enable running webapp in docker compose

EBISPOT · Nov 9, 2024 · c9ffc05 · c9ffc05
1 parent 9334180
commit c9ffc05
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Showing 2 changed files with 87 additions and 45 deletions.
diff --git a/webapp/docker-compose.yml b/webapp/docker-compose.yml
@@ -1,45 +1,58 @@
 services:
-    grebi-dataload:
-      build:
-        context: .
-        dockerfile: Dockerfile.dataload
+    grebi-ui:
+      image: ghcr.io/ebispot/grebi_ui:dev
+      ports:
+        - 8080:8080
+      environment:
+        - PUBLIC_URL=/
+        - REACT_APP_APIURL=http://localhost:8090
+    grebi-api:
+      image: ghcr.io/ebispot/grebi_api:dev
+      ports:
+        - 8090:8090
+      depends_on:
+        - grebi-neo4j
+        - grebi-solr
+        - grebi-resolver-service
+        - grebi-summary-service
+      links:
+        - grebi-neo4j
+        - grebi-solr
+        - grebi-resolver-service
+        - grebi-summary-service
       environment:
-        - GREBI_NFS_TMP=/work/tmp
-        - GREBI_HPS_TMP=/work/tmp
-        - GREBI_CONFIG=${GREBI_CONFIG:?}
-      command: bash -c "cd /work && ./scripts/run_pipeline_local.sh"
+        - GREBI_NEO4J_HOST=bolt://grebi-neo4j:7687/
+        - GREBI_SOLR_HOST=http://grebi-solr:8983/
+        - GREBI_RESOLVER_HOST=http://grebi-resolver-service:8080/
+        - GREBI_SUMMARY_HOST=http://grebi-summary-service:8081/
     grebi-neo4j:
       image: neo4j:5.18.0
       ports:
         - 7474:7474
         - 7687:7687
       volumes:
-        - grebi-neo4j-data:/var/lib/neo4j/data
+        - ${GREBI_NEO_DATA_PATH:?Need path to Neo4j data folder}:/var/lib/neo4j/data
       environment:
         - NEO4J_AUTH=none
-      depends_on:
-        grebi-dataload:
-          condition: service_completed_successfully
-    # grebi-api:
-    #   build: ./grebi_api
-    #   ports:
-    #     - 8080:8080
-    #   environment:
-    #     - GREBI_NEO4J_HOST=bolt://grebi-neo4j:7687
-    #   depends_on:
-    #     - grebi-neo4j    
-    #   links:
-    #     - grebi-neo4j 
-    # grebi-ui:
-    #   build:
-    #     context: ./grebi_ui
-    #   #env_file: ./grebi_ui/.env
-    #   ports:
-    #     - 8081:8080
-    #   depends_on:
-    #     - grebi-api
-    #   links:
-    #     - grebi-api
+        - NEO4J_PLUGINS=["apoc"]
+    grebi-solr:
+      image: solr:9.5.0
+      ports:
+        - 8983:8983
+      volumes:
+        - ${GREBI_SOLR_PATH:?Need path to Solr data}:/var/solr/data
+    grebi-resolver-service:
+      image: ghcr.io/ebispot/grebi_resolver_service:dev
+      volumes:
+        - ${GREBI_ROCKSDB_SEARCH_PATH:?Need path to search for RocksDB databases}:/rocksdbs
+      environment:
+        - GREBI_ROCKSDB_SEARCH_PATH=/rocksdbs
+    grebi-summary-service:
+      image: ghcr.io/ebispot/grebi_summary_service:dev
+      volumes:
+        - ${GREBI_SUMMARY_JSON_SEARCH_PATH:?Need path to search for summary json files}:/summaryjsons
+      environment:
+        - GREBI_SUMMARY_JSON_SEARCH_PATH=/summaryjsons
 volumes:
     grebi-neo4j-data:
 

diff --git a/webapp/grebi_api/src/main/java/uk/ac/ebi/grebi/GrebiApi.java b/webapp/grebi_api/src/main/java/uk/ac/ebi/grebi/GrebiApi.java
@@ -27,23 +27,52 @@ public class GrebiApi {
 
     public static void main(String[] args) throws ParseException, org.apache.commons.cli.ParseException, IOException {
 
