initial commit

.gitignore

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+# Created by https://www.toptal.com/developers/gitignore/api/python,linux,vim
+# Edit at https://www.toptal.com/developers/gitignore?templates=python,linux,vim
+
+### 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*
+
+### 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
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# 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
+
+
+### 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/python,linux,vim

extract/extract.py

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+import os
+import sys
+import argparse
+from typing import Dict, List, Tuple
+
+# from subprocess import Popen, PIPE, STDOUT
+# from pipes import quote as shell_quote
+
+import fitz
+
+# from ... import uis
+from ...plugins import PapersPlugin
+from ...events import PaperChangeEvent, PostCommandEvent
+
+from ... import repo
+from ...utils import resolve_citekey_list
+from ...filebroker import DocBroker
+
+
+class ExtractPlugin(PapersPlugin):
+    """Make the pubs repository also a git repository.
+
+    The git plugin creates a git repository in the pubs directory
+    and commit the changes to the pubs repository.
+
+    It also add the `pubs git` subcommand, so git commands can be executed
+    in the git repository from the command line.
+    """
+
+    name = "extract"
+    description = "Extract annotations from pubs documents"
+
+    def __init__(self, conf, ui):
+        pass
+        self.ui = ui
+        self.pubsdir = os.path.expanduser(conf["main"]["pubsdir"])
+        self.broker = DocBroker(self.pubsdir)
+        self.repository = repo.Repository(conf)
+        self.quiet = conf["plugins"].get("extract", {}).get("quiet", False)
+        # self.manual = conf['plugins'].get('git', {}).get('manual', False)
+        # self.force_color = conf['plugins'].get('git', {}).get('force_color', True)
+        # self.list_of_changes = []
+
+    def update_parser(self, subparsers, conf):
+        """Allow the usage of the pubs git subcommand"""
+        # TODO option for quiet/loud mode.
+        # TODO option for ignoring missing documents or erroring.
+        # TODO option for writing to stdout or notes
+        extract_parser = subparsers.add_parser(self.name, help=self.description)
+        extract_parser.add_argument(
+            "citekeys",
+            nargs=argparse.REMAINDER,
+            help="citekey(s) of the documents to extract from",
+        )
+        extract_parser.set_defaults(func=self.command)
+
+    def command(self, conf, args):
+        """Run the annotation extraction"""
+        citekeys = resolve_citekey_list(
+            self.repository, conf, args.citekeys, ui=self.ui, exit_on_fail=True
+        )
+        if not citekeys:
+            return
+        papers = self.gather_papers(citekeys)
+        all_annotations = self.extract(papers)
+        self.to_stdout(all_annotations)
+
+    def extract(self, papers):
+        papers_annotated: Dict = {}
+        for paper in papers:
+            file = self.get_file(paper)
+            try:
+                papers_annotated[paper.citekey] = self.get_annotations(file)
+            except fitz.FileDataError as e:
+                print(f"ERROR: Document {file} is broken: {e}")
+            if not self.quiet:
+                # TODO find pretty print functionality
+                self.ui.info(f"Extracted annotations from {paper.citekey}")
+        return papers_annotated
+
+    def gather_papers(self, citekeys):
+        papers = []
+        for key in citekeys:
+            papers.append(self.repository.pull_paper(key))
+        return papers
+
+    def get_file(self, paper):
+        path = self.broker.real_docpath(paper.docpath)
+        if not path:
+            self.ui.error(f"{paper.citekey} has no valid document.")
+        return path
+
+    def get_annotations(self, filename):
+        annotations = []
+        with fitz.Document(filename) as doc:
+            for page in doc:
+                for annot in page.annots():
+                    content = annot.get_text() or annot.info["content"].replace(
+                        "\n", ""
+                    )
+                    if content:
+                        annotations.append(f"[{page.number}] {content}")
+        return annotations
+
+    def to_stdout(self, annotated_papers):
+        for citekey, annotations in annotated_papers.items():
+            if annotations:
+                print(f"{citekey}")
+                for annot in annotations:
+                    print(f"> \"{annot}\"")
+                print("")
+
+
+    def to_notes(self, filename, annotations):
+        with open(f"{os.path.splitext(filename)[0]}.md", "w") as out:
+            out.write(f"# Annotations:\n\n")
+            out.writelines(annotations)
+            out.write(f"\n---")
+
+
+@PaperChangeEvent.listen()
+def paper_change_event(event):
+    """When a paper is changed, commit the changes to the directory."""
+    pass
+    # if ExtractPlugin.is_loaded():
+    #     git = ExtractPlugin.get_instance()
+    #     if not git.manual:
+    #         event_desc = event.description
+    #         for a, b in [('\\', '\\\\'), ('"', '\\"'), ('$', '\\$'), ('`', '\\`')]:
+    #             event_desc = event_desc.replace(a, b)
+    #         git.list_of_changes.append(event_desc)
+
+
+@PostCommandEvent.listen()
+def git_commit(event):
+    pass
+    # if ExtractPlugin.is_loaded():
+    #     try:
+    #         extract = ExtractPlugin.get_instance()
+    #         if len(extract.list_of_changes) > 0:
+    #             if not extract.manual:
+    #                 title = ' '.join(sys.argv) + '\n'
+    #                 message = '\n'.join([title] + extract.list_of_changes)
+    #
+    #                 extract.shell('add .')
+    #                 extract.shell('commit -F-', message.encode('utf-8'))
+    #     except RuntimeError as exc:
+    #         uis.get_ui().warning(exc.args[0])