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Merge pull request #566 from crim-ca/fix-cwl-enum-schema-name
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13 changes: 13 additions & 0 deletions
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tests/functional/application-packages/Finch_EnsembleGridPointWetdays/deploy.yml
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| processDescription: | ||
| process: | ||
| id: Finch_EnsembleGridPointWetdays | ||
| jobControlOptions: | ||
| - async-execute | ||
| outputTransmission: | ||
| - reference | ||
| executionUnit: | ||
| # note: This does not work by itself! The test suite injects the file dynamically. | ||
| - href: "tests/functional/application-packages/Finch_EnsembleGridPointWetdays/package.cwl" | ||
| # note: alternative for WPS (applied in tests), inspired from: | ||
| # https://finch.crim.ca/wps?service=WPS&request=DescribeProcess&version=1.0.0&identifier=ensemble_grid_point_wetdays | ||
| deploymentProfileName: "http://www.opengis.net/profiles/eoc/dockerizedApplication" |
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tests/functional/application-packages/Finch_EnsembleGridPointWetdays/describe.xml
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tests/functional/application-packages/Finch_EnsembleGridPointWetdays/execute.yml
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| lat: "45.35629610945964" | ||
| lon: "-73.98748912005094" | ||
| start_date: "1950" | ||
| end_date: "1960" | ||
| ensemble_percentiles: "" | ||
| dataset: "candcs-u6" | ||
| scenario: "ssp126" | ||
| models: "26models" | ||
| freq: "YS" | ||
| data_validation: "warn" | ||
| output_format: "csv" | ||
| csv_precision: 0 | ||
| thresh: "15 mm\/day" |
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tests/functional/application-packages/Finch_EnsembleGridPointWetdays/package.cwl
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| # NOTE: | ||
| # Inspired from (but not an exact equivalent): | ||
| # https://finch.crim.ca/wps?service=WPS&request=DescribeProcess&version=1.0.0&identifier=ensemble_grid_point_wetdays | ||
| # Outputs are modified to only collect stdout, since we don't have the expected outputs produced by the real process. | ||
| # The 'baseCommand' is also added to produce this stdout output. | ||
| # All remaining arguments are identical. | ||
| cwlVersion: v1.0 | ||
| class: CommandLineTool | ||
| requirements: | ||
| InlineJavascriptRequirement: {} | ||
| # NOTE: replaced by 'baseCommand' | ||
| #hints: | ||
| # WPS1Requirement: | ||
| # provider: https://finch.crim.ca/wps | ||
| # process: ensemble_grid_point_wetdays | ||
| baseCommand: echo | ||
| inputs: | ||
| - id: lat | ||
| type: | ||
| - string | ||
| - type: array | ||
| items: string | ||
| - id: lon | ||
| type: | ||
| - string | ||
| - type: array | ||
| items: string | ||
| - id: start_date | ||
| type: | ||
| - 'null' | ||
| - string | ||
| - id: end_date | ||
| type: | ||
| - 'null' | ||
| - string | ||
| - id: ensemble_percentiles | ||
| type: | ||
| - 'null' | ||
| - string | ||
| default: 10,50,90 | ||
| - id: average | ||
| type: | ||
| - 'null' | ||
| - boolean | ||
| default: false | ||
| - id: dataset | ||
| type: | ||
| - 'null' | ||
| - type: enum | ||
| symbols: | ||
| - humidex-daily | ||
| - candcs-u5 | ||
| - candcs-u6 | ||
| - bccaqv2 | ||
| default: candcs-u5 | ||
| # WARNING: | ||
| # Following definition combining 'enum' and its corresponding nested definition in 'array' caused a | ||
| # schema-salad name resolution error. This CWL is used particularly to validate this *valid* type resolution. | ||
| # see https://github.com/common-workflow-language/cwltool/issues/1908 | ||
| - id: scenario | ||
| type: | ||
| - 'null' | ||
| - type: enum | ||
| symbols: | ||
| - ssp126 | ||
| - rcp85 | ||
| - rcp45 | ||
| - rcp26 | ||
| - ssp585 | ||
| - ssp245 | ||
| - type: array | ||
| items: | ||
| type: enum | ||
| symbols: | ||
| - ssp126 | ||
| - rcp85 | ||
| - rcp45 | ||
| - rcp26 | ||
| - ssp585 | ||
| - ssp245 | ||
| - id: models | ||
| type: | ||
| - 'null' | ||
| - type: enum | ||
| symbols: | ||
| - KACE-1-0-G | ||
| - CCSM4 | ||
| - MIROC5 | ||
| - EC-Earth3-Veg | ||
| - TaiESM1 | ||
| - GFDL-ESM4 | ||
| - GFDL-CM3 | ||
| - CanESM5 | ||
| - HadGEM3-GC31-LL | ||
| - INM-CM4-8 | ||
| - IPSL-CM5A-MR | ||
| - EC-Earth3 | ||
| - GFDL-ESM2G | ||
| - humidex_models | ||
| - GFDL-ESM2M | ||
| - MIROC-ESM | ||
| - CSIRO-Mk3-6-0 | ||
| - MPI-ESM-LR | ||
| - NorESM1-M | ||
| - CNRM-CM5 | ||
| - all | ||
| - GISS-E2-1-G | ||
| - 24models | ||
| - MPI-ESM1-2-HR | ||
| - CNRM-ESM2-1 | ||
| - CNRM-CM6-1 | ||
| - CanESM2 | ||
| - FGOALS-g3 | ||
| - NorESM1-ME | ||
| - IPSL-CM6A-LR | ||
| - CMCC-ESM2 | ||
| - pcic12 | ||
| - EC-Earth3-Veg-LR | ||
| - ACCESS-ESM1-5 | ||
| - MRI-CGCM3 | ||
| - MIROC-ESM-CHEM | ||
| - NorESM2-MM | ||
| - bcc-csm1-1-m | ||
| - BNU-ESM | ||
| - UKESM1-0-LL | ||
| - CESM1-CAM5 | ||
| - MIROC-ES2L | ||
| - MRI-ESM2-0 | ||
| - HadGEM2-ES | ||
| - MIROC6 | ||
| - MPI-ESM-MR | ||
| - INM-CM5-0 | ||
| - bcc-csm1-1 | ||
| - BCC-CSM2-MR | ||
| - ACCESS-CM2 | ||
| - NorESM2-LM | ||
| - IPSL-CM5A-LR | ||
| - FGOALS-g2 | ||
| - HadGEM2-AO | ||
| - 26models | ||
| - MPI-ESM1-2-LR | ||
| - KIOST-ESM | ||
| - type: array | ||
| items: | ||
| type: enum | ||
| symbols: | ||
| - KACE-1-0-G | ||
| - CCSM4 | ||
| - MIROC5 | ||
| - EC-Earth3-Veg | ||
| - TaiESM1 | ||
| - GFDL-ESM4 | ||
| - GFDL-CM3 | ||
| - CanESM5 | ||
| - HadGEM3-GC31-LL | ||
| - INM-CM4-8 | ||
| - IPSL-CM5A-MR | ||
| - EC-Earth3 | ||
| - GFDL-ESM2G | ||
| - humidex_models | ||
| - GFDL-ESM2M | ||
| - MIROC-ESM | ||
| - CSIRO-Mk3-6-0 | ||
| - MPI-ESM-LR | ||
| - NorESM1-M | ||
| - CNRM-CM5 | ||
| - all | ||
| - GISS-E2-1-G | ||
| - 24models | ||
| - MPI-ESM1-2-HR | ||
| - CNRM-ESM2-1 | ||
| - CNRM-CM6-1 | ||
| - CanESM2 | ||
| - FGOALS-g3 | ||
| - NorESM1-ME | ||
| - IPSL-CM6A-LR | ||
| - CMCC-ESM2 | ||
| - pcic12 | ||
| - EC-Earth3-Veg-LR | ||
| - ACCESS-ESM1-5 | ||
| - MRI-CGCM3 | ||
| - MIROC-ESM-CHEM | ||
