Merge pull request #661 from openhealthcare/660-labs-module-move

moves the lab module accross from a plugin to part of the application…

.coveragerc

@@ -2,6 +2,7 @@
 source =
        elcid
        intrahospital_api
+       lab
 
 omit =
     */migrations/*
@@ -11,6 +12,7 @@ omit =
     elcid/settings.py
     elcid/local_settings.py
     elcid/templates/acceptance/*
+    lab/tests/*
 
 
 [report]

elcid/settings.py

@@ -210,7 +210,7 @@
 
 
 if 'test' in sys.argv:
-    INSTALLED_APPS += ('opal.tests',)
+    INSTALLED_APPS += ('lab.tests',)
     PASSWORD_HASHERS = (
         'django.contrib.auth.hashers.MD5PasswordHasher',
     )

intrahospital_api/test/test_api.py

@@ -71,7 +71,7 @@ def test_contains_empty_patient_subrecords(self):
         patient, episode = self.new_patient_and_episode_please()
         result = api.patient_to_dict(patient, self.user)
         self.assertEqual(
-            result["house_owner"], []
+            result["lab_test"], []
         )
 
     @mock.patch("intrahospital_api.api.patient_to_dict")

intrahospital_api/test/test_loader.py

@@ -179,42 +179,6 @@ def test_log_errors(self, err):
         err.assert_called_once_with("blah")
 
 
-class AnyLoadsRunningTestCase(ApiTestCase):
-    def setUp(self):
-        super(AnyLoadsRunningTestCase, self).setUp()
-        self.patient, _ = self.new_patient_and_episode_please()
-
-    def test_any_loads_running_initial_patient_load(self):
-        imodels.InitialPatientLoad.objects.create(
-            state=imodels.InitialPatientLoad.RUNNING,
-            patient=self.patient,
-            started=timezone.now()
-        )
-        self.assertTrue(loader.any_loads_running())
-
-    def test_any_loads_running_batch_patient_load(self):
-        imodels.BatchPatientLoad.objects.create(
-            state=imodels.BatchPatientLoad.RUNNING,
-            started=timezone.now()
-        )
-        self.assertTrue(loader.any_loads_running())
-
-    def test_any_loads_running_none(self):
-        self.assertFalse(loader.any_loads_running())
-
-    def test_any_loads_running_false(self):
-        imodels.InitialPatientLoad.objects.create(
-            state=imodels.InitialPatientLoad.SUCCESS,
-            patient=self.patient,
-            started=timezone.now()
-        )
-        imodels.BatchPatientLoad.objects.create(
-            state=imodels.BatchPatientLoad.SUCCESS,
-            started=timezone.now()
-        )
-        self.assertFalse(loader.any_loads_running())
-
-
 class LoadDemographicsTestCase(ApiTestCase):
 
     @mock.patch.object(loader.api, 'demographics')
@@ -614,3 +578,37 @@ def test_update_patient_from_batch_integration(self):
         self.assertEqual(
             observation["result"], "Positive"
         )
+
+
+class AnyLoadsRunningTestCase(ApiTestCase):
+    def test_any_loads_running_initial_patient_load(self):
+        patient, _ = self.new_patient_and_episode_please()
+        imodels.InitialPatientLoad.objects.create(
+            state=imodels.InitialPatientLoad.RUNNING,
+            patient=patient,
+            started=timezone.now()
+        )
+        self.assertTrue(loader.any_loads_running())
+
+    def test_any_loads_running_batch_patient_load(self):
+        imodels.BatchPatientLoad.objects.create(
+            state=imodels.BatchPatientLoad.RUNNING,
+            started=timezone.now()
+        )
+        self.assertTrue(loader.any_loads_running())
+
+    def test_any_loads_running_none(self):
+        self.assertFalse(loader.any_loads_running())
+
+    def test_any_loads_running_false(self):
+        patient, _ = self.new_patient_and_episode_please()
+        imodels.InitialPatientLoad.objects.create(
+            state=imodels.InitialPatientLoad.SUCCESS,
+            patient=patient,
+            started=timezone.now()
+        )
+        imodels.BatchPatientLoad.objects.create(
+            state=imodels.BatchPatientLoad.SUCCESS,
+            started=timezone.now()
+        )
+        self.assertFalse(loader.any_loads_running())

