fix: Default markdown atx formatter for note exporter

fix: Fixed pocketbook extractor trying to read all files
The complete read routine would work before figuring out that it is a file of xml mimetype. This means that it would try to read to memory any file as the first thing, pdfs, even binaries. Of course doing so crashed the program.
2024-01-25 22:46:38 +01:00 · 2024-01-25 21:42:34 +01:00 · 2024-01-25 21:42:33 +01:00 · 2024-01-24 14:57:10 +01:00 · 2024-01-24 14:55:28 +01:00 · 2024-01-24 13:39:01 +01:00
18 changed files with 1389 additions and 433 deletions
--- a/674
+++ b/674
@ -0,0 +1,674 @@
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    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>.
--- a/README.md
+++ b/README.md
@ -19,6 +19,8 @@ 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.
@ -198,7 +200,21 @@ 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.
-## Roadmap to first release
+## Extractors
 Currently, the program supports two annotation extractors:
 A **`pdf` extractor**, which takes highlights and annotations embedded in any PDF file.
 It should work with most PDF styles, as long as annotations are marked as such 
 (does not work if e.g. highlights are baked onto text, or there is no text in the file).
 A `pocketbook` extractor, which takes bookmarks exported from the mobile [PocketBook](https://pocketbook.ch/en-ch/app) reader applications.
 You can export bookmarks by opening a book, going to the notes list and selecting `Export notes...`.
 Then import the resulting `.html` file into the library using `papis add`
 (or `papis addto` to add it to existing documents).
 You are then ready to use extract to get those annotations from the exported list into your notes.
 ## TODO: Roadmap to first release
 Known issues to be fixed:
@ -222,16 +238,18 @@ features to be implemented:
 - [x] add page number if available
    - exists in Annotation, just need to place in output
 - [ ] show overall amount of extractions at the end
    - implemented for writing to notes (notes exporter)
    - KNOWN ISSUE: currently returns number of annotation rows (may be multiple per annot)
 - [ ] custom formatting decided by user
    - in config as { "myformatter": ">{tag}\n{quote}\n{note}\n{page} etc"}
 - [ ] improved default exporters
-    - markdown into notes
+    - [x] markdown into notes
-    - pretty display on stdout (rich?)
+    - [ ] pretty display on stdout (rich?)
-    - csv/tsv to stdout
+    - [x] 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
- [ ] `--force` mode where we simply do not drop anything
+- [x] `--force` mode where we simply do not drop anything
 - [x] `--format` option to choose from default or set up a custom formatter
    - called `--template` in current implementation
 - [ ] on_add hook to extract annotations as files are added
@ -266,6 +284,7 @@ and for myself whenever I forget. The basic building blocks currently in here ar
 - extractors
 : Extract data from a source file attached to a papis document. 
  Crawls the actual files attached to documents to put them into annotation-friendly formats.
 - annotations
 : The actual extracted blocks of text, containing some metadata
@ -275,12 +294,32 @@ and for myself whenever I forget. The basic building blocks currently in here ar
 : Put the extracted data somewhere. For now stdout or into your notes.
 - formatters
-: Make sure the exporter saves the data according to your preferred layout,
+: 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 three building blocks makes it easier to recombine them in any way,
+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 should we ever include more extractors than the one for PDFs.
+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.
 ---
--- a/papis_extract/init.py
+++ b/papis_extract/init.py
@ -7,7 +7,11 @@ import papis.notes
 import papis.strings
 from papis.document import Document
-from papis_extract import extractor, exporter
+from papis_extract.annotation import Annotation
 from papis_extract import extraction
 from papis_extract.exporter import Exporter
 from papis_extract.extractors import all_extractors
 from papis_extract.exporters import all_exporters
 from papis_extract.formatter import Formatter, formatters
 logger = papis.logging.get_logger(__name__)
@ -33,26 +37,42 @@ papis.config.register_default_settings(DEFAULT_OPTIONS)
@click.option(
    "--write/--no-write",
    "-w",
-    help="Do not write annotations to notes only print results to stdout.",
+    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.",
    show_default=True,
 )
@click.option(
    "--template",
    "-t",
    type=click.Choice(
-        ["markdown", "markdown-setext", "markdown-atx", "count", "csv"],
+        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,
@ -63,6 +83,7 @@ def main(
    doc_folder: str,
    manual: bool,
    write: bool,
    extractors: list[str],
    template: str,
    git: bool,
    force: bool,
@ -85,27 +106,47 @@ def main(
        logger.warning(papis.strings.no_documents_retrieved_message)
        return
-    formatter = formatters[template]
+    formatter = formatters.get(template)
-    run(documents, edit=manual, write=write, git=git, formatter=formatter, force=force)
+    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,
+    formatter: Formatter | None,
    extractors: list[extraction.Extractor | None],
    edit: bool = False,
    write: bool = False,
    git: bool = False,
    force: bool = False,
 ) -> None:
    annotated_docs = extractor.start(documents)
    if write:
-        exporter.to_notes(
+        exporter: Exporter = all_exporters["notes"](
-            formatter=formatter,
+            formatter=formatter or formatters["markdown-atx"],
            annotated_docs=annotated_docs,
            edit=edit,
            git=git,
            force=force,
        )
    else:
-        exporter.to_stdout(formatter=formatter, annotated_docs=annotated_docs)
+        exporter: Exporter = all_exporters["stdout"](
            formatter=formatter or formatters["markdown"]
        )
    doc_annots: list[tuple[Document, list[Annotation]]] = []
    for doc in documents:
        annotations: list[Annotation] = []
        for ext in extractors:
            if not ext:
                continue
            annotations.extend(extraction.start(ext, doc))
        doc_annots.append((doc, annotations))
    exporter.run(doc_annots)
--- a/papis_extract/annotation.py
+++ b/papis_extract/annotation.py
@ -1,19 +1,23 @@
 import math
-from dataclasses import dataclass, field
+from dataclasses import dataclass
 from typing import Any, Optional
 import chevron
 import papis.config
 from papis.document import Document
 import chevron
 TEXT_SIMILARITY_MINIMUM = 0.75
 COLOR_SIMILARITY_MINIMUM = 0.833
-COLORS = {
+COLORS: dict[str, tuple[float, float, float]] = {
    "red": (1, 0, 0),
    "green": (0, 1, 0),
    "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),
 }
@ -25,14 +29,25 @@ class Annotation:
    Contains all information necessary for the annotation itself, content and metadata.
