Switch to node-python image

Added static linting, type checking for each commit as well as pytest
testing for each master push.

Add linting and static analysis CI

Use deprecated pipeline key for server woodpecker version

Format black

Install poetry environment before pyright

Add pytest CI

Update dependencies, Fix black

Ensure tests run on master branch

.markdownlint.yaml

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

.papis.config

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

.woodpecker/lint.yml

@@ -1,4 +1,4 @@
-steps:
+pipeline:
   lint_ruff:
     image: python
     commands:

.woodpecker/static_analysis.yml

@@ -1,4 +1,4 @@
-steps:
+pipeline:
   pyright:
     image: nikolaik/python-nodejs
     commands:

.woodpecker/test.yml

@@ -1,7 +1,6 @@
-when:
+branches: master
-  branch: main
 
-steps:
+pipeline:
   pytest:
     image: ghcr.io/withlogicco/poetry:1.5.1
     commands:

COPYING

@@ -1,674 +0,0 @@
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-by the Free Software Foundation.
-
-  If the Program specifies that a proxy can decide which future
-versions of the GNU General Public License can be used, that proxy's
-public statement of acceptance of a version permanently authorizes you
-to choose that version for the Program.
-
-  Later license versions may give you additional or different
-permissions.  However, no additional obligations are imposed on any
-author or copyright holder as a result of your choosing to follow a
-later version.
-
-  15. Disclaimer of Warranty.
-
-  THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
-APPLICABLE LAW.  EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
-HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
-OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
-THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
-PURPOSE.  THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
-IS WITH YOU.  SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
-ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
-
-  16. Limitation of Liability.
-
-  IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
-WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
-THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
-GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
-USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
-DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
-PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
-EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
-SUCH DAMAGES.
-
-  17. Interpretation of Sections 15 and 16.
-
-  If the disclaimer of warranty and limitation of liability provided
-above cannot be given local legal effect according to their terms,
-reviewing courts shall apply local law that most closely approximates
-an absolute waiver of all civil liability in connection with the
-Program, unless a warranty or assumption of liability accompanies a
-copy of the Program in return for a fee.
-
-                     END OF TERMS AND CONDITIONS
-
-            How to Apply These Terms to Your New Programs
-
-  If you develop a new program, and you want it to be of the greatest
-possible use to the public, the best way to achieve this is to make it
-free software which everyone can redistribute and change under these terms.
-
-  To do so, attach the following notices to the program.  It is safest
-to attach them to the start of each source file to most effectively
-state the exclusion of warranty; and each file should have at least
-the "copyright" line and a pointer to where the full notice is found.
-
-    <one line to give the program's name and a brief idea of what it does.>
-    Copyright (C) <year>  <name of author>
-
-    This program is free software: you can redistribute it and/or modify
-    it under the terms of the GNU General Public License as published by
-    the Free Software Foundation, either version 3 of the License, or
-    (at your option) any later version.
-
-    This program is distributed in the hope that it will be useful,
-    but WITHOUT ANY WARRANTY; without even the implied warranty of
-    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-    GNU General Public License for more details.
-
-    You should have received a copy of the GNU General Public License
-    along with this program.  If not, see <https://www.gnu.org/licenses/>.
-
-Also add information on how to contact you by electronic and paper mail.
-
-  If the program does terminal interaction, make it output a short
-notice like this when it starts in an interactive mode:
-
-    <program>  Copyright (C) <year>  <name of author>
-    This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
-    This is free software, and you are welcome to redistribute it
-    under certain conditions; type `show c' for details.
-
-The hypothetical commands `show w' and `show c' should show the appropriate
-parts of the General Public License.  Of course, your program's commands
-might be different; for a GUI interface, you would use an "about box".
-
-  You should also get your employer (if you work as a programmer) or school,
-if any, to sign a "copyright disclaimer" for the program, if necessary.
-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>.

