dx upload from custom applet

Yong Qian

I tried many times to upload files through an applet and all failed. I specified in dxapp.json:

  "outputSpec": [
   {
     "name": "output_file",
     "class": "file",
     "description": "The output NPZ",
     "optional": false
   }
 ],

A python script through run.sh produced some  $snp.npz files to be uploaded to project as output_file and the file does exist in the job space (ls -l $snp.npz shows this file).  I tried in run.sh:

1. dx upload   --path "$DX_PROJECT_CONTEXT_ID:"  "${snp}.npz"
#dxpy.exceptions.PermissionDenied: UPLOAD permission required in project-GjJB3fjJ2JpZ5q92VFXkxqj7 to perform this action, code 401. Request Time=1741703687.4684954, Request ID=1741703687470-168899

2. dx-jobutil-add-output output_file "$(pwd)/${snp1}.npz"
#Error validating job's output: i/o value output_file needs to be given using DNAnexus links

3. id=`dx upload $snp1.npz --destination /out --project …..'   

   dx-jobutil-add-output "output_file" $id

 

 

Any idea how to upload the $snp.npz file to the project directory?

 
 

 

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