lab/__init__.py

@@ -0,0 +1,3 @@
+"""
+Package definition
+"""

lab/admin.py

@@ -0,0 +1,22 @@
+from reversion.admin import VersionAdmin
+from reversion import revisions as reversion
+from lab.models import LabTest, Observation
+from opal.utils import _itersubclasses
+from django.contrib import admin
+
+
+class LabTestAdmin(VersionAdmin):
+    pass
+
+
+def register_lab_tests():
+    for lab_test in LabTest.list():
+        if not getattr(lab_test, "_no_admin", False):
+            admin.site.register(lab_test, LabTestAdmin)
+
+        for obs in _itersubclasses(Observation):
+            if not reversion.is_registered(obs):
+                admin.site.register(obs, LabTestAdmin)
+
+
+register_lab_tests()

lab/context_processors.py

@@ -0,0 +1,14 @@
+from django.utils.functional import SimpleLazyObject
+from lab.models import LabTest
+
+
+class LabTestContextProcessor(object):
+    def __init__(self):
+        for i in LabTest.list():
+            setattr(self, i.__name__, i)
+
+
+def lab_tests(request):
+    return {
+        "lab_tests": SimpleLazyObject(LabTestContextProcessor)
+    }

lab/metadata.py

@@ -0,0 +1,20 @@
+from opal.core import metadata
+from lab.models import LabTest
+
+
+class LabTestMetadata(metadata.Metadata):
+    slug = "lab_tests"
+
+    @classmethod
+    def to_dict(klass, **kw):
+        result = dict(lab_tests=dict(all_tests=[]))
+        for lab_test in LabTest.list():
+            for synonym in lab_test.get_synonyms():
+                result["lab_tests"][synonym] = dict(
+                    result_form_url=lab_test.get_result_form_url(),
+                    record_url=lab_test.get_record_url(),
+                    display_name=lab_test.get_display_name()
+                )
+                if lab_test.HAS_FORM:
+                    result["lab_tests"]["all_tests"].append(synonym)
+        return result