    """
-    file: str
+    def __init__(
-    colors: tuple[float, float, float] = field(default_factory=lambda: (0.0, 0.0, 0.0))
+        self,
-    content: str = ""
+        file: str,
-    page: int = 0
+        color: tuple[float, float, float] = (0.0, 0.0, 0.0),
-    tag: str = ""
+        content: str = "",
-    text: str = ""
+        note: str = "",
-    type: str = "Highlight"
+        page: int = 0,
-    minimum_similarity_color: float = 1.0
+        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.
@ -43,8 +58,8 @@ class Annotation:
        """
        data = {
            "file": self.file,
-            "quote": self.text,
+            "quote": self.content,
-            "note": self.content,
+            "note": self.note,
            "page": self.page,
            "tag": self.tag,
            "type": self.type,
@ -52,6 +67,15 @@ class Annotation:
        }
        return chevron.render(formatting, data)
    @property
    def color(self):
        return self._color
    @color.setter
    def color(self, value: tuple[float, float, float]):
        self._color = value
        self.tag = self._tag_from_colorname(self.colorname or "")
    @property
    def colorname(self):
        """Return the stringified version of the annotation color.
@ -59,7 +83,7 @@ class Annotation:
        Finds the closest named color to the annotation and returns it,
        using euclidian distance between the two color vectors.
        """
-        annot_colors = self.colors or (0.0, 0.0, 0.0)
+        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
@ -72,7 +96,11 @@ class Annotation:
                nearest = name
        return nearest
-    def _color_similarity_ratio(self, color_one, color_two):
+    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,
@ -82,14 +110,36 @@ class Annotation:
        """
        return 1 - (abs(math.dist([*color_one], [*color_two])) / 3)
    def _tag_from_colorname(self, colorname: str) -> str:
        color_mapping: dict[str, str] = self._getdict("tags", "plugins.extract")
        if not color_mapping:
            return ""
-@dataclass
+        return color_mapping.get(colorname, "")
 class AnnotatedDocument:
    """Contains all annotations belonging to a single papis document.
-    Combines a document with a list of annotations which belong to it."""
+    # mimics the functions in papis.config.{getlist,getint,getfloat} etc.
    def _getdict(self, key: str, section: Optional[str] = None) -> dict[str, str]:
        """Dict getter
-    document: Document
+        :returns: A python dict
-    annotations: list[Annotation]
+        :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__
                    )
                )
-    # TODO could implement a from_doc() static method to generate annotation list?
+            return rawvalue
--- a/papis_extract/exporter.py
+++ b/papis_extract/exporter.py
@ -1,142 +1,28 @@
-import papis.logging
+from dataclasses import dataclass
-import papis.document
+from typing import Protocol
 import papis.notes
 import papis.commands.edit
 import papis.api
 import papis.git
 import papis.config
 import Levenshtein
 from papis_extract.annotation import AnnotatedDocument
 import papis.api
 import papis.commands.edit
 import papis.config
 import papis.document
 import papis.git
 import papis.logging
 import papis.notes
 from papis_extract.annotation import Annotation
 from papis_extract.formatter import Formatter
 logger = papis.logging.get_logger(__name__)
-def to_stdout(formatter: Formatter, annotated_docs: list[AnnotatedDocument]) -> None:
+@dataclass
-    """Pretty print annotations to stdout.
+class Exporter(Protocol):
    formatter: Formatter
    edit: bool = False
    git: bool = False
    force: bool = False
-    Gives a nice human-readable representations of
+    def run(
-    the annotations in somewhat of a list form.
+        self, annot_docs: list[tuple[papis.document.Document, list[Annotation]]]
-    Not intended for machine-readability.
+    ) -> None:
-    """
+        ...
    output: str = formatter(annotated_docs)
    print(output.rstrip("\n"))
 def to_notes(
    formatter: Formatter,
    annotated_docs: list[AnnotatedDocument],
    edit: bool,
    git: bool,
    force: bool,
 ) -> None:
    """Write annotations into document notes.
    Permanently writes the given annotations into notes
    belonging to papis documents. Creates new notes for
    documents missing a note field or appends to existing.
    """
    for entry in annotated_docs:
        formatted_annotations = formatter([entry]).split("\n")
        if formatted_annotations:
            _add_annots_to_note(entry.document, formatted_annotations, force=force)
        if edit:
            papis.commands.edit.edit_notes(entry.document, git=git)
 def _add_annots_to_note(
    document: papis.document.Document,
    formatted_annotations: list[str],
    git: bool = False,
    force: bool = False,
 ) -> None:
    """
    Append new annotations to the end of a note.
    This function appends new annotations to the end of a note file. It takes in a
    document object containing the note, a list of formatted annotations to be
    added, and optional flags git and force. If git is True, the changes will be
    committed to git. If force is True, the annotations will be added even if they
    already exist in the note.
