TB-201 Update JeMPI Docker Images Environment Variables

.github/workflows/ci-cluster.yml

@@ -72,7 +72,7 @@ jobs:
   run-e2e-tests:
     runs-on: ubuntu-20.04
     needs: configure-e2e-server
-    timeout-minutes: 80
+    timeout-minutes: 120
     steps:
       - uses: actions/checkout@v3
         with:

.github/workflows/run-tests.sh

@@ -8,6 +8,9 @@ CHANGED_FILES=($@)
 
 cd ../../test/cucumber/ || exit
 
+# This ensures that the openhim and its mediators' tests are run only once when the openhim and its mediators have all been modified
+openhimRan="false"
+
 declare -A changed_packages
 for package in "${CHANGED_FILES[@]}"; do
     if [[ $package == *"features/cluster-mode"* ]]; then
@@ -28,12 +31,10 @@ elif [[ "${!changed_packages[*]}" == *"features/single-mode"* ]] && [[ $NODE_MOD
     DOCKER_HOST=ssh://ubuntu@$GITHUB_RUN_ID.jembi.cloud yarn test:single
 elif [[ "${!changed_packages[*]}" == *"features/cluster-mode"* ]] && [[ $NODE_MODE == "cluster" ]]; then
     DOCKER_HOST=ssh://ubuntu@$GITHUB_RUN_ID.jembi.cloud yarn test:cluster
-elif [[ "${!changed_packages[*]}" == *"infrastructure"* ]]; then
-    DOCKER_HOST=ssh://ubuntu@$GITHUB_RUN_ID.jembi.cloud yarn test:"$NODE_MODE"
+elif [[ "${!changed_packages[*]}" == *"infrastructure"* ]] && [[ $openhimRan == "false" ]]; then
+    openhimRan="true"
+    DOCKER_HOST=ssh://ubuntu@$GITHUB_RUN_ID.jembi.cloud yarn test:"$NODE_MODE":openhim
 else
-    # This ensures that the openhim and its mediators' tests are run only once when the openhim and its mediators have all been modified
-    openhimRan="false"
-
     for folder_name in "${!changed_packages[@]}"; do
         echo "$folder_name was changed"
 

client-registry-jempi/README.md

@@ -0,0 +1,209 @@
+
+# JeMPI Client Registry Component - docker-swarm
+
+This component consists of two services:
+
+* JeMPI Web UI - http://localhost:3033
+* JeMPI API - http://localhost:50000/JeMPI
+
+## Api endpoints
+
+> This service uses the openhim mapping mediator to map fhir formated patients into the JeMPI format
+
+### Registering a patient
+
+via the api (in JeMPI format)
+
+```sh
+POST - http://localhost:50000/JeMPI/cr-register
+
+{
+    "candidateThreshold": 0.9,
+    "sourceId": {
+        "facility": "fac1",
+        "patient": "pat1"
+    },
+    "uniqueInteractionData": {
+        "auxDateCreated": "2016-10-30T14:22:25.285",
+        "auxId" : "1234",
+        "auxClinicalData" : "SOME DATA"
+    },
+    "demographicData": {
+        "givenName": "XXX",
+        "familyName": "YYY",
+        "gender": "female",
+        "dob": "20000101",
+        "phoneNumber": "123456789",
+        "city": "Cape Town",
+        "nationalId": "1234567890"
+    }
+}
+```
+
+via the [mapping mediator](https://github.com/jembi/openhim-mediator-mapping) (in fhir format)
+
+```sh
+
+POST http://localhost:3003/fhir/Patient
+
+{
+    "resourceType": "Patient",
+    "gender": "male",
+    "birthDate": "1968-04-15",
+    "name": [
+        {
+            "family": "cread",
+            "given": [
+                "Jacess"
+            ]
+        }
+    ],
+    "address": [
+        {
+            "city": "Indianapolis"
+        }
+    ],
+    "identifier": [
+        {
+            "system": "https://instantopenhie.org/client1",
+            "value": "6b4573e7-f9dc-49ea-9ebb-daaa6b74a534"
+        },
+        {
+            "value": "60934be6-ce88-48af-958e-02d88f77eec9",
+            "system": "NationalID"
+        }
+    ],
+    "telecom": [
+        {
+            "value": "899-882-4991",
+            "system": "phone"
+        }
+    ]
+}
+```
+> The identifier with the system 'NationalID' maps to the 'nationalId' property in JeMPI
+
+## Querying a patient by id
+
+via the api (returns patient in JeMPI formated)
+
+```sh
+GET - http://localhost:50000/JeMPI/expanded-golden-record/<PATIENT_GOLDEN_ID>
+```
+
+via the [mapping mediator](https://github.com/jembi/openhim-mediator-mapping) (returns patient in fhir format)
+
+```sh
+GET - http://localhost:3003/fhir/Patient/<PATIENT_GOLDEN_ID>
+```
+
+## Updating a patient
+
+via the api (in JeMPI format)
+
+```sh
+PATCH - http://localhost:50000/JeMPI/cr-update-fields
+
+{
+  "goldenId": "0x5",
+  "fields": [
+    {
+      "name": "givenName",
+      "value": "xxx"
+    },
+    {
+      "name": "familyName",
+      "value": "yyy"
+    }
+  ]
+}
+```
+
+via the [mapping mediator](https://github.com/jembi/openhim-mediator-mapping) (in fhir format)
+
+```sh
+PUT - http://localhost:3003/fhir/update/Patient/<PATIENT_GOLDEN_RECORD>
+
+{
+    "resourceType": "Patient",
+    "gender": "male",
+    "birthDate": "1968-04-15",
+    "name": [
+        {
+            "family": "cread",
+            "given": [
+                "Jacess"
+            ]
+        }
+    ],
+    "address": [
+        {
+            "city": "Indianapolis"
+        }
+    ],
+    "identifier": [
+        {
+            "system": "https://instantopenhie.org/client1",
+            "value": "6b4573e7-f9dc-49ea-9ebb-daaa6b74a534"
+        },
+        {
+            "value": "60934be6-ce88-48af-958e-02d88f77eec9",
+            "system": "NationalID"
+        }
+    ],
+    "telecom": [
+        {
+            "value": "899-882-4991",
+            "system": "phone"
+        }
+    ]
+}
+```
+
+## Query all patients deterministic
+
+via the api (returns in JeMPI format)
+
+```sh
+POST http://localhost:50000/JeMPI/cr-find
+
+{
+  "operand": {
+    "fn": "eq",
+    "name": "givenName",
+    "value": "xxx"
+  },
+  "operands": [
+    {
+      "operator": "and",
+      "operand": {
+        "fn": "eq",
+        "name": "familyName",
+        "value": "yyy"
+      }
+    }
+  ]
+}
+```
+
+via the [mapping mediator](https://github.com/jembi/openhim-mediator-mapping) (in fhir format)
+
+```sh
+POST http://localhost:3003/fhir/Patients
+
+{
+    "resourceType": "Parameters",
+    "parameters": [
+        {
+            "name": "and",                              // matches to the operator (options are "and" and "or")
+            "valueCode": "familyName",                  // matches to the field name (options are "givenName", "familyName", "dob", "nationalId", "gender", "city" and "phoneNumber")
+            "valueString": "creexxxeead"                // matches to value of the field
+        },
+        {
+            "name": "and",
+            "valueCode": "city",
+            "valueString": "Indianapeeolis"
+        }
+    ]
+}
+```

