papis-extract/papis_extract/__init__.py

import click
import papis.cli
import papis.config
import papis.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 AnnotatedDocument, Markdown

logger = papis.logging.get_logger(__name__)

DEFAULT_OPTIONS = {
    "plugins.extract": {
        "tags": {},
        "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

    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, Markdown(), edit=edit, git=git)
    else:
        exporter.to_stdout(doc_annotations, Markdown())