Marty Oehme
1af0f8f7bc
Since meanings assigned to highlight colors are often very personal I do not want to make any assumptions about their use. Remove any default associations.
126 lines
3.7 KiB
Python
126 lines
3.7 KiB
Python
from pathlib import Path
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import re
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import click
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import fitz_new as fitz
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import magic
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import papis.cli
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import papis.config
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import papis.document
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from papis.document import Document
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import papis.logging
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import papis.notes
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import papis.strings
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from papis_extract import extractor, exporter
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from papis_extract.annotation_data import Annotation, AnnotatedDocument
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logger = papis.logging.get_logger(__name__)
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DEFAULT_OPTIONS = {
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"plugins.extract": {
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"tags": {},
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"on_import": False,
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"minimum_similarity": 0.75, # for checking against existing annotations
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"minimum_similarity_content": 0.9, # for checking if highlight or note
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"minimum_similarity_color": 0.833, # for matching tag to color
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}
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}
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papis.config.register_default_settings(DEFAULT_OPTIONS)
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@click.command("extract")
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@click.help_option("-h", "--help")
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@papis.cli.query_argument()
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@papis.cli.doc_folder_option()
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@papis.cli.git_option(help="Add changes made to the notes files")
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@papis.cli.all_option()
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@click.option(
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"--manual/--no-manual",
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"-m",
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help="Open each note in editor for manual editing after extracting its annotations",
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)
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@click.option(
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"--write/--no-write",
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"-w",
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help="Do not write annotations to notes only print results to stdout",
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)
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def main(
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query: str,
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# info: bool,
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# _papis_id: bool,
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# _file: bool,
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# notes: bool,
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# _dir: bool,
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# _format: str,
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_all: bool,
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doc_folder: str,
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manual: bool,
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write: bool,
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git: bool,
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) -> None:
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"""Extract annotations from any pdf document
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The extract plugin allows manual or automatic extraction of all annotations
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contained in the pdf documents belonging to entries of the pubs library.
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It can write those changes to stdout or directly create and update notes
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for papis documents.
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It adds a `papis extract` subcommand through which it is invoked, but can
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optionally run whenever a new document is imported for a pubs entry.
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"""
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documents = papis.cli.handle_doc_folder_query_all_sort(
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query, doc_folder, sort_field=None, sort_reverse=False, _all=_all
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)
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if not documents:
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logger.warning(papis.strings.no_documents_retrieved_message)
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return
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doc_annotations: list[AnnotatedDocument] = _get_annotations_for_documents(documents)
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if write:
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exporter.to_notes(doc_annotations, edit=manual, git=git)
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else:
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exporter.to_stdout(doc_annotations)
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# note_file: Path = Path(papis.notes.notes_path_ensured(documents[0]))
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def is_pdf(fname: Path) -> bool:
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return magic.from_file(fname, mime=True) == "application/pdf"
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def _get_annotations_for_documents(
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documents: list[Document],
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) -> list[AnnotatedDocument]:
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output: list[AnnotatedDocument] = []
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for doc in documents:
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annotations: list[Annotation] = []
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found_pdf: bool = False
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for file in doc.get_files():
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fname = Path(file)
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if not _is_file_processable(fname):
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break
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found_pdf = True
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try:
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annotations.extend(extractor.start(fname))
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except fitz.FileDataError as e:
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print(f"File structure errors for {file}.\n{e}")
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if not found_pdf:
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# have to remove curlys or papis logger gets upset
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desc = re.sub("[{}]", "", papis.document.describe(doc))
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logger.warning("Did not find suitable PDF file for document: " f"{desc}")
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output.append(AnnotatedDocument(doc, annotations))
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return output
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def _is_file_processable(fname: Path) -> bool:
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if not fname.is_file():
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logger.error(f"File {str(fname)} not readable.")
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return False
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if not is_pdf(fname):
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return False
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return True
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