Merge 0ce132e into 61f4c09

openhealthcare · Oct 26, 2018 · 1658802 · 1658802
2 parents 61f4c09 + 0ce132e
commit 1658802
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diff --git a/.travis.yml b/.travis.yml
@@ -4,6 +4,8 @@ python:
   - "3.4"
   - "3.5"
   - "3.6"
+services:
+  - postgresql
 install:
   - python setup.py develop
   - gem install coveralls-lcov
@@ -13,6 +15,7 @@ install:
 before_script:
   - export DISPLAY=:99.0
   - sh -e /etc/init.d/xvfb start
+  - psql -c 'create database travis_ci_test;' -U postgres
 script:
   - opal test --coverage
   - flake8

diff --git a/MANIFEST.in b/MANIFEST.in
@@ -7,4 +7,5 @@ recursive-include opal/core/search/static *
 recursive-include opal/core/search/templates *
 recursive-include opal/core/pathway/static *
 recursive-include opal/core/pathway/templates *
+recursive-include opal/core/referencedata/data/lookuplists *
 recursive-include opal/tests/js_config *
diff --git a/README.md b/README.md
@@ -18,7 +18,7 @@ From there, Opal provides you with a common batteries-included architecture for
 applications, and a composable modular framework that takes advantage of generic, re-usable components.
 
 Opal is entirely open ([source](https://github.com/openhealthcare/opal) &
-[Governance](https://github.com/openhealthcare/opal/issues)) as are the wide library of plugins.
+[governance](https://github.com/openhealthcare/opal/issues)) as are the wide library of plugins.
 
 Opal was created by [Open Health Care UK](http://openhealthcare.org.uk), because it makes Healthcare IT Less Bad.
 

diff --git a/changelog.md b/changelog.md
@@ -1,9 +1,82 @@
+### 0.13.0 (Major Release)
+
+#### Removes scope.jumpToEpisode and scope.getEpisodeId from Search and Extract
+
+We no longer use these functions, instead we use an HTML link to the patient detail view.
+
+#### Removes Patient.to_dict().active_episode_id
+
+We no longer include a value for "active_episode_id" as part of the Patient to_dict serialisation.
+
+This is effectively meaningless since we moved to an episode model that allows for multiple
+concurrent episodes.
+
+
+#### Removes CopyToCategory
+
+Removes the entire CopyToCategory flow from Opal Core. If applications continue to rely on it,
+they are advised to implement at application level.
+
+In general application developers are advised to find alternative ways to display subrecords
+from multiple episodes rather than copying them however, as this is known to cause duplication
+of data that is hard to trace back later on.
+
+This includes the API endpoint at `episode/$id/actions/copyto/$category/`, the template
+`copy_to_category.html`, the Angular controller `CopyToCategoryCtrl` and service
+`CopyToCategory` and Subrecord property `_clonable`.
+
+
+#### Lookuplist data format
+
+Lookuplist entries in data files are no longer required to have an empty synonyms list
+if the entry doesn't have a synonym. This reduces the file size and makes it easier to
+hand craft data files for new applications.
+
+
+#### Removes the deprecated Model._title property
+
+Use of `Model._title` to set a display name of a subrecord has issued a warning for several
+releases - this has now been removed and will no longer work.
+
+#### Misc Changes
+
+* The undocumented Reopen Episode flow included in Opal < 0.8.0 has now been completely removed,
+including the `reopen_episode_modal.html` template and the url/view at `templates/modals/reopen_episode.html/`.
+
+* Removes the method `.deleteItem` from the `RecordEditor` service.
+
+* Adds in a footer updated/created by to the form base template
+
+
+### 0.12.0 (Major Release)
+
+#### Misc Changes
+* Adds the {% block analytics %} in the base template (opal/templates/base.html) that by default contains the google analytics code.
+
+* Adds the block {% block javascripts %} in the base template (opal/templates/base.html) that will compress all javascripts.
+
+* Adds a method `.demographics()` to `opal.models.Patient` which returns the relevant demographics instance.
+
+* Adds a `for_user` method on to the menu item. This method
+takes a user and by default returns True. Override this
+to decide if a menu item should be shown in the nav bar.
+
+### 0.11.2 (Bugfix Release)
+
+Includes referencedata JSON files in Manifest.
+
+### 0.11.1 (Bugfix Release)
+Fixes the user_options in the date picker tag to display the options as part of the text input.
+
 ### 0.11.0 (Major Release)
 
 #### Adds options of `today` and `yesterday` in the date picker
-If you pass in `user_options=True` to the date picker. You will be provided with options to select today or yesterday in the form tag.
+
+If you pass in `user_options=True` to the date picker. You will be provided with
+options to select today or yesterday in the form tag.
 
