dhti-cli 0.5.0 → 0.7.0

package/dist/resources/docker-compose-master.yml

@@ -12,7 +12,6 @@ services:
       - "80:80"
       - "9001:80"
 
-
   frontend:
     image: openmrs/openmrs-reference-application-3-frontend:3.0.0-beta.17
     # image: openmrs/openmrs-reference-application-3-frontend:${TAG:-3.0.0-beta.17} # dev3, qa, demo, 3.0.0-beta.18
@@ -59,7 +58,7 @@ services:
     restart: "unless-stopped"
     command: "mysqld --character-set-server=utf8 --collation-server=utf8_general_ci"
     healthcheck:
-      test: "mysql --user=${OMRS_DB_USER:-openmrs} --password=${OMRS_DB_PASSWORD:-openmrs} --execute \"SHOW DATABASES;\""
+      test: 'mysql --user=${OMRS_DB_USER:-openmrs} --password=${OMRS_DB_PASSWORD:-openmrs} --execute "SHOW DATABASES;"'
       interval: 3s
       timeout: 1s
       retries: 5
@@ -78,11 +77,15 @@ services:
       - "8001:8001"
     restart: "unless-stopped"
     environment:
-      - OLLAMA_SERVER_URL==http://ollama:11434
+      - OLLAMA_SERVER_URL=http://ollama:11434
       - OLLAMA_WEBUI=http://ollama-webui:8080
       - LANGFUSE_HOST=http://langfuse:3000
-      - LANGFUSE_PUBLIC_KEY=pk-lf-abcd
-      - LANGFUSE_SECRET_KEY=sk-lf-abcd
+      - LANGFUSE_PUBLIC_KEY=${LANGFUSE_PUBLIC_KEY:-pk-lf-abcd}
+      - LANGFUSE_SECRET_KEY=${LANGFUSE_SECRET_KEY:-sk-lf-abcd}
+      - GOOGLE_API_KEY=${GOOGLE_API_KEY:-google-api-key}
+      - OPENAI_API_KEY=${OPENAI_API_KEY:-openai-api-key}
+      - OPENAI_API_BASE=${OPENAI_API_BASE:-https://openrouter.ai/api/v1}
+      - OPENROUTER_API_KEY=${OPENROUTER_API_KEY:-openrouter-api-key}
 
   ollama:
     image: ollama/ollama:latest
@@ -105,7 +108,7 @@ services:
     ports:
       - 8080:8080
     environment:
-      - '/ollama/api=http://ollama:11434/api'
+      - "/ollama/api=http://ollama:11434/api"
     extra_hosts:
       - host.docker.internal:host-gateway
     restart: unless-stopped
@@ -118,19 +121,19 @@ services:
     depends_on:
       - postgres-db
     environment:
-        - "spring.datasource.url=jdbc:postgresql://postgres-db:5432/postgres"
-        - "spring.datasource.username=postgres"
-        - "spring.datasource.password=postgres"
-        - "spring.datasource.driverClassName=org.postgresql.Driver"
-        - "spring.jpa.properties.hibernate.dialect=ca.uhn.fhir.jpa.model.dialect.HapiFhirPostgres94Dialect"
-        - "hapi.fhir.fhir_version=R4"
-        - "hapi.fhir.cors.allowed-origins=*"
-        - "hapi.fhir.cors.allowCredentials=true"
-        - "hapi.fhir.bulkdata.enabled=true"
-        - "hapi.fhir.bulk_export_enabled=true"
-        - "hapi.fhir.bulk_import_enabled=true"
-        - "hapi.fhir.enforce_referential_integrity_on_write=false"
-        - "hapi.fhir.enforce_referential_integrity_on_delete=false"
+      - "spring.datasource.url=jdbc:postgresql://postgres-db:5432/postgres"
+      - "spring.datasource.username=postgres"
+      - "spring.datasource.password=postgres"
+      - "spring.datasource.driverClassName=org.postgresql.Driver"
+      - "spring.jpa.properties.hibernate.dialect=ca.uhn.fhir.jpa.model.dialect.HapiFhirPostgres94Dialect"
+      - "hapi.fhir.fhir_version=R4"
+      - "hapi.fhir.cors.allowed-origins=*"
+      - "hapi.fhir.cors.allowCredentials=true"
+      - "hapi.fhir.bulkdata.enabled=true"
+      - "hapi.fhir.bulk_export_enabled=true"
+      - "hapi.fhir.bulk_import_enabled=true"
+      - "hapi.fhir.enforce_referential_integrity_on_write=false"
+      - "hapi.fhir.enforce_referential_integrity_on_delete=false"
 
