Merge branch 'v0.17.0' into dependabot/pip/jinja2-2.10.1

.travis.yml

@@ -1,4 +1,5 @@
 language: python
+dist: trusty
 python:
   - "3.5"
   - "3.6"

changelog.md

@@ -1,3 +1,35 @@
+### 0.17.0 (Major Release)
+
+#### Javascript API removals
+
+* Removes the function Episode.isDischarged() (This was rarely if ever used, and no longer an accurate represenation of dischargedness.)
+
+#### Miscelanious changes
+
+Bumps Flake8 version to 3.7.8 - new code will now be required to pass flake8 v3.7.8
+
+#### Updates to the Dependency Graph
+
+* Psycopg2: 2.7.6.1 -> 2.8.3
+
+### 0.16.0 (Major Release)
+
+Adds serialize_date, serialize_datetime, serialize_time utility functions to serialize date/datetime/time to
+strings.
+
+Diagnosis.details is now a text field.
+
+Changes the requirements.txt files that get created when we create an opal application or plugin to use `python-dateutil==2.7.5`
+
+### 0.15.0 (Major Release)
+
+Adds an optional setting OPAL_DEFAULT_SEARCH_FIELDS that specifies the fields used to
+search in when a criteria isn't specified.
+
+### 0.14.2 (Minor Release)
+
+Documentation fix, we're on python 3.4 now.
+
 ### 0.14.1 (Minor Release)
 
 The search plugin was not excluding search strings from analytics.

doc/docs/guides/archetypes.md

@@ -67,11 +67,11 @@ frequency | FKorFT(Drugfreq)
 
 ### Diagnosis
 
-Field|Type|Length
------|----|---
+Field|Type
+-----|----
 condition | FKorFT(Condition)
 provisional | Boolean
-details | Char | 255
+details | Text
 date_of_diagnosis | Date
 
 ### PastMedicalHistory

doc/docs/guides/components_overview.md

@@ -2,7 +2,7 @@
 
 Opal applications will typically be made up of several types of components.
 
-![Layers of an Opal application](../img/OpalLayers.png)
+![Layers of an Opal application](/img/OpalLayers.png)
 
 ### Opal
 

doc/docs/guides/context_processors.md

@@ -8,15 +8,15 @@ All Opal settings are copied into the context of the template.
 
 ### Models
 
-All [subrecords](../reference/subrecords/) (the underlying clinical models of Opal) are copied into the context of the template context and can be accessed from the variable `models`, e.g. the Allergies subrecord can be referred to by 
+All [subrecords](../reference/subrecords.md) (the underlying clinical models of Opal) are copied into the context of the template context and can be accessed from the variable `models`, e.g. the Allergies subrecord can be referred to by
 
 ```html
 {{ models.Allergy }}
 ```
 
 ### Pathways
 
-Pathways are copied in to the context of the template and can be accessed from the variable `pathways`. For an example Pathway you would be able to access attributes of a Pathway thus: 
+Pathways are copied in to the context of the template and can be accessed from the variable `pathways`. For an example Pathway you would be able to access attributes of a Pathway thus:
 
 ```html
 {{ pathways.MyPathway.get_display_name }}

doc/docs/guides/datamodel.md

@@ -47,7 +47,7 @@ implement a Demographics `Subrecord` as follows:
 
 Subrecords also define various properties that will provide metadata about their
 display or structure, which are documented in the
-[Subrecord reference material](/reference/subrecords/)
+[Subrecord reference material](../reference/subrecords.md)
 
 ### Core Clinical Data Model
 

doc/docs/guides/episodes.md

@@ -52,7 +52,7 @@ More detail on customising the rest of the detail tempalte is found in the detai
 ## Default Category
 
 The default category of episodes in an Opal application is set by the
-[OpalApplication](../reference/opal_application) object's default_episode_category
+[OpalApplication](../reference/opal_application.md) object's default_episode_category
 property.
 
 ```python
@@ -62,7 +62,7 @@ class Application(application.OpalApplication):
 
 ## Defining your own EpisodeCategory
 
-As EpisodeCategory is a [discoverable](discoverable) we can define our own to
+As EpisodeCategory is a [discoverable](discoverable.md) we can define our own to
 meet custom requirements.
 
