Merge branch 'v0.20.0'

.travis.yml

@@ -4,6 +4,7 @@ python:
   - "3.5"
   - "3.6"
   - "3.7"
+  - "3.8"
 
 services:
   - postgresql

MANIFEST.in

@@ -1,8 +1,6 @@
 recursive-include opal/static *
 recursive-include opal/templates *
 recursive-include opal/scaffolding *
-recursive-include opal/core/collaborative/static *
-recursive-include opal/core/collaborative/templates *
 recursive-include opal/core/search/static *
 recursive-include opal/core/search/templates *
 recursive-include opal/core/pathway/static *

changelog.md

@@ -1,3 +1,38 @@
+### 0.20.0 (Major Release)
+
+#### Python 3 version changes.
+
+Opal now supports python 3.5 - python 3.8.
+Please note that the 0.21.0 release will drop support for python 3.5.
+
+### Scaffold application episode category
+
+The scaffolded application created by `startproject` now creates a custom
+episode category class.
+
+### Removes Django Axes
+
+Axes has been removed from the Opal core application. The package creates a database
+log of all login attempts and was installed by default. It is now considered that this
+should be an application level choice rather than a framework choice. Installing it on a
+per application basis is simple, and requires only settings and requirements changes.
+
+### Removes Letter
+
+The dependency on the letter python package has been removed from the Opal core application. If you wish to send emails, django ships with email wrappers to make this easy.
+
+#### Updates to the Dependency Graph
+
+* Django: 2.0.13 -> 2.2.16
+* Django-compressor: 2.2 -> 2.4
+* Six==1.15.0
+* Psycopg2: 2.8.3 -> 2.8.6
+* Requests: 2.22.0 -> 2.25.0
+* Python-dateutil: 2.8.0 -> 2.8.1
+* Django-rest-framework: 3.10.2 -> 3.12.2
+* Django-Axes -> Removed
+* Letter -> Removed
+
 ### 0.18.4 (Minor Release)
 
 #### Some models have translations

doc/docs/guides/episodes.md

@@ -5,7 +5,6 @@ such as a start and end date, and the type of episode. This may be an inpatient
 stay, an outpatient treatment, a telephone consultation  - or any other arbitrarily
 defined period of care.
 
-
 ## Episode Categories
 
 An episode must have a related category. An Opal `EpisodeCategory` is a discoverable
@@ -19,7 +18,7 @@ the `display_name` attribute of the relevant category.
 ```python
 episode = patient.episode_set.first()
 print episode.category
-# <opal.core.episode.InpatientEpisode object>
+# <{{ your app name }}.InpatientEpisode object>
 
 print episode.category.display_name
 # "Inpatient"
@@ -34,15 +33,6 @@ The category of an episode determines which template will be used to display it
 on the detail page for the patient. This template is determined by looking up
 the `detail_template` attribute of the `EpisodeCategory`.
 
-```python
-episode.category
-print episode.category
-# <opal.core.episode.InpatientEpisode object>
-
-print episode.category.detail_template
-# detail/inpatient.html
-```
-
 The Episode Category template does not comprise the entire
 [Patient detail view](patient_detail_views.md). This is made of multiple episodes
 and by default will display some basic demographic details as well as other episodes.

doc/docs/reference/episode_categories.md

@@ -86,10 +86,3 @@ rest of the data that's been used to update the episode.
 InpatientEpisode(episode).set_stage('Discharged', user, data_dict)
 # -> True
 ```
-
-
-## InpatientEpisode
-
-This is the default EpisodeCategory imlpementation - applications started with Opal's
-scaffolding scripts will use this as the `OpalApplication.default_episode_category`.
-It sets the detail template to `detail/inpatient.html`

doc/docs/reference/upgrading.md

@@ -3,6 +3,63 @@
 This document provides instructions for specific steps required to upgrading your Opal
 application to a later version where there are extra steps required.
 
+#### v0.18.3 -> v0.20.0
+
+##### Dependency upgrades
+
+How you do this depends on how you have configured your application. You will need to
+update both the Opal version, and versions of dependencies upgraded dependencies if
+you have specified them in for instance, a requirements.txt.
+
+(This will be the case if you use the requirements.txt originally provided by
+`opal startproject`)
+
+    # requirements.txt
+    opal==0.20.0
+    django==2.2.16
+    djangorestframework==3.12.2
+    django-compressor==2.4
+    six==1.15.0
+    psycopg2==2.8.6
+    requests==2.25.0
+    python-dateutil==2.8.1
+
+
+##### API API Changes (REST Framework)
+
+Note that the Django REST Framework update includes a breaking change to their public 
+API which may affect your application. The `base_name` attribute of a ViewSet has been 
+renamed to `basename` ([release notes](https://www.django-rest-framework.org/community/release-notes/#390)).
+
+Any APIs implemented in your application will likely need to rename this attribute as
+part of this upgrade.
+
+##### Episode Categories
+
+
+`Inpatient` is no longer provided in `opal.core.episodes`. If you are using the
+Inpatient episode category you can add it in your `{{ appname }}/episode_categories.py`
+```
+from opal.core.episodes import EpisodeCategory
+
+
+class InpatientEpisode(EpisodeCategory):
+    display_name    = 'Inpatient'
+    detail_template = 'detail/inpatient.html'
+    stages          = [
+        'Inpatient',
+        'Followup',
+        'Discharged'
+    ]
+```
+
+##### Django Axes
+
+Opal has removed the built in dependency on Django Axes. If your application wishes to
+continue using it, then the relevant settings should already be in your settings file.
+If you were relying on the entry in the opal `setup.py` to install it at deployment time,
+you will need to ensure this via some other mechanism - for instance ensuring it is in your
+application `requirements.txt`.
 
 #### v0.17.1 -> v0.18.2
 

doc/mkdocs.yml

@@ -121,7 +121,7 @@ dev_addr: 0.0.0.0:8965
 include_next_prev: false
 
 extra:
-  version: v0.18.4
+  version: v0.20.0
 
 markdown_extensions:
     - fenced_code

opal/_version.py

@@ -1,4 +1,4 @@
 """
 Declare our current version string
 """
-__version__ = '0.18.4'
+__version__ = '0.20.0'

opal/core/api.py

@@ -21,10 +21,10 @@
 
 
 class OPALRouter(routers.DefaultRouter):
-    def get_default_base_name(self, viewset):
-        name = getattr(viewset, 'base_name', None)
+    def get_default_basename(self, viewset):
+        name = getattr(viewset, 'basename', None)
         if name is None:
-            return routers.DefaultRouter.get_default_base_name(self, viewset)
+            return routers.DefaultRouter.get_default_basename(self, viewset)
         return name
 
 
@@ -81,7 +81,7 @@ class RecordViewSet(LoginRequiredViewset):
     Return the serialization of all active record types ready to
     initialize on the client side.
     """
-    base_name = 'record'
+    basename = 'record'
 
     def list(self, request):
         return json_response(schemas.list_records())
@@ -91,7 +91,7 @@ class ReferenceDataViewSet(LoginRequiredViewset):
     """
     API for referencedata
     """
-    base_name = 'referencedata'
+    basename = 'referencedata'
 
     def list(self, request):
         data = {}
@@ -141,7 +141,7 @@ class MetadataViewSet(LoginRequiredViewset):
     """
     Our metadata API
     """
-    base_name = 'metadata'
+    basename = 'metadata'
 
     def list(self, request):
         data = {}
@@ -237,7 +237,7 @@ class UserProfileViewSet(LoginRequiredViewset):
     """
     Returns the user profile details for the currently logged in user
     """
-    base_name = 'userprofile'
+    basename = 'userprofile'
 
     def list(self, request):
         profile = request.user.profile
@@ -248,7 +248,7 @@ class UserViewSet(LoginRequiredViewset):
     """
     Provides applications with information about all system users
     """
-    base_name = 'user'
+    basename = 'user'
 
     def list(self, request):
         """
@@ -269,7 +269,7 @@ class TaggingViewSet(LoginRequiredViewset):
     """
     Returns taggings associated with episodes
     """
-    base_name = 'tagging'
+    basename = 'tagging'
 
