Skip to content

Commit

Permalink
GoDocker runner:Indent fix
Browse files Browse the repository at this point in the history
  • Loading branch information
@varunshankar
varunshankar committed Jul 26, 2016
1 parent f68b17c commit d626c33
Showing 1 changed file with 20 additions and 20 deletions.
40 changes: 20 additions & 20 deletions lib/galaxy/jobs/runners/godocker.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -35,7 +35,7 @@ def http_post_request(self, query, data, header):
requests.packages.urllib3.disable_warnings()
verify_ssl = not self.noCert
try:
url = self.server+query
url = self.server + query
res = requests.post(url, data, headers=header, verify=verify_ssl)

except requests.exceptions.ConnectionError as e:
Expand All @@ -55,7 +55,7 @@ def http_get_request(self, query, header):
requests.packages.urllib3.disable_warnings()
verify_ssl = not self.noCert
try:
url = self.server+query
url = self.server + query
res = requests.get(url, headers=header, verify=verify_ssl)

except requests.exceptions.ConnectionError as e:
Expand All @@ -75,7 +75,7 @@ def http_delete_request(self, query, header):
requests.packages.urllib3.disable_warnings()
verify_ssl = not self.noCert
try:
url = self.server+query
url = self.server + query
res = requests.delete(url, headers=header, verify=verify_ssl)

except requests.exceptions.ConnectionError as e:
Expand All @@ -95,7 +95,7 @@ def http_put_request(self, query, data, header):
requests.packages.urllib3.disable_warnings()
verify_ssl = not self.noCert
try:
url = self.server+query
url = self.server + query
res = requests.put(url, data, headers=header, verify=verify_ssl)

except requests.exceptions.ConnectionError as e:
Expand Down Expand Up @@ -194,7 +194,7 @@ def check_watched_item(self, job_state):
'''
""" Get task from GoDocker """
job_status_god = self.get_task(job_state.job_id)
log.debug("Job ID: "+str(job_state.job_id)+" Job Status: "+str(job_status_god['status']['primary']))
log.debug("Job ID: " + str(job_state.job_id) + " Job Status: " + str(job_status_god['status']['primary']))

if job_status_god['status']['primary'] == "over":
job_state.running = False
Expand Down Expand Up @@ -281,16 +281,16 @@ def recover(self, job, job_wrapper):
# Helper functions

def create_log_file(self, job_state, job_status_god):
""" Create log files in galaxy, namely error_file, output_file, exit_code_file
""" Create log files in galaxy, namely error_file, output_file, exit_code_file
Return true, if all the file creations are successful
"""
path = None
for vol in job_status_god['container']['volumes']:
if vol['name'] == "go-docker":
path = str(vol['path'])
if path:
god_output_file = path+"/god.log"
god_error_file = path+"/god.err"
god_output_file = path + "/god.log"
god_error_file = path + "/god.err"
try:
# Read from GoDocker output_file and write it into galaxy output_file.
f = open(god_output_file, "r")
Expand All @@ -312,9 +312,9 @@ def create_log_file(self, job_state, job_status_god):
log_file.write(out_log)
log_file.close()
f.close()
log.debug("CREATE OUTPUT FILE: "+str(job_state.output_file))
log.debug("CREATE ERROR FILE: "+str(job_state.error_file))
log.debug("CREATE EXIT CODE FILE: "+str(job_state.exit_code_file))
log.debug("CREATE OUTPUT FILE: " + str(job_state.output_file))
log.debug("CREATE ERROR FILE: " + str(job_state.error_file))
log.debug("CREATE EXIT CODE FILE: " + str(job_state.exit_code_file))
except IOError as e:
log.error('Could not access task log file %s' % str(e))
log.debug("IO Error occurred when accessing the files!!")
Expand All @@ -328,7 +328,7 @@ def login(self, apikey, login, server, noCert=False):
Create Login model schema of GoDocker and call the http_post_request method.
"""
log.debug("LOGIN TASK TO BE EXECUTED \n")
log.debug("GODOCKER LOGIN: "+str(login))
log.debug("GODOCKER LOGIN: " + str(login))
data = json.dumps({'user': login, 'apikey': apikey})
# Create object of Godocker class
g_auth = Godocker(server, login, apikey, noCert)
Expand Down Expand Up @@ -395,11 +395,11 @@ def post_task(self, job_wrapper):
log.debug("Virtual environment is set!!!")
GALAXY_VENV_TEMPLATE = """GALAXY_VIRTUAL_ENV="%s"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi;"""
venv = GALAXY_VENV_TEMPLATE % job_wrapper.galaxy_virtual_env
command = "#!/bin/bash\n"+"cd "+job_wrapper.working_directory+"\n"+venv+"\n"+job_wrapper.runner_command_line
command = "#!/bin/bash\n" + "cd " + job_wrapper.working_directory + "\n" + venv + "\n" + job_wrapper.runner_command_line
else:
command = "#!/bin/bash\n"+"cd "+job_wrapper.working_directory+"\n"+job_wrapper.runner_command_line
command = "#!/bin/bash\n" + "cd " + job_wrapper.working_directory + "\n" + job_wrapper.runner_command_line
except:
command = "#!/bin/bash\n"+"cd "+job_wrapper.working_directory+"\n"+job_wrapper.runner_command_line
command = "#!/bin/bash\n" + "cd " + job_wrapper.working_directory + "\n" + job_wrapper.runner_command_line

