forked from scholtalbers/galaxy-test-workflows
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathrun_wf_structural.py
executable file
·191 lines (164 loc) · 7.2 KB
/
run_wf_structural.py
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
185
186
187
188
189
190
191
#!/usr/bin/env python
import argparse
import os
import time
import logging
import datetime
from justbackoff import Backoff
from bioblend import galaxy
from xunit_wrapper import xunit, xunit_suite, xunit_dump
logging.basicConfig(format='[%(asctime)s][%(lineno)d][%(module)s] %(message)s', level=logging.DEBUG)
logging.getLogger("requests").setLevel(logging.WARNING)
logging.getLogger("bioblend").setLevel(logging.WARNING)
NOW = datetime.datetime.now()
SCRIPT_DIR = os.path.dirname(os.path.realpath(__file__))
backoff = Backoff(min_ms=100, max_ms=1000 * 60 * 5, factor=2, jitter=False)
BUILD_ID = os.environ.get('BUILD_NUMBER', 'Manual')
def __main__():
parser = argparse.ArgumentParser(description="""Script to run all workflows mentioned in workflows_to_test.
It will import the shared workflows are create histories for each workflow run, prefixed with ``TEST_RUN_<date>:``
Make sure the yaml has file names identical to those in the data library.""")
parser.add_argument('-k', '--api-key', '--key', dest='key', metavar='your_api_key',
help='The account linked to this key needs to have admin right to upload by server path',
required=True)
parser.add_argument('-u', '--url', dest='url', metavar="http://galaxy_url:port",
help="Be sure to specify the port on which galaxy is running",
default="http://usegalaxy.org")
parser.add_argument('-x', '--xunit-output', dest="xunit_output", type=argparse.FileType('w'), default='report.xml',
help="""Location to store xunit report in""")
args = parser.parse_args()
gi = galaxy.GalaxyInstance(args.url, args.key)
wf = gi.workflows.get_workflows(workflow_id='7bfac6e726679b2c')[0]
# inputMap = gi.workflows.show_workflow('7bfac6e726679b2c')['inputs']
# import json
# print(json.dumps(, indent=2))
# print(wf)
# import sys; sys.exit()
org_names = ('CCS',)
test_suites = []
wf_invocations = []
for name in org_names:
hist = gi.histories.create_history(name='BuildID=%s WF=Structural Org=%s Source=Jenkins' % (BUILD_ID, name))
gi.histories.create_history_tag(hist['id'], 'Automated')
gi.histories.create_history_tag(hist['id'], 'Annotation')
gi.histories.create_history_tag(hist['id'], 'BICH464')
# Load the datasets into history
datasets, fetch_test_cases = retrieve_and_rename(gi, hist, name)
ts = xunit_suite('[%s] Fetching Data' % name, fetch_test_cases)
test_suites.append(ts)
# TODO: fix mapping to always work.
# Map our inputs for invocation
inputs = {
'0': {
'id': datasets['fasta']['id'],
'src': 'hda',
},
'1': {
'id': datasets['json']['id'],
'src': 'hda',
}
}
# Invoke Workflow
wf_test_cases, watchable_invocation = run_workflow(gi, wf, inputs, hist)
# Give galaxy time to process
time.sleep(10)
# Invoke Workflow test cases
ts = xunit_suite('[%s] Invoking workflow' % name, wf_test_cases)
test_suites.append(ts)
# Store the invocation info for watching later.
wf_invocations.append(watchable_invocation)
invoke_test_cases = []
for (wf_id, invoke_id) in wf_invocations:
with xunit('galaxy', 'workflow_watch.%s.%s' % (wf_id, invoke_id)) as tc_watch:
logging.info("Waiting on wf %s invocation %s", wf_id, invoke_id)
watch_workflow_invocation(gi, wf_id, invoke_id)
invoke_test_cases.append(tc_watch)
ts = xunit_suite('[%s] Workflow Completion' % name, invoke_test_cases)
args.xunit_output.write(xunit_dump(test_suites))
def run_workflow(gi, wf, inputs, hist):
test_cases = []
with xunit('galaxy', 'workflow_launch') as tc_invoke:
logging.info("Running wf %s in %s", wf['id'], hist['id'])
invocation = gi.workflows.invoke_workflow(
wf['id'],
inputs=inputs,
history_id=hist['id'],
)
test_cases.append(tc_invoke)
watchable_invocation = (wf['id'], invocation['id'])
return test_cases, watchable_invocation
def retrieve_and_rename(gi, hist, ORG_NAME):
logging.info("Retrieving and Renaming %s", ORG_NAME)
# Now we'll run this tool
with xunit('galaxy', 'launch_tool') as tc3:
logging.info("Running tool")
inputs = {
'org_source|source_select': 'direct',
'org_source|org_raw': ORG_NAME,
}
tool_run = gi.tools.run_tool(hist['id'], 'edu.tamu.cpt2.webapollo.export', inputs)
# Now to correct the names
datasets = {}
logging.info("Run complete, renaming outputs")
for dataset in tool_run['outputs']:
if dataset['data_type'] == 'galaxy.datatypes.text.Json':
name = '%s.json' % ORG_NAME
elif dataset['data_type'] == 'galaxy.datatypes.sequence.Fasta':
name = '%s.fasta' % ORG_NAME
elif dataset['data_type'] == 'galaxy.datatypes.interval.Gff3':
name = '%s.gff3' % ORG_NAME
else:
name = 'Unknown'
logging.debug("Renaming %s (%s, %s) to %s", dataset['id'], dataset['data_type'], dataset['file_ext'], name)
# Keep a copy by extension
datasets[dataset['file_ext']] = dataset
return datasets, [tc3]
def watch_job_invocation(gi, job_id):
latest_state = None
prev_state = None
while True:
# Fetch the current state
latest_state = gi.jobs.get_state(job_id)
# If the state changes
if latest_state != prev_state:
# Reset the backoff
backoff.reset()
prev_state = latest_state
# If it's scheduled, then let's look at steps. Otherwise steps probably don't exist yet.
logging.debug("Checking job %s state: %s", job_id, latest_state)
if latest_state == 'error':
raise Exception(latest_state)
elif latest_state == 'ok':
return
else:
time.sleep(backoff.duration())
raise Exception(latest_state)
def watch_workflow_invocation(gi, wf_id, invoke_id):
latest_state = None
prev_state = None
while True:
# Fetch the current state
latest_state = gi.workflows.show_invocation(wf_id, invoke_id)
# Get step states
states = [step['state'] for step in latest_state['steps']]
# Get a str based state representation
state_rep = '|'.join(map(str, states))
if state_rep != prev_state:
backoff.reset()
prev_state = state_rep
# If it's scheduled, then let's look at steps. Otherwise steps probably don't exist yet.
if latest_state['state'] == 'scheduled':
# If any state is in error,
logging.info("Checking workflow %s states: %s", wf_id, state_rep)
if any([state == 'error' for state in states]):
# We bail
raise Exception(latest_state)
# If all OK
if all([state is None or state == 'ok'
for state in states]):
return
# We can finish
time.sleep(backoff.duration())
raise Exception(latest_state)
if __name__ == "__main__":
__main__()