Prevent error loading pdf: Added pymupdf/fitz open to get page count

[ekcomputer]

When adding some pdfs to the Docs class, I often received the following error (in case it matters, they were docs returned by zotero.iterate). Further inspection revealed pypdf was having trouble parsing the pdf and the pypdf.PdfReader returned an object that couldn't be evaluated with the len function, which is required for the utils.count_pdf_pages function.

Although paper-qa reads pdf text with fitz by default, the utils.count_pdf_pages function is only written for pypdf. Therefore, my pull request simply modifies it to use fitz there as well.

---------------------------------------------------------------------------
KeyError                                  Traceback (most recent call last)
Cell In[15], [line 3](vscode-notebook-cell:?execution_count=15&line=3)
      [1](vscode-notebook-cell:?execution_count=15&line=1) ## Try again with only the Zotero part
      [2](vscode-notebook-cell:?execution_count=15&line=2) zotero = ZoteroDB(library_type="user")  # "group" if group library
----> [3](vscode-notebook-cell:?execution_count=15&line=3) for item in zotero.iterate(collection_name='Modeling', limit=50):
      [4](vscode-notebook-cell:?execution_count=15&line=4)     # print(f'Error parsing page count for: {item.title}')
      [5](vscode-notebook-cell:?execution_count=15&line=5)     try:
      [6](vscode-notebook-cell:?execution_count=15&line=6)         print(f' >    {item.title}')

File [~/mambaforge/envs/paperqa/lib/python3.11/site-packages/paperqa/contrib/zotero.py:259](https://file+.vscode-resource.vscode-cdn.net/Users/ekyzivat/Library/CloudStorage/Dropbox/Python/LLM-packages/~/mambaforge/envs/paperqa/lib/python3.11/site-packages/paperqa/contrib/zotero.py:259), in ZoteroDB.iterate(self, limit, start, q, qmode, since, tag, sort, direction, collection_name)
    [253](https://file+.vscode-resource.vscode-cdn.net/Users/ekyzivat/Library/CloudStorage/Dropbox/Python/LLM-packages/~/mambaforge/envs/paperqa/lib/python3.11/site-packages/paperqa/contrib/zotero.py:253) title = item["data"]["title"] if "title" in item["data"] else ""
    [254](https://file+.vscode-resource.vscode-cdn.net/Users/ekyzivat/Library/CloudStorage/Dropbox/Python/LLM-packages/~/mambaforge/envs/paperqa/lib/python3.11/site-packages/paperqa/contrib/zotero.py:254) if len(items) >= start:
    [255](https://file+.vscode-resource.vscode-cdn.net/Users/ekyzivat/Library/CloudStorage/Dropbox/Python/LLM-packages/~/mambaforge/envs/paperqa/lib/python3.11/site-packages/paperqa/contrib/zotero.py:255)     yield ZoteroPaper(
    [256](https://file+.vscode-resource.vscode-cdn.net/Users/ekyzivat/Library/CloudStorage/Dropbox/Python/LLM-packages/~/mambaforge/envs/paperqa/lib/python3.11/site-packages/paperqa/contrib/zotero.py:256)         key=_get_citation_key(item),
    [257](https://file+.vscode-resource.vscode-cdn.net/Users/ekyzivat/Library/CloudStorage/Dropbox/Python/LLM-packages/~/mambaforge/envs/paperqa/lib/python3.11/site-packages/paperqa/contrib/zotero.py:257)         title=title,
    [258](https://file+.vscode-resource.vscode-cdn.net/Users/ekyzivat/Library/CloudStorage/Dropbox/Python/LLM-packages/~/mambaforge/envs/paperqa/lib/python3.11/site-packages/paperqa/contrib/zotero.py:258)         pdf=pdf,
--> [259](https://file+.vscode-resource.vscode-cdn.net/Users/ekyzivat/Library/CloudStorage/Dropbox/Python/LLM-packages/~/mambaforge/envs/paperqa/lib/python3.11/site-packages/paperqa/contrib/zotero.py:259)         num_pages=count_pdf_pages(pdf),
    [260](https://file+.vscode-resource.vscode-cdn.net/Users/ekyzivat/Library/CloudStorage/Dropbox/Python/LLM-packages/~/mambaforge/envs/paperqa/lib/python3.11/site-packages/paperqa/contrib/zotero.py:260)         details=item,
    [261](https://file+.vscode-resource.vscode-cdn.net/Users/ekyzivat/Library/CloudStorage/Dropbox/Python/LLM-packages/~/mambaforge/envs/paperqa/lib/python3.11/site-packages/paperqa/contrib/zotero.py:261)         zotero_key=item["key"],
    [262](https://file+.vscode-resource.vscode-cdn.net/Users/ekyzivat/Library/CloudStorage/Dropbox/Python/LLM-packages/~/mambaforge/envs/paperqa/lib/python3.11/site-packages/paperqa/contrib/zotero.py:262)     )
    [263](https://file+.vscode-resource.vscode-cdn.net/Users/ekyzivat/Library/CloudStorage/Dropbox/Python/LLM-packages/~/mambaforge/envs/paperqa/lib/python3.11/site-packages/paperqa/contrib/zotero.py:263)     actual_i += 1
    [265](https://file+.vscode-resource.vscode-cdn.net/Users/ekyzivat/Library/CloudStorage/Dropbox/Python/LLM-packages/~/mambaforge/envs/paperqa/lib/python3.11/site-packages/paperqa/contrib/zotero.py:265) items.append(item)

