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Patch to use Python's tempfile library instead of 'temporary_file.temporary' #40

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Patch to use Python's tempfile library instead of 'temporary_file.temporary' #40

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15 changes: 10 additions & 5 deletions jupyterlab_slurm/slurm.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,7 @@
import asyncio
import html
import os
import tempfile

from notebook.base.handlers import IPythonHandler
from tornado.web import MissingArgumentError
Expand Down Expand Up @@ -61,10 +62,14 @@ class SbatchHandler(ShellExecutionHandler):
# Add `-H "Authorization: token <token>"` to the curl command for any POST request
async def post(self):
def string_to_file(string):
file_object = open('temporary_file.temporary', 'w')
# Helper function to convert script typed into field into a tempfile for job submission.
# Takes in the script contents of the field.
# Returns path to tempfile.
tempscript = tempfile.mkstemp()
file_object = open(tempscript[1], 'w')
file_object.write(string)
file_object.close()
return
return tempscript[1]

inputType = self.get_query_argument('inputType')
outputDir = self.get_query_argument('outputDir', default='')
Expand All @@ -81,13 +86,13 @@ def string_to_file(string):
stdout, stderr, returncode, errorMessage = ("", "Something went wrong. Check console for more details.", 1, str(e))
elif inputType == 'contents':
script_contents = self.get_body_argument('input')
string_to_file(script_contents)
tempscript = string_to_file(script_contents)
try:
stdout, stderr, returncode = await self.run_command(sbatch_command, stdin=open('temporary_file.temporary','rb'), cwd=outputDir)
stdout, stderr, returncode = await self.run_command(sbatch_command, stdin=open(tempscript,'rb'), cwd=outputDir)
errorMessage = ""
except Exception as e:
stdout, stderr, returncode, errorMessage = ("", "Something went wrong. Check console for more details.", 1, str(e))
os.remove('temporary_file.temporary')
os.remove(tempscript)
else:
raise Exception('The query argument inputType needs to be either \'path\' or \'contents\'.')
else:
Expand Down