Merge branch 'v0.10.1'

CHANGELOG.md

@@ -1,3 +1,38 @@
+### 0.10.1 (Minor Release)
+
+#### Plugin API end points can now override application end points
+
+A change to the order that APIs are registered with Django Rest Framework allows
+plugins to now override the core Opal application APIs.
+
+#### Fonts are now locally sourced
+
+Fonts are now served from Opal's static assets rather than from the Google CDN.
+
+#### print/screen stylesheets have been collapsed into opal.css
+
+Print/screen differences are now in opal.css with media tags.
+
+#### Google Analytics is now deferred
+
+The loading in of Google Analytics is now deferred to the bottom of the body
+tag to allow the page to load without waiting on analytics scripts to load.
+
+#### Scaffold version control failures
+
+The `startplugin` and `startproject` commands initialize a git repository by
+default. If we (The `subprocess` module) cannot find the `git` command, we now
+continue with a message printed to screen rather than raising an exception.
+
+#### Episode.objects.serialised now uses select_related
+
+`ForeignKeyOrFreeText` fields now have their ForeignKey items preselected when
+we use `Episode.objects.serialised`. This provides a speed boost for applications
+with moderately heavy `ForeignKeyOrFreeText` usage.
+
+(Approx 30-40% in our tests.)
+
+
 ### 0.10.0 (Major Release)
 
 This is a major release with breaking changes from upstream dependencies.

README.md

@@ -1,8 +1,8 @@
 Opal
 ====
 
-[![Build Status](https://travis-ci.org/openhealthcare/opal.svg?branch=v0.10.0)](https://travis-ci.org/openhealthcare/opal)
-[![Coverage Status](https://coveralls.io/repos/github/openhealthcare/opal/badge.svg?branch=v0.10.0)](https://coveralls.io/github/openhealthcare/opal?branch=v0.10.0)
+[![Build Status](https://travis-ci.org/openhealthcare/opal.svg?branch=v0.10.1)](https://travis-ci.org/openhealthcare/opal)
+[![Coverage Status](https://coveralls.io/repos/github/openhealthcare/opal/badge.svg?branch=v0.10.1)](https://coveralls.io/github/openhealthcare/opal?branch=v0.10.1)
 [![PyPI version](https://badge.fury.io/py/opal.svg)](https://badge.fury.io/py/opal)
 
 

doc/docs/reference/upgrading.md

@@ -3,7 +3,21 @@
 This document provides instructions for specific steps required to upgrading your Opal
 application to a later version where there are extra steps required.
 
-### 0.9.1 -> 0.10.0
+
+### 0.10.0 -> 0.10.1
+
+#### Upgrading Opal
+
+How you do this depends on how you have configured your application, but updating your
+requirements.txt to update the version should work.
+
+    # requirements.txt
+    opal==0.10.1
+
+There are no migrations or additional commands for this upgrae, and we are not aware of
+any backwards incompatible changes.
+
+### 0.9.0 -> 0.10.0
 
 #### Upgrading Opal
 
@@ -103,21 +117,6 @@ logs into second will throw a CSRF failure because Django invalidates CSRF
 tokens on login.
 
 
-### 0.9.0 -> 0.9.1
-
-#### Upgrading Opal
-
-How you do this depends on how you have configured your application, but updating your
-requirements.txt to update the version should work.
-
-    # requirements.txt
-    opal==0.9.1
-
-After re-installing (via for instance `pip install -r requirements.txt`) you will need to
-run the migrations for Opal 0.9.1
-
-    $ python manage.py migrate opal
-
 ### 0.8.3 -> 0.9.0
 
 `episode.date_of_episode`, `episode.date_of_admission` and `episode.discharge_date` are all deprecated.

doc/mkdocs.yml

@@ -117,7 +117,7 @@ dev_addr: 0.0.0.0:8965
 include_next_prev: false
 
 extra:
-  version: v0.10.0
+  version: v0.10.1
 
 markdown_extensions:
     - fenced_code

opal/_version.py

@@ -1,4 +1,4 @@
 """
 Declare our current version string
 """
-__version__ = '0.10.0'
+__version__ = '0.10.1.rc1'

opal/core/api.py

@@ -390,32 +390,39 @@ def retrieve(self, request, pk=None):
         return json_response(patientlist.to_dict(request.user))
 
 
-router.register('patient', PatientViewSet)
-router.register('episode', EpisodeViewSet)
-router.register('record', RecordViewSet)
-router.register('userprofile', UserProfileViewSet)
-router.register('user', UserViewSet)
-router.register('tagging', TaggingViewSet)
-router.register('patientlist', PatientListViewSet)
-router.register('patientrecordaccess', PatientRecordAccessViewSet)
+def register_plugin_apis():
+    for plugin in plugins.OpalPlugin.list():
+        for api in plugin.get_apis():
+            router.register(*api)
 
-router.register('referencedata', ReferenceDataViewSet)
-router.register('metadata', MetadataViewSet)
 
-for subrecord in subrecords():
-    sub_name = subrecord.get_api_name()
+def register_subrecords():
+    for subrecord in subrecords():
+        sub_name = subrecord.get_api_name()
 
-    class SubViewSet(SubrecordViewSet):
-        base_name = sub_name
-        model     = subrecord
+        class SubViewSet(SubrecordViewSet):
+            base_name = sub_name
+            model     = subrecord
 
-    router.register(sub_name, SubViewSet)
+        router.register(sub_name, SubViewSet)
 
 
-def register_plugin_apis():
-    for plugin in plugins.OpalPlugin.list():
-        for api in plugin.get_apis():
-            router.register(*api)
+def initialize_router():
+    # plugin apis get initialised first, so that plugins
+    # can
+    register_plugin_apis()
+    router.register('patient', PatientViewSet)
+    router.register('episode', EpisodeViewSet)
+    router.register('record', RecordViewSet)
+    router.register('userprofile', UserProfileViewSet)
+    router.register('user', UserViewSet)
+    router.register('tagging', TaggingViewSet)
+    router.register('patientlist', PatientListViewSet)
+    router.register('patientrecordaccess', PatientRecordAccessViewSet)
+
+    router.register('referencedata', ReferenceDataViewSet)
+    router.register('metadata', MetadataViewSet)
+    register_subrecords()
 
 
-register_plugin_apis()
+initialize_router()

opal/core/scaffold.py

@@ -2,9 +2,11 @@
 Opal scaffolding and code generation
 """
 import inspect
+import errno
 import os
 import subprocess
 import sys
+
 from django.core import management
 from django.utils.crypto import get_random_string
 from django.apps import apps
@@ -57,6 +59,9 @@ def create_lookuplists(root_dir):
 
 
 def call(cmd, **kwargs):
+    """
+    Call an external program in a subprocess
+    """
     write("Calling: {}".format(' '.join(cmd)))
     try:
         subprocess.check_call(cmd, **kwargs)
@@ -65,6 +70,26 @@ def call(cmd, **kwargs):
         sys.exit(1)
 
 
+def call_if_exists(cmd, failure_message, **kwargs):
+    """
+    Call an external program in a subprocess if it exists.
+
+    Returns True.
+
+    If it does not exist, write a failure message and return False
+    without raising an exception
+    """
+    try:
+        call(cmd, **kwargs)
+        return True
+    except OSError as e:
+        if e.errno == errno.ENOENT:
+            write(failure_message)
+            return False
+        else:
+            raise
+
+
 def start_plugin(name, USERLAND):
     name = name
 
@@ -103,7 +128,11 @@ def start_plugin(name, USERLAND):
     services = jsdir/'services'
     services.mkdir()
     # 5. Initialize git repo
-    call(('git', 'init'), cwd=root, stdout=subprocess.PIPE)
+    call_if_exists(
+        ('git', 'init'),
+        'Unable to locate git; Skipping git repository initialization.',
+        cwd=root, stdout=subprocess.PIPE
+    )
 
     write('Plugin complete at {0}'.format(reponame))
     return
@@ -252,7 +281,11 @@ def manage(command):
     manage('createopalsuperuser')
 
     # 10. Initialise git repo
-    call(('git', 'init'), cwd=project_dir, stdout=subprocess.PIPE)
+    call_if_exists(
+        ('git', 'init'),
+        'Unable to locate git; Skipping git repository initialization.',
+        cwd=project_dir, stdout=subprocess.PIPE
+    )
 
     # 11. Load referencedata shipped with Opal
     manage('load_lookup_lists')

opal/managers.py

@@ -10,6 +10,7 @@
 from opal.core.subrecords import (
     episode_subrecords, patient_subrecords
 )
+from opal.core.fields import ForeignKeyOrFreeText
 from functools import reduce
 
