Raise exception when profile is not found; Add error propagation to nextflow call

psot/default_repo/scripts/run_identity.py

 #!/usr/bin/env python3
 
 import argparse
-from os import system
 
 parser = argparse.ArgumentParser(description='Script that returns the fasta as it is inserted. Can be used for modules that have no actual analysis.')
 parser.add_argument('--fasta', '-f', required=True, help='A fasta file with aminoacid sequences')
 parser.add_argument('--output', '-o', required=True, help='The result directory. Will contain info.json and results.tsv.')
 args = parser.parse_args()
 
-print('cp ' + args.fasta + " " + args.output)
+print('cp -p ' + args.fasta + " " + args.output)

psot/main.py

@@ -55,8 +55,9 @@ def analyze(args, config):
     if args.debug:
         print(json.dumps(execution, indent=2))
     setup_execution_directory(execution)
-    execute_analysis(execution)
+    error_code = execute_analysis(execution)
     cleanup(execution)
+    exit(error_code)
 
 def cleanup(execution):
     if not execution['debug']:
@@ -88,7 +89,10 @@ def generate_execution(config, args):
     
 def generate_execution_modules_for_profile(config, profile):
     # find profile by name
-    p = [x for x in config['profiles'] if x['name'] == profile][0]
+    profiles = [x for x in config['profiles'] if x['name'] == profile]
+    if len(profiles) < 1:
+        raise Exception("Profile not found " + profile)
+    p = profiles[0]
     modules = copy.deepcopy(p['modules'])
     # generate unique ids for each module
     for module in modules:

psot/nextflow.py

@@ -4,6 +4,8 @@ import os
 import subprocess
 from copy import deepcopy
 import collections
+import sys
+
 
 # taken from https://stackoverflow.com/questions/6027558/flatten-nested-python-dictionaries-compressing-keys
 def flatten(d, parent_key='', sep='_'):
@@ -270,8 +272,14 @@ def setup_execution_directory(execution):
 def execute_analysis(execution):
     old_cwd = os.getcwd()
     os.chdir(execution['directory'])
-    os.system('nextflow run ' + execution['directory'] + '/main.nf --fasta ' + execution['fasta'] + ' --output ' + execution['output'])
+    command = 'nextflow run ' + execution['directory'] + '/main.nf --fasta ' + execution['fasta'] + ' --output ' + execution['output']
+    retcode = 1
+    try:
+      retcode = subprocess.call(command, shell= True)
+    except OSError as e:
+      print("Execution failed: ", e, file=sys.stderr)
     os.chdir(old_cwd)
+    return retcode
 
 def generate_nextflow_script(execution):
     modules = execution['modules']