Add analysis file suggestion

api/dao/containerstorage.py

@@ -24,10 +24,9 @@ class ContainerStorage(object):
         self.dbc = config.db[cont_name]
 
     def get_container(self, _id, projection=None, get_children=False):
-        cont = self._get_el(_id, projection)
+        cont = self._get_el(_id, projection=projection)
 
         if get_children:
-            # TODO: This needs to exist in one place, not several
             child_map = {
                 'groups':   'projects',
                 'projects': 'sessions',
@@ -38,8 +37,10 @@ class ContainerStorage(object):
             if not child_name:
                 raise ValueError('Children can only be listed from group, project or session level')
             else:
-                query = {cont_name: _id}
-                ContainerStorage(child_name, True)._get_all_el(query, projection)
+                query = {self.cont_name[:-1]: bson.objectid.ObjectId(_id)}
+                cont[child_name] = ContainerStorage(child_name, True).exec_op('GET', query=query, projection=projection)
+
+        return cont
 
 
     def exec_op(self, action, _id=None, payload=None, query=None, user=None,
@@ -137,18 +138,3 @@ class GroupStorage(ContainerStorage):
                 '$setOnInsert': {'roles': roles}
             },
             upsert=True)
-
-def inflate_container(cr):
-    """
-    Given a container reference, inflate its hierarchy into a map.
-    Eeventually, this might want to deduplicate with logic in hierarchy.py.
-    """
-
-    if cr.type != 'session':
-        raise Exception('Only sessions are supported for inflation right now')
-
-    oid = bson.ObjectId(cr.id)
-    root = ContainerStorage('sessions', True).exec_op('GET', oid, projection={'permissions': 0})
-    root['acquisitions'] = ContainerStorage('acquisitions', True).exec_op('GET', query={'session': oid}, projection={'permissions': 0})
-
-    return root

api/dao/hierarchy.py

@@ -72,21 +72,6 @@ def get_container(cont_name, _id):
         '_id': _id,
     })
 
-def get_children(cont_name, _id, projection=None):
-    """
-    Given a container name and id, return all children of that object in the hierarchy
-    """
-    cid = bson.ObjectId(_id)
-    if cont_name == 'session':
-        return config.db.acquisitions.find({'session': cid}, projection)
-    elif cont_name == 'project':
-        return config.db.sessions.find({'project': cid}, projection)
-    elif cont_name == 'group':
-        # groups do not use ObjectIds
-        return config.db.projects.find({'group':_id}, projection)
-    else:
-        raise ValueError('Children can only be listed from group, project or session level')
-
 def propagate_changes(cont_name, _id, query, update):
     """
     Propagates changes down the heirarchy tree.

api/handlers/containerhandler.py

@@ -7,7 +7,7 @@ from .. import util
 from .. import config
 from .. import validators
 from ..auth import containerauth, always_ok
-from ..dao import APIStorageException, containerstorage, containerutil, noop, hierarchy
+from ..dao import APIStorageException, containerstorage, containerutil, noop
 from ..dao.liststorage import AnalysesStorage
 from ..types import Origin
 from ..jobs.queue import Queue
@@ -229,11 +229,11 @@ class ContainerHandler(base.RequestHandler):
         if cont_name != 'sessions':
             self.abort(400, 'Can only request jobs at the session level.')
 
-        c = self._get_container(cid)
-        permchecker = self._get_permchecker(c)
+        cont = self._get_container(cid, projection={'permissions': 0}, get_children=True)
+        permchecker = self._get_permchecker(cont)
         permchecker(noop)('GET', cid)
 
-        children = hierarchy.get_children('session', cid)
+        children = cont.get('acquisitions')
         id_array = [str(c['_id']) for c in children]
         cont_array = [containerutil.ContainerReference('acquisition', cid) for cid in id_array]
 
@@ -502,9 +502,9 @@ class ContainerHandler(base.RequestHandler):
             parent_container = None
         return parent_container, parent_id_property
 
-    def _get_container(self, _id):
+    def _get_container(self, _id, projection=None, get_children=False):
         try:
-            container = self.storage.get_container(_id)
+            container = self.storage.get_container(_id, projection=projection, get_children=get_children)
         except APIStorageException as e:
             self.abort(400, e.message)
         if container is not None:

api/jobs/gears.py

@@ -71,12 +71,21 @@ def suggest_container(gear, cont_name, cid):
         schemas[x] = Draft4Validator(schema)
 
     # It would be nice to have use a visitor here instead of manual key loops.
-    for acq in root['acquisitions']:
+    for acq in root.get('acquisitions', []):
         for f in acq.get('files', []):
             f['suggested'] = {}
             for x in schemas:
                 f['suggested'][x] = schemas[x].is_valid(f)
 
+    for analysis in root.get('analyses',{}):
+        files = analysis.get('files', [])
+        files[:] = [x for x in files if x.get('output')]
+        for f in files:
+            f['suggested'] = {}
+            for x in schemas:
+                f['suggested'][x] = schemas[x].is_valid(f)
+        analysis['files'] = files
+
     return root
 
 def insert_gear(doc):