Add RAML for ContainerHandler based routes

.gitignore

@@ -8,3 +8,4 @@ bootstrap.json
 .cache
 /.coverage*
 coverage.xml
+node_modules/

api/api.py

@@ -145,7 +145,7 @@ routes = [
     webapp2.Route(_format(r'/api/<cont_name:{cont_name_re}>'),                          containerhandler.ContainerHandler, name='cont_list', handler_method='get_all', methods=['GET']),
     webapp2.Route(_format(r'/api/<cont_name:{cont_name_re}>'),                          containerhandler.ContainerHandler, methods=['POST']),
     webapp2.Route(_format(r'/api/<cont_name:{cont_name_re}>/<cid:{cid_re}>'),           containerhandler.ContainerHandler, name='cont_details', methods=['GET','PUT','DELETE']),
-    webapp2.Route(_format(r'/api/<cont_name:{cont_name_re}>/<cid:{cid_re}>/jobs'),           containerhandler.ContainerHandler, name='cont_jobs', handler_method='get_jobs', methods=['GET']),
+    webapp2.Route(_format(r'/api/sessions/<cid:{cid_re}>/jobs'),           containerhandler.ContainerHandler, name='cont_jobs', handler_method='get_jobs', methods=['GET']),
 
     webapp2.Route(_format(r'/api/<cont_name:groups>/<cid:{group_id_re}>/<list_name:roles>'),                                        listhandler.ListHandler, name='group_roles_post', methods=['POST']),
     webapp2.Route(_format(r'/api/<cont_name:groups>/<cid:{group_id_re}>/<list_name:roles>/<site:{site_id_re}>/<_id:{user_id_re}>'),    listhandler.ListHandler, name='group_roles', methods=['GET', 'PUT', 'DELETE']),

api/config.py

@@ -118,8 +118,11 @@ expected_mongo_schemas = set([
 ])
 expected_input_schemas = set([
     'acquisition.json',
+    'acquisition-update.json',
     'analysis.json',
+    'avatars.json',
     'collection.json',
+    'collection-update.json',
     'container.json',
     'file.json',
     'group-new.json',
@@ -129,11 +132,12 @@ expected_input_schemas = set([
     'permission.json',
     'project.json',
     'project-template.json',
+    'project-update.json',
     'session.json',
+    'session-update.json',
     'subject.json',
     'user-new.json',
     'user-update.json',
-    'avatars.json',
     'download.json',
     'tag.json',
     'enginemetadata.json',

api/handlers/collectionshandler.py

@@ -118,8 +118,15 @@ class CollectionsHandler(ContainerHandler):
         return results
 
     def curators(self):
-        curator_ids = list(set((c['curator'] for c in self.get_all('collections'))))
-        return list(config.db.users.find({'_id': {'$in': curator_ids}}, ['firstname', 'lastname']))
+        curator_ids = []
+        for collection in self.get_all():
+            if collection['curator'] not in curator_ids:
+                curator_ids.append(collection['curator'])
+        curators = config.db.users.find(
+            {'_id': {'$in': curator_ids}},
+            ['firstname', 'lastname']
+            )
+        return list(curators)
 
     def get_sessions(self, cid):
         """Return the list of sessions in a collection."""

api/handlers/containerhandler.py

@@ -172,62 +172,10 @@ class ContainerHandler(base.RequestHandler):
         if user_perm.get('access') != 'admin':
             result['permissions'] = [user_perm] if user_perm else []
 
-    def get_jobs(self, cont_name, cid):
-        """
-        .. http:get:: /api/(cont_name)/(cid)/jobs
-
-            Return any jobs that mention this container as an input.
-
-            :query states: filter results by job state
-            :type states: string
-
-            :query tags: filter results by job tags
-            :type cid: string
-
-            :statuscode 200: no error
-
-            **Example request**:
-
-            .. sourcecode:: http
-
-                GET /api/sessions/3/jobs?states=pending&states=failed&tags=a&tags=b HTTP/1.1
-                Host: demo.flywheel.io
-                Accept: */*
-
-
-            **Example response**:
-
-            .. sourcecode:: http
-
-                HTTP/1.1 200 OK
-                Vary: Accept-Encoding
-                Content-Type: application/json; charset=utf-8
-                [
-                    {
-                        "_id": "57336257ea360500272c2f11",
-                        "algorithm_id": "dicom_mr_classifier",
-                        "state": "pending",
-                        "tags": [
-                            "a"
-                        ]
-                        //...
-                    },
-                    {
-                        "_id": "57336257ea360500272c2f12",
-                        "algorithm_id": "dcm_convert",
-                        "state": "failed",
-                        "tags": [
-                            "b"
-                        ]
-                       // ...
-                    }
-                ]
-        """
-        self.config = self.container_handler_configurations[cont_name]
+    def get_jobs(self, cid):
+        # Only enabled for sessions container type per url rule in api.py
+        self.config = self.container_handler_configurations["sessions"]
         self.storage = self.config['storage']
-        if cont_name != 'sessions':
-            self.abort(400, 'Can only request jobs at the session level.')
-
         cont = self._get_container(cid, projection={'permissions': 0}, get_children=True)
 
