🐎 Query efficiency (#242)

CHANGELOG.rst

@@ -8,6 +8,11 @@ Changes
 -------
 Unreleased
 ==========
+2019-12-05: v0.7.1
+^^^^^^^^^^^^^^^^^^
+* :racehorse: Resolve some query efficiency problems
+* :fire: :books: Remove some deprecated text and illustrations from README
+
 2019-11-25: v0.6.6
 ^^^^^^^^^^^^^^^^^^
 * :ambulance: Fix `POST response/applet/activity` route

README.rst

@@ -87,83 +87,6 @@ Data Structure
 **Girder for MindLogger** uses `reprolib <https://github.com/ReproNim/schema-standardization>`_ and has the following underlying data structure:
 *Note: This project is still in version 0 and these descriptions and diagrams may sometimes diverge from the actual data structure as we develop.*
 
-Diagram
-#######
-|ERD|
-    The above `entity-relationship diagram <https://cacoo.com/blog/er-diagrams-vs-eer-diagrams-whats-the-difference/>`_ was created with `dia 0.97+git <https://live.gnome.org/Dia>`_.
-
-Glossary
-########
-
-Activity
-^^^^^^^^
-An "individual assessment", as defined in `reprolib <https://github.com/ReproNim/schema-standardization/tree/0fb4abd67d209e76325e6f42d428d7c275252ec6#20-need-for-standardizing-assessments>`_:`Activity <https://raw.githubusercontent.com/ReproNim/schema-standardization/master/schemas/Activity>`_.
-
-Activity Set
-^^^^^^^^^^^^
-A "collection[…] of `activities <#activity>`_ as defined in `reprolib <https://github.com/ReproNim/schema-standardization/tree/0fb4abd67d209e76325e6f42d428d7c275252ec6#20-need-for-standardizing-assessments>`_:`ActivitySet <https://raw.githubusercontent.com/ReproNim/schema-standardization/master/schemas/ActivitySet>`_.
-
-Applet
-^^^^^^
-A document assigning one or more `activity sets <#activity-set>`_ to one or more `users <#user>`_ with or without scheduling and other constraints.
-
-Applet-specific User ID
-^^^^^^^^^^^^^^^^^^^^^^^
-An identifier for a given `user <#user>`_ (or `reviewer <#reviewer>`_ or `subject <#subject>`_) for an `applet <#applet>`_ that does not expose that user's other data to anyone authorized to view information related to that applet.
-
-Context
-^^^^^^^
-    A set of rules for interpreting a JSON-LD document [from this database] as specified in The Context of the JSON-LD Syntax specification."
-
-This definition comes from `JSON-LD 1.1 <https://json-ld.org/spec/latest/json-ld/>`_ `context <https://json-ld.org/spec/latest/json-ld/#dfn-contexts>`_.
-
-Coordinator
-^^^^^^^^^^^
-
-Icon
-^^^^
-
-Illustration
-^^^^^^^^^^^^
-
-Manager
-^^^^^^^
-An individual responsible for setting schedules, `subjects <#subject>`_ and other constraints as well as inviting other managers, `users <#user>`_ and `reviewers <#reviewer>`_ to an `applet <#applet>`_.
-
-Protected health information
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-    Any information about health status, provision of health care, or payment for health care that […] can be linked to a specific `individual <#user>`_.
-
-This definition comes from the Wikipedia article `Protected health information <https://en.wikipedia.org/wiki/Protected_health_information>`_.
-
-Response
-^^^^^^^^
-Data collected when a `user <#user>`_ responds to an `activity <#activity>`_.
-
-Reviewer
-^^^^^^^^
-An individual authorized to review `user <#user>`_ `responses <#response>`_ to `activities <#activity>`_ in an `applet <#applet>`_.
-
-Screen
-^^^^^^
-One or more "elements of individual assessments" displayed in a single screen or page view, as defined in `reprolib <https://github.com/ReproNim/schema-standardization/tree/0fb4abd67d209e76325e6f42d428d7c275252ec6#20-need-for-standardizing-assessments>`_:`Item <https://raw.githubusercontent.com/ReproNim/schema-standardization/master/schemas/Field>`_ and `Issue #85 <https://github.com/ReproNim/schema-standardization/issues/85>`_.
-
-Skin
-^^^^
-Color scheme and other branding and appearance-related metadata.
-
-Subject
-^^^^^^^
-The person being informed about by the `user <#user>`_ `responding <#response>`_ to an `activity <#activity>`_. For self-report, the same user as the informant.
-
-Text
-^^^^
-Copy included in the mobile and web app, including "About MindLogger" and helper text.
-
-User
-^^^^
-An individual using a MindLogger mobile application or MindLogger web application to `respond <#response>`_ to `activities <#activity>`_.
-
 Links
 -----
 - `reprolib specification <https://github.com/ReproNim/schema-standardization>`_
@@ -187,10 +110,6 @@ For questions, comments, or to get in touch with the maintainers, head to their
 
 We'd love for you to `contribute to Girder <CONTRIBUTING.rst>`_.
 
-.. |ERD| image:: ./docs/images/Mindlogger-DB-ER.png
-    :alt: MindLogger database entity-relationship diagram
-    :target: ./docs/images/Mindlogger-DB-ER.dia
-
 .. |logo| image:: ./girderformindlogger/web_client/src/assets/ML-logo_25px.png
     :alt: Girder for MindLogger
     :target: https://api.mindlogger.org

girderformindlogger/api/v1/applet.py

@@ -19,6 +19,7 @@
 
 import itertools
 import re
+import threading
 import uuid
 import requests
 from ..describe import Description, autoDescribeRoute
@@ -162,36 +163,24 @@ def assignGroup(self, folder, group, role, subject):
     )
     def createApplet(self, protocolUrl=None, name=None, informant=None):
         thisUser = self.getCurrentUser()
-        # get an activity set from a URL
-        protocol = ProtocolModel().getFromUrl(
-            protocolUrl,
-            'protocol',
-            thisUser,
-            refreshCache=False
-        )[0]
-        protocol = protocol.get('protocol', protocol)
-        # create an applet for it
-        applet=AppletModel().createApplet(
-            name=name if name is not None and len(name) else ProtocolModel(
-            ).preferredName(
-                protocol
-            ),
-            protocol={
-                '_id': 'protocol/{}'.format(protocol.get('_id')),
-                'url': protocol.get(
-                    'meta',
-                    {}
-                ).get(
-                    'protocol',
-                    {}
-                ).get('url', protocolUrl)
-            },
-            user=thisUser,
-            constraints={
-                'informantRelationship': informant
-            } if informant is not None else None
+        thread = threading.Thread(
+            target=AppletModel().createAppletFromUrl,
+            kwargs={
+                'name': name,
+                'protocolUrl': protocolUrl,
+                'user': thisUser,
+                'constraints': {
+                    'informantRelationship': informant
+                } if informant is not None else None
+            }
         )
-        return(applet)
+        thread.start()
+        return({
+            "message": "The applet is being created. Please check back in "
+                       "several mintutes to see it. If you have an email "
+                       "address associated with your account, you will receive "
+                       "an email when your applet is ready."
+        })
 
     @access.user(scope=TokenScope.DATA_WRITE)
     @autoDescribeRoute(
@@ -239,8 +228,6 @@ def updateInformant(self, applet, informant):
         .errorResponse('Write access was denied for this applet.', 403)
     )
     def deactivateApplet(self, folder):
-        import threading
-
         applet = folder
         user = Applet().getCurrentUser()
         applet['meta']['applet']['deleted'] = True
@@ -251,8 +238,10 @@ def deactivateApplet(self, folder):
                 applet.get('_id')
             )
             thread = threading.Thread(
-                target=AppletModel().updateAllUserCaches(applet, user)
+                target=AppletModel().updateUserCacheAllUsersAllRoles,
+                args=(applet, user)
             )
+            thread.start()
         else:
             message = 'Could not deactivate applet {} ({}).'.format(
                 AppletModel().preferredName(applet),
@@ -264,7 +253,12 @@ def deactivateApplet(self, folder):
     @access.user(scope=TokenScope.DATA_READ)
     @autoDescribeRoute(
         Description('Get an applet by ID.')
-        .modelParam('id', model=AppletModel, level=AccessType.READ)
+        .modelParam(
+            'id',
+            model=AppletModel,
+            level=AccessType.READ,
+            destName='applet'
+        )
         .param(
             'refreshCache',
             'Reparse JSON-LD',
@@ -274,8 +268,7 @@ def deactivateApplet(self, folder):
         .errorResponse('Invalid applet ID.')
         .errorResponse('Read access was denied for this applet.', 403)
     )
-    def getApplet(self, folder, refreshCache=False):
-        applet = folder
+    def getApplet(self, applet, refreshCache=False):
         user = self.getCurrentUser()
         return(
             jsonld_expander.formatLdObject(
@@ -414,8 +407,7 @@ def invite(self, applet, role="user", idCode=None, profile=None):
         .errorResponse('Read access was denied for this applet.', 403)
     )
     def setConstraints(self, folder, activity, schedule, **kwargs):
-        import threading
-        thisUser = Applet().getCurrentUser()
+        thisUser = self.getCurrentUser()
         applet = jsonld_expander.formatLdObject(
             _setConstraints(folder, activity, schedule, thisUser),
             'applet',

girderformindlogger/api/v1/protocol.py

@@ -57,7 +57,7 @@ def __init__(self):
     def getProtocol(self, folder):
         try:
             protocol = folder
-            user = Protocol().getCurrentUser()
+            user = self.getCurrentUser()
             return(
                 jsonld_expander.formatLdObject(
                     protocol,

girderformindlogger/api/v1/screen.py

@@ -59,7 +59,7 @@ def __init__(self):
         .errorResponse('Read access was denied for the screen.', 403)
     )
     def createScreen(self, activity, screenName=None):
-        thisUser = Screen().getCurrentUser()
+        thisUser = self.getCurrentUser()
         activity = ActivityModel().load(
             activity,
             level=AccessType.WRITE,