Merge branch 'v0.11.0' into 1502-test-options

.appveyor.yml

@@ -5,7 +5,9 @@ environment:
 
 install:
   - "SET PATH=%PYTHON%;%PYTHON%\\Scripts;%PATH%"
-  - "pip install --disable-pip-version-check --user --upgrade pip"
+  # This is only pinning to a version rather than --upgrade pip until
+  # such times as the latest Pip doesn't error out with `cannot import name main`
+  - "pip install --disable-pip-version-check --user pip==9.0.3"
   - "%CMD_IN_ENV% python setup.py develop"
   - "pip install -r test-requirements.txt"
 

CHANGELOG.md

@@ -14,6 +14,9 @@ Episode manager, which no longer accepts a `episode_history` kwarg.
 A refactor in the way that the core APIs are registered by Opal means that
 importing `opal.core.api` in a plugin API no longer results in circular imports.
 
+Fixes a bug whereby episodes were serialising differently depending on whether
+the code path went via `.to_dict()` or `.objects.serialised()`.
+
 
 ### 0.10.1 (Minor Release)
 
@@ -30,11 +33,17 @@ Fonts are now served from Opal's static assets rather than from the Google CDN.
 
 Print/screen differences are now in opal.css with media tags.
 
-#### google analytics is now deferred
+#### 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

opal/core/pathway/static/js/pathway/directives.js

@@ -200,7 +200,9 @@ directives.directive("pathwayLink", function($parse){
   };
 });
 
-directives.directive("openPathway", function($parse, $rootScope, Referencedata, Metadata, $modal, episodeLoader){
+directives.directive("openPathway", function($parse, $rootScope, $modal, $q,
+                                             Referencedata, Metadata,
+                                             episodeLoader){
   /*
   * the open modal pathway directive will open a modal pathway for you
   * you can if you use the attribute pathway-callback="{{ some_function }}"
@@ -230,7 +232,10 @@ directives.directive("openPathway", function($parse, $rootScope, Referencedata,
           pathwayCallback = function(){};
         }
         var template = "/pathway/templates/" + pathwaySlug + ".html?is_modal=True";
-        return $modal.open({
+
+        var deferred = $q.defer();
+
+        $modal.open({
           controller : 'ModalPathwayCtrl',
           templateUrl: template,
           size       : 'lg',
@@ -254,7 +259,18 @@ directives.directive("openPathway", function($parse, $rootScope, Referencedata,
             metadata: function(){ return Metadata.load(); },
             referencedata: function(){ return Referencedata.load(); },
           }
-        });
+        }).result.then(
+          function(what){
+            $rootScope.state = 'normal';
+            deferred.resolve(what);
+          },
+          function(what_now){
+            $rootScope.state = 'normal';
+            deferred.resolve(what_now);
+          }
+        )
+
+        return deferred.promise;
       });
     }
   };

opal/core/pathway/static/js/test/directives.test.js

@@ -5,6 +5,7 @@ describe('pathway directives', function(){
   var referencedata, metadata, pathwayLoader;
   beforeEach(module('opal.controllers'));
   beforeEach(module('opal.directives', function($provide){
+
     mockModal = {open: function(){}};
     spyOn(mockModal, "open").and.returnValue({
       result: {
@@ -41,11 +42,11 @@ describe('pathway directives', function(){
   }));
 
   beforeEach(inject(function($injector){
-    var $rootScope = $injector.get('$rootScope');
-    scope = $rootScope.$new();
-    $httpBackend = $injector.get('$httpBackend');
-    $compile = $injector.get('$compile');
-    $parse = $injector.get('$parse');
+    $rootScope    = $injector.get('$rootScope');
+    scope         = $rootScope.$new();
+    $httpBackend  = $injector.get('$httpBackend');
+    $compile      = $injector.get('$compile');
+    $parse        = $injector.get('$parse');
     pathwayLoader = $injector.get('pathwayLoader');
   }));
 
