From bdf564639b506a7bfa47dbc478a36cf65c3eff39 Mon Sep 17 00:00:00 2001 From: Amrit Krishnan Date: Thu, 21 Nov 2024 09:23:05 -0500 Subject: [PATCH 1/6] Add FHIR server, EHR workflows --- .env.development | 2 +- adrenaline/api/patients/data.py | 12 + adrenaline/api/patients/ehr.py | 73 + adrenaline/api/routes/answer.py | 55 +- adrenaline/api/routes/patients.py | 37 + scripts/create_instruction_answers.py | 18 +- scripts/load_mimiciv_fhir.py | 197 +++ services/.env.development | 3 + services/docker-compose.dev-services.yml | 41 + services/hapi.application.yaml | 24 + ui/package-lock.json | 1621 +++++++++++++++++- ui/package.json | 2 + ui/src/app/components/ehr-workflows-card.tsx | 223 +++ ui/src/app/patient/[id]/page.tsx | 3 + 14 files changed, 2214 insertions(+), 97 deletions(-) create mode 100644 scripts/load_mimiciv_fhir.py create mode 100644 services/hapi.application.yaml create mode 100644 ui/src/app/components/ehr-workflows-card.tsx diff --git a/.env.development b/.env.development index e85b7ec..adfdab2 100644 --- a/.env.development +++ b/.env.development @@ -5,7 +5,7 @@ MEDCAT_MODELS_DIR=/Volumes/clinical-data/medcat NER_SERVICE_PORT=8003 EMBEDDING_SERVICE_PORT=8004 -EMBEDDING_SERVICE_HOST=embedding-service-dev +EMBEDDING_SERVICE_HOST=embedding-service-dev-cpu BATCH_SIZE=1 CHROMA_SERVICE_HOST=chromadb-dev diff --git a/adrenaline/api/patients/data.py b/adrenaline/api/patients/data.py index 703ea58..ee168ef 100644 --- a/adrenaline/api/patients/data.py +++ b/adrenaline/api/patients/data.py @@ -6,6 +6,18 @@ from pydantic import BaseModel, Field, field_validator +class MedicationsRequest(BaseModel): + """Request for formatting medications. + + Attributes + ---------- + medications: str + The medications to format. + """ + + medications: str + + class CohortSearchQuery(BaseModel): """Query for cohort search. diff --git a/adrenaline/api/patients/ehr.py b/adrenaline/api/patients/ehr.py index fe67c7e..b4e17a0 100644 --- a/adrenaline/api/patients/ehr.py +++ b/adrenaline/api/patients/ehr.py @@ -186,6 +186,74 @@ def fetch_patient_events_by_type( ) raise + def fetch_latest_medications(self, patient_id: int) -> str: + """Fetch medication events from the latest encounter and format them. + + Parameters + ---------- + patient_id : int + The patient ID. + + Returns + ------- + str + Comma-separated list of medications from the latest encounter. + """ + if self.lazy_df is None: + raise ValueError("LazyFrame not initialized") + + try: + # First get all events for the patient + filtered_df = ( + self.lazy_df.filter(pl.col("patient_id") == patient_id) + .select(list(self._required_columns)) + .collect(streaming=True) + ) + + if filtered_df.height == 0: + logger.info(f"No events found for patient {patient_id}") + return "" + + # Process all events first + processed_events = [ + self._process_event(row) for row in filtered_df.to_dicts() + ] + + # Find the latest encounter + latest_encounter = None + latest_timestamp = None + + for event in processed_events: + if event["event_type"] == "HOSPITAL_ADMISSION" and ( + latest_timestamp is None or event["timestamp"] > latest_timestamp + ): + latest_timestamp = event["timestamp"] + latest_encounter = event["encounter_id"] + + if latest_encounter is None: + logger.info(f"No hospital admissions found for patient {patient_id}") + return "" + + # Filter medications for the latest encounter + medications = { + event["details"] + for event in processed_events + if ( + event["event_type"] == "MEDICATION" + and event["encounter_id"] == latest_encounter + ) + } + + # Return sorted, comma-separated string + return ", ".join(sorted(medications)) + + except Exception as e: + logger.error( + f"Error fetching medications for patient {patient_id}: {str(e)}", + exc_info=True, + ) + raise + def fetch_patient_encounters(patient_id: int) -> List[dict]: """Fetch encounters with admission dates for a patient. @@ -277,3 +345,8 @@ def fetch_patient_events(patient_id: int) -> List[Event]: def fetch_patient_events_by_type(patient_id: int, event_type: str) -> List[Event]: """Fetch events filtered by event_type for a patient.""" return ehr_data_manager.fetch_patient_events_by_type(patient_id, event_type) + + +def fetch_latest_medications(patient_id: int) -> str: + """Fetch medication list from the latest encounter.""" + return ehr_data_manager.fetch_latest_medications(patient_id) diff --git a/adrenaline/api/routes/answer.py b/adrenaline/api/routes/answer.py index 66180fd..16fdbef 100644 --- a/adrenaline/api/routes/answer.py +++ b/adrenaline/api/routes/answer.py @@ -10,7 +10,7 @@ from api.pages.data import Query from api.patients.answer import generate_answer -from api.patients.data import CohortSearchQuery, CohortSearchResult +from api.patients.data import CohortSearchQuery, CohortSearchResult, MedicationsRequest from api.patients.db import get_database from api.patients.rag import ( ChromaManager, @@ -53,6 +53,59 @@ RAG_MANAGER = RAGManager(EMBEDDING_MANAGER, CHROMA_MANAGER, NER_MANAGER) +@router.post("/format_medications") +async def format_medications( + request: MedicationsRequest, + current_user: User = Depends(get_current_active_user), # noqa: B008 +) -> Dict[str, str]: + """Format medications into a markdown table. + + Parameters + ---------- + request : MedicationsRequest + Request containing