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6
.markdownlint.yaml
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@ -1,6 +0,0 @@
MD013: false
MD025: false
MD007:
indent: 4

7
.papis.config
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@ -1,7 +0,0 @@
[settings]
default-library = main
picktool = papis
formater = python
[main]
dir = temp/lib

96
README.md
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@ -8,10 +8,10 @@
Quickly extract annotations from your pdf files with the help of the [papis](https://github.com/papis/papis) bibliography manager.\ Quickly extract annotations from your pdf files with the help of the [papis](https://github.com/papis/papis) bibliography manager.\
Easily organize all your highlights and thoughts next to your documents and references.\ Easily organize all your highlights and thoughts next to your documents and references.\
## Installation ## Installation:
<!-- TODO set up pypi repository / explain git install path --> <!-- TODO set up pypi repository / explain git install path -->
You can install through pip with `pip install git+https://git.martyoeh.me/Marty/papis-extract.git`. You can install from pypi with `pip install git+https://git.martyoeh.me/Marty/papis-extract.git`.
That's it! If you have papis and papis-extract installed in the same environment (whether virtual or global), That's it! If you have papis and papis-extract installed in the same environment (whether virtual or global),
everything should now be set up. everything should now be set up.
@ -24,8 +24,7 @@ You will be set up with the default options but if you want to change anything,
> **Note** > **Note**
> This plugin is still in fairly early development. It does what I need it to do, but if you have a meticulously organized library *please* make backups before doing any operation which could affect your notes, or make use of the papis-included git options. > This plugin is still in fairly early development. It does what I need it to do, but if you have a meticulously organized library *please* make backups before doing any operation which could affect your notes, or make use of the papis-included git options.
## Usage:
## Usage
`papis extract [OPTIONS] [QUERY]` `papis extract [OPTIONS] [QUERY]`
@ -88,44 +87,16 @@ On my current laptop, extracting ~4000 annotations from ~1000 library documents
though this will vary with the length and size of the PDFs you have. though this will vary with the length and size of the PDFs you have.
For smaller workloads the process should be almost instant. For smaller workloads the process should be almost instant.
You can change the format that you want your annotations in with the `--template` option.
To output annotations in a markdown-compatible syntax (the default), do:
```bash
papis extract --template markdown
```
There are sub-variants of the formatter for atx-style headers, with `--template markdown-atx` (`# Headings`),
or setext-style with `--template markdown-setext` (the default style).
To instead see them in a csv syntax simply invoke:
```bash
papis extract --template csv
```
And if you only want to know how many annotations exist in the documents, you can invoke:
```bash
papis extract --template count
```
For now, these are the only formatters the plugin knows about.
Be aware that if you write to your notes using a different template the plugin will *not* detect old annotations and drop them,
so you will be doubling up your annotations.
## Configuration ## Configuration
### Basic configuration ### Basic configuration
Add `extract` plugin settings to your papis `config` file (usually `~/.config/papis/config`): Add `extract` plugin settings to your papis `config` file (usually `~/.config/papis/config`):
You will rarely have to set everything explained in the next few paragraphs - You will rarely have to set everything explained in the next few paragraphs -
in fact you can use the plugin without having to set up any of it if you are happy with the defaults. in fact you can use the plugin without having to set up any of it if you are happy with the defaults.
The full default settings look as follows: The full default settings look as follows:
```conf ```yaml
[plugins.extract] [plugins.extract]
on_import: False on_import: False
tags = {"important": "red", "toread": "blue"} tags = {"important": "red", "toread": "blue"}
@ -136,7 +107,7 @@ minimum_similarity_color = 0.833 # for matching tag to color
### Automatic extraction ### Automatic extraction
```conf ```yaml
[plugins.extract] [plugins.extract]
on_import: True on_import: True
``` ```
@ -148,16 +119,16 @@ if `False` extraction only happens when you explicitly invoke it.
Extraction will *not* happen automatically when you add new annotations to an existing document, Extraction will *not* happen automatically when you add new annotations to an existing document,
regardless of this setting. regardless of this setting.
### Automatic tagging #### Automatic tagging
By supplying the tags option with a valid python dictionary of the form `{"tag": "color", "tag2": "color2"}`, By supplying the tags option with a valid python dictionary of the form `{"tag": "color", "tag2": "color2"}`,
you can enable automatic tagging for your annotations. you can enable automatic tagging for your annotations.
