Merge pull request #149 from swiftss-org/fix-failing-build

Fix failing build

.pre-commit-config.yaml

@@ -6,7 +6,7 @@ repos:
   - hooks:
       - id: detect-secrets
         args: [ '--baseline', '.pre-commit/.secrets.baseline' ]
-        exclude: (config/settings/test.py|/static|.html|local|README.md)
+        exclude: (config/settings/test.py|/static|.html|local|README.md|.pre-commit/|test_views.py)
     repo: https://github.com/Yelp/detect-secrets.git
     rev: v1.4.0
 
@@ -75,6 +75,6 @@ repos:
 
   - hooks:
       - id: bandit
-        args: [ --verbose, -ll, --recursive, . ]
+        args: [ --verbose, -ll, . ]
     repo: https://github.com/PyCQA/bandit
     rev: 1.7.7

README.md

@@ -24,8 +24,8 @@ If you want to run _outside_ of Docker you will also need to:
 
 If you are on _Windows_ and not Linux (or other *nix) you will also need to have installed:
 1. [MSYS](https://www.msys2.org/) or an alternative set of Unix compatible tools that includes `make`.
-1. [Microsoft C++ Build Tools](https://visualstudio.microsoft.com/visual-cpp-build-tools/) which are required to install some of the Python [Django](https://www.djangoproject.com/) dependencies. 
- 
+1. [Microsoft C++ Build Tools](https://visualstudio.microsoft.com/visual-cpp-build-tools/) which are required to install some of the Python [Django](https://www.djangoproject.com/) dependencies.
+
 
 ### First time only
 
@@ -37,9 +37,9 @@ pyenv virtualenv registry-api
 pyenv activate registry-api
 ```
 
-Or if you prefer to use [virtualenv](https://virtualenv.pypa.io/en/latest/) directly without pyenv: 
+Or if you prefer to use [virtualenv](https://virtualenv.pypa.io/en/latest/) directly without pyenv:
 ```
-# Linux 
+# Linux
 $ virtualenv venv
 $ activate venv
 

checkInCheck.sh

@@ -0,0 +1,3 @@
+#!/usr/bin/env bash
+
+make pre-commit && make run && make test

config/asgi.py

@@ -7,6 +7,7 @@
 https://docs.djangoproject.com/en/dev/howto/deployment/asgi/
 
 """
+
 import os
 import sys
 from pathlib import Path

config/urls.py

@@ -33,9 +33,9 @@
         TemplateView.as_view(
             template_name="pages/home.html",
             extra_context={
-                "only_token_auth": True
-                if "production" in module_type
-                else False
+                "only_token_auth": (
+                    True if "production" in module_type else False
+                )
             },
         ),
         name="home",

config/wsgi.py

@@ -13,6 +13,7 @@
 framework.
 
 """
+
 import os
 import sys
 from pathlib import Path

requirements/local.txt

@@ -22,7 +22,7 @@ flake8==3.8.4  # https://github.com/PyCQA/flake8
 flake8-isort==4.0.0  # https://github.com/gforcada/flake8-isort
 coverage==5.5  # https://github.com/nedbat/coveragepy
 black==20.8b1  # https://github.com/ambv/black
-pylint-django==2.4.4  # https://github.com/PyCQA/pylint-django
+pylint-django==2.5.4  # https://github.com/PyCQA/pylint-django
 pre-commit==2.10.1  # https://github.com/pre-commit/pre-commit
 isort==4.3.21  # https://github.com/PyCQA/isort
 

tmh_registry/common/utils/functions.py

@@ -3,8 +3,12 @@ def get_text_choice_value_from_label(choices, label):
     if not label:
         return None
 
-    values = [choice[0] for choice in choices if choice[1].upper() == label.upper()]
+    values = [
+        choice[0] for choice in choices if choice[1].upper() == label.upper()
+    ]
     if len(values) == 0:
-        raise IndexError('Unable to find label "{}" in choices "{}"'.format(label, choices))
+        raise IndexError(
+            'Unable to find label "{}" in choices "{}"'.format(label, choices)
+        )
 
     return values[0]

tmh_registry/contrib/sites/migrations/0003_set_site_domain_and_name.py

@@ -3,6 +3,7 @@
 
 http://cookiecutter-django.readthedocs.io/en/latest/faq.html#why-is-there-a-django-contrib-sites-directory-in-cookiecutter-django
 """
+
 from django.conf import settings
 from django.db import migrations
 

tmh_registry/registry/admin.py

@@ -1,26 +1,29 @@
 from django.contrib import admin
-from import_export.admin import ExportMixin
-from import_export import resources
 from django.contrib.auth.admin import UserAdmin
 from django.contrib.auth.models import User
-
+from import_export import resources
+from import_export.admin import ExportMixin
 
 from tmh_registry.registry.models import (
+    Discharge,
     Episode,
+    FollowUp,
     Hospital,
     Patient,
-    PatientHospitalMapping, Discharge, FollowUp,
+    PatientHospitalMapping,
 )
 
