Error while running WfExS using a local workflow file/directory #46
Comments
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Hi @jmfernandez. I hope you had a nice weekend. As per your email, I've tried WfExS with the files above. I found 2 thing:
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In addition to the above comment, I still cannot run WfExS with an RO-Crate directly from disk. I downloaded this workflow which is same one as the file example I'm trying to run. I get a similar error to above, where is says no engine recognised. |
Hi @dcl10, did you pull this morning all the changes and updated the requirements.txt ? Because this last was updated in the commit from 15 hours ago, WfExS-backend/requirements.txt Line 24 in fde8158 |
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Thanks for the feedback, I'm trying this one later.
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Hi @jmfernandez, I pulled this morning but I pulled the wrong tag haha. Thanks for pointing this out :) |
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Hi again (again), Indeed, the local workflow is depending on other cwl file. But you are telling WfExS that the workflow is only a single file, instead of giving it a "directory" and a starting point (i.e. a context). If you try something similar to the next: # test-stage.yml
workflow_id: file:///root/hutch/workflows#subdirectory=sec-hutchx86.cwl
workflow_config:
container: 'docker'
secure: false
nickname: 'vas-workflow'
cacheDir: /tmp/wfexszn6siq2jtmpcache
crypt4gh:
key: cosifer_test1_cwl.wfex.stage.key
passphrase: mpel nite ified g
pub: cosifer_test1_cwl.wfex.stage.pub
outputs:
output_file:
c-l-a-s-s: File
glob: "output.json"
params:
body:
c-l-a-s-s: File
url:
- https://raw.githubusercontent.com/HDRUK/hutch/main/workflows/inputs/rquest-query.json
is_availability: true
db_host: "localhost"
db_name: "hutch"
db_user: "postgres"
db_password: "example"it should work (it's true, keyword |
Description
I am running WfExS with the config files shown below. When I run
WfExS-backend.py -L local-config.yml stage -W test-stage.ymlI get the following error:NotADirectoryError: [Errno 20] Not a directory: '/root/wfexs-backend-test_WorkDir/47761fdd-f06f-4260-a1f3-7351265805b3/workflow'.Looking at the path in the error message, it seems
workflowis the file inworkflow_idin the stage file. However, WfExS is expecting there to be a directory. I also tried putting a path to a directory in theworkflow_idfield, but that failed saying it couldn't work out which runner to use.Traceback
Traceback (most recent call last):
File "/root/WfExS-backend/WfExS-backend.py", line 21, in
main()
File "/root/WfExS-backend/wfexs_backend/main.py", line 1122, in main
stagedSetup = wfInstance.stageWorkDir()
File "/root/WfExS-backend/wfexs_backend/workflow.py", line 1985, in stageWorkDir
self.materializeWorkflowAndContainers(offline=offline, ignoreCache=ignoreCache)
File "/root/WfExS-backend/wfexs_backend/workflow.py", line 1233, in materializeWorkflowAndContainers
self.setupEngine(offline=offline, ignoreCache=ignoreCache)
File "/root/WfExS-backend/wfexs_backend/workflow.py", line 1191, in setupEngine
self.fetchWorkflow(
File "/root/WfExS-backend/wfexs_backend/workflow.py", line 1152, in fetchWorkflow
engineVer, candidateLocalWorkflow = engine.identifyWorkflow(
File "/root/WfExS-backend/wfexs_backend/cwl_engine.py", line 316, in identifyWorkflow
newLocalWf = self._enrichWorkflowDeps(newLocalWf, engineVer)
File "/root/WfExS-backend/wfexs_backend/cwl_engine.py", line 542, in _enrichWorkflowDeps
with subprocess.Popen(
File "/usr/lib/python3.10/subprocess.py", line 969, in init
self._execute_child(args, executable, preexec_fn, close_fds,
File "/usr/lib/python3.10/subprocess.py", line 1845, in _execute_child
raise child_exception_type(errno_num, err_msg, err_filename)
NotADirectoryError: [Errno 20] Not a directory: '/root/wfexs-backend-test_WorkDir/47761fdd-f06f-4260-a1f3-7351265805b3/workflow'
Settings
Stage file
Local config
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