test_aqs.cwl

  1#!/usr/bin/env cwl-runner
  2### Test harness for aqs.cwl
  3
  4cwlVersion: v1.2
  5class: Workflow
  6
  7requirements:
  8  InlineJavascriptRequirement: {}
  9  ScatterFeatureRequirement: {}
 10  StepInputExpressionRequirement: {}
 11  SubworkflowFeatureRequirement: {}
 12
 13
 14# All inputs of original pipeline, remove what is not needed
 15inputs:
 16  aggregation:
 17    type: string
 18  connection_name:
 19    doc: The name of the section in the database.ini file
 20    type: string
 21  database:
 22    doc: Path to database connection file, usually database.ini
 23    type: File
 24  parameter_code:
 25    doc: 'Parameter code. Either a numeric code (e.g. 88101, 44201)
 26
 27      or symbolic name (e.g. PM25, NO2).
 28
 29      See more: [AQS Code List](https://www.epa.gov/aqs/aqs-code-list)
 30
 31      '
 32    type: string
 33  proxy:
 34    default: ''
 35    doc: HTTP/HTTPS Proxy if required
 36    type: string?
 37  table:
 38    doc: Name of the table to be created in the database
 39    type: string
 40  test_script:
 41    doc: File containing SQL test script
 42    type:
 43      - File[]
 44  years:
 45    doc: Years to download
 46    type: string[]
 47
 48
 49steps:
 50  execute:
 51    run: aqs.cwl
 52    in:
 53      proxy: proxy
 54      database: database
 55      connection_name: connection_name
 56      aggregation: aggregation
 57      parameter_code: parameter_code
 58      table: table
 59      years: years
 60    out:
 61      - initdb_log
 62      - expand_log
 63      - introspect_log
 64      - ingest_log
 65      - index_log
 66      - vacuum_log
 67      - data
 68      - model
 69      - introspect_err
 70      - ingest_err
 71      - index_err
 72      - vacuum_err
 73      - export_data
 74      - export_log
 75      - export_err
 76
 77  verify:
 78    run: run_test.cwl
 79    in:
 80      database: database
 81      connection_name: connection_name
 82      script: test_script
 83      depends_on: execute/vacuum_err
 84    out:
 85      - log
 86      - errors
 87
 88outputs:
 89## Generated by nsaph/util/cwl_collect_outputs.py from aqs.cwl:
 90  execute_initdb_log:
 91    type: File
 92    outputSource: execute/initdb_log
 93  execute_expand_log:
 94    type: File
 95    outputSource: execute/expand_log
 96  execute_introspect_log:
 97    type: File
 98    outputSource: execute/introspect_log
 99  execute_ingest_log:
100    type: File
101    outputSource: execute/ingest_log
102  execute_index_log:
103    type: File
104    outputSource: execute/index_log
105  execute_vacuum_log:
106    type: File
107    outputSource: execute/vacuum_log
108  execute_data:
109    type: File
110    outputSource: execute/data
111  execute_model:
112    type: File
113    outputSource: execute/model
114  execute_introspect_err:
115    type: File
116    outputSource: execute/introspect_err
117  execute_ingest_err:
118    type: File
119    outputSource: execute/ingest_err
120  execute_index_err:
121    type: File
122    outputSource: execute/index_err
123  execute_vacuum_err:
124    type: File
125    outputSource: execute/vacuum_err
126## Generated by nsaph/util/cwl_collect_outputs.py from run_test.cwl:
127  verify_log:
128    type: File
129    outputSource: verify/log
130  verify_errors:
131    type: File
132    outputSource: verify/errors
133
134  execute_export_data:
135    type: ['File', 'Directory']
136    outputSource: execute/export_data
137  execute_export_log:
138    type: File
139    outputSource: execute/export_log
140  execute_export_err:
141    type: File
142    outputSource: execute/export_err