Basic FHIR export and release new ver

Final update for new minor version release.

Basic FHIR-compatible format export functionality is implemented, as a stepping stone to more advanced FHIR export methods.

Currently, the data in db is used to build FHIR r4 pharmacogenomic reporting IG style reports in JSON and XML format. These two new files can be found in the same reports dir.

By default this functionality is enabled, but can be explicitly set with an env flag.

Author: Zaroganos

app/api/routes/fhir_export_router.py

@@ -412,5 +412,5 @@ async def health_check():
     return {
         "status": "healthy",
         "service": "pharmcat-api",
-        "version": "0.2.2"
+        "version": "0.2.3"
     }

app/api/routes/pharmcat_router.py

@@ -37,6 +37,7 @@
 from app.api.routes.monitoring import router as monitoring_router
 from app.api.routes.workflow_router import router as workflow_router
 from app.api.routes.pharmcat_router import router as pharmcat_router
+from app.api.routes.fhir_export_router import router as fhir_export_router
 from app.pharmcat import pharmcat_client
 from app.pharmcat.pharmcat_client import call_pharmcat_service, normalize_pharmcat_results
 from app.reports.generator import create_interactive_html_report, generate_pdf_report, generate_report
@@ -99,6 +100,7 @@ def _env_flag(name: str, default: bool = False) -> bool:
 KROKI_ENABLED = _env_flag("KROKI_ENABLED", True)
 HAPI_FHIR_ENABLED = _env_flag("HAPI_FHIR_ENABLED", True)
 OUTSIDE_CALLS_OVERRIDE_ENABLED = _env_flag("OUTSIDECALLSOVERRIDE", False)
+FHIR_EXPORT_ENABLED = _env_flag("FHIR_EXPORT_ENABLED", True)  # Enable FHIR export by default
 TEMP_DIR = Path("/tmp")
 DATA_DIR = Path("/data")
 REPORTS_DIR = Path(os.getenv("REPORT_DIR", "/data/reports"))
@@ -246,6 +248,13 @@ async def ensure_docs_built_on_start() -> None:
 app.include_router(workflow_router)
 app.include_router(pharmcat_router)
 
+# Conditionally include FHIR export router (enabled by default)
+if FHIR_EXPORT_ENABLED:
+    app.include_router(fhir_export_router)
+    logger.info("FHIR export functionality enabled (endpoints at /fhir/*)")
+else:
+    logger.info("FHIR export functionality disabled (set FHIR_EXPORT_ENABLED=true to enable)")
+
 # Override and disable authentication in development mode
 if os.getenv("ZAROPGX_DEV_MODE", "true").lower() == "true":
     # Print warning about development mode
@@ -1129,7 +1138,12 @@ async def services_config():
             "optitype": {"enabled": OPTITYPE_ENABLED},
             "genome_downloader": {"enabled": GENOME_DOWNLOADER_ENABLED},
             "kroki": {"enabled": KROKI_ENABLED},
-            "hapi_fhir": {"enabled": HAPI_FHIR_ENABLED}
+            "hapi_fhir": {"enabled": HAPI_FHIR_ENABLED},
+            "fhir_export": {
+                "enabled": FHIR_EXPORT_ENABLED,
+                "description": "FHIR R4 export for pharmacogenomic reports",
+                "endpoints": "/fhir/*" if FHIR_EXPORT_ENABLED else None
+            }
         }
     }
 

app/main.py

@@ -29,6 +29,9 @@
 # Keep below import commented out; this prevents circular import
 # from app.reports.pdf_generators import generate_pdf_report_dual_lane
 
+# FHIR Export - import lazily to avoid circular imports
+# from app.services.fhir_export_service import FHIRExportService, FHIR_EXPORT_ENABLED
+
 
 # Do not hardcode; derive from pyproject when available
 __version__ = "0.0.0"
@@ -269,9 +272,13 @@ def _env_flag(name: str, default: bool = False) -> bool:
 INCLUDE_PHARMCAT_TSV = _env_flag("INCLUDE_PHARMCAT_TSV", False)
 EXECSUM_USE_TSV = _env_flag("EXECSUM_USE_TSV", False)
 
+# FHIR Export - automatically generate FHIR R4 exports during report generation
+FHIR_EXPORT_ENABLED = _env_flag("FHIR_EXPORT_ENABLED", True)
+
 # Log the configuration for debugging
 logger.info(f"PharmCAT Report Configuration - HTML: {INCLUDE_PHARMCAT_HTML}, JSON: {INCLUDE_PHARMCAT_JSON}, TSV: {INCLUDE_PHARMCAT_TSV}")
 logger.info(f"Executive Summary Configuration - Use TSV: {EXECSUM_USE_TSV}")
+logger.info(f"FHIR Export Configuration - Enabled: {FHIR_EXPORT_ENABLED}")
 