-        final GrebiNeoRepo neo = new GrebiNeoRepo();
-        final GrebiSolrRepo solr = new GrebiSolrRepo();
-        final GrebiSummaryRepo summary = new GrebiSummaryRepo();
+        GrebiNeoRepo neo;
+        GrebiSolrRepo solr;
+        GrebiSummaryRepo summary;
+
+        Set<String> rocksDbSubgraphs = null;
+        Set<String> solrSubgraphs = null;
+        Set<String> summarySubgraphs = null;
+
+        while(true) {
+            try {
+                neo = new GrebiNeoRepo();
+                solr = new GrebiSolrRepo();
+                summary = new GrebiSummaryRepo();
+                rocksDbSubgraphs = (new ResolverClient()).getSubgraphs();
+                solrSubgraphs = solr.getSubgraphs();
+                summarySubgraphs = summary.getSubgraphs();
+                if(new HashSet<>(List.of(rocksDbSubgraphs, solrSubgraphs, summarySubgraphs)).size() != 1) {
+                    throw new RuntimeException("RocksDB/Solr/the summary jsons do not seem to contain the same subgraphs. Found: " + String.join(",", rocksDbSubgraphs) + " for RocksDB (from resolver service) and " + String.join(",", solrSubgraphs) + " for Solr (from list of solr cores) and " + String.join(",", summarySubgraphs) + " for the summary jsons (from summary server)");
+                }
+                break;
+            } catch(Exception e) {
+                System.out.println("Could not get subgraphs from one of the services. Retrying in 10 seconds...");
+                e.printStackTrace();
+                try {
+                    Thread.sleep(10000);
+                } catch (InterruptedException interruptedException) {
+                    interruptedException.printStackTrace();
+                }
+            }
+        }
 
-        Gson gson = new Gson();
+        System.out.println("Found subgraphs: " + String.join(",", solrSubgraphs));
 
-        var stats = neo.getStats();
+        run(neo, solr, summary, solrSubgraphs);
+    }
 
-        var rocksDbSubgraphs = (new ResolverClient()).getSubgraphs();
-        var solrSubgraphs = solr.getSubgraphs();
-        var summarySubgraphs = summary.getSubgraphs();
+    static void run(
+        final GrebiNeoRepo neo,
+        final GrebiSolrRepo solr,
+        final GrebiSummaryRepo summary,
+        final Set<String> subgraphs
+    ) {
 
-        if(new HashSet<>(List.of(rocksDbSubgraphs, solrSubgraphs, summarySubgraphs)).size() != 1) {
-            throw new RuntimeException("RocksDB/Solr/the summary jsons do not seem to contain the same subgraphs. Found: " + String.join(",", rocksDbSubgraphs) + " for RocksDB (from resolver service) and " + String.join(",", solrSubgraphs) + " for Solr (from list of solr cores) and " + String.join(",", summarySubgraphs) + " for the summary jsons (from summary server)");
-        }
+        var stats = neo.getStats();
 
-        System.out.println("Found subgraphs: " + String.join(",", solrSubgraphs));
+        Gson gson = new Gson();
 
         Javalin.create(config -> {
                     config.bundledPlugins.enableCors(cors -> {
@@ -60,7 +89,7 @@ public static void main(String[] args) throws ParseException, org.apache.commons
                 })
                 .get("/api/v1/subgraphs", ctx -> {
                     ctx.contentType("application/json");
-                    ctx.result(gson.toJson(solrSubgraphs));
+                    ctx.result(gson.toJson(subgraphs));
                 })
                 .get("/api/v1/subgraphs/{subgraph}", ctx -> {
                     ctx.contentType("application/json");