 
 @admin.register(Discharge)
 class DischargeAdmin(ExportMixin, admin.ModelAdmin):
     model = Discharge
 
+
 @admin.register(FollowUp)
 class FollowUpAdmin(ExportMixin, admin.ModelAdmin):
     model = FollowUp
 
+
 @admin.register(Hospital)
 class HospitalAdmin(ExportMixin, admin.ModelAdmin):
     model = Hospital
@@ -44,14 +47,17 @@ class EpisodeAdmin(ExportMixin, admin.ModelAdmin):
 """
 To allow CSV export on User model
 """
+
+
 class UserResource(resources.ModelResource):
     class Meta:
         model = User
-        fields = ('first_name', 'last_name', 'email')
+        fields = ("first_name", "last_name", "email")
+
 
 class UserAdmin(ExportMixin, UserAdmin):
     resource_class = UserResource
-    pass
+
 
 admin.site.unregister(User)
 admin.site.register(User, UserAdmin)

tmh_registry/registry/api/serializers.py

@@ -1,6 +1,6 @@
 from drf_yasg.utils import swagger_serializer_method
 from rest_framework.exceptions import ValidationError
-from rest_framework.fields import CharField, IntegerField, BooleanField
+from rest_framework.fields import BooleanField, CharField, IntegerField
 from rest_framework.relations import PrimaryKeyRelatedField
 from rest_framework.serializers import ModelSerializer, SerializerMethodField
 
@@ -150,9 +150,9 @@ def create(self, validated_data):
 
         if not validated_data.get("year_of_birth", None):
             if validated_data["age"]:
-                validated_data[
-                    "year_of_birth"
-                ] = Patient.get_year_of_birth_from_age(validated_data["age"])
+                validated_data["year_of_birth"] = (
+                    Patient.get_year_of_birth_from_age(validated_data["age"])
+                )
             else:
                 raise ValidationError(
                     {
@@ -448,7 +448,7 @@ def create(self, validated_data):
                 ),
                 diathermy_used=validated_data["diathermy_used"],
                 antibiotic_used=validated_data["antibiotic_used"],
-                antibiotic_type=validated_data.get("antibiotic_type", "")
+                antibiotic_type=validated_data.get("antibiotic_type", ""),
             )
         except IndexError:
             raise ValidationError(
@@ -473,7 +473,7 @@ class Meta:
             "aware_of_mesh",
             "infection",
             "discharge_duration",
-            "comments"
+            "comments",
         ]
 
 
@@ -492,7 +492,7 @@ class Meta:
             "aware_of_mesh",
             "infection",
             "discharge_duration",
-            "comments"
+            "comments",
         ]
 
     def to_representation(self, instance):
@@ -515,7 +515,7 @@ def create(self, validated_data):
             aware_of_mesh=validated_data["aware_of_mesh"],
             infection=validated_data.get("infection", ""),
             discharge_duration=validated_data.get("discharge_duration", None),
-            comments=validated_data.get("comments", "")
+            comments=validated_data.get("comments", ""),
         )
 
         return discharge
@@ -539,7 +539,7 @@ class Meta:
             "infection",
             "numbness",
             "further_surgery_need",
-            "surgery_comments_box"
+            "surgery_comments_box",
         ]
 
 
@@ -551,7 +551,9 @@ class FollowUpWriteSerializer(ModelSerializer):
         write_only=True, many=True, queryset=MedicalPersonnel.objects.all()
     )
     pain_severity = CharField()
-    surgery_comments_box = CharField(required=False, allow_blank=True, allow_null=True)
+    surgery_comments_box = CharField(
+        required=False, allow_blank=True, allow_null=True
+    )
     further_surgery_need = BooleanField()
 
     class Meta:
@@ -566,7 +568,7 @@ class Meta:
             "infection",
             "numbness",
             "further_surgery_need",
-            "surgery_comments_box"
+            "surgery_comments_box",
         ]
 
     def to_representation(self, instance):
@@ -596,17 +598,21 @@ def create(self, validated_data):
         follow_up = FollowUp.objects.create(
             episode_id=episode.id,
             date=validated_data["date"],
-            pain_severity=get_text_choice_value_from_label(
-                FollowUp.PainSeverityChoices.choices, pain_severity
-            )
-            if pain_severity
-            else "",
+            pain_severity=(
+                get_text_choice_value_from_label(
+                    FollowUp.PainSeverityChoices.choices, pain_severity
+                )
+                if pain_severity
+                else ""
+            ),
             mesh_awareness=validated_data["mesh_awareness"],
             seroma=validated_data["seroma"],
             infection=validated_data["infection"],
             numbness=validated_data["numbness"],
             further_surgery_need=validated_data["further_surgery_need"],
-            surgery_comments_box=validated_data.get("surgery_comments_box", "")
+            surgery_comments_box=validated_data.get(
+                "surgery_comments_box", ""
+            ),
         )
 
         follow_up.attendees.set(attendees)

tmh_registry/registry/api/viewsets.py

@@ -1,13 +1,13 @@
 from django.core.exceptions import ObjectDoesNotExist
-from django.db.models import Q, CharField
+from django.db.models import CharField, Q
+from django.db.models.functions import Cast
 from django.utils.decorators import method_decorator
 from django_filters import (  # pylint: disable=E0401
     CharFilter,
     NumberFilter,
     OrderingFilter,
 )
 from django_filters.rest_framework import FilterSet  # pylint: disable=E0401
-from django.db.models.functions import Cast
 from drf_yasg import openapi
 from drf_yasg.openapi import IN_QUERY, TYPE_INTEGER, TYPE_STRING, Parameter
 from drf_yasg.utils import swagger_auto_schema
@@ -68,15 +68,26 @@ def filter_hospital(self, queryset, name, value):
         return queryset
 
     def filter_search_term(self, queryset, name, value):
-        selected_hospital_id_value = self.data.get('hospital_id')
+        selected_hospital_id_value = self.data.get("hospital_id")
         if value:
-            patient_ids = PatientHospitalMapping.objects.annotate(
-                patient_hospital_id_str=Cast('patient_hospital_id', CharField())
-            ).filter(
-                Q(patient_hospital_id_str__contains=str(value)) & Q(hospital_id=selected_hospital_id_value)
-            ).values_list("patient_id", flat=True)
+            patient_ids = (
+                PatientHospitalMapping.objects.annotate(
+                    patient_hospital_id_str=Cast(
+                        "patient_hospital_id", CharField()
+                    )
+                )
+                .filter(
+                    Q(patient_hospital_id_str__contains=str(value))
+                    & Q(hospital_id=selected_hospital_id_value)
+                )
+                .values_list("patient_id", flat=True)
+            )
+            # pylint: disable=unsupported-binary-operation
             queryset = queryset.filter(
-                Q(full_name__icontains=value) | Q(national_id__icontains=value) | Q(id__in=patient_ids)
+                Q(full_name__icontains=value)
+                | Q(national_id__iexact=value)
+                | Q(id__in=patient_ids)
+                # pylint: enable=unsupported-binary-operation
             )
             return queryset
         return queryset

tmh_registry/registry/migrations/0017_auto_20221029_1535.py

@@ -6,13 +6,24 @@
 class Migration(migrations.Migration):
 
     dependencies = [
-        ('registry', '0016_auto_20220222_1415'),
+        ("registry", "0016_auto_20220222_1415"),
     ]
 
     operations = [
         migrations.AlterField(
-            model_name='episode',
-            name='episode_type',
-            field=models.CharField(choices=[('INGUINAL', 'Inguinal Mesh Hernia Repair'), ('INCISIONAL', 'Incisional Mesh Hernia Repair'), ('FEMORAL', 'Femoral Mesh Hernia Repair'), ('UMBILICAL', 'Umbilical/Periumbilicial Mesh Hernia Repair')], max_length=128),
+            model_name="episode",
+            name="episode_type",
+            field=models.CharField(
+                choices=[
+                    ("INGUINAL", "Inguinal Mesh Hernia Repair"),
+                    ("INCISIONAL", "Incisional Mesh Hernia Repair"),
+                    ("FEMORAL", "Femoral Mesh Hernia Repair"),
+                    (
+                        "UMBILICAL",
+                        "Umbilical/Periumbilicial Mesh Hernia Repair",
+                    ),
+                ],
+                max_length=128,
+            ),
         ),
     ]

tmh_registry/registry/migrations/0018_auto_20221029_1546.py

@@ -6,18 +6,33 @@
 class Migration(migrations.Migration):
 
     dependencies = [
-        ('registry', '0017_auto_20221029_1535'),
+        ("registry", "0017_auto_20221029_1535"),
     ]
 
     operations = [
         migrations.AlterField(
-            model_name='episode',
-            name='side',
-            field=models.CharField(choices=[('NA', 'Not Applicable'), ('LEFT', 'Left'), ('RIGHT', 'Right')], max_length=16),
+            model_name="episode",
+            name="side",
+            field=models.CharField(
+                choices=[
+                    ("NA", "Not Applicable"),
+                    ("LEFT", "Left"),
+                    ("RIGHT", "Right"),
+                ],
+                max_length=16,
+            ),
         ),
         migrations.AlterField(
-            model_name='episode',
-            name='type',
-            field=models.CharField(choices=[('NA', 'Not Applicable'), ('DIRECT', 'Direct'), ('INDIRECT', 'Indirect'), ('PANTALOON', 'Pantaloon')], max_length=16),
+            model_name="episode",
+            name="type",
+            field=models.CharField(
+                choices=[
+                    ("NA", "Not Applicable"),
+                    ("DIRECT", "Direct"),
+                    ("INDIRECT", "Indirect"),
+                    ("PANTALOON", "Pantaloon"),
+                ],
+                max_length=16,
+            ),
         ),
     ]