    :param document: The document object representing the note
    :type document: class:`papis.document.Document`
    :param formatted_annotations: A list of already formatted annotations to be added
    :type formatted_annotations: list[str]
    :param git: Flag indicating whether to commit changes to git, defaults to False.
    :type git: bool, optional
    :param force:  Flag indicating whether to force adding annotations even if they
        already exist, defaults to False.
    :type force: bool, optional
    """
    logger.debug("Adding annotations to note.")
    notes_path = papis.notes.notes_path_ensured(document)
    existing: list[str] = []
    with open(notes_path, "r") as file_read:
        existing = file_read.readlines()
    new_annotations: list[str] = []
    if not force:
        new_annotations = _drop_existing_annotations(formatted_annotations, existing)
    if not new_annotations:
        return
    with open(notes_path, "a") as f:
        # add newline if theres no empty space at file end
        if len(existing) > 0 and existing[-1].strip() != "":
            f.write("\n")
        print(new_annotations)
        f.write("\n\n".join(new_annotations))
        f.write("\n")
        logger.info(
            f"Wrote {len(new_annotations)} "
            f"{'annotation' if len(new_annotations) == 1 else 'annotations'} "
            f"to {papis.document.describe(document)}"
        )
    if git:
        msg = "Update notes for '{0}'".format(papis.document.describe(document))
        folder = document.get_main_folder()
        if folder:
            papis.git.add_and_commit_resources(
                folder, [notes_path, document.get_info_file()], msg
            )
 def _drop_existing_annotations(
    formatted_annotations: list[str], file_lines: list[str]
 ) -> list[str]:
    """Returns the input annotations dropping any existing.
    Takes a list of formatted annotations and a list of strings
    (most probably existing lines in a file). If anny annotations
    match an existing line closely enough, they will be dropped.
    Returns list of annotations without duplicates.
    """
    minimum_similarity = (
        papis.config.getfloat("minimum_similarity", "plugins.extract") or 1.0
    )
    remaining: list[str] = []
    for an in formatted_annotations:
        an_split = an.splitlines()
        if an_split and not _test_similarity(
            an_split[0], file_lines, minimum_similarity
        ):
            remaining.append(an)
    return remaining
 def _test_similarity(
    string: str, lines: list[str], minimum_similarity: float = 1.0
 ) -> bool:
    for line in lines:
        ratio = Levenshtein.ratio(string, line)
        if ratio > minimum_similarity:
            return True
    return False
--- a/papis_extract/exporters/init.py
+++ b/papis_extract/exporters/init.py
@ -0,0 +1,14 @@
 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
--- a/papis_extract/exporters/notes.py
+++ b/papis_extract/exporters/notes.py
@ -0,0 +1,131 @@
 from dataclasses import dataclass
 import Levenshtein
 from papis.document import Document
 from papis_extract.annotation import Annotation
 from papis_extract.formatter import Formatter
 from papis.logging import get_logger
 import papis.notes
 import papis.document
 import papis.git
 import papis.config
 import papis.commands.edit
 logger = get_logger(__name__)
@dataclass
 class NotesExporter:
    formatter: Formatter
    edit: bool = False
    git: bool = False
    force: bool = False
    def run(self, annot_docs: list[tuple[Document, list[Annotation]]]) -> None:
        """Write annotations into document notes.
        Permanently writes the given annotations into notes
        belonging to papis documents. Creates new notes for
        documents missing a note field or appends to existing.
        """
        for doc, annots in annot_docs:
            formatted_annotations = self.formatter(doc, annots).split("\n")
            if formatted_annotations:
                self._add_annots_to_note(doc, formatted_annotations, force=self.force)
            if self.edit:
                papis.commands.edit.edit_notes(doc, git=self.git)
    def _add_annots_to_note(
        self,
        document: Document,
        formatted_annotations: list[str],
        git: bool = False,
        force: bool = False,
    ) -> None:
        """
        Append new annotations to the end of a note.
        This function appends new annotations to the end of a note file. It takes in a
        document object containing the note, a list of formatted annotations to be
        added, and optional flags git and force. If git is True, the changes will be
        committed to git. If force is True, the annotations will be added even if they
        already exist in the note.
        :param document: The document object representing the note
        :type document: class:`papis.document.Document`
        :param formatted_annotations: A list of already formatted annotations to be added
        :type formatted_annotations: list[str]
        :param git: Flag indicating whether to commit changes to git, defaults to False.
        :type git: bool, optional
        :param force:  Flag indicating whether to force adding annotations even if they
            already exist, defaults to False.
        :type force: bool, optional
        """
        logger.debug("Adding annotations to note.")
        notes_path = papis.notes.notes_path_ensured(document)
        existing: list[str] = []
        with open(notes_path, "r") as file_read:
            existing = file_read.readlines()
        new_annotations: list[str] = []
        if not force:
            new_annotations = self._drop_existing_annotations(
                formatted_annotations, existing
            )
        if not new_annotations:
            return
        with open(notes_path, "a") as f:
            # add newline if theres no empty space at file end
            if len(existing) > 0 and existing[-1].strip() != "":
                f.write("\n")
            f.write("\n\n".join(new_annotations))
            f.write("\n")
            logger.info(
                f"Wrote {len(new_annotations)} "
                f"{'line' if len(new_annotations) == 1 else 'lines'} "
                f"to {papis.document.describe(document)}"
            )
        if git:
            msg = "Update notes for '{0}'".format(papis.document.describe(document))
            folder = document.get_main_folder()
            if folder:
                papis.git.add_and_commit_resources(
                    folder, [notes_path, document.get_info_file()], msg
                )
    def _drop_existing_annotations(
        self, formatted_annotations: list[str], file_lines: list[str]
    ) -> list[str]:
        """Returns the input annotations dropping any existing.
