Expand avworkflow_run argument option

[shbrief]

Hi Martin,

Can we make the entityName argument of avworkflow_run take NULL as well? Because my bioBakery workflow doesn’t use Terra’s data model, I should set it NULL, which currently gives me this error: .is_scalar_character(entityName) is not TRUE. Thanks!

Sehyun

[LiNk-NY]

Hi Sehyun,
Can you provide a reproducible example?
Have you tried using a blank ""?
Best,
Marcel

[shbrief]

For avworkflow_run, both NULL and "" are not working:

> avworkflow_run(
+     config,
+     entityName = NULL,
+     entityType = NULL,
+     useCallCache = TRUE,
+     namespace = "waldronlab-terra-rstudio",
+     name = "biobakery_test",
+     dry = FALSE    
+ )
Error in avworkflow_run(config, entityName = NULL, entityType = NULL,  : 
  .is_scalar_character(entityName) is not TRUE
> avworkflow_run(
+     config,
+     entityName = "",
+     entityType = "",
+     useCallCache = TRUE,
+     namespace = "waldronlab-terra-rstudio",
+     name = "biobakery_test",
+     dry = FALSE    
+ )
Error in avworkflow_run(config, entityName = "", entityType = "", useCallCache = TRUE,  : 
  .is_scalar_character(entityName) is not TRUE

But Terra()$createSubmission works with NULL:

> resp <- Terra()$createSubmission(
+     workspaceNamespace = "waldronlab-terra-rstudio",
+     workspaceName = "biobakery_test",
+     methodConfigurationNamespace = "mtx_workflow_biobakery_version3",
+     methodConfigurationName = "mtx_workflow_biobakery_version3",
+     entityType = NULL,
+     entityName = NULL,
+     useCallCache = TRUE
+ )
> resp
Response [https://api.firecloud.org/api/workspaces/waldronlab-terra-rstudio/biobakery_test/submissions]
  Date: 2022-10-04 18:31
  Status: 201
  Content-Type: application/json
  Size: 3.45 kB

[mtmorgan]

Can you try with

BiocManager::install("Bioconductor/AnVIL", ref = "allow-null-workflow-entities", force = TRUE)

[shbrief]

It's taking NULL asentityName and entityType now. Thanks!