Docker

docker-compose/.env.schema

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+IMAGE_RDPC_GATEWAY=
+IMAGE_PLATFORM_GATEWAY=

docker-compose/compose.yaml

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+version: '3'
+
+services:
+  # RDPC Gateway
+  rdpc-gateway:
+    image: '${IMAGE_RDPC_GATEWAY}'
+    ports:
+      - 4000:4000
+    environment:
+      # Gateway Server Configuration
+      PORT: 4000
+      # RDPC-Gateway Services
+      WORKFLOW_API_URL: http://localhost:8088
+      SONG_SEARCH_URL: http://localhost:8081
+      # ARGO Clinical Services
+      CLINICAL_GQL_URL: http://localhost:3001
+      CLINICAL_API_URL: http://localhost:3002
+
+  # Platform Gateway
+  platform-gateway:
+    image: '${IMAGE_PLATFORM_GATEWAY}'
+    ports:
+      - 4001:4001
+    depends_on:
+      - elasticsearch
+    environment:
+      PORT: 4001
+      ELASTICSEARCH_HOST: 'http://elasticsearch:9200'
+      ELASTICSEARCH_PROGRAM_DONOR_DASHBOARD_INDEX: donor_submission_summary
+      DEV_RECAPTCHA_DISABLED: true
+
+  # Elasticsearch
+  elasticsearch:
+    image: docker.elastic.co/elasticsearch/elasticsearch:7.10.2
+    ports:
+      - 9200:9200
+    volumes:
+      - es_data:/usr/share/elasticsearch/data
+    environment:
+      - discovery.type=single-node
+      - 'ES_JAVA_OPTS=-Xms512m -Xmx2048m'
+
+  # Kibana
+  kibana:
+    image: docker.elastic.co/kibana/kibana:7.10.2
+    depends_on:
+      - elasticsearch
+    ports:
+      - 5601:5601
+
+volumes:
+  es_data:
+    driver: local

docker-compose/readme.md

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+# ES
+
+`file_centric` index needs to exist
+`npx ts-node --project tsconfig.json fileCentricEsInit.ts`

docker-compose/scripts/fileCentricEsInit.ts

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+/*
+ * Copyright (c) 2024 The Ontario Institute for Cancer Research. All rights reserved
+ *
+ * This program and the accompanying materials are made available under the terms of
+ * the GNU Affero General Public License v3.0. You should have received a copy of the
+ * GNU Affero General Public License along with this program.
+ *  If not, see <http://www.gnu.org/licenses/>.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY
+ * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT
+ * SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
+ * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED
+ * TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+ * OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER
+ * IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
+ * ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+import { Client } from '@elastic/elasticsearch';
+import indexSettings from './file_centric/file_mapping.json';
+import indexData from './file_centric/sample_file_centric.json';
+
+(async () => {
+	const TEST_INDEX = 'file_centric';
+	const ELASTICSEARCH_HOST = 'http://localhost:9200';
+	const esClient = new Client({
+		node: ELASTICSEARCH_HOST,
+		ssl: {
+			rejectUnauthorized: false,
+		},
+	});
+	try {
+		await esClient.ping();
+	} catch (err) {
+		console.log(`failing to ping elasticsearch at ${ELASTICSEARCH_HOST}: `, err);
+		throw err;
+	}
+	try {
+		console.log(`deleting index ${TEST_INDEX}`);
+		await esClient.indices.delete({
+			index: TEST_INDEX,
+		});
+	} catch (err) {
+		console.log(`could not delete index ${TEST_INDEX}: `, err);
+		if ((await esClient.indices.exists({ index: TEST_INDEX })).body) {
+			throw err;
+		}
+	}
+
+	console.log(`creating index ${TEST_INDEX}`);
+
+	await esClient.indices.create({
+		index: TEST_INDEX,
+		body: indexSettings,
+	});
+
+	console.log('index created');
+
+	await Promise.all(
+		indexData.map((doc, index) => {
+			console.log(`doc_${index}`);
+			return esClient.index({
+				index: TEST_INDEX,
+				refresh: 'wait_for',
+				body: {
+					...doc,
+					donors: [doc.donors].map((donor) => ({
+						...donor,
+						specimens: [donor.specimens].map((specimen) => ({
+							...specimen,
+							samples: [specimen.samples],
+						})),
+					})),
+					repositories: [doc.repositories],
+				},
+			});
+		}),
+	);
+
+	console.log('Complete!');
+})();