        Takes a list of formatted annotations and a list of strings
        (most probably existing lines in a file). If anny annotations
        match an existing line closely enough, they will be dropped.
        Returns list of annotations without duplicates.
        """
        minimum_similarity = (
            papis.config.getfloat("minimum_similarity", "plugins.extract") or 1.0
        )
        remaining: list[str] = []
        for an in formatted_annotations:
            an_split = an.splitlines()
            if an_split and not self._test_similarity(
                an_split[0], file_lines, minimum_similarity
            ):
                remaining.append(an)
        return remaining
    def _test_similarity(
        self, string: str, lines: list[str], minimum_similarity: float = 1.0
    ) -> bool:
        for line in lines:
            ratio = Levenshtein.ratio(string, line)
            if ratio > minimum_similarity:
                return True
        return False
--- a/papis_extract/exporters/stdout.py
+++ b/papis_extract/exporters/stdout.py
@ -0,0 +1,26 @@
 from dataclasses import dataclass
 from papis.document import Document
 from papis_extract.annotation import Annotation
 from papis_extract.formatter import Formatter
@dataclass
 class StdoutExporter:
    formatter: Formatter
    edit: bool = False
    git: bool = False
    force: bool = False
    def run(self, annot_docs: list[tuple[Document, list[Annotation]]]) -> None:
        """Pretty print annotations to stdout.
        Gives a nice human-readable representations of
        the annotations in somewhat of a list form.
        Not intended for machine-readability.
        """
        for doc, annots in annot_docs:
            output: str = self.formatter(doc, annots)
            if output:
                print("{output}\n".format(output=output.rstrip("\n")))
--- a/papis_extract/extraction.py
+++ b/papis_extract/extraction.py
@ -0,0 +1,52 @@
 import re
 from pathlib import Path
 from typing import Protocol
 import fitz
 import papis.config
 import papis.document
 import papis.logging
 from papis.document import Document
 from papis_extract.annotation import Annotation
 logger = papis.logging.get_logger(__name__)
 class Extractor(Protocol):
    def can_process(self, filename: Path) -> bool:
        ...
    def run(self, filename: Path) -> list[Annotation]:
        ...
 def start(
    extractor: Extractor,
    document: Document,
 ) -> list[Annotation]:
    """Extract all annotations from passed documents.
    Returns all annotations contained in the papis
    documents passed in.
    """
    annotations: list[Annotation] = []
    file_available: bool = False
    for file in document.get_files():
        fname = Path(file)
        if not extractor.can_process(fname):
            continue
        file_available = True
        try:
            annotations.extend(extractor.run(fname))
        except fitz.FileDataError as e:
            print(f"File structure errors for {file}.\n{e}")
    if not file_available:
        # have to remove curlys or papis logger gets upset
        desc = re.sub("[{}]", "", papis.document.describe(document))
        logger.info(f"No {type(extractor)} file for document: {desc}")
    return annotations
--- a/papis_extract/extractor.py
+++ b/papis_extract/extractor.py
@ -1,166 +0,0 @@
 import re
 from pathlib import Path
 from typing import Any, Optional
 import Levenshtein
 import magic
 import fitz
 import papis.logging
 import papis.config
 import papis.document
 from papis.document import Document
 from papis_extract.annotation import Annotation, AnnotatedDocument
 logger = papis.logging.get_logger(__name__)
 def start(
    documents: list[Document],
 ) -> list[AnnotatedDocument]:
    """Extract all annotations from passed documents.
    Returns all annotations contained in the papis
    documents passed in.
    """
    output: list[AnnotatedDocument] = []
    for doc in documents:
        annotations: list[Annotation] = []
        found_pdf: bool = False
        for file in doc.get_files():
            fname = Path(file)
            if not _is_file_processable(fname):
                break
            found_pdf = True
            try:
                annotations.extend(extract(fname))
            except fitz.FileDataError as e:
                print(f"File structure errors for {file}.\n{e}")
        if not found_pdf:
            # have to remove curlys or papis logger gets upset
            desc = re.sub("[{}]", "", papis.document.describe(doc))
            logger.warning("Did not find suitable PDF file for document: " f"{desc}")
        output.append(AnnotatedDocument(doc, annotations))
    return output
 def extract(filename: Path) -> list[Annotation]:
    """Extract annotations from a file.
    Returns all readable annotations contained in the file
    passed in. Only returns Highlight or Text annotations.
    """
    annotations = []
    with fitz.Document(filename) as doc:
        for page in doc:
            for annot in page.annots():
                quote, note = _retrieve_annotation_content(page, annot)
                if not quote and not note:
                    continue
                col = (
                    annot.colors.get("fill")
                    or annot.colors.get("stroke")
                    or (0.0, 0.0, 0.0)
                )
                a = Annotation(
                    file=str(filename),
                    text=quote or "",
                    content=note or "",
                    colors=col,
                    type=annot.type[1],
                    page=(page.number or 0) + 1,
                )
                a.tag = _tag_from_colorname(a.colorname or "")
                annotations.append(a)
    logger.debug(
        f"Found {len(annotations)} "
        f"{'annotation' if len(annotations) == 1 else 'annotations'} for {filename}."
    )
    return annotations
 def is_pdf(fname: Path) -> bool:
    """Check if file is a pdf, using mime type."""
    return magic.from_file(fname, mime=True) == "application/pdf"
 def _is_file_processable(fname: Path) -> bool:
    if not fname.is_file():
        logger.error(f"File {str(fname)} not readable.")
        return False
    if not is_pdf(fname):
        return False
    return True
 def _tag_from_colorname(colorname: str) -> str:
    color_mapping: dict[str, str] = getdict("tags", "plugins.extract")
    if not color_mapping:
        return ""
    return color_mapping.get(colorname, "")
 def _retrieve_annotation_content(
    page: fitz.Page, annotation: fitz.Annot
 ) -> tuple[str | None, str | None]:
    """Gets the text content of an annotation.
    Returns the actual content of an annotation. Sometimes
    that is only the written words, sometimes that is only
    annotation notes, sometimes it is both. Runs a similarity
    comparison between strings to find out whether they
    should both be included or are the same, using
    Levenshtein distance.
    """
    content = annotation.info["content"].replace("\n", " ")
    written = page.get_textbox(annotation.rect).replace("\n", " ")
    # highlight with selection in note
    minimum_similarity = (
        papis.config.getfloat("minimum_similarity_content", "plugins.extract") or 1.0
    )
    if Levenshtein.ratio(content, written) > minimum_similarity:
        return (content, None)
    # both a highlight and a note
    elif content and written:
        return (written, content)
    # an independent note, not a highlight
    elif content:
        return (None, content)
    # highlight with selection not in note
    elif written:
        return (written, None)
    # just a highlight without any text
    return (None, None)
 # mimics the functions in papis.config.{getlist,getint,getfloat} etc.
 def getdict(key: str, section: Optional[str] = None) -> dict[str, str]:
    """Dict getter
    :returns: A python dict
    :raises SyntaxError: Whenever the parsed syntax is either not a valid
        python object or a valid python dict.
    """
    rawvalue: Any = papis.config.general_get(key, section=section)
    if isinstance(rawvalue, dict):
        return rawvalue
    try:
        rawvalue = eval(rawvalue)
    except Exception:
        raise SyntaxError(
            "The key '{}' must be a valid Python object: {}".format(key, rawvalue)
        )
    else:
        if not isinstance(rawvalue, dict):
            raise SyntaxError(
                "The key '{}' must be a valid Python dict. Got: {} (type {!r})".format(
                    key, rawvalue, type(rawvalue).__name__
                )
            )
        return rawvalue
--- a/papis_extract/extractors/init.py
+++ b/papis_extract/extractors/init.py
@ -0,0 +1,18 @@
 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.")
--- a/papis_extract/extractors/pdf.py
+++ b/papis_extract/extractors/pdf.py
@ -0,0 +1,92 @@
 from pathlib import Path
 import fitz
 import Levenshtein
 import magic
 import papis.config
 import papis.logging
 from papis_extract.annotation import Annotation
 logger = papis.logging.get_logger(__name__)
 class PdfExtractor:
    def can_process(self, filename: Path) -> bool:
        if not filename.is_file():
            logger.error(f"File {str(filename)} not readable.")
            return False
        if not self._is_pdf(filename):
            return False
        return True
    def run(self, filename: Path) -> list[Annotation]:
        """Extract annotations from a file.
        Returns all readable annotations contained in the file
        passed in. Only returns Highlight or Text annotations.
        """
        annotations = []
        with fitz.Document(filename) as doc:
            for page in doc:
                for annot in page.annots():
                    quote, note = self._retrieve_annotation_content(page, annot)
                    if not quote and not note:
                        continue
                    col = (
                        annot.colors.get("fill")
                        or annot.colors.get("stroke")
                        or (0.0, 0.0, 0.0)
                    )
                    a = Annotation(
                        file=str(filename),
                        content=quote or "",
                        note=note or "",
                        color=col,
                        type=annot.type[1],
                        page=(page.number or 0) + 1,
                    )
                    annotations.append(a)
        logger.debug(
            f"Found {len(annotations)} "
            f"{'annotation' if len(annotations) == 1 else 'annotations'} for {filename}."
        )
        return annotations
    def _is_pdf(self, fname: Path) -> bool:
        """Check if file is a pdf, using mime type."""
        return magic.from_file(fname, mime=True) == "application/pdf"
    def _retrieve_annotation_content(
        self, page: fitz.Page, annotation: fitz.Annot
    ) -> tuple[str | None, str | None]:
        """Gets the text content of an annotation.
        Returns the actual content of an annotation. Sometimes
        that is only the written words, sometimes that is only
        annotation notes, sometimes it is both. Runs a similarity
        comparison between strings to find out whether they
        should both be included or are the same, using
        Levenshtein distance.
        """
        content = annotation.info["content"].replace("\n", " ")
        written = page.get_textbox(annotation.rect).replace("\n", " ")
        # highlight with selection in note
        minimum_similarity = (
            papis.config.getfloat("minimum_similarity_content", "plugins.extract")
            or 1.0
        )
        if Levenshtein.ratio(content, written) > minimum_similarity:
            return (content, None)
        # both a highlight and a note
        elif content and written:
            return (written, content)
        # an independent note, not a highlight
        elif content:
            return (None, content)
        # highlight with selection not in note
        elif written:
            return (written, None)
        # just a highlight without any text
        return (None, None)
--- a/papis_extract/extractors/pocketbook.py
+++ b/papis_extract/extractors/pocketbook.py
@ -0,0 +1,78 @@
 from pathlib import Path
 import magic
 import papis.config
 import papis.logging
 from bs4 import BeautifulSoup
 from papis_extract.annotation import COLORS, Annotation
 logger = papis.logging.get_logger(__name__)
 class PocketBookExtractor:
    def can_process(self, filename: Path) -> bool:
        if not magic.from_file(filename, mime=True) == "text/xml":
            return False
        content = self._read_file(filename)
        if not content:
            return False
        html = BeautifulSoup(content, features="xml")
        if not html.find(
            "meta", {"name": "generator", "content": "PocketBook Bookmarks Export"}
        ):
            return False
        return True
    def run(self, filename: Path) -> list[Annotation]:
        """Extract annotations from pocketbook html file.
