Reverted enqueue_job; added job.insert() where needed

api/dao/containerstorage.py

@@ -372,6 +372,7 @@ def create_job_and_analysis(self, cont_name, cid, analysis, job, origin, uid):
         try:
 
             job = Queue.enqueue_job(job, origin, perm_check_uid=uid)
+            job.insert()
         except Exception as e:
             # NOTE #775 remove unusable analysis - until jobs have a 'hold' state
             self.delete_el(analysis['_id'])

api/jobs/batch.py

@@ -126,108 +126,121 @@ def update(batch_id, payload):
     if result.modified_count != 1:
         raise Exception('Batch job not updated')
 
-def run(batch_job):
+def run_preconstructed_jobs(origin, preconstructed_jobs):
     """
-    Creates jobs from proposed inputs, returns jobs enqueued.
+    Enqueues jobs and returns list of created jobs
     """
+    jobs = []
 
-    proposal = batch_job.get('proposal')
-    if not proposal:
-        raise APIStorageException('The batch job is not formatted correctly.')
-    preconstructed_jobs = proposal.get('preconstructed_jobs')
-
-    # If Running a batch from already-constructed jobs
-    if preconstructed_jobs:
-        origin = batch_job.get('origin')
-        jobs = []
-        job_ids = []
+    for preconstructed_job in preconstructed_jobs:
+        job = Queue.enqueue_job(preconstructed_job, origin)
+        job.insert()
+        jobs.append(job)
 
-        for preconstructed_job in preconstructed_jobs:
-            job = Queue.enqueue_job(preconstructed_job, origin)
-            job_id = job.id_
-            jobs.append(job)
-            job_ids.append(job_id)
+    return jobs
 
-    # Otherwise create jobs from the containers and gear id provided in the proposal
-    else:
-        proposed_inputs = proposal.get('inputs', [])
-        proposed_destinations = proposal.get('destinations', [])
+def run_container_jobs(batch_job, proposal):
+    # Create jobs from the containers and gear id provided in the proposal
+    proposed_inputs = proposal.get('inputs', [])
+    proposed_destinations = proposal.get('destinations', [])
+
+    gear_id = batch_job['gear_id']
+    gear = gears.get_gear(gear_id)
+    gear_name = gear['gear']['name']
+
+    config_ = batch_job.get('config')
+    origin = batch_job.get('origin')
+    tags = proposal.get('tags', [])
+    tags.append('batch')
+
+    if gear.get('category') == 'analysis':
+        analysis_base = proposal.get('analysis', {})
+        if not analysis_base.get('label'):
+            time_now = datetime.datetime.utcnow()
+            analysis_base['label'] = {'label': '{} {}'.format(gear_name, time_now)}
+        an_storage = AnalysisStorage()
+        acq_storage = AcquisitionStorage()
+
+    jobs = []
+    job_ids = []
+
+    job_defaults = {
+        'config':   config_,
+        'gear_id':  gear_id,
+        'tags':     tags,
+        'batch':    str(batch_job.get('_id')),
+        'inputs':   {}
+    }
 
-        gear_id = batch_job['gear_id']
-        gear = gears.get_gear(gear_id)
-        gear_name = gear['gear']['name']
+    for inputs in proposed_inputs:
 
-        config_ = batch_job.get('config')
-        origin = batch_job.get('origin')
-        tags = proposal.get('tags', [])
-        tags.append('batch')
+        job_map = copy.deepcopy(job_defaults)
+        job_map['inputs'] = inputs
 
         if gear.get('category') == 'analysis':
-            analysis_base = proposal.get('analysis', {})
-            if not analysis_base.get('label'):
-                time_now = datetime.datetime.utcnow()
-                analysis_base['label'] = {'label': '{} {}'.format(gear_name, time_now)}
-            an_storage = AnalysisStorage()
-            acq_storage = AcquisitionStorage()
 
-        jobs = []
-        job_ids = []
+            analysis = copy.deepcopy(analysis_base)
 
-        job_defaults = {
-            'config':   config_,
-            'gear_id':  gear_id,
-            'tags':     tags,
-            'batch':    str(batch_job.get('_id')),
-            'inputs':   {}
-        }
+            # Create analysis
+            acquisition_id = inputs.values()[0].get('id')
+            session_id = acq_storage.get_container(acquisition_id, projection={'session':1}).get('session')
+            result = an_storage.create_job_and_analysis('sessions', session_id, analysis, job_map, origin, None)
+            job = result.get('job')
+            job_id = result.get('job_id')
 
-        for inputs in proposed_inputs:
-
-            job_map = copy.deepcopy(job_defaults)
-            job_map['inputs'] = inputs
+        else:
 
-            if gear.get('category') == 'analysis':
+            job = Queue.enqueue_job(job_map, origin)
+            job.insert()
+            job_id = job.id_
 
-                analysis = copy.deepcopy(analysis_base)
 
-                # Create analysis
-                acquisition_id = inputs.values()[0].get('id')
-                session_id = acq_storage.get_container(acquisition_id, projection={'session':1}).get('session')
-                result = an_storage.create_job_and_analysis('sessions', session_id, analysis, job_map, origin, None)
-                job = result.get('job')
-                job_id = result.get('job_id')
+        jobs.append(job)
+        job_ids.append(job_id)
 
-            else:
+    for dest in proposed_destinations:
 
-                job = Queue.enqueue_job(job_map, origin)
-                job_id = job.id_
+        job_map = copy.deepcopy(job_defaults)
+        job_map['destination'] = dest
 
+        if gear.get('category') == 'analysis':
 
-            jobs.append(job)
-            job_ids.append(job_id)
+            analysis = copy.deepcopy(analysis_base)
 
-        for dest in proposed_destinations:
+            # Create analysis
+            result = an_storage.create_job_and_analysis('sessions', bson.ObjectId(dest['id']), analysis, job_map, origin, None)
+            job = result.get('job')
+            job_id = result.get('job_id')
 
-            job_map = copy.deepcopy(job_defaults)
-            job_map['destination'] = dest
+        else:
 
-            if gear.get('category') == 'analysis':
+            job = Queue.enqueue_job(job_map, origin)
+            job.insert()
+            job_id = job.id_
 
-                analysis = copy.deepcopy(analysis_base)
 
-                # Create analysis
-                result = an_storage.create_job_and_analysis('sessions', bson.ObjectId(dest['id']), analysis, job_map, origin, None)
-                job = result.get('job')
-                job_id = result.get('job_id')
+        jobs.append(job)
+        job_ids.append(job_id)
 
-            else:
+    return jobs, job_ids
 
-                job = Queue.enqueue_job(job_map, origin)
-                job_id = job.id_
+def run(batch_job):
+    """
+    Creates jobs from proposed inputs, returns jobs enqueued.
+    """
 
+    proposal = batch_job.get('proposal')
+    if not proposal:
+        raise APIStorageException('The batch job is not formatted correctly.')
+    preconstructed_jobs = proposal.get('preconstructed_jobs')
 
-            jobs.append(job)
-            job_ids.append(job_id)
+    # If Running a batch from already-constructed jobs
+    if preconstructed_jobs:
+        origin = batch_job.get('origin')
+        jobs = run_preconstructed_jobs(origin, preconstructed_jobs)
+        jobs_ids = [job.id_ for job in jobs]
+    else:
+        jobs, job_ids = run_container_jobs(batch_job, proposal)
 
     update(batch_job['_id'], {'state': 'running', 'jobs': job_ids})
     return jobs

api/jobs/handlers.py

@@ -280,6 +280,7 @@ def add(self):
             uid = self.uid
 
         job = Queue.enqueue_job(payload,self.origin, perm_check_uid=uid)
+        job.insert()
 
         return { '_id': job.id_ }
 
@@ -713,7 +714,7 @@ def post_with_jobs(self):
 
         for job_number, job_ in enumerate(jobs_):
             try:
-                Queue.validate_job(job_, self.origin, create_job=False, perm_check_uid=uid)
+                Queue.enqueue_job(job_, self.origin, perm_check_uid=uid)
             except InputValidationException as e:
                 raise InputValidationException("Job {}: {}".format(job_number, str(e)))
 

api/jobs/queue.py

@@ -128,10 +128,11 @@ def retry(job, force=False):
 
         return new_id
 
+
     @staticmethod
-    def validate_job(job_map, origin, create_job=False, perm_check_uid=None):
+    def enqueue_job(job_map, origin, perm_check_uid=None):
         """
-        Using a payload for a proposed job, creates and returns(if create_job is True) (but does not insert)
+        Using a payload for a proposed job, creates and returns (but does not insert)
         a Job object. This preperation includes:
           - confirms gear exists
           - validates config against gear manifest
@@ -250,18 +251,8 @@ def validate_job(job_map, origin, create_job=False, perm_check_uid=None):
 
         if gear_name not in tags:
             tags.append(gear_name)
-        if create_job:
-            job = Job(str(gear['_id']), inputs, destination=destination, tags=tags, config_=config_, now=now_flag, attempt=attempt_n, previous_job_id=previous_job_id, origin=origin, batch=batch)
-            return job
-        return True
 
-    @staticmethod
-    def enqueue_job(job_map, origin, perm_check_uid=None):
-        """
-        Validates, Creates, Inserts, and Returns job
-        """
-        job = Queue.validate_job(job_map, origin, create_job=True, perm_check_uid=perm_check_uid)
-        job.insert()
+        job = Job(str(gear['_id']), inputs, destination=destination, tags=tags, config_=config_, now=now_flag, attempt=attempt_n, previous_job_id=previous_job_id, origin=origin, batch=batch)
         return job
 
     @staticmethod

api/jobs/rules.py

@@ -246,7 +246,8 @@ def create_jobs(db, container_before, container_after, container_type):
 
     for pj in potential_jobs:
         job_map = pj['job'].map()
-        Queue.enqueue_job(job_map, origin)
+        job = Queue.enqueue_job(job_map, origin)
+        job.insert()
 
         spawned_jobs.append(pj['rule']['alg'])