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Add results filtering (#935)
* introduce new component * implement component * format code * Update src/reporting/process_task_results/main.nf * Apply suggestions from code review Co-authored-by: Luke Zappia <[email protected]> * add back previously removed arguments --------- Co-authored-by: Luke Zappia <[email protected]>
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‎src/reporting/filter_results/config.vsh.yaml‎

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name: filter_results
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namespace: reporting
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description: Filter dataset, method, metric info and results based on include/exclude criteria
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argument_groups:
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- name: Inputs
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arguments:
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- name: --input_dataset_info
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type: file
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description: JSON file containing dataset information
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required: true
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example: resources_test/openproblems/task_results_v4/processed/dataset_info.json
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- name: --input_method_info
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type: file
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description: JSON file containing method information
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required: true
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example: resources_test/openproblems/task_results_v4/processed/method_info.json
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- name: --input_metric_info
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type: file
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description: JSON file containing metric information
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required: true
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example: resources_test/openproblems/task_results_v4/processed/metric_info.json
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- name: --input_results
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type: file
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description: JSON file containing results
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required: true
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example: resources_test/openproblems/task_results_v4/processed/results.json
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- name: Dataset filtering
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description: |
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Use these arguments to filter datasets by name. By default, all datasets are
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included. If `--datasets_include` is defined, only those datasets are included. If
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`--datasets_exclude` is defined, all datasets except those specified are included.
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These arguments are mutually exclusive, so only `--datasets_include` OR
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`--datasets_exclude` can be set but not both.
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arguments:
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- name: "--datasets_include"
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type: string
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multiple: true
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description: |
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A list of dataset ids to include. If specified, only these datasets will be included.
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- name: "--datasets_exclude"
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type: string
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multiple: true
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description: |
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A list of dataset ids to exclude. If specified, all datasets except the ones listed will be included.
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- name: Method filtering
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description: |
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Use these arguments to filter methods by name. By default, all methods are
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included. If `--methods_include` is defined, only those methods are included. If
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`--methods_exclude` is defined, all methods except those specified are included.
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These arguments are mutually exclusive, so only `--methods_include` OR
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`--methods_exclude` can be set but not both.
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arguments:
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- name: "--methods_include"
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type: string
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multiple: true
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description: |
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A list of method ids to include. If specified, only these methods will be included.
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- name: "--methods_exclude"
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type: string
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multiple: true
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description: |
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A list of method ids to exclude. If specified, all methods except the ones listed will be included.
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- name: Metric filtering
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description: |
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Use these arguments to filter metrics by name. By default, all metrics are
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included. If `--metrics_include` is defined, only those metrics are included. If
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`--metrics_exclude` is defined, all metrics except those specified are included.
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These arguments are mutually exclusive, so only `--metrics_include` OR
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`--metrics_exclude` can be set but not both.
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arguments:
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- name: "--metrics_include"
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type: string
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multiple: true
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description: |
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A list of metric ids to include. If specified, only these metrics will be included.
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- name: "--metrics_exclude"
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type: string
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multiple: true
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description: |
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A list of metric ids to exclude. If specified, all metrics except the ones listed will be included.
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- name: Outputs
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arguments:
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- name: --output_dataset_info
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type: file
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direction: output
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default: filtered_dataset_info.json
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description: Filtered dataset info JSON file
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info:
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format:
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type: json
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schema: /common/schemas/results_v4/dataset_info.json
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example: resources_test/openproblems/task_results_v4/processed/filtered_dataset_info.json
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- name: --output_method_info
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type: file
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direction: output
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default: filtered_method_info.json
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description: Filtered method info JSON file
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info:
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format:
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type: json
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schema: /common/schemas/results_v4/method_info.json
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example: resources_test/openproblems/task_results_v4/processed/filtered_method_info.json
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- name: --output_metric_info
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type: file
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direction: output
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default: filtered_metric_info.json
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description: Filtered metric info JSON file
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info:
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format:
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type: json
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schema: /common/schemas/results_v4/metric_info.json
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example: resources_test/openproblems/task_results_v4/processed/filtered_metric_info.json
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- name: --output_results
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type: file
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direction: output
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default: filtered_results.json
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description: Filtered results JSON file
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info:
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format:
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type: json
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schema: /common/schemas/results_v4/results.json
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example: resources_test/openproblems/task_results_v4/processed/filtered_results.json
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resources:
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- type: python_script
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path: script.py
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- path: /common/schemas
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dest: schemas
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test_resources:
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- type: python_script
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path: /common/component_tests/run_and_check_output.py
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- path: /resources_test/openproblems/task_results_v4
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dest: resources_test/openproblems/task_results_v4
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engines:
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- type: docker
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image: openproblems/base_python:1
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setup:
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- type: apt
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packages:
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- nodejs
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- npm
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- type: docker
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run: npm install -g ajv-cli
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runners:
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- type: executable
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- type: nextflow
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directives:
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label: [lowmem, lowtime, lowcpu]

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