README.md

@@ -8,10 +8,10 @@
 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.\
 
-## Installation
+## Installation:
 
 <!-- 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),
 everything should now be set up.
@@ -19,17 +19,12 @@ 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.
 
 > **Note**
-> This plugin is still in fairly early development.
+> 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.
-> 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:
-> Take care to read the Issues section of this README if you intend to run it over a large collection.
-
-## Usage
 
 `papis extract [OPTIONS] [QUERY]`
 
@@ -92,45 +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.
 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 re-write to your notes using a completely different template than the original the plugin will *not* detect old annotations and drop them,
-so you will be doubling up your annotations.
-See the `minimum_similarity_color` configuration option for more details.
-
 ## Configuration
 
 ### Basic configuration
-
 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 -
 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:
 
-```conf
+```yaml
 [plugins.extract]
 on_import: False
 tags = {"important": "red", "toread": "blue"}
@@ -141,7 +107,7 @@ minimum_similarity_color = 0.833  # for matching tag to color
 
 ### Automatic extraction
 
-```conf
+```yaml
 [plugins.extract]
 on_import: True
 ```
@@ -153,10 +119,7 @@ if `False` extraction only happens when you explicitly invoke it.
 Extraction will *not* happen automatically when you add new annotations to an existing document,
 regardless of this setting.
 
-> **Note**
+#### Automatic tagging
-> This option does not work yet due to currently missing upstream features.
-
-### Automatic tagging
 
 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.
@@ -165,7 +128,7 @@ 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:
 
-```conf
+```yaml
 [plugins.extract]
 tags = {"red": "important", "blue": "toread"}
 ```
@@ -177,7 +140,7 @@ no defaults are set here.
 
 ### Advanced configuration
 
-```conf
+```yaml
 [plugins.extract]
 minimum_similarity: 0.75,  # for checking against existing annotations
 minimum_similarity_content: 0.9,  # for checking if highlight or note
@@ -206,21 +169,7 @@ 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
+## Roadmap to first release
-
-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
 
 Known issues to be fixed:
 
@@ -228,12 +177,10 @@ Known issues to be fixed:
 - [x] Speed?
     - 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] 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!!
     - [ ] 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:
 
@@ -241,26 +188,22 @@ features to be implemented:
     - [x] static analysis (lint, typecheck etc) on pushes
     - [x] test pipeline on master pushes
     - [ ] 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
 - [ ] 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
+    - markdown into notes
-    - [ ] pretty display on stdout (rich?)
+    - pretty display on stdout (rich?)
-    - [x] csv/tsv to stdout
+    - csv/tsv to stdout
-    - [ ] table fmt 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
+- [ ] `--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
     - needs upstream help, 'on_add' hook, and pass-through of affected documents
-- [ ] target same minimum Python version as papis upstream (3.8 as of papis 0.13)
 
 upstream changes:
 
@@ -269,12 +212,6 @@ upstream changes:
 
 ## Issues
 
-First, a note in general: There is the functionality to run this plugin over your whole library in a single command and also in a way that makes permanent changes to that library.
-This is intended and, in my view, an important aspect of what this plugin provides and the batch functionality of cli programs in general.
-However, it can also lead to frustrating clean-up time if something messes up or, in the worst case, data loss.
-The extractors attempt to ascertain what files they can operate on with certain heuristics but will not be fail-safe.
-Take the note at the top of this README to heart and always have backups on hand before larger operations.
-
 A note on the extraction: Highlights in pdfs can be somewhat difficult to parse
 (as are most things in them). Sometimes they contain the selected text that is written on the
 page, sometimes they contain the annotators thoughts as a note, sometimes they contain nothing.
@@ -282,57 +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
 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. 
-  Crawls the actual files attached to documents to put them into annotation-friendly formats.
-
-- 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 annotation 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,
-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.
 
