Merge pull request #598 from scitran/jobs-endpoint

Update session jobs endpoint

api/dao/containerstorage.py

@@ -63,6 +63,8 @@ class ContainerStorage(object):
         except KeyError:
             raise APINotFoundException('Children cannot be listed from the {0} level'.format(self.cont_name))
         query = {self.cont_name[:-1]: bson.objectid.ObjectId(_id)}
+        if not projection:
+            projection = {'metadata': 0, 'files.metadata': 0, 'subject': 0}
         return self.factory(child_name, use_object_id=True).get_all_el(query, None, projection)
 
     def _from_mongo(self, cont):

api/handlers/containerhandler.py

@@ -176,36 +176,51 @@ class ContainerHandler(base.RequestHandler):
         # Only enabled for sessions container type per url rule in api.py
         self.config = self.container_handler_configurations["sessions"]
         self.storage = self.config['storage']
-        cont = self._get_container(cid, projection={'permissions': 0}, get_children=True)
+        cont = self._get_container(cid, projection={'permissions': 0, 'files': 0, 'metadata': 0}, get_children=True)
 
         permchecker = self._get_permchecker(cont)
         permchecker(noop)('GET', cid)
 
-        children = cont.get('acquisitions')
-        if not children:
-            return {}
-
-        id_array = [str(c['_id']) for c in children]
-        cont_array = [containerutil.ContainerReference('acquisition', cid) for cid in id_array]
-
-        states = self.request.GET.getall('states')
-        tags   = self.request.GET.getall('tags')
-        jobs = Queue.search(cont_array, states=states, tags=tags)
-
-        response = {}
-        for j in jobs:
-            job  = Job.load(j)
-            acqs = [] # acquisitions referenced by the current job inputs
-            for _,v in job.inputs.iteritems():
-                # Add job to the list of jobs for an acquisition if:
-                #  - the input refers to an acquisition on this session
-                #  - the job has not already been added to that acquisition's job array
-                if v.type == 'acquisition' and v.id in id_array and v.id not in acqs:
-                    if response.get(v.id) is not None:
-                        response[v.id].append(job)
-                    else:
-                        response[v.id] = [job]
-                    acqs.append(v.id)
+        analyses = cont.get('analyses', [])
+        acquisitions = cont.get('acquisitions', [])
+
+        results = []
+        if not acquisitions and not analyses:
+            # no jobs
+            return {'jobs': results}
+
+        # Get query params
+        states      = self.request.GET.getall('states')
+        tags        = self.request.GET.getall('tags')
+        join_cont   = 'containers' in self.request.params.getall('join')
+
+        # search for jobs
+        if acquisitions:
+            id_array = [str(c['_id']) for c in acquisitions]
+            cont_array = [containerutil.ContainerReference('acquisition', cid) for cid in id_array]
+            results += Queue.search(cont_array, states=states, tags=tags)
+
+        if analyses:
+            id_array = [str(c['_id']) for c in analyses]
+            cont_array = [containerutil.ContainerReference('analysis', cid) for cid in id_array]
+            results += Queue.search(cont_array, states=states, tags=tags)
+
+        # Ensure job uniqueness
+        seen_jobs = []
+        jobs = []
+        for j in results:
+            if j['_id'] not in seen_jobs:
+                job  = Job.load(j)
+                jobs.append(job)
+                seen_jobs.append(job.id_)
+
+        jobs.sort(key=lambda j: j.created)
+
+        response = {'jobs': jobs}
+        if join_cont:
+            # create a map of analyses and acquisitions by _id
+            containers = dict((str(c['_id']), c) for c in analyses+acquisitions)
+            response['containers'] = containers
 
