Refactor annotation into separate class
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2 changed files with 101 additions and 94 deletions
95
extract/annotation.py
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95
extract/annotation.py
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@ -0,0 +1,95 @@
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import math
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import re
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from dataclasses import dataclass, field
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from typing import Dict
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from pubs.paper import Paper
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from pubs import pretty
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TEXT_SIMILARITY_MINIMUM = 0.75
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COLOR_SIMILARITY_MINIMUM = 0.833
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COLORS = {
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"red": (1, 0, 0),
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"green": (0, 1, 0),
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"blue": (0, 0, 1),
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"yellow": (1, 1, 0),
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"purple": (0.5, 0, 0.5),
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"orange": (1, 0.65, 0),
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}
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@dataclass
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class Annotation:
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"""A PDF annotation object"""
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paper: Paper
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file: str
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type: str = "Highlight"
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text: str = ""
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content: str = ""
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page: int = 1
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colors: Dict = field(default_factory=lambda: {"stroke": (0.0, 0.0, 0.0)})
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tag: str = ""
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def format(self, formatting):
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"""Return a formatted string of the annotation.
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Given a provided formatting pattern, this method returns the annotation
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formatted with the correct marker replacements and removals, ready
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for display or writing.
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"""
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output = formatting
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replacements = {
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r"{quote}": self.text,
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r"{note}": self.content,
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r"{page}": str(self.page),
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r"{newline}": "\n",
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r"{tag}": self.tag,
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}
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pattern = re.compile(
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"|".join(
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[re.escape(k) for k in sorted(replacements, key=len, reverse=True)]
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),
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flags=re.DOTALL,
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)
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patt_quote_container = re.compile(r"{%quote_container(.*?)%}")
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patt_note_container = re.compile(r"{%note_container(.*?)%}")
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patt_tag_container = re.compile(r"{%tag_container(.*?)%}")
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output = patt_quote_container.sub(r"\1" if self.text else "", output)
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output = patt_note_container.sub(r"\1" if self.content else "", output)
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output = patt_tag_container.sub(r"\1" if self.tag else "", output)
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return pattern.sub(lambda x: replacements[x.group(0)], output)
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@property
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def colorname(self):
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"""Return the stringified version of the annotation color.
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Finds the closest named color to the annotation and returns it.
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"""
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annot_colors = (
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self.colors.get("stroke") or self.colors.get("fill") or (0.0, 0.0, 0.0)
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)
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nearest = None
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minimum_similarity = COLOR_SIMILARITY_MINIMUM
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for name, values in COLORS.items():
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similarity_ratio = self._color_similarity_ratio(values, annot_colors)
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if similarity_ratio > minimum_similarity:
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minimum_similarity = similarity_ratio
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nearest = name
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return nearest
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def headline(self, short=False, max_authors=3):
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headline = pretty.paper_oneliner(
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self.paper, citekey_only=short, max_authors=max_authors
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)
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return re.sub(r"\[pdf\]", "", headline).rstrip()
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def _color_similarity_ratio(self, color_one, color_two):
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"""Return the similarity of two colors between 0 and 1.
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Takes two rgb color tuples made of floats between 0 and 1, e.g. (1, 0.65, 0) for orange,
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and returns the similarity between them, with 1 being the same color and 0 being the
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difference between full black and full white, as a float.
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"""
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return 1 - (abs(math.dist([*color_one], [*color_two])) / 3)
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@ -1,108 +1,18 @@
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import os
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import re
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import argparse
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import math
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from dataclasses import dataclass, field
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from typing import Dict
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import fitz
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import Levenshtein
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from pubs.plugins import PapersPlugin
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from pubs.paper import Paper
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from pubs.events import DocAddEvent, NoteEvent
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from pubs import repo, pretty
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from pubs.utils import resolve_citekey_list
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from pubs.content import check_file, read_text_file, write_file
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from pubs.query import get_paper_filter
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from .annotation import Annotation, COLOR_SIMILARITY_MINIMUM, TEXT_SIMILARITY_MINIMUM
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CONFIRMATION_PAPER_THRESHOLD = 5
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TEXT_SIMILARITY_MINIMUM = 0.75
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COLOR_SIMILARITY_MINIMUM = 0.833
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COLORS = {
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"red": (1, 0, 0),
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"green": (0, 1, 0),
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"blue": (0, 0, 1),
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"yellow": (1, 1, 0),
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"purple": (0.5, 0, 0.5),
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"orange": (1, 0.65, 0),
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}
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@dataclass
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class Annotation:
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"""A PDF annotation object"""
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paper: Paper
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file: str
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type: str = "Highlight"
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text: str = ""
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content: str = ""
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page: int = 1
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colors: Dict = field(default_factory=lambda: {"stroke": (0.0, 0.0, 0.0)})
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tag: str = ""
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def format(self, formatting):
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"""Return a formatted string of the annotation.
