import re 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 extraction from papis_extract.annotation import Annotation from papis_extract.exporter import Exporter from papis_extract.exporters import all_exporters from papis_extract.extractors import all_extractors from papis_extract.formatter import Formatter, formatters logger = papis.logging.get_logger(__name__) DEFAULT_OPTIONS: dict[str, dict[str, bool | float | dict[str, str]]] = { "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="Commit changes made to the notes files.") @papis.cli.all_option() @click.option( "--write/--no-write", "-w", help="Write extracted annotations into papis notes.", show_default=True, ) @click.option( "--manual/--no-manual", "-m", help="Open note in editor for manual editing after annotation extraction.", show_default=True, ) @click.option( "--template", "-t", type=click.Choice( list(formatters.keys()), case_sensitive=False, ), help="Choose an output template to format annotations with.", show_default=True, ) @click.option( "--extractor", "-e", "extractors", type=click.Choice( list(all_extractors.keys()), case_sensitive=False, ), default=list(all_extractors.keys()), multiple=True, help="Choose an extractor to apply to the selected documents. [default: all]", ) @click.option( "--force/--no-force", "-f", help="Do not drop any annotations because they already exist.", show_default=True, ) def main( query: str, # _papis_id: bool, # _file: bool, # _dir: bool, _all: bool, doc_folder: str, manual: bool, write: bool, extractors: list[str], template: str, git: bool, force: bool, ) -> None: """Extract annotations from any documents. The extract plugin allows manual or automatic extraction of all annotations contained in the documents belonging to entries of the papis library, primarily targeting PDF documents currently. 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 papis entry, if set in the plugin configuration. """ 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 formatter = formatters.get(template) run( documents, edit=manual, write=write, git=git, formatter=formatter, extractors=[all_extractors.get(e) for e in extractors], force=force, ) def run( documents: list[Document], formatter: Formatter | None, extractors: list[extraction.Extractor | None], edit: bool = False, write: bool = False, git: bool = False, force: bool = False, ) -> None: exporter: Exporter if write: exporter = all_exporters["notes"]( formatter=formatter or formatters["markdown-atx"], edit=edit, git=git, force=force, ) else: exporter = all_exporters["stdout"]( formatter=formatter or formatters["markdown"] ) doc_annots: list[tuple[Document, list[Annotation]]] = [] for doc in documents: annotations: list[Annotation] = [] valid_files: int = 0 for ext in extractors: if not ext: continue added = extraction.start(ext, doc) if added is not None: valid_files += 1 annotations.extend(added) doc_annots.append((doc, annotations)) if valid_files == 0: # have to remove curlys or papis logger gets upset desc = re.sub("[{}]", "", papis.document.describe(doc)) logger.info(f"Document {desc} has no valid extractors for any of its files.") exporter.run(doc_annots)