        Export annotations from pocketbook app and load add them
        to a papis document as the exported html file.
        Returns all readable annotations contained in the file
        passed in, with highlights, notes and pages if available.
        """
        content = self._read_file(filename)
        if not content:
            return []
        html = BeautifulSoup(content, features="xml")
        annotations: list[Annotation] = []
        for bm in html.select("div.bookmark"):
            content = (bm.select_one("div.bm-text>p") or html.new_string("")).text
            note = (bm.select_one("div.bm-note>p") or html.new_string("")).text
            page = (bm.select_one("p.bm-page") or html.new_string("")).text
            el_classes = bm.attrs.get("class", "").split(" ")
            color = (0, 0, 0)
            for c in el_classes:
                if "bm-color-" in c:
                    color = COLORS.get(c.removeprefix("bm-color-"), (0, 0, 0))
                    break
            a = Annotation(
                file=str(filename),
                content=content or "",
                note=note or "",
                color=color,
                type="Highlight",
                page=int(page),
            )
            annotations.append(a)
        logger.debug(
            f"Found {len(annotations)} "
            f"{'annotation' if len(annotations) == 1 else 'annotations'} for {filename}."
        )
        return annotations
    def _read_file(self, filename: Path) -> str:
        try:
            with open(filename) as f:
                return f.read()
        except FileNotFoundError:
            logger.error(f"Could not open file {filename} for extraction.")
            return ""
--- a/papis_extract/formatter.py
+++ b/papis_extract/formatter.py
@ -1,34 +1,39 @@
 from collections.abc import Callable
-from papis_extract.annotation import AnnotatedDocument
+from papis.document import Document
-Formatter = Callable[[list[AnnotatedDocument]], str]
+from papis_extract.annotation import Annotation
 Formatter = Callable[[Document, list[Annotation]], str]
 def format_markdown(
-    docs: list[AnnotatedDocument] = [], atx_headings: bool = False
+    document: Document = Document(),
    annotations: list[Annotation] = [],
    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 = ""
    for entry in docs:
        if not entry.annotations:
            continue
-        heading = f"{entry.document['title']} - {entry.document['author']}\n"
+    heading = f"{document.get('title', '')} - {document.get('author', '')}"
-        if atx_headings:
+    if headings == "atx":
-            output += f"# {heading}\n"
+        output = f"# {heading}\n\n"
-        else:
+    elif headings == "setext":
        title_decoration = (
-                f"{'=' * len(entry.document.get('title', ''))}   "
+            f"{'=' * len(document.get('title', ''))}   "
-                f"{'-' * len(entry.document.get('author', ''))}"
+            f"{'-' * len(document.get('author', ''))}"
        )
-            output += f"{title_decoration}\n" f"{heading}" f"{title_decoration}\n\n"
+        output = f"{title_decoration}\n{heading}\n{title_decoration}\n\n"
    else:
        output = ""
-        for a in entry.annotations:
+    for a in annotations:
        output += a.format(template)
        output += "\n\n"
@ -37,49 +42,54 @@ def format_markdown(
    return output.rstrip()
-def format_markdown_atx(docs: list[AnnotatedDocument] = []) -> str:
+def format_markdown_atx(
-    return format_markdown(docs, atx_headings=True)
+    document: Document = Document(),
    annotations: list[Annotation] = [],
 ) -> str:
    return format_markdown(document, annotations, headings="atx")
-def format_markdown_setext(docs: list[AnnotatedDocument] = []) -> str:
+def format_markdown_setext(
-    return format_markdown(docs, atx_headings=False)
+    document: Document = Document(),
    annotations: list[Annotation] = [],
 ) -> str:
    return format_markdown(document, annotations, headings="setext")
-def format_count(docs: list[AnnotatedDocument] = []) -> str:
+def format_count(
-    output = ""
+    document: Document = Document(),
-    for entry in docs:
+    annotations: list[Annotation] = [],
-        if not entry.annotations:
+) -> str:
-            continue
+    if not annotations:
        return ""
    count = 0
-        for _ in entry.annotations:
+    for _ in annotations:
        count += 1
-        d = entry.document
+    return (
-        output += (
+        f"{document.get('author', '')}"
-            f"{d['author'] if 'author' in d else ''}"
+        f"{' - ' if 'author' in document else ''}"  # only put separator if author
-            f"{' - ' if 'author' in d else ''}"  # only put separator if author
+        f"{document.get('title', '')}: "
            f"{entry.document['title'] if 'title' in d else ''}: "
        f"{count}\n"
-        )
+    ).rstrip()
    return output.rstrip()
-def format_csv(docs: list[AnnotatedDocument] = []) -> str:
+def format_csv(
    document: Document = Document(),
    annotations: list[Annotation] = [],
 ) -> 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 annotations:
-        if not entry.annotations:
+        return ""
            continue
-        d = entry.document
+    for a in annotations:
-        for a in entry.annotations:
+        output += a.format(template, doc=document)
            output += a.format(template, doc=d)
        output += "\n"
    return output.rstrip()
@ -89,6 +99,6 @@ formatters: dict[str, Formatter] = {
