Merge branch 'tool-name-in-live-results' into 'develop'

Replace uuid in live results with tool name (resolves #20).

Closes #20

See merge request psot!9

psot/nextflow.py

@@ -34,7 +34,7 @@ process ${id} {
 live_results_template = Template('''
 process generate_${id}_live_results {
 
-    publishDir "${output}/live", mode: 'copy', pattern: '*????????-????-????-????-????????????.json'
+    publishDir "${output}/live", mode: 'copy', pattern: '*.*.json'
 
     input:
     file result from ${id}_json_live
@@ -44,7 +44,7 @@ process generate_${id}_live_results {
 
     script:
     """
-    split_json_into_separate_files.py --json $$result --output . --uuid
+    split_json_into_separate_files.py --json $$result --output . --tool ${id}
     """
 }
 ''')

psot/scripts/split_json_into_separate_files.py

@@ -4,11 +4,10 @@ import json
 import argparse
 import os
 import os.path
-from uuid import uuid4
 
 parser = argparse.ArgumentParser(description='Split a json file with multiple documents into single files per document')
 parser.add_argument('--json', '-j', required=True, help='json documents')
-parser.add_argument('--uuid', '-u', action='store_true', help='Include a uuid in the filename.')
+parser.add_argument('--tool', '-t', help='The name of the tool with which the results were generated')
 parser.add_argument('--output', '-o', required=True, help='The name of the output directory')
 args = parser.parse_args()
 
@@ -24,8 +23,8 @@ file = args.json
 with open(file) as f:
     doc = json.load(f)
     for k in doc:
-        if args.uuid:
-            output_filename = k + "_" + str(uuid4()) + '.json'
+        if args.tool:
+            output_filename = k + "." + args.tool + '.json'
         else:
             output_filename = k + '.json'
         with open(output_dir + '/' + output_filename, 'w') as o: