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For more information on this, and how to apply and follow the GNU GPL, see
<https://www.gnu.org/licenses/>.
The GNU General Public License does not permit incorporating your program
into proprietary programs. If your program is a subroutine library, you
may consider it more useful to permit linking proprietary applications with
the library. If this is what you want to do, use the GNU Lesser General
Public License instead of this License. But first, please read
<https://www.gnu.org/licenses/why-not-lgpl.html>.

57
README.md
View file

@ -19,8 +19,6 @@ everything should now be set up.
I am currently working towards the first release for pypi, see the below roadmap;
when that is done you will also be able to install in the usual pypi way.
If you manage your python environments with `pipx`, you can also `pipx inject --spec 'git+git+https://git.martyoeh.me/Marty/papis-extract.git` to add it to your specific papis environment.
To check if everything is working you should now see the `extract` command listed when running `papis --help`.
You will be set up with the default options but if you want to change anything, read on in configuration below.
@ -200,21 +198,7 @@ The option should generally not take too much tuning, but it is there if you nee
This should generally be an alright default but is here to be changed for example if you work with a lot of different annotation colors (where dark purple and light purple may different meanings) and get false positives in automatic tag recognition, or no tags are recognized at all.
## Extractors
Currently, the program supports two annotation extractors:
A **`pdf` extractor**, which takes highlights and annotations embedded in any PDF file.
It should work with most PDF styles, as long as annotations are marked as such
(does not work if e.g. highlights are baked onto text, or there is no text in the file).
A `pocketbook` extractor, which takes bookmarks exported from the mobile [PocketBook](https://pocketbook.ch/en-ch/app) reader applications.
You can export bookmarks by opening a book, going to the notes list and selecting `Export notes...`.
Then import the resulting `.html` file into the library using `papis add`
(or `papis addto` to add it to existing documents).
You are then ready to use extract to get those annotations from the exported list into your notes.
## TODO: Roadmap to first release
## Roadmap to first release
Known issues to be fixed:
@ -238,18 +222,16 @@ features to be implemented:
- [x] add page number if available
- exists in Annotation, just need to place in output
- [ ] show overall amount of extractions at the end
- implemented for writing to notes (notes exporter)
- KNOWN ISSUE: currently returns number of annotation rows (may be multiple per annot)
- [ ] custom formatting decided by user
- in config as { "myformatter": ">{tag}\n{quote}\n{note}\n{page} etc"}
- [ ] improved default exporters
- [x] markdown into notes
- [ ] pretty display on stdout (rich?)
- [x] csv/tsv to stdout
- [ ] table fmt stdout?
- markdown into notes
- pretty display on stdout (rich?)
- csv/tsv to stdout
- table fmt stdout?
- [ ] allow custom colors -> tag name settings not dependent on color name existing (e.g. {"important": (1.0,0.0,0.0)})
- [ ] `--overwrite` mode where existing annotations are not dropped but overwritten on same line of note
- [x] `--force` mode where we simply do not drop anything
- [ ] `--force` mode where we simply do not drop anything
- [x] `--format` option to choose from default or set up a custom formatter
- called `--template` in current implementation
- [ ] on_add hook to extract annotations as files are added
@ -284,7 +266,6 @@ and for myself whenever I forget. The basic building blocks currently in here ar
- extractors
: Extract data from a source file attached to a papis document.
Crawls the actual files attached to documents to put them into annotation-friendly formats.
- annotations
: The actual extracted blocks of text, containing some metadata
@ -294,32 +275,12 @@ and for myself whenever I forget. The basic building blocks currently in here ar
: Put the extracted data somewhere. For now stdout or into your notes.
- formatters
: Make sure the exporter saves the annotation data according to your preferred layout,
: Make sure the exporter saves the data according to your preferred layout,
such as a markdown syntax or csv-structure.
Splitting it into those building blocks makes it easier to recombine them in any way,
Splitting it into those three building blocks makes it easier to recombine them in any way,
should someone want to save highlights as csv data in their notes,
or to include additional extractors or formatters.
To develop it together with an isolated `papis` instance you can simply inject papis into your
development environment, e.g. invoking the poetry environment shell and then manually installing:
```bash
poetry shell
pip install papis
```
This will leave you with `papis` installed in the same virtual environment as your development.
However, what I do on my system instead to enable quick testing is inject it into a
system-wide (but isolated with `pipx`) papis setup:
```bash
pipx install papis # create an isolated papis installation reachable form anywhere
pipx inject --editable papis . # inject this folder into the environment and keep up with any changes
```
This for me provides the ideal compromise of clean dev environment (papis is not directly part of it)
but quickly reachable installation to test my changes.
or should we ever include more extractors than the one for PDFs.
---