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Given a provided formatting pattern, this method returns the annotation
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formatted with the correct marker replacements and removals, ready
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for display or writing.
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"""
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output = formatting
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replacements = {
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r"{quote}": self.text,
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r"{note}": self.content,
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r"{page}": str(self.page),
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r"{newline}": "\n",
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r"{tag}": self.tag,
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}
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pattern = re.compile(
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"|".join(
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[re.escape(k) for k in sorted(replacements, key=len, reverse=True)]
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),
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flags=re.DOTALL,
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)
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patt_quote_container = re.compile(r"{%quote_container(.*?)%}")
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patt_note_container = re.compile(r"{%note_container(.*?)%}")
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patt_tag_container = re.compile(r"{%tag_container(.*?)%}")
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output = patt_quote_container.sub(r"\1" if self.text else "", output)
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output = patt_note_container.sub(r"\1" if self.content else "", output)
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output = patt_tag_container.sub(r"\1" if self.tag else "", output)
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return pattern.sub(lambda x: replacements[x.group(0)], output)
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@property
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def colorname(self):
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"""Return the stringified version of the annotation color.
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Finds the closest named color to the annotation and returns it.
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"""
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annot_colors = (
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self.colors.get("stroke") or self.colors.get("fill") or (0.0, 0.0, 0.0)
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)
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nearest = None
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minimum_similarity = COLOR_SIMILARITY_MINIMUM
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for name, values in COLORS.items():
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similarity_ratio = self._color_similarity_ratio(values, annot_colors)
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if similarity_ratio > minimum_similarity:
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minimum_similarity = similarity_ratio
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nearest = name
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return nearest
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def headline(self, short=False, max_authors=3):
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headline = pretty.paper_oneliner(self.paper, citekey_only=short, max_authors=max_authors)
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return re.sub(r"\[pdf\]", "", headline).rstrip()
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def _color_similarity_ratio(self, color_one, color_two):
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"""Return the similarity of two colors between 0 and 1.
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Takes two rgb color tuples made of floats between 0 and 1, e.g. (1, 0.65, 0) for orange,
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and returns the similarity between them, with 1 being the same color and 0 being the
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difference between full black and full white, as a float.
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"""
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return 1 - (abs(math.dist([*color_one], [*color_two])) / 3)
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class ExtractPlugin(PapersPlugin):
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@ -335,7 +245,9 @@ class ExtractPlugin(PapersPlugin):
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"""
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output = ""
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for citekey, annotations in annotated_papers.items():
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output += f"\n------ {annotations[0].headline(short=short_header)} ------\n\n"
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output += (
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f"\n------ {annotations[0].headline(short=short_header)} ------\n\n"
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)
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for annotation in annotations:
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output += f"{annotation.format(self.formatting)}\n"
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output += "\n"
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@ -354,14 +266,14 @@ class ExtractPlugin(PapersPlugin):
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if check_file(notepath, fail=False):
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self._append_to_note(notepath, annotations)
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else:
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self._write_new_note(notepath, annotations)
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self._write_new_note(notepath, annotations, self.short_header)
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self.ui.info(f"Wrote annotations to {citekey} note {notepath}.")
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if edit is True:
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self.ui.edit_file(notepath, temporary=False)
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NoteEvent(citekey).send()
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def _write_new_note(self, notepath, annotations):
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def _write_new_note(self, notepath, annotations, short_header):
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"""Create a new note containing the annotations.
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Will create a new note in the notes folder of pubs
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