when i select (LAML) Acute Myeloid Leukemia as the tumor type, i get the two errors at the bottom of this post. we (richard, adit, and i) traced the error to the query
GET https://firebrowse.herokuapp.com/?http://firebrowse.org/api/v1/Metadata/Counts?&cohort=LAML&sample_type=TP,TB&data_type=mrnaseq&totals=true
this results in an empty json output (""). and this empty data probably causes the errors. we should definitely account for empty data and handle that gracefully. perhaps we could alert the user that no data was returned for that tumor and to select a different one.
sample_type=TP requests primary solid tumors, but acute myeloid leukemia is a blood cancer (ie it's an uncontrolled division of blood cells but it doesn't necessarily form a solid mass -- the cells float in the blood). we solved this by changing the sample_type to sample_type=TP,TB to include solid tumors and blood cancers. here is a list of these sample_type codes https://gdc.cancer.gov/resources-tcga-users/tcga-code-tables/sample-type-codes.
when i select
(LAML) Acute Myeloid Leukemia
as the tumor type, i get the two errors at the bottom of this post. we (richard, adit, and i) traced the error to the querythis results in an empty json output (
""
). and this empty data probably causes the errors. we should definitely account for empty data and handle that gracefully. perhaps we could alert the user that no data was returned for that tumor and to select a different one.sample_type=TP
requests primary solid tumors, but acute myeloid leukemia is a blood cancer (ie it's an uncontrolled division of blood cells but it doesn't necessarily form a solid mass -- the cells float in the blood). we solved this by changing thesample_type
tosample_type=TP,TB
to include solid tumors and blood cancers. here is a list of thesesample_type
codes https://gdc.cancer.gov/resources-tcga-users/tcga-code-tables/sample-type-codes.errors:
and