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Allow running queries for papers to be extracted from

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Marty Oehme 2022-12-24 14:23:07 +01:00
parent e201f6cf5f
commit 488dd0eb41
Signed by: Marty
GPG key ID: 73BA40D5AFAF49C9
1 changed files with 55 additions and 20 deletions
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71
extract/extract.py
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@ -11,6 +11,8 @@ from pubs.events import DocAddEvent, NoteEvent
from pubs import repo
from pubs.utils import resolve_citekey_list
from pubs.content import check_file, read_text_file, write_file
from pubs.query import get_paper_filter
class ExtractPlugin(PapersPlugin):
"""Extract annotations from any pdf document.
@ -35,10 +37,6 @@ class ExtractPlugin(PapersPlugin):
self.pubsdir = os.path.expanduser(conf["main"]["pubsdir"])
self.broker = self.repository.databroker
# TODO implement custom annotation formatting, akin to main config citekey format
# e.g. `> [{page}] {annotation}`
# or `:: {annotation} :: {page} ::`
# and so on
self.on_import = conf["plugins"].get("extract", {}).get("on_import", False)
self.minimum_similarity = float(
conf["plugins"].get("extract", {}).get("minimum_similarity", 0.75)
@ -56,11 +54,6 @@ class ExtractPlugin(PapersPlugin):
"""Allow the usage of the pubs extract subcommand"""
# TODO option for ignoring missing documents or erroring.
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.add_argument(
"-w",
"--write",
@ -75,29 +68,58 @@ class ExtractPlugin(PapersPlugin):
action="store_true",
default=False,
)
extract_parser.add_argument(
"-q",
"--query",
help="Query library instead of providing individual citekeys. For query help see pubs list command.",
action="store_true",
default=None,
dest="is_query",
)
extract_parser.add_argument(
"-i",
"--ignore-case",
action="store_false",
default=None,
dest="case_sensitive",
help="When using query mode, perform case insensitive search.",
)
extract_parser.add_argument(
"-I",
"--force-case",
action="store_true",
dest="case_sensitive",
help="When using query mode, perform case sensitive search.",
)
extract_parser.add_argument(
"--strict",
action="store_true",
default=False,
help="Force strict unicode comparison of query.",
)
extract_parser.add_argument(
"query",
nargs=argparse.REMAINDER,
help="Citekey(s)/query for the documents to extract from.",
)
extract_parser.set_defaults(func=self.command)
def command(self, conf, args):
"""Run the annotation extraction command."""
citekeys = resolve_citekey_list(
self.repository, conf, args.citekeys, ui=self.ui, exit_on_fail=True
)
if not citekeys:
return
all_annotations = self.extract(citekeys)
papers = self._gather_papers(conf, args)
all_annotations = self.extract(papers)
if args.write:
self._to_notes(all_annotations, self.note_extension, args.edit)
else:
self._to_stdout(all_annotations)
self.repository.close()
def extract(self, citekeys):
def extract(self, papers):
"""Extracts annotations from citekeys.
Returns all annotations belonging to the papers that
are described by the citekeys passed in.
"""
papers = self._gather_papers(citekeys)
papers_annotated = []
for paper in papers:
file = self._get_file(paper)
@ -107,15 +129,28 @@ class ExtractPlugin(PapersPlugin):
self.ui.error(f"Document {file} is broken: {e}")
return papers_annotated
def _gather_papers(self, citekeys):
def _gather_papers(self, conf, args):
"""Get all papers for citekeys.
Returns all Paper objects described by the citekeys
passed in.
"""
papers = []
if not args.is_query:
citekeys = resolve_citekey_list(
self.repository, conf, args.query, ui=self.ui, exit_on_fail=True
)
for key in citekeys:
papers.append(self.repository.pull_paper(key))
else:
papers = filter(
get_paper_filter(
args.query,
case_sensitive=args.case_sensitive,
strict=args.strict,
),
self.repository.all_papers(),
)
return papers
def _get_file(self, paper):