-
Notifications
You must be signed in to change notification settings - Fork 1
/
Copy pathL1-to-L2-e2e.scale.cwl
184 lines (167 loc) · 6.09 KB
/
L1-to-L2-e2e.scale.cwl
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
#!/usr/bin/env cwl-runner
cwlVersion: v1.1
class: Workflow
label: Workflow that executes the SBG L1 Workflow
$namespaces:
cwltool: http://commonwl.org/cwltool#
requirements:
SubworkflowFeatureRequirement: {}
ScatterFeatureRequirement: {}
InlineJavascriptRequirement: {}
StepInputExpressionRequirement: {}
MultipleInputFeatureRequirement: {}
## Inputs to the e2e rebinning, not to each applicaiton within the workflow
inputs:
# Generic inputs
input_processing_labels: string[]
# For CMR Search Step
input_cmr_collection_name: string
input_cmr_search_start_time: string
input_cmr_search_stop_time: string
# catalog inputs
input_unity_dapa_api: string
input_unity_dapa_client: string
#for preprocess step
input_crid: string
#isofit step
input_cores: int
input_aux_stac:
- string
- File
# For unity data stage-out step, unity catalog
output_preprocess_collection_id: string
output_isofit_collection_id: string
#output_resample_collection_id: string
#output_refcorrect_collection_id: string
#output_frcover_collection_id: string
output_data_bucket: string
outputs:
results:
type: File
outputSource: preprocess/stage_out_results
steps:
cmr-step:
run: http://awslbdockstorestack-lb-1429770210.us-west-2.elb.amazonaws.com:9998/api/ga4gh/trs/v2/tools/%23workflow%2Fdockstore.org%2Fmike-gangl%2Fcmr-trial/versions/5/PLAIN-CWL/descriptor/%2FDockstore.cwl
in:
cmr_collection : input_cmr_collection_name
cmr_start_time: input_cmr_search_start_time
cmr_stop_time: input_cmr_search_stop_time
# # Need to understand the best way of inputting this credential, nullables
# cmr_edl_user: "null"
# cmr_edl_pass: "null"
out: [results]
preprocess:
run: http://awslbdockstorestack-lb-1429770210.us-west-2.elb.amazonaws.com:9998/api/ga4gh/trs/v2/tools/%23workflow%2Fdockstore.org%2Fmike-gangl%2FSBG-unity-preprocess/versions/23/PLAIN-CWL/descriptor/%2Fworkflow.cwl
in:
# input configuration for stage-in
# edl_password_type can be either 'BASE64' or 'PARAM_STORE' or 'PLAIN'
# README available at https://github.com/unity-sds/unity-data-services/blob/main/docker/Readme.md
stage_in:
source: [cmr-step/results, input_unity_dapa_client]
valueFrom: |
${
return {
download_type: 'DAAC',
stac_json: self[0],
edl_password: '/sps/processing/workflows/edl_password',
edl_username: '/sps/processing/workflows/edl_username',
edl_password_type: 'PARAM_STORE',
downloading_keys: 'data, data1',
downloading_roles: '',
unity_stac_auth: 'NONE',
unity_client_id: self[1],
log_level: '10'
};
}
#input configuration for process
parameters:
source: [output_preprocess_collection_id, input_crid]
valueFrom: |
${
return {
crid: self[1],
sensor: 'EMIT',
temp_directory: '/tmp',
output_collection: self[0]
};
}
#input configuration for stage-out
# readme available at https://github.com/unity-sds/unity-data-services/blob/main/docker/Readme.md
stage_out:
source: [output_data_bucket, output_preprocess_collection_id]
valueFrom: |
${
return {
aws_access_key_id: '',
aws_region: 'us-west-2',
aws_secret_access_key: '',
aws_session_token: '',
collection_id: self[1],
staging_bucket: self[0],
log_level: '20',
result_path_prefix: 'stage_out'
};
}
out: [stage_out_results, stage_out_success, stage_out_failures]
isofit:
run: http://awslbdockstorestack-lb-1429770210.us-west-2.elb.amazonaws.com:9998/api/ga4gh/trs/v2/tools/%23workflow%2Fdockstore.org%2Fmike-gangl%2FSBG-unity-isofit/versions/25/PLAIN-CWL/descriptor/%2FDockstore.cwl
in:
# input configuration for stage-in
# edl_password_type can be either 'BASE64' or 'PARAM_STORE' or 'PLAIN'
# README available at https://github.com/unity-sds/unity-data-services/blob/main/docker/Readme.md
stage_in:
source: [preprocess/stage_out_success, input_unity_dapa_client]
valueFrom: |
${
return {
download_type: 'S3',
stac_json: self[0],
unity_stac_auth: 'NONE',
unity_client_id: self[1],
downloading_roles: 'data, metadata',
log_level: '20'
};
}
#input configuration for process
stage_aux_in:
source: [input_aux_stac, input_unity_dapa_client]
valueFrom: |
${
return {
download_type: 'S3',
stac_json: self[0],
unity_stac_auth: 'NONE',
unity_client_id: self[1],
downloading_roles: 'data, metadata',
log_level: '20'
};
}
parameters:
source: [output_isofit_collection_id, input_crid, input_cores]
valueFrom: |
${
return {
crid: self[1],
cores: self[2],
sensor: 'EMIT',
temp_directory: '/tmp',
output_collection: self[0]
};
}
#input configuration for stage-out
# readme available at https://github.com/unity-sds/unity-data-services/blob/main/docker/Readme.md
stage_out:
source: [output_data_bucket, output_isofit_collection_id]
valueFrom: |
${
return {
aws_access_key_id: '',
aws_region: 'us-west-2',
aws_secret_access_key: '',
aws_session_token: '',
collection_id: self[1],
staging_bucket: self[0],
log_level: '20'
};
}
out: [stage_out_results, stage_out_success, stage_out_failures]