Removed TODO's from source code.

Author: chetnieter

server/taskflows/hpccloud/taskflow/nwchem/__init__.py

@@ -88,18 +88,11 @@ def create_geometry_symlink(task, job, cluster, fileName):
 def create_json_output(task, job, cluster):
     job_dir = job_directory(cluster, job)
     cmds = ['cd %s' % job_dir]
-    # TODO: this may only work for SGE queue manager. Add a call to
-    #       AbstractQueueAdapter to get outfile name?
     outFile = '%s-%s.o%s' % (job['name'], os.path.basename(job_dir), job['queueJobId'])
-    # TODO: replace hard-coded path to the json conversion script
     nwchem_cmd = 'python /opt/NWChemOutputToJson/NWChemJsonConversion.py %s\n' % outFile
     cmds.append(nwchem_cmd)
 
-    # TODO: rename the json file since conversion script just adds .json to end
-    #       of current file name. So we end up with names like
-    #       nwchem_run-584863a80640fd46e5ec5d54.o2783.json
     with get_connection(task.taskflow.girder_token, cluster) as conn:
-    # TODO: _put_script is a 'private' function of the job module
         cmd = _put_script(conn, '\n'.join(cmds))
         conn.execute(cmd)
 
@@ -150,7 +143,6 @@ def create_job(task, upstream_result):
     task.taskflow.logger.info('Create NWChem job.')
     input_folder_id = upstream_result['input']['folder']['id']
 
-    # TODO: setup command to run with mpi
     body = {
         'name': 'nwchem_run',
         'commands': [
@@ -229,7 +221,6 @@ def monitor_nwchem_job(task, upstream_result):
     task.throws=(Retry,),
 
     job = upstream_result['job']
-    # TODO - We are currently reaching in and used a 'private' function
     _monitor_jobs(task, cluster, [job], girder_token=girder_token, monitor_interval=30)
 
     return upstream_result
@@ -241,7 +232,6 @@ def upload_output(task, upstream_result):
     cluster = upstream_result['cluster']
     job = upstream_result['job']
 
-    # TODO: does this need to be a separate workflow?
     create_json_output(task, job, cluster)
 
     client = create_girder_client(