63
papis_extract/__init__.py
View file

@ -7,11 +7,7 @@ import papis.notes
import papis.strings
from papis.document import Document
from papis_extract.annotation import Annotation
from papis_extract import extraction
from papis_extract.exporter import Exporter
from papis_extract.extractors import all_extractors
from papis_extract.exporters import all_exporters
from papis_extract import extractor, exporter
from papis_extract.formatter import Formatter, formatters
logger = papis.logging.get_logger(__name__)
@ -37,42 +33,26 @@ papis.config.register_default_settings(DEFAULT_OPTIONS)
@click.option(
"--write/--no-write",
"-w",
help="Write extracted annotations into papis notes.",
show_default=True,
help="Do not write annotations to notes only print results to stdout.",
)
@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()),
["markdown", "markdown-setext", "markdown-atx", "count", "csv"],
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,
@ -83,7 +63,6 @@ def main(
doc_folder: str,
manual: bool,
write: bool,
extractors: list[str],
template: str,
git: bool,
force: bool,
@ -106,47 +85,27 @@ def main(
logger.warning(papis.strings.no_documents_retrieved_message)
return
formatter = formatters.get(template)
formatter = formatters[template]
run(
documents,
edit=manual,
write=write,
git=git,
formatter=formatter,
extractors=[all_extractors.get(e) for e in extractors],
force=force,
)
run(documents, edit=manual, write=write, git=git, formatter=formatter, force=force)
def run(
documents: list[Document],
formatter: Formatter | None,
extractors: list[extraction.Extractor | None],
formatter: Formatter,
edit: bool = False,
write: bool = False,
git: bool = False,
force: bool = False,
) -> None:
annotated_docs = extractor.start(documents)
if write:
exporter: Exporter = all_exporters["notes"](
formatter=formatter or formatters["markdown-atx"],
exporter.to_notes(
formatter=formatter,
annotated_docs=annotated_docs,
edit=edit,
git=git,
force=force,
)
else:
exporter: Exporter = all_exporters["stdout"](
formatter=formatter or formatters["markdown"]
)
doc_annots: list[tuple[Document, list[Annotation]]] = []
for doc in documents:
annotations: list[Annotation] = []
for ext in extractors:
if not ext:
continue
annotations.extend(extraction.start(ext, doc))
doc_annots.append((doc, annotations))
exporter.run(doc_annots)
exporter.to_stdout(formatter=formatter, annotated_docs=annotated_docs)

98
papis_extract/annotation.py
View file

@ -1,23 +1,19 @@
import math
from dataclasses import dataclass
from typing import Any, Optional
from dataclasses import dataclass, field
import chevron
import papis.config
from papis.document import Document
import chevron
TEXT_SIMILARITY_MINIMUM = 0.75
COLOR_SIMILARITY_MINIMUM = 0.833
COLORS: dict[str, tuple[float, float, float]] = {
"blue": (0, 0, 1),
"green": (0, 1, 0),
COLORS = {
"red": (1, 0, 0),
"cyan": (0, 1, 1),
"green": (0, 1, 0),
"blue": (0, 0, 1),
"yellow": (1, 1, 0),
"magenta": (1, 0, 1),
"purple": (0.5, 0, 0.5),
"pink": (1, 0.75, 0.8),
"orange": (1, 0.65, 0),
}
@ -29,25 +25,14 @@ class Annotation:
Contains all information necessary for the annotation itself, content and metadata.
"""
def __init__(
self,
file: str,
color: tuple[float, float, float] = (0.0, 0.0, 0.0),
content: str = "",
note: str = "",
page: int = 0,
tag: str = "",
type: str = "Highlight",
minimum_similarity_color: float = 1.0,
) -> None:
self.minimum_similarity_color = minimum_similarity_color
self.file = file
self._color = color
self.content = content
self.note = note
self.page = page
self.tag = tag or self._tag_from_colorname(self.colorname or "")
self.type = type
file: str
colors: tuple[float, float, float] = field(default_factory=lambda: (0.0, 0.0, 0.0))
content: str = ""
page: int = 0
tag: str = ""
text: str = ""
type: str = "Highlight"
minimum_similarity_color: float = 1.0
def format(self, formatting: str, doc: Document = Document()):
"""Return a formatted string of the annotation.
@ -58,8 +43,8 @@ class Annotation:
"""
data = {
"file": self.file,
"quote": self.content,
"note": self.note,
"quote": self.text,
"note": self.content,
"page": self.page,
"tag": self.tag,
"type": self.type,
@ -67,15 +52,6 @@ class Annotation:
}
return chevron.render(formatting, data)
@property
def color(self):
return self._color
@color.setter
def color(self, value: tuple[float, float, float]):
self._color = value
self.tag = self._tag_from_colorname(self.colorname or "")
@property
def colorname(self):
"""Return the stringified version of the annotation color.
@ -83,7 +59,7 @@ class Annotation:
Finds the closest named color to the annotation and returns it,
using euclidian distance between the two color vectors.
"""
annot_colors = self.color or (0.0, 0.0, 0.0)
annot_colors = self.colors or (0.0, 0.0, 0.0)
nearest = None
minimum_similarity = (
papis.config.getfloat("minimum_similarity_color", "plugins.extract") or 1.0
@ -96,11 +72,7 @@ class Annotation:
nearest = name
return nearest
def _color_similarity_ratio(
self,
color_one: tuple[float, float, float],
color_two: tuple[float, float, float],
) -> float:
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,
@ -110,36 +82,14 @@ class Annotation:
"""
return 1 - (abs(math.dist([*color_one], [*color_two])) / 3)
def _tag_from_colorname(self, colorname: str) -> str:
color_mapping: dict[str, str] = self._getdict("tags", "plugins.extract")
if not color_mapping:
return ""
return color_mapping.get(colorname, "")
@dataclass
class AnnotatedDocument:
"""Contains all annotations belonging to a single papis document.
# mimics the functions in papis.config.{getlist,getint,getfloat} etc.
def _getdict(self, key: str, section: Optional[str] = None) -> dict[str, str]:
"""Dict getter
Combines a document with a list of annotations which belong to it."""
:returns: A python dict
:raises SyntaxError: Whenever the parsed syntax is either not a valid
python object or a valid python dict.
"""
rawvalue: Any = papis.config.general_get(key, section=section)
if isinstance(rawvalue, dict):
return rawvalue
try:
rawvalue = eval(rawvalue)
except Exception:
raise SyntaxError(
"The key '{}' must be a valid Python object: {}".format(key, rawvalue)
)
else:
if not isinstance(rawvalue, dict):
raise SyntaxError(
"The key '{}' must be a valid Python dict. Got: {} (type {!r})".format(
key, rawvalue, type(rawvalue).__name__
)
)
document: Document
annotations: list[Annotation]
return rawvalue
# TODO could implement a from_doc() static method to generate annotation list?

152
papis_extract/exporter.py
View file

@ -1,28 +1,142 @@
from dataclasses import dataclass
from typing import Protocol
import papis.api
import papis.commands.edit
import papis.config
import papis.document
import papis.git
import papis.logging
import papis.document
import papis.notes
import papis.commands.edit
import papis.api
import papis.git
import papis.config
import Levenshtein
from papis_extract.annotation import AnnotatedDocument
from papis_extract.annotation import Annotation
from papis_extract.formatter import Formatter
logger = papis.logging.get_logger(__name__)
@dataclass
class Exporter(Protocol):
formatter: Formatter
edit: bool = False
git: bool = False
force: bool = False
def to_stdout(formatter: Formatter, annotated_docs: list[AnnotatedDocument]) -> None:
"""Pretty print annotations to stdout.
def run(
self, annot_docs: list[tuple[papis.document.Document, list[Annotation]]]
) -> None:
...
Gives a nice human-readable representations of
the annotations in somewhat of a list form.
Not intended for machine-readability.
"""
output: str = formatter(annotated_docs)
print(output.rstrip("\n"))
def to_notes(
formatter: Formatter,
annotated_docs: list[AnnotatedDocument],
edit: bool,
git: bool,
force: bool,
) -> None:
"""Write annotations into document notes.
Permanently writes the given annotations into notes
belonging to papis documents. Creates new notes for
documents missing a note field or appends to existing.
"""
for entry in annotated_docs:
formatted_annotations = formatter([entry]).split("\n")
if formatted_annotations:
_add_annots_to_note(entry.document, formatted_annotations, force=force)
if edit:
papis.commands.edit.edit_notes(entry.document, git=git)
def _add_annots_to_note(
document: papis.document.Document,
formatted_annotations: list[str],
git: bool = False,
force: bool = False,
) -> None:
"""
Append new annotations to the end of a note.
This function appends new annotations to the end of a note file. It takes in a
document object containing the note, a list of formatted annotations to be
added, and optional flags git and force. If git is True, the changes will be
committed to git. If force is True, the annotations will be added even if they
already exist in the note.
:param document: The document object representing the note
:type document: class:`papis.document.Document`
:param formatted_annotations: A list of already formatted annotations to be added
:type formatted_annotations: list[str]
:param git: Flag indicating whether to commit changes to git, defaults to False.
:type git: bool, optional
:param force: Flag indicating whether to force adding annotations even if they
already exist, defaults to False.
:type force: bool, optional
"""
logger.debug("Adding annotations to note.")
notes_path = papis.notes.notes_path_ensured(document)
existing: list[str] = []
with open(notes_path, "r") as file_read:
existing = file_read.readlines()
new_annotations: list[str] = []
if not force:
new_annotations = _drop_existing_annotations(formatted_annotations, existing)
if not new_annotations:
return
with open(notes_path, "a") as f:
# add newline if theres no empty space at file end
if len(existing) > 0 and existing[-1].strip() != "":
f.write("\n")
print(new_annotations)
f.write("\n\n".join(new_annotations))
f.write("\n")
logger.info(
f"Wrote {len(new_annotations)} "
f"{'annotation' if len(new_annotations) == 1 else 'annotations'} "
f"to {papis.document.describe(document)}"
)
if git:
msg = "Update notes for '{0}'".format(papis.document.describe(document))
folder = document.get_main_folder()
if folder:
papis.git.add_and_commit_resources(
folder, [notes_path, document.get_info_file()], msg
)
def _drop_existing_annotations(
formatted_annotations: list[str], file_lines: list[str]
) -> list[str]:
"""Returns the input annotations dropping any existing.
Takes a list of formatted annotations and a list of strings
(most probably existing lines in a file). If anny annotations
match an existing line closely enough, they will be dropped.
Returns list of annotations without duplicates.
"""
minimum_similarity = (
papis.config.getfloat("minimum_similarity", "plugins.extract") or 1.0
)
remaining: list[str] = []
for an in formatted_annotations:
an_split = an.splitlines()
if an_split and not _test_similarity(
an_split[0], file_lines, minimum_similarity
):
remaining.append(an)
return remaining
def _test_similarity(
string: str, lines: list[str], minimum_similarity: float = 1.0
) -> bool:
for line in lines:
ratio = Levenshtein.ratio(string, line)
if ratio > minimum_similarity:
return True
return False

14
papis_extract/exporters/__init__.py
View file

@ -1,14 +0,0 @@
import papis.logging
from papis_extract.exporter import Exporter
from papis_extract.exporters.notes import NotesExporter
from papis_extract.exporters.stdout import StdoutExporter
logger = papis.logging.get_logger(__name__)
all_exporters: dict[str, type[Exporter]] = {}
all_exporters["stdout"] = StdoutExporter
all_exporters["notes"] = NotesExporter

131
papis_extract/exporters/notes.py
View file

@ -1,131 +0,0 @@
from dataclasses import dataclass
import Levenshtein
from papis.document import Document
from papis_extract.annotation import Annotation
from papis_extract.formatter import Formatter
from papis.logging import get_logger
import papis.notes
import papis.document
import papis.git
import papis.config
import papis.commands.edit
logger = get_logger(__name__)
@dataclass
class NotesExporter:
formatter: Formatter
edit: bool = False
git: bool = False
force: bool = False
def run(self, annot_docs: list[tuple[Document, list[Annotation]]]) -> None:
"""Write annotations into document notes.
Permanently writes the given annotations into notes
belonging to papis documents. Creates new notes for
documents missing a note field or appends to existing.
"""
for doc, annots in annot_docs:
formatted_annotations = self.formatter(doc, annots).split("\n")
if formatted_annotations:
self._add_annots_to_note(doc, formatted_annotations, force=self.force)
if self.edit:
papis.commands.edit.edit_notes(doc, git=self.git)
def _add_annots_to_note(
self,
document: Document,
formatted_annotations: list[str],
git: bool = False,
force: bool = False,
) -> None:
"""
Append new annotations to the end of a note.
This function appends new annotations to the end of a note file. It takes in a
document object containing the note, a list of formatted annotations to be
added, and optional flags git and force. If git is True, the changes will be
committed to git. If force is True, the annotations will be added even if they
already exist in the note.
:param document: The document object representing the note
:type document: class:`papis.document.Document`
:param formatted_annotations: A list of already formatted annotations to be added
:type formatted_annotations: list[str]
:param git: Flag indicating whether to commit changes to git, defaults to False.
:type git: bool, optional
:param force: Flag indicating whether to force adding annotations even if they
already exist, defaults to False.
:type force: bool, optional
"""
logger.debug("Adding annotations to note.")
notes_path = papis.notes.notes_path_ensured(document)
existing: list[str] = []
with open(notes_path, "r") as file_read:
existing = file_read.readlines()
new_annotations: list[str] = []
if not force:
new_annotations = self._drop_existing_annotations(
formatted_annotations, existing
)
if not new_annotations:
return
with open(notes_path, "a") as f:
# add newline if theres no empty space at file end
if len(existing) > 0 and existing[-1].strip() != "":
f.write("\n")
f.write("\n\n".join(new_annotations))
f.write("\n")
logger.info(
f"Wrote {len(new_annotations)} "
f"{'line' if len(new_annotations) == 1 else 'lines'} "
f"to {papis.document.describe(document)}"
)
if git:
msg = "Update notes for '{0}'".format(papis.document.describe(document))
folder = document.get_main_folder()
if folder:
papis.git.add_and_commit_resources(
folder, [notes_path, document.get_info_file()], msg
)
def _drop_existing_annotations(
self, formatted_annotations: list[str], file_lines: list[str]
) -> list[str]:
"""Returns the input annotations dropping any existing.
Takes a list of formatted annotations and a list of strings
(most probably existing lines in a file). If anny annotations
match an existing line closely enough, they will be dropped.
Returns list of annotations without duplicates.
"""
minimum_similarity = (
papis.config.getfloat("minimum_similarity", "plugins.extract") or 1.0
)
remaining: list[str] = []
for an in formatted_annotations:
an_split = an.splitlines()
if an_split and not self._test_similarity(
an_split[0], file_lines, minimum_similarity
):
remaining.append(an)
return remaining
def _test_similarity(
self, string: str, lines: list[str], minimum_similarity: float = 1.0
) -> bool:
for line in lines:
ratio = Levenshtein.ratio(string, line)
if ratio > minimum_similarity:
return True
return False

26
papis_extract/exporters/stdout.py
View file

@ -1,26 +0,0 @@
from dataclasses import dataclass
from papis.document import Document
from papis_extract.annotation import Annotation
from papis_extract.formatter import Formatter
@dataclass
class StdoutExporter:
formatter: Formatter
edit: bool = False
git: bool = False
force: bool = False
def run(self, annot_docs: list[tuple[Document, list[Annotation]]]) -> None:
"""Pretty print annotations to stdout.
Gives a nice human-readable representations of
the annotations in somewhat of a list form.
Not intended for machine-readability.
"""
for doc, annots in annot_docs:
output: str = self.formatter(doc, annots)
if output:
print("{output}\n".format(output=output.rstrip("\n")))