 # Report configuration dictionary
 REPORT_CONFIG = {
@@ -290,6 +297,9 @@ def _env_flag(name: str, default: bool = False) -> bool:
     "show_pharmcat_html_report": INCLUDE_PHARMCAT_HTML,  # Original HTML report from PharmCAT
     "show_pharmcat_json_report": INCLUDE_PHARMCAT_JSON,  # Original JSON report from PharmCAT
     "show_pharmcat_tsv_report": INCLUDE_PHARMCAT_TSV,   # Original TSV report from PharmCAT
+    
+    # FHIR Export - generate FHIR R4 compliant exports
+    "generate_fhir_export": FHIR_EXPORT_ENABLED,  # FHIR JSON/XML exports
 }
 
 # Configure WeasyPrint logging for debugging text rendering issues
@@ -2496,6 +2506,86 @@ def generate_report(pharmcat_results: Dict[str, Any], output_dir: str, patient_i
         else:
             logger.debug("PharmCAT TSV report processing disabled via INCLUDE_PHARMCAT_TSV environment variable")
 
+        # FHIR Export - Generate FHIR R4 compliant exports if enabled
+        if REPORT_CONFIG["generate_fhir_export"]:
+            logger.info("=== FHIR EXPORT GENERATION START ===")
+            try:
+                # Import lazily to avoid circular imports
+                from app.services.fhir_export_service import FHIRExportService
+                
+                # We need a database session for the FHIR export service
+                if db_session:
+                    fhir_service = FHIRExportService(db_session)
+                    
+                    # Get the PharmCAT run_id - it might be in workflow metadata or we can use patient_id
+                    pharmcat_run_id = None
+                    if workflow_id:
+                        try:
+                            from app.api.db import Workflow
+                            import uuid as uuid_module
+                            workflow_uuid = uuid_module.UUID(str(workflow_id))
+                            workflow_obj = db_session.query(Workflow).filter(Workflow.id == workflow_uuid).first()
+                            if workflow_obj and workflow_obj.workflow_metadata:
+                                pharmcat_run_id = workflow_obj.workflow_metadata.get('pharmcat_run_id')
+                                logger.info(f"Found PharmCAT run_id in workflow metadata: {pharmcat_run_id}")
+                        except Exception as e:
+                            logger.warning(f"Could not get PharmCAT run_id from workflow: {e}")
+                    
+                    if not pharmcat_run_id:
+                        logger.info("No explicit PharmCAT run_id found; using workflow data for FHIR export")
+                    
+                    # Prepare patient info for FHIR export
+                    fhir_patient_info = None
+                    if patient_info:
+                        fhir_patient_info = {
+                            "id": patient_info.get("id", patient_id),
+                            "name": patient_info.get("name"),
+                            "gender": patient_info.get("gender"),
+                            "birthDate": patient_info.get("birthDate"),
+                        }
+                    
+                    # Generate both JSON and XML FHIR exports directly from normalized data
+                    fhir_result = fhir_service.save_fhir_export(
+                        run_id=pharmcat_run_id,
+                        patient_id=patient_id,
+                        patient_info=fhir_patient_info,
+                        output_format="both",  # Generate both JSON and XML
+                        include_recommendations=True,
+                        pharmcat_data=data,
+                        workflow_id=workflow_id,
+                    )
+                    
+                    if fhir_result.get("success"):
+                        files_saved = fhir_result.get("files_saved", [])
+                        for file_info in files_saved:
+                            fmt = file_info.get("format", "")
+                            url = file_info.get("url", "")
+                            if fmt == "json":
+                                report_paths["fhir_json_path"] = url
+                                data["fhir_json_url"] = url
+                                logger.info(f"✓ FHIR JSON export generated: {url}")
+                            elif fmt == "xml":
+                                report_paths["fhir_xml_path"] = url
+                                data["fhir_xml_url"] = url
+                                logger.info(f"✓ FHIR XML export generated: {url}")
+                        
+                        # Mark workflow as having FHIR export
+                        data["exported_to_fhir"] = True
+                    else:
+                        logger.warning(f"FHIR export failed: {fhir_result.get('error', 'Unknown error')}")
+                else:
+                    logger.warning("No database session available - skipping FHIR export")
+                    
+            except ImportError as e:
+                logger.warning(f"FHIR export service not available: {e}")
+            except Exception as e:
+                logger.error(f"FHIR export generation failed: {e}", exc_info=True)
+                # Don't fail the entire report generation if FHIR export fails
+            
+            logger.info("=== FHIR EXPORT GENERATION END ===")
+        else:
+            logger.debug("FHIR export disabled via FHIR_EXPORT_ENABLED environment variable")
+        
         # Add the processed data to the report paths for reference
         report_paths["processed_data"] = data