# GoDocker Job model schema
job = {
Expand Down Expand Up @@ -442,7 +442,7 @@ def post_task(self, job_wrapper):
log.debug("\n JOB POST TASK TO BE EXECUTED \n")
result = self.auth.http_post_request(
"/api/1.0/task", json.dumps(job),
{'Authorization': 'Bearer '+self.auth.token, 'Content-type': 'application/json', 'Accept': 'application/json'}
{'Authorization': 'Bearer ' + self.auth.token, 'Content-type': 'application/json', 'Accept': 'application/json'}
)
log.debug("Response from godocker: " + str(result.json()['msg']) + " ID: " + str(result.json()['id']))
# Return job_id
Expand All @@ -454,7 +454,7 @@ def get_task(self, job_id):
"""
job = False
if self.auth.token:
result = self.auth.http_get_request("/api/1.0/task/"+str(job_id), {'Authorization': 'Bearer '+self.auth.token})
result = self.auth.http_get_request("/api/1.0/task/" + str(job_id), {'Authorization': 'Bearer ' + self.auth.token})
job = result.json()
# Return the job
return job
Expand All @@ -465,7 +465,7 @@ def task_suspend(self, job_id):
"""
job = False
if self.auth.token:
result = self.auth.http_get_request("/api/1.0/task/"+str(job_id)+"/suspend", {'Authorization': 'Bearer '+self.auth.token})
result = self.auth.http_get_request("/api/1.0/task/" + str(job_id) + "/suspend", {'Authorization': 'Bearer ' + self.auth.token})
job = result.json()
# Return the job
return job
Expand All @@ -476,7 +476,7 @@ def get_task_status(self, job_id):
"""
job = False
if self.auth.token:
result = self.auth.http_get_request("/api/1.0/task/"+str(job_id)+"/status", {'Authorization': 'Bearer '+self.auth.token})
result = self.auth.http_get_request("/api/1.0/task/" + str(job_id) + "/status", {'Authorization': 'Bearer ' + self.auth.token})
job = result.json()
# Return task status
return job
Expand All @@ -487,7 +487,7 @@ def delete_task(self, job_id):
"""
job = False
if self.auth.token:
result = self.auth.http_delete_request("/api/1.0/task/"+str(job_id), {'Authorization': 'Bearer '+self.auth.token})
result = self.auth.http_delete_request("/api/1.0/task/" + str(job_id), {'Authorization': 'Bearer ' + self.auth.token})
job = result.json()
# Return the job
return job
Expand Down

0 comments on commit d626c33

Please sign in to comment.