File [~/mambaforge/envs/paperqa/lib/python3.11/site-packages/paperqa/utils.py:68](https://file+.vscode-resource.vscode-cdn.net/Users/ekyzivat/Library/CloudStorage/Dropbox/Python/LLM-packages/~/mambaforge/envs/paperqa/lib/python3.11/site-packages/paperqa/utils.py:68), in count_pdf_pages(file_path)
     [66](https://file+.vscode-resource.vscode-cdn.net/Users/ekyzivat/Library/CloudStorage/Dropbox/Python/LLM-packages/~/mambaforge/envs/paperqa/lib/python3.11/site-packages/paperqa/utils.py:66) with open(file_path, "rb") as pdf_file:
     [67](https://file+.vscode-resource.vscode-cdn.net/Users/ekyzivat/Library/CloudStorage/Dropbox/Python/LLM-packages/~/mambaforge/envs/paperqa/lib/python3.11/site-packages/paperqa/utils.py:67)     pdf_reader = pypdf.PdfReader(pdf_file)
---> [68](https://file+.vscode-resource.vscode-cdn.net/Users/ekyzivat/Library/CloudStorage/Dropbox/Python/LLM-packages/~/mambaforge/envs/paperqa/lib/python3.11/site-packages/paperqa/utils.py:68)     num_pages = len(pdf_reader.pages)
     [69](https://file+.vscode-resource.vscode-cdn.net/Users/ekyzivat/Library/CloudStorage/Dropbox/Python/LLM-packages/~/mambaforge/envs/paperqa/lib/python3.11/site-packages/paperqa/utils.py:69) return num_pages

File [~/mambaforge/envs/paperqa/lib/python3.11/site-packages/pypdf/_page.py:2493](https://file+.vscode-resource.vscode-cdn.net/Users/ekyzivat/Library/CloudStorage/Dropbox/Python/LLM-packages/~/mambaforge/envs/paperqa/lib/python3.11/site-packages/pypdf/_page.py:2493), in _VirtualList.__len__(self)
   [2492](https://file+.vscode-resource.vscode-cdn.net/Users/ekyzivat/Library/CloudStorage/Dropbox/Python/LLM-packages/~/mambaforge/envs/paperqa/lib/python3.11/site-packages/pypdf/_page.py:2492) def __len__(self) -> int:
-> [2493](https://file+.vscode-resource.vscode-cdn.net/Users/ekyzivat/Library/CloudStorage/Dropbox/Python/LLM-packages/~/mambaforge/envs/paperqa/lib/python3.11/site-packages/pypdf/_page.py:2493)     return self.length_function()

File [~/mambaforge/envs/paperqa/lib/python3.11/site-packages/pypdf/_reader.py:462](https://file+.vscode-resource.vscode-cdn.net/Users/ekyzivat/Library/CloudStorage/Dropbox/Python/LLM-packages/~/mambaforge/envs/paperqa/lib/python3.11/site-packages/pypdf/_reader.py:462), in PdfReader._get_num_pages(self)
    [460](https://file+.vscode-resource.vscode-cdn.net/Users/ekyzivat/Library/CloudStorage/Dropbox/Python/LLM-packages/~/mambaforge/envs/paperqa/lib/python3.11/site-packages/pypdf/_reader.py:460) else:
    [461](https://file+.vscode-resource.vscode-cdn.net/Users/ekyzivat/Library/CloudStorage/Dropbox/Python/LLM-packages/~/mambaforge/envs/paperqa/lib/python3.11/site-packages/pypdf/_reader.py:461)     if self.flattened_pages is None:
--> [462](https://file+.vscode-resource.vscode-cdn.net/Users/ekyzivat/Library/CloudStorage/Dropbox/Python/LLM-packages/~/mambaforge/envs/paperqa/lib/python3.11/site-packages/pypdf/_reader.py:462)         self._flatten()
    [463](https://file+.vscode-resource.vscode-cdn.net/Users/ekyzivat/Library/CloudStorage/Dropbox/Python/LLM-packages/~/mambaforge/envs/paperqa/lib/python3.11/site-packages/pypdf/_reader.py:463)     return len(self.flattened_pages)