52
papis_extract/extraction.py
View file

@ -1,52 +0,0 @@
import re
from pathlib import Path
from typing import Protocol
import fitz
import papis.config
import papis.document
import papis.logging
from papis.document import Document
from papis_extract.annotation import Annotation
logger = papis.logging.get_logger(__name__)
class Extractor(Protocol):
def can_process(self, filename: Path) -> bool:
...
def run(self, filename: Path) -> list[Annotation]:
...
def start(
extractor: Extractor,
document: Document,
) -> list[Annotation]:
"""Extract all annotations from passed documents.
Returns all annotations contained in the papis
documents passed in.
"""
annotations: list[Annotation] = []
file_available: bool = False
for file in document.get_files():
fname = Path(file)
if not extractor.can_process(fname):
continue
file_available = True
try:
annotations.extend(extractor.run(fname))
except fitz.FileDataError as e:
print(f"File structure errors for {file}.\n{e}")
if not file_available:
# have to remove curlys or papis logger gets upset
desc = re.sub("[{}]", "", papis.document.describe(document))
logger.info(f"No {type(extractor)} file for document: {desc}")
return annotations

166
papis_extract/extractor.py Normal file
View file

@ -0,0 +1,166 @@
import re
from pathlib import Path
from typing import Any, Optional
import Levenshtein
import magic
import fitz
import papis.logging
import papis.config
import papis.document
from papis.document import Document
from papis_extract.annotation import Annotation, AnnotatedDocument
logger = papis.logging.get_logger(__name__)
def start(
documents: list[Document],
) -> list[AnnotatedDocument]:
"""Extract all annotations from passed documents.
Returns all annotations contained in the papis
documents passed in.
"""
output: list[AnnotatedDocument] = []
for doc in documents:
annotations: list[Annotation] = []
found_pdf: bool = False
for file in doc.get_files():
fname = Path(file)
if not _is_file_processable(fname):
break
found_pdf = True
try:
annotations.extend(extract(fname))
except fitz.FileDataError as e:
print(f"File structure errors for {file}.\n{e}")
if not found_pdf:
# have to remove curlys or papis logger gets upset
desc = re.sub("[{}]", "", papis.document.describe(doc))
logger.warning("Did not find suitable PDF file for document: " f"{desc}")
output.append(AnnotatedDocument(doc, annotations))
return output
def extract(filename: Path) -> list[Annotation]:
"""Extract annotations from a file.
Returns all readable annotations contained in the file
passed in. Only returns Highlight or Text annotations.
"""
annotations = []
with fitz.Document(filename) as doc:
for page in doc:
for annot in page.annots():
quote, note = _retrieve_annotation_content(page, annot)
if not quote and not note:
continue
col = (
annot.colors.get("fill")
or annot.colors.get("stroke")
or (0.0, 0.0, 0.0)
)
a = Annotation(
file=str(filename),
text=quote or "",
content=note or "",
colors=col,
type=annot.type[1],
page=(page.number or 0) + 1,
)
a.tag = _tag_from_colorname(a.colorname or "")
annotations.append(a)
logger.debug(
f"Found {len(annotations)} "
f"{'annotation' if len(annotations) == 1 else 'annotations'} for {filename}."
)
return annotations
def is_pdf(fname: Path) -> bool:
"""Check if file is a pdf, using mime type."""
return magic.from_file(fname, mime=True) == "application/pdf"
def _is_file_processable(fname: Path) -> bool:
if not fname.is_file():
logger.error(f"File {str(fname)} not readable.")
return False
if not is_pdf(fname):
return False
return True
def _tag_from_colorname(colorname: str) -> str:
color_mapping: dict[str, str] = getdict("tags", "plugins.extract")
if not color_mapping:
return ""
return color_mapping.get(colorname, "")
def _retrieve_annotation_content(
page: fitz.Page, annotation: fitz.Annot
) -> tuple[str | None, str | None]:
"""Gets the text content of an annotation.
Returns the actual content of an annotation. Sometimes
that is only the written words, sometimes that is only
annotation notes, sometimes it is both. Runs a similarity
comparison between strings to find out whether they
should both be included or are the same, using
Levenshtein distance.
"""
content = annotation.info["content"].replace("\n", " ")
written = page.get_textbox(annotation.rect).replace("\n", " ")
# highlight with selection in note
minimum_similarity = (
papis.config.getfloat("minimum_similarity_content", "plugins.extract") or 1.0
)
if Levenshtein.ratio(content, written) > minimum_similarity:
return (content, None)
# both a highlight and a note
elif content and written:
return (written, content)
# an independent note, not a highlight
elif content:
return (None, content)
# highlight with selection not in note
elif written:
return (written, None)
# just a highlight without any text
return (None, None)
# mimics the functions in papis.config.{getlist,getint,getfloat} etc.
def getdict(key: str, section: Optional[str] = None) -> dict[str, str]:
"""Dict getter
:returns: A python dict
:raises SyntaxError: Whenever the parsed syntax is either not a valid
python object or a valid python dict.
"""
rawvalue: Any = papis.config.general_get(key, section=section)
if isinstance(rawvalue, dict):
return rawvalue
try:
rawvalue = eval(rawvalue)
except Exception:
raise SyntaxError(
"The key '{}' must be a valid Python object: {}".format(key, rawvalue)
)
else:
if not isinstance(rawvalue, dict):
raise SyntaxError(
"The key '{}' must be a valid Python dict. Got: {} (type {!r})".format(
key, rawvalue, type(rawvalue).__name__
)
)
return rawvalue

18
papis_extract/extractors/__init__.py
View file

@ -1,18 +0,0 @@
from importlib.util import find_spec
import papis.logging
from papis_extract.extraction import Extractor
from papis_extract.extractors import pdf
from papis_extract.extractors.pocketbook import PocketBookExtractor
logger = papis.logging.get_logger(__name__)
all_extractors: dict[str, Extractor] = {}
all_extractors["pdf"] = pdf.PdfExtractor()
if find_spec("bs4") and find_spec("magic"):
all_extractors["pocketbook"] = PocketBookExtractor()
else:
logger.debug("pocketbook extractor not activated.")

92
papis_extract/extractors/pdf.py
View file

@ -1,92 +0,0 @@
from pathlib import Path
import fitz
import Levenshtein
import magic
import papis.config
import papis.logging
from papis_extract.annotation import Annotation
logger = papis.logging.get_logger(__name__)
class PdfExtractor:
def can_process(self, filename: Path) -> bool:
if not filename.is_file():
logger.error(f"File {str(filename)} not readable.")
return False
if not self._is_pdf(filename):
return False
return True
def run(self, filename: Path) -> list[Annotation]:
"""Extract annotations from a file.
Returns all readable annotations contained in the file
passed in. Only returns Highlight or Text annotations.
"""
annotations = []
with fitz.Document(filename) as doc:
for page in doc:
for annot in page.annots():
quote, note = self._retrieve_annotation_content(page, annot)
if not quote and not note:
continue
col = (
annot.colors.get("fill")
or annot.colors.get("stroke")
or (0.0, 0.0, 0.0)
)
a = Annotation(
file=str(filename),
content=quote or "",
note=note or "",
color=col,
type=annot.type[1],
page=(page.number or 0) + 1,
)
annotations.append(a)
logger.debug(
f"Found {len(annotations)} "
f"{'annotation' if len(annotations) == 1 else 'annotations'} for {filename}."
)
return annotations
def _is_pdf(self, fname: Path) -> bool:
"""Check if file is a pdf, using mime type."""
return magic.from_file(fname, mime=True) == "application/pdf"
def _retrieve_annotation_content(
self, page: fitz.Page, annotation: fitz.Annot
) -> tuple[str | None, str | None]:
"""Gets the text content of an annotation.
Returns the actual content of an annotation. Sometimes
that is only the written words, sometimes that is only
annotation notes, sometimes it is both. Runs a similarity
comparison between strings to find out whether they
should both be included or are the same, using
Levenshtein distance.
"""
content = annotation.info["content"].replace("\n", " ")
written = page.get_textbox(annotation.rect).replace("\n", " ")
# highlight with selection in note
minimum_similarity = (
papis.config.getfloat("minimum_similarity_content", "plugins.extract")
or 1.0
)
if Levenshtein.ratio(content, written) > minimum_similarity:
return (content, None)
# both a highlight and a note
elif content and written:
return (written, content)
# an independent note, not a highlight
elif content:
return (None, content)
# highlight with selection not in note
elif written:
return (written, None)
# just a highlight without any text
return (None, None)

78
papis_extract/extractors/pocketbook.py
View file

@ -1,78 +0,0 @@
from pathlib import Path
import magic
import papis.config
import papis.logging
from bs4 import BeautifulSoup
from papis_extract.annotation import COLORS, Annotation
logger = papis.logging.get_logger(__name__)
class PocketBookExtractor:
def can_process(self, filename: Path) -> bool:
if not magic.from_file(filename, mime=True) == "text/xml":
return False
content = self._read_file(filename)
if not content:
return False
html = BeautifulSoup(content, features="xml")
if not html.find(
"meta", {"name": "generator", "content": "PocketBook Bookmarks Export"}
):
return False
return True
def run(self, filename: Path) -> list[Annotation]:
"""Extract annotations from pocketbook html file.
Export annotations from pocketbook app and load add them
to a papis document as the exported html file.
Returns all readable annotations contained in the file
passed in, with highlights, notes and pages if available.
"""
content = self._read_file(filename)
if not content:
return []
html = BeautifulSoup(content, features="xml")
annotations: list[Annotation] = []
for bm in html.select("div.bookmark"):
content = (bm.select_one("div.bm-text>p") or html.new_string("")).text
note = (bm.select_one("div.bm-note>p") or html.new_string("")).text
page = (bm.select_one("p.bm-page") or html.new_string("")).text
el_classes = bm.attrs.get("class", "").split(" ")
color = (0, 0, 0)
for c in el_classes:
if "bm-color-" in c:
color = COLORS.get(c.removeprefix("bm-color-"), (0, 0, 0))
break
a = Annotation(
file=str(filename),
content=content or "",
note=note or "",
color=color,
type="Highlight",
page=int(page),
)
annotations.append(a)
logger.debug(
f"Found {len(annotations)} "
f"{'annotation' if len(annotations) == 1 else 'annotations'} for {filename}."
)
return annotations
def _read_file(self, filename: Path) -> str:
try:
with open(filename) as f:
return f.read()
except FileNotFoundError:
logger.error(f"Could not open file {filename} for extraction.")
return ""

94
papis_extract/formatter.py
View file

@ -1,39 +1,34 @@
from collections.abc import Callable
from papis.document import Document
from papis_extract.annotation import AnnotatedDocument
from papis_extract.annotation import Annotation
Formatter = Callable[[Document, list[Annotation]], str]
Formatter = Callable[[list[AnnotatedDocument]], str]
def format_markdown(
document: Document = Document(),
annotations: list[Annotation] = [],
headings: str = "setext", # setext | atx | None
docs: list[AnnotatedDocument] = [], atx_headings: bool = False
) -> str:
if not annotations:
return ""
template = (
"{{#tag}}#{{tag}}\n{{/tag}}"
"{{#quote}}> {{quote}}{{/quote}}{{#page}} [p. {{page}}]{{/page}}"
"{{#note}}\n NOTE: {{note}}{{/note}}"
)
output = ""
for entry in docs:
if not entry.annotations:
continue
heading = f"{document.get('title', '')} - {document.get('author', '')}"
if headings == "atx":
output = f"# {heading}\n\n"
elif headings == "setext":
title_decoration = (
f"{'=' * len(document.get('title', ''))} "
f"{'-' * len(document.get('author', ''))}"
)
output = f"{title_decoration}\n{heading}\n{title_decoration}\n\n"
heading = f"{entry.document['title']} - {entry.document['author']}\n"
if atx_headings:
output += f"# {heading}\n"
else:
output = ""
title_decoration = (
f"{'=' * len(entry.document.get('title', ''))} "
f"{'-' * len(entry.document.get('author', ''))}"
)
output += f"{title_decoration}\n" f"{heading}" f"{title_decoration}\n\n"
for a in annotations:
for a in entry.annotations:
output += a.format(template)
output += "\n\n"
@ -42,54 +37,49 @@ def format_markdown(
return output.rstrip()
def format_markdown_atx(
document: Document = Document(),
annotations: list[Annotation] = [],
) -> str:
return format_markdown(document, annotations, headings="atx")
def format_markdown_atx(docs: list[AnnotatedDocument] = []) -> str:
return format_markdown(docs, atx_headings=True)
def format_markdown_setext(
document: Document = Document(),
annotations: list[Annotation] = [],
) -> str:
return format_markdown(document, annotations, headings="setext")
def format_markdown_setext(docs: list[AnnotatedDocument] = []) -> str:
return format_markdown(docs, atx_headings=False)
def format_count(
document: Document = Document(),
annotations: list[Annotation] = [],
) -> str:
if not annotations:
return ""
def format_count(docs: list[AnnotatedDocument] = []) -> str:
output = ""
for entry in docs:
if not entry.annotations:
continue
count = 0
for _ in annotations:
for _ in entry.annotations:
count += 1
return (
f"{document.get('author', '')}"
f"{' - ' if 'author' in document else ''}" # only put separator if author
f"{document.get('title', '')}: "
d = entry.document
output += (
f"{d['author'] if 'author' in d else ''}"
f"{' - ' if 'author' in d else ''}" # only put separator if author
f"{entry.document['title'] if 'title' in d else ''}: "
f"{count}\n"
).rstrip()
)
return output.rstrip()
def format_csv(
document: Document = Document(),
annotations: list[Annotation] = [],
) -> str:
def format_csv(docs: list[AnnotatedDocument] = []) -> str:
header: str = "type,tag,page,quote,note,author,title,ref,file"
template: str = (
'{{type}},{{tag}},{{page}},"{{quote}}","{{note}}",'
'"{{doc.author}}","{{doc.title}}","{{doc.ref}}","{{file}}"'
)
output = f"{header}\n"
if not annotations:
return ""
for entry in docs:
if not entry.annotations:
continue
for a in annotations:
output += a.format(template, doc=document)
d = entry.document
for a in entry.annotations:
output += a.format(template, doc=d)
output += "\n"
return output.rstrip()
@ -99,6 +89,6 @@ formatters: dict[str, Formatter] = {
"count": format_count,
"csv": format_csv,
"markdown": format_markdown,
"markdown-atx": format_markdown_atx,
"markdown-setext": format_markdown_setext,
"markdown_atx": format_markdown_atx,
"markdown_setext": format_markdown_setext,
}

2
poetry.lock generated
View file

@ -1084,4 +1084,4 @@ whoosh = ["whoosh"]
[metadata]
lock-version = "2.0"
python-versions = "^3.11"
content-hash = "273c651cac44163ca183313ce3c7384577f090fd98fa6d28e6a3496cb28254ac"
content-hash = "02d5ac314a19f14103372c7ceccdaec080df3fdc2fdb1381f2f6343cd6d17db4"

