown_setext( def format_count( document: Document = Document(), annotations: list[Annotation] = [], + first: bool = False, ) -> str: if not annotations: return "" @@ -76,13 +93,14 @@ def format_count( def format_csv( document: Document = Document(), annotations: list[Annotation] = [], + first: bool = False, ) -> str: header: str = "type,tag,page,quote,note,author,title,ref,file" template: str = ( '{{type}},{{tag}},{{page}},"{{quote}}","{{note}}",' '"{{doc.author}}","{{doc.title}}","{{doc.ref}}","{{file}}"' ) - output = f"{header}\n" + output = f"{header}\n" if first else "" if not annotations: return "" diff --git a/tests/test_formatting.py b/tests/test_formatting.py index b018041..ac7f2c3 100644 --- a/tests/test_formatting.py +++ b/tests/test_formatting.py @@ -54,6 +54,15 @@ def test_count_default(): def test_csv_default(): fmt = format_csv assert fmt(document, annotations) == ( + 'Highlight,,0,"my lovely text","","document-author",' + '"document-title","","myfile.pdf"\n' + 'Highlight,,0,"my second text","with note","document-author",' + '"document-title","","myfile.pdf"' + ) + +def test_csv_with_header(): + fmt = format_csv + assert fmt(document, annotations, first=True) == ( "type,tag,page,quote,note,author,title,ref,file\n" 'Highlight,,0,"my lovely text","","document-author",' '"document-title","","myfile.pdf"\n' From 19599a66d734b40417336f7c0cab300192162fab Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Wed, 12 Jun 2024 11:46:39 +0200 Subject: [PATCH 066/107] chore: Black formatting --- papis_extract/exporter.py | 3 +-- papis_extract/exporters/__init__.py | 1 - papis_extract/exporters/notes.py | 4 +++- papis_extract/extraction.py | 6 ++---- papis_extract/formatter.py | 7 +++++-- tests/test_formatting.py | 1 + 6 files changed, 12 insertions(+), 10 deletions(-) diff --git a/papis_extract/exporter.py b/papis_extract/exporter.py index de1fe6c..8358480 100644 --- a/papis_extract/exporter.py +++ b/papis_extract/exporter.py @@ -24,5 +24,4 @@ class Exporter(Protocol): def run( self, annot_docs: list[tuple[papis.document.Document, list[Annotation]]] - ) -> None: - ... + ) -> None: ... diff --git a/papis_extract/exporters/__init__.py b/papis_extract/exporters/__init__.py index 6b5208b..b9980e5 100644 --- a/papis_extract/exporters/__init__.py +++ b/papis_extract/exporters/__init__.py @@ -1,4 +1,3 @@ - import papis.logging from papis_extract.exporter import Exporter diff --git a/papis_extract/exporters/notes.py b/papis_extract/exporters/notes.py index 22b4ce0..3b2726d 100644 --- a/papis_extract/exporters/notes.py +++ b/papis_extract/exporters/notes.py @@ -29,7 +29,9 @@ class NotesExporter: """ for doc, annots in annot_docs: # first always true since we write single doc per note - formatted_annotations: list[str] = self.formatter(doc, annots, first=True).split("\n") + formatted_annotations: list[str] = self.formatter( + doc, annots, first=True + ).split("\n") if formatted_annotations: self._add_annots_to_note(doc, formatted_annotations, force=self.force) diff --git a/papis_extract/extraction.py b/papis_extract/extraction.py index 79c6d6a..1c69026 100644 --- a/papis_extract/extraction.py +++ b/papis_extract/extraction.py @@ -14,11 +14,9 @@ logger = papis.logging.get_logger(__name__) class Extractor(Protocol): - def can_process(self, filename: Path) -> bool: - ... + def can_process(self, filename: Path) -> bool: ... - def run(self, filename: Path) -> list[Annotation]: - ... + def run(self, filename: Path) -> list[Annotation]: ... def start( diff --git a/papis_extract/formatter.py b/papis_extract/formatter.py index 18e15b2..515a2c7 100644 --- a/papis_extract/formatter.py +++ b/papis_extract/formatter.py @@ -3,6 +3,7 @@ from papis.document import Document from papis_extract.annotation import Annotation + class Formatter(Protocol): """Basic formatter protocol. @@ -16,8 +17,10 @@ class Formatter(Protocol): exporter is used, if multiple entries are printed. This can be useful for adding a header if necessary for the format. """ - def __call__(self, document: Document, annotations: list[Annotation], first: bool) -> str: - ... + + def __call__( + self, document: Document, annotations: list[Annotation], first: bool + ) -> str: ... def format_markdown( diff --git a/tests/test_formatting.py b/tests/test_formatting.py index ac7f2c3..27eb702 100644 --- a/tests/test_formatting.py +++ b/tests/test_formatting.py @@ -60,6 +60,7 @@ def test_csv_default(): '"document-title","","myfile.pdf"' ) + def test_csv_with_header(): fmt = format_csv assert fmt(document, annotations, first=True) == ( From 7261e7d80cbad416318fe7de5e1f4a666d943b46 Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Thu, 13 Jun 2024 21:20:53 +0200 Subject: [PATCH 067/107] chore: Refactor for strict pyright analysis --- papis_extract/__init__.py | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/papis_extract/__init__.py b/papis_extract/__init__.py index 855d80f..3e4792d 100644 --- a/papis_extract/__init__.py +++ b/papis_extract/__init__.py @@ -7,16 +7,16 @@ import papis.notes import papis.strings from papis.document import Document -from papis_extract.annotation import Annotation from papis_extract import extraction +from papis_extract.annotation import Annotation from papis_extract.exporter import Exporter -from papis_extract.extractors import all_extractors from papis_extract.exporters import all_exporters +from papis_extract.extractors import all_extractors from papis_extract.formatter import Formatter, formatters logger = papis.logging.get_logger(__name__) -DEFAULT_OPTIONS = { +DEFAULT_OPTIONS: dict[str, dict[str, bool | float | dict[str, str]]] = { "plugins.extract": { "tags": {}, "on_import": False, @@ -129,15 +129,16 @@ def run( git: bool = False, force: bool = False, ) -> None: + exporter: Exporter if write: - exporter: Exporter = all_exporters["notes"]( + exporter = all_exporters["notes"]( formatter=formatter or formatters["markdown-atx"], edit=edit, git=git, force=force, ) else: - exporter: Exporter = all_exporters["stdout"]( + exporter = all_exporters["stdout"]( formatter=formatter or formatters["markdown"] ) From 809325955185da98e12edbcc3ced11fc63ff16dc Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Fri, 14 Jun 2024 14:59:39 +0200 Subject: [PATCH 068/107] refactor: Remove pymupdf coupling in extraction The library is only needed for pdf extraction which is taken care of in its own extractor plugin. In the overall extraction routine we do not need any knowledge of the existence of pymupdf. --- papis_extract/extraction.py | 6 +-- papis_extract/extractors/__init__.py | 10 +++++ papis_extract/extractors/pdf.py | 65 +++++++++++++++++----------- 3 files changed, 52 insertions(+), 29 deletions(-) diff --git a/papis_extract/extraction.py b/papis_extract/extraction.py index 1c69026..74a6636 100644 --- a/papis_extract/extraction.py +++ b/papis_extract/extraction.py @@ -2,13 +2,13 @@ import re from pathlib import Path from typing import Protocol -import fitz import papis.config import papis.document import papis.logging from papis.document import Document from papis_extract.annotation import Annotation +from papis_extract.extractors import ExtractionError logger = papis.logging.get_logger(__name__) @@ -39,8 +39,8 @@ def start( try: annotations.extend(extractor.run(fname)) - except fitz.FileDataError as e: - print(f"File structure errors for {file}.\n{e}") + except ExtractionError as e: + print(f"File extraction errors for {file}.\n{e}") if not file_available: # have to remove curlys or papis logger gets upset diff --git a/papis_extract/extractors/__init__.py b/papis_extract/extractors/__init__.py index 47ead33..40af703 100644 --- a/papis_extract/extractors/__init__.py +++ b/papis_extract/extractors/__init__.py @@ -16,3 +16,13 @@ if find_spec("bs4") and find_spec("magic"): all_extractors["pocketbook"] = PocketBookExtractor() else: logger.debug("pocketbook extractor not activated.") + + +class ExtractionError(Exception): + """Raised for exceptions during extraction. + + Something went wrong during the extraction process in the extractor + run routine itself. + """ + + pass diff --git a/papis_extract/extractors/pdf.py b/papis_extract/extractors/pdf.py index a5f8de4..f61cefc 100644 --- a/papis_extract/extractors/pdf.py +++ b/papis_extract/extractors/pdf.py @@ -7,6 +7,7 @@ import papis.config import papis.logging from papis_extract.annotation import Annotation +from papis_extract.extractors import ExtractionError logger = papis.logging.get_logger(__name__) @@ -26,31 +27,43 @@ class PdfExtractor: Returns all readable annotations contained in the file passed in. Only returns Highlight or Text annotations. """ - annotations = [] - with fitz.Document(filename) as doc: - for page in doc: - for annot in page.annots(): - quote, note = self._retrieve_annotation_content(page, annot) - if not quote and not note: - continue - col = ( - annot.colors.get("fill") - or annot.colors.get("stroke") - or (0.0, 0.0, 0.0) - ) - a = Annotation( - file=str(filename), - content=quote or "", - note=note or "", - color=col, - type=annot.type[1], - page=(page.number or 0) + 1, - ) - annotations.append(a) - logger.debug( - f"Found {len(annotations)} " - f"{'annotation' if len(annotations) == 1 else 'annotations'} for {filename}." - ) + annotations: list[Annotation] = [] + try: + with mu.Document(filename) as doc: + for page in doc: # pyright: ignore [reportUnknownVariableType] - missing stub + page = cast(mu.Page, page) + annot: mu.Annot + for annot in page.annots(): + quote, note = self._retrieve_annotation_content(page, annot) + if not quote and not note: + continue + color: tuple[float, float, float] = cast( + tuple[float, float, float], + ( + annot.colors.get("fill") + or annot.colors.get("stroke") + or (0.0, 0.0, 0.0) + ), + ) + page_nr: int = cast(int, page.number or 0) + highlight_type: str = cast(str, annot.type[1] or "") + a = Annotation( + file=str(filename), + content=quote or "", + note=note or "", + color=color, + type=highlight_type, + page=page_nr, + ) + annotations.append(a) + logger.debug( + f"Found {len(annotations)} " + f"{'annotation' if len(annotations) == 1 else 'annotations'} for {filename}." + ) + + except mu.FileDataError as e: + raise ExtractionError + return annotations def _is_pdf(self, fname: Path) -> bool: @@ -58,7 +71,7 @@ class PdfExtractor: return magic.from_file(fname, mime=True) == "application/pdf" def _retrieve_annotation_content( - self, page: fitz.Page, annotation: fitz.Annot + self, page: mu.Page, annotation: mu.Annot ) -> tuple[str | None, str | None]: """Gets the text content of an annotation. From 6b35b2f918f06a36c67d5b36f7594bb26892e744 Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Fri, 14 Jun 2024 15:13:24 +0200 Subject: [PATCH 069/107] chore: Fix strict pyright analysis errors --- papis_extract/annotation.py | 6 +++--- papis_extract/extractors/pdf.py | 12 ++++++++---- papis_extract/extractors/pocketbook.py | 22 ++++++++++++++++------ tests/test_annotation.py | 6 +++--- 4 files changed, 30 insertions(+), 16 deletions(-) diff --git a/papis_extract/annotation.py b/papis_extract/annotation.py index 666c1bb..54b216d 100644 --- a/papis_extract/annotation.py +++ b/papis_extract/annotation.py @@ -1,6 +1,6 @@ import math from dataclasses import dataclass -from typing import Any, Optional +from typing import Any, Optional, cast import chevron import papis.config @@ -127,7 +127,7 @@ class Annotation: """ rawvalue: Any = papis.config.general_get(key, section=section) if isinstance(rawvalue, dict): - return rawvalue + return cast(dict[str, str], rawvalue) try: rawvalue = eval(rawvalue) except Exception: @@ -142,4 +142,4 @@ class Annotation: ) ) - return rawvalue + return cast(dict[str, str], rawvalue) diff --git a/papis_extract/extractors/pdf.py b/papis_extract/extractors/pdf.py index f61cefc..55c13f1 100644 --- a/papis_extract/extractors/pdf.py +++ b/papis_extract/extractors/pdf.py @@ -1,10 +1,12 @@ +# pyright: strict, reportMissingTypeStubs=false, reportUnknownMemberType=false from pathlib import Path +from typing import cast -import fitz import Levenshtein import magic import papis.config import papis.logging +import pymupdf as mu from papis_extract.annotation import Annotation from papis_extract.extractors import ExtractionError @@ -30,7 +32,9 @@ class PdfExtractor: annotations: list[Annotation] = [] try: with mu.Document(filename) as doc: - for page in doc: # pyright: ignore [reportUnknownVariableType] - missing stub + for ( + page + ) in doc: # pyright: ignore [reportUnknownVariableType] - missing stub page = cast(mu.Page, page) annot: mu.Annot for annot in page.annots(): @@ -61,7 +65,7 @@ class PdfExtractor: f"{'annotation' if len(annotations) == 1 else 'annotations'} for {filename}." ) - except mu.FileDataError as e: + except mu.FileDataError: raise ExtractionError return annotations @@ -82,7 +86,7 @@ class PdfExtractor: should both be included or are the same, using Levenshtein distance. """ - content = annotation.info["content"].replace("\n", " ") + content = cast(str, annotation.info["content"].replace("\n", " ")) written = page.get_textbox(annotation.rect).replace("\n", " ") # highlight with selection in note diff --git a/papis_extract/extractors/pocketbook.py b/papis_extract/extractors/pocketbook.py index 56ab17c..ad73ad7 100644 --- a/papis_extract/extractors/pocketbook.py +++ b/papis_extract/extractors/pocketbook.py @@ -1,3 +1,4 @@ +# pyright: strict, reportUnknownMemberType=false from pathlib import Path import magic @@ -42,9 +43,18 @@ class PocketBookExtractor: annotations: list[Annotation] = [] for bm in html.select("div.bookmark"): - content = (bm.select_one("div.bm-text>p") or html.new_string("")).text - note = (bm.select_one("div.bm-note>p") or html.new_string("")).text - page = (bm.select_one("p.bm-page") or html.new_string("")).text + content = str( + (bm.select_one("div.bm-text>p") or html.new_string("")).text + or "" # pyright: ignore [reportUnknownArgumentType] + ) + note = str( + (bm.select_one("div.bm-note>p") or html.new_string("")).text + or "" # pyright: ignore [reportUnknownArgumentType] + ) + page = int( + (bm.select_one("p.bm-page") or html.new_string("")).text + or 0 # pyright: ignore [reportUnknownArgumentType] + ) el_classes = bm.attrs.get("class", "").split(" ") color = (0, 0, 0) @@ -55,11 +65,11 @@ class PocketBookExtractor: a = Annotation( file=str(filename), - content=content or "", - note=note or "", + content=content, + note=note, color=color, type="Highlight", - page=int(page), + page=page, ) annotations.append(a) diff --git a/tests/test_annotation.py b/tests/test_annotation.py index 98e7f31..ceb0c0e 100644 --- a/tests/test_annotation.py +++ b/tests/test_annotation.py @@ -18,7 +18,7 @@ from papis_extract.annotation import Annotation ), ], ) -def test_formatting_replacements(fmt_string, expected): +def test_formatting_replacements(fmt_string: str, expected: str): sut = Annotation( "myfile", content="I am the text value", @@ -36,7 +36,7 @@ def test_formatting_replacements(fmt_string, expected): ("{{quote}} ({{doc.author}})", "I am the text value (document-author)"), ], ) -def test_formatting_document_access(fmt_string, expected): +def test_formatting_document_access(fmt_string: str, expected: str): sut = Annotation( "myfile", content="I am the text value", @@ -64,7 +64,7 @@ def test_colorname_matches_exact(): (0.51, 0.0, 0.0), ], ) -def test_matches_inexact_colorname(color_value): +def test_matches_inexact_colorname(color_value: tuple[float, float, float]): sut = Annotation("testfile", color=color_value, minimum_similarity_color=0.833) c_name = sut.colorname assert c_name == "red" From 9e713193a85b1342c76a6f1cf7c3f204bb65cef1 Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Fri, 14 Jun 2024 15:18:02 +0200 Subject: [PATCH 070/107] refactor: Fix circular exception import --- papis_extract/exceptions.py | 8 ++++++++ papis_extract/extraction.py | 2 +- papis_extract/extractors/__init__.py | 10 ---------- papis_extract/extractors/pdf.py | 2 +- 4 files changed, 10 insertions(+), 12 deletions(-) create mode 100644 papis_extract/exceptions.py diff --git a/papis_extract/exceptions.py b/papis_extract/exceptions.py new file mode 100644 index 0000000..0c5ff3f --- /dev/null +++ b/papis_extract/exceptions.py @@ -0,0 +1,8 @@ +class ExtractionError(Exception): + """Raised for exceptions during extraction. + + Something went wrong during the extraction process in the extractor + run routine itself. + """ + + pass diff --git a/papis_extract/extraction.py b/papis_extract/extraction.py index 74a6636..2054323 100644 --- a/papis_extract/extraction.py +++ b/papis_extract/extraction.py @@ -8,7 +8,7 @@ import papis.logging from papis.document import Document from papis_extract.annotation import Annotation -from papis_extract.extractors import ExtractionError +from papis_extract.exceptions import ExtractionError logger = papis.logging.get_logger(__name__) diff --git a/papis_extract/extractors/__init__.py b/papis_extract/extractors/__init__.py index 40af703..47ead33 100644 --- a/papis_extract/extractors/__init__.py +++ b/papis_extract/extractors/__init__.py @@ -16,13 +16,3 @@ if find_spec("bs4") and find_spec("magic"): all_extractors["pocketbook"] = PocketBookExtractor() else: logger.debug("pocketbook extractor not activated.") - - -class ExtractionError(Exception): - """Raised for exceptions during extraction. - - Something went wrong during the extraction process in the extractor - run routine itself. - """ - - pass diff --git a/papis_extract/extractors/pdf.py b/papis_extract/extractors/pdf.py index 55c13f1..906fdec 100644 --- a/papis_extract/extractors/pdf.py +++ b/papis_extract/extractors/pdf.py @@ -9,7 +9,7 @@ import papis.logging import pymupdf as mu from papis_extract.annotation import Annotation -from papis_extract.extractors import ExtractionError +from papis_extract.exceptions import ExtractionError logger = papis.logging.get_logger(__name__) From 97b7ec0dc90daef42dbe5ccadd9bbe1570e1f51c Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Fri, 14 Jun 2024 15:19:57 +0200 Subject: [PATCH 071/107] chore: Update dependencies --- poetry.lock | 692 +++++++++++++++++++++++++++++----------------------- 1 file changed, 381 insertions(+), 311 deletions(-) diff --git a/poetry.lock b/poetry.lock index 2d8d498..ff17e4d 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. [[package]] name = "arxiv2bib" @@ -46,13 +46,13 @@ pyparsing = ">=2.0.3" [[package]] name = "certifi" -version = "2023.11.17" +version = "2024.6.2" description = "Python package for providing Mozilla's CA Bundle." optional = false python-versions = ">=3.6" files = [ - {file = "certifi-2023.11.17-py3-none-any.whl", hash = "sha256:e036ab49d5b79556f99cfc2d9320b34cfbe5be05c5871b51de9329f0603b0474"}, - {file = "certifi-2023.11.17.tar.gz", hash = "sha256:9b469f3a900bf28dc19b8cfbf8019bf47f7fdd1a65a1d4ffb98fc14166beb4d1"}, + {file = "certifi-2024.6.2-py3-none-any.whl", hash = "sha256:ddc6c8ce995e6987e7faf5e3f1b02b302836a0e5d98ece18392cb1a36c72ad56"}, + {file = "certifi-2024.6.2.tar.gz", hash = "sha256:3cd43f1c6fa7dedc5899d69d3ad0398fd018ad1a17fba83ddaf78aa46c747516"}, ] [[package]] @@ -203,63 +203,63 @@ files = [ [[package]] name = "coverage" -version = "7.4.0" +version = "7.5.3" description = "Code coverage measurement for Python" optional = false python-versions = ">=3.8" files = [ - {file = 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"sha256:d0570876c61ab9e520d776c38acbbb5b05a776d3f9ff98a5c8fd5162a444cf19"}, ] [package.extras] brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)"] +h2 = ["h2 (>=4,<5)"] socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"] zstd = ["zstandard (>=0.18.0)"] From 779519f580bba71ea51b98e9a456cea1c8634e86 Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Fri, 14 Jun 2024 20:02:52 +0200 Subject: [PATCH 072/107] fix: Only inform if no extractor finds valid files Until now whenever an extractor could not find any valid files for a document it would inform the user of this case. However, this is not very useful: if you have a pdf and an epub extractor running, it would inform you for each document which only had one of the two formats as well as those which actually did not have any valid files for *any* of the extractors running. This commit changes the behavior to only inform the user when none of the running extractors find a valid file, since that is the actual case a user might want to be informed about. --- papis_extract/__init__.py | 11 ++++++++++- papis_extract/extraction.py | 13 ++++++------- 2 files changed, 16 insertions(+), 8 deletions(-) diff --git a/papis_extract/__init__.py b/papis_extract/__init__.py index 3e4792d..043d3b5 100644 --- a/papis_extract/__init__.py +++ b/papis_extract/__init__.py @@ -1,3 +1,4 @@ +import re import click import papis.cli import papis.config @@ -145,10 +146,18 @@ def run( doc_annots: list[tuple[Document, list[Annotation]]] = [] for doc in documents: annotations: list[Annotation] = [] + valid_files: int = 0 for ext in extractors: if not ext: continue - annotations.extend(extraction.start(ext, doc)) + added = extraction.start(ext, doc) + if added is not None: + valid_files += 1 + annotations.extend(added) doc_annots.append((doc, annotations)) + if valid_files == 0: + # have to remove curlys or papis logger gets upset + desc = re.sub("[{}]", "", papis.document.describe(doc)) + logger.info(f"Document {desc} has no valid extractors for any of its files.") exporter.run(doc_annots) diff --git a/papis_extract/extraction.py b/papis_extract/extraction.py index 2054323..c0b93c3 100644 --- a/papis_extract/extraction.py +++ b/papis_extract/extraction.py @@ -1,4 +1,3 @@ -import re from pathlib import Path from typing import Protocol @@ -22,11 +21,13 @@ class Extractor(Protocol): def start( extractor: Extractor, document: Document, -) -> list[Annotation]: +) -> list[Annotation] | None: """Extract all annotations from passed documents. Returns all annotations contained in the papis - documents passed in. + documents passed in (empty list if no annotations). + If there are no files that the extractor can process, + returns None instead. """ annotations: list[Annotation] = [] file_available: bool = False @@ -40,11 +41,9 @@ def start( try: annotations.extend(extractor.run(fname)) except ExtractionError as e: - print(f"File extraction errors for {file}.\n{e}") + logger.error(f"File extraction errors for {file}. File may be damaged.\n{e}") if not file_available: - # have to remove curlys or papis logger gets upset - desc = re.sub("[{}]", "", papis.document.describe(document)) - logger.info(f"No {type(extractor)} file for document: {desc}") + return None return annotations From 103c2ea2fc9f356afddd1bbc1cffbe29bce90d9a Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Fri, 15 Nov 2024 11:28:50 +0100 Subject: [PATCH 073/107] chore: Switch to uv packaging and hatch backend Switching this project over to the uv package manager as a pilot project for my personal use. Since this project is not yet widely used I can use it as an experimental playground for discovering uv further without interrupting anybody's workflow. --- README.md | 24 +- papis_extract/__init__.py | 5 +- poetry.lock | 1146 ------------------------------------- pyproject.toml | 63 +- uv.lock | 767 +++++++++++++++++++++++++ 5 files changed, 819 insertions(+), 1186 deletions(-) delete mode 100644 poetry.lock create mode 100644 uv.lock diff --git a/README.md b/README.md index 44d48b8..47aea8d 100644 --- a/README.md +++ b/README.md @@ -211,7 +211,7 @@ This should generally be an alright default but is here to be changed for exampl Currently, the program supports two annotation extractors: A **`pdf` extractor**, which takes highlights and annotations embedded in any PDF file. -It should work with most PDF styles, as long as annotations are marked as such +It should work with most PDF styles, as long as annotations are marked as such (does not work if e.g. highlights are baked onto text, or there is no text in the file). A `pocketbook` extractor, which takes bookmarks exported from the mobile [PocketBook](https://pocketbook.ch/en-ch/app) reader applications. @@ -261,6 +261,8 @@ features to be implemented: - [ ] on_add hook to extract annotations as files are added - needs upstream help, 'on_add' hook, and pass-through of affected documents - [ ] target same minimum Python version as papis upstream (3.8 as of papis 0.13) +- [ ] change detection: + - how does it handle updated citations? updated colors? should it be configurable? upstream changes: @@ -295,10 +297,14 @@ I am not sure if there is much I can do about these issues for now. and for myself whenever I forget. The basic building blocks currently in here are three: -- extractors -: Extract data from a source file attached to a papis document. +- extractors (= input format) +: Extract data from a source file attached to a papis document. Crawls the actual files attached to documents to put them into annotation-friendly formats. +- formatters (= output format) +: Make sure the exporter saves the annotation data according to your preferred layout, + such as a markdown syntax or csv-structure. + - annotations : The actual extracted blocks of text, containing some metadata info as well, such as their color, type, page. @@ -306,24 +312,20 @@ and for myself whenever I forget. The basic building blocks currently in here ar - exporters : Put the extracted data somewhere. For now stdout or into your notes. -- formatters -: Make sure the exporter saves the annotation data according to your preferred layout, - such as a markdown syntax or csv-structure. - Splitting it into those building blocks makes it easier to recombine them in any way, should someone want to save highlights as csv data in their notes, or to include additional extractors or formatters. -To develop it together with an isolated `papis` instance you can simply inject papis into your -development environment, e.g. invoking the poetry environment shell and then manually installing: +To develop it together with an isolated `papis` instance you can simply inject papis into your +development environment, e.g. invoking the uv environment shell and then manually installing: ```bash -poetry shell +uv shell pip install papis ``` This will leave you with `papis` installed in the same virtual environment as your development. -However, what I do on my system instead to enable quick testing is inject it into a +However, what I do on my system instead to enable quick testing is inject it into a system-wide (but isolated with `pipx`) papis setup: ```bash diff --git a/papis_extract/__init__.py b/papis_extract/__init__.py index 043d3b5..7ccf649 100644 --- a/papis_extract/__init__.py +++ b/papis_extract/__init__.py @@ -1,4 +1,5 @@ import re + import click import papis.cli import papis.config @@ -159,5 +160,7 @@ def run( if valid_files == 0: # have to remove curlys or papis logger gets upset desc = re.sub("[{}]", "", papis.document.describe(doc)) - logger.info(f"Document {desc} has no valid extractors for any of its files.") + logger.info( + f"Document {desc} has no valid extractors for any of its files." + ) exporter.run(doc_annots) diff --git a/poetry.lock b/poetry.lock deleted file mode 100644 index ff17e4d..0000000 --- a/poetry.lock +++ /dev/null @@ -1,1146 +0,0 @@ -# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. - -[[package]] -name = "arxiv2bib" -version = "1.0.8" -description = "Get arXiv.org metadata in BibTeX format" -optional = false -python-versions = "*" -files = [ - {file = "arxiv2bib-1.0.8.tar.gz", hash = "sha256:137608ed8aa4da6594350152964b9b0f46c6efcb07f8a4dfd50309c968b647a8"}, -] - -[[package]] -name = "beautifulsoup4" -version = "4.12.3" -description = "Screen-scraping library" -optional = false -python-versions = ">=3.6.0" -files = [ - {file = "beautifulsoup4-4.12.3-py3-none-any.whl", hash = "sha256:b80878c9f40111313e55da8ba20bdba06d8fa3969fc68304167741bbf9e082ed"}, - {file = "beautifulsoup4-4.12.3.tar.gz", hash = "sha256:74e3d1928edc070d21748185c46e3fb33490f22f52a3addee9aee0f4f7781051"}, -] - -[package.dependencies] -soupsieve = ">1.2" - -[package.extras] -cchardet = ["cchardet"] -chardet = ["chardet"] -charset-normalizer = ["charset-normalizer"] -html5lib = ["html5lib"] -lxml = ["lxml"] - -[[package]] -name = "bibtexparser" -version = "1.4.1" -description = "Bibtex parser for python 3" -optional = false -python-versions = "*" -files = [ - {file = "bibtexparser-1.4.1.tar.gz", hash = "sha256:e00e29e24676c4808e0b4333b37bb55cca9cbb7871a56f63058509281588d789"}, -] - -[package.dependencies] -pyparsing = ">=2.0.3" - -[[package]] -name = "certifi" -version = "2024.6.2" -description = "Python package for providing Mozilla's CA Bundle." -optional = false -python-versions = ">=3.6" -files = [ - {file = "certifi-2024.6.2-py3-none-any.whl", hash = "sha256:ddc6c8ce995e6987e7faf5e3f1b02b302836a0e5d98ece18392cb1a36c72ad56"}, - {file = "certifi-2024.6.2.tar.gz", hash = "sha256:3cd43f1c6fa7dedc5899d69d3ad0398fd018ad1a17fba83ddaf78aa46c747516"}, -] - -[[package]] -name = "chardet" -version = "5.2.0" -description = "Universal encoding detector for Python 3" -optional = false -python-versions = ">=3.7" -files = [ - {file = "chardet-5.2.0-py3-none-any.whl", hash = "sha256:e1cf59446890a00105fe7b7912492ea04b6e6f06d4b742b2c788469e34c82970"}, - {file = "chardet-5.2.0.tar.gz", hash = "sha256:1b3b6ff479a8c414bc3fa2c0852995695c4a026dcd6d0633b2dd092ca39c1cf7"}, -] - -[[package]] -name = "charset-normalizer" -version = "3.3.2" -description = "The Real First Universal Charset Detector. 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Renamed the template selection from the cli to '--output' since it control the output format that annotations are displayed/written in. This also somewhat more closely mirrors pandoc cli options, which are generally a good guide to follow. --- README.md | 24 ++++++++++++------------ papis_extract/__init__.py | 16 ++++++++-------- 2 files changed, 20 insertions(+), 20 deletions(-) diff --git a/README.md b/README.md index 47aea8d..2aea597 100644 --- a/README.md +++ b/README.md @@ -92,33 +92,33 @@ On my current laptop, extracting ~4000 annotations from ~1000 library documents though this will vary with the length and size of the PDFs you have. For smaller workloads the process should be almost instant. -You can change the format that you want your annotations in with the `--template` option. +You can change the format that you want your annotations in with the `--output` option. To output annotations in a markdown-compatible syntax (the default), do: ```bash -papis extract --template markdown +papis extract --output markdown ``` -There are sub-variants of the formatter for atx-style headers, with `--template markdown-atx` (`# Headings`), -or setext-style with `--template markdown-setext` (the default style). +There are sub-variants of the formatter for atx-style headers, with `--output markdown-atx` (`# Headings`), +or setext-style with `--output markdown-setext` (the default style). To instead see them in a csv syntax simply invoke: ```bash -papis extract --template csv +papis extract --output csv ``` And if you only want to know how many annotations exist in the documents, you can invoke: ```bash -papis extract --template count +papis extract --output count ``` For now, these are the only formatters the plugin knows about. -Be aware that if you re-write to your notes using a completely different template than the original the plugin will *not* detect old annotations and drop them, +Be aware that if you re-write to your notes using a completely different output format than the original the plugin will *not* detect old annotations and drop them, so you will be doubling up your annotations. -See the `minimum_similarity_color` configuration option for more details. +See the `minimum_similarity` configuration option for more details. ## Configuration @@ -185,7 +185,7 @@ minimum_similarity_color: 0.833, # for matching tag to color ``` `minimum_similarity` sets the required similarity of an annotation with existing annotations in your notes to be dropped. -Annotations you have in notes might change if you for example fix small spacing mistakes or a letter/punctuation that has been falsely recognized in the PDF or change similar things. +Annotations you have in notes might change if you, for example, fix small spacing mistakes or a letter/punctuation that has been falsely recognized in the PDF or change similar things. Generally, this should be fine as it is but you should change this value if you either get new annotations dropped though they should be added (decrease the value) or annotations are added duplicating existing ones (increase the value). --- @@ -216,8 +216,8 @@ It should work with most PDF styles, as long as annotations are marked as such A `pocketbook` extractor, which takes bookmarks exported from the mobile [PocketBook](https://pocketbook.ch/en-ch/app) reader applications. You can export bookmarks by opening a book, going to the notes list and selecting `Export notes...