Script to format .bib from Zotero(bibtex)

usage: bibtex_organizer.py [-h] [-f <file>] [-o <string>] [-m <string>]

%prog [options] -f filein -o fileout -m mode

optional arguments:
  -h, --help            show this help message and exit
  -f <file>, --filein <file>
                        in file name,.gz would gzip, none|stdin|- means stdin (default: None)
  -o <string>, --fileout <string>
                        out file name,.gz would gzip, none|stdout|- means stdout (default: None)
  -m <string>, --mode <string>
                        abbr(get Journal Abbreviation),fig get 1st figure from PMC (default: abbr,fig)

1. Step1: Collect Manuscript using Zotero along with Chrome Extension

• Option1: Zotero Plugin PMCID Fetcher could help you get PMCID quickly.
• Option2: Manual fill in Extra region of Zotero such as

  PMCID: PMC6842117
  PMID: 31493975
  

• Option3: Other Tags(Extra region of Zotero) could be converted to links
  • 'tex.' prefix were only needed in Zotero for export using Zotero Plugin zotero-better-bibtex (case insensitive). If you manually change .bib file, then no need 'tex.' (lowercase)
  • Most support multiple links seperated by ';'
  • 'LinkID,Name' will show 'Name' as text of link, 'LinkID' will show default as text of links (usually 'LinkID')
  • tex.cofirst:
    • 2 means first 2 authors equally contributed
    • 2,3 means 2nd and 3rd author equally contributed
    • 2;1,-1 means first 2 authors equally contributed, last author and 1st author corresponding
    • 2;-2,-1 means first 2 authors equally contributed, last 2 authors corresponding
    • negative corresponding max support to -5, not sure how to implement variable in jekyll liquid plus.
  • tex.highlight:
    • You could write short summary of paper you'd like highlight.
    • Only entries with 'highlight' in .bib will be highlighted with Figure.
    • If use 'none', will use first 2 and last 2 sentences of abstract.
  • Examples

    tex.GEOID: GSE87064,Mouse;GSE87065,CHIP
    tex.SRAID: PRJNA473990,Human;PRJNA473991,Mouse
    tex.EGAID:  EGAS00001000514,Link1;EGAS00001000654
    tex.Browser: https://pecan.stjude.cloud/proteinpaint/study/retina_hic_2018,Mouse_mm9;https://viz.stjude.cloud/stjude/visualization/human-retina-wgbs-chipseq-chromhmmgene-fpkm-hg19,Human_hg19
    tex.Extralinks: https://platform.stjude.cloud/workflows/methylation-to-activity,STJUDE.CLOUD.workflow;https://github.com/chenlab-sj/M2A,Code
    tex.cofirst: 2
    tex.highlight: none
  

2. Step2: In Zotero, Select Entries Export better-bibtex (or bibtex) as .bib file

3. Step3:

conda env create -f .condaenv.xml
conda activate iobuild
cd _bibliography
python ../script/bibtex_organizer.py -f papers.bib -m abbr,fig
mv *.jpg *.jpg *.gif ../images/pubpic/

Details:

• Highlight template in _layouts/bib_highlight.html
• Full list template in _layouts/bib.html

• Recommend export using Zotero Plugin zotero-better-bibtex
• Using jabref Database API
• Alt: CSL Abbreviations Data
• Alt: Canismarko's API using CASSI and LTWA

cd _bibliography
python ../script/bibtex_organizer.py -f papers.bib -m abbr
#Results papers.clean.bib (with abbr property) will be used (defined in _config.yml -> scholar -> bibliography)

cd _bibliography
python ../script/bibtex_organizer.py -f papers.bib -m fig
#Will automactially download first figure if it have PMCID
#Results papers.clean.bib (with fig1 property)