@@ -141,6 +142,37 @@ describe('pathway directives', function(){
       var resolves = mockModal.open.calls.mostRecent().args[0].resolve;
       expect(resolves.episode()).toBe('trees');
     });
+
+    it('should set up the state variable', function() {
+      var markup = '<a href="#" open-pathway="someFakePathway"></a>';
+      mockModal.open.and.returnValue({result: {then:function(cb, eb){
+        // Conspicuously not calling cb();
+      }}})
+      element = $compile(markup)(scope);
+      $(element).click();
+      expect($rootScope.state).toEqual('modal');
+    });
+
+    it('should reset the state variable', function() {
+      var markup = '<a href="#" open-pathway="someFakePathway"></a>';
+      element = $compile(markup)(scope);
+      scope.$digest();
+      $(element).click();
+      scope.$digest();
+      expect($rootScope.state).toEqual('normal');
+    });
+
+    it('should reset the state variable in case of rejection', function() {
+      var markup = '<a href="#" open-pathway="someFakePathway"></a>';
+      mockModal.open.and.returnValue({result: {then:function(cb, eb){
+        eb() // Conspicuously calling the rejection case
+      }}})
+      element = $compile(markup)(scope);
+      $(element).click();
+      scope.$digest();
+      expect($rootScope.state).toEqual('normal');
+    });
+
   });
 
 

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

@@ -65,10 +65,16 @@ def serialised_episode_subrecords(self, episodes, user):
         in a nested hashtable where the outer key is the episode id,
         the inner key the subrecord API name.
         """
-        episode_subs = defaultdict(lambda: defaultdict(list))
+        episode_subs = defaultdict(dict)
+        episode_ids = [e.id for e in episodes]
 
         for model in episode_subrecords():
             name = model.get_api_name()
+
+            # Ensure there is an empty list for serialisation
+            for episode_id in episode_ids:
+                episode_subs[episode_id][name] = []
+
             subrecords = prefetch(
                 model.objects.filter(episode__in=episodes)
             )
@@ -78,6 +84,7 @@ def serialised_episode_subrecords(self, episodes, user):
 
             for sub in subrecords:
                 episode_subs[sub.episode_id][name].append(sub.to_dict(user))
+
         return episode_subs
 
     def serialised(self, user, episodes, historic_tags=False):
@@ -87,11 +94,15 @@ def serialised(self, user, episodes, historic_tags=False):
         If HISTORIC_TAGS is Truthy, return deleted tags as well.
         """
         patient_ids = [e.patient_id for e in episodes]
-        patient_subs = defaultdict(lambda: defaultdict(list))
+        patient_subs = defaultdict(dict)
 
         episode_subs = self.serialised_episode_subrecords(episodes, user)
         for model in patient_subrecords():
             name = model.get_api_name()
+
+            for patient_id in patient_ids:
+                patient_subs[patient_id][name] = []
+
             subrecords = prefetch(
                 model.objects.filter(patient__in=patient_ids)
             )

opal/models.py

@@ -874,28 +874,28 @@ def to_dict(self, user, shallow=False):
         for model in patient_subrecords():
             subrecords = model.objects.filter(patient_id=self.patient.id)
 
-            if subrecords:
-                d[model.get_api_name()] = [
-                    subrecord.to_dict(user) for subrecord in subrecords
-                ]
+            d[model.get_api_name()] = [
+                subrecord.to_dict(user) for subrecord in subrecords
+            ]
+
         for model in episode_subrecords():
             subrecords = model.objects.filter(episode_id=self.id)
 
-            if subrecords:
-                d[model.get_api_name()] = [
-                    subrecord.to_dict(user) for subrecord in subrecords
-                ]
+            d[model.get_api_name()] = [
+                subrecord.to_dict(user) for subrecord in subrecords
+            ]
 
         d['tagging'] = self.tagging_dict(user)
         return d
 
 
 class Subrecord(UpdatesFromDictMixin, ToDictMixin, TrackedModel, models.Model):
-    consistency_token = models.CharField(max_length=8)
-    _is_singleton = False
-    _advanced_searchable = True
+    _is_singleton            = False
+    _advanced_searchable     = True
     _exclude_from_subrecords = False
 
