this repo has no description
Add API's for Specimen and Observation Definition
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.cursorignore
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.cursorignore
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data/*
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.cursorrules
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.cursorrules
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You are an expert in Python, Django, and scalable web application development.
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Key Principles
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- Write clear, technical responses with precise Django examples.
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- Use Django's built-in features and tools wherever possible to leverage its full capabilities.
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- Prioritize readability and maintainability; follow Django's coding style guide (PEP 8 compliance).
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- Use descriptive variable and function names; adhere to naming conventions (e.g., lowercase with underscores for functions and variables).
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- Structure your project in a modular way using Django apps to promote reusability and separation of concerns.
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Django/Python
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- Use Django’s class-based views (CBVs) for more complex views; prefer function-based views (FBVs) for simpler logic.
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- Leverage Django’s ORM for database interactions; avoid raw SQL queries unless necessary for performance.
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- Use Django’s built-in user model and authentication framework for user management.
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- Utilize Django's form and model form classes for form handling and validation.
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- Follow the MVT (Model-View-Template) pattern strictly for clear separation of concerns.
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- Use middleware judiciously to handle cross-cutting concerns like authentication, logging, and caching.
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Error Handling and Validation
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- Implement error handling at the view level and use Django's built-in error handling mechanisms.
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- Use Django's validation framework to validate form and model data.
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- Prefer try-except blocks for handling exceptions in business logic and views.
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- Customize error pages (e.g., 404, 500) to improve user experience and provide helpful information.
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- Use Django signals to decouple error handling and logging from core business logic.
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Dependencies
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- Django
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- Django REST Framework (for API development)
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- Celery (for background tasks)
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- Redis (for caching and task queues)
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- PostgreSQL or MySQL (preferred databases for production)
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Django-Specific Guidelines
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- Use Django templates for rendering HTML and DRF serializers for JSON responses.
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- Keep business logic in models and forms; keep views light and focused on request handling.
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- Use Django's URL dispatcher (urls.py) to define clear and RESTful URL patterns.
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- Apply Django's security best practices (e.g., CSRF protection, SQL injection protection, XSS prevention).
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- Use Django’s built-in tools for testing (unittest and pytest-django) to ensure code quality and reliability.
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- Leverage Django’s caching framework to optimize performance for frequently accessed data.
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- Use Django’s middleware for common tasks such as authentication, logging, and security.
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Performance Optimization
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- Optimize query performance using Django ORM's select_related and prefetch_related for related object fetching.
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- Use Django’s cache framework with backend support (e.g., Redis or Memcached) to reduce database load.
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- Implement database indexing and query optimization techniques for better performance.
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- Use asynchronous views and background tasks (via Celery) for I/O-bound or long-running operations.
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Key Conventions
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1. Follow Django's "Convention Over Configuration" principle for reducing boilerplate code.
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2. Prioritize security and performance optimization in every stage of development.
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3. Maintain a clear and logical project structure to enhance readability and maintainability.
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Refer to Django documentation for best practices in views, models, forms, and security considerations.
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care/emr/api/viewsets/observation_definition.py
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care/emr/api/viewsets/observation_definition.py
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care/emr/api/viewsets/specimen_definition.py
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care/emr/api/viewsets/specimen_definition.py
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from django_filters import rest_framework as filters
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from rest_framework.exceptions import PermissionDenied
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from rest_framework.generics import get_object_or_404
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from care.emr.api.viewsets.base import (
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EMRBaseViewSet,
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EMRCreateMixin,
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EMRListMixin,
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EMRRetrieveMixin,
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EMRUpdateMixin,
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)
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from care.emr.models.specimen_definition import SpecimenDefinition
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from care.emr.resources.specimen_definition.spec import (
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BaseSpecimenDefinitionSpec,
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SpecimenDefinitionReadSpec,
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)
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from care.facility.models import Facility
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from care.security.authorization import AuthorizationController
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class SpecimenDefinitionFilters(filters.FilterSet):
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status = filters.CharFilter(field_name="status", lookup_expr="iexact")
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class SpecimenDefinitionViewSet(
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EMRCreateMixin, EMRRetrieveMixin, EMRUpdateMixin, EMRListMixin, EMRBaseViewSet
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):
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database_model = SpecimenDefinition
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pydantic_model = BaseSpecimenDefinitionSpec
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pydantic_read_model = SpecimenDefinitionReadSpec
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filterset_class = SpecimenDefinitionFilters
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filter_backends = [filters.DjangoFilterBackend]
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def get_facility_obj(self):
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return get_object_or_404(
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Facility, external_id=self.kwargs["facility_external_id"]
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)
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def perform_create(self, instance):
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instance.facility = self.get_facility_obj()
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super().perform_create(instance)
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def authorize_create(self, instance):
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"""
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The user must have permission to create specimen definition in the facility.
