Merge pull request #614 from Apurva-Nagar/master

Sample Test: added sample choices, patient object for sample report details and file permissions for staff user

.pre-commit-config.yaml

@@ -1,4 +1,4 @@
-exclude: 'docs|node_modules|migrations|.git|.tox'
+exclude: "docs|node_modules|migrations|.git|.tox"
 default_stages: [commit]
 fail_fast: true
 
@@ -15,7 +15,6 @@ repos:
         name: fix end of files.
         description: Ensures that a file is either empty, or ends with one newline.
 
-
   - repo: https://github.com/asottile/seed-isort-config
     rev: v2.1.0
     hooks:
@@ -31,7 +30,7 @@ repos:
     hooks:
       - id: black
         args: [--line-length=120, --safe]
-        language_version: python3.7
+        language_version: python3
 
   - repo: https://github.com/myint/autoflake
     rev: v1.4
@@ -41,12 +40,12 @@ repos:
 
   - repo: local
     hooks:
-#      - id: flake8
-#        name: flake8
-#        entry: flake8
-#        language: python
-#        types: [python]
-#        args: ['--config=setup.cfg']
+      #      - id: flake8
+      #        name: flake8
+      #        entry: flake8
+      #        language: python
+      #        types: [python]
+      #        args: ['--config=setup.cfg']
 
       - id: pre-commit-django-migrations
         name: Check django migrations
@@ -55,7 +54,6 @@ repos:
         types: [python]
         pass_filenames: false
         require_serial: true
-
 #      - id: pre-commit-django-tests
 #        name: Run Django unit tests
 #        entry: python manage.py test --settings=config.settings.test -n

care/facility/api/serializers/file_upload.py

@@ -1,22 +1,13 @@
-from care.facility.models.patient_sample import PatientSample
-from care.facility.api.serializers import facility
-from django.core.exceptions import ValidationError
-from django.db.models import F
 from rest_framework import serializers
 
-
-from care.facility.models.file_upload import FileUpload
-
-from care.users.api.serializers.user import UserBaseMinimumSerializer
-from config.serializers import ChoiceField
+from care.facility.api.serializers.shifting import has_facility_permission
+from care.facility.models.facility import Facility
 from care.facility.models.file_upload import FileUpload
-
 from care.facility.models.patient import PatientRegistration
 from care.facility.models.patient_consultation import PatientConsultation
-
+from care.facility.models.patient_sample import PatientSample
 from care.users.api.serializers.user import UserBaseMinimumSerializer
-
-from care.facility.api.serializers.shifting import has_facility_permission
+from config.serializers import ChoiceField
 
 
 def check_permissions(file_type, associating_id, user):
@@ -57,6 +48,9 @@ def check_permissions(file_type, associating_id, user):
                 if sample.consultation.assigned_to:
                     if user == sample.consultation.assigned_to:
                         return sample.id
+            if sample.testing_facility:
+                if has_facility_permission(user, Facility.objects.get(external_id=sample.testing_facility.external_id)):
+                    return sample.id
             if not has_facility_permission(user, patient.facility):
                 raise Exception("No Permission")
             return sample.id

care/facility/api/serializers/patient_sample.py

@@ -4,7 +4,8 @@
 
 from care.facility.api.serializers import TIMESTAMP_FIELDS
 from care.facility.api.serializers.facility import FacilityBasicInfoSerializer
-from care.facility.models import PatientConsultation, PatientRegistration, Facility
+from care.facility.api.serializers.patient import PatientDetailSerializer
+from care.facility.models import Facility, PatientConsultation, PatientRegistration
 from care.facility.models.patient_sample import SAMPLE_TYPE_CHOICES, PatientSample, PatientSampleFlow
 from care.utils.serializer.external_id_field import ExternalIdSerializerField
 from config.serializers import ChoiceField
@@ -19,6 +20,7 @@ class Meta:
 
 
 class PatientSampleSerializer(serializers.ModelSerializer):
+    patient_object = PatientDetailSerializer(source="patient", read_only=True)
     id = serializers.UUIDField(source="external_id", read_only=True)
     patient_name = serializers.CharField(read_only=True, source="patient.name")
     patient_has_sari = serializers.BooleanField(read_only=True, source="patient.has_SARI")

