Updated module generator to corerctly create download jobs.

chipathlon/generators/module_generator.py

@@ -80,9 +80,7 @@ class ModuleGenerator(object):
             job_info = job_dict[job_name]
             all_jobs.append(self.workflow_jobs[job_name])
             if job_info.get("outputs"):
-                for output_dict in job_info["outputs"]:
-                    logical_name = output_dict.keys()[0]
-                    output_info = output_dict[logical_name]
+                for logical_name, output_info in job_info["outputs"].iteritems():
                     # We have to explicitly compare since None evalutes to False.
                     if not output_info.get("final_result") == True:
                         result = Result(
@@ -128,16 +126,32 @@ class ModuleGenerator(object):
         Download the target result from gridfs.
         """
         db_result = result.get_db_result(self.mdb, run.genome)
-        inputs = [
-            {"name": "host", "type": "string", "value": self.mdb.host},
-            {"name": "username", "type": "string", "value": self.mdb.username},
-            {"name": "password", "type": "string", "value": self.mdb.password},
-            {"name": "id", "type": "string", "value": db_result["gridfs_id"]}
-        ]
-        outputs = [
-            {"name": result.full_name, "type": "file", "file": result.pegasus_file, "transfer": False}
-        ]
-        download_job = self.workflow_jobs["download_from_gridfs"].create_job(inputs, [], outputs)
+        inputs = {
+            "host": {
+                "name": "host",
+                "value": self.mdb.host
+            },
+            "username": {
+                "name": "username",
+                "value": self.mdb.username
+            },
+            "password": {
+                "name": "password",
+                "value": self.mdb.password
+            },
+            "id": {
+                "name": "id",
+                "value": db_result["gridfs_id"]
+            }
+        }
+        outputs = {
+            "downloaded_result": {
+                "name": result.full_name,
+                "file": result.pegasus_file,
+                "transfer": False
+            }
+        }
+        download_job = self.workflow_jobs["download_from_gridfs"].create_job(inputs, outputs)
         if download_job is not None:
             self.master_files[result.full_name] = result.pegasus_file
             self.dax.addJob(download_job)
@@ -153,14 +167,24 @@ class ModuleGenerator(object):
         """
         # Assuming we only call on a result file with 1 accession
         sample = result.control_samples[0] if len(result.control_samples) > 0 else result.signal_samples[0]
-        inputs = [
-            {"name": "url", "type": "string", "value": sample["hcc_url"] if "hcc_url" in sample else sample["url"]},
-            {"name": "md5", "type": "string", "value": sample["md5sum"]}
-        ]
-        outputs = [
-            {"name": result.full_name, "type": "file", "file": result.pegasus_file, "transfer": False}
-        ]
-        download_job = self.workflow_jobs["download_from_encode"].create_job(inputs, [], outputs)
+        inputs = {
+            "url": {
+                "name": "url",
+                "value": sample["hcc_url"] if "hcc_url" in sample else sample["url"]
+            },
+            "md5": {
+                "name": "md5",
+                "value": sample["md5sum"]
+            }
+        }
+        outputs = {
+            "downloaded_file": {
+                "name": result.full_name,
+                "file": result.pegasus_file,
+                "transfer": False
+            }
+        }
+        download_job = self.workflow_jobs["download_from_encode"].create_job(inputs, outputs)
         if download_job is not None:
             self.master_files[result.full_name] = result.pegasus_file
             self.dax.addJob(download_job)