GitLab

See #29 .

library.sh(fetch): Updated.

(fetch_one_die,fetch_one_warn): New functions.

Added mapping file for the Use_Type category

...with new S74 version

New PFAS TPs from @parviel.chirsir plus fixed ref info from previous entries

... in SLE mapping files

PFAS TPs added to S74, thanks to @parviel.chirsir

Added 4 new SMILES to the badlist based on latest deposition failure. Removing these manually resulted in successful deposition (110674).

New proposed CCS template (also on PubChem FTP site)

Updated mapping files with info needed for S81 ...

SLE files plus transformations, from Carla, Noelia & co

Added license ...

updated to Top 5 too...

Updated MassBank files on Zenodo to contain Top5 information ... and consequently updated the links here!

minor updates to script, could not reproduce error reported by @anjana.elapavalore in #26 so no modifications there (yet?).

...with Leucomalachite green and Malachite green entries from Anca Baesu. Added DTXSIDs now we have more than 1.

...new pesticide TP permission information (NA = not applicable instead of FALSE for several entries)

Added script to create files for PubChem, plus associated SMILES badlist. Deposited necessary files on Zenodo and added mapping file. Moved out-of-date files to archive and Zenodo.

First go at categorising MassBankEU instrument types into PubChem TOC Mass Spectrometry categories

Added / updated DOI

This hopefully solves the issue of missing manifest file.

File manifest.yaml in the input directory will now be consulted for
metfrag path and benchmar url by read_manifest.pl .

eval4pub.sh correctly transports PCL_FN_METFRAG_JAR and
PCL_URL_ZENODO_BENCH to Rscript.

Also updated READMEs where required.

The driver script `pb-lite-driver.sh` now takes the following arguments:

-i <input-directory-path>
-s stage1 -s stage2 -s ...
-a
where stageN is one of `cleanup`, `prepare`, `fetch_scripts_and_sources`,
`build`, `sanity_postbuild`, `eval4pub` and `epilog`.

If `-a` was given, all stages are run in the appropriate order.

Updated SLOD file with new annotations too.

added annotations for the two new entries ...