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When py-tes unmarshall service-info of TES 1.0.0(TESK), it creates error.
service-info
py-tes is installed with this command
pip install "py-tes @ git+https://github.com/ohsu-comp-bio/py-tes.git@5379b2a08bc911f7af55bd835dbd85aad0124c6a"
Actual error log is here. This error occurred when I throw CWL job using toil.
$ toil-cwl-runner --batchSystem tes --tesEndpoint=http://10.152.183.122:8080/ga4gh/tes/ hello_world_fileoutput.cwl hello_world_fileoutput.yaml [2023-11-02T20:36:09+0900] [MainThread] [I] [cwltool] Resolved 'hello_world_fileoutput.cwl' to 'file:///home/ubuntu/work/cwl-samples-2023/hello_world_fileoutput.cwl' SUCCESS Traceback (most recent call last): File "/home/ubuntu/work/venv-toil/lib/python3.10/site-packages/tes/utils.py", line 93, in unmarshal output = o(**r) TypeError: ServiceInfo.__init__() got an unexpected keyword argument 'id' During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/home/ubuntu/work/venv-toil/bin/toil-cwl-runner", line 8, in <module> sys.exit(main()) File "/home/ubuntu/work/venv-toil/lib/python3.10/site-packages/toil/cwl/cwltoil.py", line 3860, in main outobj = toil.start(wf1) File "/home/ubuntu/work/venv-toil/lib/python3.10/site-packages/toil/common.py", line 1043, in start self._batchSystem = self.createBatchSystem(self.config) File "/home/ubuntu/work/venv-toil/lib/python3.10/site-packages/toil/common.py", line 1192, in createBatchSystem return batch_system(**kwargs) File "/home/ubuntu/work/venv-toil/lib/python3.10/site-packages/toil/batchSystems/tes.py", line 86, in __init__ server_info = self.tes.get_service_info() File "/home/ubuntu/work/venv-toil/lib/python3.10/site-packages/tes/client.py", line 127, in get_service_info return unmarshal(response.json(), ServiceInfo) File "/home/ubuntu/work/venv-toil/lib/python3.10/site-packages/tes/utils.py", line 98, in unmarshal raise UnmarshalError(msg) tes.utils.UnmarshalError: {'id': 'uk.ac.ebi.tsc.tesk', 'name': 'TESK', 'type': {'group': 'org.ga4gh', 'artifact': 'tes', 'version': '1.0'}, 'description': 'GA4GH TES Server implementation for Kubernetes', 'organization': {'name': 'EMBL-EBI', 'url': 'https://www.ebi.ac.uk/'}, 'contactUrl': 'https://github.com/EMBL-EBI-TSI/TESK/issues', 'documentationUrl': 'https://github.com/EMBL-EBI-TSI/TESK', 'createdAt': '2021-04-06T00:00:00Z', 'environment': 'dev', 'version': '1.0', 'storage': ['ftp://ftp-private.ebi.ac.uk']} could not be unmarshalled to type: ServiceInfo TypeError: ServiceInfo.__init__() got an unexpected keyword argument 'id'
I disccussed with @uniqueg we see these documents (maybe these).
https://github.com/ga4gh/task-execution-schemas/blob/9e9c5aa2648d683d5574f9dbd63a025b4aea285d/openapi/task_execution_service.openapi.yaml#L540-L556
https://raw.githubusercontent.com/ga4gh-discovery/ga4gh-service-info/v1.0.0/service-info.yaml#/components/schemas/Service
my TES server's service-info is here my TES server is TESK.
$ curl http://10.152.183.122:8080/ga4gh/tes/v1/service-info { "id" : "uk.ac.ebi.tsc.tesk", "name" : "TESK", "type" : { "group" : "org.ga4gh", "artifact" : "tes", "version" : "1.0" }, "description" : "GA4GH TES Server implementation for Kubernetes", "organization" : { "name" : "EMBL-EBI", "url" : "https://www.ebi.ac.uk/" }, "contactUrl" : "https://github.com/EMBL-EBI-TSI/TESK/issues", "documentationUrl" : "https://github.com/EMBL-EBI-TSI/TESK", "createdAt" : "2021-04-06T00:00:00Z", "environment" : "dev", "version" : "1.0", "storage" : [ "ftp://ftp-private.ebi.ac.uk" ] }
The text was updated successfully, but these errors were encountered:
Update support for Service Info (#55)
4d12b82
- Fix version to match PyPi release (#59)
lbeckman314
No branches or pull requests
When py-tes unmarshall
service-info
of TES 1.0.0(TESK), it creates error.py-tes is installed with this command
Actual error log is here.
This error occurred when I throw CWL job using toil.
I disccussed with @uniqueg we see these documents (maybe these).
https://github.com/ga4gh/task-execution-schemas/blob/9e9c5aa2648d683d5574f9dbd63a025b4aea285d/openapi/task_execution_service.openapi.yaml#L540-L556
https://raw.githubusercontent.com/ga4gh-discovery/ga4gh-service-info/v1.0.0/service-info.yaml#/components/schemas/Service
my TES server's
service-info
is heremy TES server is TESK.
The text was updated successfully, but these errors were encountered: