forked from HopkinsIDD/flepimop_sample
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathmetadata-output.json
119 lines (119 loc) · 9.21 KB
/
metadata-output.json
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
{
"workflowName": "modelWorkflow",
"workflowProcessingEvents": [{
"cromwellId": "cromid-ddbcb6c",
"description": "PickedUp",
"timestamp": "2024-05-06T19:00:08.586Z",
"cromwellVersion": "86"
}, {
"cromwellId": "cromid-ddbcb6c",
"description": "Finished",
"timestamp": "2024-05-06T19:29:40.017Z",
"cromwellVersion": "86"
}],
"actualWorkflowLanguageVersion": "1.0",
"submittedFiles": {
"workflow": "version 1.0\n\ntask run_Model {\n input {\n File setup_os_script\n File install_git_script\n File clone_repository_script\n File copy_model_output_script\n String model_git_repository\n File install_model_script\n File model_configuration_yml\n String model_executable\n File run_model_script\n String model_output_folder\n String model_runtime_docker\n }\n\n String model_output_files = \"model_output_files.txt\"\n\n command {\n ${setup_os_script}\n ${install_git_script}\n ${clone_repository_script} \"${model_git_repository}\"\n ${install_model_script}\n ${run_model_script} \"${model_executable}\" \"${model_configuration_yml}\"\n find ./\"${model_output_folder}\" -name '*.parquet' > \"${model_output_files}\"\n python3 ${copy_model_output_script} \"${model_output_files}\"\n }\n\n runtime {\n docker: \"${model_runtime_docker}\"\n }\n\n output {\n Array[File] output_files = read_lines(model_output_files)\n }\n}\n\nworkflow modelWorkflow {\n input {\n File setup_os_script\n File install_git_script\n File clone_repository_script\n File copy_model_output_script\n }\n\n call run_Model {\n input:\n setup_os_script = setup_os_script,\n install_git_script = install_git_script,\n clone_repository_script = clone_repository_script,\n copy_model_output_script = copy_model_output_script\n }\n}\n",
"root": "",
"options": "{\n\n}",
"inputs": "{\n \"modelWorkflow.run_Model.model_configuration_yml\": \"config_sample_2pop.yml\",\n \"modelWorkflow.run_Model.model_executable\": \"gempyor-simulate\",\n \"modelWorkflow.run_Model.model_git_repository\": \"https://github.com/HopkinsIDD/flepiMoP.git\",\n \"modelWorkflow.run_Model.model_output_folder\": \"model_output\",\n \"modelWorkflow.run_Model.install_model_script\": \"./scripts/sh/flepimop/install_model.sh\",\n \"modelWorkflow.run_Model.run_model_script\": \"./scripts/sh/flepimop/run_model.sh\",\n \"modelWorkflow.run_Model.model_runtime_docker\": \"rocker/verse:latest\",\n \"modelWorkflow.setup_os_script\": \"./scripts/sh/setup_os.sh\",\n \"modelWorkflow.install_git_script\": \"./scripts/sh/install_git.sh\",\n \"modelWorkflow.clone_repository_script\": \"./scripts/sh/clone_git_repository.sh\",\n \"modelWorkflow.copy_model_output_script\": \"scripts/python/copy_model_output.py\"\n}\n\n",
"workflowUrl": "modelWorkflow.wdl",
"labels": "{}"
},
"calls": {
"modelWorkflow.run_Model": [{
"executionStatus": "Done",
"stdout": "/Users/jbs82/Documents/dev/cromwell_flepimop_project/cromwell-executions/modelWorkflow/565fbcef-5a14-4aa3-9487-1edc33517443/call-run_Model/execution/stdout",
"backendStatus": "Done",
"commandLine": "/cromwell-executions/modelWorkflow/565fbcef-5a14-4aa3-9487-1edc33517443/call-run_Model/inputs/-710979368/setup_os.sh\n/cromwell-executions/modelWorkflow/565fbcef-5a14-4aa3-9487-1edc33517443/call-run_Model/inputs/-710979368/install_git.sh\n/cromwell-executions/modelWorkflow/565fbcef-5a14-4aa3-9487-1edc33517443/call-run_Model/inputs/-710979368/clone_git_repository.sh \"https://github.com/HopkinsIDD/flepiMoP.git\"\n/cromwell-executions/modelWorkflow/565fbcef-5a14-4aa3-9487-1edc33517443/call-run_Model/inputs/-1095727923/install_model.sh\n/cromwell-executions/modelWorkflow/565fbcef-5a14-4aa3-9487-1edc33517443/call-run_Model/inputs/-1095727923/run_model.sh \"gempyor-simulate\" \"/cromwell-executions/modelWorkflow/565fbcef-5a14-4aa3-9487-1edc33517443/call-run_Model/inputs/-1556192397/config_sample_2pop.yml\"\nfind ./\"model_output\" -name '*.parquet' > \"model_output_files.txt\"\npython3 /cromwell-executions/modelWorkflow/565fbcef-5a14-4aa3-9487-1edc33517443/call-run_Model/inputs/1566734815/copy_model_output.py \"model_output_files.txt\"",
"shardIndex": -1,
"outputs": {
"output_files": ["/Users/jbs82/Documents/dev/cromwell_flepimop_project/cromwell-executions/modelWorkflow/565fbcef-5a14-4aa3-9487-1edc33517443/call-run_Model/execution/./model_output/sample_2pop/20240506_192641/seir/000000001.20240506_192641.seir.parquet", "/Users/jbs82/Documents/dev/cromwell_flepimop_project/cromwell-executions/modelWorkflow/565fbcef-5a14-4aa3-9487-1edc33517443/call-run_Model/execution/./model_output/sample_2pop/20240506_192641/spar/000000001.20240506_192641.spar.parquet"]
},
"runtimeAttributes": {
"maxRetries": "0",
"failOnStderr": "false",
"continueOnReturnCode": "0",
"docker": "rocker/verse:latest"
},
"callCaching": {
"allowResultReuse": false,
"effectiveCallCachingMode": "CallCachingOff"
},
"inputs": {
"copy_model_output_script": "scripts/python/copy_model_output.py",
"clone_repository_script": "./scripts/sh/clone_git_repository.sh",
"model_output_folder": "model_output",
"setup_os_script": "./scripts/sh/setup_os.sh",
"run_model_script": "./scripts/sh/flepimop/run_model.sh",
"install_model_script": "./scripts/sh/flepimop/install_model.sh",
"model_configuration_yml": "config_sample_2pop.yml",
"model_git_repository": "https://github.com/HopkinsIDD/flepiMoP.git",
"model_executable": "gempyor-simulate",
"install_git_script": "./scripts/sh/install_git.sh",
"model_runtime_docker": "rocker/verse:latest",
"model_output_files": "model_output_files.txt"
},
"returnCode": 0,
"jobId": "97250",
"backend": "LocalExample",
"start": "2024-05-06T19:00:11.257Z",
"end": "2024-05-06T19:29:39.331Z",
"dockerImageUsed": "rocker/verse@sha256:ceae16a621386e24189b993f002e150adf55ddd8255cf0b6f8f6a89ee0cf2d9d",
"stderr": "/Users/jbs82/Documents/dev/cromwell_flepimop_project/cromwell-executions/modelWorkflow/565fbcef-5a14-4aa3-9487-1edc33517443/call-run_Model/execution/stderr",
"callRoot": "/Users/jbs82/Documents/dev/cromwell_flepimop_project/cromwell-executions/modelWorkflow/565fbcef-5a14-4aa3-9487-1edc33517443/call-run_Model",
"attempt": 1,
"executionEvents": [{
"startTime": "2024-05-06T19:00:11.265Z",
"description": "Pending",
"endTime": "2024-05-06T19:00:11.273Z"
}, {
"startTime": "2024-05-06T19:00:20.457Z",
"description": "RunningJob",
"endTime": "2024-05-06T19:29:39.330Z"
}, {
"startTime": "2024-05-06T19:00:18.546Z",
"description": "WaitingForValueStore",
"endTime": "2024-05-06T19:00:18.551Z"
}, {
"startTime": "2024-05-06T19:00:18.551Z",
"description": "PreparingJob",
"endTime": "2024-05-06T19:00:20.457Z"
}, {
"startTime": "2024-05-06T19:00:11.273Z",
"description": "RequestingExecutionToken",
"endTime": "2024-05-06T19:00:18.546Z"
}, {
"startTime": "2024-05-06T19:29:39.330Z",
"description": "UpdatingJobStore",
"endTime": "2024-05-06T19:29:39.331Z"
}]
}]
},
"outputs": {
"modelWorkflow.run_Model.output_files": ["/Users/jbs82/Documents/dev/cromwell_flepimop_project/cromwell-executions/modelWorkflow/565fbcef-5a14-4aa3-9487-1edc33517443/call-run_Model/execution/./model_output/sample_2pop/20240506_192641/seir/000000001.20240506_192641.seir.parquet", "/Users/jbs82/Documents/dev/cromwell_flepimop_project/cromwell-executions/modelWorkflow/565fbcef-5a14-4aa3-9487-1edc33517443/call-run_Model/execution/./model_output/sample_2pop/20240506_192641/spar/000000001.20240506_192641.spar.parquet"]
},
"workflowRoot": "/Users/jbs82/Documents/dev/cromwell_flepimop_project/cromwell-executions/modelWorkflow/565fbcef-5a14-4aa3-9487-1edc33517443",
"actualWorkflowLanguage": "WDL",
"status": "Succeeded",
"end": "2024-05-06T19:29:40.017Z",
"start": "2024-05-06T19:00:08.616Z",
"id": "565fbcef-5a14-4aa3-9487-1edc33517443",
"inputs": {
"modelWorkflow.run_Model.model_git_repository": "https://github.com/HopkinsIDD/flepiMoP.git",
"install_git_script": "./scripts/sh/install_git.sh",
"clone_repository_script": "./scripts/sh/clone_git_repository.sh",
"setup_os_script": "./scripts/sh/setup_os.sh",
"modelWorkflow.run_Model.install_model_script": "./scripts/sh/flepimop/install_model.sh",
"modelWorkflow.run_Model.model_runtime_docker": "rocker/verse:latest",
"modelWorkflow.run_Model.run_model_script": "./scripts/sh/flepimop/run_model.sh",
"modelWorkflow.run_Model.model_configuration_yml": "config_sample_2pop.yml",
"modelWorkflow.run_Model.model_output_folder": "model_output",
"modelWorkflow.run_Model.model_executable": "gempyor-simulate",
"copy_model_output_script": "scripts/python/copy_model_output.py"
},
"labels": {
"cromwell-workflow-id": "cromwell-565fbcef-5a14-4aa3-9487-1edc33517443"
},
"submission": "2024-05-06T19:00:08.561Z"
}