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"""
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facility = self.get_facility_obj()
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if not AuthorizationController.call(
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"can_write_facility_specimen_definition",
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self.request.user,
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facility,
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):
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raise PermissionDenied("Access Denied to Specimen Definition")
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def authorize_update(self, request_obj, model_instance):
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self.authorize_create(model_instance)
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def get_queryset(self):
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"""
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If no facility filters are applied, all objects must be returned without a facility filter.
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If facility filter is applied, check for read permission and return all inside facility.
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"""
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base_queryset = self.database_model.objects.all()
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facility_obj = self.get_facility_obj()
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if not AuthorizationController.call(
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"can_list_facility_specimen_definition",
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self.request.user,
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facility_obj,
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):
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raise PermissionDenied("Access Denied to Specimen Definition")
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return base_queryset.filter(facility=facility_obj)
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care/emr/migrations/0022_observationdefinition.py
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care/emr/migrations/0022_observationdefinition.py
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# Generated by Django 5.1.4 on 2025-04-07 07:16
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import django.db.models.deletion
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import uuid
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from django.conf import settings
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from django.db import migrations, models
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class Migration(migrations.Migration):
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dependencies = [
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('emr', '0021_metaartifact'),
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('facility', '0476_facility_default_internal_organization_and_more'),
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migrations.swappable_dependency(settings.AUTH_USER_MODEL),
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]
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operations = [
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migrations.CreateModel(
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name='ObservationDefinition',
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fields=[
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('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
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('external_id', models.UUIDField(db_index=True, default=uuid.uuid4, unique=True)),
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('created_date', models.DateTimeField(auto_now_add=True, db_index=True, null=True)),
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('modified_date', models.DateTimeField(auto_now=True, db_index=True, null=True)),
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('deleted', models.BooleanField(db_index=True, default=False)),
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('history', models.JSONField(default=dict)),
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('meta', models.JSONField(default=dict)),
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('version', models.IntegerField(default=1)),
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('slug', models.CharField(max_length=255)),
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('name', models.CharField(max_length=1024)),
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('status', models.CharField(max_length=255)),
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('description', models.TextField()),
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('derived_from_uri', models.TextField()),
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('category', models.JSONField()),
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('code', models.JSONField()),
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('permitted_data_type', models.JSONField()),
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('body_site', models.JSONField()),
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('method', models.JSONField()),
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('permitted_unit', models.JSONField()),
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('component', models.JSONField()),
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('created_by', models.ForeignKey(blank=True, default=None, null=True, on_delete=django.db.models.deletion.SET_NULL, related_name='%(app_label)s_%(class)s_created_by', to=settings.AUTH_USER_MODEL)),
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('facility', models.ForeignKey(blank=True, default=None, null=True, on_delete=django.db.models.deletion.PROTECT, to='facility.facility')),
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('updated_by', models.ForeignKey(blank=True, default=None, null=True, on_delete=django.db.models.deletion.SET_NULL, related_name='%(app_label)s_%(class)s_updated_by', to=settings.AUTH_USER_MODEL)),
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],
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options={
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'abstract': False,
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},
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),
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]
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care/emr/migrations/0030_observationdefinition_specimen_specimendefinition.py
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care/emr/migrations/0030_observationdefinition_specimen_specimendefinition.py
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# Generated by Django 5.1.4 on 2025-04-08 19:21
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import django.db.models.deletion
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import uuid
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from django.conf import settings
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from django.db import migrations, models
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class Migration(migrations.Migration):
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dependencies = [
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('emr', '0029_encounter_discharge_summary_advice'),
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('facility', '0476_facility_default_internal_organization_and_more'),
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migrations.swappable_dependency(settings.AUTH_USER_MODEL),
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]
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operations = [
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migrations.CreateModel(
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name='ObservationDefinition',
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fields=[
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('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
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('external_id', models.UUIDField(db_index=True, default=uuid.uuid4, unique=True)),
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('created_date', models.DateTimeField(auto_now_add=True, db_index=True, null=True)),
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('modified_date', models.DateTimeField(auto_now=True, db_index=True, null=True)),
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('deleted', models.BooleanField(db_index=True, default=False)),
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('history', models.JSONField(default=dict)),
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('meta', models.JSONField(default=dict)),
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('version', models.IntegerField(default=1)),
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('slug', models.CharField(max_length=255)),
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('title', models.CharField(max_length=1024)),
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('status', models.CharField(max_length=255)),
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('description', models.TextField()),
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('derived_from_uri', models.TextField()),
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('category', models.JSONField()),
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('code', models.JSONField()),
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('permitted_data_type', models.JSONField()),
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('body_site', models.JSONField()),
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('method', models.JSONField()),
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('permitted_unit', models.JSONField()),
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('component', models.JSONField()),
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('created_by', models.ForeignKey(blank=True, default=None, null=True, on_delete=django.db.models.deletion.SET_NULL, related_name='%(app_label)s_%(class)s_created_by', to=settings.AUTH_USER_MODEL)),
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('facility', models.ForeignKey(blank=True, default=None, null=True, on_delete=django.db.models.deletion.PROTECT, to='facility.facility')),
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('updated_by', models.ForeignKey(blank=True, default=None, null=True, on_delete=django.db.models.deletion.SET_NULL, related_name='%(app_label)s_%(class)s_updated_by', to=settings.AUTH_USER_MODEL)),
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],
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options={
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'abstract': False,
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},
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),
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migrations.CreateModel(
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name='Specimen',
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fields=[
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('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
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('external_id', models.UUIDField(db_index=True, default=uuid.uuid4, unique=True)),
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('created_date', models.DateTimeField(auto_now_add=True, db_index=True, null=True)),
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('modified_date', models.DateTimeField(auto_now=True, db_index=True, null=True)),
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('deleted', models.BooleanField(db_index=True, default=False)),
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('history', models.JSONField(default=dict)),
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('meta', models.JSONField(default=dict)),
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('accession_identifier', models.JSONField(default=list)),
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('status', models.CharField(max_length=20)),
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('specimen_type', models.JSONField()),
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('received_time', models.DateTimeField(blank=True, null=True)),
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('note', models.TextField(blank=True, null=True)),
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('condition', models.JSONField(default=list)),
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('processing', models.JSONField(default=list)),
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('collection', models.JSONField(default=dict)),
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('created_by', models.ForeignKey(blank=True, default=None, null=True, on_delete=django.db.models.deletion.SET_NULL, related_name='%(app_label)s_%(class)s_created_by', to=settings.AUTH_USER_MODEL)),
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('encounter', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='emr.encounter')),
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('facility', models.ForeignKey(blank=True, default=None, null=True, on_delete=django.db.models.deletion.PROTECT, to='facility.facility')),
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('patient', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='emr.patient')),
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('updated_by', models.ForeignKey(blank=True, default=None, null=True, on_delete=django.db.models.deletion.SET_NULL, related_name='%(app_label)s_%(class)s_updated_by', to=settings.AUTH_USER_MODEL)),
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],
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options={
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'abstract': False,
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},
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),
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migrations.CreateModel(
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name='SpecimenDefinition',
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fields=[
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('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
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('external_id', models.UUIDField(db_index=True, default=uuid.uuid4, unique=True)),
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('created_date', models.DateTimeField(auto_now_add=True, db_index=True, null=True)),
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('modified_date', models.DateTimeField(auto_now=True, db_index=True, null=True)),
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('deleted', models.BooleanField(db_index=True, default=False)),
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('history', models.JSONField(default=dict)),
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('meta', models.JSONField(default=dict)),
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('version', models.IntegerField(default=1)),
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('slug', models.CharField(max_length=255)),
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('title', models.CharField(max_length=1024)),
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('derived_from_uri', models.TextField(blank=True, null=True)),
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('status', models.CharField(max_length=255)),
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('description', models.TextField()),
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('type_collected', models.JSONField(blank=True, null=True)),
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('patient_preparation', models.JSONField(default=list)),
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('collection', models.JSONField(blank=True, null=True)),
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('type_tested', models.JSONField(default=dict)),
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('created_by', models.ForeignKey(blank=True, default=None, null=True, on_delete=django.db.models.deletion.SET_NULL, related_name='%(app_label)s_%(class)s_created_by', to=settings.AUTH_USER_MODEL)),
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('facility', models.ForeignKey(blank=True, default=None, null=True, on_delete=django.db.models.deletion.PROTECT, to='facility.facility')),
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('updated_by', models.ForeignKey(blank=True, default=None, null=True, on_delete=django.db.models.deletion.SET_NULL, related_name='%(app_label)s_%(class)s_updated_by', to=settings.AUTH_USER_MODEL)),
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],
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options={
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'abstract': False,
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},
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),
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]
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care/emr/models/__init__.py
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care/emr/models/__init__.py
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care/emr/models/observation_definition.py
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care/emr/models/observation_definition.py
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)
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version = models.IntegerField(default=1)
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slug = models.CharField(max_length=255)
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name = models.CharField(max_length=1024)
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title = models.CharField(max_length=1024)
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status = models.CharField(max_length=255)
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description = models.TextField()
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derived_from_uri = models.TextField()
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care/emr/models/specimen.py
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care/emr/models/specimen.py
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from django.db import models
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from care.emr.models import EMRBaseModel
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class Specimen(EMRBaseModel):
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facility = models.ForeignKey(
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"facility.Facility",
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on_delete=models.PROTECT,
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default=None,
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null=True,
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blank=True,
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)
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accession_identifier = models.JSONField(default=list)
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status = models.CharField(max_length=20)
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specimen_type = models.JSONField()
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patient = models.ForeignKey("emr.Patient", on_delete=models.CASCADE)
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encounter = models.ForeignKey(
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"emr.Encounter", on_delete=models.CASCADE, null=True, blank=True
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)
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received_time = models.DateTimeField(null=True, blank=True)
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note = models.TextField(null=True, blank=True)
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condition = models.JSONField(default=list)
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processing = models.JSONField(default=list)
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collection = models.JSONField(default=dict)
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care/emr/models/specimen_definition.py
+23
care/emr/models/specimen_definition.py
···
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from django.db import models
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from care.emr.models import EMRBaseModel
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class SpecimenDefinition(EMRBaseModel):
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facility = models.ForeignKey(
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"facility.Facility",
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on_delete=models.PROTECT,
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default=None,
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null=True,
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blank=True,
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)
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version = models.IntegerField(default=1)
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slug = models.CharField(max_length=255)
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title = models.CharField(max_length=1024)
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derived_from_uri = models.TextField(null=True, blank=True)
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status = models.CharField(max_length=255)
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description = models.TextField()
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type_collected = models.JSONField(null=True, blank=True)
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patient_preparation = models.JSONField(default=list)
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collection = models.JSONField(null=True, blank=True)
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type_tested = models.JSONField(default=dict)
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care/emr/resources/observation_definition/spec.py
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care/emr/resources/observation_definition/spec.py
care/emr/resources/specimen/__init__.py
care/emr/resources/specimen/__init__.py
This is a binary file and will not be displayed.
+130
care/emr/resources/specimen/spec.py
+130
care/emr/resources/specimen/spec.py
···
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import datetime
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from enum import Enum
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from pydantic import UUID4, BaseModel, field_validator
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from care.emr.models.specimen import Specimen
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from care.emr.resources.base import EMRResource
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from care.emr.resources.common import Coding
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from care.emr.resources.observation.valueset import CARE_BODY_SITE_VALUESET
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from care.emr.resources.specimen.valueset import (
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COLLECTION_METHOD_VALUESET,
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FASTING_STATUS_VALUESET,
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SPECIMEN_CONDITION_VALUESET,
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)
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from care.emr.resources.specimen_definition.valueset import SPECIMEN_TYPE_CODE_VALUESET
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from care.emr.utils.valueset_coding_type import ValueSetBoundCoding
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from care.facility.models import Facility
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from care.users.models import User
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class SpecimenStatusOptions(str, Enum):
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"""Status options for specimen"""
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available = "available"
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unavailable = "unavailable"
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unsatisfactory = "unsatisfactory"
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entered_in_error = "entered_in_error"
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class QuantitySpec(BaseModel):
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"""Represents a quantity with value and unit"""
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value: float
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unit: Coding
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class DurationSpec(BaseModel):
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"""Duration specification using value and unit"""
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# Needs to be moved into the common specs, with datetime based valueset check
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value: int
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unit: Coding
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class CollectionSpec(BaseModel):
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"""Specimen collection details"""
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collector: UUID4 | None = None
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collected_date_time: datetime.datetime | None = None # Check for TZ
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quantity: QuantitySpec | None = None
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method: ValueSetBoundCoding[COLLECTION_METHOD_VALUESET.slug] | None = None
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procedure: UUID4 | None = None
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body_site: ValueSetBoundCoding[CARE_BODY_SITE_VALUESET.slug] | None = None
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fasting_status_codeable_concept: (
55
+
ValueSetBoundCoding[FASTING_STATUS_VALUESET.slug] | None
56
+
) = None
57
+
fasting_status_duration: DurationSpec | None = None
58
+
59
+
@field_validator("collector")
60
+
@classmethod
61
+
def validate_collector(cls, collector):
62
+
if collector and not User.objects.filter(external_id=collector).exists():
63
+
raise ValueError("Collector user not found")
64
+
return collector
65
+
66
+
67
+
class ProcessingSpec(BaseModel):
68
+
"""Specimen processing details"""
69
+
70
+
description: str
71
+
method: Coding | None = None
72
+
performer: UUID4 | None = None
73
+
time_date_time: str
74
+
75
+
@field_validator("performer")
76
+
@classmethod
77
+
def validate_performer(cls, performer):
78
+
if performer and not User.objects.filter(external_id=performer).exists():
79
+
raise ValueError("Performer user not found")
80
+
return performer
81
+
82
+
83
+
class BaseSpecimenSpec(EMRResource):
84
+
"""Base model for specimen"""
85
+
86
+
__model__ = Specimen
87
+
__exclude__ = ["facility", "subject", "request", "collection", "processing"]
88
+
89
+
id: str | None = None
90
+
accession_identifier: list[str] = []
91
+
status: SpecimenStatusOptions
92
+
specimen_type: ValueSetBoundCoding[SPECIMEN_TYPE_CODE_VALUESET.slug]
93
+
subject: dict | None = None
94
+
received_time: str | None = None
95
+
request: dict | None = None
96
+
collection: CollectionSpec
97
+
processing: list[ProcessingSpec] = []
98
+
condition: list[ValueSetBoundCoding[SPECIMEN_CONDITION_VALUESET.slug]] = []
99
+
note: str | None = None
100
+
101
+
102
+
class SpecimenCreateSpec(BaseSpecimenSpec):
103
+
"""Specimen creation specification"""
104
+
105
+
facility: UUID4 | None = None
106
+
subject_patient: UUID4
107
+
subject_encounter: UUID4 | None = None
108
+
request: UUID4 | None = None
109
+
collection: CollectionSpec
110
+
processing: list[ProcessingSpec] = []
111
+
112
+
@field_validator("facility")
113
+
@classmethod
114
+
def validate_facility_exists(cls, facility):
115
+
if not Facility.objects.filter(external_id=facility).exists():
116
+
# Check if user is in the given facility
117
+
raise ValueError("Facility not found")
118
+
return facility
119
+
120
+
def perform_extra_deserialization(self, is_update, obj):
121
+
if self.facility:
122
+
obj.facility = Facility.objects.get(external_id=self.facility)
123
+
124
+
125
+
class SpecimenReadSpec(BaseSpecimenSpec):
126
+
"""Specimen read specification"""
127
+
128
+
@classmethod
129
+
def perform_extra_serialization(cls, mapping, obj):
130
+
mapping["id"] = obj.external_id
+86
care/emr/resources/specimen/valueset.py
+86
care/emr/resources/specimen/valueset.py
···
1
+
from care.emr.registries.care_valueset.care_valueset import CareValueset
2
+
from care.emr.resources.common.valueset import ValueSetCompose, ValueSetInclude
3
+
from care.emr.resources.valueset.spec import ValueSetStatusOptions
4
+
5
+
# Collection method valueset (SNOMED)
6
+
COLLECTION_METHOD_VALUESET = CareValueset(
7
+
"Collection Method",
8
+
"system-collection-method-code",
9
+
ValueSetStatusOptions.active.value,
10
+
)
11
+
12
+
COLLECTION_METHOD_VALUESET.register_valueset(
13
+
ValueSetCompose(
14
+
include=[
15
+
ValueSetInclude(
16
+
system="http://snomed.info/sct",
17
+
concept=[
18
+
{
19
+
"code": "129316008",
20
+
"display": "Aspiration - action",
21
+
},
22
+
{"code": "129314006", "display": "Biopsy - action"},
23
+
{"code": "129300006", "display": "Puncture - action"},
24
+
{"code": "129304002", "display": "Excision - action"},
25
+
{"code": "129323009", "display": "Scraping - action"},
26
+
{
27
+
"code": "73416001",
28
+
"display": "Urine specimen collection, clean catch",
29
+
},
30
+
{"code": "225113003", "display": "Timed urine collection"},
31
+
{
32
+
"code": "70777001",
33
+
"display": "Urine specimen collection, catheterized",
34
+
},
35
+
{"code": "386089008", "display": "Collection of coughed sputum"},
36
+
{
37
+
"code": "278450005",
38
+
"display": "Finger-prick sampling",
39
+
},
40
+
],
41
+
)
42
+
]
43
+
)
44
+
)
45
+
46
+
COLLECTION_METHOD_VALUESET.register_as_system()
47
+
48
+
# Fasting status valueset
49
+
FASTING_STATUS_VALUESET = CareValueset(
50
+
"Fasting Status",
51
+
"system-fasting-status-code",
52
+
ValueSetStatusOptions.active.value,
53
+
)
54
+
55
+
FASTING_STATUS_VALUESET.register_valueset(
56
+
ValueSetCompose(
57
+
include=[
58
+
ValueSetInclude(
59
+
system="http://terminology.hl7.org/CodeSystem/v2-0916",
60
+
version="2.0.0",
61
+
)
62
+
]
63
+
)
64
+
)
65
+
66
+
FASTING_STATUS_VALUESET.register_as_system()
67
+
68
+
# Specimen condition valueset
69
+
SPECIMEN_CONDITION_VALUESET = CareValueset(
70
+
"Specimen Condition",
71
+
"system-specimen-condition-code",
72
+
ValueSetStatusOptions.active.value,
73
+
)
74
+
75
+
SPECIMEN_CONDITION_VALUESET.register_valueset(
76
+
ValueSetCompose(
77
+
include=[
78
+
ValueSetInclude(
79
+
system="http://terminology.hl7.org/CodeSystem/v2-0493",
80
+
version="2.0.0",
81
+
)
82
+
]
83
+
)
84
+
)
85
+
86
+
SPECIMEN_CONDITION_VALUESET.register_as_system()
care/emr/resources/specimen_definition/__init__.py
care/emr/resources/specimen_definition/__init__.py
This is a binary file and will not be displayed.
+112
care/emr/resources/specimen_definition/spec.py
+112
care/emr/resources/specimen_definition/spec.py
···
1
+
from enum import Enum
2
+
3
+
from pydantic import BaseModel, model_validator
4
+
5
+
from care.emr.models.specimen_definition import SpecimenDefinition
6
+
from care.emr.resources.base import EMRResource
7
+
from care.emr.resources.common import Coding
8
+
from care.emr.resources.specimen_definition.valueset import (
9
+
CONTAINER_CAP_VALUESET,
10
+
PREPARE_PATIENT_PRIOR_SPECIMEN_CODE_VALUESET,
11
+
SPECIMEN_COLLECTION_CODE_VALUESET,
12
+
SPECIMEN_TYPE_CODE_VALUESET,
13
+
)
14
+
from care.emr.utils.valueset_coding_type import ValueSetBoundCoding
15
+
16
+
17
+
class SpecimenDefinitionStatusOptions(str, Enum):
18
+
"""Status options for specimen definition"""
19
+
20
+
draft = "draft"
21
+
active = "active"
22
+
retired = "retired"
23
+
unknown = "unknown"
24
+
25
+
26
+
class PreferenceOptions(str, Enum):
27
+
"""Preference options for specimen type testing"""
28
+
29
+
preferred = "preferred"
30
+
alternate = "alternate"
31
+
32
+
33
+
class QuantitySpec(BaseModel):
34
+
"""Represents a quantity with value and unit"""
35
+
36
+
value: float
37
+
unit: Coding
38
+
39
+
40
+
class MinimumVolumeSpec(BaseModel):
41
+
"""Specification for minimum volume with support for quantity or string representation"""
42
+
43
+
quantity: QuantitySpec | None = None
44
+
string: str | None = None
45
+
46
+
@model_validator(mode="after")
47
+
def validate_minimum_volume(self):
48
+
"""Validates that only one minimum volume field is provided"""
49
+
if self.quantity and self.string:
50
+
raise ValueError("Only one of quantity or string should be provided")
51
+
return self
52
+
53
+
54
+
class ContainerSpec(BaseModel):
55
+
"""Container specification for specimen collection"""
56
+
57
+
description: str | None = None
58
+
capacity: QuantitySpec | None = None
59
+
minimum_volume: MinimumVolumeSpec | None = None
60
+
cap: ValueSetBoundCoding[CONTAINER_CAP_VALUESET.slug] | None = None
61
+
preparation: str | None = None
62
+
63
+
64
+
class DurationSpec(BaseModel):
65
+
"""Duration specification using value and unit"""
66
+
67
+
value: int
68
+
unit: Coding # Nees to be restricted to Datetime Units
69
+
70
+
71
+
class TypeTestedSpec(BaseModel):
72
+
"""Specification for tested specimen types"""
73
+
74
+
is_derived: bool
75
+
specimen_type: ValueSetBoundCoding[SPECIMEN_TYPE_CODE_VALUESET.slug]
76
+
preference: PreferenceOptions
77
+
container: ContainerSpec | None = None
78
+
requirement: str | None = None
79
+
retention_time: DurationSpec | None = None
80
+
single_use: bool | None = None
81
+
82
+
83
+
class BaseSpecimenDefinitionSpec(EMRResource):
84
+
"""Base model for specimen definition"""
85
+
86
+
__model__ = SpecimenDefinition
87
+
__exclude__ = ["facility"]
88
+
89
+
id: str | None = None
90
+
slug: str
91
+
title: str
92
+
derived_from_uri: str | None = None
93
+
status: SpecimenDefinitionStatusOptions
94
+
description: str
95
+
type_collected: ValueSetBoundCoding[SPECIMEN_TYPE_CODE_VALUESET.slug] | None = None
96
+
patient_preparation: list[
97
+
ValueSetBoundCoding[PREPARE_PATIENT_PRIOR_SPECIMEN_CODE_VALUESET.slug]
98
+
] = []
99
+
collection: ValueSetBoundCoding[SPECIMEN_COLLECTION_CODE_VALUESET.slug] | None = (
100
+
None
101
+
)
102
+
type_tested: TypeTestedSpec | None = None
103
+
104
+
105
+
class SpecimenDefinitionReadSpec(BaseSpecimenDefinitionSpec):
106
+
"""Specimen definition read specification"""
107
+
108
+
version: int | None = None
109
+
110
+
@classmethod
111
+
def perform_extra_serialization(cls, mapping, obj):
112
+
mapping["id"] = obj.external_id
+107
care/emr/resources/specimen_definition/valueset.py
+107
care/emr/resources/specimen_definition/valueset.py
···
1
+
from care.emr.registries.care_valueset.care_valueset import CareValueset
2
+
from care.emr.resources.common.valueset import ValueSetCompose, ValueSetInclude
3
+
from care.emr.resources.valueset.spec import ValueSetStatusOptions
4
+
5
+
SPECIMEN_TYPE_CODE_VALUESET = CareValueset(
6
+
"Specimen Type Code",
7
+
"system-specimen_type-code",
8
+
ValueSetStatusOptions.active.value,
9
+
)
10
+
11
+
SPECIMEN_TYPE_CODE_VALUESET.register_valueset(
12
+
ValueSetCompose(
13
+
include=[
14
+
ValueSetInclude(
15
+
system="http://terminology.hl7.org/CodeSystem/v2-0487",
16
+
version="2.0.0",
17
+
)
18
+
]
19
+
)
20
+
)
21
+
22
+
SPECIMEN_TYPE_CODE_VALUESET.register_as_system()
23
+
24
+
25
+
PREPARE_PATIENT_PRIOR_SPECIMEN_CODE_VALUESET = CareValueset(
26
+
"Prepare Patient Prior Specimen Code",
27
+
"system-prepare_patient_prior_specimen_code",
28
+
ValueSetStatusOptions.active.value,
29
+
)
30
+
31
+
PREPARE_PATIENT_PRIOR_SPECIMEN_CODE_VALUESET.register_valueset(
32
+
ValueSetCompose(
33
+
include=[
34
+
ValueSetInclude(
35
+
system="http://snomed.info/sct",
36
+
filter=[
37
+
{
38
+
"property": "concept",
39
+
"op": "is-a",
40
+
"value": "703763000",
41
+
}
42
+
],
43
+
)
44
+
]
45
+
)
46
+
)
47
+
48
+
PREPARE_PATIENT_PRIOR_SPECIMEN_CODE_VALUESET.register_as_system()
49
+
50
+
51
+
SPECIMEN_COLLECTION_CODE_VALUESET = CareValueset(
52
+
"Specimen Collection Code",
53
+
"system-specimen_collection_code",
54
+
ValueSetStatusOptions.active.value,
55
+
)
56
+
57
+
SPECIMEN_COLLECTION_CODE_VALUESET.register_valueset(
58
+
ValueSetCompose(
59
+
include=[
60
+
ValueSetInclude(
61
+
system="http://snomed.info/sct",
62
+
concept=[
63
+
{
64
+
"code": "129316008",
65
+
"display": "Aspiration - action",
66
+
},
67
+
{"code": "129314006", "display": "Biopsy - action"},
68
+
{"code": "129300006", "display": "Puncture - action"},
69
+
{"code": "129304002", "display": "Excision - action"},
70
+
{"code": "129323009", "display": "Scraping - action"},
71
+
{
72
+
"code": "73416001",
73
+
"display": "Urine specimen collection, clean catch",
74
+
},
75
+
{"code": "225113003", "display": "Timed urine collection"},
76
+
{
77
+
"code": "70777001",
78
+
"display": "Urine specimen collection, catheterized",
79
+
},
80
+
{"code": "386089008", "display": "Collection of coughed sputum"},
81
+
{"code": "278450005", "display": "Finger-prick sampling"},
82
+
],
83
+
)
84
+
]
85
+
)
86
+
)
87
+
88
+
SPECIMEN_COLLECTION_CODE_VALUESET.register_as_system()
89
+
90
+
91
+
CONTAINER_CAP_VALUESET = CareValueset(
92
+
"Container Cap",
93
+
"system-container_cap-code",
94
+
ValueSetStatusOptions.active.value,
95
+
)
96
+
97
+
CONTAINER_CAP_VALUESET.register_valueset(
98
+
ValueSetCompose(
99
+
include=[
100
+
ValueSetInclude(
101
+
system="http://terminology.hl7.org/CodeSystem/container-cap"
102
+
)
103
+
]
104
+
)
105
+
)
106
+
107
+
CONTAINER_CAP_VALUESET.register_as_system()
+3
-1
care/security/permissions/base.py
+3
-1
care/security/permissions/base.py
···
11
11
from care.security.permissions.organization import OrganizationPermissions
12
12
from care.security.permissions.patient import PatientPermissions
13
13
from care.security.permissions.questionnaire import QuestionnairePermissions
14
+
from care.security.permissions.specimen_definition import SpecimenDefinitionPermissions
14
15
from care.security.permissions.user import UserPermissions
15
16
from care.security.permissions.user_schedule import UserSchedulePermissions
16
17
···
39
40
UserSchedulePermissions,
40
41
FacilityLocationPermissions,
41
42
ObservationDefinitionPermissions,
42
-
DevicePermissions
43
+
DevicePermissions,
44
+
SpecimenDefinitionPermissions,
43
45
]
44
46
45
47
cache = {}
+2
-2
care/security/permissions/observation_definition.py
+2
-2
care/security/permissions/observation_definition.py
···
5
5
ADMIN_ROLE,
6
6
DOCTOR_ROLE,
7
7
FACILITY_ADMIN_ROLE,
8
-
GEO_ADMIN,
8
+
ADMINISTRATOR,
9
9
NURSE_ROLE,
10
10
STAFF_ROLE,
11
11
VOLUNTEER_ROLE,
···
25
25
PermissionContext.FACILITY,
26
26
[
27
27
FACILITY_ADMIN_ROLE,
28
-
GEO_ADMIN,
28
+
ADMINISTRATOR,
29
29
ADMIN_ROLE,
30
30
STAFF_ROLE,
31
31
DOCTOR_ROLE,
+35
care/security/permissions/specimen_definition.py
+35
care/security/permissions/specimen_definition.py
···
1
+
import enum
2
+
3
+
from care.security.permissions.constants import Permission, PermissionContext
4
+
from care.security.roles.role import (
5
+
ADMIN_ROLE,
6
+
DOCTOR_ROLE,
7
+
FACILITY_ADMIN_ROLE,
8
+
ADMINISTRATOR,
9
+
NURSE_ROLE,
10
+
STAFF_ROLE,
11
+
VOLUNTEER_ROLE,
12
+
)
13
+
14
+
15
+
class SpecimenDefinitionPermissions(enum.Enum):
16
+
can_write_specimen_definition = Permission(
17
+
"Can Create Specimen Definition on Facility",
18
+
"",
19
+
PermissionContext.FACILITY,
20
+
[FACILITY_ADMIN_ROLE, ADMIN_ROLE],
21
+
)
22
+
can_read_specimen_definition = Permission(
23
+
"Can Read Specimen Definition",
24
+
"",
25
+
PermissionContext.FACILITY,
26
+
[
27
+
FACILITY_ADMIN_ROLE,
28
+
ADMINISTRATOR,
29
+
ADMIN_ROLE,
30
+
STAFF_ROLE,
31
+
DOCTOR_ROLE,
32
+
NURSE_ROLE,
33
+
VOLUNTEER_ROLE,
34
+
],
35
+
)
+12
config/api_router.py
+12
config/api_router.py
···
44
44
from care.emr.api.viewsets.mfa_login import MFALoginViewSet
45
45
from care.emr.api.viewsets.notes import NoteMessageViewSet, NoteThreadViewSet
46
46
from care.emr.api.viewsets.observation import ObservationViewSet
47
+
from care.emr.api.viewsets.observation_definition import ObservationDefinitionViewSet
47
48
from care.emr.api.viewsets.organization import (
48
49
OrganizationPublicViewSet,
49
50
OrganizationUsersViewSet,
···
69
70
AvailabilityExceptionsViewSet,
70
71
)
71
72
from care.emr.api.viewsets.scheduling.booking import TokenBookingViewSet
73
+
from care.emr.api.viewsets.specimen_definition import SpecimenDefinitionViewSet
72
74
from care.emr.api.viewsets.totp import TOTPViewSet
73
75
from care.emr.api.viewsets.user import UserViewSet
74
76
from care.emr.api.viewsets.valueset import ValueSetViewSet
···
99
101
router.register(
100
102
"questionnaire_tag", QuestionnaireTagsViewSet, basename="questionnaire_tags"
101
103
)
104
+
105
+
router.register(
106
+
"observation_definition", ObservationDefinitionViewSet, basename="observation_definition"
107
+
)
108
+
102
109
103
110
router.register("organization", OrganizationViewSet, basename="organization")
104
111
···
186
193
basename="device",
187
194
)
188
195
196
+
facility_nested_router.register(
197
+
r"specimen_definition",
198
+
SpecimenDefinitionViewSet,
199
+
basename="specimen_definition",
200
+
)
189
201
device_nested_router = NestedSimpleRouter(
190
202
facility_nested_router, r"device", lookup="device"
191
203
)