You thus ascribe specific meanings to the colors you use in highlighting. You thus ascribe specific meanings to the colors you use in highlighting.
For example, if you always highlight the most essential arguments and findings in red and always highlight things you have to follow up on in blue, you can assign the meanings 'important' and 'todo' to them respectively as follows: For example, if you always highlight the most essential arguments and findings in red and always highlight things you have to follow up on in blue, you can assign the meanings 'important' and 'todo' to them respectively as follows:
```conf ```yaml
[plugins.extract] [plugins.extract]
tags = {"red": "important", "blue": "toread"} tags = {"red": "important", "blue": "toread"}
``` ```
@ -169,14 +140,14 @@ no defaults are set here.
### Advanced configuration ### Advanced configuration
```conf ```yaml
[plugins.extract] [plugins.extract]
minimum_similarity: 0.75, # for checking against existing annotations minimum_similarity: 0.75, # for checking against existing annotations
minimum_similarity_content: 0.9, # for checking if highlight or note minimum_similarity_content: 0.9, # for checking if highlight or note
minimum_similarity_color: 0.833, # for matching tag to color minimum_similarity_color: 0.833, # for matching tag to color
``` ```
`minimum_similarity` sets the required similarity of an annotation with existing annotations in your notes to be dropped. `minimum_similarity` sets the required similarity of an annotation with existing annotations in your notes to be dropped.
Annotations you have in notes might change if you for example fix small spacing mistakes or a letter/punctuation that has been falsely recognized in the PDF or change similar things. Annotations you have in notes might change if you for example fix small spacing mistakes or a letter/punctuation that has been falsely recognized in the PDF or change similar things.
Generally, this should be fine as it is but you should change this value if you either get new annotations dropped though they should be added (decrease the value) or annotations are added duplicating existing ones (increase the value). Generally, this should be fine as it is but you should change this value if you either get new annotations dropped though they should be added (decrease the value) or annotations are added duplicating existing ones (increase the value).
@ -206,12 +177,10 @@ Known issues to be fixed:
- [x] Speed? - [x] Speed?
- should be fine, on my machine (old i5 laptop) it takes around 90s for ~1000 documents with ~4000 annotations - should be fine, on my machine (old i5 laptop) it takes around 90s for ~1000 documents with ~4000 annotations
- [x] ensure all cmdline options do what they should - [x] ensure all cmdline options do what they should
- [x] annotations carry over color object from fitz, should just be Color object or simple tuple with rgb vals - [ ] annotations carry over color object from fitz, should just be Color object or simple tuple with rgb vals
- [x] docstrings, docstrings! - [ ] docstrings, docstrings!
- [ ] testing testing testing!! - [ ] testing testing testing!!
- [ ] refactor into some better abstractions (e.g. Exporter Protocol -> stdout/markdown implementations; Extractor Protocol -> PDF implementation) - [ ] refactor into some better abstractions (e.g. Exporter Protocol -> stdout/markdown implementations; Extractor Protocol -> PDF implementation)
- [ ] dependency injection for extractor/exporter/formatter/annotation modules
- [ ] any call to papis.config should start from init and be injected?
features to be implemented: features to be implemented:
@ -219,7 +188,7 @@ features to be implemented:
- [x] static analysis (lint, typecheck etc) on pushes - [x] static analysis (lint, typecheck etc) on pushes
- [x] test pipeline on master pushes - [x] test pipeline on master pushes
- [ ] release pipeline to pypi on tags - [ ] release pipeline to pypi on tags
- [x] add page number if available - [ ] add page number if available
- exists in Annotation, just need to place in output - exists in Annotation, just need to place in output
- [ ] show overall amount of extractions at the end - [ ] show overall amount of extractions at the end
- [ ] custom formatting decided by user - [ ] custom formatting decided by user
@ -232,8 +201,7 @@ features to be implemented:
- [ ] allow custom colors -> tag name settings not dependent on color name existing (e.g. {"important": (1.0,0.0,0.0)}) - [ ] 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 - [ ] `--overwrite` mode where existing annotations are not dropped but overwritten on same line of note
- [ ] `--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 - [ ] `--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 - [ ] on_add hook to extract annotations as files are added
- needs upstream help, 'on_add' hook, and pass-through of affected documents - needs upstream help, 'on_add' hook, and pass-through of affected documents
@ -251,36 +219,12 @@ This plugin makes an effort to find the right combination and extract the writte
as well as any additional notes made - but things *will* slip through or extract weirdly every now as well as any additional notes made - but things *will* slip through or extract weirdly every now
and again. and again.