client-registry-jempi/docker-compose.api.yml

@@ -4,17 +4,18 @@ services:
   jempi-api:
     image: jembi/jempi-api:${JEMPI_API_IMAGE_TAG}
     environment:
-      KC_REALM_NAME: ${KC_REALM_NAME}
-      KC_JEMPI_CLIENT_ID: ${KC_JEMPI_CLIENT_ID}
-      KC_JEMPI_CLIENT_SECRET: ${KC_JEMPI_CLIENT_SECRET}
-      KC_API_URL: ${KC_API_URL}
-      KC_JEMPI_ROOT_URL: ${KC_JEMPI_ROOT_URL}
-      JEMPI_SESSION_SECRET: ${JEMPI_SESSION_SECRET}
-      kafka.bootstrap.servers: ${KAFKA_HOSTS}
-      JEMPI_FILE_IMPORT_MAX_SIZE_BYTE: ${JEMPI_FILE_IMPORT_MAX_SIZE_BYTE}
-      JEMPI_SESSION_SECURE: ${JEMPI_SESSION_SECURE}
-      JEMPI_SESSION_DOMAIN_NAME: ${DOMAIN_NAME}
-      postgres.server: ${JEMPI_REPMGR_PARTNER_NODES}
+      POSTGRESQL_USER: ${POSTGRESQL_USERNAME} 
+      POSTGRESQL_PASSWORD: ${POSTGRESQL_PASSWORD} 
+      POSTGRESQL_DATABASE: ${POSTGRESQL_DATABASE}
+      KAFKA_BOOTSTRAP_SERVERS: ${KAFKA_HOSTS}
+      KAFKA_APPLICATION_ID: ${KAFKA_APPLICATION_ID_API}
+      DGRAPH_HOSTS: ${DGRAPH_HOSTS}
+      DGRAPH_PORTS: ${DGRAPH_PORTS}
+      HTTP_SERVER_PORT: ${HTTP_SERVER_PORT}
+      LOG4J2_LEVEL: ${LOG4J2_LEVEL}
+      LINKER_HOST: ${LINKER_HOST}
+    volumes:
+      - "jempi-shared-data:/app/csv"
     deploy:
       replicas: ${JEMPI_API_INSTANCES}
       resources:
@@ -24,18 +25,16 @@ services:
           memory: ${JEMPI_API_MEMORY_RESERVE}
     networks:
       reverse-proxy:
-      keycloak:
       kafka:
       default:
 
+volumes:
+  jempi-shared-data: 
 
 networks:
   reverse-proxy:
     name: reverse-proxy_public
     external: true
-  keycloak:
-    name: keycloak_public
-    external: true
   kafka:
     name: kafka_public
     external: true

client-registry-jempi/docker-compose.combined-dev.yml

@@ -1,12 +1,6 @@
 version: '3.9'
 
 services:
-  jempi-sync-receiver:
-    ports:
-      - published: 50040
-        target: 50000
-        protocol: tcp
-        mode: host
 
   jempi-controller:
     ports: