reads_json does not work

Whenever I try to use read_json it does not work. For instance, when I make a simple wdl like:

workflow quantification {

    File references
    Map[String, String] indexes = read_json(references)
}
where test.json is:
```json
{
  "quantification.references": "/home/antonkulaga/rna-seq/workflows/rna-seq/quantification/inputs/test.json"
}

it tells

Unable to build WOM node for Declaration ‘indexes’: Return type of read_json() can’t be known statically at cromwell.engine.workflow.lifecycle.materialization.MaterializeWorkflowDescriptorActor.cromwell$engine$workflow$lifecycle$materialization$MaterializeWorkflowDescriptorActor$$workflowInitializationFailed(MaterializeWorkflowDescriptorActor.scala:211) at cromwell.engine.workflow.lifecycle.materialization.MaterializeWorkflowDescriptorActor$$anonfun$2.applyOrElse(MaterializeWorkflowDescriptorActor.scala:181) at cromwell.engine.workflow.lifecycle.materialization.MaterializeWorkflowDescriptorActor$$anonfun$2.applyOrElse(MaterializeWorkflowDescriptorActor.scala:176) at scala.runtime.AbstractPartialFunction.apply(AbstractPartialFunction.scala:34)

That means I cannot just load a file and parse it, so how else can I read JSON then?

[antonkulaga]

Looks like read_json in current trunk still has some issues. When I give a json like this:

{
  "Homo sapiens": {
    "transcriptome" : "/pipelines/indexes/HUMAN/27/gencode.v27.transcripts.fa",
    "gtf": "/pipelines/indexes/HUMAN/27/",
    "salmon": "/pipelines/indexes/HUMAN/27/salmon"
  },
  "Mus musculus": {
    "transcriptome" : "/pipelines/indexes/MOUSE/M16/gencode.vM16.transcripts.fa",
    "gtf": "/pipelines/indexes/MOUSE/M16/gencode.vM16.annotation.gtf",
    "salmon": "/pipelines/indexes/MOUSE/M16/salmon"
  }
}

with wdl like this

Map[String, Map[String, String]] indexes = read_json(references)   

I get:

Workflow input processing failed
WorkflowFailure(ERROR: indexes is declared as a Map[String, Map[String, String]] but the expression evaluates to a Object: Map[String, Map[String, String]] indexes = read_json(references) ^ ,List())

I do not get what is wrong there, I’ve tried different type combinations.

[cjllanwarne]

Hi @antonkulaga - sorry to come to this so late. It does look like the coercion function might require a little bit of a fixup here. In the mean time did you try using the Object type?

Object indexes = read_json(references)