Secondly, a note on the pages: I use the page number that the mupdf library gives me when it The easiest extraction is provided if your program writes the selection itself into the highlight
extracts anything from the pdf file. Sometimes that number will be correct for the document, content, because then we can just use that. It is harder to parse if it does not and will sometimes
sometimes it will however be the number of the *pdf document* internally. This can happen if get additional words in front or behind (especially if the highlight ends in the middle of a line)
e.g. an article or a book has frontmatter without numbering scheme or with a different one. or even cut a few off.
Sometimes the correct pages will still be embedded in the pdf and everything will work,
others it won't. So always double check your page numbers!
I am not sure if there is much I can do about these issues for now. I am not sure if there is much I can do about this.
## For developers
and for myself whenever I forget. The basic building blocks currently in here are three:
- extractors
: Extract data from a source file attached to a papis document.
- annotations
: The actual extracted blocks of text, containing some metadata
info as well, such as their color, type, page.
- exporters
: Put the extracted data somewhere. For now stdout or into your notes.
- formatters
: Make sure the exporter saves the data according to your preferred layout,
such as a markdown syntax or csv-structure.
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 should we ever include more extractors than the one for PDFs.
--- ---

55
papis_extract/__init__.py
View file

@ -8,10 +8,7 @@ import papis.strings
from papis.document import Document from papis.document import Document
from papis_extract import extractor, exporter from papis_extract import extractor, exporter
from papis_extract.formatter import ( from papis_extract.annotation_data import AnnotatedDocument
Formatter,
formatters
)
logger = papis.logging.get_logger(__name__) logger = papis.logging.get_logger(__name__)
@ -31,54 +28,41 @@ papis.config.register_default_settings(DEFAULT_OPTIONS)
@click.help_option("-h", "--help") @click.help_option("-h", "--help")
@papis.cli.query_argument() @papis.cli.query_argument()
@papis.cli.doc_folder_option() @papis.cli.doc_folder_option()
@papis.cli.git_option(help="Commit changes made to the notes files.") @papis.cli.git_option(help="Add changes made to the notes files")
@papis.cli.all_option() @papis.cli.all_option()
@click.option(
"--write/--no-write",
"-w",
help="Do not write annotations to notes only print results to stdout.",
)
@click.option( @click.option(
"--manual/--no-manual", "--manual/--no-manual",
"-m", "-m",
help="Open note in editor for manual editing after annotation extraction.", help="Open each note in editor for manual editing after extracting its annotations",
) )
@click.option( @click.option(
"--template", "--write/--no-write",
"-t", "-w",
type=click.Choice( help="Do not write annotations to notes only print results to stdout",
["markdown", "markdown-setext", "markdown-atx", "count", "csv"],
case_sensitive=False,
),
help="Choose an output template to format annotations with.",
)
@click.option(
"--force/--no-force",
"-f",
help="Do not drop any annotations because they already exist.",
) )
def main( def main(
query: str, query: str,
# info: bool,
# _papis_id: bool, # _papis_id: bool,
# _file: bool, # _file: bool,
# notes: bool,
# _dir: bool, # _dir: bool,
# _format: str,
_all: bool, _all: bool,
doc_folder: str, doc_folder: str,
manual: bool, manual: bool,
write: bool, write: bool,
template: str,
git: bool, git: bool,
) -> None: ) -> None:
"""Extract annotations from any pdf document. """Extract annotations from any pdf document
The extract plugin allows manual or automatic extraction of all annotations The extract plugin allows manual or automatic extraction of all annotations
contained in the pdf documents belonging to entries of the papis library. contained in the pdf documents belonging to entries of the pubs library.
It can write those changes to stdout or directly create and update notes It can write those changes to stdout or directly create and update notes
for papis documents. for papis documents.
It adds a `papis extract` subcommand through which it is invoked, but can It adds a `papis extract` subcommand through which it is invoked, but can
optionally run whenever a new document is imported for a papis entry, optionally run whenever a new document is imported for a pubs entry.
if set in the plugin configuration.
""" """
documents = papis.cli.handle_doc_folder_query_all_sort( documents = papis.cli.handle_doc_folder_query_all_sort(
query, doc_folder, sort_field=None, sort_reverse=False, _all=_all query, doc_folder, sort_field=None, sort_reverse=False, _all=_all
@ -87,22 +71,19 @@ def main(
logger.warning(papis.strings.no_documents_retrieved_message) logger.warning(papis.strings.no_documents_retrieved_message)
return return
formatter = formatters[template] run(documents, edit=manual, write=write, git=git)
run(documents, edit=manual, write=write, git=git, formatter=formatter)
def run( def run(
documents: list[Document], documents: list[Document],
formatter: Formatter,
edit: bool = False, edit: bool = False,
write: bool = False, write: bool = False,
git: bool = False, git: bool = False,
) -> None: ) -> None:
annotated_docs = extractor.start(documents)
doc_annotations: list[AnnotatedDocument] = extractor.start(documents)
if write: if write:
exporter.to_notes( exporter.to_notes(doc_annotations, edit=edit, git=git)
formatter=formatter, annotated_docs=annotated_docs, edit=edit, git=git
)
else: else:
exporter.to_stdout(formatter=formatter, annotated_docs=annotated_docs) exporter.to_stdout(doc_annotations)

18
papis_extract/annotation.py → papis_extract/annotation_data.py
View file

@ -20,10 +20,7 @@ COLORS = {
@dataclass @dataclass
class Annotation: class Annotation:
"""A PDF annotation object. """A PDF annotation object"""
Contains all information necessary for the annotation itself, content and metadata.
"""
file: str file: str
colors: tuple[float, float, float] = field(default_factory=lambda: (0.0, 0.0, 0.0)) colors: tuple[float, float, float] = field(default_factory=lambda: (0.0, 0.0, 0.0))
@ -34,7 +31,7 @@ class Annotation:
type: str = "Highlight" type: str = "Highlight"
minimum_similarity_color: float = 1.0 minimum_similarity_color: float = 1.0
def format(self, formatting: str, doc: Document = Document()): def format(self, formatting):
"""Return a formatted string of the annotation. """Return a formatted string of the annotation.
Given a provided formatting pattern, this method returns the annotation Given a provided formatting pattern, this method returns the annotation
@ -48,7 +45,6 @@ class Annotation:
"page": self.page, "page": self.page,
"tag": self.tag, "tag": self.tag,
"type": self.type, "type": self.type,
"doc": doc,
} }
return chevron.render(formatting, data) return chevron.render(formatting, data)
@ -59,7 +55,9 @@ class Annotation:
Finds the closest named color to the annotation and returns it, Finds the closest named color to the annotation and returns it,
using euclidian distance between the two color vectors. using euclidian distance between the two color vectors.
""" """
annot_colors = self.colors or (0.0, 0.0, 0.0) annot_colors = (
self.colors or (0.0, 0.0, 0.0)
)
nearest = None nearest = None
minimum_similarity = ( minimum_similarity = (
papis.config.getfloat("minimum_similarity_color", "plugins.extract") or 1.0 papis.config.getfloat("minimum_similarity_color", "plugins.extract") or 1.0
@ -85,11 +83,5 @@ class Annotation:
@dataclass @dataclass
class AnnotatedDocument: class AnnotatedDocument:
"""Contains all annotations belonging to a single papis document.
Combines a document with a list of annotations which belong to it."""
document: Document document: Document
annotations: list[Annotation] annotations: list[Annotation]
# TODO could implement a from_doc() static method to generate annotation list?

97
papis_extract/exporter.py
View file

@ -6,41 +6,64 @@ import papis.api
import papis.git import papis.git
import papis.config import papis.config
import Levenshtein import Levenshtein
from papis_extract.annotation import AnnotatedDocument
from papis_extract.formatter import Formatter from papis_extract.annotation_data import AnnotatedDocument, Annotation
logger = papis.logging.get_logger(__name__) logger = papis.logging.get_logger(__name__)
def to_stdout(formatter: Formatter, annotated_docs: list[AnnotatedDocument]) -> None: def _format_annotation(annotation: Annotation) -> str:
note = f"NOTE: {annotation.content}" if annotation.content else ""
return f"> {annotation.text}\n {note}"
def to_stdout(annots: list[AnnotatedDocument]) -> None:
"""Pretty print annotations to stdout. """Pretty print annotations to stdout.
