This script updates the Human Metabolites Database (HMDB) files for OpenMS

It generates a HMDBMappingFile.tsv and a HMDB2StructMapping.tsv that is used by the AccurateMassSearch tool

Steps to do:

git clone this repo
Download "All Metabolites" files as XML from http://www.hmdb.ca/downloads
extract into any folder, e.g, default: /your/path/hmdb_metabolites
delete hmdb_metabolites.xml unless it is the only file
execute python script:

python generateHMDBFilesForOpenMS.py /your/path/hmdb_metabolites/

double-check
create a pull request to the OpenMS/OpenMS repository

Requires:

python 3.6+
lxml