 #### Adds `dateHelper` to the rootScope
+
 The dateHelper has the functions `now` and `yesterday` that return javascript Dates for
 the current time and the current time - 1 day.
 
@@ -21,11 +94,13 @@ Fixes a bug whereby episodes were serialising differently depending on whether
 the code path went via `.to_dict()` or `.objects.serialised()`.
 
 #### HelpTextStep can now use a custom template
+
 The `opal.core.pathway.steps.HelpTextStep` can now have a `help_text_template` passed in.
 
 This is the template for what will be placed in the side bar.
 
 #### Adds in a radio_vertical template tag
+
 This displays the label and then the radio
 buttons as a vertical list.
 
@@ -65,7 +140,6 @@ for a method named `get_$attr` and will call that if it exists.
 Adds the method `.get_absolute_url()` to `opal.core.pathways.Pathway` and
 `opal.core.patient_lists.PatientList`.
 
-
 #### Template removals
 
 We removed a number of superfluous templates:
@@ -96,11 +170,9 @@ override `base.html`in your application we advise that you add this `<meta>` tag
 a generator function which will yield all subrecord singletons.
 * Fixes a URI encoding bug in the `Episode.findByHospitalNumber()` method that
 made hospital numbers including `#` or `/` raise an error.
-
 * Adds the methods `.get_absolute_url()`, `.get_icon()` and `get_display_name()`
 to `opal.core.pathways.Pathway` and `opal.core.patient_lists.PatientList`.
 
-
 #### Updates to the Dependency Graph
 
 * Django compressor: 1.5 -> 2.2

diff --git a/config/karma.conf.js b/config/karma.conf.js
@@ -10,8 +10,6 @@ module.exports = function(config){
     var includedFiles = [
       'opal/app.js',
       'opal/routes.js',
-      '../../core/pathway/static/js/pathway/**/*.js',
-      '../../core/search/static/js/search/**/*.js',
       'test/*.js',
       '../../core/search/static/js/test/*',
       '../../core/pathway/static/js/test/*',

diff --git a/doc/docs/guides/flow.md b/doc/docs/guides/flow.md
@@ -34,7 +34,7 @@ wish to be called.
     enter: function(){
             return {
                 'controller': 'HospitalNumberCtrl',
-                'template'  : '/templates/modals/hospital_number.html/'
+                'template'  : '/templates/hospital_number_modal.html/'
             }
         }
 
@@ -64,6 +64,6 @@ that acts differently for deceased patients might look as follows
           }
           return {
               'controller': 'DischargeEpisodeCtrl',
-              'template'  : '/templates/modals/discharge_episode.html/'
+              'template'  : '/templates/discharge_episode_modal.html'
           }
         }
diff --git a/doc/docs/guides/releasing.md b/doc/docs/guides/releasing.md
@@ -1,25 +1,26 @@
 # Making a Release
+1. Make and deploy a version to test it on a windows machines.
 
-1. Tag the HEAD of the release branch and push to github: `git tag <version> && git push --tags`.
+2. Tag the HEAD of the release branch and push to github: `git tag <version> && git push --tags`.
 Opal branch names are in the format `vX.Y.Z` the tag for a release should be the `X.Y.Z` component
 of the branch name.
 
-1. Check version is correct in `_version.py`.
+3. Check version is correct in `_version.py`.
 
-1. Make sure you have `twine` installed and then: `make release`
+4. Make sure you have `twine` installed and then: `make release`
 
-1. Merge the branch you are releasing into `master`
+5. Merge the branch you are releasing into `master`
 
-1. Update the Github release page and make sure that it has the relevant Changelog contents.
+6. Update the Github release page and make sure that it has the relevant Changelog contents.
 
