initial commit

.gitignore

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+/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

papis_extract/__init__.py

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+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

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]

papis_extract/exporter.py

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+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

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, "")

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. Open, modern and actively maintained alternative to Chardet."
+optional = false
+python-versions = ">=3.7.0"
+files = [
+    {file = "charset-normalizer-3.2.0.tar.gz", hash = "sha256:3bb3d25a8e6c0aedd251753a79ae98a093c7e7b471faa3aa9a93a81431987ace"},
+    {file = "charset_normalizer-3.2.0-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:0b87549028f680ca955556e3bd57013ab47474c3124dc069faa0b6545b6c9710"},
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pyproject.toml

@@ -0,0 +1,23 @@
+[tool.poetry]
+name = "papis-extract"
+version = "0.1.0"
+description = ""
+authors = ["Marty Oehme <marty.oehme@gmail.com>"]
+readme = "README.md"
+packages = [{include = "papis_extract"}]
+
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+levenshtein = "^0.21.1"
+papis = "^0.13"
+click = "^8.1.7"
+whoosh = "^2.7.4"
+python-magic = "^0.4.27"
+
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+extract = "papis_extract:main"
+
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+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"