Build the application

## Build
Validate custom genomics research observation instances against FHIR StructureDefinition rules. Detect schema deviations, cardinality errors, and missing mandatory molecular codes.

## User
Clinical Interoperability Engineer

## Workflow
1. Ingest FHIR R5 StructureDefinition profiles specifying required molecular observation attributes.
2. Parse incoming research observation JSON objects to check datatype conformity and cardinality.
3. Inspect terminology bindings to verify standard code systems for gene symbols and sequence types.
4. Generate conformance reports highlighting valid elements and actionable validation errors.

## Interface
Developer terminal CLI and web-based diff viewer comparing observed resources against StructureDefinition.

## Data
Use official HL7 FHIR R5 core StructureDefinition JSON schemas downloaded from the published standard.
Starter examples below are synthetic. They are not downloaded records.

## Source
[HL7 FHIR overview](https://hl7.org/fhir/overview.html)
Directly implements StructureDefinition constraints, cardinality checks, and terminology bindings from FHIR specification Section 2.1.15.3.1.

## Tools
pydantic-ai, fastapi, pytest.
Provides deterministic type validation and model enforcement matching FHIR StructureDefinition constraints.
Local open LLM or standard hosted API used only for generating human-readable remediations.

## Deliverables
Submit runnable source, pinned dependencies, setup commands, a working interface, example outputs, and a recorded end-to-end demo. Include tests and an action log.

## Acceptance
- Validates JSON payloads against FHIR R5 Observation StructureDefinition cardinality rules.
- Flags missing mandatory fields such as 'status', 'code', and 'resourceType'.
- Produces a structured conformance score with explicit JSON-pointer error locations.

## Starter Examples
```json
[
  {
    "input": {
      "resourceType": "Observation",
      "status": "final",
      "code": {
        "coding": [
          {
            "system": "http://loinc.org",
            "code": "48018-6",
            "display": "Gene studied [Identifier]"
          }
        ]
      },
      "valueString": "BRCA1"
    },
    "expected_output": {
      "conforms": true,
      "schema": "FHIR-R5-Observation",
      "missing_elements": [],
      "cardinality_violations": [],
      "conformance_score": 1
    }
  },
  {
    "input": {
      "resourceType": "Observation",
      "valueString": "BRCA1"
    },
    "expected_output": {
      "conforms": false,
      "schema": "FHIR-R5-Observation",
      "missing_elements": [
        "status",
        "code"
      ],
      "cardinality_violations": [
        "Observation.status: minimum cardinality 1, found 0"
      ],
      "conformance_score": 0.33
    }
  }
]
```

## Safety
Technical schema validation of synthetic research payloads; strictly excludes clinical health records.
Use mock external writes. Require human review before any real deployment.