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 - File[]
45 years:
46 doc: Years to download
47 type: string[]
48
49
50steps:
51 execute:
52 run: aqs.cwl
53 in:
54 proxy: proxy
55 database: database
56 connection_name: connection_name
57 aggregation: aggregation
58 parameter_code: parameter_code
59 table: table
60 years: years
61 out:
62 - initdb_log
63 - expand_log
64 - introspect_log
65 - ingest_log
66 - index_log
67 - vacuum_log
68 - data
69 - model
70 - introspect_err
71 - ingest_err
72 - index_err
73 - vacuum_err
74
75 verify:
76 run: run_test.cwl
77 in:
78 database: database
79 connection_name: connection_name
80 script: test_script
81 depends_on: execute/vacuum_err
82 out:
83 - log
84 - errors
85
86outputs:
87## Generated by nsaph/util/cwl_collect_outputs.py from aqs.cwl:
88 execute_initdb_log:
89 type: File
90 outputSource: execute/initdb_log
91 execute_expand_log:
92 type: File
93 outputSource: execute/expand_log
94 execute_introspect_log:
95 type: File
96 outputSource: execute/introspect_log
97 execute_ingest_log:
98 type: File
99 outputSource: execute/ingest_log
100 execute_index_log:
101 type: File
102 outputSource: execute/index_log
103 execute_vacuum_log:
104 type: File
105 outputSource: execute/vacuum_log
106 execute_data:
107 type: File
108 outputSource: execute/data
109 execute_model:
110 type: File
111 outputSource: execute/model
112 execute_introspect_err:
113 type: File
114 outputSource: execute/introspect_err
115 execute_ingest_err:
116 type: File
117 outputSource: execute/ingest_err
118 execute_index_err:
119 type: File
120 outputSource: execute/index_err
121 execute_vacuum_err:
122 type: File
123 outputSource: execute/vacuum_err
124## Generated by nsaph/util/cwl_collect_outputs.py from run_test.cwl:
125 verify_log:
126 type: File
127 outputSource: verify/log
128 verify_errors:
129 type: File
130 outputSource: verify/errors