We try to annotate a serum_host column in tdb on ingest of CDC titers. The serum_host column in fauna is usually null and recent “HUMAN” pooled data don’t get labeled as “human” since the annotation in the tdb ingest requires an exact match to “Human” to be added.
We also have some mouse-based data that appear with serum id values like L20MouseS0007.
Expected behavior
We should parse the host species from the serum id based on a standard set of expected values and set the default host to "ferret" in the absence of other details.
Possible solution
We need to minimally update the lines referenced above to apply a regex or other search to the serum id and set the host to "human" or "mouse" for the cases we know about.
@joverlee521 notes that: "if we update the upload scripts to not do exact matches, [we] can re-upload the titer data. Since the index fields do not include serum_host, these records should get updated in place."
Current Behavior
We try to annotate a
serum_hostcolumn in tdb on ingest of CDC titers. Theserum_hostcolumn in fauna is usuallynulland recent “HUMAN” pooled data don’t get labeled as “human” since the annotation in the tdb ingest requires an exact match to “Human” to be added.We also have some mouse-based data that appear with serum id values like
L20MouseS0007.Expected behavior
We should parse the host species from the serum id based on a standard set of expected values and set the default host to "ferret" in the absence of other details.
Possible solution
We need to minimally update the lines referenced above to apply a regex or other search to the serum id and set the host to "human" or "mouse" for the cases we know about.
@joverlee521 notes that: "if we update the upload scripts to not do exact matches, [we] can re-upload the titer data. Since the index fields do not include serum_host, these records should get updated in place."
Additional context
See related Slack thread.