medications string + current_user : User + The current authenticated user + + Returns + ------- + Dict[str, str] + Formatted markdown table of medications + """ + try: + if not request.medications.strip(): + return {"formatted_medications": "No medications found"} + + # Prepare the prompt for the LLM + prompt = f""" + Convert this comma-separated list of medications into a well-formatted markdown table with columns for Medication Name and Status. + Sort them alphabetically by medication name. Remove any duplicate entries. + + Medications: {request.medications} + + Format the table like this: + | Medication Name | Status | + |----------------|---------| + | Med 1 | Status 1 | + """ + + # Generate the formatted table + formatted_table = await generate_answer( + user_query=prompt, + mode="general", + context="", + ) + + return {"formatted_medications": formatted_table[0]} + + except Exception as e: + logger.error(f"Error formatting medications: {str(e)}") + raise HTTPException( + status_code=500, + detail="An error occurred while formatting medications", + ) from e + + @router.post("/generate_answer") async def generate_answer_endpoint( query: Query = Body(...), # noqa: B008 diff --git a/adrenaline/api/routes/patients.py b/adrenaline/api/routes/patients.py index 97bd64a..2b501b8 100644 --- a/adrenaline/api/routes/patients.py +++ b/adrenaline/api/routes/patients.py @@ -10,6 +10,7 @@ from api.patients.data import ClinicalNote, Event, PatientData, QAPair from api.patients.db import get_database from api.patients.ehr import ( + fetch_latest_medications, fetch_patient_encounters, fetch_patient_events, fetch_patient_events_by_type, @@ -37,6 +38,42 @@ init_lazy_df(MEDS_DATA_DIR) +@router.get("/patient_data/{patient_id}/medications", response_model=str) +async def get_latest_medications( + patient_id: int, + db: AsyncIOMotorDatabase[Any] = Depends(get_database), # noqa: B008 + current_user: User = Depends(get_current_active_user), # noqa: B008 +) -> str: + """Retrieve latest medications for a specific patient. + + Parameters + ---------- + patient_id : int + The ID of the patient. + db : AsyncIOMotorDatabase + The database connection. + current_user : User + The current authenticated user. + + Returns + ------- + str + The latest medications for the patient. + """ + try: + medications = fetch_latest_medications(patient_id) + logger.info(f"Retrieved medications for patient ID {patient_id} {medications}") + return medications + except Exception as e: + logger.error( + f"Error retrieving medications for patient ID {patient_id}: {str(e)}" + ) + raise HTTPException( + status_code=status.HTTP_500_INTERNAL_SERVER_ERROR, + detail="An error occurred while retrieving medications", + ) from e + + @router.get( "/patient_data/{patient_id}/events/{event_type}", response_model=List[Event] ) diff --git a/scripts/create_instruction_answers.py b/scripts/create_instruction_answers.py index e1a3747..d66f445 100644 --- a/scripts/create_instruction_answers.py +++ b/scripts/create_instruction_answers.py @@ -1,22 +1,12 @@ """Script to create instruction answers for EHR data.""" import os -from api.patients.ehr import init_lazy_df, fetch_recent_encounter_events +from api.patients.ehr import init_lazy_df, fetch_latest_medications -MEDS_DATA_DIR = os.getenv( - "MEDS_DATA_DIR", "/mnt/data/odyssey/meds/hosp/merge_to_MEDS_cohort/train" -) +MEDS_DATA_DIR = os.getenv("MEDS_DATA_DIR", "/Volumes/clinical-data/train") init_lazy_df(MEDS_DATA_DIR) -events = fetch_recent_encounter_events(10000032) -events_str = "" -for event in events: - event_type = event.code.split("//")[0] - if event_type == "MEDICATION": - medication = event.code.split("//")[1] - events_str += f"{medication} \n" - - -print(events_str) +meds = fetch_latest_medications(10000032) +print(meds) diff --git a/scripts/load_mimiciv_fhir.py b/scripts/load_mimiciv_fhir.py new file mode 100644 index 0000000..3856614 --- /dev/null +++ b/scripts/load_mimiciv_fhir.py @@ -0,0 +1,197 @@ +"""Script to load MIMIC-IV data into a FHIR server.""" + +import gzip +import json +import requests +from pathlib import Path +import logging +from rich.logging import RichHandler +from rich.progress import Progress, SpinnerColumn, TimeElapsedColumn + +logging.basicConfig( + level=logging.INFO, + format="%(message)s", + handlers=[RichHandler(rich_tracebacks=True)], +) +logger = logging.getLogger("MIMIC FHIR Loader") + +# Define MIMIC-IV FHIR resource loading order based on dependencies +RESOURCE_LOAD_ORDER = [ + # Base resources with no dependencies + "MimicOrganization", # Healthcare organization info + "MimicLocation", # Hospital locations + "MimicPatient", # Patient demographics + # Encounter resources + "MimicEncounter", # Hospital admissions + "MimicEncounterED", # Emergency department visits + "MimicEncounterICU", # ICU stays + # Medication-related resources + "MimicMedication", # Medication catalog + "MimicMedicationMix", # Medication mixtures + "MimicMedicationRequest", # Medication orders + "MimicMedicationDispense", # Medication dispensing + "MimicMedicationDispenseED", # ED medication dispensing + "MimicMedicationAdministration", # Medication administration + "MimicMedicationAdministrationICU", # ICU medication administration + "MimicMedicationStatementED", # ED medication statements + # Clinical resources + "MimicSpecimen", # Specimen collection + "MimicSpecimenLab", # Laboratory specimens + "MimicCondition", # Diagnoses and conditions + "MimicConditionED", # ED diagnoses + "MimicProcedure", # Hospital procedures + "MimicProcedureED", # ED procedures + "MimicProcedureICU", # ICU procedures + # Observation resources (largest files last) + "MimicObservationED", # ED observations + "MimicObservationVitalSignsED", # ED vital signs + "MimicObservationMicroOrg", # Microbiology organisms + "MimicObservationMicroTest", # Microbiology tests + "MimicObservationMicroSusc", # Microbiology susceptibilities + "MimicObservationDatetimeevents", # Datetime events + "MimicObservationOutputevents", # Output events + "MimicObservationLabevents", # Laboratory results + "MimicObservationChartevents", # Charted events +] + + +def send_to_fhir(bundle, fhir_base_url): + """Send bundle to FHIR server.""" + headers = {"Content-Type": "application/fhir+json"} + try: + response = requests.post(fhir_base_url, json=bundle, headers=headers) + if response.status_code not in [200, 201]: + logger.error(f"Error response: {response.status_code} - {response.text}") + response.raise_for_status() + return response + except requests.RequestException as e: + logger.error(f"Failed to send bundle to FHIR server: {e}") + return None + + +def create_transaction_bundle(resources): + """Create a FHIR transaction bundle from a list of resources.""" + entries = [] + for res in resources: + # Ensure the resource has an id + if "id" not in res: + logger.warning(f"Resource missing id: {res.get('resourceType', 'Unknown')}") + continue + + entries.append( + { + "resource": res, + "request": { + "method": "PUT", # Use PUT instead of POST to ensure id is preserved + "url": f"{res['resourceType']}/{res['id']}", + }, + } + ) + + return {"resourceType": "Bundle", "type": "transaction", "entry": entries} + + +def load_ndjson_to_fhir(file_path, fhir_base_url, batch_size=50): # Smaller batch size + """Load NDJSON file into FHIR server.""" + logger.info(f"Loading data from {file_path}...") + file_size = file_path.stat().st_size / (1024 * 1024) # Size in MB + logger.info(f"File size: {file_size:.1f} MB") + + with gzip.open(file_path, "rt") as f: + batch = [] + total_loaded = 0 + failed_batches = 0 + + with Progress( + SpinnerColumn(), + *Progress.get_default_columns(), + TimeElapsedColumn(), + transient=True, + ) as progress: + task = progress.add_task(f"Loading {file_path.name}", total=None) + + for line_number, line in enumerate(f, 1): + try: + resource = json.loads(line) + + # Ensure resource has an id + if "id" not in resource: + resource["id"] = f"{line_number}" + + batch.append(resource) + + if len(batch) >= batch_size: + bundle = create_transaction_bundle(batch) + response = send_to_fhir(bundle, fhir_base_url) + + if response and response.status_code in [200, 201]: + total_loaded += len(batch) + progress.update(task, advance=len(batch)) + else: + failed_batches += 1 + logger.error(f"Failed to load batch at line {line_number}") + batch = [] + + except json.JSONDecodeError: + logger.error(f"Invalid JSON at line {line_number}: {line[:100]}...") + except Exception as e: + logger.error(f"Error processing line {line_number}: {str(e)}") + + # Process remaining resources + if batch: + bundle = create_transaction_bundle(batch) + response = send_to_fhir(bundle, fhir_base_url) + + if response and response.status_code in [200, 201]: + total_loaded += len(batch) + progress.update(task, advance=len(batch)) + else: + failed_batches += 1 + logger.error("Failed to load final batch") + + logger.info( + f"✅ Completed loading {total_loaded} resources from {file_path.name}" + f" ({failed_batches} failed batches)" + ) + return total_loaded, failed_batches + + +def main(): + port = "8087" # Change this to match your FHIR server port + fhir_base_url = f"http://localhost:{port}/fhir" + data_dir = Path("/Volumes/clinical-data/physionet.org/files/mimic-iv-fhir/1.0/fhir") + + if not data_dir.exists(): + logger.error(f"Data directory not found: {data_dir}") + return + + # Test server connection + try: + response = requests.get(f"{fhir_base_url}/metadata") + response.raise_for_status() + logger.info("Successfully connected to FHIR server") + except requests.RequestException as e: + logger.error(f"Failed to connect to FHIR server: {e}") + return + + # Process files in the specified order + total_resources = 0 + total_failed = 0 + + for resource_type in RESOURCE_LOAD_ORDER: + resource_file = data_dir / f"{resource_type}.ndjson.gz" + if resource_file.exists(): + logger.info(f"\n=== Loading {resource_type} resources ===") + loaded, failed = load_ndjson_to_fhir(resource_file, fhir_base_url) + total_resources += loaded + total_failed += failed + else: + logger.warning(f"File not found: {resource_file}") + + logger.info("\n=== Loading Complete ===") + logger.info(f"Total resources loaded: {total_resources}") + logger.info(f"Total failed batches: {total_failed}") + + +if __name__ == "__main__": + main() diff --git a/services/.env.development b/services/.env.development index fc17fc4..f527602 100644 --- a/services/.env.development +++ b/services/.env.development @@ -12,3 +12,6 @@ CHROMA_SERVICE_PORT=8000 MONGO_USERNAME=root MONGO_PASSWORD=password + +FHIR_SERVICE_HOST=fhir-dev +FHIR_SERVICE_PORT=8080 