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Refactor extraction to use PaperAnnotated class

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Marty Oehme 2022-12-25 12:17:05 +01:00
parent 7a415b4d7d
commit 04c8a8ed0b
Signed by: Marty
GPG key ID: 73BA40D5AFAF49C9
3 changed files with 52 additions and 30 deletions
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1
README.md
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@ -160,6 +160,7 @@ content, because then we can just use that. It is harder to parse if it does not
- [ ] needs some way to delimit where it puts stuff and user stuff is in note
- [ ] one way is to have it look at `> [17] here be extracted annotation from page seventeen` annotations and put it in between
- [x] another, probably simpler first, is to just append missing annotations to the end of the note
- [ ] use similarity search instead of literal search for existing annotation (levenshtein)
- [x] some highlights (or annotations in general) do not contain text as content
- [x] pymupdf can extract the content of the underlying rectangle (mostly)
- [x] issue is that sometimes the highlight contents are in content, sometimes a user comment instead

30
extract/annotation.py
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@ -19,11 +19,33 @@ COLORS = {
}
class PaperAnnotated(Paper):
def __init__(self, citekey, bibdata, metadata=None, annotations=[]):
super(PaperAnnotated, self).__init__(citekey, bibdata, metadata)
self.annotations = annotations
@classmethod
def from_paper(cls, paper, annotations=[]):
return cls(paper.citekey, paper.bibdata, paper.metadata, annotations)
def __repr__(self):
return "PaperAnnotated(%s, %s, %s)" % (
self.citekey,
self.bibdata,
self.metadata,
)
def headline(self, short=False, max_authors=3):
headline = pretty.paper_oneliner(
self, citekey_only=short, max_authors=max_authors
)
return re.sub(r"\[pdf\]", "", headline).rstrip()
@dataclass
class Annotation:
"""A PDF annotation object"""
paper: Paper
file: str
type: str = "Highlight"
text: str = ""
@ -79,12 +101,6 @@ class Annotation:
nearest = name
return nearest
def headline(self, short=False, max_authors=3):
headline = pretty.paper_oneliner(
self.paper, citekey_only=short, max_authors=max_authors
)
return re.sub(r"\[pdf\]", "", headline).rstrip()
def _color_similarity_ratio(self, color_one, color_two):
"""Return the similarity of two colors between 0 and 1.

51
extract/extract.py
View file

@ -10,7 +10,12 @@ from pubs import repo, pretty
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
from .annotation import Annotation, COLOR_SIMILARITY_MINIMUM, TEXT_SIMILARITY_MINIMUM
from .annotation import (
PaperAnnotated,
Annotation,
COLOR_SIMILARITY_MINIMUM,
TEXT_SIMILARITY_MINIMUM,
)
CONFIRMATION_PAPER_THRESHOLD = 5
@ -34,6 +39,7 @@ class ExtractPlugin(PapersPlugin):
def __init__(self, conf, ui):
self.ui = ui
self.note_extension = conf["main"]["note_extension"]
self.max_authors = conf["main"]["max_authors"]
self.repository = repo.Repository(conf)
self.pubsdir = os.path.expanduser(conf["main"]["pubsdir"])
self.broker = self.repository.databroker
@ -123,12 +129,12 @@ class ExtractPlugin(PapersPlugin):
Returns all annotations belonging to the papers that
are described by the citekeys passed in.
"""
papers_annotated = {}
papers_annotated = []
for paper in papers:
file = self._get_file(paper)
try:
annotations = self._get_annotations(file, paper)
papers_annotated[paper.citekey] = annotations
annotations = self._get_annotations(file)
papers_annotated.append(PaperAnnotated.from_paper(paper, annotations))
except fitz.FileDataError as e:
self.ui.error(f"Document {file} is broken: {e}")
return papers_annotated
@ -166,7 +172,7 @@ class ExtractPlugin(PapersPlugin):
self.ui.message(
"\n".join(
pretty.paper_oneliner(
p, citekey_only=False, max_authors=conf["main"]["max_authors"]
p, citekey_only=False, max_authors=self.max_authors
)
for p in papers
)
@ -188,7 +194,7 @@ class ExtractPlugin(PapersPlugin):
self.ui.warning(f"{paper.citekey} has no valid document.")
return path
def _get_annotations(self, filename, paper):
def _get_annotations(self, filename):
"""Extract annotations from a file.
Returns all readable annotations contained in the file
@ -202,7 +208,6 @@ class ExtractPlugin(PapersPlugin):
quote, note = self._retrieve_annotation_content(page, annot)
a = Annotation(
file=filename,
paper=paper,
text=quote,
content=note,
colors=annot.colors,
@ -237,18 +242,18 @@ class ExtractPlugin(PapersPlugin):
# highlight with selection not in note
return (written, "")
def _to_stdout(self, annotated_papers, short_header=True):
def _to_stdout(self, annotated_papers, short_header=False):
"""Write annotations to stdout.
Simply outputs the gathered annotations over stdout
ready to be passed on through pipelines etc.
"""
output = ""
for citekey, annotations in annotated_papers.items():
for paper in annotated_papers:
output += (
f"\n------ {annotations[0].headline(short=short_header)} ------\n\n"
f"\n------ {paper.headline(self.short_header, self.max_authors)} ------\n\n"
)
for annotation in annotations:
for annotation in paper.annotations:
output += f"{annotation.format(self.formatting)}\n"
output += "\n"
self.ui.message(output.strip())
@ -260,31 +265,31 @@ class ExtractPlugin(PapersPlugin):
in the pubs notes directory. Creates new notes for
citekeys missing a note or appends to existing.
"""
for citekey, annotations in annotated_papers.items():
if annotations:
notepath = self.broker.real_notepath(citekey, note_extension)
for paper in annotated_papers:
if paper.annotations:
notepath = self.broker.real_notepath(paper.citekey, note_extension)
if check_file(notepath, fail=False):
self._append_to_note(notepath, annotations)
self._append_to_note(notepath, paper)
else:
self._write_new_note(notepath, annotations, self.short_header)
self.ui.info(f"Wrote annotations to {citekey} note {notepath}.")
self._write_new_note(notepath, paper, paper.headline(short=True, max_authors=self.max_authors))
self.ui.info(f"Wrote annotations to {paper.citekey} note {notepath}.")
if edit is True:
self.ui.edit_file(notepath, temporary=False)
NoteEvent(citekey).send()
NoteEvent(paper.citekey).send()
def _write_new_note(self, notepath, annotations, short_header):
def _write_new_note(self, notepath, paper, headline):
"""Create a new note containing the annotations.
Will create a new note in the notes folder of pubs
and fill it with the annotations extracted from pdf.
"""
output = f"# {annotations[0].headline(short=short_header)}\n\n"
for annotation in annotations:
output = f"# {headline}\n\n"
for annotation in paper.annotations:
output += f"{annotation.format(self.formatting)}\n\n"
write_file(notepath, output, "w")
def _append_to_note(self, notepath, annotations):
def _append_to_note(self, notepath, paper):
"""Append new annotations to the end of a note.
Looks through note to determine any new annotations which should be
@ -293,7 +298,7 @@ class ExtractPlugin(PapersPlugin):
existing = read_text_file(notepath)
# removed annotations already found in the note
existing_dropped = [
x for x in annotations if x.format(self.formatting) not in existing
x for x in paper.annotations if x.format(self.formatting) not in existing
]
if not existing_dropped:
return