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Unicorninputjson #243

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Unicorninputjson #243

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642751a
unicorninputjson before checking dependency
SooLee Sep 20, 2019
dba1ba1
added runjson/unicorninputjson option to cli log
SooLee Sep 20, 2019
bc6f335
minor fix
SooLee Sep 20, 2019
1c2ec59
typo
SooLee Sep 20, 2019
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11 changes: 8 additions & 3 deletions tibanna/__main__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -99,7 +99,11 @@ def args(self):
"your current default is %s)" % TIBANNA_DEFAULT_STEP_FUNCTION_NAME,
'default': TIBANNA_DEFAULT_STEP_FUNCTION_NAME},
{'flag': ["-p", "--postrunjson"],
'help': "print out postrun json instead", 'action': "store_true"}],
'help': "print out postrun json instead", 'action': "store_true"},
{'flag': ["-r", "--runjson"],
'help': "print out run json instead", 'action': "store_true"},
{'flag': ["-u", "--unicorn-input-json"],
'help': "print out unicorn input json instead", 'action': "store_true"}],
'add_user':
[{'flag': ["-u", "--user"],
'help': "user to add to a Tibanna usergroup"},
Expand Down Expand Up @@ -300,9 +304,10 @@ def list_sfns(numbers=False):
API().list_sfns(numbers=numbers)


def log(exec_arn=None, job_id=None, exec_name=None, sfn=TIBANNA_DEFAULT_STEP_FUNCTION_NAME, postrunjson=False):
def log(exec_arn=None, job_id=None, exec_name=None, sfn=TIBANNA_DEFAULT_STEP_FUNCTION_NAME,
postrunjson=False, runjson=False, unicorn_input_json=False):
"""print execution log or postrun json (-p) for a job"""
print(API().log(exec_arn, job_id, exec_name, sfn, postrunjson))
print(API().log(exec_arn, job_id, exec_name, sfn, postrunjson, runjson, unicorn_input_json))


def kill_all(sfn=TIBANNA_DEFAULT_STEP_FUNCTION_NAME):
Expand Down
5 changes: 4 additions & 1 deletion tibanna/core.py
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Original file line number Diff line number Diff line change
Expand Up @@ -350,11 +350,14 @@ def kill_all(self, sfn=None):
else:
break

def log(self, exec_arn=None, job_id=None, exec_name=None, sfn=None, postrunjson=False, runjson=False, quiet=False):
def log(self, exec_arn=None, job_id=None, exec_name=None, sfn=None, postrunjson=False,
runjson=False, unicorn_input_json=False, quiet=False):
if postrunjson:
suffix = '.postrun.json'
elif runjson:
suffix = '.run.json'
elif unicorn_input_json:
suffix = '.unicorn.input.json'
else:
suffix = '.log'
if not sfn:
Expand Down
7 changes: 4 additions & 3 deletions tibanna/ec2_utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -330,6 +330,7 @@ def input_dict(self):
return self.unicorn_input.as_dict()

def prelaunch(self, profile=None):
self.upload_run_json(self.input_dict, suffix='unicorn.input.json')
self.check_dependency(**self.args.dependency)
runjson = self.create_run_json_dict()
self.upload_run_json(runjson)
Expand Down Expand Up @@ -605,9 +606,9 @@ def create_run_json_dict(self):
del(pre['config']['key_name'])
return pre

def upload_run_json(self, runjson):
def upload_run_json(self, runjson, suffix = 'run.json'):
jsonbody = json.dumps(runjson, indent=4, sort_keys=True)
jsonkey = self.jobid + '.run.json'
jsonkey = self.jobid + '.' + suffix
# Keep log of the final json
logger.info("jsonbody=\n" + jsonbody)
# copy the json file to the s3 bucket
Expand All @@ -619,7 +620,7 @@ def upload_run_json(self, runjson):
try:
res = s3.put_object(Body=jsonbody.encode('utf-8'), Bucket=self.cfg.json_bucket, Key=jsonkey)
except Exception:
raise Exception("boto3 client error: Failed to upload run.json %s to s3: %s" % (jsonkey, str(res)))
raise Exception("boto3 client error: Failed to upload %s %s to s3: %s" % (suffix, jsonkey, str(res)))

def create_userdata(self, profile=None):
"""Create a userdata script to pass to the instance. The userdata script is run_workflow.$JOBID.sh.
Expand Down
6 changes: 4 additions & 2 deletions tibanna_4dn/__main__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -68,8 +68,10 @@ def list_sfns(numbers=False):
API().list_sfns(numbers=numbers)


def log(exec_arn=None, job_id=None, exec_name=None, sfn=TIBANNA_DEFAULT_STEP_FUNCTION_NAME, postrunjson=False):
API().log(exec_arn, job_id, exec_name, sfn, postrunjson)
def log(exec_arn=None, job_id=None, exec_name=None, sfn=TIBANNA_DEFAULT_STEP_FUNCTION_NAME,
postrunjson=False, runjson=False, unicorn_input_json=False):
"""print execution log or postrun json (-p) for a job"""
print(API().log(exec_arn, job_id, exec_name, sfn, postrunjson, runjson, unicorn_input_json))


def kill_all(sfn=TIBANNA_DEFAULT_STEP_FUNCTION_NAME):
Expand Down
6 changes: 4 additions & 2 deletions tibanna_cgap/__main__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -69,8 +69,10 @@ def list_sfns(numbers=False):
API().list_sfns(numbers=numbers)


def log(exec_arn=None, job_id=None, exec_name=None, sfn=TIBANNA_DEFAULT_STEP_FUNCTION_NAME, postrunjson=False):
API().log(exec_arn, job_id, exec_name, sfn, postrunjson)
def log(exec_arn=None, job_id=None, exec_name=None, sfn=TIBANNA_DEFAULT_STEP_FUNCTION_NAME,
postrunjson=False, runjson=False, unicorn_input_json=False):
"""print execution log or postrun json (-p) for a job"""
print(API().log(exec_arn, job_id, exec_name, sfn, postrunjson, runjson, unicorn_input_json))


def kill_all(sfn=TIBANNA_DEFAULT_STEP_FUNCTION_NAME):
Expand Down