Generate formula late

api/jobs.py

@@ -117,41 +117,16 @@ def queue_job(db, algorithm_id, container_type, container_id, filename, filehash
         'created':  now,
         'modified': now,
 
-         # We need all these keys to re-run this job if it fails.
-        'algorithm_id': algorithm_id,
-        'container_type': container_type,
-        'container_id': container_id,
-        'filename': filename,
-        'filehash': filehash,
-        'attempt': attempt_n,
-
-        'formula': {
-            'inputs': [
-                {
-                    'type': 'file',
-                    'uri': '/tmp/deja/flak/0/dcm_convert-0.1.1.tar',
-                    'location': '/',
-                },
-                {
-                    'type': 'scitran',
-                    'uri': '/' + container_type + '/' + container_id + '/file/' + filename,
-                    'location': '/input/' + filename,
-                }
-            ],
-            'transform': {
-                'command': ['bash', '-c', 'mkdir /output; /scripts/run /input/' + filename + ' /output/'],
-                'env': { },
-                'dir': "/",
-            },
+         # Everything required to generate a job formula.
+        'intent': {
+            'algorithm_id': algorithm_id,
+            'container_type': container_type,
+            'container_id': container_id,
+            'filename': filename,
+            'filehash': filehash,
+        },
 
-            'outputs': [
-                {
-                    'type': 'scitran',
-                    'uri': '/' + container_type + '/' + container_id + '/file/',
-                    'location': '/output',
-                },
-            ],
-        }
+        'attempt': attempt_n,
     }
 
     if previous_job_id is not None:
@@ -169,13 +144,59 @@ def retry_job(db, j):
     TODO: make max attempts configurable
     """
 
+    i = j['intent']
+
     if j['attempt'] < 3:
-        job_id = queue_job(db, j['algorithm_id'], j['container_type'], j['container_id'], j['filename'], j['filehash'], j['attempt']+1, j['_id'])
+        job_id = queue_job(db, i['algorithm_id'], i['container_type'], i['container_id'], i['filename'], i['filehash'], j['attempt']+1, j['_id'])
         log.info('respawned job %s as %s (attempt %d)' % (j['_id'], job_id, j['attempt']+1))
     else:
         log.info('permanently failed job %s (after %d attempts)' % (j['_id'], j['attempt']))
 
 
+def generate_formula(i):
+    """
+    Given an intent, generates a formula to execute a job.
+
+    Parameters
+    ----------
+    i: map
+        A job's intent that holds everything needed to generate a formula.
+    """
+
+    if i['algorithm_id'] not in ALGORITHMS:
+        raise Exception('Usupported algorithm ' + algorithm_id)
+
+    # Currently hard-coded for a single algorithm: dcm2nii
+    f = {
+        'inputs': [
+            {
+                'type': 'file',
+                'uri': '/tmp/deja/flak/0/dcm_convert-0.1.1.tar',
+                'location': '/',
+            },
+            {
+                'type': 'scitran',
+                'uri': '/' + i['container_type'] + '/' + i['container_id'] + '/file/' + i['filename'],
+                'location': '/input/' + i['filename'],
+            }
+        ],
+        'transform': {
+            'command': ['bash', '-c', 'mkdir /output; /scripts/run /input/' + i['filename'] + ' /output/'],
+            'env': { },
+            'dir': "/",
+        },
+
+        'outputs': [
+            {
+                'type': 'scitran',
+                'uri': '/' + i['container_type'] + '/' + i['container_id'] + '/file/',
+                'location': '/output',
+            },
+        ],
+    }
+
+    return f
+
 class Jobs(base.RequestHandler):
 
     """Provide /jobs API routes."""
@@ -214,8 +235,7 @@ class Jobs(base.RequestHandler):
         if not self.superuser_request:
             self.abort(401, 'Request requires superuser')
 
-        # REVIEW: is this atomic?
-        # REVIEW: semantics are not documented as to this mutation's behaviour when filter matches no docs.
+        # First, atomically mark document as running.
         result = self.app.db.jobs.find_one_and_update(
             {
                 'state': 'pending'
@@ -231,6 +251,20 @@ class Jobs(base.RequestHandler):
         if result == None:
             self.abort(400, 'No jobs to process')
 
+        # Second, update document to store formula request.
+        result = self.app.db.jobs.find_one_and_update(
+            {
+                '_id': result['_id']
+            },
+            { '$set': {
+                'request': generate_formula(result['intent'])}
+            },
+            return_document=pymongo.collection.ReturnDocument.AFTER
+        )
+
+        if result == None:
+            self.abort(500, 'Marked job as running but could not generate and save formula')
+
         return result
 
 class Job(base.RequestHandler):