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VEuPathDB / microbiomeComputations

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ranked abundance: collections with one var give 500 #15

Closed asizemore closed 2 years ago

asizemore commented 2 years ago

Checked two studies that have both assay types. The latter one causes 500s in ranked abundance.

Not sure why yet, but making ticket so we don't forget.

Screen Shot 2022-04-14 at 8 04 14 PM
asizemore commented 2 years ago

(look at https://github.com/VEuPathDB/web-eda/pull/1068 for the web-eda branch)

asizemore commented 2 years ago

Might be a plot.data issue, or could be that the abundance app response is weird. Here's the backend error:

Rserve: 2022-04-20 16:20:48 Ranked abundance computation completed with parameters recordIdColumn= EUPATH_0000813.entity_16SRRNASequencingAssayTargetingV4Region_stable_id , method = median , cutoff = 10 , naToZero =  TRUE , verbose = TRUE
Rserve:
Rserve: 2022-04-20 16:20:48 Map has been validated.
Rserve: Error in box.dt(data, map, points = points, mean = mean, computeStats = computeStats,  :
Rserve:   Must provide xAxisVariable for plot type box.
Rserve: In addition: Warning messages:
Rserve: 1: In fread("compute_input_dataset", select = c(EUPATH_0000813.entity_16SRRNASequencingAssayTargetingV4Region_stable_id = "double",  :
Rserve:   Attempt to override column 1 <<EUPATH_0000813.entity_16SRRNASequencingAssayTargetingV4Region_stable_id>> of inherent type 'string' down to 'float64' ignored. Only overrides to a higher type are currently supported. If this was intended, please coerce to the lower type afterwards.
Rserve: 2: In fread("single_tabular_dataset", select = c(EUPATH_0000813.entity_16SRRNASequencingAssayTargetingV4Region_stable_id = "double",  :
Rserve:   Attempt to override column 1 <<EUPATH_0000813.entity_16SRRNASequencingAssayTargetingV4Region_stable_id>> of inherent type 'string' down to 'float64' ignored. Only overrides to a higher type are currently supported. If this was intended, please coerce to the lower type afterwards.
Rserve:
asizemore commented 2 years ago

Sometimes the collections only have one var. See VEuPathDB/MicrobiomeWorkflow#16 for discussion on how to proceed

asizemore commented 2 years ago

Decided to remove collections with one var. Closing.