| - NorESM2-MM | ||
| - bcc-csm1-1-m | ||
| - BNU-ESM | ||
| - UKESM1-0-LL | ||
| - CESM1-CAM5 | ||
| - MIROC-ES2L | ||
| - MRI-ESM2-0 | ||
| - HadGEM2-ES | ||
| - MIROC6 | ||
| - MPI-ESM-MR | ||
| - INM-CM5-0 | ||
| - bcc-csm1-1 | ||
| - BCC-CSM2-MR | ||
| - ACCESS-CM2 | ||
| - NorESM2-LM | ||
| - IPSL-CM5A-LR | ||
| - FGOALS-g2 | ||
| - HadGEM2-AO | ||
| - 26models | ||
| - MPI-ESM1-2-LR | ||
| - KIOST-ESM | ||
| default: all | ||
| - id: thresh | ||
| type: | ||
| - 'null' | ||
| - string | ||
| default: 1.0 mm/day | ||
| - id: freq | ||
| type: | ||
| - 'null' | ||
| - type: enum | ||
| symbols: | ||
| - YS | ||
| - QS-DEC | ||
| - AS-JUL | ||
| - MS | ||
| default: YS | ||
| - id: op | ||
| type: | ||
| - 'null' | ||
| - type: enum | ||
| symbols: | ||
| - '>=' | ||
| - '>' | ||
| - gt | ||
| - ge | ||
| default: '>=' | ||
| - id: month | ||
| type: | ||
| - 'null' | ||
| - int | ||
| - type: array | ||
| items: int | ||
| inputBinding: | ||
| valueFrom: "\n ${\n const values = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12];\n if (Array.isArray(self)) {\n \n if (self.every(item => values.includes(item))) {\n return self;\n }\n else {\n throw \"invalid value(s) in [\" + self + \"] are not all allowed values from [\" + values + \"]\";\n }\n \n }\n else {\n \n if (values.includes(self)) {\n return self;\n }\n else {\n throw \"invalid value \" + self + \" is not an allowed value from [\" + values + \"]\";\n }\n \n }\n }\n " | ||
| - id: season | ||
| type: | ||
| - 'null' | ||
| - type: enum | ||
| symbols: | ||
| - SON | ||
| - MAM | ||
| - JJA | ||
| - DJF | ||
| - id: check_missing | ||
| type: | ||
| - 'null' | ||
| - type: enum | ||
| symbols: | ||
| - pct | ||
| - at_least_n | ||
| - wmo | ||
| - skip | ||
| - from_context | ||
| - any | ||
| default: any | ||
| - id: missing_options | ||
| type: | ||
| - 'null' | ||
| - File | ||
| format: iana:application/json | ||
| - id: cf_compliance | ||
| type: | ||
| - 'null' | ||
| - type: enum | ||
| symbols: | ||
| - raise | ||
| - log | ||
| - warn | ||
| default: warn | ||
| - id: data_validation | ||
| type: | ||
| - 'null' | ||
| - type: enum | ||
| symbols: | ||
| - raise | ||
| - log | ||
| - warn | ||
| default: raise | ||
| - id: output_name | ||
| type: | ||
| - 'null' | ||
| - string | ||
| - id: output_format | ||
| type: | ||
| - 'null' | ||
| - type: enum | ||
| symbols: | ||
| - csv | ||
| - netcdf | ||
| default: netcdf | ||
| - id: csv_precision | ||
| type: | ||
| - 'null' | ||
| - int | ||
| # NOTE: | ||
| # Following structure is permitted in standard CWL, but not supported in Weaver. | ||
| # Must use the equivalent 'long form' in the meantime. | ||
| #outputs: | ||
| #- id: output | ||
| # type: stdout | ||
| outputs: | ||
| - id: output | ||
| type: File | ||
| outputBinding: | ||
| glob: "stdout.log" | ||
| stdout: stdout.log | ||
| $namespaces: | ||
| iana: https://www.iana.org/assignments/media-types/ | ||
| edam: http://edamontology.org/ |
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