Upgrade to pypi acmc v0.1.2 (latest)
The MELDB 3.2.10 phenotype and concept sets need to be upgraded using the refactored acmc concept processing tool published in pypi, and then republished at v4.0.0
The task list
-
check latest tag in repo is 3.2.10, acmc now updated to deal with last tags beginning with or without a v -
Checkout latest concepts used for SAIL into workspace/phen directory -
Manually create the acmc directory structure - rename codes to concepts
- add concept-sets directory
-
Write converter from concepts configuration file to acmc configuration file config.yaml - need to split excel sheets for drugs as not supported by acmc
- need to duplicate hanlon for 1-1 mapping between concept-set and codes
-
Add desired maps to config.yaml, read2, read3, snomed -
validate phenotype: acmc phen validate -
map phenotype: acmc map -
check consistency of concepts of v3.2.10 to the new maps, ideally using: acmc phen diff, to do this will require restructuring of the 3.2.10 directories but the maps should be the same -
Exclude unwanted Readv2 codes with Black list -
delete all of the old files from 3.2.10 -
publish phen as major release, should increment from last v3.2.10 tag to 4.0.0 : acmc phen publish -i major
Edited by Jakub Dylag