`. -Then import the resulting `.html` file into the library using `papis add` -(or `papis addto` to add it to existing documents). +Then import the resulting `.html` file into the library like any other document using `papis add` +(or `papis addto` to add it to existing document references). You are then ready to use extract to get those annotations from the exported list into your notes. ## TODO: Roadmap to first release @@ -257,7 +257,7 @@ features to be implemented: - [ ] `--overwrite` mode where existing annotations are not dropped but overwritten on same line of note - [x] `--force` mode where we simply do not drop anything - [x] `--format` option to choose from default or set up a custom formatter - - called `--template` in current implementation + - called `--output` in current implementation - [ ] on_add hook to extract annotations as files are added - needs upstream help, 'on_add' hook, and pass-through of affected documents - [ ] target same minimum Python version as papis upstream (3.8 as of papis 0.13) diff --git a/papis_extract/__init__.py b/papis_extract/__init__.py index 7ccf649..8464b76 100644 --- a/papis_extract/__init__.py +++ b/papis_extract/__init__.py @@ -49,18 +49,18 @@ papis.config.register_default_settings(DEFAULT_OPTIONS) show_default=True, ) @click.option( - "--template", - "-t", + "--output", + "-o", type=click.Choice( list(formatters.keys()), case_sensitive=False, ), - help="Choose an output template to format annotations with.", + help="Choose which format to output annotations in.", show_default=True, ) @click.option( - "--extractor", - "-e", + "--input", + "-i", "extractors", type=click.Choice( list(all_extractors.keys()), @@ -68,7 +68,7 @@ papis.config.register_default_settings(DEFAULT_OPTIONS) ), default=list(all_extractors.keys()), multiple=True, - help="Choose an extractor to apply to the selected documents. [default: all]", + help="Choose which input formats to gather annotations from. [default: all]", ) @click.option( "--force/--no-force", @@ -86,7 +86,7 @@ def main( manual: bool, write: bool, extractors: list[str], - template: str, + output: str, git: bool, force: bool, ) -> None: @@ -109,7 +109,7 @@ def main( logger.warning(papis.strings.no_documents_retrieved_message) return - formatter = formatters.get(template) + formatter = formatters.get(output) run( documents, From 9c80281220474329c5599e39a7b5ebc00cf4d0b5 Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Sat, 30 Nov 2024 21:22:45 +0100 Subject: [PATCH 076/107] fix: Respect minimum color similarity option Previously we would always assign a minimum color similarity of 1.0, regardless of the option set. Now we set a minimum similarity according to the option set in the configuration, otherwise the default set for that option and fall back to a simple default value declared at the top of the file. --- papis_extract/annotation.py | 13 ++++++------- 1 file changed, 6 insertions(+), 7 deletions(-) diff --git a/papis_extract/annotation.py b/papis_extract/annotation.py index 54b216d..8fd63ac 100644 --- a/papis_extract/annotation.py +++ b/papis_extract/annotation.py @@ -6,8 +6,7 @@ import chevron import papis.config from papis.document import Document -TEXT_SIMILARITY_MINIMUM = 0.75 -COLOR_SIMILARITY_MINIMUM = 0.833 +COLOR_SIMILARITY_MINIMUM_FALLBACK = 0.833 COLORS: dict[str, tuple[float, float, float]] = { "blue": (0, 0, 1), @@ -38,14 +37,17 @@ class Annotation: page: int = 0, tag: str = "", type: str = "Highlight", - minimum_similarity_color: float = 1.0, + minimum_similarity_color: float | None = None, ) -> None: - self.minimum_similarity_color = minimum_similarity_color self.file = file self._color = color self.content = content self.note = note self.page = page + self.minimum_similarity_color = minimum_similarity_color or ( + papis.config.getfloat("minimum_similarity_color", "plugins.extract") + or COLOR_SIMILARITY_MINIMUM_FALLBACK + ) self.tag = tag or self._tag_from_colorname(self.colorname or "") self.type = type @@ -85,9 +87,6 @@ class Annotation: """ annot_colors = self.color or (0.0, 0.0, 0.0) nearest = None - minimum_similarity = ( - papis.config.getfloat("minimum_similarity_color", "plugins.extract") or 1.0 - ) minimum_similarity = self.minimum_similarity_color for name, values in COLORS.items(): similarity_ratio = self._color_similarity_ratio(values, annot_colors) From ddaa75f44b9c598894e01074ebc0cd82df223e1c Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Sat, 30 Nov 2024 21:45:59 +0100 Subject: [PATCH 077/107] chore: Change woodpecker ci to use uv --- .woodpecker/static_analysis.yml | 6 +++--- .woodpecker/test.yml | 8 ++++---- 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/.woodpecker/static_analysis.yml b/.woodpecker/static_analysis.yml index b817624..5244d3a 100644 --- a/.woodpecker/static_analysis.yml +++ b/.woodpecker/static_analysis.yml @@ -3,7 +3,7 @@ steps: image: nikolaik/python-nodejs commands: - npm install --global pyright - - poetry install - - python --version && poetry --version && pyright --version + - uv sync + - python --version && uv version && pyright --version - echo "------------- running pyright typecheck -------------" - - poetry run pyright + - uv run pyright diff --git a/.woodpecker/test.yml b/.woodpecker/test.yml index 0dc8073..5ae9b1d 100644 --- a/.woodpecker/test.yml +++ b/.woodpecker/test.yml @@ -3,9 +3,9 @@ when: steps: pytest: - image: ghcr.io/withlogicco/poetry:1.5.1 + image: nikolaik/python-nodejs commands: - - poetry install - - python --version && poetry --version + - uv sync + - python --version && uv version - echo "------------- running pytest -------------" - - poetry run pytest + - uv run pytest From 7a69bd509f283dbc1000884dc547ae18656782bd Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Sat, 30 Nov 2024 21:47:38 +0100 Subject: [PATCH 078/107] chore: Remove redundant cast --- papis_extract/extraction.py | 4 +++- papis_extract/extractors/pdf.py | 1 - 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/papis_extract/extraction.py b/papis_extract/extraction.py index c0b93c3..19c4ccc 100644 --- a/papis_extract/extraction.py +++ b/papis_extract/extraction.py @@ -41,7 +41,9 @@ def start( try: annotations.extend(extractor.run(fname)) except ExtractionError as e: - logger.error(f"File extraction errors for {file}. File may be damaged.\n{e}") + logger.error( + f"File extraction errors for {file}. File may be damaged.\n{e}" + ) if not file_available: return None diff --git a/papis_extract/extractors/pdf.py b/papis_extract/extractors/pdf.py index 906fdec..8caaf5c 100644 --- a/papis_extract/extractors/pdf.py +++ b/papis_extract/extractors/pdf.py @@ -35,7 +35,6 @@ class PdfExtractor: for ( page ) in doc: # pyright: ignore [reportUnknownVariableType] - missing stub - page = cast(mu.Page, page) annot: mu.Annot for annot in page.annots(): quote, note = self._retrieve_annotation_content(page, annot) From 1f65317d65bad2f5bd882d602bc29c5be36886a9 Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Wed, 10 Sep 2025 22:27:05 +0200 Subject: [PATCH 079/107] chore: Update to papis 0.14 --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index c869ea7..ca3daf8 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -7,7 +7,7 @@ requires-python = "<4.0,>=3.11" dependencies = [ "pymupdf<2.0.0,>=1.24.2", "levenshtein<1.0.0,>=0.25.1", - "papis<1.0,>=0.13", + "papis<1.0,>=0.14", "click<9.0.0,>=8.1.7", "python-magic<1.0.0,>=0.4.27", "chevron<1.0.0,>=0.14.0", From 5350b9215e0210141715da82d378042f8176e28e Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Wed, 10 Sep 2025 22:50:48 +0200 Subject: [PATCH 080/107] docs: Update README --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 2aea597..45a9b88 100644 --- a/README.md +++ b/README.md @@ -5,7 +5,7 @@ ![PyPI](https://img.shields.io/pypi/v/papis-extract) --> -Quickly extract annotations from your pdf files with the help of the [papis](https://github.com/papis/papis) bibliography manager.\ +Quickly extract annotations from your files with the help of the [papis](https://github.com/papis/papis) bibliography manager.\ Easily organize all your highlights and thoughts next to your documents and references.\ ## Installation From 3ef45e24f7bd08d4bc4eb83fecb31a75167d380f Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Wed, 10 Sep 2025 22:50:48 +0200 Subject: [PATCH 081/107] feat: Add ReadEra extractor For the readera epub/pdf reader application for android and ios. --- papis_extract/extractors/__init__.py | 2 + papis_extract/extractors/readera.py | 85 ++++++++++++++++++++++++++++ 2 files changed, 87 insertions(+) create mode 100644 papis_extract/extractors/readera.py diff --git a/papis_extract/extractors/__init__.py b/papis_extract/extractors/__init__.py index 47ead33..da84829 100644 --- a/papis_extract/extractors/__init__.py +++ b/papis_extract/extractors/__init__.py @@ -5,12 +5,14 @@ import papis.logging from papis_extract.extraction import Extractor from papis_extract.extractors import pdf from papis_extract.extractors.pocketbook import PocketBookExtractor +from papis_extract.extractors import readera logger = papis.logging.get_logger(__name__) all_extractors: dict[str, Extractor] = {} all_extractors["pdf"] = pdf.PdfExtractor() +all_extractors["readera"] = readera.ReadEraExtractor() if find_spec("bs4") and find_spec("magic"): all_extractors["pocketbook"] = PocketBookExtractor() diff --git a/papis_extract/extractors/readera.py b/papis_extract/extractors/readera.py new file mode 100644 index 0000000..0d94d35 --- /dev/null +++ b/papis_extract/extractors/readera.py @@ -0,0 +1,85 @@ +# pyright: strict, reportUnknownMemberType=false +import re +from pathlib import Path + +import magic +import papis.logging + +from papis_extract.annotation import Annotation + +logger = papis.logging.get_logger(__name__) + + +class ReadEraExtractor: + """Extracts exported annotations from the ReadEra book reading app for Android and iOS. + + https://readera.org/ + """ + + def can_process(self, filename: Path) -> bool: + if not magic.from_file(filename, mime=True) == "text/plain": + return False + + content = self._read_file(filename) + if not content: + return False + + if not content[0] or not content[1]: + return False + + patt = re.compile(r"\n\*\*\*\*\*\n") + if not patt.search("".join(content)): + return False + + logger.debug( + f"Found annotation file processable with ReadEraExtractor: {filename}" + ) + return True + + def run(self, filename: Path) -> list[Annotation]: + """Extract annotations from readera txt file. + + Returns all readable annotations contained in the file + passed in, with highlights and notes if available. + Could theoretically return the annotation color but I + do not have access to a premium version of ReadEra so + I cannot add this feature. + """ + content = self._read_file(filename)[2:] + if not content: + return [] + + annotations: list[Annotation] = [] + + split = "\n".join(content).split("\n*****\n") + note_pattern = re.compile(r"\n--.*") + for entry in split: + entry = entry.strip() + note = note_pattern.search(entry) + if note: + entry = note_pattern.sub("", entry) + note = re.sub(r"\n--", "", note.group()) + + entry = re.sub(r"\n", " ", entry) + + a = Annotation( + file=str(filename), + content=entry, + note=note if note else "", + # color=color, # TODO: Implement for premium ReadEra version + ) + annotations.append(a) + + logger.debug( + f"Found {len(annotations)} " + f"{'annotation' if len(annotations) == 1 else 'annotations'} for {filename}." + ) + return annotations + + def _read_file(self, filename: Path) -> list[str]: + try: + with open(filename, encoding="utf-8") as f: + return f.readlines() + except FileNotFoundError: + logger.error(f"Could not open file {filename} for extraction.") + return [] From 5f01aa1f2b7c3c0c241abc5e17706a2574a1fdd7 Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Thu, 11 Sep 2025 10:14:10 +0200 Subject: [PATCH 082/107] feat: Add eof heuristic for readera extractor Every exported ReadEra annotation file also _ends_ with the ubiquitous `*****` pattern, so we look for that to detect the file. --- papis_extract/extractors/readera.py | 9 +++++++-- tests/extractors/ReadEra_sample.txt | 25 +++++++++++++++++++++++++ 2 files changed, 32 insertions(+), 2 deletions(-) create mode 100644 tests/extractors/ReadEra_sample.txt diff --git a/papis_extract/extractors/readera.py b/papis_extract/extractors/readera.py index 0d94d35..0e9bd63 100644 --- a/papis_extract/extractors/readera.py +++ b/papis_extract/extractors/readera.py @@ -24,11 +24,16 @@ class ReadEraExtractor: if not content: return False + # look for title and author lines up top if not content[0] or not content[1]: return False - patt = re.compile(r"\n\*\*\*\*\*\n") - if not patt.search("".join(content)): + # look for star-shaped divider pattern + if not re.search(r"\n\*\*\*\*\*\n", "".join(content)): + return False + + # look for star-shaped pattern at end of file + if not re.search(r"\n\*\*\*\*\*\n\n$", "".join(content)): return False logger.debug( diff --git a/tests/extractors/ReadEra_sample.txt b/tests/extractors/ReadEra_sample.txt new file mode 100644 index 0000000..de84412 --- /dev/null +++ b/tests/extractors/ReadEra_sample.txt @@ -0,0 +1,25 @@ +The Circle of the Snake +Grafton Tanner + +digital technologies of the twenty-first century can only exist thanks to this kind of outsourced labor. The relative invisibility of the tech supply chain is part of the ruse; American consumers do not see where smartphones come from. They do not see the conflict zones where coltan is mined to be used in electronic devices, or the sweatshops in which digital products are manufactured. The latest technologies arrive instead in pristine condition, as if delivered from on high. + +***** + +We don’t necessarily want our leaders to be average persons like us, even though we often enjoy hearing that famous celebrities eat the same fast food as regular people. But in the beginning of the twenty-first century, we carefully watch our public figures to ensure they do not commit an unconscionable act. Doing so helps to rid the public stage of bigots, even as it also threatens the last known walls of privacy. This is an inevitable tension that must be maintained as we open the door on the private lives of others +--We continuously demystify our leaders - first through television, now through social media, streams, docus, etc. this brings them down to our level, which is what this paragraph talks about + +***** + +Initially, the Internet was praised as a freer way to encounter information. In the early 1990s, digital theorist George Landow saw hypertext as a liberatory reading strategy.¹⁶ He embraced it as a common good and thought hyperlinks would emancipate readers from the prison of the fixed word, allowing them to flow freely between various information sources. But what Landow never imagined is the exhaustion that could come from the endless, rootless process of reading in this way. Not everyone wants to jump from point to point without any center. Infinity might not always be alluring. +Landow puts the agency in the reader when he writes, ‘anyone who uses hypertext makes his or her own interests the de facto organizing principle (or center) for the investigation at the moment.’¹⁷ But how much agency do we actually have when falling down the rabbit hole? What if we get lost in the hole where the center was? How much attention do we end up losing in a world where we must always multi-task and where reading itself is disrupted by one hyperlink after another? And who + +***** + +In the Dust of This Planet +Horror of Philosophy vol. 1 +Eugene Thacker +In the first of a series of three books on the Horror of Philosophy,In the Dust of This Planetoffers the genre of horror as a way of thinking about the unthinkable. +Paperback: 978-1-84694-676-9 ebook: 978-1-78099-010-1 + +***** + From e90a123f8871ca901a9c0f73d2264e46bc942a0f Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Thu, 11 Sep 2025 10:17:53 +0200 Subject: [PATCH 083/107] chore!: Rename force option to duplicates BREAKING CHANGE: Change the `--force/--no-force` cli option to `--duplicates/--no-duplicates` since it describes a little clearer what using it actually achieves (adding quote duplicates or not to output). --- papis_extract/__init__.py | 12 ++++++------ papis_extract/exporter.py | 2 +- papis_extract/exporters/notes.py | 18 +++++++++--------- papis_extract/exporters/stdout.py | 2 +- 4 files changed, 17 insertions(+), 17 deletions(-) diff --git a/papis_extract/__init__.py b/papis_extract/__init__.py index 8464b76..041a86a 100644 --- a/papis_extract/__init__.py +++ b/papis_extract/__init__.py @@ -71,8 +71,8 @@ papis.config.register_default_settings(DEFAULT_OPTIONS) help="Choose which input formats to gather annotations from. [default: all]", ) @click.option( - "--force/--no-force", - "-f", + "--duplicates/--no-duplicates", + "-d", help="Do not drop any annotations because they already exist.", show_default=True, ) @@ -88,7 +88,7 @@ def main( extractors: list[str], output: str, git: bool, - force: bool, + duplicates: bool, ) -> None: """Extract annotations from any documents. @@ -118,7 +118,7 @@ def main( git=git, formatter=formatter, extractors=[all_extractors.get(e) for e in extractors], - force=force, + duplicates=duplicates, ) @@ -129,7 +129,7 @@ def run( edit: bool = False, write: bool = False, git: bool = False, - force: bool = False, + duplicates: bool = False, ) -> None: exporter: Exporter if write: @@ -137,7 +137,7 @@ def run( formatter=formatter or formatters["markdown-atx"], edit=edit, git=git, - force=force, + duplicates=duplicates, ) else: exporter = all_exporters["stdout"]( diff --git a/papis_extract/exporter.py b/papis_extract/exporter.py index 8358480..13fe082 100644 --- a/papis_extract/exporter.py +++ b/papis_extract/exporter.py @@ -20,7 +20,7 @@ class Exporter(Protocol): formatter: Formatter edit: bool = False git: bool = False - force: bool = False + duplicates: bool = False def run( self, annot_docs: list[tuple[papis.document.Document, list[Annotation]]] diff --git a/papis_extract/exporters/notes.py b/papis_extract/exporters/notes.py index 3b2726d..e27bc78 100644 --- a/papis_extract/exporters/notes.py +++ b/papis_extract/exporters/notes.py @@ -18,7 +18,7 @@ class NotesExporter: formatter: Formatter edit: bool = False git: bool = False - force: bool = False + duplicates: bool = False def run(self, annot_docs: list[tuple[Document, list[Annotation]]]) -> None: """Write annotations into document notes. @@ -33,7 +33,7 @@ class NotesExporter: doc, annots, first=True ).split("\n") if formatted_annotations: - self._add_annots_to_note(doc, formatted_annotations, force=self.force) + self._add_annots_to_note(doc, formatted_annotations, duplicates=self.duplicates) if self.edit: papis.commands.edit.edit_notes(doc, git=self.git) @@ -43,15 +43,15 @@ class NotesExporter: document: Document, formatted_annotations: list[str], git: bool = False, - force: bool = False, + duplicates: bool = False, ) -> None: """ Append new annotations to the end of a note. This function appends new annotations to the end of a note file. It takes in a document object containing the note, a list of formatted annotations to be - added, and optional flags git and force. If git is True, the changes will be - committed to git. If force is True, the annotations will be added even if they + added, and optional flags git and duplicates. If git is True, the changes will be + committed to git. If duplicates is True, the annotations will be added even if they already exist in the note. :param document: The document object representing the note @@ -60,9 +60,9 @@ class NotesExporter: :type formatted_annotations: list[str] :param git: Flag indicating whether to commit changes to git, defaults to False. :type git: bool, optional - :param force: Flag indicating whether to force adding annotations even if they - already exist, defaults to False. - :type force: bool, optional + :param duplicates: Flag indicating whether to force adding annotations as duplicates + even if they already exist, defaults to False. + :type duplicates: bool, optional """ logger.debug("Adding annotations to note.") notes_path = papis.notes.notes_path_ensured(document) @@ -72,7 +72,7 @@ class NotesExporter: existing = file_read.readlines() new_annotations: list[str] = [] - if not force: + if not duplicates: new_annotations = self._drop_existing_annotations( formatted_annotations, existing ) diff --git a/papis_extract/exporters/stdout.py b/papis_extract/exporters/stdout.py index f8a229f..a9f2d95 100644 --- a/papis_extract/exporters/stdout.py +++ b/papis_extract/exporters/stdout.py @@ -11,7 +11,7 @@ class StdoutExporter: formatter: Formatter edit: bool = False git: bool = False - force: bool = False + duplicates: bool = False def run(self, annot_docs: list[tuple[Document, list[Annotation]]]) -> None: """Pretty print annotations to stdout. 