-1. If the branch for the next version does not already exist, create that branch. For instance, if you
+7. If the branch for the next version does not already exist, create that branch. For instance, if you
 have released `x.y.z` then create `x.y.(z+1)`. If you are creating a new version branch, ensure you have
 also changed the version number in the documentation, `opal._version.__version__`, and the branches that
 any badges in the project README are pointing at.
 
-1. Change the github default branch to be the new in development version
+8. Change the github default branch to be the new in development version
 
-1. Update the Opal website: Change the current release and development version on the homepage, and run
+9. Update the Opal website: Change the current release and development version on the homepage, and run
 `rake docs` to regenerate the documentation site with a new latest stable release version.
 
-1. Post to the Opal mailing list to announce the new release.
+10. Post to the Opal mailing list to announce the new release.
diff --git a/doc/docs/guides/working_with_data_in_angular.md b/doc/docs/guides/working_with_data_in_angular.md
@@ -40,9 +40,6 @@ episode.recordEditor.newItem('diagnosis'):
 
 episode.recordEditor.editItem('diagnosis', 0);
 // -> Opens a modal that allows the user to edit the first diagnosis
-
-episode.recordEditor.deleteItem('diagnosis', 0);
-// -> Prompts the user to confirm the deletion of the first diagnosis
 ```
 
 ## Customising Subrecords

diff --git a/doc/docs/img/detail_1.png b/doc/docs/img/detail_1.png
diff --git a/doc/docs/reference/core_menus.md b/doc/docs/reference/core_menus.md
@@ -2,7 +2,7 @@
 
 Opal provides classes and methods to define application menus programatically.
 
-## opal.core.MenuItem
+### opal.core.MenuItem
 
 An item in an application menu.
 
@@ -15,7 +15,12 @@ An item in an application menu.
 * display - the text to display in this menu item
 * index - a number to use as the primary sort order for your menu items
 
-## opal.core.Menu
+**Methods**
+
+#### for_user
+A method that takes a user and returns True by default. Override this if you want menu items hidden for certain users.
+
+### opal.core.Menu
 
 The menu for an Opal application. On initialization it will construct a menu
 for the current user, pulling items from the current app, and any plugins.
diff --git a/doc/docs/reference/javascript/episode_service.md b/doc/docs/reference/javascript/episode_service.md
@@ -61,14 +61,6 @@ episode.recordEditor.newItem('diagnosis'):
 // -> Opens a modal with the diagnosis form and will create a new diagnosis on save
 ```
 
-#### Episode.recordEditor.deleteItem(name, index)
-
-Delete the `index-th` item of type `name`. Prompt the user to confirm this with a dialog.
-
-```js
-episode.recordEditor.deleteItem('diagnosis', 0);
-// -> Prompts the user to confirm the deletion of the first diagnosis
-```
 #### Episode.recordEditor.editItem(name, index)
 
 Open a modal from which the user may edit the `index-th` item of type `name`.

diff --git a/doc/docs/reference/panels_templatetags.md b/doc/docs/reference/panels_templatetags.md
@@ -11,7 +11,7 @@ instances of the given model, as well as editing any existing ones.
 Render a panel for a given record that will allow the user to view, create, update and delete instances.
 
 The record panel template expects the relevant Angular `$scope` to have `newNamedItem(name, index)`,
-`editNamedItem(name, index)` and `deleteItem(name, index)` methods implemented. Default
+`editNamedItem(name, index)` methods implemented. Default
 implementations of these are available from the `EpisodeDetailMixin`.
 
     {% load panels %}

diff --git a/doc/docs/reference/patient.md b/doc/docs/reference/patient.md
@@ -2,7 +2,11 @@
 
 ### methods
 
-#### create_episode
+#### `Patient.demographics()`
+
+Returns the relevant Demographics instance for the patient.
+
+#### `Patient.create_episode()`
 
 Returns a new `Episode` for this patient.
 

