Sedish haiti server (#59)

* Workflow fix * Fix * Fixed postgres setup * Fixed postgres setup * Fix * Fix * Fix * Fixes #54 * Fixes * Fixes * Fixed wait for isanteplus * Fixed wait for isanteplus * Fixed wait for isanteplus * Fixed wait for isanteplus * Fixed wait for isanteplus * Fixed wait for isanteplus * Fixed wait for isanteplus * Fixed wait for isanteplus * Fixed wait for isanteplus * Fixed wait for isanteplus * Fixed wait for isanteplus * Fixed wait for isanteplus * Fixed isanteplus wait * Fixed isanteplus wait * fix * Version Update * Haiti server updates * Ton of cleanup * Reverted to nginx due to ssl issues * Reverted to nginx due to ssl issues * Bumped iSantePlus to v2.3.4 * wait fix * Internal ID fix * Small fix * Small fix * Small fix
I-TECH-UW · Aug 19, 2022 · 8fd4a0e · 8fd4a0e
1 parent 4ea52a7
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diff --git a/.env b/.env
@@ -1,6 +1,6 @@
 # Versions
-ISANTEPLUS_DOCKER_VERSION=v2.0.2
-ISANTEPLUS_DB_VERSION=v2.0.2
+ISANTEPLUS_DOCKER_VERSION=v2.3.4
+ISANTEPLUS_DB_VERSION=v2.2.1
 ISANTEPLUS_QA_VERSION=v1.0.2
 
 # Port Assignments

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -17,51 +17,59 @@ jobs:
       - name: Checkout
         uses: actions/checkout@v1
 
+      - name: Copy config templates
+        run: |
+          cp ${GITHUB_WORKSPACE}/configs/opencr/.env.template ${GITHUB_WORKSPACE}/configs/opencr/.env
+          cp ${GITHUB_WORKSPACE}/configs/shr/.env.template ${GITHUB_WORKSPACE}/configs/shr/.env
+          cp ${GITHUB_WORKSPACE}/configs/isanteplus/isanteplus.env.template ${GITHUB_WORKSPACE}/configs/isanteplus/isanteplus.env
+
       - name: Set up Docker Buildx
         uses: docker/setup-buildx-action@v1
 
       - name: Pull containers
-        run: docker-compose -f docker-compose.ports.yml pull
+        run: docker-compose pull
 
       - name: Cache containers
         uses: satackey/[email protected]
         continue-on-error: true
 
-      - name: generate certs
-        run: docker-compose -f docker-compose.ports.yml up -d certgen
-
-      - name: Start core containers
-        run: docker-compose -f docker-compose.ports.yml up -d nginx openhim-core openhim-console mongo-db openhim-config
+      - name: Start all containers
+        run: docker-compose up -d
 
-      - name: Sleep for 10 seconds
-        run: sleep 30
+      - name: Sleep for 120 seconds
+        run: sleep 120
         shell: bash
 
       - name: Display docker logs for openhim config
-        run: docker-compose -f docker-compose.ports.yml logs openhim-config
-
-      - name: Start up support containers
-        run: docker-compose -f docker-compose.ports.yml up -d shr-fhir opencr-fhir opencr-es kafka zookeeper isanteplus isanteplus-mysql chrome 
-
-      - name: Sleep for 1200 seconds
-        run: sleep 1200
-        shell: bash
+        run: docker-compose logs openhim-config
 
+      - name: Show docker logs for isanteplus
+        run: docker logs isanteplus
+
       - name: Display docker logs for SHR & OpenCR
-        run: docker-compose -f docker-compose.ports.yml logs shr-fhir opencr-fhir
-
-      - name: Start up mediators
-        run: docker-compose -f docker-compose.ports.yml up -d shr opencr streaming-pipeline
+        run: docker-compose logs shr-fhir opencr-fhir
 
-      - name: Sleep for 120 seconds
-        run: sleep 120
+      - name: Wait For OpenMRS
+        run: docker-compose --profile=utility up  --exit-code-from wait-for-openmrs wait-for-openmrs
+
+      - name: Restart streaming pipeline
+        run: docker-compose up -d --force-recreate streaming-pipeline
+
+      - name: Sleep for 30 seconds
+        run: sleep 30
         shell: bash
+
+      - name: Display docker logs for iSantePlus
+        run: docker-compose logs isanteplus
+
+      - name: Display docker logs for Streaming Pipeline
+        run: docker-compose logs streaming-pipeline
 
       - name: Display docker logs for OpenCR
-        run: docker-compose -f docker-compose.ports.yml logs opencr
+        run: docker-compose logs opencr
 
       - name: Display docker logs for SHR
-        run: docker-compose -f docker-compose.ports.yml logs shr
+        run: docker-compose logs shr
 
       - name: Display docker logs for isanteplus mysql
         run: docker logs -n 500 isanteplus-mysql
@@ -70,25 +78,25 @@ jobs:
         run: docker logs isanteplus
 