diff --git a/services/docker-compose.dev-services.yml b/services/docker-compose.dev-services.yml index 2d31f46..7f261be 100644 --- a/services/docker-compose.dev-services.yml +++ b/services/docker-compose.dev-services.yml @@ -138,9 +138,50 @@ services: start_period: 40s restart: unless-stopped + fhir-dev: + image: "hapiproject/hapi:latest" + ports: + - "8087:8080" + configs: + - source: hapi + target: /app/config/application.yaml + depends_on: + fhir-db-dev: + condition: service_healthy + networks: + - services-network + healthcheck: + test: ["CMD", "curl", "-f", "http://localhost:8080/fhir/metadata"] + interval: 30s + timeout: 10s + retries: 3 + start_period: 30s + + fhir-db-dev: + image: postgres:17 + restart: always + environment: + POSTGRES_PASSWORD: admin + POSTGRES_USER: admin + POSTGRES_DB: hapi + volumes: + - hapi_fhir_data:/var/lib/postgresql/data + networks: + - services-network + healthcheck: + test: ["CMD-SHELL", "pg_isready -U admin -d hapi"] + interval: 10s + timeout: 5s + retries: 5 + +configs: + hapi: + file: ./hapi.application.yaml + volumes: mongodb_data: chroma_data: + hapi_fhir_data: networks: services-network: diff --git a/services/hapi.application.yaml b/services/hapi.application.yaml new file mode 100644 index 0000000..14e1f0d --- /dev/null +++ b/services/hapi.application.yaml @@ -0,0 +1,24 @@ +spring: + datasource: + url: 'jdbc:postgresql://fhir-db-dev:5432/hapi' + username: admin + password: admin + driverClassName: org.postgresql.Driver + jpa: + properties: + hibernate.dialect: ca.uhn.fhir.jpa.model.dialect.HapiFhirPostgresDialect + hibernate.search.enabled: false + +hapi: + fhir: + version: R4 + server_address: 'http://localhost:8080/fhir' + allow_external_references: true + allow_multiple_delete: true + bulk_export_enabled: true + tester: + home: + name: Local Tester + server_address: 'http://localhost:8080/fhir' + refuse_to_fetch_third_party_urls: false + fhir_version: R4 diff --git a/ui/package-lock.json b/ui/package-lock.json index f7a49d6..6063710 100644 --- a/ui/package-lock.json +++ b/ui/package-lock.json @@ -21,10 +21,12 @@ "react-chartjs-2": "^5.2.0", "react-dom": "^18", "react-icons": "^5.3.0", + "react-markdown": "^9.0.1", "react-plotly.js": "^2.6.0", "react-table": "^7.8.0", "react-textarea-autosize": "^8.5.3", "reactflow": "^11.11.4", + "remark-gfm": "^4.0.0", "swr": "^2.2.5", "zod": "^3.23.8", "zod-formik-adapter": "^1.3.0" @@ -2505,11 +2507,44 @@ "@types/d3-selection": "*" } }, + "node_modules/@types/debug": { + "version": "4.1.12", + "resolved": "https://registry.npmjs.org/@types/debug/-/debug-4.1.12.tgz", + "integrity": "sha512-vIChWdVG3LG1SMxEvI/AK+FWJthlrqlTu7fbrlywTkkaONwk/UAGaULXRlf8vkzFBLVm0zkMdCquhL5aOjhXPQ==", + "license": "MIT", + "dependencies": { + "@types/ms": "*" + } + }, + "node_modules/@types/estree": { + "version": "1.0.6", + "resolved": "https://registry.npmjs.org/@types/estree/-/estree-1.0.6.tgz", + "integrity": "sha512-AYnb1nQyY49te+VRAVgmzfcgjYS91mY5P0TKUDCLEM+gNnA+3T6rWITXRLYCpahpqSQbN5cE+gHpnPyXjHWxcw==", + "license": "MIT" + }, + "node_modules/@types/estree-jsx": { + "version": "1.0.5", + "resolved": "https://registry.npmjs.org/@types/estree-jsx/-/estree-jsx-1.0.5.tgz", + "integrity": "sha512-52CcUVNFyfb1A2ALocQw/Dd1BQFNmSdkuC3BkZ6iqhdMfQz7JWOFRuJFloOzjk+6WijU56m9oKXFAXc7o3Towg==", + "license": "MIT", + "dependencies": { + "@types/estree": "*" + } + }, "node_modules/@types/geojson": { "version": "7946.0.14", "resolved": "https://registry.npmjs.org/@types/geojson/-/geojson-7946.0.14.tgz", "integrity": "sha512-WCfD5Ht3ZesJUsONdhvm84dmzWOiOzOAqOncN0++w0lBw1o8OuDNJF2McvvCef/yBqb/HYRahp1BYtODFQ8bRg==" }, + "node_modules/@types/hast": { + "version": "3.0.4", + "resolved": "https://registry.npmjs.org/@types/hast/-/hast-3.0.4.tgz", + "integrity": "sha512-WPs+bbQw5aCj+x6laNGWLH3wviHtoCv/P3+otBhbOhJgG8qtpdAMlTCxLtsTWA7LH1Oh/bFCHsBn0TPS5m30EQ==", + "license": "MIT", + "dependencies": { + "@types/unist": "*" + } + }, "node_modules/@types/hoist-non-react-statics": { "version": "3.3.5", "resolved": "https://registry.npmjs.org/@types/hoist-non-react-statics/-/hoist-non-react-statics-3.3.5.tgz", @@ -2538,6 +2573,21 @@ "@types/lodash": "*" } }, + "node_modules/@types/mdast": { + "version": "4.0.4", + "resolved": "https://registry.npmjs.org/@types/mdast/-/mdast-4.0.4.tgz", + "integrity": "sha512-kGaNbPh1k7AFzgpud/gMdvIm5xuECykRR+JnWKQno9TAXVa6WIVCGTPvYGekIDL4uwCZQSYbUxNBSb1aUo79oA==", + "license": "MIT", + "dependencies": { + "@types/unist": "*" + } + }, + "node_modules/@types/ms": { + "version": "0.7.34", + "resolved": "https://registry.npmjs.org/@types/ms/-/ms-0.7.34.tgz", + "integrity": "sha512-nG96G3Wp6acyAgJqGasjODb+acrI7KltPiRxzHPXnP3NgI28bpQDRv53olbqGXbfcgF5aiiHmO3xpwEpS5Ld9g==", + "license": "MIT" + }, "node_modules/@types/node": 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"url": "https://github.com/sponsors/wooorm" + } } } } diff --git a/ui/package.json b/ui/package.json index 778b972..e781b34 100644 --- a/ui/package.json +++ b/ui/package.json @@ -22,10 +22,12 @@ "react-chartjs-2": "^5.2.0", "react-dom": "^18", "react-icons": "^5.3.0", + "react-markdown": "^9.0.1", "react-plotly.js": "^2.6.0", "react-table": "^7.8.0", "react-textarea-autosize": "^8.5.3", "reactflow": "^11.11.4", + "remark-gfm": "^4.0.0", "swr": "^2.2.5", "zod": "^3.23.8", "zod-formik-adapter": "^1.3.0" diff --git a/ui/src/app/components/ehr-workflows-card.tsx b/ui/src/app/components/ehr-workflows-card.tsx new file mode 100644 index 0000000..c037b88 --- /dev/null +++ b/ui/src/app/components/ehr-workflows-card.tsx @@ -0,0 +1,223 @@ +import React, { useState } from 'react' +import { + Card, + CardBody, + Heading, + VStack, + Button, + Text, + useColorModeValue, + useToast, + Box, + Spinner, + Table, + Thead, + Tbody, + Tr, + Th, + Td, +} from '@chakra-ui/react' +import { FaMedkit } from 'react-icons/fa' +import ReactMarkdown from 'react-markdown' +import remarkGfm from 'remark-gfm' + +interface EHRWorkflowsCardProps { + patientId: string +} + +const EHRWorkflowsCard: React.FC = ({ patientId }) => { + const [isLoading, setIsLoading] = useState(false) + const [medicationsTable, setMedicationsTable] = useState(null) + const toast = useToast() + + // Color mode values + const cardBgColor = useColorModeValue('white', 'gray.800') + const borderColor = useColorModeValue('gray.200', 'gray.600') + const headerBgColor = useColorModeValue('gray.50', 'gray.700') + const hoverBgColor = useColorModeValue('blue.50', 'blue.900') + const textColor = useColorModeValue('gray.800', 'white') + + const handleRetrieveMedications = async () => { + setIsLoading(true) + try { + const token = localStorage.getItem('token') + if (!token) throw new Error('No token found') + + // Fetch medications + const medsResponse = await fetch(`/api/patient_data/${patientId}/medications`, { + headers: { + 'Authorization': `Bearer ${token}`, + 'Accept': 'text/plain' + }, + }) + + if (!medsResponse.ok) { + const errorText = await medsResponse.text() + throw new Error(`Failed to fetch medications: ${errorText}`) + } + + const medications = await medsResponse.text() + + if (!medications.trim()) { + setMedicationsTable("No medications found for this patient.") + return + } + + // Format medications into table + const formatResponse = await fetch('/api/format_medications', { + method: 'POST', + headers: { + 'Authorization': `Bearer ${token}`, + 'Content-Type': 'application/json', + }, + body: JSON.stringify({ + medications: medications.replace(/^"|"$/g, '') + }), + }) + + if (!formatResponse.ok) { + const errorText = await formatResponse.text() + throw new Error(`Failed to format medications: ${errorText}`) + } + + const { formatted_medications } = await formatResponse.json() + setMedicationsTable(formatted_medications) + } catch (error) { + console.error('Error:', error) + toast({ + title: "Error", + description: error instanceof Error ? error.message : "An error occurred", + status: "error", + duration: 3000, + isClosable: true, + }) + setMedicationsTable(null) + } finally { + setIsLoading(false) + } + } + + // Custom components for ReactMarkdown + const MarkdownComponents = { + table: ({ children }: { children: React.ReactNode }) => ( + + {children} +
+ ), + thead: ({ children }: { children: React.ReactNode }) => ( + {children} + ), + tbody: ({ children }: { children: React.ReactNode }) => ( + {children} + ), + tr: ({ children }: { children: React.ReactNode }) => ( + + {children} + + ), + th: ({ children }: { children: React.ReactNode }) => ( + + {children} + + ), + td: ({ children }: { children: React.ReactNode }) => ( + + {children} + + ), + } + + return ( + + + + + EHR Workflows + + + + + {isLoading && ( + + + + Processing medications... + + + )} + + {medicationsTable && !isLoading && ( + + + Current Medications + + + {medicationsTable} + + + )} + + + + ) +} + +export default EHRWorkflowsCard diff --git a/ui/src/app/patient/[id]/page.tsx b/ui/src/app/patient/[id]/page.tsx index 9732e9f..731fc85 100644 --- a/ui/src/app/patient/[id]/page.tsx +++ b/ui/src/app/patient/[id]/page.tsx @@ -34,6 +34,7 @@ import PatientDetailsCard from '../../components/patient-details-card' import PatientEncountersTable from '../../components/patient-encounters-table' import SearchBox from '../../components/search-box' import AnswerCard from '../../components/answer-card' +import EHRWorkflowsCard from '../../components/ehr-workflows-card' const MotionBox = motion(Box) @@ -229,6 +230,8 @@ const PatientPage: React.FC = () => { isLoading={isLoadingEncounters} /> + + From 77fef4cec87c4ca9843d11c83401a3a52495f2b2 Mon Sep 17 00:00:00 2001 From: Amrit Krishnan Date: Thu, 21 Nov 2024 10:23:02 -0500 Subject: [PATCH 2/6] Improvements and type annotations --- adrenaline/api/patients/answer.py | 36 ++++++---------------------- adrenaline/api/patients/ehr.py | 2 +- adrenaline/api/patients/llm.py | 33 +++++++++++++++++++++++++ adrenaline/api/patients/workflows.py | 3 +++ adrenaline/api/routes/answer.py | 4 ++-- adrenaline/api/routes/pages.py | 12 +++++----- scripts/cot_endpoint.py | 5 +++- services/embedding/api/routes.py | 2 +- 8 files changed, 57 insertions(+), 40 deletions(-) create mode 100644 adrenaline/api/patients/llm.py create mode 100644 adrenaline/api/patients/workflows.py diff --git a/adrenaline/api/patients/answer.py b/adrenaline/api/patients/answer.py index b50b7b1..b958eb6 100644 --- a/adrenaline/api/patients/answer.py +++ b/adrenaline/api/patients/answer.py @@ -2,15 +2,14 @@ import json import logging -import os from typing import Tuple from langchain_core.output_parsers import PydanticOutputParser from langchain_core.prompts import