Question: Workflow API - first step fails to receive dataset execute_workflow.py
0
gravatar for eric
22 months ago by
eric0
UC Berkeley
eric0 wrote:

I'm having no luck executing a workflow in the example:

python workflow_execute.py 2bb67717b99a37e92e59003f93625c9b http://localhost:8080/api/workflows f2db41e1fa331b3e 'hist_id=f597429621d6eb2b' '1=hda=dc4d617ef0d54eb6'

The entire workflow is queued properly, but in the first step fails because it's never able to find the file (dataset id) I pass it. The input that is passed on the command line is 'None'.

blastn -query "None" -db "/var/www/html/galaxy/data/blastdb/nt/17apr2014/nt" -task blastn -evalue 0.001 -out "/var/www/html/galaxy/database/files/000/dataset_422.dat" -outfmt 5 -num_threads "${GALAXY_SLOTS:-8}"

where the last parameter is <step>-<src>-<dataset id="">, as I understand.

  • I wasn't sure if I the step was zero-based so I tried both 0 and 1
  • also tried all varients of src (hda, ldda, ld), although my dataset
  • is hda the dataset-id is grabbed from the dataset's "id:" field

from: https://wiki.galaxyproject.org/Learn/API/Examples

The POST payload:

{
  "url": "http://192.168.56.102:8080/api/workflows?key=2bb67717b99a37e92e59003f93625c9b",
  "method": "POST",
  "headers": {
    "Accept-Encoding": "gzip, deflate",
    "Accept-Language": "en-US,en;q=0.5",
    "Content-Length": 124
  },
  "json": {
    "workflow_id": "f2db41e1fa331b3e",
    "history": "hist_id=f597429621d6eb2b",
    "ds_map": {
      "0": {
        "src": "hda",
        "id": "dc4d617ef0d54eb6"
      }
    }
  }
}

200

The other example exhibits the same problem: example_watch_folder.py any help much appreciated

workflow api galaxy • 584 views
ADD COMMENTlink modified 22 months ago • written 22 months ago by eric0
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