Merge upstream v0.13.0

openhealthcare · Nov 2, 2018 · f1c0d76 · f1c0d76
2 parents e3cc92a + b13c275
commit f1c0d76
Show file tree

Hide file tree

Showing 17 changed files with 235 additions and 85 deletions.
diff --git a/changelog.md b/changelog.md
@@ -6,6 +6,20 @@ Due to the upgrade to Django 2.x, Opal no longer supports Python 2.x.
 
 Opal is now tested against Python 3.5, 3.6
 
+#### Episode.active
+
+The field `Episode.active` was previously implicitly set when calling `.set_tag_names()` to
+something equivalent to the value of `bool(len(tag_names) > 0)`.
+
+As of 0.13.0 the value of `Episode.active` is checked whenever `.save()` is called, prior
+to the database call. The correct value is looked up via `Episode.category.is_active()`.
+
+The default calculation of `.active` has also changed to be roughly equivalent to
+` bool(self.episode.end is None)`.
+
+Applications are now able to easily _change_ this behaviour by overriding the `.is_active`
+method of the relevant `EpisodeCategory`.
+
 #### Coding systems for lookuplists
 
 Lookuplist entries may now have an associated coding system and code value stored against them.

diff --git a/doc/custom_theme/base.html b/doc/custom_theme/base.html
@@ -12,10 +12,16 @@
 
 	<title>{% if page_title %}{{ page_title }} - {% endif %}{{ site_name }}</title>
 
-        <link href="{{ base_url }}/css/bootstrap-custom.min.css" rel="stylesheet">
-        <link href="{{ base_url }}/css/font-awesome-4.0.3.css" rel="stylesheet">
-        <link rel="stylesheet" href="{{ base_url }}/css/highlight.css">
-        <link href="{{ base_url }}/css/base.css" rel="stylesheet">
+        <link href="{{ 'css/bootstrap-custom.min.css'|url }}" rel="stylesheet">
+        <link href="{{ 'css/font-awesome.min.css'|url }}" rel="stylesheet">
+        <link href="{{ 'css/base.css'|url }}" rel="stylesheet">
+        {%- if config.theme.highlightjs %}
+        <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/highlight.js/9.12.0/styles/{{ config.theme.hljs_style }}.min.css">
+        {%- endif %}
+        <!-- <link href="{{ base_url }}/css/bootstrap-custom.min.css" rel="stylesheet"> -->
+        <!-- <link href="{{ base_url }}/css/font-awesome-4.0.3.css" rel="stylesheet"> -->
+        <!-- <link rel="stylesheet" href="{{ base_url }}/css/highlight.css"> -->
+        <!-- <link href="{{ base_url }}/css/base.css" rel="stylesheet"> -->
         {%- for path in extra_css %}
         <link href="{{ path }}" rel="stylesheet">
         {%- endfor %}
@@ -26,21 +32,9 @@
             <script src="https://oss.maxcdn.com/libs/respond.js/1.3.0/respond.min.js"></script>
         <![endif]-->
 
-        {% if google_analytics %}
-        <script>
-            (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
-            (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
-            m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
-            })(window,document,'script','//www.google-analytics.com/analytics.js','ga');
-
-            ga('create', '{{ google_analytics[0] }}', '{{ google_analytics[1] }}');
-            ga('send', 'pageview');
-        </script>
-        {% endif %}
     </head>
 
     <body>
-
         {% include "nav.html" %}
 
         <div class="container">
@@ -57,11 +51,20 @@
               <a href="http://openhealthcare.org.uk" target="_blank">Open Health Care UK</i></a>.
             </center>
         </footer>
+        <script>
+            var base_url = {{ base_url | tojson }},
+                shortcuts = {{ config.theme.shortcuts | tojson }};
+        </script>
 
-        <script src="{{ base_url }}/js/jquery-1.10.2.min.js"></script>
-        <script src="{{ base_url }}/js/bootstrap-3.0.3.min.js"></script>
-        <script src="{{ base_url }}/js/highlight.pack.js"></script>
-        <script src="{{ base_url }}/js/base.js"></script>
+        <script src="{{ 'js/jquery-1.10.2.min.js'|url }}" defer></script>
+        <script src="{{ 'js/bootstrap-3.0.3.min.js'|url }}" defer></script>
+        {%- if config.theme.highlightjs %}
+        <script src="https://cdnjs.cloudflare.com/ajax/libs/highlight.js/9.12.0/highlight.min.js"></script>
+        {%- for lang in config.theme.hljs_languages %}
+        <script src="https://cdnjs.cloudflare.com/ajax/libs/highlight.js/9.12.0/languages/{{lang}}.min.js"></script>
+        {%- endfor %}
+        <script>hljs.initHighlightingOnLoad();</script>
+        {%- endif %}
         {%- for path in extra_javascript %}
         <script src="{{ path }}"></script>
         {%- endfor %}

