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Enable unit tests #5

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merged 2 commits into from
Dec 4, 2024
Merged

Enable unit tests #5

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ee75e9a
enable unit tests
rcannood Dec 4, 2024
eaa8f98
fix data path
rcannood Dec 4, 2024
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3 changes: 2 additions & 1 deletion scripts/create_resources/test_resources.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -110,5 +110,6 @@ viash run src/data_processors/process_dataset/config.vsh.yaml -- \

# # only run this if you have access to the openproblems-data bucket
aws s3 sync --profile op \
"$DATASET_DIR" s3://openproblems-data/resources_test/task_cyto_batch_integration \
resources_test/task_cyto_batch_integration/starter_file \
s3://openproblems-data/resources_test/task_cyto_batch_integration/starter_file \
--delete --dryrun
14 changes: 7 additions & 7 deletions src/api/comp_control_method.yaml
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Expand Up @@ -24,10 +24,10 @@ arguments:
__merge__: file_integrated.yaml
required: true
direction: output
# test_resources:
# - type: python_script
# path: /common/component_tests/run_and_check_output.py
# - type: python_script
# path: /common/component_tests/check_config.py
# - path: /resources_test/task_cyto_batch_integration/cxg_mouse_pancreas_atlas
# dest: resources_test/task_cyto_batch_integration/cxg_mouse_pancreas_atlas
test_resources:
- type: python_script
path: /common/component_tests/run_and_check_output.py
- type: python_script
path: /common/component_tests/check_config.py
- path: /resources_test/task_cyto_batch_integration/starter_file
dest: resources_test/task_cyto_batch_integration/starter_file
10 changes: 5 additions & 5 deletions src/api/comp_data_processor.yaml
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Expand Up @@ -23,9 +23,9 @@ arguments:
__merge__: file_validation.yaml
direction: output
required: true
# test_resources:
# - path: /resources_test/common/cxg_mouse_pancreas_atlas
# dest: resources_test/common/cxg_mouse_pancreas_atlas
# - type: python_script
# path: /common/component_tests/run_and_check_output.py
test_resources:
- type: python_script
path: /common/component_tests/run_and_check_output.py
- path: /resources_test/task_cyto_batch_integration/starter_file
dest: resources_test/task_cyto_batch_integration/starter_file

18 changes: 9 additions & 9 deletions src/api/comp_method.yaml
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Expand Up @@ -3,9 +3,9 @@ info:
type: method
type_info:
label: Method
summary: A method.
summary: A method for integrating batch effects in cytometry data.
description: |
A method to predict the task effects.
A method for integrating batch effects in cytometry data.
arguments:
- name: --input
__merge__: file_unintegrated_censored.yaml
Expand All @@ -15,10 +15,10 @@ arguments:
__merge__: file_integrated.yaml
required: true
direction: output
# test_resources:
# - type: python_script
# path: /common/component_tests/run_and_check_output.py
# - type: python_script
# path: /common/component_tests/check_config.py
# - path: /resources_test/task_cyto_batch_integration/cxg_mouse_pancreas_atlas
# dest: resources_test/task_cyto_batch_integration/cxg_mouse_pancreas_atlas
test_resources:
- type: python_script
path: /common/component_tests/run_and_check_output.py
- type: python_script
path: /common/component_tests/check_config.py
- path: /resources_test/task_cyto_batch_integration/starter_file
dest: resources_test/task_cyto_batch_integration/starter_file
14 changes: 7 additions & 7 deletions src/api/comp_metric.yaml
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Expand Up @@ -23,10 +23,10 @@ arguments:
__merge__: file_score.yaml
direction: output
required: true
# test_resources:
# - type: python_script
# path: /common/component_tests/run_and_check_output.py
# - type: python_script
# path: /common/component_tests/check_config.py
# - path: /resources_test/task_cyto_batch_integration/cxg_mouse_pancreas_atlas
# dest: resources_test/task_cyto_batch_integration/cxg_mouse_pancreas_atlas
test_resources:
- type: python_script
path: /common/component_tests/run_and_check_output.py
- type: python_script
path: /common/component_tests/check_config.py
- path: /resources_test/task_cyto_batch_integration/starter_file
dest: resources_test/task_cyto_batch_integration/starter_file
2 changes: 2 additions & 0 deletions src/metrics/accuracy/config.vsh.yaml
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Expand Up @@ -10,6 +10,8 @@ __merge__: ../../api/comp_metric.yaml
# Can contain only lowercase letters or underscores.
name: accuracy

status: disabled

# Metadata for your component
info:
metrics:
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