 Episode categories should be defined in a file named `episode_categories` of

doc/docs/guides/forms.md

@@ -82,4 +82,4 @@ forms, with less verbose templates.
     </form>
 
 
-For full documentation of the options, please see the [Form templatetags reference material](/reference/form_templatetags/)
+For full documentation of the options, please see the [Form templatetags reference material](../reference/form_templatetags.md)

doc/docs/reference/core_serialization.md

@@ -2,6 +2,30 @@
 
 Helpers for serializing and deserializing data
 
+## `serialize_date(value)`
+Given a date, serialize it to a string using the
+`settings.DATE_FORMAT`
+
+```python
+    as_date_str = serialize_date(datetime.date(2019, 4, 1))
+```
+
+## `serialize_datetime(value)`
+Given a datetime, serialize it to a string using the
+`settings.DATETIME_FORMAT`
+
+```python
+    as_datetime_str = serialize_datetime(datetime.datetime(2019, 4, 1, 10, 30))
+```
+
+## `serialize_time(value)`
+Given a time, serialize it to a string using the
+`settings.TIME_FORMAT`
+
+```python
+    as_datetime_str = serialize_time(datetime.time(10, 30))
+```
+
 ## `deserialize_datetime(value)`
 
 Given a string which represents a date time, deserialize it to a Python datetime

doc/docs/reference/opal_application.md

@@ -8,7 +8,7 @@ Returns the application class for the currently active application.
 
 #### get_all_components
 
-Returns an iterator of all the of the [plugins](/guides/plugins/) and the current application
+Returns an iterator of all the of the [plugins](../guides/plugins.md) and the current application
 
 ## OpalApplication
 

doc/docs/reference/settings.md

@@ -12,6 +12,18 @@ The human readable form of your application name.
 Displayed in the header by default.
 Scaffolded applications start with whatever is passed in to `opal startproject`.
 
+## OPAL_DEFAULT_SEARCH_FIELDS
+
+Search fields that we look in by default when a user enters a search term.
+Defaults to
+```python
+ [
+    "demographics__hospital_number",
+    "demographics__first_name",
+    "demographics__surname"
+]
+```
+
 ## OPAL_LOG_OUT_DURATION
 
 Opal will log users out if they have been inactive for greater than this value.

doc/docs/reference/upgrading.md

@@ -3,6 +3,13 @@
 This document provides instructions for specific steps required to upgrading your Opal
 application to a later version where there are extra steps required.
 
+#### v0.15.0 -> v0.16.0
+Diagnosis.details is now a text field. Please make and run migrations if you are
+using it in your app.
+
+The record template for diagnosis now shows the details on the next row.
+
+
 ### 0.13.1 -> 0.14.0
 If you were creating a UserProfile, this will now fail as a UserProfile is created automatically after creating a user (by a signal).
 

doc/docs/tutorial.md

@@ -47,7 +47,7 @@ Let's have a look at what that created for you:
             urls.py             # Django Urlconf
             wsgi.py
 
-            patient_lists.py    # these create the [lists](/guides/list_views/) for you application
+            patient_lists.py    # these create the [lists](guides/list_views.md) for you application
 
             assets/             # Your static files directory
             templates/          # Your template directory
@@ -88,16 +88,16 @@ front-end Angular single page apps.
 Most clinical services will need at some stage to generate a list of patients - so Opal provides
 this functionality enabled by default.
 
-The [list view](/guides/list_views/) is a spreadsheet-style list of patients - try navigating
-to the list view and adding a patient with the `add patient` button.
+The [list view](guides/list_views.md) is a spreadsheet-style list of patients - try navigating
+to the list view and adding a patient with the `add patient` button. [episode](guides/datamodel.md)
 
 <img src="/img/tutorial-list.png" width="600" style="margin: 12px auto; border: 1px solid black;"/>
 
 Each column contains a different type of information about a patient, while each
 row represents one patient.
 
 <blockquote><small>
-Strictly speaking each row is an <a href="/guides/datamodel/">episode</a>
+Strictly speaking each row is an <a href="../guides/datamodel.md">episode</a>
 of care for a patient - but we'll come to that in a second.
 </small></blockquote>
 
@@ -120,7 +120,7 @@ class Diagnosis(EpisodeSubrecord):
 
 You will notice that the condition field has a custom field type - `ForeignKeyOrFreeText`.
 This is a custom field type that we use with Opal when we want to use a
-[Lookup List](/guides/referencedata/).
+[Lookup List](guides/referencedata.md).
 
 
 Lookup Lists allow us to reference canonical lists of available terminology as a foreign key, while
@@ -147,7 +147,7 @@ For more details consult the
 So far we've begun to get a sense of the batteries-included parts of Opal,
 but before long, you're going to need to create models for your own needs.
 
-Most Opal models are [Subrecords](/guides/datamodel/) - they relate to either a patient, or
+Most Opal models are [Subrecords](guides/datamodel.md) - they relate to either a patient, or
 an episode (an episode is for example, an admission to hospital).
 
