bmc/README.md

BiblioManager

BiblioManager is a simple script to download and store your articles. Read on if you want more info :)

Note : This script is currently a work in progress.

What is BiblioManager (or what it is not) ?

I used to have a folder with poorly named papers and books and wanted something to help me handle it. I don't like Mendeley and Zotero and so on, which are heavy and overkill for my needs. I just want to feed a script with PDF files of papers and books, or URLs to PDF files, and I want it to automatically maintain a BibTeX index of these files, to help me cite them and find them back. Then, I want it to give me a way to easily retrieve a file, either by author, by title or with some other search method, and give me the associated bibtex entry.

This is the goal of BiblioManager. This script can :

• Download or import PDF/Djvu files
• Try to get automatically the metadata of the files (keywords, author, review, …)
• Store all the metadata in a BibTex file
• Rename your files to store them in a logical and homogeneous way according to a user-defined mask
• Help you find them back
• Give you directly the bibtex entry necessary to cite them
• Remove some of the watermarks included in those files (the front page with your ip address from IOP for instance)

BiblioManager will always use standard formats such as BibTeX, so that you can easily edit your library, export it and manage it by hand, even if you quit this software for any reason.

Current status

• Able to import a PDF / djvu file, automagically find the DOI / ISBN, get the bibtex entry back and add it to the library. If DOI / ISBN search fails, it will prompt you for it.
• Able to download a URL, using any specified proxy (you can list many and it will try all of them) and store the pdf file with its metadata.

Should be almost working and usable now, although still to be considered as experimental.

Important note : I use it for personal use, but I don't read articles from many journals. If you find any file which is not working, please fill an issue or send me an e-mail with the relevant information. There are alternative ways to get the metadata for example, and I didn't know really which one was the best one as writing this code.

Installation

• Clone this git repository where you want : git clone https://github.com/Phyks/BMC
• Install requesocks, PyPDF2 and isbntools via Pypi
• Install pdftotext (provided by Xpdf) and djvulibre via your package manager the way you want
• Copy params.py.example to params.py and customize it to fit your needs

Usage

To import an existing PDF / Djvu file

Run ./main.py import PATH_TO_FILE [article|book]. [article|book] is an optional argument (article or book) to search only for DOI or ISBN and thus, speed up the import.

It will get automatically the bibtex entry corresponding to the document, and you will be prompted for confirmation. It will then copy the file to your papers dir, renaming it according to the specified mask in params.py.

To download a PDF / Djvu file

Run ./main.py download URL_TO_PDF [article|book], where [article|book] (article or book) is again a parameter to specify to search only for DOI or ISBN only, and thus speed up the import. The URL_TO_PDF parameter should be a direct link to the PDF file (meaning it should be the link to the pdf page, which may have an authentication portal and not the page with abstract on many publishers websites).

The script will try to download the file with the proxies specified in params.py until it manages to get the file, or runs out of available proxies.

It will get automatically the bibtex entry corresponding to the document, and you will be prompted for confirmation. It will then put the file in your papers dir, renaming it according to the specified mask in params.py.

Delete an entry

Run ./main.py delete PARAM where PARAM should be either a path to a paper file, or an ident in the bibtex index. This will remove the corresponding entry in the bibtex index, and will remove the file from your papers dir. Although it will prompt you for confirmation, there's no way to recover your file after deletion, so use with care.

Search for an entry

TODO

List all entries

TODO

Edit entries

TODO

Data storage

All your documents will be stored in the papers dir specified in params.py. All the bibtex entries will be added to the index.bib file. You should not add entries to this file (but you can edit existing entries without any problem), as this will break synchronization between documents in papers dir and the index. If you do so, you can rebuild the index fie with ./main.py rebuild.

License

All the source code I wrote is under a no-alcoohol beer-ware license. All functions that I didn't write myself are under the original license and their origin is specified in the function itself.

* --------------------------------------------------------------------------------
* "THE NO-ALCOHOL BEER-WARE LICENSE" (Revision 42):
* Phyks (webmaster@phyks.me) wrote this file. As long as you retain this notice you
* can do whatever you want with this stuff (and you can also do whatever you want
* with this stuff without retaining it, but that's not cool...). If we meet some 
* day, and you think this stuff is worth it, you can buy me a <del>beer</del> soda 
* in return.
*																		Phyks
* ---------------------------------------------------------------------------------

I used the tearpages.py script from sciunto, which can be found here and is released under a GNU GPLv3 license.

Inspiration

Here are some sources of inspirations for this project :

• MPC
• http://en.dogeno.us/2010/02/release-a-python-script-for-organizing-scientific-papers-pyrenamepdf-py/
• Bibsoup
• Paperbot

Ideas, TODO

A list of ideas and TODO. Don't hesitate to give feedback on the ones you really want or to propose your owns.

10. Refactor 11. Use bibtex-parser lib to write bibtex, instead of parsed2BibTex 12. Rebuild function
11. No DOI for arXiv / HAL
12. Parameter to disable remote search
13. Open file
14. Doc / Man
15. Webserver interface
16. Categories
17. Edit an entry instead of deleting it and adding it again

Issues ?

• Remove the watermarks on pdf files => done, some warning in okular on generated pdf, but seems ok. Seems to be a bug in Okular.