 ---
 

papis_extract/__init__.py

@@ -1,23 +1,23 @@
+from pathlib import Path
 import re
+
 import click
+import fitz_new as fitz
+import magic
 import papis.cli
 import papis.config
 import papis.document
+from papis.document import Document
 import papis.logging
 import papis.notes
 import papis.strings
-from papis.document import Document
 
-from papis_extract import extraction
+from papis_extract import extractor, exporter
-from papis_extract.annotation import Annotation
+from papis_extract.annotation_data import Annotation, AnnotatedDocument
-from papis_extract.exporter import Exporter
-from papis_extract.exporters import all_exporters
-from papis_extract.extractors import all_extractors
-from papis_extract.formatter import Formatter, formatters
 
 logger = papis.logging.get_logger(__name__)
 
-DEFAULT_OPTIONS: dict[str, dict[str, bool | float | dict[str, str]]] = {
+DEFAULT_OPTIONS = {
     "plugins.extract": {
         "tags": {},
         "on_import": False,
@@ -33,73 +33,41 @@ papis.config.register_default_settings(DEFAULT_OPTIONS)
 @click.help_option("-h", "--help")
 @papis.cli.query_argument()
 @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()
-@click.option(
-    "--write/--no-write",
-    "-w",
-    help="Write extracted annotations into papis notes.",
-    show_default=True,
-)
 @click.option(
     "--manual/--no-manual",
     "-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",
-    show_default=True,
 )
 @click.option(
-    "--template",
+    "--write/--no-write",
-    "-t",
+    "-w",
-    type=click.Choice(
+    help="Do not write annotations to notes only print results to stdout",
-        list(formatters.keys()),
-        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,
+    # info: bool,
     # _papis_id: bool,
     # _file: bool,
+    # notes: bool,
     # _dir: bool,
+    # _format: str,
     _all: bool,
     doc_folder: str,
     manual: bool,
     write: bool,
-    extractors: list[str],
-    template: str,
     git: bool,
-    force: bool,
 ) -> None:
-    """Extract annotations from any documents.
+    """Extract annotations from any pdf document
 
     The extract plugin allows manual or automatic extraction of all annotations
-    contained in the documents belonging to entries of the papis library,
+    contained in the pdf documents belonging to entries of the pubs library.
-    primarily targeting PDF documents currently.
     It can write those changes to stdout or directly create and update notes
     for papis documents.
 
     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(
         query, doc_folder, sort_field=None, sort_reverse=False, _all=_all
@@ -108,56 +76,50 @@ def main(
         logger.warning(papis.strings.no_documents_retrieved_message)
         return
 
-    formatter = formatters.get(template)
+    doc_annotations: list[AnnotatedDocument] = _get_annotations_for_documents(documents)
 
-    run(
-        documents,
-        edit=manual,
-        write=write,
-        git=git,
-        formatter=formatter,
-        extractors=[all_extractors.get(e) for e in extractors],
-        force=force,
-    )
-
-
-def run(
-    documents: list[Document],
-    formatter: Formatter | None,
-    extractors: list[extraction.Extractor | None],
-    edit: bool = False,
-    write: bool = False,
-    git: bool = False,
-    force: bool = False,
-) -> None:
-    exporter: Exporter
     if write:
-        exporter = all_exporters["notes"](
+        exporter.to_notes(doc_annotations, edit=manual, git=git)
-            formatter=formatter or formatters["markdown-atx"],
-            edit=edit,
-            git=git,
-            force=force,
-        )
     else:
-        exporter = all_exporters["stdout"](
+        exporter.to_stdout(doc_annotations)
-            formatter=formatter or formatters["markdown"]
-        )
 
-    doc_annots: list[tuple[Document, list[Annotation]]] = []
+    # note_file: Path = Path(papis.notes.notes_path_ensured(documents[0]))
+
+
+def is_pdf(fname: Path) -> bool:
+    return magic.from_file(fname, mime=True) == "application/pdf"
+
+
+def _get_annotations_for_documents(
+    documents: list[Document],
+) -> list[AnnotatedDocument]:
+    output: list[AnnotatedDocument] = []
     for doc in documents:
         annotations: list[Annotation] = []
-        valid_files: int = 0
+        found_pdf: bool = False
-        for ext in extractors:
+        for file in doc.get_files():
-            if not ext:
+            fname = Path(file)
-                continue
+            if not _is_file_processable(fname):
-            added = extraction.start(ext, doc)
+                break
-            if added is not None:
+            found_pdf = True
-                valid_files += 1
-                annotations.extend(added)
-        doc_annots.append((doc, annotations))
 
