This is a little utility that helps to create templated notes from the pdf file of scientific papers using their autoextracted metadata. By default the tool also renames the pdf file to the title of the paper.
The tool is based on the great pdf2bib library.
I use this tool extensively in conjuction with logseq to create a knowledge base of scientific papers without any need to use separate reference management software.
You can have a look at the step by step guide for more information.
This README is structured in the following way:
To install the package, you can use pip:
pip install git+https://github.com/m0dd0/paper2note.gitThe tool can be used as a command line utility, as a context menu entry or as a python library.
To create a reference note from a paper, you can use the following command:
paper2note path/to/paper.pdfWithout any additional options, the utility will set the name of the pdf file to the title of the paper and create a markdown file in the same folder as the pdf which corresponds to this template. If a file with the same name already exists, the utility will not overwrite.
A couple of configuration options are available to customize the behavior of the utility.
positional arguments:
pdf Path to the pdf file of the paper.
options:
-h, --help show this help message and exit
--pdf-rename-pattern PDF_RENAME_PATTERN
Pattern to rename the pdf file. All entries of the metadata can be used as placeholders.
Placeholder must be in curly braces. Defaults to the title of the paper. Set to an empty
string to not rename the pdf file.
--note-target-folder NOTE_TARGET_FOLDER
Folder where the note should be saved to. Can be an absolute path or relative to the
directory from wich the script is called. Defaults to the directory of the pdf file.
--note-template-path NOTE_TEMPLATE_PATH
Path to the note template. Can be an absolute path or relative to the directory from wich
the script is called. Defaults to a default note template.
--note-filename-pattern NOTE_FILENAME_PATTERN
Pattern to name the note file. All entries of the metadata can be used as placeholders.
Placeholder must be in curly braces. Defaults to the same name as the (renamed) pdf file. As of now, the context menu entry is only available on windows. (I am happy to accept pull requests to add this functionality for other operating systems.)
The (default) command described above can also be executed by right-clicking on a pdf file and selecting the "paper2note" option. To enable this functionality, execute the following command in a terminal with administrator rights:
paper2note-context-menuTo remove the context menu entry, execute the following command in a terminal with administrator rights:
paper2note-context-menu --removeIf you want to customize the behavior of the context menu entry, you can pass the arguments for the paper2note command to the paper2note-context-menu command. In this case all the invocations of the context menu entry will use the passed arguments.
For example:
paper2note-context-menu '--pdf-rename-pattern "{title} - {author}" --note-target-folder "path/to/notes" --note-template-path "path/to/template.md" --note-filename-pattern "{title} - {year}"'You can adapt the behavior of the context menu entry further with the following options:
positional arguments:
arguments The command args to configure the context menu entry with. If nothing given all the default args will be used.
options:
-h, --help show this help message and exit
--entry-name ENTRY_NAME
The displayed name of the context menu entry.
--remove Remove the context menu entry instead of creating it.
--keep-open Keep the command prompt open after the command has been executed.The utility can also be used as a python library.
The library contains exactly one function, paper2note.
The following example shows how to create a reference note from a paper:
from paper2note import paper2note
paper2note("path/to/paper.pdf", pdf_rename_pattern="{title} - {author}", note_target_folder="path/to/notes", note_template_path="path/to/template.md", note_filename_pattern="{title} - {author}")Have a look at the docstring of the function for more information.
The following keys can be used as placeholders in the pdf_rename_pattern, note_filename_pattern and the note template.
Sometimes not all metadata can be extracted from the pdf file. In this case the respective key will be filled with a placeholder string such as e.g. <no journal found>.
title: The title of the paperauthors: A string of comma separated full author namesyear: The year of publicationmonth: The month of publicationday: The day of publicationjournal: The journal in which the paper was publisheddoi: The doi of the paperurl: The url of the papervolume: The volume of the journalpage: The page of the journalabstract: The abstract of the paperbibtex: The full unmodified bibtex entry of the papertype: The type of the paperauthor_i: The i-th author of the paper were i is a number between 1 and the number of authorsauthor_last: The last named author of the paperlogseq_author_listing: A string of comma separated author names in the form [[author1]], [[author2]], ... for use in logseqextraction_method: The method used to extract the metadata from the pdf filepath: The path to the (renamed) pdf filerelative_logseq_path: If the pdf is located in a subdirectory of the logseq directory, this key contains the relative path to the pdf file from the logseq directory. Otherwise it is an empty string.
This utility uses the pdf2bib library to extract metadata from the pdf file. The pdf2bib library tries 5 different methods one after another to extract metadata is described on the respective github page. For my usecase, the results were accurate in most cases, but there were also cases where the metadata was not extracted correctly. This was especially the case for papers from the Neurips conference. Emprically I found that one of the methods used by pdf2bib to extract metadata from the pdf file results in many false positives. For this reason this library uses a fork of pdf2bib in which I disabled this method. See this issue for more information.
If you install the package into an environment like conda or venv the command line utility will only be available in this environment. However, once you have added the context menu entry, you can use the context menu regardless of the environment you are in.
Feel free to open an issue or a pull request if you have any suggestions or found a bug.
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