The script uses the
-f parameter with a start-anchored prefixed ontology id
to retrieve samples, and then to update the prefix-determined biocharacteristics.
This isn’t a “general use” function but requires some diligent use …
Changing this to make use of direct Python data manipulation using the standard
bycon query generation/exacution would be possible; however, the greater
execution transparency seems to be an advantage for now.
pgx_cmd_modify_biosamples.py -d progenetix -f "icdom-97323" -i "icdot-C42.1" -l "Bone marrow"
"mongostring": True setting leads to the query being prepared as
MongoDB string literal, instead of a dictionary for
In a first instance, biocharacteristics are updated by replacing the one
with a matching prefix.
Since sometimes no biocharacteristic with matching prefix may exist, in
a second step such samples receive a new one.