         permchecker = self._get_permchecker(cont)

bin/install-dev-osx.sh

@@ -87,4 +87,4 @@ fi
 # Install testing dependencies
 echo "Installing testing dependencies"
 pip install -r "test/integration_tests/requirements-integration-test.txt"
-npm install -g test/integration_tests
+npm install test/integration_tests

raml/api.raml

@@ -11,6 +11,10 @@ traits:
                 description: |
                     JSON did not validate against schema for this endpoint
 
+resourceTypes:
+  - container: !include resourceTypes/container.raml
+  - container-item: !include resourceTypes/container-item.raml
+
 /download: !include resources/download.raml
 /upload/label: !include resources/upload-by-label.raml
 /upload/uid: !include resources/upload-by-uid.raml
@@ -26,4 +30,7 @@ traits:
 /gears: !include resources/gears.raml
 /rules: !include resources/rules.raml
 /groups: !include resources/groups.raml
+/collections: !include resources/collections.raml
+/sessions: !include resources/sessions.raml
+/acquisitions: !include resources/acquisitions.raml
 /projects: !include resources/projects.raml

raml/examples/input/acquisition-update.json

+{
+	"label": "example-acquisition-new-label"
+}

raml/examples/input/acquisition.json

+{
+	"label": "example-acquisition",
+	"session": "57e45328466d8e000e33a85b",
+	"public": false
+}

raml/examples/input/collection-update.json

+{
+	"contents": {
+		"operation": "add",
+		"nodes": [{
+			"level": "session",
+			"_id": "57dc50b0931cefd8ac2a371e"
+		}]
+	}
+}

raml/examples/input/collection.json

+{"label":"control-group"}

raml/examples/input/project-update.json

+{"label":"test2-project-new-label"}

raml/examples/input/project.json

+{"group":"scitran","label":"test2"}

raml/examples/input/session.json

+{
+  "subject": {
+    "code": "a subject"
+  },
+  "label": "a session",
+  "project": "57e29f8aa479a44d25f28c47",
+  "public": false
+}

raml/examples/output/acquisition-list.json

+[
+  {
+    "files": [
+      {
+        "origin": {
+          "method": "importer",
+          "type": "device",
+          "id": "importer_Admin_Import",
+          "name": "Admin Import"
+        },
+        "mimetype": "application/zip",
+        "measurements": [],
+        "hash": "v0-sha384-dd3c97bfe0ad1fcba75ae6718c6e81038c59af4f447f5db194d52732efa4f955b28455db02eb64cad3e4e55f11e3679f",
+        "name": "4784_1_1_localizer_dicom.zip",
+        "tags": [],
+        "created": "2016-09-21T14:56:09.943000+00:00",
+        "modified": "2016-09-21T14:56:09.943000+00:00",
+        "instrument": null,
+        "metadata": {},
+        "type": "dicom",
+        "size": 989933
+      }
+    ],
+    "created": "2016-09-21T14:56:10.026000+00:00",
+    "timestamp": "2016-09-21T19:24:45.539570+00:00",
+    "modified": "2016-09-21T14:56:10.026000+00:00",
+    "label": "4784_1_1_localizer",
+    "session": "57e29f8afab726000f7ec6b1",
+    "collections": [
+      "57e2a026675ca0000f0eeb0c"
+    ],
+    "_id": "57e29f8afab726000f7ec6b2",
+    "public": false,
+    "permissions": [
+      {
+        "access": "admin",
+        "_id": "coltonlw@flywheel.io",
+        "site": "local"
+      }
+    ]
+  },
+  {
+    "files": [
+      {
+        "origin": {
+          "method": "importer",
+          "type": "device",
+          "id": "importer_Admin_Import",
+          "name": "Admin Import"
+        },
+        "mimetype": "application/zip",
+        "measurements": [],
+        "hash": "v0-sha384-ca055fb36845db86e4278cf6e185f8674d11a96f4b29af27e401fc495cc82ef6b53a5729c3757713064649dc71c8c725",
+        "name": "4784_3_1_t1_dicom.zip",
+        "tags": [],
+        "created": "2016-09-21T14:56:11.224000+00:00",
+        "modified": "2016-09-21T14:56:11.224000+00:00",
+        "instrument": null,
+        "metadata": {},
+        "type": "dicom",
+        "size": 2921881
+      }
+    ],
+    "created": "2016-09-21T14:56:11.452000+00:00",
+    "timestamp": "2016-09-21T19:24:45.539580+00:00",
+    "modified": "2016-09-21T14:56:11.452000+00:00",
+    "label": "4784_3_1_t1",
+    "session": "57e29f8afab726000f7ec6b1",
+    "collections": [
+      "57e2a026675ca0000f0eeb0c"
+    ],
+    "_id": "57e29f8bfab726000e7ec6b0",
+    "public": false,
+    "permissions": [
+      {
+        "access": "admin",
+        "_id": "coltonlw@flywheel.io",
+        "site": "local"
+      }
+    ]
+  },
+  {
+    "files": [
+      {
+        "origin": {
+          "method": "importer",
+          "type": "device",
+          "id": "importer_Admin_Import",
+          "name": "Admin Import"
+        },
+        "mimetype": "application/zip",
+        "measurements": [],
+        "hash": "v0-sha384-537e42b1dd8f1feef9844fbfb4f60461361e71cafa7055556097e9d0b9f7fac68c8f234ed126af9412bd43a548948847",
+        "name": "4784_5_1_fmri_dicom.zip",
+        "tags": [],
+        "created": "2016-09-21T14:56:13.580000+00:00",
+        "modified": "2016-09-21T14:56:13.580000+00:00",
+        "instrument": null,
+        "metadata": {},
+        "type": "dicom",
+        "size": 4525137
+      }
+    ],
+    "created": "2016-09-21T14:56:13.886000+00:00",
+    "timestamp": "2016-09-21T19:24:45.539582+00:00",
+    "modified": "2016-09-21T14:56:13.886000+00:00",
+    "label": "4784_5_1_fmri",
+    "session": "57e29f8afab726000f7ec6b1",
+    "collections": [
+      "57e2a026675ca0000f0eeb0c"
+    ],
+    "_id": "57e29f8dfab726000e7ec6b3",
+    "public": false,
+    "permissions": [
+      {
+        "access": "admin",
+        "_id": "coltonlw@flywheel.io",
+        "site": "local"
+      }
+    ]
+  }
+]

raml/examples/output/acquisition.json

+{
+  "files": [
+    {
+      "origin": {
+        "method": "importer",
+        "type": "device",
+        "id": "importer_Admin_Import",
+        "name": "Admin Import"
+      },
+      "mimetype": "application/zip",
+      "measurements": [],
+      "hash": "v0-sha384-dd3c97bfe0ad1fcba75ae6718c6e81038c59af4f447f5db194d52732efa4f955b28455db02eb64cad3e4e55f11e3679f",
+      "name": "4784_1_1_localizer_dicom.zip",
+      "tags": [],
+      "created": "2016-09-21T14:56:09.943000+00:00",
+      "modified": "2016-09-21T14:56:09.943000+00:00",
+      "instrument": null,
+      "metadata": {},
+      "type": "dicom",
+      "size": 989933
+    }
+  ],
+  "created": "2016-09-21T14:56:10.026000+00:00",
+  "timestamp": "2016-09-21T19:24:45.539570+00:00",
+  "modified": "2016-09-21T14:56:10.026000+00:00",
+  "label": "4784_1_1_localizer",
+  "session": "57e29f8afab726000f7ec6b1",
+  "collections": [
+    "57e2a026675ca0000f0eeb0c"
+  ],
+  "_id": "57e29f8afab726000f7ec6b2",
+  "public": false,
+  "permissions": [
+    {
+      "access": "admin",
+      "_id": "coltonlw@flywheel.io",
+      "site": "local"
+    }
+  ]
+}

raml/examples/output/collection-curators-list.json

+[
+  {
+    "lastname": "LW",
+    "_id": "coltonlw@flywheel.io",
+    "firstname": "Colton"
+  }
+]

raml/examples/output/collection-new.json

+{
+    "_id":"57bb486a9e512c41c8b7fdd5"
+}

raml/examples/output/collection.json

+{
+	"created": "2016-08-30T17:22:05.299000+00:00",
+	"curator": "user@test.com",
+	"label": "test",
+	"modified": "2016-08-30T17:22:05.299000+00:00",
+	"_id": "57c5c0bd9e512c606dd3df09",
+	"permissions": [{
+		"access": "admin",
+		"_id": "user@test.com",
+		"site": "local"
+	}]
+}