fix: Default markdown atx formatter for note exporter

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.

COPYING

@@ -0,0 +1,674 @@
+                    GNU GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
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+
+  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

@@ -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
-    - pretty display on stdout (rich?)
-    - csv/tsv to stdout
-    - table fmt stdout?
+    - [x] markdown into notes
+    - [ ] pretty display on stdout (rich?)
+    - [x] csv/tsv to stdout
+    - [ ] table fmt stdout?
 - [ ] allow custom colors -> tag name settings not dependent on color name existing (e.g. {"important": (1.0,0.0,0.0)})
 - [ ] `--overwrite` mode where existing annotations are not dropped but overwritten on same line of note
-- [ ] `--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
@@ -265,7 +283,8 @@ I am not sure if there is much I can do about these issues for now.
 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.
+: 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.
 
 ---
 

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(
-            formatter=formatter,
-            annotated_docs=annotated_docs,
+        exporter: Exporter = all_exporters["notes"](
+            formatter=formatter or formatters["markdown-atx"],
             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)

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 = {
-    "red": (1, 0, 0),
-    "green": (0, 1, 0),
+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),
 }
 
@@ -25,14 +29,25 @@ class Annotation:
     Contains all information necessary for the annotation itself, content and metadata.
     """
 
-    file: str
-    colors: tuple[float, float, float] = field(default_factory=lambda: (0.0, 0.0, 0.0))
-    content: str = ""
-    page: int = 0
-    tag: str = ""
-    text: str = ""
-    type: str = "Highlight"
-    minimum_similarity_color: float = 1.0
+    def __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.
@@ -43,8 +58,8 @@ class Annotation:
         """
         data = {
             "file": self.file,
-            "quote": self.text,
-            "note": self.content,
+            "quote": 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
-class AnnotatedDocument:
-    """Contains all annotations belonging to a single papis document.
+        return color_mapping.get(colorname, "")
 
-    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
-    annotations: list[Annotation]
+        :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__
+                    )
+                )
 
-    # TODO could implement a from_doc() static method to generate annotation list?
+            return rawvalue

papis_extract/exporter.py

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

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

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

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")))

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

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

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.")

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)

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 ""

papis_extract/formatter.py

@@ -1,86 +1,96 @@
 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"
-        if atx_headings:
-            output += f"# {heading}\n"
-        else:
-            title_decoration = (
-                f"{'=' * len(entry.document.get('title', ''))}   "
-                f"{'-' * len(entry.document.get('author', ''))}"
-            )
-            output += f"{title_decoration}\n" f"{heading}" f"{title_decoration}\n\n"
-
-        for a in entry.annotations:
-            output += a.format(template)
-            output += "\n\n"
-
-        output += "\n\n\n"
-
-    return output.rstrip()
-
-
-def format_markdown_atx(docs: list[AnnotatedDocument] = []) -> str:
-    return format_markdown(docs, atx_headings=True)
-
-
-def format_markdown_setext(docs: list[AnnotatedDocument] = []) -> str:
-    return format_markdown(docs, atx_headings=False)
-
-
-def format_count(docs: list[AnnotatedDocument] = []) -> str:
-    output = ""
-    for entry in docs:
-        if not entry.annotations:
-            continue
-
-        count = 0
-        for _ in entry.annotations:
-            count += 1
-
-        d = entry.document
-        output += (
-            f"{d['author'] if 'author' in d else ''}"
-            f"{' - ' if 'author' in d else ''}"  # only put separator if author
-            f"{entry.document['title'] if 'title' in d else ''}: "
-            f"{count}\n"
+    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"
+    else:
+        output = ""
+
+    for a in annotations:
+        output += a.format(template)
+        output += "\n\n"
+
+    output += "\n\n\n"
 
     return output.rstrip()
 
 
-def format_csv(docs: list[AnnotatedDocument] = []) -> str:
+def format_markdown_atx(
+    document: Document = Document(),
+    annotations: list[Annotation] = [],
+) -> str:
+    return format_markdown(document, annotations, headings="atx")
+
+
+def format_markdown_setext(
+    document: Document = Document(),
+    annotations: list[Annotation] = [],
+) -> str:
+    return format_markdown(document, annotations, headings="setext")
+
+
+def format_count(
+    document: Document = Document(),
+    annotations: list[Annotation] = [],
+) -> str:
+    if not annotations:
+        return ""
+
+    count = 0
+    for _ in annotations:
+        count += 1
+
+    return (
+        f"{document.get('author', '')}"
+        f"{' - ' if 'author' in document else ''}"  # only put separator if author
+        f"{document.get('title', '')}: "
+        f"{count}\n"
+    ).rstrip()
+
+
+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 entry.annotations:
-            continue
+    if not annotations:
+        return ""
 
-        d = entry.document
-        for a in entry.annotations:
-            output += a.format(template, doc=d)
-            output += "\n"
+    for a in annotations:
+        output += a.format(template, doc=document)
+        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_setext": format_markdown_setext,
+    "markdown-atx": format_markdown_atx,
+    "markdown-setext": format_markdown_setext,
 }

poetry.lock

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

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"

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="Whereas I represent the note",
+        content="I am the text value",
+        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="Whereas I represent the note",
+        content="I am the text value",
+        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"

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(data={"author": "document-author", "title": "document-title"}),
-    [
-        Annotation("myfile.pdf", text="my lovely text"),
-        Annotation("myfile.pdf", text="my second text", content="with note"),
-    ],
-)
+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
 ==============   ---------------
@@ -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([d]) == ""
+    assert format_markdown(document, []) == ""
 
 
 def test_count_no_annotations():
-    d: AnnotatedDocument = AnnotatedDocument(Document(data={}), [])
-    assert format_count([d]) == ""
+    assert format_count(document, []) == ""
 
 
 def test_csv_no_annotations():
-    d: AnnotatedDocument = AnnotatedDocument(Document(data={}), [])
-    assert format_csv([d]) == "type,tag,page,quote,note,author,title,ref,file"
+    assert format_csv(document, []) == ""