+    consistency_token = models.CharField(max_length=8)
+
     class Meta:
         abstract = True
 

opal/templates/forms/investigation_form.html

@@ -15,7 +15,7 @@
 {% radio label="IgG" model="editing.investigation.vca_igg" show="testType == 'micro_test_ebv_serology'" lookuplist="['pending', 'positive', 'negative', 'equivocal', 'not done']" %}
 {% radio label="EBNA IgG" model="editing.investigation.ebna_igg" show="testType == 'micro_test_ebv_serology'" lookuplist="['pending', 'positive', 'negative', 'equivocal', 'not done']" %}
 
-{% radio label="Result" model="editing.investigation.result" show="testType == 'micro_test_hiv'" lookuplist="['pending', 'antibody positive', 'p24 antigen only', 'negative']" %}
+{% radio label="Result" model="editing.investigation.result" show="testType == 'micro_test_hiv'" lookuplist="['pending', 'antibody positive', 'p24 antigen only', 'negative']" element_name="micro_test_hiv" %}
 
 {% radio label="HBsAg" model="editing.investigation.hbsag" show="testType == 'micro_test_hepititis_b_serology'" lookuplist="['pending', 'positive', 'negative', 'equivocal', 'not done']" %}
 {% radio label="anti-HbS" model="editing.investigation.anti_hbs" show="testType == 'micro_test_hepititis_b_serology'" lookuplist="['pending', 'positive', 'negative', 'equivocal', 'not done']" %}
@@ -25,9 +25,9 @@
 {% input label="RPR" model="editing.investigation.rpr" show="testType == 'micro_test_syphilis_serology'" %}
 {% radio label="TPPA" model="editing.investigation.tppa" show="testType == 'micro_test_syphilis_serology'" lookuplist="['pending', 'positive', 'negative']" %}
 
-{% radio label="Result" model="editing.investigation.result" show="testType == 'micro_test_single_test_pos_neg'" lookuplist="['pending', 'positive', 'negative']" element_name="test_pos_neg" %}
+{% radio label="Result" model="editing.investigation.result" show="testType == 'micro_test_single_test_pos_neg'" lookuplist="['pending', 'positive', 'negative']" element_name="micro_test_single_test_pos_neg" %}
 
-{% radio label="Result" model="editing.investigation.result" show="testType == 'micro_test_single_test_pos_neg_equiv'" lookuplist="['pending', 'positive', 'negative', 'equivocal', 'not done']" element_name="test_pos_neg_equiv" %}
+{% radio label="Result" model="editing.investigation.result" show="testType == 'micro_test_single_test_pos_neg_equiv'" lookuplist="['pending', 'positive', 'negative', 'equivocal', 'not done']" element_name="micro_test_single_test_pos_neg_equiv" %}
 
 {% radio label="IgG" model="editing.investigation.igg" show="testType == 'micro_test_single_igg_test'" lookuplist="['pending', 'positive', 'negative', 'equivocal', 'not done']" %}
 
@@ -101,17 +101,17 @@
     <div class="col-sm-8">
 
       <label class="radio-inline">
-        <input class="" type="radio" value="pending" ng-model="editing.investigation.result" name="leish_pcr">
+        <input class="" type="radio" value="pending" ng-model="editing.investigation.result" name="micro_test_leishmaniasis_pcr">
         pending
       </label>
 
       <label class="radio-inline">
-        <input class="" type="radio" value="positive" ng-model="editing.investigation.result" name="leish_pcr">
+        <input class="" type="radio" value="positive" ng-model="editing.investigation.result" name="micro_test_leishmaniasis_pcr">
         positive
       </label>
 
       <label class="radio-inline">
-        <input class="" type="radio" value="negative" ng-model="editing.investigation.result" name="leish_pcr">
+        <input class="" type="radio" value="negative" ng-model="editing.investigation.result" name="micro_test_leishmaniasis_pcr">
         negative
       </label>
 
@@ -538,7 +538,7 @@
   <div class="form-group">
     <label class="control-label col-sm-3">Result</label>
     <div class="col-sm-8">
-      <input class="form-control" type="text" ng-model="editing.investigation.result">
+      <input class="form-control" type="text" ng-model="editing.investigation.result" name="micro_test_other">
     </div>
   </div>