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Merge pull request #9 from DCAN-Labs/test
Implementing pytest
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,4 +1,5 @@ | ||
| /temp/ | ||
| /src/__pycache__/ | ||
| /test-param-jsons/ | ||
| /__pycache__ | ||
| /__pycache__/ | ||
| /.pytest_cache/ |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,137 @@ | ||
| { | ||
| "cabinet": { | ||
| "container_type": "singularity", | ||
| "stages": ["bibsnet", "solve_world_hunger", "nibabies"], | ||
| "verbose": true, | ||
| "handle_missing_host_paths": "make_directories" | ||
| }, | ||
|
|
||
| "stages": { | ||
| "bibsnet": { | ||
| "container_filepath": "/home/faird/shared/code/internal/pipelines/cabinet_container/cabinet_v2.4.3.sif", | ||
| "container_args": { | ||
| "--cleanenv": true, | ||
| "--nv": true | ||
| }, | ||
| "binds": [ | ||
| { | ||
| "host_path":"/home/faird/shared/data/BCP-MVP_BIBSNet/input/", | ||
| "container_path":"/input" | ||
| }, | ||
| { | ||
| "host_path":"/home/feczk001/shared/projects/segpipeline_testing/Barry_test/cbaw-test/derivatives/" | ||
| }, | ||
| { | ||
| "host_path":"/home/feczk001/shared/projects/segpipeline_testing/Barry_test/cbaw-test/work/", | ||
| "container_path":"/work" | ||
| } | ||
| ], | ||
| "positional_args": [ | ||
| "/input", "/output", "participant" | ||
| ], | ||
| "flags": { | ||
| "--parameter-json":"/home/cabinet/parameter-file-container.json", | ||
| "-start":"prebibsnet", | ||
| "-end":"postbibsnet", | ||
| "-v": true, | ||
| "--participant-label":"470437", | ||
| "-w":"/work" | ||
| } | ||
| }, | ||
| "nibabies": { | ||
| "container_filepath": "/home/faird/shared/code/external/pipelines/nibabies/nibabies_t1-t2-derivatives_08102023.sif", | ||
| "container_args": { | ||
| "--cleanenv": true | ||
| }, | ||
| "binds": [ | ||
| { | ||
| "host_path":"/home/faird/shared/data/BCP-MVP_BIBSNet/input/", | ||
| "container_path":"/bids_dir" | ||
| }, | ||
| { | ||
| "host_path":"/home/feczk001/shared/projects/segpipeline_testing/Barry_test/cbaw-test/derivatives/nibabies/", | ||
| "container_path":"/output_dir" | ||
| }, | ||
| { | ||
| "host_path":"/home/feczk001/shared/projects/segpipeline_testing/Barry_test/cbaw-test/work/", | ||
| "container_path":"/work" | ||
| }, | ||
| { | ||
| "host_path":"/home/faird/shared/code/external/utilities/freesurfer_license/license.txt", | ||
| "container_path":"/opt/freesurfer/license.txt" | ||
| }, | ||
| { | ||
| "host_path":"/home/feczk001/shared/projects/segpipeline_testing/Barry_test/cbaw-test/derivatives/bibsnet/", | ||
| "container_path":"/derivatives" | ||
| }, | ||
| { | ||
| "host_path":"/home/faird/tikal004/fake/file/path/", | ||
| "container_path":"/fake_path" | ||
| } | ||
| ], | ||
| "positional_args": [ | ||
| "/bids_dir", "/output_dir", "participant" | ||
| ], | ||
| "flags": { | ||
| "--project-goodvoxels": true, | ||
| "--surface-recon-method": "mcribs", | ||
| "--omp-nthreads": 3, | ||
| "--resource-monitor": true, | ||
| "--cifti-output": "91k", | ||
| "-vv": true, | ||
| "-w": "/work", | ||
| "--fd-radius": 35, | ||
| "--derivatives": "/derivatives", | ||
| "--age-months": 1, | ||
| "--participant-label":"470437" | ||
| } | ||
| }, | ||
| "xcpd": { | ||
| "container_args": { | ||
| "--cleanenv": true | ||
| }, | ||
| "binds": [ | ||
| { | ||
| "host_path":"/home/feczk001/shared/projects/segpipeline_testing/Barry_test/cbaw-test/work/", | ||
| "container_path":"/work" | ||