    "count": format_count,
    "csv": format_csv,
    "markdown": format_markdown,
-    "markdown_atx": format_markdown_atx,
+    "markdown-atx": format_markdown_atx,
-    "markdown_setext": format_markdown_setext,
+    "markdown-setext": format_markdown_setext,
 }
--- a/poetry.lock
+++ b/poetry.lock
@ -1084,4 +1084,4 @@ whoosh = ["whoosh"]
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.11"
-content-hash = "02d5ac314a19f14103372c7ceccdaec080df3fdc2fdb1381f2f6343cd6d17db4"
+content-hash = "273c651cac44163ca183313ce3c7384577f090fd98fa6d28e6a3496cb28254ac"
--- a/pyproject.toml
+++ b/pyproject.toml
@ -3,8 +3,21 @@ name = "papis-extract"
 version = "0.2.0"
 description = ""
 authors = ["Marty Oehme <marty.oehme@gmail.com>"]
 license = "GPL-3.0-or-later"
 readme = "README.md"
-packages = [{include = "papis_extract"}]
+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"
@ -15,9 +28,11 @@ click = "^8.1.7"
 whoosh = { version = "^2.7.4", optional = true }
 python-magic = "^0.4.27"
 chevron = "^0.14.0"
 beautifulsoup4 = { version = "^4.12.3", optional = true }
 [tool.poetry.extras]
 whoosh = ["whoosh"]
 pocketbook = ["beautifulsoup4"]
 [tool.poetry.group.dev.dependencies]
 pytest = "^7.4.0"
--- a/tests/test_annotation.py
+++ b/tests/test_annotation.py
@ -1,5 +1,6 @@
 from papis.document import Document
 import pytest
 from papis.document import Document
 from papis_extract.annotation import Annotation
@ -20,8 +21,8 @@ from papis_extract.annotation import Annotation
 def test_formatting_replacements(fmt_string, expected):
    sut = Annotation(
        "myfile",
-        text="I am the text value",
+        content="I am the text value",
-        content="Whereas I represent the note",
+        note="Whereas I represent the note",
    )
    assert sut.format(fmt_string) == expected
@ -38,8 +39,8 @@ def test_formatting_replacements(fmt_string, expected):
 def test_formatting_document_access(fmt_string, expected):
    sut = Annotation(
        "myfile",
-        text="I am the text value",
+        content="I am the text value",
-        content="Whereas I represent the note",
+        note="Whereas I represent the note",
    )
    doc = Document(data={"title": "document-title", "author": "document-author"})
@ -47,7 +48,7 @@ def test_formatting_document_access(fmt_string, expected):
 def test_colorname_matches_exact():
-    sut = Annotation("testfile", colors=(1.0, 0.0, 0.0), minimum_similarity_color=1.0)
+    sut = Annotation("testfile", color=(1.0, 0.0, 0.0), minimum_similarity_color=1.0)
    c_name = sut.colorname
    assert c_name == "red"
@ -64,6 +65,6 @@ def test_colorname_matches_exact():
    ],
 )
 def test_matches_inexact_colorname(color_value):
-    sut = Annotation("testfile", colors=color_value, minimum_similarity_color=0.833)
+    sut = Annotation("testfile", color=color_value, minimum_similarity_color=0.833)
    c_name = sut.colorname
    assert c_name == "red"
--- a/tests/test_formatting.py
+++ b/tests/test_formatting.py
@ -1,5 +1,5 @@
 from papis.document import Document
-from papis_extract.annotation import AnnotatedDocument, Annotation
+from papis_extract.annotation import Annotation
 from papis_extract.formatter import (
    format_count,
@ -9,13 +9,11 @@ from papis_extract.formatter import (
    format_markdown_setext,
 )
-an_doc: AnnotatedDocument = AnnotatedDocument(
+document = Document(data={"author": "document-author", "title": "document-title"})
-    Document(data={"author": "document-author", "title": "document-title"}),
+annotations = [
-    [
+    Annotation("myfile.pdf", content="my lovely text"),
-        Annotation("myfile.pdf", text="my lovely text"),
+    Annotation("myfile.pdf", content="my second text", note="with note"),
-        Annotation("myfile.pdf", text="my second text", content="with note"),
+]
    ],
 )
 md_default_output = """==============   ---------------
 document-title - document-author
 ==============   ---------------
@ -28,12 +26,12 @@ document-title - document-author
 def test_markdown_default():
    fmt = format_markdown
-    assert fmt([an_doc]) == md_default_output
+    assert fmt(document, annotations) == md_default_output
 def test_markdown_atx():
    fmt = format_markdown_atx
-    assert fmt([an_doc]) == (
+    assert fmt(document, annotations) == (
        """# document-title - document-author
 > my lovely text
@ -45,17 +43,17 @@ def test_markdown_atx():
 def test_markdown_setext():
    fmt = format_markdown_setext
-    assert fmt([an_doc]) == md_default_output
+    assert fmt(document, annotations) == md_default_output
 def test_count_default():
    fmt = format_count
-    assert fmt([an_doc]) == ("""document-author - document-title: 2""")
+    assert fmt(document, annotations) == ("""document-author - document-title: 2""")
 def test_csv_default():
    fmt = format_csv
-    assert fmt([an_doc]) == (
+    assert fmt(document, annotations) == (
        "type,tag,page,quote,note,author,title,ref,file\n"
        'Highlight,,0,"my lovely text","","document-author",'
        '"document-title","","myfile.pdf"\n'
@ -66,15 +64,12 @@ def test_csv_default():
 # sadpath - no annotations contained for each format
 def test_markdown_no_annotations():
-    d: AnnotatedDocument = AnnotatedDocument(Document(data={}), [])
+    assert format_markdown(document, []) == ""
    assert format_markdown([d]) == ""
 def test_count_no_annotations():
-    d: AnnotatedDocument = AnnotatedDocument(Document(data={}), [])
+    assert format_count(document, []) == ""
    assert format_count([d]) == ""