PromptTemplate from langchain_core.runnables import RunnableSequence -from langchain_openai import ChatOpenAI from api.pages.data import Answer +from api.patients.llm import LLM from api.patients.prompts import ( general_answer_template, patient_answer_template, @@ -21,27 +20,6 @@ logging.basicConfig(level=logging.INFO) logger = logging.getLogger(__name__) -# Set up OpenAI client with custom endpoint -LLM_SERVICE_URL = os.getenv("LLM_SERVICE_URL") -if not LLM_SERVICE_URL: - raise ValueError("LLM_SERVICE_URL is not set") -logger.info(f"LLM_SERVICE_URL is set to: {LLM_SERVICE_URL}") - -os.environ["OPENAI_API_KEY"] = "EMPTY" - -# Initialize LLM with increased timeout -try: - llm = ChatOpenAI( - base_url=LLM_SERVICE_URL, - model_name="Meta-Llama-3.1-70B-Instruct", - temperature=0.3, - max_tokens=4096, - request_timeout=60, - ) - logger.info("ChatOpenAI initialized successfully") -except Exception as e: - logger.error(f"Error initializing ChatOpenAI: {str(e)}") - raise answer_parser = PydanticOutputParser(pydantic_object=Answer) patient_answer_prompt = PromptTemplate( @@ -54,8 +32,8 @@ ) # Initialize the LLMChains -patient_answer_chain = RunnableSequence(patient_answer_prompt | llm) -general_answer_chain = RunnableSequence(general_answer_prompt | llm) +patient_answer_chain = RunnableSequence(patient_answer_prompt | LLM) +general_answer_chain = RunnableSequence(general_answer_prompt | LLM) def parse_llm_output_answer(output: str) -> Tuple[str, str]: @@ -139,7 +117,7 @@ async def generate_answer( raise -async def test_llm_connection(): +async def test_llm_connection() -> bool: """Test the connection to the LLM. Returns @@ -158,12 +136,12 @@ async def test_llm_connection(): return False -async def initialize_llm(): +async def initialize_llm() -> bool: """Initialize the LLM. Returns ------- bool - True if the connection is successful, False otherwise. + True if the LLM is initialized successfully, False otherwise. """ - await test_llm_connection() + return await test_llm_connection() diff --git a/adrenaline/api/patients/ehr.py b/adrenaline/api/patients/ehr.py index b4e17a0..43bf345 100644 --- a/adrenaline/api/patients/ehr.py +++ b/adrenaline/api/patients/ehr.py @@ -240,7 +240,7 @@ def fetch_latest_medications(self, patient_id: int) -> str: for event in processed_events if ( event["event_type"] == "MEDICATION" - and event["encounter_id"] == latest_encounter + and event["timestamp"] > latest_timestamp ) } diff --git a/adrenaline/api/patients/llm.py b/adrenaline/api/patients/llm.py new file mode 100644 index 0000000..6dfceb1 --- /dev/null +++ b/adrenaline/api/patients/llm.py @@ -0,0 +1,33 @@ +"""LLM module for patients API.""" + +import logging +import os + +from langchain_openai import ChatOpenAI + + +# Configure logging +logging.basicConfig(level=logging.INFO) +logger = logging.getLogger(__name__) + +# Set up OpenAI client with custom endpoint +LLM_SERVICE_URL = os.getenv("LLM_SERVICE_URL") +if not LLM_SERVICE_URL: + raise ValueError("LLM_SERVICE_URL is not set") +logger.info(f"LLM_SERVICE_URL is set to: {LLM_SERVICE_URL}") + +os.environ["OPENAI_API_KEY"] = "EMPTY" + +# Initialize LLM with increased timeout +try: + LLM = ChatOpenAI( + base_url=LLM_SERVICE_URL, + model_name="Meta-Llama-3.1-70B-Instruct", + temperature=0.3, + max_tokens=4096, + request_timeout=60, + ) + logger.info("ChatOpenAI initialized successfully") +except Exception as e: + logger.error(f"Error initializing ChatOpenAI: {str(e)}") + raise \ No newline at end of file diff --git a/adrenaline/api/patients/workflows.py b/adrenaline/api/patients/workflows.py new file mode 100644 index 0000000..0cebd81 --- /dev/null +++ b/adrenaline/api/patients/workflows.py @@ -0,0 +1,3 @@ +"""EHR workflow functions.""" + + diff --git a/adrenaline/api/routes/answer.py b/adrenaline/api/routes/answer.py index 16fdbef..7e456aa 100644 --- a/adrenaline/api/routes/answer.py +++ b/adrenaline/api/routes/answer.py @@ -3,7 +3,7 @@ import logging import os from datetime import datetime -from typing import Dict, List +from typing import Any, Dict, List from fastapi import APIRouter, Body, Depends, HTTPException from motor.motor_asyncio import AsyncIOMotorDatabase @@ -109,7 +109,7 @@ async def format_medications( @router.post("/generate_answer") async def generate_answer_endpoint( query: Query = Body(...), # noqa: B008 - db: AsyncIOMotorDatabase = Depends(get_database), # noqa: B008 + db: AsyncIOMotorDatabase[Any] = Depends(get_database), # noqa: B008 current_user: User = Depends(get_current_active_user), # noqa: B008 ) -> Dict[str, str]: """Generate an answer using RAG.""" diff --git a/adrenaline/api/routes/pages.py b/adrenaline/api/routes/pages.py index 9fbe5e2..842e56d 100644 --- a/adrenaline/api/routes/pages.py +++ b/adrenaline/api/routes/pages.py @@ -2,7 +2,7 @@ import logging from datetime import UTC, datetime -from typing import Dict, List, Optional +from typing import Any, Dict, List, Optional from bson import ObjectId from fastapi import APIRouter, Body, Depends, HTTPException @@ -32,7 +32,7 @@ class CreatePageRequest(BaseModel): @router.post("/pages/create") async def create_page( request: CreatePageRequest, - db: AsyncIOMotorDatabase = Depends(get_database), # noqa: B008 + db: AsyncIOMotorDatabase[Any] = Depends(get_database), # noqa: B008 current_user: User = Depends(get_current_active_user), # noqa: B008 ) -> Dict[str, str]: """Create a new page for a user.""" @@ -63,9 +63,9 @@ async def append_to_page( page_id: str, question: str = Body(...), answer: str = Body(...), - db: AsyncIOMotorDatabase = Depends(get_database), # noqa: B008 + db: AsyncIOMotorDatabase[Any] = Depends(get_database), # noqa: B008 current_user: User = Depends(get_current_active_user), # noqa: B008 -) -> dict: +) -> Dict[str, str]: """Append a follow-up question and answer to an existing page.""" existing_page = await db.pages.find_one( {"_id": ObjectId(page_id), "user_id": str(current_user.id)} @@ -89,7 +89,7 @@ async def append_to_page( @router.get("/pages/history", response_model=List[Page]) async def get_user_page_history( - db: AsyncIOMotorDatabase = Depends(get_database), # noqa: B008 + db: AsyncIOMotorDatabase[Any] = Depends(get_database), # noqa: B008 current_user: User = Depends(get_current_active_user), # noqa: B008 ) -> List[Page]: """Retrieve all pages for the current user. @@ -114,7 +114,7 @@ async def get_user_page_history( @router.get("/pages/{page_id}", response_model=Page) async def get_page( page_id: str, - db: AsyncIOMotorDatabase = Depends(get_database), # noqa: B008 + db: AsyncIOMotorDatabase[Any] = Depends(get_database), # noqa: B008 current_user: User = Depends(get_current_active_user), # noqa: B008 ) -> Page: """Retrieve a specific page. diff --git a/scripts/cot_endpoint.py b/scripts/cot_endpoint.py index ff73407..f475042 100644 --- a/scripts/cot_endpoint.py +++ b/scripts/cot_endpoint.py @@ -1,4 +1,7 @@ +"""Test a chain of thought endpoint.""" + import os +from typing import Dict from langchain_openai import OpenAI from langchain.prompts import PromptTemplate from langchain_core.output_parsers import StrOutputParser @@ -47,7 +50,7 @@ class Query(BaseModel): # Define endpoint @app.post("/cot") -async def chain_of_thought(query: Query): +async def chain_of_thought(query: Query) -> Dict[str, str]: try: result = chain.invoke({"query": query.text}) diff --git a/services/embedding/api/routes.py b/services/embedding/api/routes.py index d5711e5..fcf2789 100644 --- a/services/embedding/api/routes.py +++ b/services/embedding/api/routes.py @@ -96,7 +96,7 @@ async def create_embeddings(request: EmbeddingRequest) -> Dict[str, List[List[fl raise HTTPException(status_code=500, detail=str(e)) from e -def initialize_model(): +def initialize_model() -> None: """Initialize the model.""" global model model = load_model() From 1dad75a1036eaf90280847dda43105c4fa132186 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Thu, 21 Nov 2024 15:23:39 +0000 Subject: [PATCH 3/6] [pre-commit.ci] Add auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- adrenaline/api/patients/llm.py | 2 +- adrenaline/api/patients/workflows.py | 2 -- 2 files changed, 1 insertion(+), 3 deletions(-) diff --git a/adrenaline/api/patients/llm.py b/adrenaline/api/patients/llm.py index 6dfceb1..d00874e 100644 --- a/adrenaline/api/patients/llm.py +++ b/adrenaline/api/patients/llm.py @@ -30,4 +30,4 @@ logger.info("ChatOpenAI initialized successfully") except Exception as e: logger.error(f"Error initializing ChatOpenAI: {str(e)}") - raise \ No newline at end of file + raise diff --git a/adrenaline/api/patients/workflows.py b/adrenaline/api/patients/workflows.py index 0cebd81..73603b8 100644 --- a/adrenaline/api/patients/workflows.py +++ b/adrenaline/api/patients/workflows.py @@ -1,3 +1 @@ """EHR workflow functions.""" - - From 2119c62467624e92820a7a6fed1f192695a87e60 Mon Sep 17 00:00:00 2001 From: Amrit Krishnan Date: Thu, 21 Nov 2024 13:55:26 -0500 Subject: [PATCH 4/6] Improve date formatting --- adrenaline/api/patients/llm.py | 2 +- adrenaline/api/patients/workflows.py | 2 - ui/src/app/components/ehr-workflows-card.tsx | 12 +- .../components/patient-encounters-table.tsx | 112 +++++++++++++----- ui/src/app/patient/[id]/page.tsx | 43 ++++++- ui/src/app/types/patient.ts | 10 ++ 6 files changed, 141 insertions(+), 40 deletions(-) diff --git a/adrenaline/api/patients/llm.py b/adrenaline/api/patients/llm.py index 6dfceb1..d00874e 100644 --- a/adrenaline/api/patients/llm.py +++ b/adrenaline/api/patients/llm.py @@ -30,4 +30,4 @@ logger.info("ChatOpenAI initialized successfully") except Exception as e: logger.error(f"Error initializing ChatOpenAI: {str(e)}") - raise \ No newline at end of file + raise diff --git a/adrenaline/api/patients/workflows.py b/adrenaline/api/patients/workflows.py index 0cebd81..73603b8 100644 --- a/adrenaline/api/patients/workflows.py +++ b/adrenaline/api/patients/workflows.py @@ -1,3 +1 @@ """EHR workflow functions.""" - - diff --git a/ui/src/app/components/ehr-workflows-card.tsx b/ui/src/app/components/ehr-workflows-card.tsx index c037b88..45c8c69 100644 --- a/ui/src/app/components/ehr-workflows-card.tsx +++ b/ui/src/app/components/ehr-workflows-card.tsx @@ -43,12 +43,17 @@ const EHRWorkflowsCard: React.FC = ({ patientId }) => { const token = localStorage.getItem('token') if (!token) throw new Error('No token found') - // Fetch medications + // Create AbortController with longer timeout + const controller = new AbortController() + const timeoutId = setTimeout(() => controller.abort(), 300000) // 5 minute timeout + + // Fetch medications with timeout const medsResponse = await fetch(`/api/patient_data/${patientId}/medications`, { headers: { 'Authorization': `Bearer ${token}`, 'Accept': 'text/plain' }, + signal: controller.signal }) if (!medsResponse.ok) { @@ -63,18 +68,21 @@ const EHRWorkflowsCard: React.FC = ({ patientId }) => { return } - // Format medications into table + // Format medications with timeout const formatResponse = await fetch('/api/format_medications', { method: 'POST', headers: { 'Authorization': `Bearer ${token}`, 'Content-Type': 'application/json', }, + signal: controller.signal, body: JSON.stringify({ medications: medications.replace(/^"|"$/g, '') }), }) + clearTimeout(timeoutId) + if (!formatResponse.ok) { const errorText = await formatResponse.text() throw new Error(`Failed to format medications: ${errorText}`) diff --git a/ui/src/app/components/patient-encounters-table.tsx b/ui/src/app/components/patient-encounters-table.tsx index cc55189..bcb6118 100644 --- a/ui/src/app/components/patient-encounters-table.tsx +++ b/ui/src/app/components/patient-encounters-table.tsx @@ -12,17 +12,20 @@ import { Td, Skeleton, Text, - useColorModeValue + useColorModeValue, + Box } from '@chakra-ui/react' +import { Encounter, PatientEncountersTableProps } from '../types/patient' -interface Encounter { - encounter_id: string; - admission_date: string; -} -interface PatientEncountersTableProps { - encounters: Encounter[]; - isLoading: boolean; +const formatDate = (dateString: string): string => { + const date = new Date(dateString) + return new Intl.DateTimeFormat('en-US', { + weekday: 'long', + year: 'numeric', + month: 'long', + day: 'numeric', + }).format(date) } const PatientEncountersTable: React.FC = ({ @@ -31,53 +34,104 @@ const PatientEncountersTable: React.FC = ({ }) => { const cardBgColor = useColorModeValue('white', 'gray.800') const borderColor = useColorModeValue('gray.200', 'gray.600') - const headerBgColor = useColorModeValue('gray.50', 'gray.700') + const headerBgColor = useColorModeValue('blue.50', 'blue.900') + const rowHoverBg = useColorModeValue('gray.50', 'gray.700') + const textColor = useColorModeValue('gray.800', 'gray.100') + const headerTextColor = useColorModeValue('blue.700', 'blue.100') return ( - - - Patient Encounters - + + + + Patient Encounters + + + {isLoading ? ( - + + + ) : encounters.length > 0 ? ( - +
- - - + + + {encounters.map((encounter, index) => ( - - + + ))}
Encounter IDAdmission Date
+ Encounter ID + + Admission Date +
{encounter.encounter_id}{new Date(encounter.admission_date).toLocaleDateString()} + {encounter.encounter_id} + + {formatDate(encounter.admission_date)} +
) : ( - No encounters found + + + No encounters found + + )} diff --git a/ui/src/app/patient/[id]/page.tsx b/ui/src/app/patient/[id]/page.tsx index 731fc85..14e07b7 100644 --- a/ui/src/app/patient/[id]/page.tsx +++ b/ui/src/app/patient/[id]/page.tsx @@ -200,7 +200,7 @@ const PatientPage: React.FC = () => { return ( - + @@ -225,12 +225,43 @@ const PatientPage: React.FC = () => { )} - + + {isLoading ? ( + + ) : patientData ? ( + + ) : ( + + + No patient data found + + + )} + - + + {isLoading ? ( + + ) : patientData ? ( + + ) : ( + + + No patient data found + + + )} + diff --git a/ui/src/app/types/patient.ts b/ui/src/app/types/patient.ts index 4b7571f..2abc681 100644 --- a/ui/src/app/types/patient.ts +++ b/ui/src/app/types/patient.ts @@ -1,3 +1,13 @@ +export interface Encounter { + encounter_id: string; + admission_date: string; +} + +export interface PatientEncountersTableProps { + encounters: Encounter[]; + isLoading: boolean; +} + export interface ClinicalNote { note_id: string; encounter_id: string; From 90e29e880c48d3a4c3eb103c20973820bd2d21c9 Mon Sep 17 00:00:00 2001 From: Amrit Krishnan Date: Thu, 21 Nov 2024 13:58:23 -0500 Subject: [PATCH 5/6] Remove unused imports --- ui/src/app/patient/[id]/page.tsx | 7 ------- 1 file changed, 7 deletions(-) diff --git a/ui/src/app/patient/[id]/page.tsx b/ui/src/app/patient/[id]/page.tsx index 14e07b7..affe4ac 100644 --- a/ui/src/app/patient/[id]/page.tsx +++ b/ui/src/app/patient/[id]/page.tsx @@ -17,13 +17,6 @@ import { GridItem, Progress, Heading, - Table, - Thead, - Tbody, - Tr, - Th, - Td, - TableContainer } from '@chakra-ui/react' import { motion, AnimatePresence } from 'framer-motion' import Sidebar from '../../components/sidebar' From 16f6d466d65d06fc23daa1838289792374a822f3 Mon Sep 17 00:00:00 2001 From: Amrit Krishnan Date: Thu, 21 Nov 2024 14:01:26 -0500 Subject: [PATCH 6/6] Fix formatting of encounter ID --- ui/src/app/components/clinical-notes-table.tsx | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/ui/src/app/components/clinical-notes-table.tsx b/ui/src/app/components/clinical-notes-table.tsx index b336021..2582157 100644 --- a/ui/src/app/components/clinical-notes-table.tsx +++ b/ui/src/app/components/clinical-notes-table.tsx @@ -22,6 +22,11 @@ const ClinicalNotesTable: React.FC = ({ notes, patientI router.push(`/note/${patientId}/${noteId}`); }, [router, patientId]); + const formatEncounterId = (encounterId: string | number): string => { + const numericId = parseInt(encounterId.toString(), 10); + return numericId === -1 ? 'N/A' : numericId.toString(); + }; + return ( @@ -49,7 +54,7 @@ const ClinicalNotesTable: React.FC = ({ notes, patientI
- {note.encounter_id === '-1' ? 'N/A' : note.encounter_id} + {formatEncounterId(note.encounter_id)}