| }, | ||
| { | ||
| "host_path":"/home/faird/shared/code/external/utilities/freesurfer_license/license.txt", | ||
| "container_path":"/opt/freesurfer/license.txt" | ||
| }, | ||
| { | ||
| "host_path":"/home/feczk001/shared/projects/segpipeline_testing/Barry_test/cbaw-test/derivatives/", | ||
| "container_path":"/output_dir" | ||
| }, | ||
| { | ||
| "host_path":"/home/faird/shared/code/external/pipelines/xcp_d_test_binds/20230712_fix-collection/xcp_d/xcp_d", | ||
| "container_path":"/usr/local/miniconda/lib/python3.8/site-packages/xcp_d" | ||
| } | ||
| ], | ||
| "positional_args": [ | ||
| "/output_dir/nibabies", "/output_dir/", "participant" | ||
| ], | ||
| "flags": { | ||
| "--input-type": "nibabies", | ||
| "--cifti": true, | ||
| "--despike":true, | ||
| "--resource-monitor": true, | ||
| "--dcan-qc": true, | ||
| "-w": "/work", | ||
| "--omp-nthreads": 3, | ||
| "--warp-surfaces-native2std": true, | ||
| "-f": 0.3, | ||
| "-m": true, | ||
| "-vv": true, | ||
| "--participant-label": "470437" | ||
| } | ||
| }, | ||
| "lolcow": { | ||
| "container_filepath": "/home/faird/tikal004/lolcow.sif", | ||
| "action": "exe", | ||
| "positional_args": [ | ||
| "cowsay", "\"Thank you for testing CABINET\"" | ||
| ] | ||
| } | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,22 @@ | ||
| { | ||
| "cabinet": { | ||
| "container_type": "singularity", | ||
| "stages": ["lolcow", "dockerfail", "lolcow", "lolcow-exec"] | ||
| }, | ||
|
|
||
| "stages": { | ||
| "lolcow": { | ||
| "container_filepath": "/home/faird/shared/code/internal/utilities/test_containers/lolcow.sif" | ||
| }, | ||
| "dockerfail": { | ||
| "container_filepath": "/home/faird/shared/code/internal/utilities/test_containers/dockerfail.sif" | ||
| }, | ||
| "lolcow-exec": { | ||
| "action": "exec", | ||
| "container_filepath": "/home/faird/shared/code/internal/utilities/test_containers/lolcow.sif", | ||
| "positional_args": [ | ||
| "cowsay", "Thank you for testing CABINET" | ||
| ] | ||
| } | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,19 @@ | ||
| #!/usr/bin/env python3 | ||
| # coding: utf-8 | ||
|
|
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| from src.valid_jargs_class import ValidJargs | ||
| from src.wrapper_class import Wrapper | ||
|
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| param_json = "lolcow_test.json" | ||
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| Jargs = ValidJargs(param_json) | ||
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| Test = Wrapper(Jargs) | ||
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| def test_run_stage_pass(): | ||
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| assert Test.run_stage("lolcow") | ||
|
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| def test_run_stage_fail(): | ||
|
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| assert not Test.run_stage("dockerfail") |
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| @@ -0,0 +1,10 @@ | ||
| #!/usr/bin/env python3 | ||
| # coding: utf-8 | ||
|
|
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| from src.valid_jargs_class import ValidJargs | ||
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| param_json = "invalid-example.json" | ||
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| Jargs = ValidJargs(param_json) | ||
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| assert not Jargs.validate_cabinet_options() |