         return response
 

raml/examples/output/session-jobs.json

 {
-    "57ebe5adf0a2c90027d2bd44": [
-        {
-            "inputs": {
-                "dicom": {
-                    "type": "acquisition",
-                    "id": "57ebe5adf0a2c90027d2bd44",
-                    "name": "1_1_dicom.zip"
-                }
-            },
-            "attempt": 1,
-            "name": "dcm_convert",
-            "tags": [
-                "dcm_convert",
-                "spectroscopy"
-            ],
-            "destination": {
-                "type": "acquisition",
-                "id": "57ebe5adf0a2c90027d2bd44"
-            },
-            "request": {
-                "inputs": [
-                    {
-                        "type": "scitran",
-                        "uri": "/jobs/57ebe5adf0a2c90027d2bd48/config.json",
-                        "location": "/flywheel/v0"
-                    },
-                    {
-                        "type": "scitran",
-                        "uri": "/acquisitions/57ebe5adf0a2c90027d2bd44/files/1_1_dicom.zip",
-                        "location": "/flywheel/v0/input/dicom"
-                    }
-                ],
-                "target": {
-                    "command": [
-                        "bash",
-                        "-c",
-                        "rm -rf output; mkdir -p output; ./run; echo \"Exit was $?\""
-                    ],
-                    "env": {
-                        "PATH": "/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin"
-                    },
-                    "dir": "/flywheel/v0"
-                },
-                "outputs": [
-                    {
-                        "type": "scitran",
-                        "uri": "/engine?level=acquisition&id=57ebe5adf0a2c90027d2bd44&job=57ebe5adf0a2c90027d2bd48",
-                        "location": "/flywheel/v0/output"
-                    }
-                ]
-            },
-            "modified": "2016-09-28T15:45:52.607000+00:00",
-            "created": "2016-09-28T15:45:49.975000+00:00",
-            "state": "running",
-            "config": {},
-            "id": "57ebe5adf0a2c90027d2bd48"
+  "jobs": [
+    {
+      "origin": {
+        "type": "system",
+        "id": null
+      },
+      "inputs": {
+        "dcm2niix": {
+          "type": "acquisition",
+          "id": "582cbe5a5740eb00162cf3d2",
+          "name": "6879_1_2_localizer.dicom.zip"
         }
-    ]
+      },
+      "attempt": 1,
+      "name": "dcm2niix",
+      "tags": [
+        "dcm2niix"
+      ],
+      "destination": {
+        "type": "acquisition",
+        "id": "582cbe5a5740eb00162cf3d2"
+      },
+      "modified": "2016-11-16T20:15:22.742000+00:00",
+      "created": "2016-11-16T20:15:22.742000+00:00",
+      "saved_files": [],
+      "state": "pending",
+      "config": null,
+      "id": "582cbe5a5740eb00162cf3d3"
+    },
+    {
+      "origin": {
+        "type": "system",
+        "id": null
+      },
+      "inputs": {
+        "dicom": {
+          "type": "acquisition",
+          "id": "582cbe5a5740eb00162cf3d2",
+          "name": "6879_1_2_localizer.dicom.zip"
+        }
+      },
+      "attempt": 1,
+      "name": "dicom-mr-classifier",
+      "tags": [
+        "dicom-mr-classifier"
+      ],
+      "destination": {
+        "type": "acquisition",
+        "id": "582cbe5a5740eb00162cf3d2"
+      },
+      "modified": "2016-11-16T20:15:22.756000+00:00",
+      "created": "2016-11-16T20:15:22.756000+00:00",
+      "saved_files": [],
+      "state": "pending",
+      "config": null,
+      "id": "582cbe5a5740eb00162cf3d4"
+    },
+    {
+      "origin": {
+        "type": "system",
+        "id": null
+      },
+      "inputs": {
+        "dcm2niix": {
+          "type": "acquisition",
+          "id": "582cbe5d5740eb00132cf3d6",
+          "name": "6879_3_1_t1.dicom.zip"
+        }
+      },
+      "attempt": 1,
+      "name": "dcm2niix",
+      "tags": [
+        "dcm2niix"
+      ],
+      "destination": {
+        "type": "acquisition",
+        "id": "582cbe5d5740eb00132cf3d6"
+      },
+      "modified": "2016-11-16T20:15:25.899000+00:00",
+      "created": "2016-11-16T20:15:25.899000+00:00",
+      "saved_files": [],
+      "state": "pending",
+      "config": null,
+      "id": "582cbe5d5740eb00132cf3d7"
+    }
+  ],
+  "containers": {
+    "582cbe5a5740eb00162cf3d2": {
+      "created": "2016-11-16T20:15:22.629000+00:00",
+      "modified": "2016-11-16T20:15:22.629000+00:00",
+      "label": "6879_1_2_localizer",
+      "session": "582cbe5a5740eb00162cf3d1",
+      "_id": "582cbe5a5740eb00162cf3d2",
+      "public": false
+    },
+    "582cbe5d5740eb00132cf3d6": {
+      "created": "2016-11-16T20:15:25.858000+00:00",
+      "modified": "2016-11-16T20:15:25.858000+00:00",
+      "label": "6879_3_1_t1",
+      "session": "582cbe5a5740eb00162cf3d1",
+      "_id": "582cbe5d5740eb00132cf3d6",
+      "public": false
+    }
+  }
 }

raml/schemas/output/session-jobs.json

 {
   "$schema": "http://json-schema.org/draft-04/schema#",
   "type": "object",
-  "patternProperties": {
-    "^[a-fA-F0-9]{24}$":{
+  "properties":{
+    "jobs":{
       "type":"array",
       "items":{
         "type":"object",
@@ -27,6 +27,13 @@
            "destination", "tags", "state", "attempt"
         ]
       }
+    },
+    "containers":{
+       "patternProperties": {
+        "^[a-fA-F0-9]{24}$":{
+          "type": "object"
+        }
+      }
     }
   },
   "additionalProperties":false