diff --git a/doc/custom_theme/content.html b/doc/custom_theme/content.html
@@ -0,0 +1 @@
+{{ page.content }}
diff --git a/doc/custom_theme/nav.html b/doc/custom_theme/nav.html
@@ -35,7 +35,7 @@
                 <!-- </li> -->
             {% else %}
                 <li {% if nav_item.active %}class="active"{% endif %}>
-                    <a href="{{ nav_item.url }}">{{ nav_item.title }}</a>
+                    <a href="{{ nav_item.url | url }}">{{ nav_item.title }}</a>
                 </li>
             {% endif %}
             {% endfor %}

diff --git a/doc/custom_theme/toc.html b/doc/custom_theme/toc.html
@@ -1,7 +1,7 @@
 <div class="bs-sidebar hidden-print affix well" role="complementary">
   <h3>Contents</h3>
     <ul class="nav bs-sidenav">
-    {% for toc_item in toc %}
+    {% for toc_item in page.toc %}
         <li class="main {% if toc_item.active %}active{% endif %}"><a href="{{ toc_item.url }}">{{ toc_item.title }}</a></li>
         {% for toc_item in toc_item.children %}
             <li><a href="{{ toc_item.url }}">{{ toc_item.title }}</a></li>

diff --git a/doc/docs/guides/episodes.md b/doc/docs/guides/episodes.md
@@ -54,25 +54,6 @@ class Application(application.OpalApplication):
     default_episode_category = MyCategory.display_name
 ```
 
-## Episode stages
-
-An Episode will frequently consist of a number of possible stages. For instance,
-for an inpatient episode, a patient will first be an inpatient, and then an
-be discharged, with an optional interim follow up stage for inpatients who have been
-discharged but requrie further follow up.
-
-Opal stores the stage of an episode as a string in the `stage` property of an
-`Episode`. The valid possible stages for a category are accessed from the
-`get_stages` method of the category.
-
-```
-episode.category.get_stages()
-# ['Inpatient', 'Followup', 'Discharged']
-
-episode.category.has_stage('Followup')
-# True
-```
-
 ## Defining your own EpisodeCategory
 
 As EpisodeCategory is a [discoverable](discoverable) we can define our own to
@@ -92,3 +73,55 @@ class DropInClinicEpisode(episodes.EpisodeCategory):
     detail_template = "detail/drop_in.html"
 