File [~/mambaforge/envs/paperqa/lib/python3.11/site-packages/pypdf/_reader.py:1228](https://file+.vscode-resource.vscode-cdn.net/Users/ekyzivat/Library/CloudStorage/Dropbox/Python/LLM-packages/~/mambaforge/envs/paperqa/lib/python3.11/site-packages/pypdf/_reader.py:1228), in PdfReader._flatten(self, pages, inherit, indirect_reference)
   [1224](https://file+.vscode-resource.vscode-cdn.net/Users/ekyzivat/Library/CloudStorage/Dropbox/Python/LLM-packages/~/mambaforge/envs/paperqa/lib/python3.11/site-packages/pypdf/_reader.py:1224)     inherit = {}
   [1225](https://file+.vscode-resource.vscode-cdn.net/Users/ekyzivat/Library/CloudStorage/Dropbox/Python/LLM-packages/~/mambaforge/envs/paperqa/lib/python3.11/site-packages/pypdf/_reader.py:1225) if pages is None:
   [1226](https://file+.vscode-resource.vscode-cdn.net/Users/ekyzivat/Library/CloudStorage/Dropbox/Python/LLM-packages/~/mambaforge/envs/paperqa/lib/python3.11/site-packages/pypdf/_reader.py:1226)     # Fix issue 327: set flattened_pages attribute only for
   [1227](https://file+.vscode-resource.vscode-cdn.net/Users/ekyzivat/Library/CloudStorage/Dropbox/Python/LLM-packages/~/mambaforge/envs/paperqa/lib/python3.11/site-packages/pypdf/_reader.py:1227)     # decrypted file
-> [1228](https://file+.vscode-resource.vscode-cdn.net/Users/ekyzivat/Library/CloudStorage/Dropbox/Python/LLM-packages/~/mambaforge/envs/paperqa/lib/python3.11/site-packages/pypdf/_reader.py:1228)     catalog = self.trailer[TK.ROOT].get_object()
   [1229](https://file+.vscode-resource.vscode-cdn.net/Users/ekyzivat/Library/CloudStorage/Dropbox/Python/LLM-packages/~/mambaforge/envs/paperqa/lib/python3.11/site-packages/pypdf/_reader.py:1229)     pages = catalog["[/Pages](https://file+.vscode-resource.vscode-cdn.net/Pages)"].get_object()  # type: ignore
   [1230](https://file+.vscode-resource.vscode-cdn.net/Users/ekyzivat/Library/CloudStorage/Dropbox/Python/LLM-packages/~/mambaforge/envs/paperqa/lib/python3.11/site-packages/pypdf/_reader.py:1230)     self.flattened_pages = []

File [~/mambaforge/envs/paperqa/lib/python3.11/site-packages/pypdf/generic/_data_structures.py:333](https://file+.vscode-resource.vscode-cdn.net/Users/ekyzivat/Library/CloudStorage/Dropbox/Python/LLM-packages/~/mambaforge/envs/paperqa/lib/python3.11/site-packages/pypdf/generic/_data_structures.py:333), in DictionaryObject.__getitem__(self, key)
    [332](https://file+.vscode-resource.vscode-cdn.net/Users/ekyzivat/Library/CloudStorage/Dropbox/Python/LLM-packages/~/mambaforge/envs/paperqa/lib/python3.11/site-packages/pypdf/generic/_data_structures.py:332) def __getitem__(self, key: Any) -> PdfObject:
--> [333](https://file+.vscode-resource.vscode-cdn.net/Users/ekyzivat/Library/CloudStorage/Dropbox/Python/LLM-packages/~/mambaforge/envs/paperqa/lib/python3.11/site-packages/pypdf/generic/_data_structures.py:333)     return dict.__getitem__(self, key).get_object()

KeyError: '/Root'

[whitead]

Awesome! Great find, thanks!