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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
The text was updated successfully, but these errors were encountered:
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:
Expected behavior
Perhaps an error message:
Provenance link is missing for method x
The text was updated successfully, but these errors were encountered: