massive refactor app structure and move to mongodb

README.md

@@ -59,26 +59,13 @@ foobar:~foo$ pip install -r requirements/development-requirements
 
 ### Running the database
 
-We advise running the postgresql database from within Docker on port 5432, the default for Django
-
 ```command
-foobar:~foo$ docker run --name [container_name] -e POSTGRES_USER=username -e POSTGRES_PASSWORD=[mysecretpassword] -p 5432:5432 -d postgres
-```
-
-## Connect to the docker container
-
-```console
-foobar:~foo$ docker exec -it [container_name] bash
-root@175d895153ab:/#  psql -U [username]
+foobar:~foo$ docker run --name epilepsy12-mongo-docker -p 27017:27017 -d mongo:latest
 ```
 
 ## Create the database
 
 ```console
-psql (14.0 (Debian 14.0-1.pgdg110+1))
-Type "help" for help.
-
-epilepsy12user=# CREATE DATABASE epilepsy12db;
 ```
 
 ## Prepare the database for use
@@ -103,6 +90,12 @@ you may need to allow permissions to run the bash script in that folder first:
 foobar:~foo$ chmod +x ./s/runserver
 ```
 
+## Create superuser to enable logging into admin section
+
+```console
+python manage.py createsuperuser
+```
+
 ##  Stated Aims of the Audit
 
 * Continue to measure and improve care and outcomes for children and young people with

epilepsy12/general_functions/postcode.py

@@ -0,0 +1,29 @@
+import re
+
+
+def valid_postcode(postcode) -> bool:
+    """
+    Validation function for UK postcodes
+    Returns either a regexp match or 'not matched'
+    ACKNOWLEDGEMENT: with thanks to https://kodey.co.uk/2020/09/03/a-uk-postcode-validation-script-in-python/
+    """
+    pattern = 'not matched'
+    #e.g. W27XX
+    if len(postcode.replace(" ", "")) == 5:
+        pattern = re.compile("^[a-zA-Z]{1}[0-9]{2}[a-zA-Z]{2}")
+    #e.g. TW27XX
+    elif len(postcode.replace(" ", "")) == 6:
+        pattern = re.compile("^[a-zA-Z]{2}[0-9]{2}[a-zA-Z]{2}")
+    #e.g. TW218FF
+    elif len(postcode.replace(" ", "")) == 7:
+        pattern = re.compile("^[a-zA-Z]{2}[0-9]{3}[a-zA-Z]{2}")
+
+    return pattern
+
+
+def validate_postcode(postcode: str) -> bool:
+    valid_postcode_regex = valid_postcode(postcode=postcode)
+    if(valid_postcode_regex.match('not matched')):
+        return False
+    else:
+        return True

rcpch-audit-engine/epilepsy12/migrations/0001_initial.py → epilepsy12/migrations/0001_initial.py

@@ -1,9 +1,7 @@
-# Generated by Django 4.0 on 2022-03-09 07:56
+# Generated by Django 4.0 on 2022-03-09 13:11
 
-import django.core.validators
 from django.db import migrations, models
 import django.db.models.deletion
-import epilepsy12.general_functions.postcode
 import uuid
 
 
@@ -48,21 +46,21 @@ class Migration(migrations.Migration):
         migrations.CreateModel(
             name='Case',
             fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
                 ('created_at', models.DateTimeField(auto_now_add=True)),
                 ('updated_at', models.DateTimeField(auto_now=True)),
-                ('case_uuid', models.UUIDField(default=uuid.uuid4, editable=False, primary_key=True, serialize=False, verbose_name='Unique case identifier')),
                 ('locked', models.BooleanField(default=False, verbose_name='Locked')),
                 ('locked_at', models.DateTimeField(auto_now_add=True, verbose_name='Date record locked')),
                 ('nhs_patient', models.BooleanField(verbose_name='Is an NHS patient?')),
-                ('nhs_number', models.IntegerField(validators=[django.core.validators.MinLengthValidator(limit_value=10, message='The NHS number must be 10 digits long.')], verbose_name='NHS Number')),
+                ('nhs_number', models.IntegerField(verbose_name='NHS Number')),
                 ('first_name', models.CharField(max_length=100, verbose_name='first name')),
                 ('surname', models.CharField(max_length=100, verbose_name='surname')),
-                ('gender', models.CharField(choices=[(0, 'Not Known'), (1, 'Male'), (2, 'Female'), (9, 'Not Specified')], max_length=2, verbose_name='gender')),
+                ('gender', models.IntegerField(choices=[(0, 'Not Known'), (1, 'Male'), (2, 'Female'), (9, 'Not Specified')])),
                 ('date_of_birth', models.DateField(verbose_name='date of birth (YYYY-MM-DD)')),
-                ('postcode', models.CharField(max_length=7, validators=[epilepsy12.general_functions.postcode.validate_postcode], verbose_name='postcode')),
+                ('postcode', models.CharField(max_length=7, verbose_name='postcode')),
                 ('ethnicity', models.CharField(choices=[('N', 'African'), ('L', 'Any other Asian background'), ('P', 'Any other Black background'), ('S', 'Any other ethnic group'), ('G', 'Any other mixed background'), ('C', 'Any other White background'), ('K', 'Bangladeshi or British Bangladeshi'), ('A', 'British, Mixed British'), ('M', 'Caribbean'), ('R', 'Chinese'), ('H', 'Indian or British Indian'), ('B', 'Irish'), ('NULL', 'Not Recorded'), ('Z', 'Not Stated'), ('J', 'Pakistani or British Pakistani'), ('F', 'White and Asian'), ('E', 'White and Black African'), ('D', 'White and Black Caribbean')], max_length=4)),
                 ('created_by', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, related_name='created%(app_label)s_%(class)s_related', to='auth.user', verbose_name='record created by user in %(class)')),
-                ('locked_by', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='auth.user', verbose_name='locked by')),
+                ('locked_by', models.ForeignKey(default=None, on_delete=django.db.models.deletion.CASCADE, to='auth.user', verbose_name='locked by')),
                 ('updated_by', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, related_name='updated%(app_label)s_%(class)s_related', to='auth.user', verbose_name='record updated by user in %(class)')),
             ],
             options={
@@ -419,8 +417,4 @@ class Migration(migrations.Migration):
             model_name='hospitaltrust',
             index=models.Index(fields=['hospital_trust_name'], name='epilepsy12__hospita_a838eb_idx'),
         ),
-        migrations.AddIndex(
-            model_name='case',
-            index=models.Index(fields=['case_uuid'], name='epilepsy12__case_uu_5b975e_idx'),
-        ),
     ]

epilepsy12/migrations/0002_alter_case_options.py

@@ -0,0 +1,17 @@
+# Generated by Django 4.0 on 2022-03-09 13:36
+
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('epilepsy12', '0001_initial'),
+    ]
+
+    operations = [
+        migrations.AlterModelOptions(
+            name='case',
+            options={'verbose_name': 'case', 'verbose_name_plural': 'cases'},
+        ),
+    ]

rcpch-audit-engine/epilepsy12/models/case.py → epilepsy12/models/case.py

@@ -4,10 +4,13 @@
 from django.contrib.auth.models import User
 from django.core.validators import MinLengthValidator
 import uuid
+
+from django.forms import IntegerField
 from ..constants import *
 from ..general_functions import *
 from .time_and_user_abstract_base_classes import *
 
+
 class Case(TimeStampAbstractBaseClass, UserStampAbstractBaseClass):
     """
     This class holds information about each child or young person
@@ -25,75 +28,76 @@ class Case(TimeStampAbstractBaseClass, UserStampAbstractBaseClass):
 
     ?analysis flag
     """
-    case_uuid=models.UUIDField(
-        "Unique case identifier",
-        primary_key=True, 
-        default=uuid.uuid4, 
-        editable=False
-    )
-    locked=models.BooleanField( # this determines if the case is locked from editing ? are cases or only registrations locked?
-        "Locked", 
+    # case_uuid=models.UUIDField(
+    #     "Unique case identifier",
+    #     primary_key=True,
+    #     default=uuid.uuid4,
+    #     editable=False
+    # )
+    locked = models.BooleanField(  # this determines if the case is locked from editing ? are cases or only registrations locked?
+        "Locked",
         default=False
     )
     locked_at = models.DateTimeField(
         "Date record locked",
         auto_now_add=True
     )
     locked_by = models.ForeignKey(
-        User, 
+        User,
         on_delete=CASCADE,
-        verbose_name="locked by"
+        verbose_name="locked by",
+        default=None
     )
     nhs_patient = models.BooleanField(
         "Is an NHS patient?"
     )
-    nhs_number = models.IntegerField( # the NHS number for England and Wales - THIS IS NOT IN THE ORIGINAL TABLES
+    nhs_number = models.IntegerField(  # the NHS number for England and Wales - THIS IS NOT IN THE ORIGINAL TABLES
         "NHS Number",
-        validators=[MinLengthValidator( # should be other validation before saving - need to strip out spaces
-            limit_value=10,
-            message="The NHS number must be 10 digits long."
-        )]
-    ) # TODO #13 NHS Number must be hidden - use case_uuid as proxy
-    first_name=CharField(
+        # validators=[MinLengthValidator(  # should be other validation before saving - need to strip out spaces
+        #     limit_value=10,
+        #     message="The NHS number must be 10 digits long."
+        # )]
+    )  # TODO #13 NHS Number must be hidden - use case_uuid as proxy
+    first_name = CharField(
         "first name",
         max_length=100
     )
-    surname=CharField(
+    surname = CharField(
         "surname",
         max_length=100
     )
-    gender=CharField(
-        "gender",
-        max_length=2,
+    gender = models.IntegerField(
         choices=SEX_TYPE
     )
-    date_of_birth=DateField(
+    date_of_birth = DateField(
         "date of birth (YYYY-MM-DD)"
     )
-    postcode=CharField(
+    postcode = CharField(
         "postcode",
         max_length=7,
-        validators=[validate_postcode]
+        # validators=[validate_postcode]
     )
-    
-    ethnicity=CharField(
+
+    ethnicity = CharField(
         max_length=4,
         choices=ETHNICITIES
     )
 
-    def _imd_quintile_from_postcode(self)->int:
-        "index of multiple deprivation calculated from MySociety data.",
-        if (self.postcode):
-            postcode=validate_postcode(self.postcode)
-            imd_quintile=imd_for_postcode(postcode)
-            return imd_quintile
+    # This field requires the deprivare api to be running
+    # def _imd_quintile_from_postcode(self) -> int:
+    #     "index of multiple deprivation calculated from MySociety data.",
+    #     if (self.postcode):
+    #         postcode = valid_postcode(self.postcode)
+    #         imd_quintile = imd_for_postcode(postcode)
+    #         return imd_quintile
 
-    index_of_multiple_deprivation_quintile=property(_imd_quintile_from_postcode)
+    # index_of_multiple_deprivation_quintile = property(
+    #     _imd_quintile_from_postcode)
 
     class Meta:
-        indexes=[models.Index(fields=['case_uuid'])]
-        verbose_name = 'child or young person'
-        verbose_name_plural = 'children and young people'
+        # indexes = [models.Index(fields=['case_uuid'])]
+        verbose_name = 'case'
+        verbose_name_plural = 'cases'
 
     def __str__(self) -> str:
-        return self.hospital_trust_name
+        return self.first_name + " " + self.surname

rcpch-audit-engine/epilepsy12/models/electroclinical_syndrome.py → epilepsy12/models/electroclinical_syndrome.py

@@ -1,20 +1,23 @@
 from django.db import models
 from ..constants import *
 from .time_and_user_abstract_base_classes import *
+
+
 class ElectroClinicalSyndrome(TimeStampAbstractBaseClass, UserStampAbstractBaseClass):
     """
     This class records information on electroclinical syndromes.
     It references the episode class, since one episode can have features of a single electroclinical syndrome.
     """
-    electroclinical_syndrome=models.IntegerField(choices=ELECTROCLINICAL_SYNDROMES)
-    electroclinical_sydrome_other=models.CharField(
+    electroclinical_syndrome = models.IntegerField(
+        choices=ELECTROCLINICAL_SYNDROMES)
+    electroclinical_syndrome_other = models.CharField(
         default=None,
         max_length=250
     )
 
     class Meta:
-        verbose_name="electroclinical syndrome",
-        verbose_name_plural="electroclinical syndromes"
-    
+        verbose_name = 'electroclinical syndrome'
+        verbose_name_plural = 'electroclinical syndromes'
+
     def __str__(self) -> str:
-        return self.electroclinical_syndrome
+        return self.electroclinical_syndrome

rcpch-audit-engine/epilepsy12/models/epilepsy_context.py → epilepsy12/models/epilepsy_context.py

@@ -1,44 +1,41 @@
 
 from datetime import date
 from django.db import models
-from django.db.models.deletion import CASCADE
 from ..constants import *
 from .time_and_user_abstract_base_classes import *
 
-# other tables
-from .case import Case
 
 class EpilepsyContext(TimeStampAbstractBaseClass, UserStampAbstractBaseClass):
     """
     This class records contextual information that defines epilepsy risk.
     It references the InitialAssessment class, as each case optionally has a single epilepsy context.
     """
-    previous_febrile_seizure=models.CharField(
+    previous_febrile_seizure = models.CharField(
         "has there been a previous febrile seizure?",
         max_length=2,
         choices=OPT_OUT_UNCERTAIN
     )
-    previous_acute_symptomatic_seizure=models.CharField(
+    previous_acute_symptomatic_seizure = models.CharField(
         "has there been a previous acute symptomatic seizure?",
         max_length=2,
         choices=OPT_OUT_UNCERTAIN
     )
-    is_there_a_family_history_of_epilepsy=models.CharField(
+    is_there_a_family_history_of_epilepsy = models.CharField(
         "is there a family history of epilepsy?",
-        max_length=3, 
+        max_length=3,
         choices=OPT_OUT_UNCERTAIN
     )
-    previous_neonatal_seizures=models.CharField(
+    previous_neonatal_seizures = models.CharField(
         "were there seizures in the neonatal period?",
         max_length=2,
         choices=OPT_OUT_UNCERTAIN
     )
-    diagnosis_of_epilepsy_withdrawn=models.CharField(
+    diagnosis_of_epilepsy_withdrawn = models.CharField(
         "has the diagnosis of epilepsy been withdrawn?",
-        max_length=2, 
+        max_length=2,
         choices=OPT_OUT
     )
-    date_of_first_epileptic_seizure=models.DateField(
+    date_of_first_epileptic_seizure = models.DateField(
         "What date was the first reported epileptic seizure?"
     )
 
@@ -49,9 +46,10 @@ def calculate_epilepsy_years(self):
             today = date.today()
             days_between = abs(today-self.date_of_first_epileptic_seizure).days
             return days_between
+
     class Meta:
         verbose_name = 'epilepsy context'
         verbose_name_plural = 'epilepsy contexts'
-    
+
     def __str__(self) -> str:
         return self.date_of_first_epileptic_seizure