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Simon-Harris-IBM / ChallengeWorkflowTemplatesSimon

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Add in check for empty prediction file generated. #21

Open thomasyu888 opened 4 years ago

thomasyu888 commented 4 years ago

@Simon-Harris-IBM The log for 9700807 you sent me had errors:

File size must be at least one bytes

The workflow failed on the upload step because you cannot upload files into Synapse if it is empty

Submission 9700804 generated a prediction file that was invalid. The check_status tool intentionally quits the workflow. In the log you can see:

STDERR: 2020-03-02T04:56:53.149231447Z 12504aee8408 2020-03-02 04:56:53,149 MainThread WARNING toil.leader: kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.1_check_status.cwl/instancem4rggvk6    17   if(inputs.status == "INVALID"){
STDERR: 2020-03-02T04:56:53.149313839Z 12504aee8408 2020-03-02 04:56:53,149 MainThread WARNING toil.leader: kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.1_check_status.cwl/instancem4rggvk6    18     throw 'invalid submission';
STDERR: 2020-03-02T04:56:53.149406601Z 12504aee8408 2020-03-02 04:56:53,149 MainThread WARNING toil.leader: kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.1_check_status.cwl/instancem4rggvk6    19   } else {
STDERR: 2020-03-02T04:56:53.149489540Z 12504aee8408 2020-03-02 04:56:53,149 MainThread WARNING toil.leader: kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.1_check_status.cwl/instancem4rggvk6    20     return {finished: true};
STDERR: 2020-03-02T04:56:53.149577906Z 12504aee8408 2020-03-02 04:56:53,149 MainThread WARNING toil.leader: kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.1_check_status.cwl/instancem4rggvk6    21   }
STDERR: 2020-03-02T04:56:53.149659129Z 12504aee8408 2020-03-02 04:56:53,149 MainThread WARNING toil.leader: kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.1_check_status.cwl/instancem4rggvk6    22 })()
STDERR: 2020-03-02T04:56:53.149750582Z 12504aee8408 2020-03-02 04:56:53,149 MainThread WARNING toil.leader: kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.1_check_status.cwl/instancem4rggvk6    stdout was: ''
STDERR: 2020-03-02T04:56:53.149832871Z 12504aee8408 2020-03-02 04:56:53,149 MainThread WARNING toil.leader: kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v2.1_check_status.cwl/instancem4rggvk6    stderr was: 'invalid submission'
thomasyu888 commented 4 years ago

It really helps to put the log files in an environment that doesn't have any text wrapping