 ```
+
+## Episode.active
+
+The field `.active` is used to distinguish Episodes which are ongoing. This field
+is set implicitly by the `Episode.save()` method, and there will generally be no
+need to set this field directly as part of application code.
+
+Whether an Episode is considered active is determined by the `.is_active()` method
+of the relevant EpisodeCategory.
+
+The default implementation considers any Episode without an `.end` date to be active
+and any Episode with one to be inactive.
+
+Applications may customise this behaviour by overriding the `.is_active()` method.
+
+For instance, to create a category which considered any Episode older than 2 weeks to
+be inactive, one might override the method as follows:
+
+```python
+# yourapp/episode_categories.py
+import datetime
+from opal.core import episodes
+
+
+class TwoWeeksAndStopCaringEpisode(episodes.EpisodeCategory):
+    def is_active(self):
+        delta = datetime.date.today() - self.episode.start
+        return bool(delta >= datetime.timedelta(days=14))
+
+```
+
+(Note that this would not alter the value in the database immediately after those 2
+weeks, but would alter the value the next time the `Episode.save()` method was called.)
+
+## Episode stages
+
+An Episode will frequently consist of a number of possible stages. For instance,
+for an inpatient episode, a patient will first be an inpatient, and then an
+be discharged, with an optional interim follow up stage for inpatients who have been
+discharged but requrie further follow up.
+
+Opal stores the stage of an episode as a string in the `stage` property of an
+`Episode`. The valid possible stages for a category are accessed from the
+`get_stages` method of the category.
+
+```
+episode.category.get_stages()
+# ['Inpatient', 'Followup', 'Discharged']
+
+episode.category.has_stage('Followup')
+# True
+```
diff --git a/doc/docs/reference/episode_categories.md b/doc/docs/reference/episode_categories.md
@@ -65,6 +65,17 @@ InpatientEpisode(episode).has_stage('Inpatient')
 # -> True
 ```
 
+### EpisodeCategory.is_active()
+
+Predicate function to determine whether this episode is active.
+
+The default implementation looks to see whether an end date has
+been set on the episode.
+
+```python
+InpatientEpisode(Episode()).is_active()
+# -> True
+```
 
 ### EpisodeCategory.set_stage(stage, user, data)
 

diff --git a/doc/mkdocs.yml b/doc/mkdocs.yml
@@ -1,5 +1,6 @@
 site_name: Opal
 docs_dir: docs
+
 pages:
   - Home: index.md
   - installation.md
@@ -110,11 +111,13 @@ pages:
 
 
 
-theme: mkdocs
-theme: cerulean
-theme: cosmo
-theme_dir: 'custom_theme'
+#theme: mkdocs
+theme:
+  name: cosmo
+  custom_dir: 'custom_theme/'
 
+extra_css:
+  - opaldocs.css
 
 dev_addr: 0.0.0.0:8965
 include_next_prev: false

diff --git a/doc/requirements.txt b/doc/requirements.txt
@@ -1,3 +1,3 @@
-mkdocs-bootstrap==0.1.1
-mkdocs-bootswatch==0.4.0
-mkdocs==0.15.3
+mkdocs-bootstrap==1.0.1
+mkdocs-bootswatch==1.0
+mkdocs==1.0.4
diff --git a/opal/core/episodes.py b/opal/core/episodes.py
@@ -50,6 +50,15 @@ def episode_visible_to(kls, episode, user):
     def __init__(self, episode):
         self.episode = episode
 
+    def is_active(self):
+        """
+        Predicate function to determine whether this episode is active.
+
+        The default implementation looks to see whether an end date has
+        been set on the episode.
+        """
+        return bool(self.episode.end is None)
+
     def get_stages(self):
         """
         Return the list of string stages for this category

diff --git a/opal/core/exceptions.py b/opal/core/exceptions.py
@@ -39,5 +39,9 @@ class MissingTemplateError(Error):
     pass
 
 
+class UnexpectedEpisodeCategoryNameError(Error):
+    pass
+
+
 class InvalidDataError(Error):
     pass
diff --git a/opal/models.py b/opal/models.py
@@ -689,14 +689,42 @@ class Episode(UpdatesFromDictMixin, TrackedModel):
 
     objects = managers.EpisodeQueryset.as_manager()
 
+    def __init__(self, *args, **kwargs):
+        super(Episode, self).__init__(*args, **kwargs)
+        self.__original_active = self.active
+
     def __unicode__(self):
         return 'Episode {0}: {1} - {2}'.format(
             self.pk, self.start, self.end
         )
 
     def save(self, *args, **kwargs):
         created = not bool(self.id)
+
+        current_active_value = self.active
+        category_active_value = self.category.is_active()
+
+        if current_active_value != category_active_value:  # Disagreement
+            if current_active_value != self.__original_active:
+                # The value of self.active has been set by some code somewhere
+                # not by __init__() e.g. the original database value at the
+                # time of instance initalization.
+                #
+                # Rather than overriding this silently we should raise a
+                # ValueError.
+                msg = "Value of Episode.active has been set to {} but " \
+                      "category.is_active() returns {}"
+                raise ValueError(
+                    msg.format(current_active_value, category_active_value)
+                )
+
+        self.active = category_active_value
         super(Episode, self).save(*args, **kwargs)
+
+        # Re-set this in case we changed it once post initialization and then
+        # the user subsequently saves this instance again
+        self.__original_active = self.active
+
         if created:
             for subclass in episode_subrecords():
                 if subclass._is_singleton:
@@ -705,10 +733,16 @@ def save(self, *args, **kwargs):
     @property
     def category(self):
         from opal.core import episodes
-        category = episodes.EpisodeCategory.filter(
+        categories = episodes.EpisodeCategory.filter(
             display_name=self.category_name
-        )[0]
-        return category(self)
+        )
+        if len(categories) == 0:
+            msg = "Unable to find EpisodeCategory for category name {0}"
+            msg = msg.format(self.category_name)
+            raise exceptions.UnexpectedEpisodeCategoryNameError(msg)
+        else:
+            category = categories[0]
+            return category(self)
 
     def visible_to(self, user):
         """
@@ -731,20 +765,12 @@ def set_stage(self, stage, user, data):
 
     def set_tag_names(self, tag_names, user):
         """
-        1. Set the episode.active status
-        2. Special case mine
-        3. Archive dangling tags not in our current list.
-        4. Add new tags.
-        5. Ensure that we're setting the parents of child tags
-        6. There is no step 6.
+        1. Special case mine
+        2. Archive dangling tags not in our current list.
+        3. Add new tags.
+        4. Ensure that we're setting the parents of child tags
+        5. There is no step 6.
         """
-        if len(tag_names) and not self.active:
-            self.active = True
-            self.save()
-        elif not len(tag_names) and self.active:
-            self.active = False
-            self.save()
-
         if "mine" not in tag_names:
             self.tagging_set.filter(user=user,
                                     value='mine').update(archived=True)

diff --git a/opal/tests/test_core_episodes.py b/opal/tests/test_core_episodes.py
@@ -1,6 +1,8 @@
 """
 Unittests for opal.core.episodes
 """
+import datetime
+
 from django.contrib.auth.models import User
 
 from opal.core import test
@@ -17,7 +19,7 @@ def setUp(self):
         )
         self.patient = Patient.objects.create()
         self.inpatient_episode = self.patient.create_episode(
-            category_name=episodes.InpatientEpisode
+            category_name=episodes.InpatientEpisode.display_name
         )
 
     def test_episode_categories(self):
@@ -42,6 +44,15 @@ def test_for_category(self):
         self.assertEqual(episodes.InpatientEpisode,
                          episodes.EpisodeCategory.get('inpatient'))
 
+    def test_is_active(self):
+        category = episodes.InpatientEpisode(self.inpatient_episode)
+        self.assertTrue(category.is_active())
+
+    def test_is_active_end_date_set(self):
+        self.inpatient_episode.end = datetime.date.today()
+        category = episodes.InpatientEpisode(self.inpatient_episode)
+        self.assertFalse(category.is_active())
+
     def test_get_stages(self):
         stages = [
             'Inpatient',