added resolve_dbxrefs.py to nextflow.py (not working yet)

psot/nextflow.py

@@ -74,6 +74,21 @@ process convert_${id}_to_json {
     """
 }
 ''')
+fetch_template = Template('''
+process fetch_dbxrefs {
+
+    input:
+    file result from ${id}_fetch_json
+
+    output:
+    file "$${result}_fetched.json" into ${id}_json
+
+    script:
+    """
+    resolve_dbxrefs.py --input $$result --retreiver ../dbxref/scripts --output $${result}_fetched.json
+    """
+}
+''')
 input_template = Template('''    file ${id}_result from ${id}_json''')
 join_jsons_template = Template('''
 process join_documents {
@@ -153,8 +168,9 @@ Channel.fromPath(params.fasta).set{fasta}''')
     for m in modules:
         json_inputs.append(input_template.substitute(m))
 
+#    fragments.append(fetch_template.substitute(flatten(m)))
     fragments.append(join_jsons_template.substitute({'inputs': '\n'.join(json_inputs)}))
     fragments.append(split_jsons_template.substitute(execution))
-        
+
     nextflow_script = '\n'.join(fragments)
     return nextflow_script

scripts/resolve_dbxrefs.py

@@ -7,6 +7,7 @@ import sys
 parser = argparse.ArgumentParser(description='Resolve dbxrefs from json file')
 parser.add_argument('--input', '-i', required=True, help='The json input document')
 parser.add_argument('--retriever', '-s', required=True, help='Location of retriever')
+parser.add_argument('--output', '-o', required=True, help='The json output document')
 args = parser.parse_args()
 
 basename = args.retriever.replace('scripts/', '')
@@ -30,6 +31,7 @@ for c in j['computations']:
         if 'target'in r and 'dbxref' in r['target']:
             r['target']['dbxref'] = {'dbxref': r['target']['dbxref'], 'informations': next(entry for entry in entries if entry['id'] == r['target']['dbxref'])}
 
-with open(args.input, 'w') as o:
+#with open(args.input, 'w') as o:
+with open(args.output, 'w') as o:
     json.dump(j, o)