#!/usr/bin/env cwl-runner
### Test harness for aqs.cwl
cwlVersion: v1.2
class: Workflow
requirements:
InlineJavascriptRequirement: {}
ScatterFeatureRequirement: {}
StepInputExpressionRequirement: {}
SubworkflowFeatureRequirement: {}
# All inputs of original pipeline, remove what is not needed
inputs:
aggregation:
type: string
connection_name:
doc: The name of the section in the database.ini file
type: string
database:
doc: Path to database connection file, usually database.ini
type: File
parameter_code:
doc: 'Parameter code. Either a numeric code (e.g. 88101, 44201)
or symbolic name (e.g. PM25, NO2).
See more: [AQS Code List](https://www.epa.gov/aqs/aqs-code-list)
'
type: string
proxy:
default: ''
doc: HTTP/HTTPS Proxy if required
type: string?
table:
doc: Name of the table to be created in the database
type: string
test_script:
doc: File containing SQL test script
type: File
years:
doc: Years to download
type: string[]
steps:
execute:
run: aqs.cwl
in:
proxy: proxy
database: database
connection_name: connection_name
aggregation: aggregation
parameter_code: parameter_code
table: table
years: years
out:
- initdb_log
- expand_log
- introspect_log
- ingest_log
- index_log
- vacuum_log
- data
- model
- introspect_err
- ingest_err
- index_err
- vacuum_err
verify:
run: run_test.cwl
in:
database: database
connection_name: connection_name
script: test_script
depends_on: execute/vacuum_err
out:
- log
- errors
outputs:
## Generated by nsaph/util/cwl_collect_outputs.py from aqs.cwl:
execute_initdb_log:
type: File
outputSource: execute/initdb_log
execute_expand_log:
type: File
outputSource: execute/expand_log
execute_introspect_log:
type: File
outputSource: execute/introspect_log
execute_ingest_log:
type: File
outputSource: execute/ingest_log
execute_index_log:
type: File
outputSource: execute/index_log
execute_vacuum_log:
type: File
outputSource: execute/vacuum_log
execute_data:
type: File
outputSource: execute/data
execute_model:
type: File
outputSource: execute/model
execute_introspect_err:
type: File
outputSource: execute/introspect_err
execute_ingest_err:
type: File
outputSource: execute/ingest_err
execute_index_err:
type: File
outputSource: execute/index_err
execute_vacuum_err:
type: File
outputSource: execute/vacuum_err
## Generated by nsaph/util/cwl_collect_outputs.py from run_test.cwl:
verify_log:
type: File
outputSource: verify/log
verify_errors:
type: File
outputSource: verify/errors