Gives a nice human-readable representations of Gives a nice human-readable representations of
the annotations in somewhat of a list form. the annotations in somewhat of a list form.
Not intended for machine-readability. Not intended for machine-readability.
""" """
output: str = formatter(annotated_docs) if not annots:
print(output.rstrip("\n")) return
for entry in annots:
if not entry.annotations:
continue
title_decoration = (
f"{'=' * len(entry.document.get('title', ''))} "
f"{'-' * len(entry.document.get('author', ''))}"
)
print(
f"{title_decoration}\n{papis.document.describe(entry.document)}\n{title_decoration}\n"
)
for a in entry.annotations:
print(_format_annotation(a))
if entry != annots[-1]:
print("\n")
def to_notes( def to_notes(annots: list[AnnotatedDocument], edit: bool, git: bool) -> None:
formatter: Formatter,
annotated_docs: list[AnnotatedDocument],
edit: bool,
git: bool,
force: bool,
) -> None:
"""Write annotations into document notes. """Write annotations into document notes.
Permanently writes the given annotations into notes Permanently writes the given annotations into notes
belonging to papis documents. Creates new notes for belonging to papis documents. Creates new notes for
documents missing a note field or appends to existing. documents missing a note field or appends to existing.
""" """
for entry in annotated_docs: if not annots:
formatted_annotations = formatter([entry]).split("\n") return
if formatted_annotations:
_add_annots_to_note(entry.document, formatted_annotations, force=force) for entry in annots:
if not entry.annotations:
continue
formatted_annotations: list[str] = []
for a in entry.annotations:
formatted_annotations.append(_format_annotation(a))
_add_annots_to_note(entry.document, formatted_annotations)
if edit: if edit:
papis.commands.edit.edit_notes(entry.document, git=git) papis.commands.edit.edit_notes(entry.document, git=git)
@ -50,26 +73,11 @@ def _add_annots_to_note(
document: papis.document.Document, document: papis.document.Document,
formatted_annotations: list[str], formatted_annotations: list[str],
git: bool = False, git: bool = False,
force: bool = False,
) -> None: ) -> None:
""" """Append new annotations to the end of a note.
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 Looks through note to determine any new annotations which should be
document object containing the note, a list of formatted annotations to be added and adds them to the end of the note file.
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.") logger.debug("Adding annotations to note.")
notes_path = papis.notes.notes_path_ensured(document) notes_path = papis.notes.notes_path_ensured(document)
@ -78,9 +86,9 @@ def _add_annots_to_note(
with open(notes_path, "r") as file_read: with open(notes_path, "r") as file_read:
existing = file_read.readlines() existing = file_read.readlines()
new_annotations: list[str] = [] new_annotations: list[str] = _drop_existing_annotations(
if not force: formatted_annotations, existing
new_annotations = _drop_existing_annotations(formatted_annotations, existing) )
if not new_annotations: if not new_annotations:
return return
@ -88,8 +96,7 @@ def _add_annots_to_note(
# add newline if theres no empty space at file end # add newline if theres no empty space at file end
if len(existing) > 0 and existing[-1].strip() != "": if len(existing) > 0 and existing[-1].strip() != "":
f.write("\n") f.write("\n")
print(new_annotations) f.write("\n".join(new_annotations))
f.write("\n\n".join(new_annotations))
f.write("\n") f.write("\n")
logger.info( logger.info(
f"Wrote {len(new_annotations)} " f"Wrote {len(new_annotations)} "
@ -109,14 +116,6 @@ def _add_annots_to_note(
def _drop_existing_annotations( def _drop_existing_annotations(
formatted_annotations: list[str], file_lines: list[str] formatted_annotations: list[str], file_lines: list[str]
) -> 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 = ( minimum_similarity = (
