Platform beta release

config.yaml

@@ -44,6 +44,8 @@ profiles:
       - openhim-mapping-mediator
       - kafka-mapper-consumer
       - kafka-unbundler-consumer
+      - fhir-ig-importer
+      - reprocess-mediator
     envFiles:
       - cdr-dw.env
 
@@ -75,4 +77,3 @@ profiles:
       - openhim-mapping-mediator
     envFiles:
       - mpi.env
-

fhir-ig-importer/docker-compose.dev.yml

@@ -10,5 +10,5 @@ services:
   fhir-ig-importer-ui:
     ports:
       - target: 8080
-        published: 3000
+        published: 3334
         mode: host

fhir-ig-importer/importer/volume/ig-importer-app.json

@@ -3,7 +3,7 @@
   "description": "FHIR IG microfrontend app",
   "category": "HIE Configuration",
   "type": "esmodule",
-  "url": "http://localhost:3000/jembi-fhir-ig-importer.js",
+  "url": "http://localhost:3334/jembi-fhir-ig-importer.js",
   "showInPortal": true,
   "showInSideBar": true,
   "access_roles": ["admin"],

fhir-ig-importer/package-metadata.json

@@ -14,7 +14,7 @@
     "FHIR_IG_IMPORTER_CORE_PORT": 3001,
     "FHIR_IG_IMPORTER_CORE_HOST": "0.0.0.0",
     "FHIR_IG_IMPORTER_CORE_URL": "http://0.0.0.0:3001/fhir/ig/v1.0",
-    "FHIR_IG_IMPORTER_UI_VERSION": "0.1.0",
-    "FHIR_IG_IMPORTER_CORE_VERSION": "1.0.0"
+    "FHIR_IG_IMPORTER_UI_VERSION": "v1.0.0",
+    "FHIR_IG_IMPORTER_CORE_VERSION": "v1.0.0"
   }
 }

interoperability-layer-openhim/package-metadata.json

@@ -6,8 +6,8 @@
   "type": "infrastructure",
   "dependencies": [],
   "environmentVariables": {
-    "OPENHIM_CORE_IMAGE": "jembi/openhim-core:microfrontends-3.0.0-beta",
-    "OPENHIM_CONSOLE_IMAGE": "jembi/openhim-console:v1.18.2",
+    "OPENHIM_CORE_IMAGE": "jembi/openhim-core:v8.4.3",
+    "OPENHIM_CONSOLE_IMAGE": "jembi/openhim-console:poc-microfrontend",
     "MONGO_IMAGE": "mongo:4.2",
     "AWAIT_HELPER_IMAGE": "jembi/await-helper:1.0.1",
     "MONGO_1_PLACEMENT": "node-1",

kafka-mapper-consumer/package-metadata.json

@@ -17,7 +17,7 @@
     "REGISTER_MEDIATOR": "true",
     "CLICKHOUSE_HOST": "analytics-datastore-clickhouse",
     "CLICKHOUSE_PORT": "8123",
-    "KAFKA_CONSUMER_MAPPER_MEDIATOR_VERSION": "jembi/kafka-mapper-consumer:0.1.0",
-    "KAFKA_CONSUMER_MAPPER_UI_VERSION": "jembi/kafka-mapper-consumer-ui:0.1.1-alpha"
+    "KAFKA_CONSUMER_MAPPER_MEDIATOR_VERSION": "jembi/kafka-mapper-consumer:v0.0.1",
+    "KAFKA_CONSUMER_MAPPER_UI_VERSION": "jembi/kafka-mapper-consumer-ui:v0.0.1"
   }
 }

mpi-mediator/docker-compose.yml

@@ -2,7 +2,7 @@ version: '3.9'
 
 services:
   mpi-mediator:
-    image: jembi/mpi-mediator:v2.1.1
+    image: jembi/mpi-mediator:v2.2.0
     networks:
       openhim:
       kafka:

mpi-mediator/importer/volume/openhim-import.json

@@ -5,9 +5,7 @@
       "surname": "User",
       "email": "[email protected]",
       "provider": "token",
-      "groups": [
-        "admin"
-      ],
+      "groups": ["admin"],
       "passwordAlgorithm": "sha512",
       "passwordHash": "ea3824f17cf1379eb118a36bc7c8cf0f45712e2af7748567fca5313dec6fa66d61064e82a5e5cb88e998486ee3c7d0dac235bbeda8c341d6edc1c77406be2ab6",
       "passwordSalt": "d4f622c0404f09bd959bfb263efa3452",
@@ -21,9 +19,7 @@
     {
       "clientID": "test",
       "name": "Test Client",
-      "roles": [
-        "instant"
-      ],
+      "roles": ["instant"],
       "customTokenID": "test"
     }
   ],
@@ -98,7 +94,7 @@
       "urlPattern": "^/fhir.*$",
       "methods": ["GET", "POST"],
       "type": "http",
-      "priority": null,
+      "priority": 2,
       "tcpPort": null,
       "tcpHost": null,
       "pollingSchedule": null,
@@ -147,19 +143,15 @@
     {
       "name": "MPI Orchestration for fhir bundles - Asynchronous flow",
       "urlPattern": "^/async/fhir/?$",
-      "methods": [
-        "POST"
-      ],
+      "methods": ["POST"],
       "type": "http",
       "priority": null,
       "tcpPort": null,
       "tcpHost": null,
       "pollingSchedule": null,
       "requestBody": true,
       "responseBody": true,
-      "allow": [
-        "instant"
-      ],
+      "allow": ["instant"],
       "whitelist": [],
       "authType": "private",
       "routes": [
@@ -240,9 +232,7 @@
       "pollingSchedule": null,
       "requestBody": true,
       "responseBody": true,
-      "allow": [
-        "instant"
-      ],
+      "allow": ["instant"],
       "whitelist": [],
       "authType": "private",
       "routes": [
@@ -328,14 +318,9 @@
         {
           "name": "MPI mediator",
           "urlPattern": "^(/async)?/fhir.*$",
-          "methods": [
-            "POST",
-            "GET"
-          ],
+          "methods": ["POST", "GET"],
           "type": "http",
-          "allow": [
-            "instant"
-          ],
+          "allow": ["instant"],
           "whitelist": [],
           "authType": "private",
           "routes": [

reprocess-mediator/docker-compose.dev.yml

@@ -4,7 +4,7 @@ services:
   reprocess-mediator:
     ports:
       - target: 3000
-        published: 3000
+        published: 3335
         mode: host
 
   reprocess-mediator-ui:

reprocess-mediator/package-metadata.json

@@ -1,18 +1,18 @@
 {
-    "id": "reprocess-mediator",
-    "name": "Reprocess Mediator",
-    "description": "A mediator that allows for configuring and reprocessing of transactions",
-    "type": "use-case",
-    "version": "1.4.2",
-    "dependencies": ["interoperability-layer-openhim"],
-    "environmentVariables": {
-      "TRUST_SELF_SIGNED": "true",
-      "OPENHIM_MEDIATOR_URL": "https://openhim-core:8080",
-      "OPENHIM_USERNAME": "[email protected]",
-      "OPENHIM_PASSWORD": "instant101",
-      "REGISTER_MEDIATOR": "true",
-      "REPROCESSOR_API_BASE_URL": "http://reprocess-mediator:3000",
-      "REPROCESS_CORE_VERSION": "latest",
-      "REPROCESS_UI_VERSION": "latest"
-    }
+  "id": "reprocess-mediator",
+  "name": "Reprocess Mediator",
+  "description": "A mediator that allows for configuring and reprocessing of transactions",
+  "type": "use-case",
+  "version": "1.4.2",
+  "dependencies": ["interoperability-layer-openhim"],
+  "environmentVariables": {
+    "TRUST_SELF_SIGNED": "true",
+    "OPENHIM_MEDIATOR_URL": "https://openhim-core:8080",
+    "OPENHIM_USERNAME": "[email protected]",
+    "OPENHIM_PASSWORD": "instant101",
+    "REGISTER_MEDIATOR": "true",
+    "REPROCESSOR_API_BASE_URL": "http://reprocess-mediator:3000",
+    "REPROCESS_CORE_VERSION": "v0.1.0",
+    "REPROCESS_UI_VERSION": "v0.1.0"
   }
+}

test/cucumber/features/steps/recipesSteps.js

@@ -1,16 +1,15 @@
-"use strict"
+"use strict";
 
 const axios = require("axios");
 const fs = require("fs");
-const path = require('path');
+const path = require("path");
 const chai = require("chai");
-const { ClickHouse } = require('clickhouse');
+const { ClickHouse } = require("clickhouse");
 const { Given, When, Then, setDefaultTimeout } = require("@cucumber/cucumber");
 setDefaultTimeout(30 * 60 * 1000);
 
-const HOST =
-  process.env.HOST || 'localhost';
-const CLICKHOUSE_PORT = parseInt(process.env.CLICKHOUSE_PORT || '8124');
+const HOST = process.env.HOST || "localhost";
+const CLICKHOUSE_PORT = parseInt(process.env.CLICKHOUSE_PORT || "8124");
 const CLICKHOUSE_DEBUG = Boolean(process.env.CLICKHOUSE_DEBUG || false);
 
 const { expect } = chai;
@@ -22,69 +21,99 @@ const clickhouse = new ClickHouse({
   raw: true,
 });
 
-const query = table => `SELECT * FROM ${table}`;
+const query = (table) => `SELECT * FROM ${table}`;
 
-const sendRequest = (url, method='POST', data={}) => {
+const sendRequest = (url, method = "POST", data = {}) => {
   return axios({
     url,
     headers: {
-      'Content-Type': 'application/fhir+json',
-      Authorization: `Custom test`
+      "Content-Type": "application/fhir+json",
+      Authorization: `Custom test`,
     },
     data,
-    method
-  })
+    method,
+  });
 };
 
 let PatientID;
 
