commit a22cc635b2c784e7e66372e641490c179670d8ee Author: Marty Oehme Date: Mon Aug 28 10:28:06 2023 +0200 initial commit diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..56951dd --- /dev/null +++ b/.gitignore @@ -0,0 +1,230 @@ +/temp/ + +# Created by https://www.toptal.com/developers/gitignore/api/-f,python,linux,vim,quarto,markdown,jupyternotebooks +# Edit at https://www.toptal.com/developers/gitignore?templates=-f,python,linux,vim,quarto,markdown,jupyternotebooks + +#!! ERROR: -f is undefined. Use list command to see defined gitignore types !!# + +### JupyterNotebooks ### +# gitignore template for Jupyter Notebooks +# website: http://jupyter.org/ + +.ipynb_checkpoints +*/.ipynb_checkpoints/* + +# IPython +profile_default/ +ipython_config.py + +# Remove previous ipynb_checkpoints +# git rm -r .ipynb_checkpoints/ + +### Linux ### +*~ + +# temporary files which can be created if a process still has a handle open of a deleted file +.fuse_hidden* + +# KDE directory preferences +.directory + +# Linux trash folder which might appear on any partition or disk +.Trash-* + +# .nfs files are created when an open file is removed but is still being accessed +.nfs* + +#!! ERROR: markdown is undefined. Use list command to see defined gitignore types !!# + +### Python ### +# Byte-compiled / optimized / DLL files +__pycache__/ +*.py[cod] +*$py.class + +# C extensions +*.so + +# Distribution / packaging +.Python +build/ +develop-eggs/ +dist/ +downloads/ +eggs/ +.eggs/ +lib/ +lib64/ +parts/ +sdist/ +var/ +wheels/ +share/python-wheels/ +*.egg-info/ +.installed.cfg +*.egg +MANIFEST + +# PyInstaller +# Usually these files are written by a python script from a template +# before PyInstaller builds the exe, so as to inject date/other infos into it. +*.manifest +*.spec + +# Installer logs +pip-log.txt +pip-delete-this-directory.txt + +# Unit test / coverage reports +htmlcov/ +.tox/ +.nox/ +.coverage +.coverage.* +.cache +nosetests.xml +coverage.xml +*.cover +*.py,cover +.hypothesis/ +.pytest_cache/ +cover/ + +# Translations +*.mo +*.pot + +# Django stuff: +*.log +local_settings.py +db.sqlite3 +db.sqlite3-journal + +# Flask stuff: +instance/ +.webassets-cache + +# Scrapy stuff: +.scrapy + +# Sphinx documentation +docs/_build/ + +# PyBuilder +.pybuilder/ +target/ + +# Jupyter Notebook + +# IPython + +# pyenv +# For a library or package, you might want to ignore these files since the code is +# intended to run in multiple environments; otherwise, check them in: +# .python-version + +# pipenv +# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. +# However, in case of collaboration, if having platform-specific dependencies or dependencies +# having no cross-platform support, pipenv may install dependencies that don't work, or not +# install all needed dependencies. +#Pipfile.lock + +# poetry +# Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control. +# This is especially recommended for binary packages to ensure reproducibility, and is more +# commonly ignored for libraries. +# https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control +#poetry.lock + +# pdm +# Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control. +#pdm.lock +# pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it +# in version control. +# https://pdm.fming.dev/#use-with-ide +.pdm.toml + +# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm +__pypackages__/ + +# Celery stuff +celerybeat-schedule +celerybeat.pid + +# SageMath parsed files +*.sage.py + +# Environments +.env +.venv +env/ +venv/ +ENV/ +env.bak/ +venv.bak/ + +# Spyder project settings +.spyderproject +.spyproject + +# Rope project settings +.ropeproject + +# mkdocs documentation +/site + +# mypy +.mypy_cache/ +.dmypy.json +dmypy.json + +# Pyre type checker +.pyre/ + +# pytype static type analyzer +.pytype/ + +# Cython debug symbols +cython_debug/ + +# PyCharm +# JetBrains specific template is maintained in a separate JetBrains.gitignore that can +# be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore +# and can be added to the global gitignore or merged into this file. For a more nuclear +# option (not recommended) you can uncomment the following to ignore the entire idea folder. +#.idea/ + +### Python Patch ### +# Poetry local configuration file - https://python-poetry.org/docs/configuration/#local-configuration +poetry.toml + +# ruff +.ruff_cache/ + +# LSP config files +pyrightconfig.json + +#!! ERROR: quarto is undefined. Use list command to see defined gitignore types !!