 def test_csv_no_annotations():
-    d: AnnotatedDocument = AnnotatedDocument(Document(data={}), [])
+    assert format_csv(document, []) == ""
    assert format_csv([d]) == "type,tag,page,quote,note,author,title,ref,file"
Author	SHA1	Message	Date
Marty Oehme	905b20a79c	fix: Default markdown atx formatter for note exporter Some checks failed ci/woodpecker/push/lint Pipeline failed Details ci/woodpecker/push/static_analysis Pipeline failed Details ci/woodpecker/push/test Pipeline was successful Details	2024-01-25 22:46:38 +01:00
Marty Oehme	163fd63038	fix: Fixed pocketbook extractor trying to read all files The complete read routine would work before figuring out that it is a file of xml mimetype. This means that it would try to read to memory any file as the first thing, pdfs, even binaries. Of course doing so crashed the program.	2024-01-25 21:42:34 +01:00
Marty Oehme	72ddaaf1bc	refactor: Extract exporters to separate module	2024-01-25 21:42:33 +01:00
Marty Oehme	c8e8453b68	feat: Add advanced pocketbook detection heuristic Added heuristic which checks for the existence of a specific meta tag written to the pocketbook XHTML file.	2024-01-24 14:57:10 +01:00
Marty Oehme	6a8f8a03bc	refactor: Extract pocketbook file opening method	2024-01-24 14:55:28 +01:00
Marty Oehme	86d53a19d4	chore: Fix import lint error	2024-01-24 13:39:01 +01:00
Marty Oehme	c2a5190237	refactor: Improve module availability checks Followed ruff (Pyflakes) suggestion to use importlib utils directly instead of try and erroring with imports.	2024-01-24 12:27:21 +01:00
Marty Oehme	2f41906e6a	docs: Add extractor and install info Added extractor info for the two currently existing extractors. Added install recommendation for pipx.	2024-01-24 12:21:51 +01:00
Marty Oehme	e7e5258b34	feat: Only activate pocketbook extractor optionally Since we make the dependencies for pocketbook html extraction optional as an extra, this commit ensures the extractor (and cli option) only gets loaded when they exist.	2024-01-24 12:07:04 +01:00
Marty Oehme	e1e09b6011	chore: Format pyproject	2024-01-24 12:05:41 +01:00
Marty Oehme	f6c0189529	fix: Tag automation on tag creation Tagging by color only worked on manually invoking the `annotation.color = ()` setter. Now it works on initial instance creation.	2024-01-24 11:20:00 +01:00
Marty Oehme	333bd279b9	fix: Fix test fixtures for new annotation structure	2024-01-24 11:15:10 +01:00
Marty Oehme	67bfc30396	refactor: Switch annotation away from dataclass To ease employing getters and setters, we switch the dataclass to a normal python undecorated class.	2024-01-24 11:15:10 +01:00
Marty Oehme	f4a26292a0	fix: Remove debug print statement	2024-01-24 11:13:35 +01:00
Marty Oehme	c53cd563b7	feat: Add pocketbook extraction	2024-01-24 08:56:21 +01:00
Marty Oehme	ddb34fca7b	refactor: Move tagging by color to Annotation	2024-01-24 08:53:54 +01:00
Marty Oehme	3bd6247888	chore: Add license and dev instructions	2024-01-23 10:15:51 +01:00
Marty Oehme	11d570f9d8	refactor: Rename annotation content variables Renamed the two variables describing an annotation's highlighted PDF-text and its appended note if any exists. Previously called 'text' (for the in-PDF highlighted content) and 'content' (for the additional supplied content). Now they are called 'content' for the IN PDF words, highlighted. and 'note' for the appended note given (or not) in an annotation.	2024-01-23 09:54:36 +01:00
Marty Oehme	9169e1c98a	chore: Improve stdout newline handling Always strip all newlines of the end of all entries, and then add a single newline back between entries.	2024-01-23 09:49:31 +01:00
Marty Oehme	2880c06f53	chore: Improve cli option help texts Fixed the write option text to be without wrong negation. Show default settings for flag options.	2024-01-23 09:27:26 +01:00
Marty Oehme	a51205954c	refactor: Extract extractor list to extractor module	2024-01-23 09:21:46 +01:00
Marty Oehme	629932a5e8	feat: Loop through all chosen extractors	2024-01-23 09:10:42 +01:00
Marty Oehme	f477deea7c	feat: Add extractor cli choice Can only choose pdf for the time being, but allows additional extractors to be added in the future.	2024-01-23 08:58:32 +01:00
Marty Oehme	3b4db7b6b8	refactor: Extract PDF extractor into class Extractor is a general protocol with the PDF extraction routine now being one implementation of the protocol. Preparation for adding multiple extractors (epub,djvu, or specific progammes) in the future.	2024-01-20 18:02:51 +01:00
Marty Oehme	765de505bb	refactor: Remove AnnotatedDocument class The AnnotatedDocument class was, essentially, a simple tuple of a document and a list of annotations. While not bad in a vacuum, it is unwieldy and passing this around instead of a document, annotations, or both where necessary is more restrictive and frankly unnecessary. This commit removes the data class and any instances of its use. Instead, we now pass the individual components around to anything that needs them. This also frees us up to pass only annotations around for example. We also do not iterate through the selected papis documents to work on in each exporter anymore (since we only pass a single document), but in the main function itself. This leads to less duplication and makes the overall run function the overall single source of iteration through selected documents. Everything else only knows about a single document - the one it is operating on - which seems much neater. For now, it does not change much, but should make later work on extra exporters or extractors easier.	2024-01-20 16:36:24 +01:00