/tex2jats

Primary LanguagePythonGNU General Public License v3.0GPL-3.0

TeX 2 JATS XML for Seismica

Dependencies

These ones are shared dependencies with the docx/odt parsing for Seismica module:

  • python 3.n (preferably 3.8+)
  • numpy
  • pandoc

Other dependencies:

  • python3 datetime (often already installed)
  • GNU sed, v4.8
  • perl, v>5 (below not tested)

SCE requirements

Before running the TeX2JATS converter, you need to have produced:

  • final .tex galleys (proof accepted by authors)
  • corrected list of references
  • have the final metadata on hand (you can replace it in the JATS galley)
  • check that the dates format is correct (Month dd, YYYY)

Workflow

  1. Copy tex2xml.sh, apa.csl, cleanidjats.py and metatex2jats.py to your current working directory (CWD, where the TeX galley is):
    cd /cwd/
    cp /path/to/tex2jats/tex2xml.sh ./
    cp /path/to/tex2jats/*.py ./
    cp /path/to/tex2jats/apa.csl ./

  2. In your CWD, use tex2xml.sh to convert the TeX to JATS XML:
    ./tex2xml.sh proof biblio
    with:

    • proof, the name of the TeX galley without the extension (which should be .tex)
    • biblio, the name of the corrected list of references, without the extension (which should be .bib)

  3. This will output:

    • proof.xml
    • proof_metadata.jats
    • proof_credits.jats
    • proof_galley.xml
    • proof_tab1.tex if you have one table (see point (5)), and one similar file per table
    • proof_tab1.xml
      You will then work with the XML galley only (proof_galley.xml). Other files are only here for correction if needed.

  4. How to view the XML galley? To my knowledge, there is no open-source and easy-to-use tool, so the best way is to open it with a text editor. You will be able to view the galley before publishing on OJS. If you open it with a web browser, it should not show any error. You can use the web browser to debug (will show the line of every error).

  5. If there are TABLES in your TeX galley, tex2xml.sh will export two files for each table: tabxx.tex and tabxx.xml, xx ranging from 1 to the total number of arrays present in the article.
    If there are equations or math expressions in your table, tex2xml might not behave correctly. I would suggest removing them before running the scrip. For each table:

    1. Correct any unwanted symbol in tabxx.tex
    2. Translate the tabxx.tex to HTML with https://tableconvert.com/latex-to-html
    3. Copy the HTML code in the XML table file tabxx.xml, where indicated
    4. Replace the wrong table code in the XML galley proof_galley.xml with the updated tabxx.xml. In the XML galley, tables are under a boxed-text environnement.

  6. Proofread XML galley and add metadata if necessary. Some things to check by visual inspection of the XML galley:

    • Metadata, author names, credits, affiliations are here
    • Abstracts are here
    • Reference list is here
    • Every figure is here

  7. Convert every figure to PNG format if not already done. You can use the following bash command (converts every PDF file which starts with fig to a PNG format, requires imagemagick, you can adjust density if needed):
    mogrify -verbose -quality 00 -density 250 -format png ./fig*.pdf

  8. Optional. Check your galley on the Seismica test website. No need to upload the figures. If you can open the XML galley with a web browser without errors, it will load fine in OJS.

  9. Upload the galley PDF and XML files to the OJS website.

    • For the XML galley, images need to be uploaded separately (no need to fill in the caption etc.)
    • Don't forget the uploading order:
      1. PDF galley
      2. XML galley
      3. Supplementary Materials (any)
      4. Review reports

TO DO

  • Don't use regex, because it is unstable with XML? Oops…
  • Correctly parse math expressions within tables