     @episode_from_pk
     def retrieve(self, request, episode):
@@ -293,7 +293,7 @@ class EpisodeViewSet(LoginRequiredViewset):
     """
     Episodes of care
     """
-    base_name = 'episode'
+    basename = 'episode'
 
     def list(self, request):
         return json_response(
@@ -357,7 +357,7 @@ def retrieve(self, request, episode):
 
 
 class PatientViewSet(LoginRequiredViewset):
-    base_name = 'patient'
+    basename = 'patient'
 
     @patient_from_pk
     def retrieve(self, request, patient):
@@ -366,7 +366,7 @@ def retrieve(self, request, patient):
 
 
 class PatientRecordAccessViewSet(LoginRequiredViewset):
-    base_name = 'patientrecordaccess'
+    basename = 'patientrecordaccess'
 
     def retrieve(self, request, pk=None):
         return json_response([
@@ -376,7 +376,7 @@ def retrieve(self, request, pk=None):
 
 
 class PatientListViewSet(LoginRequiredViewset):
-    base_name = 'patientlist'
+    basename = 'patientlist'
     permission_classes = (IsAuthenticated,)
 
     def retrieve(self, request, pk=None):
@@ -401,7 +401,7 @@ def register_subrecords():
         sub_name = subrecord.get_api_name()
 
         class SubViewSet(SubrecordViewSet):
-            base_name = sub_name
+            basename  = sub_name
             model     = subrecord
 
         router.register(sub_name, SubViewSet)

opal/core/application.py

@@ -92,7 +92,7 @@ class OpalApplication(object):
             index=0
         )
     ]
-    default_episode_category = 'Inpatient'
+    default_episode_category = None
 
     @classmethod
     def get_core_javascripts(klass, namespace):
@@ -113,10 +113,8 @@ def get_menu_items(klass, user=None):
         """
         Default implementation of get_menu_items()
         """
-        # we import here as settings must be set before this is imported
-        from django.contrib.auth.views import logout as logout_view
         logout = menus.MenuItem(
-            href=reverse(logout_view), icon="fa-sign-out", index=1000
+            href=reverse("logout"), icon="fa-sign-out", index=1000
         )
         admin = menus.MenuItem(
             href="/admin/", icon="fa-cogs", display=_("Admin"),

opal/core/commandline.py

@@ -8,6 +8,7 @@
 import os
 import subprocess
 import sys
+import logging
 
 from django.core import management
 import ffs
@@ -242,5 +243,14 @@ def parse_args(args):
     sys.exit(0)
 
 
+def warn_for_python_35():
+    vi = sys.version_info
+    if vi.major == 3 and vi.minor == 5:
+        logging.warn(
+            "Python 3.5 will be deprecated in Opal 0.21.0",
+        )
+
+
 def main():
+    warn_for_python_35()
     parse_args(sys.argv[1:])

opal/core/episodes.py

@@ -85,13 +85,3 @@ def set_stage(self, stage, user, data):
                 )
                 raise ValueError(msg)
         self.episode.stage = stage
-
-
-class InpatientEpisode(EpisodeCategory):
-    display_name    = 'Inpatient'
-    detail_template = 'detail/inpatient.html'
-    stages          = [
-        'Inpatient',
-        'Followup',
-        'Discharged'
-    ]

opal/core/pathway/tests/pathway_test/pathways.py

@@ -6,7 +6,7 @@
 class SomeComplicatedStep(steps.Step):
     display_name = "Some complicated step"
     step_controller = "SomeController"
-    template = "Sometemplate.html"
+    template = "complicated_step_template.html"
 
 
 class PagePathwayExample(pathways.PagePathway):

opal/core/patient_lists.py

@@ -298,17 +298,17 @@ def get_member_lists(klass):
         Returns an iterable of PatientLists
         Defaults to the `.member_lists` property
         """
-        for l in klass.member_lists:
-            yield l
+        for member_list in klass.member_lists:
+            yield member_list
 
     @classmethod
     def get_member_lists_for_user(klass, user):
         """
         Returns an iterable of the visible member lists for a given USER
         """
-        for l in klass.get_member_lists():
-            if l.visible_to(user):
-                yield l
+        for member_list in klass.get_member_lists():
+            if member_list.visible_to(user):
+                yield member_list
 
     @classmethod
     def visible_to(klass, user):