papis.config.getfloat("minimum_similarity", "plugins.extract") or 1.0 papis.config.getfloat("minimum_similarity", "plugins.extract") or 1.0
) )
@ -124,9 +123,7 @@ def _drop_existing_annotations(
remaining: list[str] = [] remaining: list[str] = []
for an in formatted_annotations: for an in formatted_annotations:
an_split = an.splitlines() an_split = an.splitlines()
if an_split and not _test_similarity( if not _test_similarity(an_split[0], file_lines, minimum_similarity):
an_split[0], file_lines, minimum_similarity
):
remaining.append(an) remaining.append(an)
return remaining return remaining

3
papis_extract/extractor.py
View file

@ -10,7 +10,7 @@ import papis.config
import papis.document import papis.document
from papis.document import Document from papis.document import Document
from papis_extract.annotation import Annotation, AnnotatedDocument from papis_extract.annotation_data import Annotation, AnnotatedDocument
logger = papis.logging.get_logger(__name__) logger = papis.logging.get_logger(__name__)
@ -83,7 +83,6 @@ def extract(filename: Path) -> list[Annotation]:
def is_pdf(fname: Path) -> bool: def is_pdf(fname: Path) -> bool:
"""Check if file is a pdf, using mime type."""
return magic.from_file(fname, mime=True) == "application/pdf" return magic.from_file(fname, mime=True) == "application/pdf"

94
papis_extract/formatter.py
View file

@ -1,94 +0,0 @@
from collections.abc import Callable
from papis_extract.annotation import AnnotatedDocument
Formatter = Callable[[list[AnnotatedDocument]], str]
def format_markdown(
docs: list[AnnotatedDocument] = [], atx_headings: bool = False
) -> str:
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"{entry.document['title']} - {entry.document['author']}\n"
if atx_headings:
output += f"# {heading}\n"
else:
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 entry.annotations:
output += a.format(template)
output += "\n\n"
output += "\n\n\n"
return output.rstrip()
def format_markdown_atx(docs: list[AnnotatedDocument] = []) -> str:
return format_markdown(docs, atx_headings=True)
def format_markdown_setext(docs: list[AnnotatedDocument] = []) -> str:
return format_markdown(docs, atx_headings=False)
def format_count(docs: list[AnnotatedDocument] = []) -> str:
output = ""
for entry in docs:
if not entry.annotations:
continue
count = 0
for _ in entry.annotations:
count += 1
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"
)
return output.rstrip()
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"
for entry in docs:
if not entry.annotations:
continue
d = entry.document
for a in entry.annotations:
output += a.format(template, doc=d)
output += "\n"
return output.rstrip()
formatters: dict[str, Formatter] = {
"count": format_count,
"csv": format_csv,
"markdown": format_markdown,
"markdown_atx": format_markdown_atx,
"markdown_setext": format_markdown_setext,
}

387
poetry.lock generated
View file

@ -1,4 +1,4 @@
# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand. # This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand.
[[package]] [[package]]
name = "arxiv2bib" name = "arxiv2bib"
@ -183,70 +183,6 @@ files = [
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] ]
[[package]]
name = "coverage"
version = "7.3.1"
description = "Code coverage measurement for Python"
optional = false
python-versions = ">=3.8"
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[package.extras]
toml = ["tomli"]
[[package]] [[package]]
name = "dominate" name = "dominate"
version = "2.8.0" version = "2.8.0"
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{file = "rapidfuzz-3.3.0.tar.gz", hash = "sha256:5e71bc5829f41e78b2d009431aedeb308ee3699d2bbbc68b7739db9b40bd1465"},
] ]
[package.extras] [package.extras]
@ -981,13 +883,13 @@ use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"]
[[package]] [[package]]
name = "soupsieve" name = "soupsieve"
version = "2.5" version = "2.4.1"
description = "A modern CSS selector implementation for Beautiful Soup." description = "A modern CSS selector implementation for Beautiful Soup."