       - name: Display container status
-        run: docker-compose -f docker-compose.ports.yml ps
+        run: docker-compose ps
 
       # - name: Run iSantePlus QA Framework (https://github.com/IsantePlus/isanteplus-qaframework)
-      #   run: docker-compose -f docker-compose.ports.yml up --exit-code-from qa qa
+      #   run: docker-compose up --exit-code-from qa qa
 
       - name: Run General Tests (https://www.postman.com/itechuw/workspace/haiti-sedish/collection/1525496-943a668e-664f-44a3-86b5-a4d4bc14c0e9)
         env:
           POSTMAN_COLLECTION: https://www.getpostman.com/collections/46fd37386092a9f460e4
-        run: docker-compose --profile test -f docker-compose.ports.yml up --exit-code-from newman newman
+        run: docker-compose --profile test up --exit-code-from newman newman
 
-      # - name: Run CR Tests (https://www.postman.com/itechuw/workspace/haiti-sedish/collection/1525496-943a668e-664f-44a3-86b5-a4d4bc14c0e9)
-      #   env:
-      #     POSTMAN_COLLECTION: https://www.getpostman.com/collections/4d682cbb222bb538d365
-      #   run: docker-compose --profile test -f docker-compose.ports.yml up --exit-code-from newman newman
+      - name: Run CR Tests (https://www.postman.com/itechuw/workspace/haiti-sedish/collection/1525496-943a668e-664f-44a3-86b5-a4d4bc14c0e9)
+        env:
+          POSTMAN_COLLECTION: https://www.getpostman.com/collections/4d682cbb222bb538d365
+        run: docker-compose --profile test up --exit-code-from newman newman
 
-      # - name: Run iSantePlus Tests (https://www.postman.com/itechuw/workspace/haiti-sedish/collection/1525496-ed828464-9287-4f1f-8bf0-61444f186c61)
-      #   env:
-      #     POSTMAN_COLLECTION: https://www.getpostman.com/collections/d3ccb73c1a402b1f6dd4
-      #   run: docker-compose --profile test -f docker-compose.ports.yml up --exit-code-from newman newman
+      - name: Run iSantePlus Tests (https://www.postman.com/itechuw/workspace/haiti-sedish/collection/1525496-ed828464-9287-4f1f-8bf0-61444f186c61)
+        env:
+          POSTMAN_COLLECTION: https://www.getpostman.com/collections/d3ccb73c1a402b1f6dd4
+        run: docker-compose --profile test up --exit-code-from newman newman
 
       - name: Display docker logs for OpenCR
         if: always()
@@ -102,6 +110,14 @@ jobs:
         if: always()
         run: docker logs -n 100 isanteplus
 
+      - name: Display docker logs for OpenHIM
+        if: always()
+        run: docker-compose logs openhim-core openhim-console
+
+      - name: Display docker logs for SHR FHIR
+        if: always()
+        run: docker-compose logs -n 500 shr-fhir
+
       - name: Stop containers
         if: always()
-        run: docker-compose -f docker-compose.ports.yml down -v
+        run: docker-compose down -v
diff --git a/.gitignore b/.gitignore
@@ -54,4 +54,8 @@ configs/isanteplus/custom_modules/*.omod
 configs/isanteplus/*.env
 configs/isanteplus/db/*.sql
 
-configs/streaming-pipeline/data*
+configs/streaming-pipeline/data*
+
+*.bak
+
+parquet
diff --git a/configs/nginx/nginx.conf b/configs/nginx/nginx.conf
@@ -57,7 +57,7 @@ http {
 
   server {
     listen              443 ssl;
-    server_name         core.sedish-haiti.org;
+    server_name         openhim-api.sedish-haiti.org;
 
     location / {
       resolver 127.0.0.11 valid=30s;  
@@ -141,5 +141,21 @@ http {
     }
   }
 
+  server {
+    listen              443 ssl;
+    server_name         opencr-fhir.sedish-haiti.org;
+
+    location / {
+      resolver 127.0.0.11 valid=30s;  
+
+      proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
+      proxy_set_header X-Forwarded-Proto $scheme;
+      proxy_set_header Host $http_host;
+      proxy_redirect off;
+
+      set $upstream opencr-fhir;
+      proxy_pass http://$upstream:8080;
+    }
+  }
 
 }
diff --git a/configs/opencr/PatientRelationship.json b/configs/opencr/PatientRelationship.json
@@ -0,0 +1,155 @@
+{
+  "resourceType": "Basic",
+  "id": "patientreport",
+  "meta": {
+    "versionId": "1",
+    "lastUpdated": "2019-07-30T07:34:24.098+00:00",
+    "profile": [
+      "http://ihris.org/fhir/StructureDefinition/iHRISRelationship"
+    ]
+  },
+  "extension": [
+    {
+      "url": "http://ihris.org/fhir/StructureDefinition/iHRISReportDetails",
+      "extension": [
+        {
+          "url": "label",
+          "valueString": "Patient Report"
+        },
+        {
+          "url": "name",
+          "valueString": "patients"
+        },
+        {
+          "url": "http://ihris.org/fhir/StructureDefinition/iHRISReportElement",
+          "extension": [
+            {
+              "url": "label",
+              "valueString": "gender"
+            },
+            {
+              "url": "name",
+              "valueString": "gender"
+            }
+          ]
+        },
+        {
+          "url": "http://ihris.org/fhir/StructureDefinition/iHRISReportElement",
+          "extension": [
+            {
+              "url": "label",
+              "valueString": "birthDate"
+            },
+            {
+              "url": "name",
+              "valueString": "birthDate"
+            }
+          ]
+        },
+        {
+          "url": "http://ihris.org/fhir/StructureDefinition/iHRISReportElement",
+          "extension": [
+            {
+              "url": "label",
+              "valueString": "given"
+            },
+            {
+              "url": "name",
+              "valueString": "name.where(use='official').last().given"
+            }
+          ]
+        },
+        {
+          "url": "http://ihris.org/fhir/StructureDefinition/iHRISReportElement",
+          "extension": [
+            {
+              "url": "label",
+              "valueString": "family"
+            },
+            {
+              "url": "name",
+              "valueString": "name.where(use='official').last().family"
+            }
+          ]
+        },
+        {
+          "url": "http://ihris.org/fhir/StructureDefinition/iHRISReportElement",
+          "extension": [
+            {
+              "url": "label",
+              "valueString": "fullname"
+            },
+            {
+              "url": "name",
+              "valueString": "name.where(use='official').last().text"
+            }
+          ]
+        },
+        {
+          "url": "http://ihris.org/fhir/StructureDefinition/iHRISReportElement",
+          "extension": [
+            {
+              "url": "label",
+              "valueString": "phone"
+            },
+            {
+              "url": "name",
+              "valueString": "telecom.where(system='phone').value"
+            }
+          ]
+        },
+        {
+          "url": "http://ihris.org/fhir/StructureDefinition/iHRISReportElement",
+          "extension": [
+            {
+              "url": "label",
+              "valueString": "art"
+            },
+            {
+              "url": "name",
+              "valueString": "identifier.where(system='http://clientregistry.org/artnumber').value"
+            }
+          ]
+        },
+        {
+          "url": "http://ihris.org/fhir/StructureDefinition/iHRISReportElement",
+          "extension": [
+            {
+              "url": "label",
+              "valueString": "biometric"
+            },
+            {
+              "url": "name",
+              "valueString": "identifier.where(system='http://isanteplus.org/openmrs/fhir2/6-biometrics-national-reference-code').value"
+            }
+          ]
+        },
+        {
+          "url": "http://ihris.org/fhir/StructureDefinition/iHRISReportElement",
+          "extension": [
+            {
+              "url": "label",
+              "valueString": "codeNational"
+            },
+            {
+              "url": "name",
+              "valueString": "identifier.where(system='http://isanteplus.org/openmrs/fhir2/5-code-national').value"
+            }
+          ]
+        }
+      ]
+    }
+  ],
+  "code": {
+    "coding": [
+      {
+        "system": "http://ihris.org/fhir/ValueSet/ihris-resource",
+        "code": "iHRISRelationship"
+      }
+    ],
+    "text": "iHRISRelationship"
+  },
+  "subject": {
+    "reference": "StructureDefinition/Patient"
+  }
+}
diff --git a/configs/opencr/application.yml b/configs/opencr/application.yml
@@ -0,0 +1,40 @@
+spring:
+  datasource:
+    hikari:
+      maximum-pool-size: 10
+  flyway:
+    check-location: false
+    baselineOnMigrate: true
+  jpa:
+    properties:
+      hibernate.format_sql: false
+      hibernate.show_sql: false
+  batch:
+    job:
+      enabled: false
+hapi:
+  fhir:
+    openapi_enabled: true
+    fhir_version: R4
+    server_address: http://opencr-fhir:8080/fhir
+    allow_cascading_deletes: true
+    allow_contains_searches: true
+    allow_external_references: true
+    allow_multiple_delete: true
+    narrative_enabled: false
+    auto_create_placeholder_reference_targets: true
+    default_page_size: 50
+    cors:
+      allow_Credentials: true
+      allowed_origin:
+        - '*'
+    search-coord-core-pool-size: 20
+    search-coord-max-pool-size: 100
+    search-coord-queue-capacity: 200
+    tester:
+      home:
+        name: Local Tester
+        server_address: 'http://localhost:8080/fhir'
+        refuse_to_fetch_third_party_urls: false
+        fhir_version: R4
+