care/facility/migrations/0272_auto_20210825_1248.py

@@ -0,0 +1,18 @@
+# Generated by Django 2.2.11 on 2021-08-25 07:18
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('facility', '0271_auto_20210815_1617'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='patientsample',
+            name='sample_type',
+            field=models.IntegerField(choices=[(0, 'UNKNOWN'), (1, 'BA/ETA'), (2, 'TS/NPS/NS'), (3, 'Blood in EDTA'), (4, 'Acute Sera'), (5, 'Covalescent sera'), (6, 'Biopsy'), (7, 'AMR'), (8, 'Communicable'), (9, 'OTHER TYPE')], default=0),
+        ),
+    ]

care/facility/migrations/0273_auto_20210825_1829.py

@@ -0,0 +1,18 @@
+# Generated by Django 2.2.11 on 2021-08-25 12:59
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('facility', '0272_auto_20210825_1248'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='patientsample',
+            name='sample_type',
+            field=models.IntegerField(choices=[(0, 'UNKNOWN'), (1, 'BA/ETA'), (2, 'TS/NPS/NS'), (3, 'Blood in EDTA'), (4, 'Acute Sera'), (5, 'Covalescent sera'), (6, 'Biopsy'), (7, 'AMR'), (8, 'Communicable Diseases'), (9, 'OTHER TYPE')], default=0),
+        ),
+    ]

care/facility/models/patient_sample.py

@@ -10,7 +10,10 @@
     (3, "Blood in EDTA"),
     (4, "Acute Sera"),
     (5, "Covalescent sera"),
-    (6, "OTHER TYPE"),
+    (6, "Biopsy"),
+    (7, "AMR"),
+    (8, "Communicable Diseases"),
+    (9, "OTHER TYPE"),
 ]
 
 
@@ -40,13 +43,16 @@ class PatientSample(FacilityBaseModel):
     SAMPLE_TEST_FLOW_CHOICES = [(v, k) for k, v in SAMPLE_TEST_FLOW_MAP.items()]
     SAMPLE_FLOW_RULES = {
         # previous rule      # next valid rules
-        "REQUEST_SUBMITTED": {"APPROVED", "DENIED",},
+        "REQUEST_SUBMITTED": {
+            "APPROVED",
+            "DENIED",
+        },
         "APPROVED": {"SENT_TO_COLLECTON_CENTRE", "RECEIVED_AND_FORWARED", "RECEIVED_AT_LAB", "COMPLETED"},
         "DENIED": {"REQUEST_SUBMITTED"},
         "SENT_TO_COLLECTON_CENTRE": {"RECEIVED_AND_FORWARED", "RECEIVED_AT_LAB", "COMPLETED"},
         "RECEIVED_AND_FORWARED": {"RECEIVED_AT_LAB", "COMPLETED"},
         "RECEIVED_AT_LAB": {"COMPLETED"},
-        "COMPLETED" : {"COMPLETED"}
+        "COMPLETED": {"COMPLETED"},
     }
 
     patient = models.ForeignKey(PatientRegistration, on_delete=models.PROTECT)

setup.cfg

@@ -26,4 +26,4 @@ django_settings_module = config.settings.test
 ignore_errors = True
 
 [isort]
-known_third_party = allauth,boto3,celery,crispy_forms,dateparser,dateutil,django,django_filters,django_rest_passwordreset,djangoql,djqscsv,drf_extra_fields,drf_yasg,dry_rest_permissions,environ,fernet_fields,freezegun,hardcopy,location_field,multiselectfield,partial_index,phonenumber_field,phonenumbers,pytz,pywebpush,ratelimit,requests,rest_framework,rest_framework_nested,rest_framework_simplejwt,sentry_sdk,simple_history
+known_third_party = allauth,boto3,celery,crispy_forms,dateparser,dateutil,django,django_filters,django_rest_passwordreset,djangoql,djqscsv,drf_extra_fields,drf_yasg,dry_rest_permissions,environ,fernet_fields,freezegun,hardcopy,jsonschema,location_field,multiselectfield,partial_index,phonenumber_field,phonenumbers,pytz,pywebpush,ratelimit,requests,rest_framework,rest_framework_nested,rest_framework_simplejwt,sentry_sdk,simple_history