optional = false optional = false
python-versions = ">=3.8" python-versions = ">=3.7"
files = [ files = [
{file = "soupsieve-2.5-py3-none-any.whl", hash = "sha256:eaa337ff55a1579b6549dc679565eac1e3d000563bcb1c8ab0d0fefbc0c2cdc7"}, {file = "soupsieve-2.4.1-py3-none-any.whl", hash = "sha256:1c1bfee6819544a3447586c889157365a27e10d88cde3ad3da0cf0ddf646feb8"},
{file = "soupsieve-2.5.tar.gz", hash = "sha256:5663d5a7b3bfaeee0bc4372e7fc48f9cff4940b3eec54a6451cc5299f1097690"}, {file = "soupsieve-2.4.1.tar.gz", hash = "sha256:89d12b2d5dfcd2c9e8c22326da9d9aa9cb3dfab0a83a024f05704076ee8d35ea"},
] ]
[[package]] [[package]]
@ -1037,13 +939,13 @@ telegram = ["requests"]
[[package]] [[package]]
name = "typing-extensions" name = "typing-extensions"
version = "4.8.0" version = "4.7.1"
description = "Backported and Experimental Type Hints for Python 3.8+" description = "Backported and Experimental Type Hints for Python 3.7+"
optional = false optional = false
python-versions = ">=3.8" python-versions = ">=3.7"
files = [ files = [
{file = "typing_extensions-4.8.0-py3-none-any.whl", hash = "sha256:8f92fc8806f9a6b641eaa5318da32b44d401efaac0f6678c9bc448ba3605faa0"}, {file = "typing_extensions-4.7.1-py3-none-any.whl", hash = "sha256:440d5dd3af93b060174bf433bccd69b0babc3b15b1a8dca43789fd7f61514b36"},
{file = "typing_extensions-4.8.0.tar.gz", hash = "sha256:df8e4339e9cb77357558cbdbceca33c303714cf861d1eef15e1070055ae8b7ef"}, {file = "typing_extensions-4.7.1.tar.gz", hash = "sha256:b75ddc264f0ba5615db7ba217daeb99701ad295353c45f9e95963337ceeeffb2"},
] ]
[[package]] [[package]]
@ -1078,7 +980,7 @@ files = [
name = "whoosh" name = "whoosh"
version = "2.7.4" version = "2.7.4"
description = "Fast, pure-Python full text indexing, search, and spell checking library." description = "Fast, pure-Python full text indexing, search, and spell checking library."
optional = true optional = false
python-versions = "*" python-versions = "*"
files = [ files = [
{file = "Whoosh-2.7.4-py2.py3-none-any.whl", hash = "sha256:aa39c3c3426e3fd107dcb4bde64ca1e276a65a889d9085a6e4b54ba82420a852"}, {file = "Whoosh-2.7.4-py2.py3-none-any.whl", hash = "sha256:aa39c3c3426e3fd107dcb4bde64ca1e276a65a889d9085a6e4b54ba82420a852"},
@ -1086,10 +988,7 @@ files = [
{file = "Whoosh-2.7.4.zip", hash = "sha256:e0857375f63e9041e03fedd5b7541f97cf78917ac1b6b06c1fcc9b45375dda69"}, {file = "Whoosh-2.7.4.zip", hash = "sha256:e0857375f63e9041e03fedd5b7541f97cf78917ac1b6b06c1fcc9b45375dda69"},
] ]
[extras]
whoosh = ["whoosh"]
[metadata] [metadata]
lock-version = "2.0" lock-version = "2.0"
python-versions = "^3.11" python-versions = "^3.11"
content-hash = "02d5ac314a19f14103372c7ceccdaec080df3fdc2fdb1381f2f6343cd6d17db4" content-hash = "a3af36ed2941235df158c20ba9b66bdf5a0af0554235fd004ec77c3e88def3c3"

14
pyproject.toml
View file

@ -12,21 +12,17 @@ pymupdf = "^1.23.1"
levenshtein = "^0.21.1" levenshtein = "^0.21.1"
papis = "^0.13" papis = "^0.13"
click = "^8.1.7" click = "^8.1.7"
whoosh = { version = "^2.7.4", optional = true } whoosh = "^2.7.4"
python-magic = "^0.4.27" python-magic = "^0.4.27"
chevron = "^0.14.0" chevron = "^0.14.0"
[tool.poetry.extras]
whoosh = ["whoosh"]
[tool.poetry.group.dev.dependencies]
pytest = "^7.4.0"
coverage = "^7.3.1"
pytest-cov = "^4.1.0"
[tool.poetry.plugins."papis.command"] [tool.poetry.plugins."papis.command"]
extract = "papis_extract:main" extract = "papis_extract:main"
[tool.poetry.group.dev.dependencies]
pytest = "^7.4.0"
[build-system] [build-system]
requires = ["poetry-core"] requires = ["poetry-core"]
build-backend = "poetry.core.masonry.api" build-backend = "poetry.core.masonry.api"

32
tests/test_annotation.py
