Integrate OpenElis with a FHIR-Based Open Client Registry

README.md

@@ -1,25 +1,29 @@
-# ci-hie-demo
+# OpenELIS-OpenCR-HIE-Setup
+This integration aims to connect OpenELIS, a laboratory information system, with a FHIR-Based Open Client Registry which will allow users to search for patients within their local OpenELIS system, If the patient isn't found locally, search the client registry then Import patient information from the client registry to OpenELIS. 
 
+In simpler terms, this lets users find patients within their local system and if not found, search for them in a central database and bring their information back into the local system.
 
 ## How-Tos
 
 ### Pre-Requesites 
-1. Git: https://git-scm.com/book/en/v2/Getting-Started-Installing-Git
-2. Git Large File Storage: https://docs.github.com/en/repositories/working-with-files/managing-large-files/installing-git-large-file-storage
-3. Docker: https://docs.docker.com/engine/install/
+- Git: https://git-scm.com/book/en/v2/Getting-Started-Installing-Git
+- Git Large File Storage: https://docs.github.com/en/repositories/working-with-files/managing-large-files/installing-git-large-file-storage
+- Docker: https://docs.docker.com/engine/install/
 
 ### Startup
 
-```sh
-git clone https://github.com/I-TECH-UW/ci-hie-demo.git
-
-git lfs fetch
-
-git lfs checkout
-
-git lfs pull
-
-```
+- ```
+    git clone https://github.com/mherman22/OpenELIS-OpenCR-HIE-Setup
+    ```
+- ```
+    git lfs fetch
+    ```
+-  ```
+    git lfs checkout
+    ```
+- ```
+    git lfs pull
+    ```
 In the file found at "./configs/opencr/config.json" change the
 installed flag under app to false to load configs for Opencr  
 ```
@@ -31,26 +35,32 @@ installed flag under app to false to load configs for Opencr
 
 
 ### Resetting and Clearing OpenCR 
-```sh
-docker stop opencr opencr-fhir es
-docker system prune --volumes
-```
+- ```
+    docker stop opencr opencr-fhir es
+  ```
+- ```
+    docker system prune --volumes
+  ```
 ## Local setup
 
-Unzip esplugin plugin
+- ```
+  cd esplugin/string-similarity
+  ```
+- ```
+  unzip string-similarity-scoring-0.0.6-es7.9.1.zip
+  ```
 
-Spin up the services
+## Spin up the services
 
-```
-docker compose -f docker-compose-local.yml up -d
-```
-### You should be able to acces the Sigdep (OpenMRS) ,OpenHIM and Hapi-Fhir instances  at the following urls
+- ```
+    docker compose -f openelis-opencr-hie-docker-compose.yml up -d
+    ```
+### You should be able to acces the OpenELIS ,OpenHIM , OpenCR and Hapi-Fhir instances  at the following urls
 | Instance  |     URL       | credentials (user : password)|
 |---------- |:-------------:|------:                       |
-| Sigdep (OpenMRS)   | http://localhost:8080/openmrs  |  admin : Dppeis@pnls_16 |
 | OpenHIM   | http://localhost:9000  |  [email protected] : openhim |
 | OpenCR    | http://localhost:3000/crux  |  [email protected]  : intrahealth|
-| OpenELIS | https://localhost:8443/OpenELIS-Global/ |    admin : adminADMIN!| 
+| OpenELIS | https://localhost/login |    admin : adminADMIN!| 
 
 ### Restart the Streaming pipeline to work Properly
 After spinning up the Sigdep3 , restart the Streaming pipeline to Stream all Changes to the SHR (Fixed by adding depends-on meta in compose file)
@@ -99,7 +109,9 @@ ansible-playbook -i inventory.ini deployment.yml
 
 Run the following command in the test folder using newman to preload the client registry
 
-```
-npm install -g newman
-newman run postman_collection.json -e postman_environment.json --iteration-data pims_rule_test_dataset.csv --insecure
+- ```
+    npm install -g newman
+    ```
+- ```
+    newman run postman_collection.json -e postman_environment.json --iteration-data pims_rule_test_dataset.csv --insecure
 ```

configs/hapi/properties/hapi_application.yaml

@@ -0,0 +1,215 @@
+#Adds the option to go to eg. http://localhost:8080/actuator/health for seeing the running configuration
+#see https://docs.spring.io/spring-boot/docs/current/reference/html/actuator.html#actuator.endpoints
+management:
+  endpoints:
+    web:
+      exposure:
+        include: "health,prometheus"
+spring:
+  main:
+    allow-circular-references: true
+    #allow-bean-definition-overriding: true
+  flyway:
+    enabled: false
+    check-location: false
+    baselineOnMigrate: true
+  datasource:
+    url: 'jdbc:postgresql://database:5432/clinlims?currentSchema=clinlims'
+    #url: jdbc:h2:mem:test_mem
+    username: clinlims
+    password: clinlims
+
+    driverClassName: org.postgresql.Driver
+    max-active: 15
+
+    # database connection pool size
+    hikari:
+      maximum-pool-size: 10
+  jpa:
+    properties:
+      hibernate.format_sql: false
+      hibernate.show_sql: false
+
+      #Hibernate dialect is automatically detected except Postgres and H2.
+      #If using H2, then supply the value of ca.uhn.fhir.jpa.model.dialect.HapiFhirH2Dialect
+      #If using postgres, then supply the value of ca.uhn.fhir.jpa.model.dialect.HapiFhirPostgres94Dialect
+      hibernate.dialect: org.hibernate.dialect.PostgreSQLDialect
+      hibernate.hbm2ddl.auto: update
+  #      hibernate.jdbc.batch_size: 20
+  #      hibernate.cache.use_query_cache: false
+  #      hibernate.cache.use_second_level_cache: false
+  #      hibernate.cache.use_structured_entries: false
+  #      hibernate.cache.use_minimal_puts: false
+
+  ###    These settings will enable fulltext search with lucene or elastic
+      hibernate.search.enabled: true
+  ### lucene parameters
+#      hibernate.search.backend.type: lucene
+#      hibernate.search.backend.analysis.configurer: ca.uhn.fhir.jpa.search.HapiHSearchAnalysisConfigurers$HapiLuceneAnalysisConfigurer
+#      hibernate.search.backend.directory.type: local-filesystem
+#      hibernate.search.backend.directory.root: target/lucenefiles
+#      hibernate.search.backend.lucene_version: lucene_current
+  ### elastic parameters ===> see also elasticsearch section below <===
+#      hibernate.search.backend.type: elasticsearch
+#      hibernate.search.backend.analysis.configurer: ca.uhn.fhir.jpa.search.HapiHSearchAnalysisConfigurers$HapiElasticAnalysisConfigurer
+hapi:
+  fhir:
+
+    ### This enables the swagger-ui at /fhir/swagger-ui/index.html as well as the /fhir/api-docs (see https://hapifhir.io/hapi-fhir/docs/server_plain/openapi.html)
+    openapi_enabled: true
+    ### This is the FHIR version. Choose between, DSTU2, DSTU3, R4 or R5
+    fhir_version: R4
+    ### This flag when enabled to true, will avail evaluate measure operations from CR Module.
+    ### Flag is false by default, can be passed as command line argument to override.
+    cr_enabled: "${CR_ENABLED: false}"
+    ### enable to use the ApacheProxyAddressStrategy which uses X-Forwarded-* headers
+    ### to determine the FHIR server address
+    #   use_apache_address_strategy: false
+    ### forces the use of the https:// protocol for the returned server address.
+    ### alternatively, it may be set using the X-Forwarded-Proto header.
+    #   use_apache_address_strategy_https: false
+    ### enables the server to host content like HTML, css, etc. under the url pattern of /static/**
+    ### the deepest folder level will be used. E.g. - if you put file:/foo/bar/bazz as value then the files are resolved under /static/bazz/**
+    #staticLocation: file:/foo/bar/bazz
+    ### enable to set the Server URL
+    server_address: https://fhir.openelis.org:8443/fhir/
+    #    defer_indexing_for_codesystems_of_size: 101
+    #    install_transitive_ig_dependencies: true
+    ### tells the server whether to attempt to load IG resources that are already present
+    #    reload_existing_implementationGuides : false
+    #    implementationguides:
+    ###    example from registry (packages.fhir.org)
+    #      swiss:
+    #        name: swiss.mednet.fhir
+    #        version: 0.8.0
+    #      example not from registry
+    #      ips_1_0_0:
+    #        url: https://build.fhir.org/ig/HL7/fhir-ips/package.tgz
+    #        name: hl7.fhir.uv.ips
+    #        version: 1.0.0
+    #    supported_resource_types:
+    #      - Patient
+    #      - Observation
+    ##################################################
+    # Allowed Bundle Types for persistence (defaults are: COLLECTION,DOCUMENT,MESSAGE)
+    ##################################################
+    #    allowed_bundle_types: COLLECTION,DOCUMENT,MESSAGE,TRANSACTION,TRANSACTIONRESPONSE,BATCH,BATCHRESPONSE,HISTORY,SEARCHSET
+    #    allow_cascading_deletes: true
+    #    allow_contains_searches: true
+    allow_external_references: true
+    #    allow_multiple_delete: true
+    #    allow_override_default_search_params: true
+    auto_create_placeholder_reference_targets: true
+    ### tells the server to automatically append the current version of the target resource to references at these paths
+    #    auto_version_reference_at_paths: Device.patient, Device.location, Device.parent, DeviceMetric.parent, DeviceMetric.source, Observation.device, Observation.subject
+    #    cr_enabled: true
+    #    ips_enabled: false
+    #    default_encoding: JSON
+    default_pretty_print: false
+    default_page_size: 100
+    #    delete_expunge_enabled: true
+    #    enable_repository_validating_interceptor: true
+    #    enable_index_missing_fields: false
+    #    enable_index_of_type: true
+    #    enable_index_contained_resource: false
+    ###  !!Extended Lucene/Elasticsearch Indexing is still a experimental feature, expect some features (e.g. _total=accurate) to not work as expected!!
+    ###  more information here: https://hapifhir.io/hapi-fhir/docs/server_jpa/elastic.html
+    advanced_lucene_indexing: false
+    bulk_export_enabled: false
+    bulk_import_enabled: false
+    #    enforce_referential_integrity_on_delete: false
+    # This is an experimental feature, and does not fully support _total and other FHIR features.
+    #    enforce_referential_integrity_on_delete: false
+    #    enforce_referential_integrity_on_write: false
+    #    etag_support_enabled: true
+    #    expunge_enabled: true
+    #    client_id_strategy: ALPHANUMERIC
+    fhirpath_interceptor_enabled: false
+    #    filter_search_enabled: true
+    #    graphql_enabled: true
+    narrative_enabled: false
+    #    mdm_enabled: true
+    #    local_base_urls:
+    #      - https://hapi.fhir.org/baseR4
+    mdm_enabled: false
+    #    partitioning:
+    #      allow_references_across_partitions: false
+    #      partitioning_include_in_search_hashes: false
+    cors:
+      allow_Credentials: true
+      # These are allowed_origin patterns, see: https://docs.spring.io/spring-framework/docs/current/javadoc-api/org/springframework/web/cors/CorsConfiguration.html#setAllowedOriginPatterns-java.util.List-
+      allowed_origin:
+        - '*'
+
+    # Search coordinator thread pool sizes
+    search-coord-core-pool-size: 20
+    search-coord-max-pool-size: 100
+    search-coord-queue-capacity: 200
+
+    # comma-separated package names, will be @ComponentScan'ed by Spring to allow for creating custom Spring beans
+    #custom-bean-packages:
+
+    # comma-separated list of fully qualified interceptor classes. 
+    # classes listed here will be fetched from the Spring context when combined with 'custom-bean-packages', 
+    # or will be instantiated via reflection using an no-arg contructor; then registered with the server  
+    #custom-interceptor-classes:  
+
+    # Threadpool size for BATCH'ed GETs in a bundle.
+    #    bundle_batch_pool_size: 10
+    #    bundle_batch_pool_max_size: 50
+
+    #    logger:
+    #      error_format: 'ERROR - ${requestVerb} ${requestUrl}'
+    #      format: >-
+    #        Path[${servletPath}] Source[${requestHeader.x-forwarded-for}]
+    #        Operation[${operationType} ${operationName} ${idOrResourceName}]
+    #        UA[${requestHeader.user-agent}] Params[${requestParameters}]
+    #        ResponseEncoding[${responseEncodingNoDefault}]
+    #      log_exceptions: true
+    #      name: fhirtest.access
+    #    max_binary_size: 104857600
+    max_page_size: 200
+    retain_cached_searches_mins: 60
+    reuse_cached_search_results_millis: 1
+    tester:
+      home:
+        name: OE adjacent FHIR Store
+        server_address: 'https://fhir.openelis.org:8443/fhir/'
+        refuse_to_fetch_third_party_urls: false
+        fhir_version: R4
+    #    validation:
+    #      requests_enabled: true
+    #      responses_enabled: true
+    #    binary_storage_enabled: true
+    inline_resource_storage_below_size: 4000
+#    bulk_export_enabled: true
+    subscription:
+      resthook_enabled: true
+#      websocket_enabled: false
+#      email:
+#        from: [email protected]
+#        host: google.com
+#        port:
+#        username:
+#        password:
+#        auth:
+#        startTlsEnable:
+#        startTlsRequired:
+#        quitWait:
+#    lastn_enabled: true
+#    store_resource_in_lucene_index_enabled: true
+###  This is configuration for normalized quantity search level default is 0
+###   0: NORMALIZED_QUANTITY_SEARCH_NOT_SUPPORTED - default
+###   1: NORMALIZED_QUANTITY_STORAGE_SUPPORTED
+###   2: NORMALIZED_QUANTITY_SEARCH_SUPPORTED
+#    normalized_quantity_search_level: 2
+#elasticsearch:
+#  debug:
+#    pretty_print_json_log: false
+#    refresh_after_write: false
+#  enabled: false
+#  password: SomePassword
+#  required_index_status: YELLOW
+#  rest_url: 'localhost:9200'
+#  protocol: 'http'
+#  schema_management_strategy: CREATE