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JJ: Enter a description for the selected changes. --- papis_extract/exporters/notes.py | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/papis_extract/exporters/notes.py b/papis_extract/exporters/notes.py index e27bc78..29a2ed2 100644 --- a/papis_extract/exporters/notes.py +++ b/papis_extract/exporters/notes.py @@ -64,14 +64,14 @@ class NotesExporter: even if they already exist, defaults to False. :type duplicates: bool, optional """ - logger.debug("Adding annotations to note.") + logger.debug("Adding annotations to note...") notes_path = papis.notes.notes_path_ensured(document) existing: list[str] = [] with open(notes_path, "r") as file_read: existing = file_read.readlines() - new_annotations: list[str] = [] + new_annotations: list[str] = formatted_annotations if not duplicates: new_annotations = self._drop_existing_annotations( formatted_annotations, existing @@ -85,8 +85,7 @@ class NotesExporter: f.write("\n") # FIXME this either joins them too close or moves them too far apart # We need a better algorithm which knows what a full 'annotation' is. - f.write("\n".join(new_annotations)) - f.write("\n") + f.write("\n\n".join(new_annotations)) logger.info( f"Wrote {len(new_annotations)} " f"{'line' if len(new_annotations) == 1 else 'lines'} " From 96cd4929c9960cef1066ca472fcf6636d73cad07 Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Thu, 11 Sep 2025 10:53:50 +0200 Subject: [PATCH 086/107] chore: Format files with ruff --- papis_extract/__init__.py | 1 - papis_extract/exporters/__init__.py | 1 - papis_extract/exporters/notes.py | 32 +++++++++++++++----------- papis_extract/extractors/__init__.py | 3 +-- papis_extract/extractors/pdf.py | 4 +--- papis_extract/extractors/pocketbook.py | 9 +++----- papis_extract/formatter.py | 1 + pyproject.toml | 19 ++++----------- 8 files changed, 29 insertions(+), 41 deletions(-) diff --git a/papis_extract/__init__.py b/papis_extract/__init__.py index 041a86a..ae04015 100644 --- a/papis_extract/__init__.py +++ b/papis_extract/__init__.py @@ -5,7 +5,6 @@ import papis.cli import papis.config import papis.document import papis.logging -import papis.notes import papis.strings from papis.document import Document diff --git a/papis_extract/exporters/__init__.py b/papis_extract/exporters/__init__.py index b9980e5..7a1b343 100644 --- a/papis_extract/exporters/__init__.py +++ b/papis_extract/exporters/__init__.py @@ -4,7 +4,6 @@ from papis_extract.exporter import Exporter from papis_extract.exporters.notes import NotesExporter from papis_extract.exporters.stdout import StdoutExporter - logger = papis.logging.get_logger(__name__) all_exporters: dict[str, type[Exporter]] = {} diff --git a/papis_extract/exporters/notes.py b/papis_extract/exporters/notes.py index 29a2ed2..2a753d3 100644 --- a/papis_extract/exporters/notes.py +++ b/papis_extract/exporters/notes.py @@ -1,14 +1,16 @@ from dataclasses import dataclass + import Levenshtein -from papis.document import Document -from papis_extract.annotation import Annotation -from papis_extract.formatter import Formatter -from papis.logging import get_logger -import papis.notes +import papis.commands.edit +import papis.config import papis.document import papis.git -import papis.config -import papis.commands.edit +import papis.notes +from papis.document import Document +from papis.logging import get_logger + +from papis_extract.annotation import Annotation +from papis_extract.formatter import Formatter logger = get_logger(__name__) @@ -33,7 +35,9 @@ class NotesExporter: doc, annots, first=True ).split("\n") if formatted_annotations: - self._add_annots_to_note(doc, formatted_annotations, duplicates=self.duplicates) + self._add_annots_to_note( + doc, formatted_annotations, duplicates=self.duplicates + ) if self.edit: papis.commands.edit.edit_notes(doc, git=self.git) @@ -83,12 +87,12 @@ class NotesExporter: # add newline if theres no empty space at file end if len(existing) > 0 and existing[-1].strip() != "": f.write("\n") - # FIXME this either joins them too close or moves them too far apart - # We need a better algorithm which knows what a full 'annotation' is. - f.write("\n\n".join(new_annotations)) + # We filter out any empty lines from the annotations + filtered_annotations = [annot for annot in new_annotations if annot != ""] + f.write("\n\n".join(filtered_annotations)) logger.info( - f"Wrote {len(new_annotations)} " - f"{'line' if len(new_annotations) == 1 else 'lines'} " + f"Wrote {len(filtered_annotations)} " + f"{'line' if len(filtered_annotations) == 1 else 'lines'} " f"to {papis.document.describe(document)}" ) @@ -106,7 +110,7 @@ class NotesExporter: """Returns the input annotations dropping any existing. Takes a list of formatted annotations and a list of strings - (most probably existing lines in a file). If anny annotations + (most probably existing lines in a file). If any annotations match an existing line closely enough, they will be dropped. Returns list of annotations without duplicates. diff --git a/papis_extract/extractors/__init__.py b/papis_extract/extractors/__init__.py index da84829..b943913 100644 --- a/papis_extract/extractors/__init__.py +++ b/papis_extract/extractors/__init__.py @@ -3,9 +3,8 @@ from importlib.util import find_spec import papis.logging from papis_extract.extraction import Extractor -from papis_extract.extractors import pdf +from papis_extract.extractors import pdf, readera from papis_extract.extractors.pocketbook import PocketBookExtractor -from papis_extract.extractors import readera logger = papis.logging.get_logger(__name__) diff --git a/papis_extract/extractors/pdf.py b/papis_extract/extractors/pdf.py index 8caaf5c..887a88b 100644 --- a/papis_extract/extractors/pdf.py +++ b/papis_extract/extractors/pdf.py @@ -32,9 +32,7 @@ class PdfExtractor: annotations: list[Annotation] = [] try: with mu.Document(filename) as doc: - for ( - page - ) in doc: # pyright: ignore [reportUnknownVariableType] - missing stub + for page in doc: # pyright: ignore [reportUnknownVariableType] - missing stub annot: mu.Annot for annot in page.annots(): quote, note = self._retrieve_annotation_content(page, annot) diff --git a/papis_extract/extractors/pocketbook.py b/papis_extract/extractors/pocketbook.py index ad73ad7..4f4b73a 100644 --- a/papis_extract/extractors/pocketbook.py +++ b/papis_extract/extractors/pocketbook.py @@ -44,16 +44,13 @@ class PocketBookExtractor: annotations: list[Annotation] = [] for bm in html.select("div.bookmark"): content = str( - (bm.select_one("div.bm-text>p") or html.new_string("")).text - or "" # pyright: ignore [reportUnknownArgumentType] + (bm.select_one("div.bm-text>p") or html.new_string("")).text or "" # pyright: ignore [reportUnknownArgumentType] ) note = str( - (bm.select_one("div.bm-note>p") or html.new_string("")).text - or "" # pyright: ignore [reportUnknownArgumentType] + (bm.select_one("div.bm-note>p") or html.new_string("")).text or "" # pyright: ignore [reportUnknownArgumentType] ) page = int( - (bm.select_one("p.bm-page") or html.new_string("")).text - or 0 # pyright: ignore [reportUnknownArgumentType] + (bm.select_one("p.bm-page") or html.new_string("")).text or 0 # pyright: ignore [reportUnknownArgumentType] ) el_classes = bm.attrs.get("class", "").split(" ") diff --git a/papis_extract/formatter.py b/papis_extract/formatter.py index 515a2c7..1bfd286 100644 --- a/papis_extract/formatter.py +++ b/papis_extract/formatter.py @@ -1,4 +1,5 @@ from typing import Protocol + from papis.document import Document from papis_extract.annotation import Annotation diff --git a/pyproject.toml b/pyproject.toml index ca3daf8..2988dd5 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,8 +1,6 @@ [project] -authors = [ - {name = "Marty Oehme", email = "contact@martyoeh.me"}, -] -license = {text = "GPL-3.0-or-later"} +authors = [{ name = "Marty Oehme", email = "contact@martyoeh.me" }] +license = { text = "GPL-3.0-or-later" } requires-python = "<4.0,>=3.11" dependencies = [ "pymupdf<2.0.0,>=1.24.2", @@ -35,18 +33,11 @@ repository = "https://github.com/marty-oehme/papis-extract" extract = "papis_extract:main" [project.optional-dependencies] -whoosh = [ - "whoosh<3.0.0,>=2.7.4", -] -pocketbook = [ - "beautifulsoup4<5.0.0,>=4.12.3", -] +whoosh = ["whoosh<3.0.0,>=2.7.4"] +pocketbook = ["beautifulsoup4<5.0.0,>=4.12.3"] [tool.uv] -dev-dependencies = [ - "pytest<9.0.0,>=8.0.0", - "pytest-cov<7.0.0,>=6.0.0", -] +dev-dependencies = ["pytest<9.0.0,>=8.0.0", "pytest-cov<7.0.0,>=6.0.0"] [build-system] requires = ["hatchling"] From f5455b6946c8c25c275075e905a8a17e35295c2f Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Thu, 11 Sep 2025 13:38:47 +0200 Subject: [PATCH 087/107] chore: Fix for additional linting rules --- papis_extract/__init__.py | 7 +++++-- papis_extract/annotation.py | 14 ++++++-------- papis_extract/exporters/notes.py | 18 ++++++++++-------- papis_extract/extractors/pdf.py | 18 ++++++++---------- papis_extract/extractors/pocketbook.py | 17 ++++++++--------- papis_extract/extractors/readera.py | 6 +++--- pyproject.toml | 18 ++++++++++++++++++ 7 files changed, 58 insertions(+), 40 deletions(-) diff --git a/papis_extract/__init__.py b/papis_extract/__init__.py index ae04015..d1292c9 100644 --- a/papis_extract/__init__.py +++ b/papis_extract/__init__.py @@ -1,4 +1,9 @@ import re +from typing import TYPE_CHECKING + +if TYPE_CHECKING: + from papis_extract.annotation import Annotation + from papis_extract.exporter import Exporter import click import papis.cli @@ -9,8 +14,6 @@ import papis.strings from papis.document import Document from papis_extract import extraction -from papis_extract.annotation import Annotation -from papis_extract.exporter import Exporter from papis_extract.exporters import all_exporters from papis_extract.extractors import all_extractors from papis_extract.formatter import Formatter, formatters diff --git a/papis_extract/annotation.py b/papis_extract/annotation.py index 8fd63ac..97bd950 100644 --- a/papis_extract/annotation.py +++ b/papis_extract/annotation.py @@ -1,6 +1,6 @@ import math from dataclasses import dataclass -from typing import Any, Optional, cast +from typing import Any, cast import chevron import papis.config @@ -117,7 +117,7 @@ class Annotation: return color_mapping.get(colorname, "") # mimics the functions in papis.config.{getlist,getint,getfloat} etc. - def _getdict(self, key: str, section: Optional[str] = None) -> dict[str, str]: + def _getdict(self, key: str, section: str | None = None) -> dict[str, str]: """Dict getter :returns: A python dict @@ -126,19 +126,17 @@ class Annotation: """ rawvalue: Any = papis.config.general_get(key, section=section) if isinstance(rawvalue, dict): - return cast(dict[str, str], rawvalue) + return cast("dict[str, str]", rawvalue) try: rawvalue = eval(rawvalue) except Exception: raise SyntaxError( - "The key '{}' must be a valid Python object: {}".format(key, rawvalue) + f"The configuration key '{key}' must be a valid Python dict: {rawvalue}" ) else: if not isinstance(rawvalue, dict): raise SyntaxError( - "The key '{}' must be a valid Python dict. Got: {} (type {!r})".format( - key, rawvalue, type(rawvalue).__name__ - ) + f"The configuration key '{key}' must be a valid Python dict. Got: {rawvalue} (type {type(rawvalue).__name__})" ) - return cast(dict[str, str], rawvalue) + return cast("dict[str, str]", rawvalue) diff --git a/papis_extract/exporters/notes.py b/papis_extract/exporters/notes.py index 2a753d3..ff92c3d 100644 --- a/papis_extract/exporters/notes.py +++ b/papis_extract/exporters/notes.py @@ -1,4 +1,5 @@ from dataclasses import dataclass +from pathlib import Path import Levenshtein import papis.commands.edit @@ -69,11 +70,11 @@ class NotesExporter: :type duplicates: bool, optional """ logger.debug("Adding annotations to note...") - notes_path = papis.notes.notes_path_ensured(document) + notes_path = Path(papis.notes.notes_path_ensured(document)) existing: list[str] = [] - with open(notes_path, "r") as file_read: - existing = file_read.readlines() + with notes_path.open("r") as fr: + existing = fr.readlines() new_annotations: list[str] = formatted_annotations if not duplicates: @@ -81,15 +82,16 @@ class NotesExporter: formatted_annotations, existing ) if not new_annotations: + logger.debug("No new annotations to be added.") return - with open(notes_path, "a") as f: + with notes_path.open("a") as fa: # add newline if theres no empty space at file end if len(existing) > 0 and existing[-1].strip() != "": - f.write("\n") + fa.write("\n") # We filter out any empty lines from the annotations filtered_annotations = [annot for annot in new_annotations if annot != ""] - f.write("\n\n".join(filtered_annotations)) + fa.write("\n\n".join(filtered_annotations)) logger.info( f"Wrote {len(filtered_annotations)} " f"{'line' if len(filtered_annotations) == 1 else 'lines'} " @@ -97,11 +99,11 @@ class NotesExporter: ) if git: - msg = "Update notes for '{0}'".format(papis.document.describe(document)) + msg = f"Update annotations for '{papis.document.describe(document)}'" folder = document.get_main_folder() if folder: papis.git.add_and_commit_resources( - folder, [notes_path, document.get_info_file()], msg + folder, [str(notes_path), document.get_info_file()], msg ) def _drop_existing_annotations( diff --git a/papis_extract/extractors/pdf.py b/papis_extract/extractors/pdf.py index 887a88b..6d9acc2 100644 --- a/papis_extract/extractors/pdf.py +++ b/papis_extract/extractors/pdf.py @@ -19,9 +19,7 @@ class PdfExtractor: if not filename.is_file(): logger.error(f"File {str(filename)} not readable.") return False - if not self._is_pdf(filename): - return False - return True + return self._is_pdf(filename) def run(self, filename: Path) -> list[Annotation]: """Extract annotations from a file. @@ -39,15 +37,15 @@ class PdfExtractor: if not quote and not note: continue color: tuple[float, float, float] = cast( - tuple[float, float, float], + "tuple[float, float, float]", ( annot.colors.get("fill") or annot.colors.get("stroke") or (0.0, 0.0, 0.0) ), ) - page_nr: int = cast(int, page.number or 0) - highlight_type: str = cast(str, annot.type[1] or "") + page_nr: int = cast("int", page.number or 0) + highlight_type: str = cast("str", annot.type[1] or "") a = Annotation( file=str(filename), content=quote or "", @@ -83,7 +81,7 @@ class PdfExtractor: should both be included or are the same, using Levenshtein distance. """ - content = cast(str, annotation.info["content"].replace("\n", " ")) + content = cast("str", annotation.info["content"].replace("\n", " ")) written = page.get_textbox(annotation.rect).replace("\n", " ") # highlight with selection in note @@ -94,13 +92,13 @@ class PdfExtractor: if Levenshtein.ratio(content, written) > minimum_similarity: return (content, None) # both a highlight and a note - elif content and written: + if content and written: return (written, content) # an independent note, not a highlight - elif content: + if content: return (None, content) # highlight with selection not in note - elif written: + if written: return (written, None) # just a highlight without any text return (None, None) diff --git a/papis_extract/extractors/pocketbook.py b/papis_extract/extractors/pocketbook.py index 4f4b73a..46ba66b 100644 --- a/papis_extract/extractors/pocketbook.py +++ b/papis_extract/extractors/pocketbook.py @@ -2,7 +2,6 @@ from pathlib import Path import magic -import papis.config import papis.logging from bs4 import BeautifulSoup @@ -13,7 +12,7 @@ logger = papis.logging.get_logger(__name__) class PocketBookExtractor: def can_process(self, filename: Path) -> bool: - if not magic.from_file(filename, mime=True) == "text/xml": + if magic.from_file(filename, mime=True) != "text/xml": return False content = self._read_file(filename) @@ -21,11 +20,11 @@ class PocketBookExtractor: return False html = BeautifulSoup(content, features="xml") - if not html.find( - "meta", {"name": "generator", "content": "PocketBook Bookmarks Export"} - ): - return False - return True + return bool( + html.find( + "meta", {"name": "generator", "content": "PocketBook Bookmarks Export"} + ) + ) def run(self, filename: Path) -> list[Annotation]: """Extract annotations from pocketbook html file. @@ -78,8 +77,8 @@ class PocketBookExtractor: def _read_file(self, filename: Path) -> str: try: - with open(filename) as f: - return f.read() + with filename.open("r") as fr: + return fr.read() except FileNotFoundError: logger.error(f"Could not open file {filename} for extraction.") return "" diff --git a/papis_extract/extractors/readera.py b/papis_extract/extractors/readera.py index 0e9bd63..a968255 100644 --- a/papis_extract/extractors/readera.py +++ b/papis_extract/extractors/readera.py @@ -17,7 +17,7 @@ class ReadEraExtractor: """ def can_process(self, filename: Path) -> bool: - if not magic.from_file(filename, mime=True) == "text/plain": + if magic.from_file(filename, mime=True) != "text/plain": return False content = self._read_file(filename) @@ -83,8 +83,8 @@ class ReadEraExtractor: def _read_file(self, filename: Path) -> list[str]: try: - with open(filename, encoding="utf-8") as f: - return f.readlines() + with filename.open("r") as fr: + return fr.readlines() except FileNotFoundError: logger.error(f"Could not open file {filename} for extraction.") return [] diff --git a/pyproject.toml b/pyproject.toml index 2988dd5..0c84bea 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -39,6 +39,24 @@ pocketbook = ["beautifulsoup4<5.0.0,>=4.12.3"] [tool.uv] dev-dependencies = ["pytest<9.0.0,>=8.0.0", "pytest-cov<7.0.0,>=6.0.0"] +[tool.ruff.lint] +extend-select = [ + "C4", # Catch incorrect use of comprehensions, dict, list, etc + "F", # Pyflakes rules + "FA", # Enforce from __future__ import annotations + "I", # Sort imports properly + "ICN", # Use common import conventions + "ISC", # Good use of string concatenation + "NPY", # Some numpy-specific things + "PTH", # Use pathlib instead of os.path + "RET", # Good return practices + "SIM", # Common simplification rules + "TC", # Enforce importing certain types in a TYPE_CHECKING block + "TID", # Some good import practices + "UP", # Warn if certain things can changed due to newer Python versions + "W", # PyCodeStyle warnings +] + [build-system] requires = ["hatchling"] build-backend = "hatchling.build" From ff36d30f91e5ffa4d2f3a1ca4fec8fa36328f6c4 Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Thu, 11 Sep 2025 17:05:35 +0200 Subject: [PATCH 088/107] docs: Add CHANGELOG --- CHANGELOG.md | 57 ++++++++++++++++++++++++++++++++++++++++++++++++++ pyproject.toml | 2 +- uv.lock | 2 +- 3 files changed, 59 insertions(+), 2 deletions(-) create mode 100644 CHANGELOG.md diff --git a/CHANGELOG.md b/CHANGELOG.md new file mode 100644 index 0000000..12ee011 --- /dev/null +++ b/CHANGELOG.md @@ -0,0 +1,57 @@ +# Changelog + +All notable changes to this project will be documented in this file. + +## [Unreleased] + +### Added + +### Changed + +### Fixed + +### Removed + +## [0.2.1] + +### Added + +- Add option to force-add duplicated annotations +- Add cli option to choose extractor +- Add CSV formatter +- Add count formatter (displays the annotation count per item) + +### Changed + +- Switch to uv packaging and hatch backend + +### Fixed + +- Only inform if no extractor finds valid files +- Respect minimum color similarity option + +## [0.2.0] + +### Added + +- Add pocketbook extractor (requires BeautifulSoup4) +- Add ReadEra extractor +- Allow different formatting for first format entry +- Add Markdown style formatting +- Add stdout or write to note exporters + +### Changed + +- Update dependencies +- Update to papis 0.14 +- Refactor and simplify test dependencies + +## [0.1.0] + +### Added + +- Add extractor and install info +- Add pdf extractor +- Allow cli option for choosing a template +- Add mustache templating +- Add preliminary README diff --git a/pyproject.toml b/pyproject.toml index 0c84bea..f9fc3c1 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -11,7 +11,7 @@ dependencies = [ "chevron<1.0.0,>=0.14.0", ] name = "papis-extract" -version = "0.2.0" +version = "0.2.1" description = "" readme = "README.md" keywords = [ diff --git a/uv.lock b/uv.lock index 083b67a..a1744be 100644 --- a/uv.lock +++ b/uv.lock @@ -408,7 +408,7 @@ wheels = [ [[package]] name = "papis-extract" -version = "0.2.0" +version = "0.2.1" source = { editable = "." } dependencies = [ { name = "chevron" }, From e46219151bf8278d701464e717a1d81e53ca3ea1 Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Thu, 11 Sep 2025 17:25:20 +0200 Subject: [PATCH 089/107] refactor: Use generator for PDF extractor --- papis_extract/extractors/pdf.py | 68 +++++++++++++++++++-------------- 1 file changed, 40 insertions(+), 28 deletions(-) diff --git a/papis_extract/extractors/pdf.py b/papis_extract/extractors/pdf.py index 6d9acc2..5df854e 100644 --- a/papis_extract/extractors/pdf.py +++ b/papis_extract/extractors/pdf.py @@ -1,6 +1,7 @@ # pyright: strict, reportMissingTypeStubs=false, reportUnknownMemberType=false +from collections.abc import Generator from pathlib import Path -from typing import cast +from typing import NamedTuple, cast import Levenshtein import magic @@ -14,6 +15,11 @@ from papis_extract.exceptions import ExtractionError logger = papis.logging.get_logger(__name__) +class PdfAnnot(NamedTuple): + page: mu.Page + annot: mu.Annot + + class PdfExtractor: def can_process(self, filename: Path) -> bool: if not filename.is_file(): @@ -29,32 +35,24 @@ class PdfExtractor: """ annotations: list[Annotation] = [] try: - with mu.Document(filename) as doc: - for page in doc: # pyright: ignore [reportUnknownVariableType] - missing stub - annot: mu.Annot - for annot in page.annots(): - quote, note = self._retrieve_annotation_content(page, annot) - if not quote and not note: - continue - color: tuple[float, float, float] = cast( - "tuple[float, float, float]", - ( - annot.colors.get("fill") - or annot.colors.get("stroke") - or (0.0, 0.0, 0.0) - ), - ) - page_nr: int = cast("int", page.number or 0) - highlight_type: str = cast("str", annot.type[1] or "") - a = Annotation( - file=str(filename), - content=quote or "", - note=note or "", - color=color, - type=highlight_type, - page=page_nr, - ) - annotations.append(a) + for page, annot in self._all_pdf_annots(filename): + quote, note = self._get_annotation_content(page, annot) + if not quote and not note: + continue + + color = self._get_correct_color(annot) + page_nr: int = cast("int", page.number or 0) + highlight_type: str = cast("str", annot.type[1] or "") + + a = Annotation( + file=str(filename), + content=quote or "", + note=note or "", + color=color, + type=highlight_type, + page=page_nr, + ) + annotations.append(a) logger.debug( f"Found {len(annotations)} " f"{'annotation' if len(annotations) == 1 else 'annotations'} for {filename}." @@ -65,11 +63,18 @@ class PdfExtractor: return annotations + def _all_pdf_annots(self, filename: Path) -> Generator[PdfAnnot]: + with mu.Document(filename) as doc: + for page in doc: + annot: mu.Annot + for annot in page.annots(): + yield PdfAnnot(page, annot) + def _is_pdf(self, fname: Path) -> bool: """Check if file is a pdf, using mime type.""" return magic.from_file(fname, mime=True) == "application/pdf" - def _retrieve_annotation_content( + def _get_annotation_content( self, page: mu.Page, annotation: mu.Annot ) -> tuple[str | None, str | None]: """Gets the text content of an annotation. @@ -102,3 +107,10 @@ class PdfExtractor: return (written, None) # just a highlight without any text return (None, None) + + def _get_correct_color(self, annot: mu.Annot): + color: tuple[float, float, float] = cast( + "tuple[float, float, float]", + (annot.colors.get("fill") or annot.colors.get("stroke") or (0.0, 0.0, 0.0)), + ) + return color From 3344147f1f2cfc39a10a10b5507e8ca95f6b2938 Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Thu, 11 Sep 2025 18:05:08 +0200 Subject: [PATCH 090/107] test: Add tests for readera extractor --- tests/extractors/test_readera.py | 17 +++++ .../ReadEra_sample.txt | 0 tests/resources/Readest_sample.txt | 70 +++++++++++++++++++ 3 files changed, 87 insertions(+) create mode 100644 tests/extractors/test_readera.py rename tests/{extractors => resources}/ReadEra_sample.txt (100%) create mode 100644 tests/resources/Readest_sample.txt diff --git a/tests/extractors/test_readera.py b/tests/extractors/test_readera.py new file mode 100644 index 0000000..92fc5b7 --- /dev/null +++ b/tests/extractors/test_readera.py @@ -0,0 +1,17 @@ +from pathlib import Path + +from papis_extract.extractors.readera import ReadEraExtractor + +valid_file = Path("tests/resources/ReadEra_sample.txt") +invalid_file = Path("tests/resources/Readest_sample.txt") + + +def test_identifies_readera_exports(): + ex = ReadEraExtractor() + assert ex.can_process(valid_file) + + +# Readest exports are very similar so we should ensure it ignores them +def test_ignores_readest_exports(): + ex = ReadEraExtractor() + assert not ex.can_process(invalid_file) diff --git a/tests/extractors/ReadEra_sample.txt b/tests/resources/ReadEra_sample.txt similarity index 100% rename from tests/extractors/ReadEra_sample.txt rename to tests/resources/ReadEra_sample.txt diff --git a/tests/resources/Readest_sample.txt b/tests/resources/Readest_sample.txt new file mode 100644 index 0000000..6e0ab8f --- /dev/null +++ b/tests/resources/Readest_sample.txt @@ -0,0 +1,70 @@ +# Ideology and the Virtual City +**Author**: + +**Exported from Readest**: 2025-09-10 + +--- + +## Highlights & Annotations + +### 5 No More Heroes: The City as Wasteland +> "As an ideological response, this “escapist defeatism” contains elements of cynicism, in that it also involves an outward rejection of normal social demands and a pessimistic outlook. The difference between it and cynical self-interest, however, is that the defeatist doesn’t still want to thrive within the existing order. Whereas cynical self-interest distances behaviour from moral values only to really enjoy following dominant demands after all, the defeatist is less excited by regular notions of success, but cannot imagine a way out. I believe this position embodies various features of what Mark Fisher calls “capitalist realism,” which is less about competitive spirit or “making it” and more a kind of depressed state of low expectation within a totalizing capitalist reality." + +> "As an ideological response, this “escapist defeatism” contains elements of cynicism, in that it also involves an outward rejection of normal social demands and a pessimistic outlook. The difference between it and cynical self-interest, however, is that the defeatist doesn’t still want to thrive within the existing order. Whereas cynical self-interest distances behaviour from moral values only to really enjoy following dominant demands after all, the defeatist is less excited by regular notions of success, but cannot imagine a way out. I believe this position embodies various features of what Mark Fisher calls “capitalist realism,” which is less about competitive spirit or “making it” and more a kind of depressed state of low expectation within a totalizing capitalist reality." +**Note**:: Opposing cynical defeatism to cynical self-interest + +> "As he says, this modern depression “is constituted not by an inability to get pleasure so much as it is by an inability to do anything else except pursue pleasure. There is a sense that ‘something is missing’—but no appreciation that this mysterious, missing enjoyment can only be accessed beyond the pleasure principle.”22 And of course, the obsessive retreat into consumer pleasures only connects the defeatist even more deeply to the depressing reality, as it becomes part of the work-leisure cycle in which body and mind are allowed to relax, only to be rejuvenated for more draining labour. Even in strictly economic terms, if the escape is all we live for it still must be funded through labour; the only way to get more escape time is to return to the prison and earn it." +**Note**:: cf. Mark Fisher + +> "As he says, this modern depression “is constituted not by an inability to get pleasure so much as it is by an inability to do anything else except pursue pleasure. There is a sense that ‘something is missing’—but no appreciation that this mysterious, missing enjoyment can only be accessed beyond the pleasure principle.”22 And of course, the obsessive retreat into consumer pleasures only connects the defeatist even more deeply to the depressing reality, as it becomes part of the work-leisure cycle in which body and mind are allowed to relax, only to be rejuvenated for more draining labour. Even in strictly economic terms, if the escape is all we live for it still must be funded through labour; the only way to get more escape time is to return to the prison and earn it." + +> "His position then reflects the idea developed by Žižek through the terminology of psychoanalyst Jacques Lacan that, in placing increasing emphasis on personal responsibility for success and enjoyment, neoliberalized societies appear to have no “big Other,” or no generalized symbolic guarantee of meaning that explicitly prescribes standards of behaviour. With no singular authoritative voice to aid our decision-making, the attraction of consumerist distractions is perhaps unsurprising, but as the seductive promises of consumer entertainment remain unfulfilled, the pressure remains on us to take responsibility for this dissatisfaction as well. Neoliberalism’s constant demand to do more, without telling us what to do or where we might find it, means we are always guilty of failure, and can’t really identify once and for all what we wish to become" + +> "NMH highlights how consumerist escapist fantasies must be funded by the very normality we wish to escape, and the deeper the escape the more funding is required. The paradox is represented superbly in the kind of jobs Travis must do between matches. While there are extra contract killing jobs on offer, the game only grants access to these after the player completes more menial tasks taken from the local job centre, from picking coconuts and mowing lawns to collecting litter and cleaning graffiti. At these points, Travis is plunged back into an ideological normalcy where work is deemed valuable and fulfilling" + +> "NMH highlights how consumerist escapist fantasies must be funded by the very normality we wish to escape, and the deeper the escape the more funding is required. The paradox is represented superbly in the kind of jobs Travis must do between matches. While there are extra contract killing jobs on offer, the game only grants access to these after the player completes more menial tasks taken from the local job centre, from picking coconuts and mowing lawns to collecting litter and cleaning graffiti. At these points, Travis is plunged back into an ideological normalcy where work is deemed valuable and fulfilling" +**Note**:: 'No more heroes' + +> "“something deeper” may be seen in psychoanalytic terms as “death drive,” or a kind of gap in our subjective identities that means we are never quite fully reconciled with ourselves. It is an inevitable sense of uncertainty that emerges because there is no final truth about what things mean, only different understandings that emerge in human consciousness through language. No matter how knowledgeable we are, each of us only has our own perspective and cannot know the innermost feelings and thoughts of others. Moreover, our own deepest desires are not even compatible (for example, the desires for risk and security), so that satisfying one may leave us unsatisfied in another way. In short, nothing is ever really, conclusively fulfilling, and our ideological fantasies which make us feel that there is some absolute meaning merely distract us from that realization." + +--- + +### 6 Persona 5: The City as Prison +> "missing here is any appreciation of the extent to which neoliberalized political, financial, legal and cultural institutions themselves cause social disengagement, or how the logic of profit actively works against deeper democratic participation. In other words, it does not ask whether democracy may itself be problematic in its existing form, or whether people might be politically disengaged because of privatized media’s tendency to trivialize politics, the influence of corporate money on political parties, or the excessive demands on other aspects of their lives. Indeed, meaningful political change is unlikely, as Jodi Dean points out, when “the appeal to democracy presupposes democracy is the solution to the problems of democracy, because it incorporates in advance any hope things might be otherwise as already the fundamental democratic promise and provision.”25 " + +> "one is represented by the general public, who are shown to be uncommitted, fickle, apathetic and ignorant individuals that may want a just society, but take no responsibility for it. In what Žižek calls the “culture of complaint” in modern societies, they constantly ask some authority figure to make life better, and even “enjoy” playing the perpetual victim, effectively recognizing themselves as subordinates, rather than as agents who could actually affect change. Likewise, in P5, public opinion first imagines the Phantom Thieves as saviours, but later disowns them when they appear to have become too radical, and when Shido promises to restore order through conventional political means." + +--- + +### 7 Conclusion: Conformism and Critique +> "“hedonism,” in the context of neoliberalism I am thinking of a lifestyle that focuses substantially on consumerist entertainment or pleasure. This hedonist need not be an extreme thrill seeker or a wild party-goer. It would be equally “hedonistic,” in the sense I am defining here, for someone to fixate on what they might want for dinner every night, be genuinely excited about seeing the latest superhero movie, or constantly want to go shopping. In this way, for this hedonist, work is predominantly a means to an end that must be done to pay for enjoyment. The hedonist wouldn’t think twice about stopping work if they came into a large amount of money, but until then work is on balance a good thing, because it enables the purchase of pleasurable goods and services. At the same time, many big social issues, including politics, would appear boring to the hedonist. It is of course better when the economy is thriving, but it makes more sense to leave that stuff to the experts. In all this, such hedonism is not necessarily motivated by pure self-interest. Rather, it involves lines of rationalization based on neoliberal ideas, including consumerist concepts of identity creation but also an understanding of freedom in individual terms and a notion that there are no political alternatives." + +> "while it recognizes the hypocrisy when powerful figures claim to be acting in the best interests of all, it has no time for radical critique, whether left or right, that actually seeks significant changes to the status quo. Instead, the cynic wants things to stay as they are and to exploit them to his/her advantage. This self-interest is supported by pragmatic “realism.” The market is flawed, so the argument goes, but better than the alternative; at least we aren’t subjected to the oppressive and broken systems of, say, Soviet Russia or North Korea. We must remember that humans are a selfish and aggressive bunch, and grand social projects always fail, so we should make the most of what we have." +**Note**:: Cynical self-interest + +> "while it recognizes the hypocrisy when powerful figures claim to be acting in the best interests of all, it has no time for radical critique, whether left or right, that actually seeks significant changes to the status quo. Instead, the cynic wants things to stay as they are and to exploit them to his/her advantage. This self-interest is supported by pragmatic “realism.” The market is flawed, so the argument goes, but better than the alternative; at least we aren’t subjected to the oppressive and broken systems of, say, Soviet Russia or North Korea. We must remember that humans are a selfish and aggressive bunch, and grand social projects always fail, so we should make the most of what we have." + +> "it obscures that many people in the world still do have it bad, and that their situation is deeply connected to the wealth and freedoms elsewhere, so could improve under a different social order. Here, the cynic may claim that nothing can be done about this, or that someone somewhere always gets a raw deal, so we may as well just enjoy our luck. What is still missing, however, is any consideration that “human nature” has other aspects and adapts to different conditions, or that humans also share and act collectively, and are more likely to do so in more equal societies, where everyone has a stake and a reasonable quality of life." +**Note**:: Cynical self-interest + +> "it obscures that many people in the world still do have it bad, and that their situation is deeply connected to the wealth and freedoms elsewhere, so could improve under a different social order. Here, the cynic may claim that nothing can be done about this, or that someone somewhere always gets a raw deal, so we may as well just enjoy our luck. What is still missing, however, is any consideration that “human nature” has other aspects and adapts to different conditions, or that humans also share and act collectively, and are more likely to do so in more equal societies, where everyone has a stake and a reasonable quality of life." + +> "Central to cynicism is an idea that it rejects ideology for rationality, because ideologies are dogmatic and lead to authoritarianism. But with this alibi it fails to account for its own presumption of neoliberal ideas, particularly its onus on individual self-sufficiency and the impossibility of even potentially workable political or economic alternatives" + +> "In “escapist defeatism” there is also recognition of social problems and also a notion that not much can be done about them, at least by the average citizen. It does perhaps entail more of a historical dimension than cynical self-interest, in focusing less on human nature and more on the way things are now, under a seemingly omnipotent global capitalist system. Moreover, for the defeatist, taking advantage of the situation isn’t the most attractive option, because dominant notions of success simply don’t seem that satisfying, or because an outward pursuit of self-interest remains ethically abhorrent." + +> "Such media consumption goes beyond the throwaway pleasures of hedonism to a deeper identification with the chosen material, even if, deep down, the defeatist knows it is meaningless" + +> "how heavily tied they are to the economy, forcing the individuals concerned back into the normalcy of work-leisure routines to financially maintain their obsession. Another possible aspect of this lifestyle is a kind of victim complex, in which the powers that be are held responsible for life’s difficulties, but cannot be resisted, only mocked or angrily reproached. Either way, the defeatist does not take responsibility for his/her part in reproducing the status quo through excessive consumerist habits, or make any attempt to organize politically and create change." + +> "he answer is somewhere in between: the system works in principle but needs attention if it’s ever going to run smoothly enough to produce a proper meritocracy. What is required, therefore, is collective vigilance and effort to get involved in improving the system, to stop anyone from having an overly corruptive impact. In short, no major overhaul is required, merely greater commitment to properly enforce the concepts of justice and equal opportunity that already exist. This position involves strong political commitment and a good working knowledge of existing systems. But it also implies strict adherence to a particular set of principles, specifically ones that do not question the actual political, social and economic institutions that are currently in place. In addition, the very idea of “making it” inscribed into its meritocratic ideal is limited by neoliberal notions of success: fulfilling career potentials, accumulating property, developing personal relationships and expressing identities through consumerist" +**Note**:: Political reformism + +> "he answer is somewhere in between: the system works in principle but needs attention if it’s ever going to run smoothly enough to produce a proper meritocracy. What is required, therefore, is collective vigilance and effort to get involved in improving the system, to stop anyone from having an overly corruptive impact. In short, no major overhaul is required, merely greater commitment to properly enforce the concepts of justice and equal opportunity that already exist. This position involves strong political commitment and a good working knowledge of existing systems. But it also implies strict adherence to a particular set of principles, specifically ones that do not question the actual political, social and economic institutions that are currently in place. In addition, the very idea of “making it” inscribed into its meritocratic ideal is limited by neoliberal notions of success: fulfilling career potentials, accumulating property, developing personal relationships and expressing identities through consumerist" + +> "It does not consider whether these aims are really universal, or whether some people may have valid alternate desires that would require extensive social change to realize. Nor does it question whether meritocracy is fair in the first place, or whether people who simply lack marketable personal attributes deserve a lesser standard of life." + +> "Such a perspective may, for example, contemplate whether the kinds of work we are generally obliged to do are socially necessary or personally fulfilling. It may ask whether the demand to “enjoy responsibly” by balancing ever growing work and consumer pressures actually constitutes a meaningful or coherent life goal, or whether alternative goals could be more satisfactory. It can also imagine the possibility of greater political engagement from the majority of people, and what it means to take collective responsibility for social conditions, rather than following individual desires. And if all these ideas are framed in relation to neoliberal capitalist systems of economics, politics and culture, they can even consider whether the systems as such produce demands that are inherently unrealistic, antagonistic and socially destructive. + The specific questions that then arise from such critical thinking are many and varied. For example, are there even enough jobs, especially satisfying, well-paid jobs, for everyone to do today? Is throwaway mass consumerism environmentally sustainable? Does an individualized focus on employment and consumerism detract from more meaningful social activity? Are the demands of globalized markets compatible with free and effective political decision-making? To what extent does corporate advertising, PR and lobbying help frame our political desires? And how might we need to change society to provide the kind of meaning, involvement and satisfaction we desire? If some of these questions seem overly radical even for progressives who perceive a need to address existing social problems, it should be clear by now that getting to the root of these problems may require re-evaluation of even the most deeply embedded assumptions about how societies work and how they could work." + +--- From d840609ecb974a2348c7c8f29c1d88003a1554d1 Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Thu, 11 Sep 2025 18:38:59 +0200 Subject: [PATCH 091/107] fix: Fix annotation value comparison --- papis_extract/annotation.py | 8 ++++++-- tests/test_annotation.py | 6 ++++++ 2 files changed, 12 insertions(+), 2 deletions(-) diff --git a/papis_extract/annotation.py b/papis_extract/annotation.py index 97bd950..d3dadb9 100644 --- a/papis_extract/annotation.py +++ b/papis_extract/annotation.py @@ -1,5 +1,4 @@ import math -from dataclasses import dataclass from typing import Any, cast import chevron @@ -21,7 +20,6 @@ COLORS: dict[str, tuple[float, float, float]] = { } -@dataclass class Annotation: """A PDF annotation object. @@ -140,3 +138,9 @@ class Annotation: ) return cast("dict[str, str]", rawvalue) + + def __str__(self) -> str: + return f"Annotation({self.type}: '{self.file}', color: {self.color}, tag: '{self.tag}', page: {self.page}, content: '{self.content}', note: '{self.note}', minimum_similarity_color: {self.minimum_similarity_color})" + + def __repr__(self) -> str: + return f"Annotation(type={self.type}, file='{self.file}', color={self.color}, tag='{self.tag}', page={self.page}, content='{self.content}', note='{self.note}', minimum_similarity_color={self.minimum_similarity_color})" diff --git a/tests/test_annotation.py b/tests/test_annotation.py index ceb0c0e..6d177a5 100644 --- a/tests/test_annotation.py +++ b/tests/test_annotation.py @@ -4,6 +4,12 @@ from papis.document import Document from papis_extract.annotation import Annotation +def test_value_comparison_works(): + sut = Annotation("myfile", content="Here be content!", note="and a note") + other = Annotation("myfile", content="Here be different content!", note="but still a note") + assert sut != other + + @pytest.mark.parametrize( "fmt_string,expected", [ From db47ad686d6ca934379d58e5e3e5cafd48bb1f07 Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Thu, 11 Sep 2025 20:16:05 +0200 Subject: [PATCH 092/107] chore: Implement Annotation sort and equality dunders --- papis_extract/annotation.py | 35 +++++++++++++++++++++++++++++++++++ tests/test_annotation.py | 34 ++++++++++++++++++++++++++++++++-- 2 files changed, 67 insertions(+), 2 deletions(-) diff --git a/papis_extract/annotation.py b/papis_extract/annotation.py index d3dadb9..212f103 100644 --- a/papis_extract/annotation.py +++ b/papis_extract/annotation.py @@ -1,4 +1,6 @@ import math +from functools import total_ordering +from types import NotImplementedType from typing import Any, cast import chevron @@ -20,6 +22,7 @@ COLORS: dict[str, tuple[float, float, float]] = { } +@total_ordering class Annotation: """A PDF annotation object. @@ -144,3 +147,35 @@ class Annotation: def __repr__(self) -> str: return f"Annotation(type={self.type}, file='{self.file}', color={self.color}, tag='{self.tag}', page={self.page}, content='{self.content}', note='{self.note}', minimum_similarity_color={self.minimum_similarity_color})" + + def __eq__(self, other: object) -> bool | NotImplementedType: + if not isinstance(other, Annotation): + return NotImplemented + + return ( + self.content.lower(), + self.note.lower(), + self.type, + self.file, + self.color, + self.tag, + self.page, + ) == ( + other.content.lower(), + other.note.lower(), + other.type, + other.file, + other.color, + other.tag, + other.page, + ) + + def __lt__(self, other: object) -> bool: + if not hasattr(other, "page"): + return NotImplemented + + other = cast("Annotation", other) + selfpage = self.page if self.page != 0 else float("inf") + otherpage = other.page if other.page != 0 else float("inf") + + return selfpage < otherpage diff --git a/tests/test_annotation.py b/tests/test_annotation.py index 6d177a5..efc2403 100644 --- a/tests/test_annotation.py +++ b/tests/test_annotation.py @@ -4,12 +4,42 @@ from papis.document import Document from papis_extract.annotation import Annotation -def test_value_comparison_works(): +def test_value_inequality_comparison(): sut = Annotation("myfile", content="Here be content!", note="and a note") - other = Annotation("myfile", content="Here be different content!", note="but still a note") + other = Annotation( + "myfile", content="Here be different content!", note="but still a note" + ) assert sut != other +def test_oder_lt_comparison(): + sut = Annotation("myfile", content="Here be content!", note="and a note", page=2) + other = Annotation( + "myfile", content="Here be different content!", note="but still a note", page=10 + ) + assert sut < other + + +def test_oder_ge_comparison(): + big = Annotation("mf", content="ct", note="nt", page=10) + small = Annotation("mf", content="ct", note="nt", page=2) + alsosmall = Annotation("mf", content="ct", note="nt", page=2) + assert big >= small + assert small >= alsosmall + + +def test_oder_gt_comparison_single_nopage(): + zeropage = Annotation("mf", content="ct", note="nt", page=0) + small = Annotation("mf", content="ct", note="nt", page=2) + assert zeropage > small + + +def test_oder_le_comparison_all_nopage(): + zeropage = Annotation("mf", content="ct", note="nt", page=0) + small = Annotation("mf", content="ct", note="nt", page=0) + assert zeropage <= small + + @pytest.mark.parametrize( "fmt_string,expected", [ From a9ff4152affa32cb2b8a0307c178cb7f4eecba2a Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Thu, 11 Sep 2025 18:38:59 +0200 Subject: [PATCH 093/107] fix: Do not parse the last ReadEra section --- papis_extract/extractors/readera.py | 13 +++++++------ tests/extractors/test_readera.py | 23 +++++++++++++++++++++++ tests/resources/ReadEra_sample.txt | 18 +++++------------- 3 files changed, 35 insertions(+), 19 deletions(-) diff --git a/papis_extract/extractors/readera.py b/papis_extract/extractors/readera.py index a968255..b6159ff 100644 --- a/papis_extract/extractors/readera.py +++ b/papis_extract/extractors/readera.py @@ -44,11 +44,10 @@ class ReadEraExtractor: def run(self, filename: Path) -> list[Annotation]: """Extract annotations from readera txt file. - Returns all readable annotations contained in the file - passed in, with highlights and notes if available. - Could theoretically return the annotation color but I - do not have access to a premium version of ReadEra so - I cannot add this feature. + Returns all readable annotations contained in the file passed in, with + highlights and notes if available. Could theoretically return the + annotation color but I do not have access to a premium version of + ReadEra so I cannot add this feature. """ content = self._read_file(filename)[2:] if not content: @@ -56,7 +55,9 @@ class ReadEraExtractor: annotations: list[Annotation] = [] - split = "\n".join(content).split("\n*****\n") + # split for *** separators and remove the last entry since it is always + # empty + split = "\n".join(content).split("\n*****\n")[:-1] note_pattern = re.compile(r"\n--.*") for entry in split: entry = entry.strip() diff --git a/tests/extractors/test_readera.py b/tests/extractors/test_readera.py index 92fc5b7..1061666 100644 --- a/tests/extractors/test_readera.py +++ b/tests/extractors/test_readera.py @@ -1,10 +1,27 @@ from pathlib import Path +from papis_extract.annotation import Annotation from papis_extract.extractors.readera import ReadEraExtractor valid_file = Path("tests/resources/ReadEra_sample.txt") invalid_file = Path("tests/resources/Readest_sample.txt") +expected = [ + Annotation( + file="tests/resources/ReadEra_sample.txt", + content="digital technologies of the twenty-first century can only exist thanks to this kind of outsourced labor. The relative invisibility of the tech supply chain is part of the ruse; American consumers do not see where smartphones come from.", + ), + Annotation( + file="tests/resources/ReadEra_sample.txt", + content="We don’t necessarily want our leaders to be average persons like us, even though we often enjoy hearing that famous celebrities eat the same fast food as regular people. ", + note="We continuously demystify our leaders - first through television, now through social media", + ), + Annotation( + file="tests/resources/ReadEra_sample.txt", + content="Initially, the Internet was praised as a freer way to encounter information. In the early 1990s, digital theorist George Landow saw hypertext as a liberatory reading strategy.", + ), +] + def test_identifies_readera_exports(): ex = ReadEraExtractor() @@ -15,3 +32,9 @@ def test_identifies_readera_exports(): def test_ignores_readest_exports(): ex = ReadEraExtractor() assert not ex.can_process(invalid_file) + + +def test_entry_extractions(): + ex = ReadEraExtractor() + result = ex.run(valid_file) + assert result == expected diff --git a/tests/resources/ReadEra_sample.txt b/tests/resources/ReadEra_sample.txt index de84412..c73029f 100644 --- a/tests/resources/ReadEra_sample.txt +++ b/tests/resources/ReadEra_sample.txt @@ -1,25 +1,17 @@ The Circle of the Snake Grafton Tanner -digital technologies of the twenty-first century can only exist thanks to this kind of outsourced labor. The relative invisibility of the tech supply chain is part of the ruse; American consumers do not see where smartphones come from. They do not see the conflict zones where coltan is mined to be used in electronic devices, or the sweatshops in which digital products are manufactured. The latest technologies arrive instead in pristine condition, as if delivered from on high. +digital technologies of the twenty-first century can only exist thanks to this kind of outsourced labor. The relative invisibility of the tech supply chain is part of the ruse; American consumers do not see where smartphones come from. ***** -We don’t necessarily want our leaders to be average persons like us, even though we often enjoy hearing that famous celebrities eat the same fast food as regular people. But in the beginning of the twenty-first century, we carefully watch our public figures to ensure they do not commit an unconscionable act. Doing so helps to rid the public stage of bigots, even as it also threatens the last known walls of privacy. This is an inevitable tension that must be maintained as we open the door on the private lives of others ---We continuously demystify our leaders - first through television, now through social media, streams, docus, etc. this brings them down to our level, which is what this paragraph talks about +We don’t necessarily want our leaders to be average persons like us, even though we often enjoy hearing that famous celebrities eat the same fast food as regular people. +--We continuously demystify our leaders - first through television, now through social media ***** -Initially, the Internet was praised as a freer way to encounter information. In the early 1990s, digital theorist George Landow saw hypertext as a liberatory reading strategy.¹⁶ He embraced it as a common good and thought hyperlinks would emancipate readers from the prison of the fixed word, allowing them to flow freely between various information sources. But what Landow never imagined is the exhaustion that could come from the endless, rootless process of reading in this way. Not everyone wants to jump from point to point without any center. Infinity might not always be alluring. -Landow puts the agency in the reader when he writes, ‘anyone who uses hypertext makes his or her own interests the de facto organizing principle (or center) for the investigation at the moment.’¹⁷ But how much agency do we actually have when falling down the rabbit hole? What if we get lost in the hole where the center was? How much attention do we end up losing in a world where we must always multi-task and where reading itself is disrupted by one hyperlink after another? And who - -***** - -In the Dust of This Planet -Horror of Philosophy vol. 1 -Eugene Thacker -In the first of a series of three books on the Horror of Philosophy,In the Dust of This Planetoffers the genre of horror as a way of thinking about the unthinkable. -Paperback: 978-1-84694-676-9 ebook: 978-1-78099-010-1 +Initially, the Internet was praised as a freer way to encounter information. +In the early 1990s, digital theorist George Landow saw hypertext as a liberatory reading strategy. ***** From fd714825260b747d5292d10dcace5fc25710fa08 Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Thu, 11 Sep 2025 21:37:18 +0200 Subject: [PATCH 094/107] chore: Log found files for extractors to debug logger --- papis_extract/extractors/pdf.py | 7 ++++++- papis_extract/extractors/pocketbook.py | 12 +++++++----- papis_extract/extractors/readera.py | 2 +- 3 files changed, 14 insertions(+), 7 deletions(-) diff --git a/papis_extract/extractors/pdf.py b/papis_extract/extractors/pdf.py index 5df854e..3ba9873 100644 --- a/papis_extract/extractors/pdf.py +++ b/papis_extract/extractors/pdf.py @@ -25,7 +25,12 @@ class PdfExtractor: if not filename.is_file(): logger.error(f"File {str(filename)} not readable.") return False - return self._is_pdf(filename) + + if not self._is_pdf(filename): + return False + + logger.debug(f"Found processable annotation file: {filename}") + return True def run(self, filename: Path) -> list[Annotation]: """Extract annotations from a file. diff --git a/papis_extract/extractors/pocketbook.py b/papis_extract/extractors/pocketbook.py index 46ba66b..5fc0585 100644 --- a/papis_extract/extractors/pocketbook.py +++ b/papis_extract/extractors/pocketbook.py @@ -20,11 +20,13 @@ class PocketBookExtractor: return False html = BeautifulSoup(content, features="xml") - return bool( - html.find( - "meta", {"name": "generator", "content": "PocketBook Bookmarks Export"} - ) - ) + if not html.find( + "meta", {"name": "generator", "content": "PocketBook Bookmarks Export"} + ): + return False + + logger.debug(f"Found processable annotation file: {filename}") + return True def run(self, filename: Path) -> list[Annotation]: """Extract annotations from pocketbook html file. diff --git a/papis_extract/extractors/readera.py b/papis_extract/extractors/readera.py index b6159ff..d992512 100644 --- a/papis_extract/extractors/readera.py +++ b/papis_extract/extractors/readera.py @@ -37,7 +37,7 @@ class ReadEraExtractor: return False logger.debug( - f"Found annotation file processable with ReadEraExtractor: {filename}" + f"Found processable annotation file: {filename}" ) return True From 3eb7f3f1c777b1aa4acad4c0fbba4e15df854415 Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Thu, 11 Sep 2025 21:37:18 +0200 Subject: [PATCH 095/107] feat: Add Readest extractor --- papis_extract/extractors/__init__.py | 3 +- papis_extract/extractors/readest.py | 78 ++++++++++++++++++++++++++++ 2 files changed, 80 insertions(+), 1 deletion(-) create mode 100644 papis_extract/extractors/readest.py diff --git a/papis_extract/extractors/__init__.py b/papis_extract/extractors/__init__.py index b943913..a49d010 100644 --- a/papis_extract/extractors/__init__.py +++ b/papis_extract/extractors/__init__.py @@ -3,7 +3,7 @@ from importlib.util import find_spec import papis.logging from papis_extract.extraction import Extractor -from papis_extract.extractors import pdf, readera +from papis_extract.extractors import pdf, readera, readest from papis_extract.extractors.pocketbook import PocketBookExtractor logger = papis.logging.get_logger(__name__) @@ -12,6 +12,7 @@ all_extractors: dict[str, Extractor] = {} all_extractors["pdf"] = pdf.PdfExtractor() all_extractors["readera"] = readera.ReadEraExtractor() +all_extractors["readest"] = readest.ReadestExtractor() if find_spec("bs4") and find_spec("magic"): all_extractors["pocketbook"] = PocketBookExtractor() diff --git a/papis_extract/extractors/readest.py b/papis_extract/extractors/readest.py new file mode 100644 index 0000000..1d0df08 --- /dev/null +++ b/papis_extract/extractors/readest.py @@ -0,0 +1,78 @@ +# pyright: strict, reportUnknownMemberType=false +import re +from pathlib import Path + +import magic +import papis.logging + +from papis_extract.annotation import Annotation + +logger = papis.logging.get_logger(__name__) + + +class ReadestExtractor: + """Extracts exported annotations from the FOSS Readest book reading app. + + https://readest.com/ + """ + + def can_process(self, filename: Path) -> bool: + if magic.from_file(filename, mime=True) != "text/plain": + return False + + content = self._read_file(filename) + if not content: + return False + + # look for star-shaped divider pattern + if not re.search( + r"\n\*\*Exported from Readest\*\*: \d{4}-\d{2}-\d{2}\n", "".join(content) + ): + return False + + logger.debug(f"Found processable annotation file: {filename}") + return True + + def run(self, filename: Path) -> list[Annotation]: + """Extract annotations from readest txt file. + + Returns all readable annotations contained in the file passed in, with + highlights and notes if available. + """ + content = self._read_file(filename)[2:] + if not content: + return [] + + annotations: list[Annotation] = [] + + for i, line in enumerate(content): + entry_content: str = "" + entry_note: str = "" + if line.startswith("> "): + entry_content = line.lstrip('> "').rstrip('\n" ') + nextline = content[i + 1] + if nextline.startswith("**Note**:: "): + entry_note = nextline.removeprefix("**Note**:: ").strip() + + a = Annotation( + file=str(filename), + content=entry_content, + note=entry_note, + # NOTE: Unfortunately Readest currently does not export color information + # color=color, + ) + annotations.append(a) + + logger.debug( + f"Found {len(annotations)} " + f"{'annotation' if len(annotations) == 1 else 'annotations'} for {filename}." + ) + return annotations + + def _read_file(self, filename: Path) -> list[str]: + try: + with filename.open("r") as fr: + return fr.readlines() + except FileNotFoundError: + logger.error(f"Could not open file {filename} for extraction.") + return [] From 17c6fefd897c52dc64fdfc2c1b534395079fd83d Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Thu, 11 Sep 2025 23:28:47 +0200 Subject: [PATCH 096/107] chore: Remove unnecessary imports --- papis_extract/exporter.py | 5 ----- papis_extract/extraction.py | 2 -- 2 files changed, 7 deletions(-) diff --git a/papis_extract/exporter.py b/papis_extract/exporter.py index 13fe082..5cb0221 100644 --- a/papis_extract/exporter.py +++ b/papis_extract/exporter.py @@ -1,13 +1,8 @@ from dataclasses import dataclass from typing import Protocol -import papis.api -import papis.commands.edit -import papis.config import papis.document -import papis.git import papis.logging -import papis.notes from papis_extract.annotation import Annotation from papis_extract.formatter import Formatter diff --git a/papis_extract/extraction.py b/papis_extract/extraction.py index 19c4ccc..139aabf 100644 --- a/papis_extract/extraction.py +++ b/papis_extract/extraction.py @@ -1,8 +1,6 @@ from pathlib import Path from typing import Protocol -import papis.config -import papis.document import papis.logging from papis.document import Document From 1a4b5e3a70888426da262dc80b39488cc6a1ffdc Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Fri, 12 Sep 2025 09:47:41 +0200 Subject: [PATCH 097/107] chore: Remove python-magic dependency It relies on the libmagic module which is not necessarily installed everywhere. Most of the functionality that we need for our purposes can be recreated with lighter-weight methods. --- papis_extract/extractors/pdf.py | 4 ++-- papis_extract/extractors/pocketbook.py | 7 +++++-- papis_extract/extractors/readera.py | 11 ++++++----- papis_extract/extractors/readest.py | 22 ++++++++++++++++++++-- pyproject.toml | 1 - 5 files changed, 33 insertions(+), 12 deletions(-) diff --git a/papis_extract/extractors/pdf.py b/papis_extract/extractors/pdf.py index 3ba9873..d161229 100644 --- a/papis_extract/extractors/pdf.py +++ b/papis_extract/extractors/pdf.py @@ -1,10 +1,10 @@ # pyright: strict, reportMissingTypeStubs=false, reportUnknownMemberType=false +import mimetypes from collections.abc import Generator from pathlib import Path from typing import NamedTuple, cast import Levenshtein -import magic import papis.config import papis.logging import pymupdf as mu @@ -77,7 +77,7 @@ class PdfExtractor: def _is_pdf(self, fname: Path) -> bool: """Check if file is a pdf, using mime type.""" - return magic.from_file(fname, mime=True) == "application/pdf" + return mimetypes.guess_type(fname)[0] == "application/pdf" def _get_annotation_content( self, page: mu.Page, annotation: mu.Annot diff --git a/papis_extract/extractors/pocketbook.py b/papis_extract/extractors/pocketbook.py index 5fc0585..928aad1 100644 --- a/papis_extract/extractors/pocketbook.py +++ b/papis_extract/extractors/pocketbook.py @@ -1,7 +1,7 @@ # pyright: strict, reportUnknownMemberType=false +import mimetypes from pathlib import Path -import magic import papis.logging from bs4 import BeautifulSoup @@ -12,7 +12,7 @@ logger = papis.logging.get_logger(__name__) class PocketBookExtractor: def can_process(self, filename: Path) -> bool: - if magic.from_file(filename, mime=True) != "text/xml": + if not self._is_html(filename): return False content = self._read_file(filename) @@ -28,6 +28,9 @@ class PocketBookExtractor: logger.debug(f"Found processable annotation file: {filename}") return True + def _is_html(self, filename: Path) -> bool: + return mimetypes.guess_type(filename)[0] == "text/html" + def run(self, filename: Path) -> list[Annotation]: """Extract annotations from pocketbook html file. diff --git a/papis_extract/extractors/readera.py b/papis_extract/extractors/readera.py index d992512..c8905fe 100644 --- a/papis_extract/extractors/readera.py +++ b/papis_extract/extractors/readera.py @@ -1,8 +1,8 @@ # pyright: strict, reportUnknownMemberType=false +import mimetypes import re from pathlib import Path -import magic import papis.logging from papis_extract.annotation import Annotation @@ -17,7 +17,7 @@ class ReadEraExtractor: """ def can_process(self, filename: Path) -> bool: - if magic.from_file(filename, mime=True) != "text/plain": + if not self._is_txt(filename): return False content = self._read_file(filename) @@ -36,11 +36,12 @@ class ReadEraExtractor: if not re.search(r"\n\*\*\*\*\*\n\n$", "".join(content)): return False - logger.debug( - f"Found processable annotation file: {filename}" - ) + logger.debug(f"Found processable annotation file: {filename}") return True + def _is_txt(self, filename: Path) -> bool: + return mimetypes.guess_type(filename)[0] == "text/plain" + def run(self, filename: Path) -> list[Annotation]: """Extract annotations from readera txt file. diff --git a/papis_extract/extractors/readest.py b/papis_extract/extractors/readest.py index 1d0df08..f387721 100644 --- a/papis_extract/extractors/readest.py +++ b/papis_extract/extractors/readest.py @@ -2,13 +2,15 @@ import re from pathlib import Path -import magic import papis.logging from papis_extract.annotation import Annotation logger = papis.logging.get_logger(__name__) +ACCEPTED_EXTENSIONS = [".txt", ".md", ".qmd", ".rmd"] +TEXTCHARS = bytearray({7, 8, 9, 10, 12, 13, 27} | set(range(0x20, 0x100)) - {0x7F}) + class ReadestExtractor: """Extracts exported annotations from the FOSS Readest book reading app. @@ -17,7 +19,7 @@ class ReadestExtractor: """ def can_process(self, filename: Path) -> bool: - if magic.from_file(filename, mime=True) != "text/plain": + if not self._is_readable_text(filename): return False content = self._read_file(filename) @@ -33,6 +35,22 @@ class ReadestExtractor: logger.debug(f"Found processable annotation file: {filename}") return True + def _is_readable_text(self, filename: Path) -> bool: + """Checks whether a file has a valid text extension and is not a binary file. + + A file is considered a valid text file if its extension is in + :data:`ACCEPTED_EXTENSIONS` and does not contain any non-text characters. + + :returns: A boolean indicating whether the file is a valid text file. + """ + if filename.suffix not in ACCEPTED_EXTENSIONS: + return False + try: + with filename.open("rb") as rb: + return not bool(rb.read(1024).translate(None, TEXTCHARS)) + except (FileNotFoundError, PermissionError): + return False + def run(self, filename: Path) -> list[Annotation]: """Extract annotations from readest txt file. diff --git a/pyproject.toml b/pyproject.toml index f9fc3c1..bf39ddf 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -22,7 +22,6 @@ keywords = [ "bibliography", "reference manager", "research", - "science", ] [project.urls] From ecb999a49eaa4b7fc2aff751a32a62de9e9493cb Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Fri, 12 Sep 2025 10:19:49 +0200 Subject: [PATCH 098/107] chore: Formatting for ruff check --- tests/test_formatting.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/test_formatting.py b/tests/test_formatting.py index 27eb702..7c4b381 100644 --- a/tests/test_formatting.py +++ b/tests/test_formatting.py @@ -1,6 +1,6 @@ from papis.document import Document -from papis_extract.annotation import Annotation +from papis_extract.annotation import Annotation from papis_extract.formatter import ( format_count, format_csv, From ff6cdf3ccaf01a81c59d0d336340eac93ff33dac Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Fri, 12 Sep 2025 10:19:49 +0200 Subject: [PATCH 099/107] ci: Update woodpecker ci to use uv images --- .woodpecker/lint.yml | 18 +++++++++--------- .woodpecker/static_analysis.yml | 8 ++++---- .woodpecker/test.yml | 6 +++--- 3 files changed, 16 insertions(+), 16 deletions(-) diff --git a/.woodpecker/lint.yml b/.woodpecker/lint.yml index 4400de4..3601016 100644 --- a/.woodpecker/lint.yml +++ b/.woodpecker/lint.yml @@ -1,16 +1,16 @@ steps: lint_ruff: - image: python + image: ghcr.io/astral-sh/uv:python3.11-trixie-slim commands: - - pip install ruff - - python --version && poetry --version && ruff --version + - uv tool install ruff + - python --version && uv --version && ruff --version - echo "----------------- running ruff lint ------------------" - ruff check . - lint_black: - image: python + format_ruff: + image: ghcr.io/astral-sh/uv:python3.11-trixie-slim commands: - - pip install black - - python --version && poetry --version && black --version - - echo "----------------- running black lint ----------------" - - black --check . + - uv tool install ruff + - python --version && uv --version && ruff --version + - echo "----------------- running ruff format ------------------" + - ruff format --check . diff --git a/.woodpecker/static_analysis.yml b/.woodpecker/static_analysis.yml index 5244d3a..037007b 100644 --- a/.woodpecker/static_analysis.yml +++ b/.woodpecker/static_analysis.yml @@ -1,9 +1,9 @@ steps: pyright: - image: nikolaik/python-nodejs + image: ghcr.io/astral-sh/uv:python3.11-trixie-slim commands: - 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a/.woodpecker/lint.yml +++ b/.woodpecker/lint.yml @@ -1,3 +1,6 @@ +when: + - event: push + steps: lint_ruff: image: ghcr.io/astral-sh/uv:python3.11-trixie-slim diff --git a/.woodpecker/static_analysis.yml b/.woodpecker/static_analysis.yml index 037007b..95bf928 100644 --- a/.woodpecker/static_analysis.yml +++ b/.woodpecker/static_analysis.yml @@ -1,3 +1,6 @@ +when: + - event: push + steps: pyright: image: ghcr.io/astral-sh/uv:python3.11-trixie-slim diff --git a/.woodpecker/test.yml b/.woodpecker/test.yml index b8d5947..3315ac4 100644 --- a/.woodpecker/test.yml +++ b/.woodpecker/test.yml @@ -1,5 +1,5 @@ when: - branch: main + - event: push steps: pytest: From 81f8690b184612a4da873e2efa46a70bd55d8cd8 Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Fri, 12 Sep 2025 13:25:42 +0200 Subject: [PATCH 103/107] docs: Extract ROADMAP from README --- README.md | 49 ------------------------------------------------- ROADMAP | 49 +++++++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 49 insertions(+), 49 deletions(-) create mode 100644 ROADMAP diff --git a/README.md b/README.md index 45a9b88..0772665 100644 --- a/README.md +++ b/README.md @@ -220,55 +220,6 @@ Then import the resulting `.html` file into the library like any other document (or `papis addto` to add it to existing document references). You are then ready to use extract to get those annotations from the exported list into your notes. -## TODO: Roadmap to first release - -Known issues to be fixed: - -- [x] if both content and text are empty, do not extract an annotation -- [x] Speed? - - should be fine, on my machine (old i5 laptop) it takes around 90s for ~1000 documents with ~4000 annotations -- [x] ensure all cmdline options do what they should -- [x] annotations carry over color object from fitz, should just be Color object or simple tuple with rgb vals -- [x] docstrings, docstrings! -- [ ] testing testing testing!! - - [ ] refactor into some better abstractions (e.g. Exporter Protocol -> stdout/markdown implementations; Extractor Protocol -> PDF implementation) -- [ ] dependency injection for extractor/exporter/formatter/annotation modules - - [ ] any call to papis.config should start from init and be injected? - -features to be implemented: - -- [ ] CICD - - [x] static analysis (lint, typecheck etc) on pushes - - [x] test pipeline on master pushes - - [ ] release pipeline to pypi on tags -- [x] add page number if available - - exists in Annotation, just need to place in output -- [ ] show overall amount of extractions at the end - - implemented for writing to notes (notes exporter) - - KNOWN ISSUE: currently returns number of annotation rows (may be multiple per annot) -- [ ] custom formatting decided by user - - in config as { "myformatter": ">{tag}\n{quote}\n{note}\n{page} etc"} -- [ ] improved default exporters - - [x] markdown into notes - - [ ] pretty display on stdout (rich?) - - [x] csv/tsv to stdout - - [ ] table fmt stdout? -- [ ] allow custom colors -> tag name settings not dependent on color name existing (e.g. {"important": (1.0,0.0,0.0)}) -- [ ] `--overwrite` mode where existing annotations are not dropped but overwritten on same line of note -- [x] `--force` mode where we simply do not drop anything -- [x] `--format` option to choose from default or set up a custom formatter - - called `--output` in current implementation -- [ ] on_add hook to extract annotations as files are added - - needs upstream help, 'on_add' hook, and pass-through of affected documents -- [ ] target same minimum Python version as papis upstream (3.8 as of papis 0.13) -- [ ] change detection: - - how does it handle updated citations? updated colors? should it be configurable? - -upstream changes: - -- [ ] need a hook for adding a document/file -- [ ] need hooks to actually pass through information on the thing they worked on (i.e. their document) - ## Issues First, a note in general: There is the functionality to run this plugin over your whole library in a single command and also in a way that makes permanent changes to that library. diff --git a/ROADMAP b/ROADMAP new file mode 100644 index 0000000..77b6160 --- /dev/null +++ b/ROADMAP @@ -0,0 +1,49 @@ +# ROADMAP to first release + +Known issues to be fixed: + +- [x] if both content and text are empty, do not extract an annotation +- [x] Speed? + - should be fine, on my machine (old i5 laptop) it takes around 90s for ~1000 documents with ~4000 annotations +- [x] ensure all cmdline options do what they should +- [x] annotations carry over color object from fitz, should just be Color object or simple tuple with rgb vals +- [x] docstrings, docstrings! +- [ ] testing testing testing!! + - [ ] refactor into some better abstractions (e.g. Exporter Protocol -> stdout/markdown implementations; Extractor Protocol -> PDF implementation) +- [ ] dependency injection for extractor/exporter/formatter/annotation modules + - [ ] any call to papis.config should start from init and be injected? + +features to be implemented: + +- [ ] CICD + - [x] static analysis (lint, typecheck etc) on pushes + - [x] test pipeline on master pushes + - [ ] release pipeline to pypi on tags +- [x] add page number if available + - exists in Annotation, just need to place in output +- [ ] show overall amount of extractions at the end + - implemented for writing to notes (notes exporter) + - KNOWN ISSUE: currently returns number of annotation rows (may be multiple per annot) +- [ ] custom formatting decided by user + - in config as { "myformatter": ">{tag}\n{quote}\n{note}\n{page} etc"} +- [ ] improved default exporters + - [x] markdown into notes + - [ ] pretty display on stdout (rich?) + - [x] csv/tsv to stdout + - [ ] table fmt stdout? +- [ ] allow custom colors -> tag name settings not dependent on color name existing (e.g. {"important": (1.0,0.0,0.0)}) +- [ ] `--overwrite` mode where existing annotations are not dropped but overwritten on same line of note +- [x] `--force` mode where we simply do not drop anything + - called `--duplicates` in current implementation +- [x] `--format` option to choose from default or set up a custom formatter + - called `--output` in current implementation +- [ ] on_add hook to extract annotations as files are added + - needs upstream help, 'on_add' hook, and pass-through of affected documents +- [ ] target same minimum Python version as papis upstream (3.8 as of papis 0.14, 3.10 for upcoming papis ~0.15) +- [ ] change detection: + - how does it handle updated citations? updated colors? should it be configurable? + +upstream changes: + +- [ ] need a hook for adding a document/file +- [ ] need hooks to actually pass through information on the thing they worked on (i.e. their document) From 9e88054736472966764601a018b38144ee6b5f6c Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Wed, 10 Sep 2025 22:27:05 +0200 Subject: [PATCH 104/107] test: Update local papisconf used for manual testing --- .papis.config | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/.papis.config b/.papis.config index 5e61770..5f55f09 100644 --- a/.papis.config +++ b/.papis.config @@ -1,7 +1,12 @@ [settings] default-library = main picktool = papis -formater = python +formatter = python [main] +database-backend = whoosh +use-cache = False dir = temp/lib + +[plugins.extract] +tags = {"red": 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00:00:00 2001 From: Marty Oehme Date: Fri, 12 Sep 2025 13:34:59 +0200 Subject: [PATCH 106/107] docs: Format README --- README.md | 30 ++++++++++++++++-------------- 1 file changed, 16 insertions(+), 14 deletions(-) diff --git a/README.md b/README.md index 0772665..4216956 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,7 @@ # papis-extract [![status-badge](https://ci.martyoeh.me/api/badges/Marty/papis-extract/status.svg)](https://ci.martyoeh.me/Marty/papis-extract) + @@ -11,6 +12,7 @@ Easily organize all your highlights and thoughts next to your documents and refe ## Installation + You can install through pip with `pip install git+https://git.martyoeh.me/Marty/papis-extract.git`. That's it! If you have papis and papis-extract installed in the same environment (whether virtual or global), @@ -26,7 +28,7 @@ You will be set up with the default options but if you want to change anything, > **Note** > This plugin is still in fairly early development. -> It does what I need it to do, but if you have a meticulously organized library *please* make backups before doing any operation which could affect your notes, or make use of the papis-included git options. +> It does what I need it to do, but if you have a meticulously organized library _please_ make backups before doing any operation which could affect your notes, or make use of the papis-included git options. > Take care to read the Issues section of this README if you intend to run it over a large collection. ## Usage @@ -66,7 +68,7 @@ use `--all` as usual with papis: papis extract --all "author:Einstein" ``` -The above command will print out your annotations made on *all* papers by Einstein. +The above command will print out your annotations made on _all_ papers by Einstein. You can invoke the command with `--manual` to instantly edit the notes in your editor: @@ -85,7 +87,7 @@ papis extract --write --all ``` However, the warning for your notes' safety goes doubly for this command since it will touch -*most* or *all* of your notes, depending on how many entries in your library have pdfs with annotations attached. +_most_ or _all_ of your notes, depending on how many entries in your library have pdfs with annotations attached. While I have not done extensive optimizations the process should be relatively quick even for larger libraries: On my current laptop, extracting ~4000 annotations from ~1000 library documents takes around 90 seconds, @@ -116,7 +118,7 @@ papis extract --output count For now, these are the only formatters the plugin knows about. -Be aware that if you re-write to your notes using a completely different output format than the original the plugin will *not* detect old annotations and drop them, +Be aware that if you re-write to your notes using a completely different output format than the original the plugin will _not_ detect old annotations and drop them, so you will be doubling up your annotations. See the `minimum_similarity` configuration option for more details. @@ -150,7 +152,7 @@ If you set `on_import` to `True`, extraction into notes is automatically run whenever a new document is added to the library, if `False` extraction only happens when you explicitly invoke it. -Extraction will *not* happen automatically when you add new annotations to an existing document, +Extraction will _not_ happen automatically when you add new annotations to an existing document, regardless of this setting. > **Note** @@ -190,11 +192,11 @@ Generally, this should be fine as it is but you should change this value if you --- -`minimum_similarity_content` sets the required similarity of an annotation's note and in-pdf written words to be viewed as one. Any annotation that has both and is *under* the minimum similarity will be added in the following form: +`minimum_similarity_content` sets the required similarity of an annotation's note and in-pdf written words to be viewed as one. Any annotation that has both and is _under_ the minimum similarity will be added in the following form: ```markdown > my annotation -Note: my additional thoughts +> Note: my additional thoughts ``` That is, the extractor detects additional written words by whoever annotated and adds them to the extraction. @@ -232,12 +234,12 @@ A note on the extraction: Highlights in pdfs can be somewhat difficult to parse (as are most things in them). Sometimes they contain the selected text that is written on the page, sometimes they contain the annotators thoughts as a note, sometimes they contain nothing. This plugin makes an effort to find the right combination and extract the written words, -as well as any additional notes made - but things *will* slip through or extract weirdly every now +as well as any additional notes made - but things _will_ slip through or extract weirdly every now and again. Secondly, a note on the pages: I use the page number that the mupdf library gives me when it extracts anything from the pdf file. Sometimes that number will be correct for the document, -sometimes it will however be the number of the *pdf document* internally. This can happen if +sometimes it will however be the number of the _pdf document_ internally. This can happen if e.g. an article or a book has frontmatter without numbering scheme or with a different one. Sometimes the correct pages will still be embedded in the pdf and everything will work, others it won't. So always double check your page numbers! @@ -249,19 +251,19 @@ I am not sure if there is much I can do about these issues for now. and for myself whenever I forget. The basic building blocks currently in here are three: - extractors (= input format) -: Extract data from a source file attached to a papis document. + : Extract data from a source file attached to a papis document. Crawls the actual files attached to documents to put them into annotation-friendly formats. - formatters (= output format) -: Make sure the exporter saves the annotation data according to your preferred layout, + : Make sure the exporter saves the annotation data according to your preferred layout, such as a markdown syntax or csv-structure. - annotations -: The actual extracted blocks of text, containing some metadata + : The actual extracted blocks of text, containing some metadata info as well, such as their color, type, page. - exporters -: Put the extracted data somewhere. For now stdout or into your notes. + : Put the extracted data somewhere. For now stdout or into your notes. Splitting it into those building blocks makes it easier to recombine them in any way, should someone want to save highlights as csv data in their notes, @@ -280,7 +282,7 @@ However, what I do on my system instead to enable quick testing is inject it int system-wide (but isolated with `pipx`) papis setup: ```bash -pipx install papis # create an isolated papis installation reachable form anywhere +pipx install papis # create an isolated papis installation reachable form anywhere pipx inject --editable papis . # inject this folder into the environment and keep up with any changes ``` From 15606b293f200855e608d3e7676f5dd768c81274 Mon Sep 17 00:00:00 2001 From: Marty Oehme Date: Fri, 12 Sep 2025 15:26:13 +0200 Subject: [PATCH 107/107] test: Ignore swig 4.3 deprecation warnings in pytest --- pyproject.toml | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/pyproject.toml b/pyproject.toml index 27c5743..77b630a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -62,3 +62,11 @@ build-backend = "hatchling.build" [tool.pyright] typeCheckingMode = "strict" + +[tool.pytest.ini_options] +filterwarnings = [ + # see https://github.com/swig/swig/issues/2881#issuecomment-2877988848 + # should hopefully be redundant with swig-4.4 + "ignore:.*builtin type SwigPy\\w* has no __module__ attribute.*:DeprecationWarning", + "ignore:.*builtin type swigvarlink has no __module__ attribute.*:DeprecationWarning" +]