lab/migrations/0001_initial.py

@@ -0,0 +1,142 @@
+# -*- coding: utf-8 -*-
+from __future__ import unicode_literals
+
+from django.db import migrations, models
+import jsonfield.fields
+import opal.models
+from django.conf import settings
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        migrations.swappable_dependency(settings.AUTH_USER_MODEL),
+        ('opal', '0025_merge'),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name='LabTest',
+            fields=[
+                ('id', models.AutoField(verbose_name='ID', serialize=False, auto_created=True, primary_key=True)),
+                ('created', models.DateTimeField(null=True, blank=True)),
+                ('updated', models.DateTimeField(null=True, blank=True)),
+                ('consistency_token', models.CharField(max_length=8)),
+                ('status', models.CharField(blank=True, max_length=256, null=True, choices=[(b'pending', b'pending'), (b'complete', b'complete')])),
+                ('lab_test_type', models.CharField(max_length=256, null=True, blank=True)),
+                ('date_ordered', models.DateField(null=True, blank=True)),
+                ('date_received', models.DateField(null=True, blank=True)),
+                ('extras', jsonfield.fields.JSONField(null=True, blank=True)),
+                ('created_by', models.ForeignKey(related_name='created_lab_labtest_subrecords', blank=True, to=settings.AUTH_USER_MODEL, null=True)),
+                ('patient', models.ForeignKey(to='opal.Patient')),
+                ('resistant_antibiotics', models.ManyToManyField(related_name='test_resistant', to='opal.Antimicrobial')),
+                ('sensitive_antibiotics', models.ManyToManyField(related_name='test_sensitive', to='opal.Antimicrobial')),
+                ('updated_by', models.ForeignKey(related_name='updated_lab_labtest_subrecords', blank=True, to=settings.AUTH_USER_MODEL, null=True)),
+            ],
+            options={
+                'abstract': False,
+            },
+            bases=(opal.models.UpdatesFromDictMixin, opal.models.ToDictMixin, models.Model),
+        ),
+        migrations.CreateModel(
+            name='Observation',
+            fields=[
+                ('id', models.AutoField(verbose_name='ID', serialize=False, auto_created=True, primary_key=True)),
+                ('created', models.DateTimeField(null=True, blank=True)),
+                ('updated', models.DateTimeField(null=True, blank=True)),
+                ('consistency_token', models.CharField(max_length=8)),
+                ('observation_type', models.CharField(max_length=256)),
+                ('extras', jsonfield.fields.JSONField(null=True, blank=True)),
+                ('result', models.CharField(max_length=256, null=True, blank=True)),
+                ('name', models.CharField(max_length=255)),
+                ('created_by', models.ForeignKey(related_name='created_lab_observation_subrecords', blank=True, to=settings.AUTH_USER_MODEL, null=True)),
+                ('lab_test', models.ForeignKey(related_name='observations', to='lab.LabTest')),
+                ('updated_by', models.ForeignKey(related_name='updated_lab_observation_subrecords', blank=True, to=settings.AUTH_USER_MODEL, null=True)),
+            ],
+            options={
+                'abstract': False,
+            },
+            bases=(opal.models.UpdatesFromDictMixin, opal.models.ToDictMixin, models.Model),
+        ),
+        migrations.CreateModel(
+            name='Antimicrobial',
+            fields=[
+            ],
+            options={
+                'proxy': True,
+            },
+            bases=('lab.observation',),
+        ),
+        migrations.CreateModel(
+            name='DynamicLookupList',
+            fields=[
+            ],
+            options={
+                'proxy': True,
+            },
+            bases=('lab.observation',),
+        ),
+        migrations.CreateModel(
+            name='DynamicResultChoices',
+            fields=[
+            ],
+            options={
+                'proxy': True,
+            },
+            bases=('lab.observation',),
+        ),
+        migrations.CreateModel(
+            name='GenericInput',
+            fields=[
+            ],
+            options={
+                'proxy': True,
+            },
+            bases=('lab.observation',),
+        ),
+        migrations.CreateModel(
+            name='Organism',
+            fields=[
+            ],
+            options={
+                'proxy': True,
+            },
+            bases=('lab.observation',),
+        ),
+        migrations.CreateModel(
+            name='PendingPosNeg',
+            fields=[
+            ],
+            options={
+                'proxy': True,
+            },
+            bases=('lab.observation',),
+        ),
+        migrations.CreateModel(
+            name='PosNeg',
+            fields=[
+            ],
+            options={
+                'proxy': True,
+            },
+            bases=('lab.observation',),
+        ),
+        migrations.CreateModel(
+            name='PosNegEquivicalNotDone',
+            fields=[
+            ],
+            options={
+                'proxy': True,
+            },
+            bases=('lab.observation',),
+        ),
+        migrations.CreateModel(
+            name='PosNegUnknown',
+            fields=[
+            ],
+            options={
+                'proxy': True,
+            },
+            bases=('lab.observation',),
+        ),
+    ]

lab/migrations/0002_auto_20161127_1849.py

@@ -0,0 +1,24 @@
+# -*- coding: utf-8 -*-
+from __future__ import unicode_literals
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('lab', '0001_initial'),
+    ]
+
+    operations = [
+        migrations.RenameField(
+            model_name='labtest',
+            old_name='extras',
+            new_name='details',
+        ),
+        migrations.RenameField(
+            model_name='observation',
+            old_name='extras',
+            new_name='details',
+        ),
+    ]

lab/migrations/0003_auto_20161127_1952.py

@@ -0,0 +1,24 @@
+# -*- coding: utf-8 -*-
+from __future__ import unicode_literals
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('lab', '0002_auto_20161127_1849'),
+    ]
+
+    operations = [
+        migrations.RenameField(
+            model_name='labtest',
+            old_name='details',
+            new_name='extras',
+        ),
+        migrations.RenameField(
+            model_name='observation',
+            old_name='details',
+            new_name='extras',
+        ),
+    ]

lab/migrations/0004_auto_20161206_1255.py

@@ -0,0 +1,19 @@
+# -*- coding: utf-8 -*-
+from __future__ import unicode_literals
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('lab', '0003_auto_20161127_1952'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='observation',
+            name='result',
+            field=models.CharField(default=None, max_length=256, null=True, blank=True),
+        ),
+    ]