Refactor annotation into separate class

extract/annotation.py

@@ -0,0 +1,95 @@
+import math
+import re
+from dataclasses import dataclass, field
+from typing import Dict
+
+from pubs.paper import Paper
+from pubs import pretty
+
+TEXT_SIMILARITY_MINIMUM = 0.75
+COLOR_SIMILARITY_MINIMUM = 0.833
+
+COLORS = {
+    "red": (1, 0, 0),
+    "green": (0, 1, 0),
+    "blue": (0, 0, 1),
+    "yellow": (1, 1, 0),
+    "purple": (0.5, 0, 0.5),
+    "orange": (1, 0.65, 0),
+}
+
+
+@dataclass
+class Annotation:
+    """A PDF annotation object"""
+
+    paper: Paper
+    file: str
+    type: str = "Highlight"
+    text: str = ""
+    content: str = ""
+    page: int = 1
+    colors: Dict = field(default_factory=lambda: {"stroke": (0.0, 0.0, 0.0)})
+    tag: str = ""
+
+    def format(self, formatting):
+        """Return a formatted string of the annotation.
+
+        Given a provided formatting pattern, this method returns the annotation
+        formatted with the correct marker replacements and removals, ready
+        for display or writing.
+        """
+        output = formatting
+        replacements = {
+            r"{quote}": self.text,
+            r"{note}": self.content,
+            r"{page}": str(self.page),
+            r"{newline}": "\n",
+            r"{tag}": self.tag,
+        }
+        pattern = re.compile(
+            "|".join(
+                [re.escape(k) for k in sorted(replacements, key=len, reverse=True)]
+            ),
+            flags=re.DOTALL,
+        )
+        patt_quote_container = re.compile(r"{%quote_container(.*?)%}")
+        patt_note_container = re.compile(r"{%note_container(.*?)%}")
+        patt_tag_container = re.compile(r"{%tag_container(.*?)%}")
+        output = patt_quote_container.sub(r"\1" if self.text else "", output)
+        output = patt_note_container.sub(r"\1" if self.content else "", output)
+        output = patt_tag_container.sub(r"\1" if self.tag else "", output)
+        return pattern.sub(lambda x: replacements[x.group(0)], output)
+
+    @property
+    def colorname(self):
+        """Return the stringified version of the annotation color.
+
+        Finds the closest named color to the annotation and returns it.
+        """
+        annot_colors = (
+            self.colors.get("stroke") or self.colors.get("fill") or (0.0, 0.0, 0.0)
+        )
+        nearest = None
+        minimum_similarity = COLOR_SIMILARITY_MINIMUM
+        for name, values in COLORS.items():
+            similarity_ratio = self._color_similarity_ratio(values, annot_colors)
+            if similarity_ratio > minimum_similarity:
+                minimum_similarity = similarity_ratio
+                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.
+
+        Takes two rgb color tuples made of floats between 0 and 1, e.g. (1, 0.65, 0) for orange,
+        and returns the similarity between them, with 1 being the same color and 0 being the
+        difference between full black and full white, as a float.
+        """
+        return 1 - (abs(math.dist([*color_one], [*color_two])) / 3)

extract/extract.py

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