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add_activity_batch fails with missing link #55

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allaway opened this issue Jul 27, 2022 · 0 comments
Open

add_activity_batch fails with missing link #55

allaway opened this issue Jul 27, 2022 · 0 comments
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@allaway
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allaway commented Jul 27, 2022

Describe the bug
When add_activity_batch is missing a provenance link, e.g. in the deepvariant example below, it fails with a confusing error (' ValueError: NA is not a valid Synapse id'). A check for completion or some other handling strategy might be helpful here. This is a low-priorty issue IMO.

To Reproduce
Steps to reproduce the behavior:
Try to upload activity with a missing link, eg:

> sample_io$workflow %>% unique()
[1] "DeepVariant" "FreeBayes"   "Mutect2"     "Strelka2"   
> wf_link <- c(FreeBayes = "https://nf-co.re/sarek/2.7.1/output#freebayes",
+              Mutect2 = "https://nf-co.re/sarek/2.7.1/output#gatk-mutect2",
+              Strelka2 = "https://nf-co.re/sarek/2.7.1/output#strelka2")
> add_activity_batch(sample_io$output_id, 
+                    sample_io$workflow, 
+                    wf_link[sample_io$workflow], 
+                    sample_io$input_id)
Error in py_call_impl(callable, dots$args, dots$keywords) : 
  ValueError: NA is not a valid Synapse id

Expected behavior
Perhaps an error message: Provenance link is missing for method x

@allaway allaway added the bug Something isn't working label Jul 27, 2022
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