sasurfer/to_openehr_converter

from different formats to openehr

TO_OPENEHR_CONVERTER

Convert from BBMRI XML to OpenEHR template by @fra and @ceci (current template version mycrc_cohort7)

For ehrbase (0.18.3-0.19) use flag --ehrbase For earlier version there's a problem with null_flavour not supported. For Marand simply omit the flag --ehrbase

Flags in brief: loglevel=set level for the log file conversion.log inputfile=xml input file webtemplate=template for the flat format composition outputfilebasename=basename for the flat composition(s) created check=check the leafs created and warn if some compulsory ones are missing ehrbase=flag to be used with ehrbase. In some input files one or more therapies exist but response_to_therapy is missing. EHRBase do not work on these so with the flag we add a complete null flavour response.

Use example for ehrbase: python3 main.py --loglevel=INFO --inputfile=/usr/local/data/WORK/OPENEHR/ECOSYSTEM/TO_AND_FROM_CONVERTER/CODE/FROM_DB_CSV_TO_XML_CONVERTER/patientsFromDb_8.xml --webtemplate=/usr/local/data/WORK/OPENEHR/ECOSYSTEM/TO_AND_FROM_CONVERTER/CODE/RESULTS/TEST/NEWTEMPLATE/mycrc_cohort6mod.json --outputfilebasename=myoutputceciDB8 --check --ehrbase