fix bootstrap job creation to match api

bootstrap.py

@@ -95,31 +95,63 @@ example:
 ./scripts/bootstrap.py dbinit mongodb://cnifs.stanford.edu/nims?replicaSet=cni -j nims_users_and_groups.json
 """
 
-
+# TODO: this should use util.create_job to eliminate duplicate code
 def jobsinit(args):
     """Create a job entry for every acquisition's orig dataset."""
     db_client = connect_db(args.db_uri)
     db = db_client.get_default_database()
 
     if args.force:
-        db_client.drop_database(db)
+        db.drop_collection('jobs')
 
     counter = db.jobs.count() + 1   # where to start creating jobs
 
+    dbc = db.jobs
+
     for a in db.acquisitions.find({'files.state': ['orig']}, {'files.$': 1, 'session': 1, 'series': 1, 'acquisition': 1}):
         if a.get('files')[0].get('kinds')[0] == 'screenshot':
             print 'no default app set for screenshots. skipping...'
             continue
 
+        else:
+            app_id = 'scitran/dcm2nii:latest'
+            app_outputs = [
+                {
+                    'fext': '.nii.gz',
+                    'state': ['derived', ],
+                    'type': 'nifti',
+                    'kinds': a.get('files')[0].get('kinds'),  # there should be someway to indicate 'from parent file'
+                },
+                {
+                    'fext': '.bvec',
+                    'state': ['derived', ],
+                    'type': 'text',
+                    'kinds': ['bvec', ],
+                },
+                {
+                    'fext': '.bval',
+                    'state': ['derived', ],
+                    'type': 'text',
+                    'kinds': ['bval', ],
+                },
+            ]
+
         aid = a.get('_id')
         session = db.sessions.find_one({'_id': bson.ObjectId(a.get('session'))})
         project = db.projects.find_one({'_id': bson.ObjectId(session.get('project'))})
+        output_url = '%s/%s/%s' % ('acquisitions', aid, 'file')
         db.jobs.insert({
             '_id': counter,
             'group': project.get('group_id'),
-            'project': project.get('_id'),
+            'project': {
+                '_id': project.get('_id'),
+                'name': project.get('name'),
+            },
             'exam': session.get('exam'),
-            'app_id': 'scitran/dcm2nii:latest',
+            'app': {
+                '_id': 'scitran/dcm2nii:latest',
+                'type': 'docker',
+            },
             'inputs': [
                 {
                     'url': '%s/%s/%s' % ('acquisitions', aid, 'file'),
@@ -130,16 +162,7 @@ def jobsinit(args):
                     },
                 }
             ],
-            'outputs': [
-                {
-                    'url': '%s/%s/%s' % ('acquisitions', aid, 'file'),
-                    'payload': {
-                        'type': 'nifti',
-                        'state': ['derived', ],
-                        'kinds': a['files'][0]['kinds'],
-                    },
-                },
-            ],
+            'outputs': [{'url': output_url, 'payload': i} for i in app_outputs],
             'status': 'pending',     # queued
             'activity': None,
             'added': datetime.datetime.now(),