-        if valid_files == 0:
+            try:
+                annotations.extend(extractor.start(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.info(f"Document {desc} has no valid extractors for any of its files.")
+            logger.warning("Did not find suitable PDF file for document: " f"{desc}")
-    exporter.run(doc_annots)
+        output.append(AnnotatedDocument(doc, annotations))
+    return output
+
+
+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

papis_extract/annotation.py

@@ -1,145 +0,0 @@
-import math
-from dataclasses import dataclass
-from typing import Any, Optional, cast
-
-import chevron
-import papis.config
-from papis.document import Document
-
-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),
-    "red": (1, 0, 0),
-    "cyan": (0, 1, 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),
-}
-
-
-@dataclass
-class Annotation:
-    """A PDF annotation object.
-
-    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
-
-    def format(self, formatting: str, doc: Document = Document()):
-        """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.
-        """
-        data = {
-            "file": self.file,
-            "quote": self.content,
-            "note": self.note,
-            "page": self.page,
-            "tag": self.tag,
-            "type": self.type,
-            "doc": doc,
-        }
-        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.
-
-        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)
-        nearest = None
-        minimum_similarity = (
-            papis.config.getfloat("minimum_similarity_color", "plugins.extract") or 1.0
-        )
-        minimum_similarity = self.minimum_similarity_color
-        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 _color_similarity_ratio(
-        self,
-        color_one: tuple[float, float, float],
-        color_two: tuple[float, float, float],
-    ) -> float:
-        """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)
-
-    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, "")
-
-    # mimics the functions in papis.config.{getlist,getint,getfloat} etc.
-    def _getdict(self, 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 cast(dict[str, str], 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 cast(dict[str, str], rawvalue)

papis_extract/annotation_data.py

@@ -0,0 +1,97 @@
+import re
+import math
+from dataclasses import dataclass, field
+
+import papis.config
+from papis.document import Document
+
+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"""
+
+    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,
+        using euclidian distance between the two color vectors.
+        """
+        annot_colors = (
+            self.colors.get("stroke") or self.colors.get("fill") or (0.0, 0.0, 0.0)
+        )
+        nearest = None
+        minimum_similarity = (
+            papis.config.getfloat("minimum_similarity_color", "plugins.extract") or 1.0
+        )
+        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 _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)
+
+
+@dataclass
+class AnnotatedDocument:
+    document: Document
+    annotations: list[Annotation]

papis_extract/exceptions.py

@@ -1,8 +0,0 @@
-class ExtractionError(Exception):
-    """Raised for exceptions during extraction.
-
-    Something went wrong during the extraction process in the extractor
-    run routine itself.
-    """
-
-    pass

papis_extract/exporter.py

@@ -1,27 +1,139 @@
-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 Annotation
+from papis_extract.annotation_data import AnnotatedDocument, Annotation
-from papis_extract.formatter import Formatter
 
 logger = papis.logging.get_logger(__name__)
 
 
-@dataclass
+def _format_annotation(annotation: Annotation) -> str:
-class Exporter(Protocol):
+    note = f"NOTE: {annotation.content}" if annotation.content else ""
-    formatter: Formatter
+    return f"> {annotation.text}\n  {note}"
-    edit: bool = False
-    git: bool = False
-    force: bool = False
 
-    def run(
+
-        self, annot_docs: list[tuple[papis.document.Document, list[Annotation]]]
+def to_stdout(annots: list[AnnotatedDocument]) -> None:
-    ) -> 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.
+    """
+    if not annots:
+        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(annots: list[AnnotatedDocument], edit: bool, git: 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.
+    """
+    if not annots:
+        return
+
+    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:
+            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,
+) -> None:
+    """Append new annotations to the end of a note.
+
+    Looks through note to determine any new annotations which should be
+    added and adds them to the end of the note file.
+    """
+    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] = _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".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]:
+    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 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

papis_extract/exporters/__init__.py

@@ -1,13 +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

papis_extract/exporters/notes.py

@@ -1,136 +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:
-            # first always true since we write single doc per note
-            formatted_annotations: list[str] = self.formatter(
-                doc, annots, first=True
-            ).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")
-            # FIXME this either joins them too close or moves them too far apart
-            # We need a better algorithm which knows what a full 'annotation' is.
-            f.write("\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

papis_extract/exporters/stdout.py

@@ -1,28 +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.
-        """
-        first_entry = True
-        for doc, annots in annot_docs:
-            output: str = self.formatter(doc, annots, first=first_entry)
-            if output:
-                print("{output}\n".format(output=output.rstrip("\n")))
-                first_entry = False

papis_extract/extraction.py

@@ -1,49 +0,0 @@
-from pathlib import Path
-from typing import Protocol
-
-import papis.config
-import papis.document
-import papis.logging
-from papis.document import Document
-
-from papis_extract.annotation import Annotation
-from papis_extract.exceptions import ExtractionError
-
-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] | None:
-    """Extract all annotations from passed documents.
-
-    Returns all annotations contained in the papis
-    documents passed in (empty list if no annotations).
-    If there are no files that the extractor can process,
-    returns None instead.
-    """
-    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 ExtractionError as e:
-            logger.error(f"File extraction errors for {file}. File may be damaged.\n{e}")
-
-    if not file_available:
-        return None
-
-    return annotations

papis_extract/extractor.py

@@ -0,0 +1,111 @@
+from pathlib import Path
+from typing import Any, Optional
+
+import Levenshtein
+import fitz_new as fitz
+import papis.logging
+import papis.config
+
+from papis_extract.annotation_data import Annotation
+
+logger = papis.logging.get_logger(__name__)
+
+
+def start(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
+                a = Annotation(
+                    file=str(filename),
+                    text=quote or "",
+                    content=note or "",
+                    colors=annot.colors,
+                    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 _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

papis_extract/extractors/__init__.py

@@ -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.")

papis_extract/extractors/pdf.py

@@ -1,109 +0,0 @@
-# pyright: strict, reportMissingTypeStubs=false, reportUnknownMemberType=false
-from pathlib import Path
-from typing import cast
-
-import Levenshtein
-import magic
-import papis.config
-import papis.logging
-import pymupdf as mu
-
-from papis_extract.annotation import Annotation
-from papis_extract.exceptions import ExtractionError
-
-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: list[Annotation] = []
-        try:
-            with mu.Document(filename) as doc:
-                for (
-                    page
-                ) in doc:  # pyright: ignore [reportUnknownVariableType] - missing stub
-                    page = cast(mu.Page, page)
-                    annot: mu.Annot
-                    for annot in page.annots():
-                        quote, note = self._retrieve_annotation_content(page, annot)
-                        if not quote and not note:
-                            continue
-                        color: tuple[float, float, float] = cast(
-                            tuple[float, float, float],
-                            (
-                                annot.colors.get("fill")
-                                or annot.colors.get("stroke")
-                                or (0.0, 0.0, 0.0)
-                            ),
-                        )
-                        page_nr: int = cast(int, page.number or 0)
-                        highlight_type: str = cast(str, annot.type[1] or "")
-                        a = Annotation(
-                            file=str(filename),
-                            content=quote or "",
-                            note=note or "",
-                            color=color,
-                            type=highlight_type,
-                            page=page_nr,
-                        )
-                        annotations.append(a)
-            logger.debug(
-                f"Found {len(annotations)} "
-                f"{'annotation' if len(annotations) == 1 else 'annotations'} for {filename}."
-            )
-
-        except mu.FileDataError:
-            raise ExtractionError
-
-        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: mu.Page, annotation: mu.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 = cast(str, 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)