diff --git a/doc/docs/reference/subrecords.md b/doc/docs/reference/subrecords.md
@@ -58,16 +58,6 @@ Name of the field by which we want to sort these records when displaying.
         _sort = 'start_date'
 ```
 
-#### Subrecord._clonable
-
-A Boolean that is True by default used by `opal.views.EpisodeCopyToCategoryView`
-to determine if instances of this record should be copied across.
-
-```python
-    class Antimicrobial(EpisodeSubrecord):
-        _clonable = 'False'
-```
-
 #### Subrecord._exclude_from_extract
 
 Boolean to specify that this subrecord should be excluded from any standard data extract.
@@ -104,7 +94,7 @@ Classmethod that returns the display name of the subrecord.
 This is used as the user visible title of subrecord panels and modals amongst other places.
 
 By default this uses the Django
-[Meta verbose_name](https://docs.djangoproject.com/en/dev/ref/models/options/#verbose-name) 
+[Meta verbose_name](https://docs.djangoproject.com/en/dev/ref/models/options/#verbose-name)
 property
 
 ```python

diff --git a/doc/docs/reference/upgrading.md b/doc/docs/reference/upgrading.md
@@ -3,6 +3,14 @@
 This document provides instructions for specific steps required to upgrading your Opal
 application to a later version where there are extra steps required.
 
+### 0.11.1 -> 0.11.2
+
+This bugfix release should be entirely backwards compatible.
+
+### 0.11.0 -> 0.11.1
+
+This bugfix release should be entirely backwards compatible.
+
 ### 0.10.1 -> 0.11.0
 
 Please upgrade django-compressor version to 2.2, ie update your requirements to

diff --git a/doc/docs/tutorial.md b/doc/docs/tutorial.md
@@ -120,7 +120,8 @@ 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/lookup_lists/).
+[Lookup List](/guides/referencedata/).
+
 
 Lookup Lists allow us to reference canonical lists of available terminology as a foreign key, while
 also allowing synonymous terms, and a free text override. That means that we can ensure that
@@ -262,7 +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_helpers/). 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
@@ -295,7 +296,7 @@ We also have a detail view for our patients, which you can access via search res
 view will typically allow for a more detailed display and editing of all the events
 comprising a patient's care than is available on the list page.
 
-<img src="/img/detail.png" style="margin: 12px auto; border: 1px solid black; width: 600px;"/>
+<img src="/img/detail_1.png" style="margin: 12px auto; border: 1px solid black; width: 600px;"/>
 
 
 #### JSON APIs

diff --git a/doc/mkdocs.yml b/doc/mkdocs.yml
@@ -120,7 +120,7 @@ dev_addr: 0.0.0.0:8965
 include_next_prev: false
 
 extra:
-  version: v0.11.0
+  version: v0.13.0
 
 markdown_extensions:
     - fenced_code
diff --git a/opal/_version.py b/opal/_version.py
@@ -1,4 +1,4 @@
 """
 Declare our current version string
 """
-__version__ = '0.11.0'
+__version__ = '0.13.0'
diff --git a/opal/core/api.py b/opal/core/api.py
@@ -319,7 +319,7 @@ def create(self, request):
             patient, created = Patient.objects.get_or_create(
                 demographics__hospital_number=hospital_number)
             if created:
-                demographics = patient.demographics_set.get()
+                demographics = patient.demographics()
                 demographics.hospital_number = hospital_number
                 demographics.save()
         else:

diff --git a/opal/core/application.py b/opal/core/application.py
@@ -66,7 +66,6 @@ class OpalApplication(object):
             "js/opal/services/patient_loader.js",
             "js/opal/services/episode_resource.js",
             "js/opal/services/record_editor.js",
-            "js/opal/services/copy_to_category.js",
             "js/opal/services/patientlist_loader.js",
             'js/opal/services/fields_translater.js',
             'js/opal/services/referencedata.js',
@@ -86,7 +85,6 @@ class OpalApplication(object):
             "js/opal/controllers/account.js",
             "js/opal/controllers/discharge.js",
             "js/opal/controllers/undischarge.js",
-            "js/opal/controllers/copy_to_category.js",
             "js/opal/controllers/keyboard_shortcuts.js",
             "js/opal/controllers/patient_access_log.js",
             "js/opal/controllers/lookup_list_reference.js"
@@ -142,7 +140,7 @@ def get_menu_items(klass, user=None):
                 items.append(logout)
                 if user.is_staff:
                     items.append(admin)
-        return items
+        return [item for item in items if item.for_user(user)]
 
     @classmethod
     def get_menu(klass, user=None):