In a meeting with the MicrobeTrace team, they flagged that they were unable to view the ANDV dataset in MicrobeTrace. I traced this back to the "Los Rios" province missing the lat/long entry causing an error in the MicrobeTrace parsing of the JSON. I've recommended that they update their parser to handle missing lat/longs, but this also prompted me to look into the ANDV dataset itself.
I was going to add a lat/long entry but realize "Los Rios" is the same as "Region de Los Rios" based on
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# if curated region is 'los rios' set to 'region de los rios' |
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if curated_region.lower() == "los rios": |
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curated_region = "region de los rios" |
The script only replaces the value if the original metadata has a null value, so since both values are coming from Pathoplexus, these are not getting standardized in the script.
Should this be fixed in the add_curated_metadata.py script or upstream in PPX?
In a meeting with the MicrobeTrace team, they flagged that they were unable to view the ANDV dataset in MicrobeTrace. I traced this back to the "Los Rios" province missing the lat/long entry causing an error in the MicrobeTrace parsing of the JSON. I've recommended that they update their parser to handle missing lat/longs, but this also prompted me to look into the ANDV dataset itself.
I was going to add a lat/long entry but realize "Los Rios" is the same as "Region de Los Rios" based on
andv/scripts/add_curated_metadata.py
Lines 86 to 88 in 5215893
The script only replaces the value if the original metadata has a null value, so since both values are coming from Pathoplexus, these are not getting standardized in the script.
Should this be fixed in the add_curated_metadata.py script or upstream in PPX?