papis_extract/extractors/pocketbook.py

@@ -1,88 +0,0 @@
-# pyright: strict, reportUnknownMemberType=false
-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 = str(
-                (bm.select_one("div.bm-text>p") or html.new_string("")).text
-                or ""  # pyright: ignore [reportUnknownArgumentType]
-            )
-            note = str(
-                (bm.select_one("div.bm-note>p") or html.new_string("")).text
-                or ""  # pyright: ignore [reportUnknownArgumentType]
-            )
-            page = int(
-                (bm.select_one("p.bm-page") or html.new_string("")).text
-                or 0  # pyright: ignore [reportUnknownArgumentType]
-            )
-
-            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,
-                note=note,
-                color=color,
-                type="Highlight",
-                page=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 ""

papis_extract/formatter.py

@@ -1,123 +0,0 @@
-from typing import Protocol
-from papis.document import Document
-
-from papis_extract.annotation import Annotation
-
-
-class Formatter(Protocol):
-    """Basic formatter protocol.
-
-    Every valid formatter must implement at least this protocol.
-    A formatter is a function which receives a document and a list
-    of annotations and spits them out in some formatted way.
-
-    Formatters additionally must take the (often optional) passed
-    parameter 'first' which signals to the formatter that the current
-    document entry is the very first one to be printed in whatever
-    exporter is used, if multiple entries are printed.
-    This can be useful for adding a header if necessary for the format.
-    """
-
-    def __call__(
-        self, document: Document, annotations: list[Annotation], first: bool
-    ) -> str: ...
-
-
-def format_markdown(
-    document: Document = Document(),
-    annotations: list[Annotation] = [],
-    first: bool = False,
-    headings: str = "setext",  # setext | atx | None
-) -> str:
-    if not annotations:
-        return ""
-    template = (
-        "{{#tag}}#{{tag}}\n{{/tag}}"
-        "{{#quote}}> {{quote}}{{/quote}}{{#page}} [p. {{page}}]{{/page}}"
-        "{{#note}}\n  NOTE: {{note}}{{/note}}"
-    )
-    output = ""
-
-    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"
-
-    for a in annotations:
-        output += a.format(template)
-        output += "\n\n"
-
-    output += "\n\n\n"
-
-    return output.rstrip()
-
-
-def format_markdown_atx(
-    document: Document = Document(),
-    annotations: list[Annotation] = [],
-    first: bool = False,
-) -> str:
-    return format_markdown(document, annotations, headings="atx")
-
-
-def format_markdown_setext(
-    document: Document = Document(),
-    annotations: list[Annotation] = [],
-    first: bool = False,
-) -> str:
-    return format_markdown(document, annotations, headings="setext")
-
-
-def format_count(
-    document: Document = Document(),
-    annotations: list[Annotation] = [],
-    first: bool = False,
-) -> str:
-    if not annotations:
-        return ""
-
-    count = 0
-    for _ in annotations:
-        count += 1
-
-    return (
-        f"{count} "
-        f"{document.get('author', '')}"
-        f"{': ' if 'author' in document else ''}"  # only put separator if author
-        f"{document.get('title', '')}"
-    ).rstrip()
-
-
-def format_csv(
-    document: Document = Document(),
-    annotations: list[Annotation] = [],
-    first: bool = False,
-) -> 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 first else ""
-    if not annotations:
-        return ""
-
-    for a in annotations:
-        output += a.format(template, doc=document)
-        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,
-}

pyproject.toml

@@ -1,50 +1,27 @@
 [tool.poetry]
 name = "papis-extract"
-version = "0.2.0"
+version = "0.1.0"
 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",
-]
 
 [tool.poetry.dependencies]
 python = "^3.11"
-pymupdf = "^1.24.2"
+pymupdf = "^1.23.1"
-levenshtein = "^0.25.1"
+levenshtein = "^0.21.1"
 papis = "^0.13"
 click = "^8.1.7"
-whoosh = { version = "^2.7.4", optional = true }
+whoosh = "^2.7.4"
 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"
-coverage = "^7.3.1"
-pytest-cov = "^4.1.0"
 
 [tool.poetry.plugins."papis.command"]
 extract = "papis_extract:main"
 
+
+[tool.poetry.group.dev.dependencies]
+pytest = "^7.4.0"
+
 [build-system]
 requires = ["poetry-core"]
 build-backend = "poetry.core.masonry.api"
-
-[tool.pyright]
-typeCheckingMode = "strict"

tests/test_annotation.py

@@ -1,70 +1,7 @@
-import pytest
+from papis_extract.annotation_data import Annotation
-from papis.document import Document
-
-from papis_extract.annotation import Annotation
 
 
-@pytest.mark.parametrize(
+def test_matches_colorname_exact():
-    "fmt_string,expected",
+    sut = Annotation("testfile", colors={"stroke": (1.0, 0.0, 0.0)})
-    [
-        ("{{quote}}", "I am the text value"),
-        (
-            "> {{quote}}\n{{#note}}Note: {{note}}{{/note}}",
-            "> I am the text value\nNote: Whereas I represent the note",
-        ),
-        (
-            "{{#note}}Note: {{note}}{{/note}}{{#page}}, p. {{page}}{{/page}}",
-            "Note: Whereas I represent the note",
-        ),
-    ],
-)
-def test_formatting_replacements(fmt_string: str, expected: str):
-    sut = Annotation(
-        "myfile",
-        content="I am the text value",
-        note="Whereas I represent the note",
-    )
-
-    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: str, expected: str):
-    sut = Annotation(
-        "myfile",
-        content="I am the text value",
-        note="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():
-    sut = Annotation("testfile", color=(1.0, 0.0, 0.0), minimum_similarity_color=1.0)
-    c_name = sut.colorname
-    assert c_name == "red"
-
-
-# TODO inject closeness value instead of relying on default
-@pytest.mark.parametrize(
-    "color_value",
-    [
-        (1.0, 0.0, 0.0),
-        (0.9, 0.0, 0.0),
-        (0.8, 0.0, 0.0),
-        (0.7, 0.0, 0.0),
-        (0.51, 0.0, 0.0),
-    ],
-)
-def test_matches_inexact_colorname(color_value: tuple[float, float, float]):
-    sut = Annotation("testfile", color=color_value, minimum_similarity_color=0.833)
     c_name = sut.colorname
     assert c_name == "red"

tests/test_formatting.py

@@ -1,85 +0,0 @@
-from papis.document import Document
-from papis_extract.annotation import Annotation
-
-from papis_extract.formatter import (
-    format_count,
-    format_csv,
-    format_markdown,
-    format_markdown_atx,
-    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"),
-]
-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(document, annotations) == md_default_output
-
-
-def test_markdown_atx():
-    fmt = format_markdown_atx
-    assert fmt(document, annotations) == (
-        """# document-title - document-author
-
-> my lovely text
-
-> my second text
-  NOTE: with note"""
-    )
-
-
-def test_markdown_setext():
-    fmt = format_markdown_setext
-    assert fmt(document, annotations) == md_default_output
-
-
-def test_count_default():
-    fmt = format_count
-    assert fmt(document, annotations) == ("""2 document-author: document-title""")
-
-
-def test_csv_default():
-    fmt = format_csv
-    assert fmt(document, annotations) == (
-        '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"'
-    )
-
-
-def test_csv_with_header():
-    fmt = format_csv
-    assert fmt(document, annotations, first=True) == (
-        "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():
-    assert format_markdown(document, []) == ""
-
-
-def test_count_no_annotations():
-    assert format_count(document, []) == ""
-
-
-def test_csv_no_annotations():
-    assert format_csv(document, []) == ""