 Given("I have configured the cdr", async function () {
   await new Promise((resolve) => {
-    setTimeout(() => resolve(), 300000)
+    setTimeout(() => resolve(), 300000);
   });
   const organization = JSON.parse(
-    fs.readFileSync(path.resolve(__dirname, '..' , 'resources', 'organization.json'))
+    fs.readFileSync(
+      path.resolve(__dirname, "..", "resources", "organization.json")
+    )
   );
 
-  this.cdrConfigResult = await sendRequest(`http://${HOST}:5001/fhir`, 'POST', organization);
+  this.cdrConfigResult = await sendRequest(
+    `http://${HOST}:5001/fhir`,
+    "POST",
+    organization
+  );
 });
 
 When("I send a fhir patient bundle", async function () {
   const fhirBundle = JSON.parse(
-    fs.readFileSync(path.resolve(__dirname, '..' , 'resources', 'fhirBundle.json'))
+    fs.readFileSync(
+      path.resolve(__dirname, "..", "resources", "fhirBundle.json")
+    )
   );
 
-  this.fhirBundleSentResult = await sendRequest(`http://${HOST}:5001/fhir`, 'POST', fhirBundle);
+  this.fhirBundleSentResult = await sendRequest(
+    `http://${HOST}:5001/fhir`,
+    "POST",
+    fhirBundle
+  );
 });
 
 When("I then send a fhir patient summary request", async function () {
-  this.IPSResult = await sendRequest(`http://${HOST}:5001/fhir/Patient/${PatientID}/$summary`, 'GET');
-});
-
-When("I then send a request for all the patient's clinical data", async function () {
-  this.EverythingResult = await sendRequest(`http://${HOST}:5001/fhir/Patient/${PatientID}/$everything?_mdm=true`, 'GET');
+  this.IPSResult = await sendRequest(
+    `http://${HOST}:5001/fhir/Patient/${PatientID}/$summary`,
+    "GET"
+  );
 });
 
-When("I wait for the services to start up", async function() {
+When(
+  "I then send a request for all the patient's clinical data",
+  async function () {
+    this.EverythingResult = await sendRequest(
+      `http://${HOST}:5001/fhir/Patient/${PatientID}/$everything?_mdm=true`,
+      "GET"
+    );
+  }
+);
+
+When("I wait for the services to start up", async function () {
   await new Promise((resolve) => {
     setTimeout(() => resolve(), 1500000);
   });
 });
 
 Then("the clinical data should be stored in hapi fhir", async function () {
-  this.fhirBundleSentResult.data.entry.forEach(rec => {
+  this.fhirBundleSentResult.data.entry.forEach((rec) => {
     expect(rec.response.status).to.match(/201|200/);
   });
 });
 
 Then("the patient data in the Jempi client registry", async function () {
-  const patientResource = this.fhirBundleSentResult.data.entry.filter(rec => rec.response.location.match('Patient'))[0];
+  const patientResource = this.fhirBundleSentResult.data.entry.filter((rec) =>
+    rec.response.location.match("Patient")
+  )[0];
 
-  PatientID = patientResource.response.location.split('/')[1];
+  PatientID = patientResource.response.location.split("/")[1];
 
-  const patient = await sendRequest(`http://${HOST}:5001/fhir/links/Patient/${PatientID}`, 'GET');
+  const patient = await sendRequest(
+    `http://${HOST}:5001/fhir/Patient/${PatientID}`,
+    "GET"
+  );
 
-  expect(patient.data.link.filter(pat => pat.other.reference.match(`Patient/${PatientID}`)).length).to.equal(1);
+  expect(
+    patient.data.link.filter((pat) =>
+      pat.other.reference.match(`Patient/${PatientID}`)
+    ).length
+  ).to.equal(1);
 });
 
 Then("I should get a successful summary response", function () {
@@ -96,22 +125,22 @@ Then("I should get a successful everything response", function () {
 });
 
 Then("a request to fetch data from the cdr should fail", async function () {
-  await sendRequest(`http://${HOST}:5001/fhir/links/Patient/${PatientID}`).catch(err => {
-    expect(err.message).to.match(/ECONNREFUSED|socket hang up|ETIMEDOUT/);
-  });
+  await sendRequest(`http://${HOST}:5001/fhir/Patient/${PatientID}`).catch(
+    (err) => {
+      expect(err.message).to.match(/ECONNREFUSED|socket hang up|ETIMEDOUT/);
+    }
+  );
 });
 
 Then("the data should be stored in clickhouse", async function () {
   await new Promise((resolve) => {
-    setTimeout(() => resolve(), 20000)
+    setTimeout(() => resolve(), 20000);
   });
 
-  const patient = await clickhouse.query(
-    query("patient_example"),
-  ).toPromise();
-  const observation = await clickhouse.query(
-    query("observation_example")
-  ).toPromise();
+  const patient = await clickhouse.query(query("patient_example")).toPromise();
+  const observation = await clickhouse
+    .query(query("observation_example"))
+    .toPromise();
 
   expect(JSON.parse(patient).rows).to.be.greaterThan(0);
   expect(JSON.parse(observation).rows).to.be.greaterThan(0);