# + +### Vim ### +# Swap +[._]*.s[a-v][a-z] +!*.svg # comment out if you don't need vector files +[._]*.sw[a-p] +[._]s[a-rt-v][a-z] +[._]ss[a-gi-z] +[._]sw[a-p] + +# Session +Session.vim +Sessionx.vim + +# Temporary +.netrwhist +# Auto-generated tag files +tags +# Persistent undo +[._]*.un~ + +# End of https://www.toptal.com/developers/gitignore/api/-f,python,linux,vim,quarto,markdown,jupyternotebooks diff --git a/README.md b/README.md new file mode 100644 index 0000000..e69de29 diff --git a/papis_extract/__init__.py b/papis_extract/__init__.py new file mode 100644 index 0000000..cd19bc8 --- /dev/null +++ b/papis_extract/__init__.py @@ -0,0 +1,125 @@ +from pathlib import Path + +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_extract import extractor, exporter +from papis_extract.annotation_data import Annotation, AnnotatedDocument + +logger = papis.logging.get_logger(__name__) + +DEFAULT_OPTIONS = { + "plugins.extract": { + "tags": {"important": "red", "toread": "blue"}, + "on_import": False, + "minimum_similarity": 0.75, # for checking against existing annotations + "minimum_similarity_content": 0.9, # for checking if highlight or note + "minimum_similarity_color": 0.833 # for matching tag to color + } +} +papis.config.register_default_settings(DEFAULT_OPTIONS) + + +@click.command("extract") +@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.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", +) +def main( + query: str, + # info: bool, + # _papis_id: bool, + # _file: bool, + # notes: bool, + # _dir: bool, + # _format: str, + _all: bool, + doc_folder: str, + manual: bool, + write: bool, + git: bool, +) -> None: + """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. + 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. + """ + documents = papis.cli.handle_doc_folder_query_all_sort( + query, doc_folder, sort_field=None, sort_reverse=False, _all=_all + ) + if not documents: + logger.warning(papis.strings.no_documents_retrieved_message) + return + + doc_annotations: list[AnnotatedDocument] = _get_annotations_for_documents(documents) + + if write: + exporter.to_notes(doc_annotations, edit=manual, 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: + logger.warning( + "Did not find suitable PDF file for document: " + f"{papis.document.describe(doc)}" + ) + 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/annotation_data.py b/papis_extract/annotation_data.py new file mode 100644 index 0000000..3036ff1 --- /dev/null +++ b/papis_extract/annotation_data.py @@ -0,0 +1,98 @@ +import re +import math +from dataclasses import dataclass, field + +import papis.config +from papis.document import Document + +TEXT_SIMILARITY_MINIMUM = 0.75 +COLOR_SIMILARITY_MINIMUM = 0.833 + +COLORS = { + "red": (1, 0, 0), + "green": (0, 1, 0), + "blue": (0, 0, 1), + "yellow": (1, 1, 0), + "purple": (0.5, 0, 0.5), + "orange": (1, 0.65, 0), +} + + +@dataclass +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)}) + tag: str = "" + + def format(self, formatting): + """Return a formatted string of the annotation. + + Given a provided formatting pattern, this method returns the 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, + } + 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) + + @property + def colorname(self): + """Return the stringified version of the annotation color. + + Finds the closest named color to the annotation and returns it, + 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) + ) + nearest = None + minimum_similarity = ( + papis.config.getfloat("minimum_similarity_color", "plugins.extract") + or 1.0 + ) + for name, values in COLORS.items(): + similarity_ratio = self._color_similarity_ratio(values, annot_colors) + if similarity_ratio > minimum_similarity: + minimum_similarity = similarity_ratio + nearest = name + return nearest + + def _color_similarity_ratio(self, color_one, color_two): + """Return the similarity of two colors between 0 and 1. + + Takes two rgb color tuples made of floats between 0 and 1, + e.g. (1, 0.65, 0) for orange, and returns the similarity + between them, with 1 being the same color and 0 being the + difference between full black and full white, as a float. + """ + return 1 - (abs(math.dist([*color_one], [*color_two])) / 3) + + +@dataclass +class AnnotatedDocument: + document: Document + annotations: list[Annotation] diff --git a/papis_extract/exporter.py b/papis_extract/exporter.py new file mode 100644 index 0000000..cb5c883 --- /dev/null +++ b/papis_extract/exporter.py @@ -0,0 +1,128 @@ +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_data import AnnotatedDocument, Annotation + +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: + if not annots: + return + + for entry in annots: + if not entry.annotations: + continue + + title_decoration = "=" * len(entry.document.get("title", "")) + print( + f"{title_decoration}\n{papis.document.describe(entry.document)}\n{title_decoration}\n" + ) + for a in entry.annotations: + print(_format_annotation(a)) + print("\n") + + +def to_notes(annots: 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. + """ + 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(_format_annotation(a)) + + _add_annots_to_note(entry.document, formatted_annotations) + + if edit: + papis.commands.edit.edit_notes(entry.document, git=git) + + +def _add_annots_to_note( + document: papis.document.Document, + formatted_annotations: list[str], + git: bool = False, +) -> None: + """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. + """ + 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] = _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".join(new_annotations)) + f.write("\n") + logger.info( + f"Wrote {len(new_annotations)} annotations "\ + 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]: + 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 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 diff --git a/papis_extract/extractor.py b/papis_extract/extractor.py new file mode 100644 index 0000000..e9a1451 --- /dev/null +++ b/papis_extract/extractor.py @@ -0,0 +1,66 @@ +from pathlib import Path + +import Levenshtein +import fitz_new as fitz +import papis.config + +from papis_extract.annotation_data import Annotation + +COLOR_MAPPING = {} + + +def start(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) + a = Annotation( + file=str(filename), + text=quote, + content=note, + colors=annot.colors, + type=annot.type[1], + page=(page.number or 0) + 1, + ) + a.tag = _tag_from_colorname(a.colorname) + annotations.append(a) + return annotations + + +def _tag_from_colorname(colorname): + return COLOR_MAPPING.get(colorname, "") + + +def _retrieve_annotation_content(page, annotation): + """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, "") + # an independent note, not a highlight + elif content and not written: + return ("", content) + # both a highlight and a note + elif content: + return (written, content) + # highlight with selection not in note + return (written, "") diff --git a/poetry.lock b/poetry.lock new file mode 100644 index 0000000..e225e20 --- /dev/null +++ b/poetry.lock @@ -0,0 +1,926 @@ +# This file is automatically @generated by Poetry 1.5.1 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 = "4.12.2" +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"}, +] + +[package.dependencies] +soupsieve = ">1.2" + +[package.extras] +html5lib = ["html5lib"] +lxml = ["lxml"] + +[[package]] +name = "bibtexparser" +version = "1.4.0" +description = "Bibtex parser for python 3" +optional = false +python-versions = "*" +files = [ + {file = "bibtexparser-1.4.0.tar.gz", hash = "sha256:ca7ce2bc34e7c48a678dd49416429bb567441f26dbb13b3609082d8cd109ace6"}, +] + +[package.dependencies] +pyparsing = ">=2.0.3" + +[[package]] +name = "certifi" +version = "2023.7.22" +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"}, +] + +[[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 = "3.2.0" +description = "The Real First Universal Charset Detector. 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