   mcp-fhir:
     image: beapen/fhir-mcp-server:4.0
@@ -173,7 +176,7 @@ services:
       - LANGFUSE_ENABLE_EXPERIMENTAL_FEATURES=${LANGFUSE_ENABLE_EXPERIMENTAL_FEATURES:-false}
 
   postgres-db:
-    image: postgres
+    image: postgres:17
     restart: "unless-stopped"
     environment:
       - POSTGRES_USER=postgres
@@ -183,6 +186,12 @@ services:
       - 5432:5432
     volumes:
       - postgres-db:/var/lib/postgresql/data
+    healthcheck:
+      test: ["CMD-SHELL", "pg_isready -U postgres -d postgres"]
+      interval: 10s
+      timeout: 5s
+      retries: 5
+      start_period: 10s
 
   redis:
     image: redislabs/redisearch:2.8.8
@@ -191,6 +200,12 @@ services:
     restart: "unless-stopped"
     volumes:
       - redis-db:/data
+    healthcheck:
+      test: ["CMD", "redis-cli", "ping"]
+      interval: 10s
+      timeout: 5s
+      retries: 3
+      start_period: 10s
 
   redis-commander:
     image: rediscommander/redis-commander:latest
@@ -234,14 +249,111 @@ services:
       - "3000:3000"
     # environment:
     #   - MCPX_PORT=9000
-    #   - MCPX_SERVER_URL="http://10.0.0.211:9000"
+    #   - MCPX_SERVER_URL="http://localhost:9000"
     #   - VITE_MCPX_SERVER_PORT=9000
-    #   - VITE_MCPX_SERVER_URL="http://10.0.0.211:9000"
+    #   - VITE_MCPX_SERVER_URL="http://localhost:9000"
     restart: unless-stopped
     volumes:
       - mcpx-config:/lunar/packages/mcpx-server/config
     privileged: true
 
+  # Medplum server container
+  medplum-server:
+    image: medplum/medplum-server:latest
+    restart: always
+    depends_on:
+      postgres-db:
+        condition: service_healthy
+      redis:
+        condition: service_healthy
+    ports:
+      - "8103:8103"
+    volumes:
+      # Conditionally define a volume for a `medplum.config.json` if one is specified by the MEDPLUM_CONFIG_PATH env var
+      - ${MEDPLUM_CONFIG_PATH:-./medplum.config.json}:/usr/src/medplum/packages/server/medplum.config.json
+    entrypoint: >
+      sh -c "
+      if [ -n '${MEDPLUM_CONFIG_PATH}' ]; then
+        echo 'Config file found, running with custom config'
+        node --require ./packages/server/dist/otel/instrumentation.js packages/server/dist/index.js file:/usr/src/medplum/packages/server/medplum.config.json
+      else
+        echo 'No config file found, running with default env settings'
+        node --require ./packages/server/dist/otel/instrumentation.js packages/server/dist/index.js env
+      fi
+      "
+    environment:
+      MEDPLUM_PORT: 8103
+      MEDPLUM_BASE_URL: "http://localhost:8103/"
+      MEDPLUM_APP_BASE_URL: "http://localhost:3103/"
+      MEDPLUM_STORAGE_BASE_URL: "http://localhost:8103/storage/"
+
+      MEDPLUM_DATABASE_HOST: "postgres-db"
+      MEDPLUM_DATABASE_PORT: 5432
+      MEDPLUM_DATABASE_DBNAME: "postgres"
+      MEDPLUM_DATABASE_USERNAME: "postgres"
+      MEDPLUM_DATABASE_PASSWORD: "postgres"
+
+      MEDPLUM_REDIS_HOST: "redis"
+      MEDPLUM_REDIS_PORT: 6379
+      # MEDPLUM_REDIS_PASSWORD: 'medplum'
+
+      MEDPLUM_BINARY_STORAGE: "file:./binary/"
+      MEDPLUM_SUPPORT_EMAIL: '\"Medplum\" <support@medplum.com>'
+      MEDPLUM_GOOGLE_CLIENT_ID: "397236612778-c0b5tnjv98frbo1tfuuha5vkme3cmq4s.apps.googleusercontent.com"
+      MEDPLUM_GOOGLE_CLIENT_SECRET: ""
+      MEDPLUM_RECAPTCHA_SITE_KEY: "6LfHdsYdAAAAAC0uLnnRrDrhcXnziiUwKd8VtLNq"
+      MEDPLUM_RECAPTCHA_SECRET_KEY: "6LfHdsYdAAAAAH9dN154jbJ3zpQife3xaiTvPChL"
+      MEDPLUM_MAX_JSON_SIZE: "1mb"
+      MEDPLUM_MAX_BATCH_SIZE: "50mb"
+      MEDPLUM_BOT_LAMBDA_ROLE_ARN: ""
+      MEDPLUM_BOT_LAMBDA_LAYER_NAME: "medplum-bot-layer"
+      MEDPLUM_VM_CONTEXT_BOTS_ENABLED: "true"
+      MEDPLUM_DEFAULT_BOT_RUNTIME_VERSION: "vmcontext"
+      MEDPLUM_ALLOWED_ORIGINS: "*"
+      MEDPLUM_INTROSPECTION_ENABLED: "true"
+      MEDPLUM_SHUTDOWN_TIMEOUT_MILLISECONDS: 30000
+
+    healthcheck:
+      test:
+        # We use Node's fetch for healthcheck because this image doesn't have a curl or wget installed
+        [
+          "CMD",
+          "node",
+          "-e",
+          'fetch("http://localhost:8103/healthcheck").then(r => r.json()).then(console.log).catch(() => { process.exit(1); })',
+        ]
+      interval: 30s
+      timeout: 10s
+      retries: 5
+
+  # Medplum app container (web UI)
+  medplum-app:
+    image: medplum/medplum-app:latest
+    restart: always
+    # depends_on:
+    #   medplum-server:
+    #     condition: service_healthy
+    ports:
+      - "3103:3000"
+    healthcheck:
+      test: ["CMD", "curl", "-f", "http://localhost:3103"]
+      interval: 10s
+      timeout: 5s
+      retries: 5
+
+  mpclient:
+    image: beapen/mpclient:15.0
+    ports:
+      - "8111:8111"
+    restart: "unless-stopped"
+    environment:
+      - PORT=8111
+      - MPCLIENT_BASE_URL=http://localhost:8111
+      - MEDPLUM_TOKEN_URL=http://medplum-server:8103/oauth2/token
+      - MEDPLUM_CLIENT_ID=client-id
+      - MEDPLUM_CLIENT_SECRET=secret
+    depends_on:
+      - medplum-server
 
 volumes:
   openmrs-data: ~
@@ -253,4 +365,4 @@ volumes:
   ollama-code: ~
   ollama-root: ~
   ollama-webui: ~
-  mcpx-config: ~
+  mcpx-config: ~

package/oclif.manifest.json

@@ -457,6 +457,14 @@
           "name": "dry-run",
           "allowNo": false,
           "type": "boolean"
+        },
+        "token": {
+          "char": "t",
+          "description": "Bearer token for authentication (optional)",
+          "name": "token",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
         }
       },
       "hasDynamicHelp": false,
@@ -474,6 +482,173 @@
         "mimic.js"
       ]
     },
+    "synthea": {
+      "aliases": [],
+      "args": {
+        "subcommand": {
+          "description": "Subcommand to execute: install, generate, upload, delete, download",
+          "name": "subcommand",
+          "options": [
+            "install",
+            "generate",
+            "upload",
+            "delete",
+            "download"
+          ],
+          "required": true
+        }
+      },
+      "description": "Manage Synthea synthetic FHIR data generation",
+      "examples": [
+        "<%= config.bin %> <%= command.id %> install",
+        "<%= config.bin %> <%= command.id %> generate -p 10",
+        "<%= config.bin %> <%= command.id %> upload -e http://fhir:8005/baseR4",
+        "<%= config.bin %> <%= command.id %> delete",
+        "<%= config.bin %> <%= command.id %> download --covid19"
+      ],
+      "flags": {
+        "age": {
+          "char": "a",
+          "description": "Generate patients with specific age range (e.g., \"0-18\" for pediatric)",
+          "name": "age",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "city": {
+          "char": "c",
+          "description": "City for patient generation",
+          "name": "city",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "covid19": {
+          "description": "Download COVID-19 dataset (1k patients)",
+          "name": "covid19",
+          "allowNo": false,
+          "type": "boolean"
+        },
+        "covid19_10k": {
+          "description": "Download COVID-19 dataset (10k patients)",
+          "name": "covid19_10k",
+          "allowNo": false,
+          "type": "boolean"
+        },
+        "covid19_csv": {
+          "description": "Download COVID-19 CSV dataset (1k patients)",
+          "name": "covid19_csv",
+          "allowNo": false,
+          "type": "boolean"
+        },
+        "covid19_csv_10k": {
+          "description": "Download COVID-19 CSV dataset (10k patients)",
+          "name": "covid19_csv_10k",
+          "allowNo": false,
+          "type": "boolean"
+        },
+        "dry-run": {
+          "description": "Show what changes would be made without actually making them",
+          "name": "dry-run",
+          "allowNo": false,
+          "type": "boolean"
+        },
+        "endpoint": {
+          "char": "e",
+          "description": "FHIR server endpoint URL",
+          "name": "endpoint",
+          "default": "http://fhir:8005/baseR4",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "gender": {
+          "char": "g",
+          "description": "Generate patients of specific gender (M or F)",
+          "name": "gender",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "options": [
+            "M",
+            "F"
+          ],
+          "type": "option"
+        },
+        "population": {
+          "char": "p",
+          "description": "Number of patients to generate",
+          "name": "population",
+          "default": 1,
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "seed": {
+          "char": "s",
+          "description": "Random seed for reproducible generation",
+          "name": "seed",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "state": {
+          "description": "State for patient generation (default: Massachusetts)",
+          "name": "state",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "synthea_sample_data_csv_latest": {
+          "description": "Download latest CSV sample data",
+          "name": "synthea_sample_data_csv_latest",
+          "allowNo": false,
+          "type": "boolean"
+        },
+        "synthea_sample_data_fhir_latest": {
+          "description": "Download latest FHIR sample data",
+          "name": "synthea_sample_data_fhir_latest",
+          "allowNo": false,
+          "type": "boolean"
+        },
+        "synthea_sample_data_fhir_stu3_latest": {
+          "description": "Download latest FHIR STU3 sample data",
+          "name": "synthea_sample_data_fhir_stu3_latest",
+          "allowNo": false,
+          "type": "boolean"
+        },
+        "token": {
+          "char": "t",
+          "description": "Bearer token for FHIR server authentication",
+          "name": "token",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "workdir": {
+          "char": "w",
+          "description": "Working directory for Synthea files",
+          "name": "workdir",
+          "default": "/home/runner/dhti",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        }
+      },
+      "hasDynamicHelp": false,
+      "hiddenAliases": [],
+      "id": "synthea",
+      "pluginAlias": "dhti-cli",
+      "pluginName": "dhti-cli",
+      "pluginType": "core",
+      "strict": true,
+      "enableJsonFlag": false,
+      "isESM": true,
+      "relativePath": [
+        "dist",
+        "commands",
+        "synthea.js"
+      ]
+    },
     "synthetic": {
       "aliases": [],
       "args": {
@@ -566,5 +741,5 @@
       ]
     }
   },
-  "version": "0.5.0"
+  "version": "0.7.0"
 }

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "dhti-cli",
   "description": "DHTI CLI",
-  "version": "0.5.0",
+  "version": "0.7.0",
   "author": "Bell Eapen",
   "bin": {
     "dhti-cli": "bin/run.js"
@@ -83,7 +83,8 @@
     "postpack": "shx rm -f oclif.manifest.json",
     "posttest": "echo 'npm run lint'",
     "prepack": "npx oclif manifest && npx oclif readme --readme-path notes/README.md",
-    "test": "mocha --forbid-only \"test/**/*.test.ts\"",
+    "test": "mocha --forbid-only \"test/**/*.test.ts\" --exclude \"test/e2e/**/*.test.ts\"",
+    "test-e2e": "mocha --forbid-only \"test/**/*.test.ts\"",
     "readme": "npx oclif readme --readme-path notes/README.md && git add notes/README.md",
     "docs": "typedoc --exclude src/tool.ts --html docs src"
   },