 
@@ -32,6 +33,23 @@ def search(self, some_query):
         return qs
 
 
+def prefetch(qs):
+    """
+    Given a Queryset QS, examine the model for `ForeignKeyOrFreetext`
+    fields or `ManyToMany` fields and add `select_related` or
+    `prefetch_related` calls to the queryset as appropriate to reduce
+    the total number of database queries required to serialise the
+    contents of the queryset.
+    """
+    for name, value in list(vars(qs.model).items()):
+        if isinstance(value, ForeignKeyOrFreeText):
+            qs = qs.select_related(value.fk_field_name)
+
+    for related in qs.model._meta.many_to_many:
+        qs = qs.prefetch_related(related.attname)
+    return qs
+
+
 class EpisodeQueryset(models.QuerySet):
 
     def search(self, some_query):
@@ -51,7 +69,9 @@ def serialised_episode_subrecords(self, episodes, user):
 
         for model in episode_subrecords():
             name = model.get_api_name()
-            subrecords = model.objects.filter(episode__in=episodes)
+            subrecords = prefetch(
+                model.objects.filter(episode__in=episodes)
+            )
 
             for related in model._meta.many_to_many:
                 subrecords = subrecords.prefetch_related(related.attname)
@@ -74,7 +94,9 @@ def serialised(self, user, episodes,
         episode_subs = self.serialised_episode_subrecords(episodes, user)
         for model in patient_subrecords():
             name = model.get_api_name()
-            subrecords = model.objects.filter(patient__in=patient_ids)
+            subrecords = prefetch(
+                model.objects.filter(patient__in=patient_ids)
+            )
 
             for sub in subrecords:
                 patient_subs[sub.patient_id][name].append(sub.to_dict(user))

opal/static/css/opal.css

@@ -1,3 +1,82 @@
+/* lato-300 - latin */
+@font-face {
+  font-family: 'Lato';
+  font-style: normal;
+  font-weight: 300;
+  src: url('../fonts/lato-v14-latin-300.eot'); /* IE9 Compat Modes */
+  src: local('Lato Light'), local('Lato-Light'),
+       url('../fonts/lato-v14-latin-300.eot?#iefix') format('embedded-opentype'), /* IE6-IE8 */
+       url('../fonts/lato-v14-latin-300.woff2') format('woff2'), /* Super Modern Browsers */
+       url('../fonts/lato-v14-latin-300.woff') format('woff'), /* Modern Browsers */
+       url('../fonts/lato-v14-latin-300.ttf') format('truetype'), /* Safari, Android, iOS */
+       url('../fonts/lato-v14-latin-300.svg#Lato') format('svg'); /* Legacy iOS */
+}
+/* lato-regular - latin */
+@font-face {
+  font-family: 'Lato';
+  font-style: normal;
+  font-weight: 400;
+  src: url('../fonts/lato-v14-latin-regular.eot'); /* IE9 Compat Modes */
+  src: local('Lato Regular'), local('Lato-Regular'),
+       url('../fonts/lato-v14-latin-regular.eot?#iefix') format('embedded-opentype'), /* IE6-IE8 */
+       url('../fonts/lato-v14-latin-regular.woff2') format('woff2'), /* Super Modern Browsers */
+       url('../fonts/lato-v14-latin-regular.woff') format('woff'), /* Modern Browsers */
+       url('../fonts/lato-v14-latin-regular.ttf') format('truetype'), /* Safari, Android, iOS */
+       url('../fonts/lato-v14-latin-regular.svg#Lato') format('svg'); /* Legacy iOS */
+}
+/* lato-700 - latin */
+@font-face {
+  font-family: 'Lato';
+  font-style: normal;
+  font-weight: 700;
+  src: url('../fonts/lato-v14-latin-700.eot'); /* IE9 Compat Modes */
+  src: local('Lato Bold'), local('Lato-Bold'),
+       url('../fonts/lato-v14-latin-700.eot?#iefix') format('embedded-opentype'), /* IE6-IE8 */
+       url('../fonts/lato-v14-latin-700.woff2') format('woff2'), /* Super Modern Browsers */
+       url('../fonts/lato-v14-latin-700.woff') format('woff'), /* Modern Browsers */
+       url('../fonts/lato-v14-latin-700.ttf') format('truetype'), /* Safari, Android, iOS */
+       url('../fonts/lato-v14-latin-700.svg#Lato') format('svg'); /* Legacy iOS */
+}
+
+
+@media print{
+  @page {
+  	size: landscape;
+  }
+  .patient-list-container {
+      overflow: visible;
+      overflow-y: visible;
+  }
+
+  li {
+  	padding-top: 0px;
+  	padding-bottom: 0px;
+      line-height: 12px;
+  }
+
+  .screen-only {
+  	display: none;
+  }
+
+  /*
+  * it needs important because bootstrap
+  */
+  .always-on-print-block{
+  	display: block !important;
+  }
+
+  table {
+      font-size: 12px
+  }
+}
+
+@media screen{
+  .print-only {
+  	display: none;
+  }
+}
+
+
 /* Bootstrap resets */
 html, .outer-container{
     height: 100%;