 Let's see how that works by creating a TODO list model that is assigned to
@@ -263,7 +263,7 @@ application.
 
 For us, you'll notice that the value of `TODOItem.completed` simply displays as false -
 which is not particularly useful. So let's update that using the Opal
-[Boxed filter](/reference/javascript/javascript_helpers/#boxed). In `mynewapp/templates/records/todo_item.html`
+[Boxed filter](../reference/javascript/javascript_helpers/#boxed). In `mynewapp/templates/records/todo_item.html`
 change the last `span` to look like this:
 
 ```html
@@ -312,4 +312,4 @@ in your application. You can inspect these APIs interactively at the url:
 ### What next?
 
 This is just a glimpse at the full range of functionality that comes with Opal - there is
-much more to discover in the [Topic Guides](/guides/topic-guides/).
+much more to discover in the [Topic Guides](guides/topic-guides.md).

doc/mkdocs.yml

@@ -123,7 +123,7 @@ dev_addr: 0.0.0.0:8965
 include_next_prev: false
 
 extra:
-  version: v0.14.0
+  version: v0.17.0
 
 markdown_extensions:
     - fenced_code

opal/_version.py

@@ -1,4 +1,4 @@
 """
 Declare our current version string
 """
-__version__ = '0.14.1'
+__version__ = '0.17.0'

opal/admin.py

@@ -27,10 +27,6 @@ class UserProfileInline(admin.StackedInline):
     filter_horizontal = ('roles',)
 
 
-class FilterInline(admin.StackedInline):
-    model = models.Filter
-
-
 class UserProfileAdmin(UserAdmin):
     add_fieldsets = (
         (None, {
@@ -42,7 +38,7 @@ class UserProfileAdmin(UserAdmin):
             )
         }),
     )
-    inlines = [UserProfileInline, FilterInline, ]
+    inlines = [UserProfileInline]
 
     def get_actions(self, request):
         actions = super(UserProfileAdmin, self).get_actions(request)
@@ -63,6 +59,23 @@ def has_delete_permission(self, request, obj=None):
                 return False
         return True
 
+    def save_formset(self, request, form, formset, change):
+        """
+        The user profile is already created by a signal so
+        attatch the existing user profile if after the user
+        has been saved.
+        """
+        if change:
+            super().save_formset(request, form, formset, change)
+        else:
+            instances = formset.save(commit=False)
+            profile = UserProfile.objects.get(user_id=form.instance.id)
+            for i in instances:
+                i.id = profile.id
+                i.user = profile.user
+                i.save()
+            formset.save_m2m()
+
 
 class MyAdmin(VersionAdmin):
     pass

opal/core/patient_lists.py

@@ -284,7 +284,7 @@ def for_list(klass, patient_list):
             if not issubclass(patient_list, PatientList):
                 raise ValueError(msg)
         except TypeError:
-                raise ValueError(msg)
+            raise ValueError(msg)
 
         for group in klass.list():
             if patient_list in group.get_member_lists():

opal/core/search/tests/test_views.py

@@ -295,6 +295,29 @@ def test_with_multiple_patient_episodes(self):
         }
         self.assertEqual(response, expected)
 
+    @patch('opal.core.search.views.PAGINATION_AMOUNT', 2)
+    def test_patients_more_than_pagination_amount(self):
+        """
+        Prior to 0.16.0 the implementation would sometimes
+        return results with fewer than the number of results
+        that should have been on that page.
+
+        This is because a subquery was paginating by the
+        number of episodes rather than the number of
+        patients.
+        """
+        blofeld_patient, blofeld_episode = self.create_patient(
+            "Ernst", "Blofeld", "23422"
+        )
+        blofeld_patient.create_episode()
+
+        response = json.loads(
+            self.get_response(
+                '{}/?query=o'.format(self.url)
+            ).content.decode('UTF-8')
+        )
+        self.assertEqual(len(response["object_list"]), 2)
+
 
 class SearchTemplateTestCase(OpalTestCase):
 

opal/core/search/views.py

@@ -109,8 +109,9 @@ def simple_search_view(request):
     # on postgres it blows up if we don't manually manage this
     if not paginated_patients:
         paginated_patients = models.Patient.objects.none()
+
     episodes = models.Episode.objects.filter(
-        id__in=paginated_patients.values_list("episode__id", flat=True)
+        patient__in=paginated_patients
     )
     paginated["object_list"] = query.get_aggregate_patients_from_episodes(
         episodes