View file

@ -1,6 +1,5 @@
from papis.document import Document
import pytest import pytest
from papis_extract.annotation import Annotation from papis_extract.annotation_data import Annotation
@pytest.mark.parametrize( @pytest.mark.parametrize(
@ -17,7 +16,7 @@ from papis_extract.annotation import Annotation
), ),
], ],
) )
def test_formatting_replacements(fmt_string, expected): def test_formatting(fmt_string, expected):
sut = Annotation( sut = Annotation(
"myfile", "myfile",
text="I am the text value", text="I am the text value",
@ -26,30 +25,13 @@ def test_formatting_replacements(fmt_string, expected):
assert sut.format(fmt_string) == expected assert sut.format(fmt_string) == expected
@pytest.mark.parametrize(
"fmt_string,expected",
[
("{{doc.title}}", "document-title"),
("{{doc.title}}-{{doc.author}}", "document-title-document-author"),
("{{quote}} ({{doc.author}})", "I am the text value (document-author)"),
]
)
def test_formatting_document_access(fmt_string, expected):
sut = Annotation(
"myfile",
text="I am the text value",
content="Whereas I represent the note",
)
doc = Document(data= {"title": "document-title", "author": "document-author"})
assert sut.format(fmt_string, doc=doc) == expected
def test_colorname_matches_exact(): def test_colorname_matches_exact():
sut = Annotation("testfile", colors=(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 c_name = sut.colorname
assert c_name == "red" assert c_name == "red"
# TODO inject closeness value instead of relying on default # TODO inject closeness value instead of relying on default
@pytest.mark.parametrize( @pytest.mark.parametrize(
"color_value", "color_value",
@ -62,6 +44,8 @@ def test_colorname_matches_exact():
], ],
) )
def test_matches_inexact_colorname(color_value): def test_matches_inexact_colorname(color_value):
sut = Annotation("testfile", colors=color_value, minimum_similarity_color=0.833) sut = Annotation(
"testfile", colors=color_value, minimum_similarity_color=0.833
)
c_name = sut.colorname c_name = sut.colorname
assert c_name == "red" assert c_name == "red"

80
tests/test_formatting.py
View file

@ -1,80 +0,0 @@
from papis.document import Document
from papis_extract.annotation import AnnotatedDocument, Annotation
from papis_extract.formatter import (
format_count,
format_csv,
format_markdown,
format_markdown_atx,
format_markdown_setext,
)
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
============== ---------------
> my lovely text
> my second text
NOTE: with note"""
def test_markdown_default():
fmt = format_markdown
assert fmt([an_doc]) == md_default_output
def test_markdown_atx():
fmt = format_markdown_atx
assert fmt([an_doc]) == (
"""# document-title - document-author
> my lovely text
> my second text
NOTE: with note"""
)
def test_markdown_setext():
fmt = format_markdown_setext
assert fmt([an_doc]) == md_default_output
def test_count_default():
fmt = format_count
assert fmt([an_doc]) == ("""document-author - document-title: 2""")
def test_csv_default():
fmt = format_csv
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'
'Highlight,,0,"my second text","with note","document-author",'
'"document-title","","myfile.pdf"'
)
# sadpath - no annotations contained for each format
def test_markdown_no_annotations():
d: AnnotatedDocument = AnnotatedDocument(Document(data={}), [])
assert format_markdown([d]) == ""
def test_count_no_annotations():
d: AnnotatedDocument = AnnotatedDocument(Document(data={}), [])
assert format_count([d]) == ""
def test_csv_no_annotations():
d: AnnotatedDocument = AnnotatedDocument(Document(data={}), [])
assert format_csv([d]) == "type,tag,page,quote,note,author,title,ref,file"