17
pyproject.toml
View file

@ -3,21 +3,8 @@ name = "papis-extract"
version = "0.2.0"
description = ""
authors = ["Marty Oehme <marty.oehme@gmail.com>"]
license = "GPL-3.0-or-later"
readme = "README.md"
packages = [{ include = "papis_extract" }]
homepage = "https://git.martyoeh.me/Marty/papis-extract"
repository = "https://github.com/marty-oehme/papis-extract"
keywords = [
"papis",
"pdf",
"biblatex",
"bibtex",
"bibliography",
"reference manager",
"research",
"science",
]
packages = [{include = "papis_extract"}]
[tool.poetry.dependencies]
python = "^3.11"
@ -28,11 +15,9 @@ click = "^8.1.7"
whoosh = { version = "^2.7.4", optional = true }
python-magic = "^0.4.27"
chevron = "^0.14.0"
beautifulsoup4 = { version = "^4.12.3", optional = true }
[tool.poetry.extras]
whoosh = ["whoosh"]
pocketbook = ["beautifulsoup4"]
[tool.poetry.group.dev.dependencies]
pytest = "^7.4.0"

15
tests/test_annotation.py
View file

@ -1,6 +1,5 @@
import pytest
from papis.document import Document
import pytest
from papis_extract.annotation import Annotation
@ -21,8 +20,8 @@ from papis_extract.annotation import Annotation
def test_formatting_replacements(fmt_string, expected):
sut = Annotation(
"myfile",
content="I am the text value",
note="Whereas I represent the note",
text="I am the text value",
content="Whereas I represent the note",
)
assert sut.format(fmt_string) == expected
@ -39,8 +38,8 @@ def test_formatting_replacements(fmt_string, expected):
def test_formatting_document_access(fmt_string, expected):
sut = Annotation(
"myfile",
content="I am the text value",
note="Whereas I represent the note",
text="I am the text value",
content="Whereas I represent the note",
)
doc = Document(data={"title": "document-title", "author": "document-author"})
@ -48,7 +47,7 @@ def test_formatting_document_access(fmt_string, expected):
def test_colorname_matches_exact():
sut = Annotation("testfile", color=(1.0, 0.0, 0.0), minimum_similarity_color=1.0)
sut = Annotation("testfile", colors=(1.0, 0.0, 0.0), minimum_similarity_color=1.0)
c_name = sut.colorname
assert c_name == "red"
@ -65,6 +64,6 @@ def test_colorname_matches_exact():
],
)
def test_matches_inexact_colorname(color_value):
sut = Annotation("testfile", color=color_value, minimum_similarity_color=0.833)
sut = Annotation("testfile", colors=color_value, minimum_similarity_color=0.833)
c_name = sut.colorname
assert c_name == "red"

33
tests/test_formatting.py
View file

@ -1,5 +1,5 @@
from papis.document import Document
from papis_extract.annotation import Annotation
from papis_extract.annotation import AnnotatedDocument, Annotation
from papis_extract.formatter import (
format_count,
@ -9,11 +9,13 @@ from papis_extract.formatter import (
format_markdown_setext,
)
document = Document(data={"author": "document-author", "title": "document-title"})
annotations = [
Annotation("myfile.pdf", content="my lovely text"),
Annotation("myfile.pdf", content="my second text", note="with note"),
]
an_doc: AnnotatedDocument = AnnotatedDocument(
Document(data={"author": "document-author", "title": "document-title"}),
[
Annotation("myfile.pdf", text="my lovely text"),
Annotation("myfile.pdf", text="my second text", content="with note"),
],
)
md_default_output = """============== ---------------
document-title - document-author
============== ---------------
@ -26,12 +28,12 @@ document-title - document-author
def test_markdown_default():
fmt = format_markdown
assert fmt(document, annotations) == md_default_output
assert fmt([an_doc]) == md_default_output
def test_markdown_atx():
fmt = format_markdown_atx
assert fmt(document, annotations) == (
assert fmt([an_doc]) == (
"""# document-title - document-author
> my lovely text
@ -43,17 +45,17 @@ def test_markdown_atx():
def test_markdown_setext():
fmt = format_markdown_setext
assert fmt(document, annotations) == md_default_output
assert fmt([an_doc]) == md_default_output
def test_count_default():
fmt = format_count
assert fmt(document, annotations) == ("""document-author - document-title: 2""")
assert fmt([an_doc]) == ("""document-author - document-title: 2""")
def test_csv_default():
fmt = format_csv
assert fmt(document, annotations) == (
assert fmt([an_doc]) == (
"type,tag,page,quote,note,author,title,ref,file\n"
'Highlight,,0,"my lovely text","","document-author",'
'"document-title","","myfile.pdf"\n'
@ -64,12 +66,15 @@ def test_csv_default():
# sadpath - no annotations contained for each format
def test_markdown_no_annotations():
assert format_markdown(document, []) == ""
d: AnnotatedDocument = AnnotatedDocument(Document(data={}), [])
assert format_markdown([d]) == ""
def test_count_no_annotations():
assert format_count(document, []) == ""
d: AnnotatedDocument = AnnotatedDocument(Document(data={}), [])
assert format_count([d]) == ""
def test_csv_no_annotations():
assert format_csv(document, []) == ""
d: AnnotatedDocument = AnnotatedDocument(Document(data={}), [])
assert format_csv([d]) == "type,tag,page,quote,note,author,title,ref,file"