Merge pull request #234 from geneontology/api_hack_1

Adding search API at /search to minerva
geneontology · Jul 11, 2019 · 41879e6 · 41879e6
2 parents 781ef94 + 737cb86
commit 41879e6
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Showing 8 changed files with 497 additions and 18 deletions.
diff --git a/minerva-cli/.DS_Store b/minerva-cli/.DS_Store
diff --git a/minerva-core/src/main/java/org/geneontology/minerva/BlazegraphMolecularModelManager.java b/minerva-core/src/main/java/org/geneontology/minerva/BlazegraphMolecularModelManager.java
@@ -135,6 +135,7 @@ private BigdataSailRepository initializeRepository(String pathToJournal) {
 			properties.setProperty(Options.FILE, pathToJournal);
 			BigdataSail sail = new BigdataSail(properties);
 			BigdataSailRepository repository = new BigdataSailRepository(sail);
+
 			repository.initialize();
 			return repository;
 		} catch (RepositoryException e) {

diff --git a/minerva-server/pom.xml b/minerva-server/pom.xml
@@ -118,5 +118,10 @@
 			<groupId>org.glassfish.jersey.containers</groupId>
 			<artifactId>jersey-container-servlet-core</artifactId>
 		</dependency>
+		<dependency>
+    		<groupId>org.glassfish.jersey.media</groupId>
+    		<artifactId>jersey-media-json-processing</artifactId>
+    		<version>2.28</version>
+		</dependency>
 	</dependencies>
 </project>
diff --git a/minerva-server/src/main/java/org/geneontology/minerva/server/StartUpTool.java b/minerva-server/src/main/java/org/geneontology/minerva/server/StartUpTool.java
@@ -1,8 +1,11 @@
 package org.geneontology.minerva.server;
 
 import org.apache.log4j.Logger;
+import org.eclipse.jetty.server.HttpConfiguration;
+import org.eclipse.jetty.server.HttpConnectionFactory;
 import org.eclipse.jetty.server.Server;
-import org.eclipse.jetty.server.nio.SelectChannelConnector;
+import org.eclipse.jetty.server.ServerConnector;
+//import org.eclipse.jetty.server.nio.SelectChannelConnector;
 import org.eclipse.jetty.servlet.ServletContextHandler;
 import org.eclipse.jetty.servlet.ServletHolder;
 import org.geneontology.minerva.ModelReaderHelper;
@@ -83,7 +86,7 @@ public static class MinervaStartUpConfig {
 
 		public String prefixesFile = null;
 
-		public int sparqlEndpointTimeout = 10;
+		public int sparqlEndpointTimeout = 100;
 	}
 
 	public static void main(String[] args) throws Exception {
@@ -379,15 +382,25 @@ public static Server startUp(UndoAwareMolecularModelManager models, MinervaStart
 		SimpleEcoMapper ecoMapper = EcoMapperFactory.createSimple();
 		JsonOrJsonpSeedHandler seedHandler = new JsonOrJsonpSeedHandler(models, conf.defaultModelState, conf.golrSeedUrl, ecoMapper );
 		SPARQLHandler sparqlHandler = new SPARQLHandler(models, conf.sparqlEndpointTimeout);
-		resourceConfig = resourceConfig.registerInstances(batchHandler, seedHandler, sparqlHandler);
+		ModelSearchHandler searchHandler = new ModelSearchHandler(models, conf.sparqlEndpointTimeout);
+		resourceConfig = resourceConfig.registerInstances(batchHandler, seedHandler, sparqlHandler, searchHandler);
 
 		// setup jetty server port, buffers and context path
 		Server server = new Server();
 		// create connector with port and custom buffer sizes
-		SelectChannelConnector connector = new SelectChannelConnector();
+		//old jetty
+		//SelectChannelConnector connector = new SelectChannelConnector();	
+		//old jetty - they must be configured somewhere else in new jetty
+		//connector.setRequestHeaderSize(conf.requestHeaderSize);
+		//connector.setRequestBufferSize(conf.requestBufferSize);
+		//new jetty - does not have setRequestBufferSize at all
+		//seems to push defaults harder here.
+		//to change request header size need to create a new connector and manipulate httpconfiguration
+        HttpConfiguration http_config = new HttpConfiguration();  
+        http_config.setRequestHeaderSize(conf.requestHeaderSize);
+		ServerConnector connector = new ServerConnector(server, new HttpConnectionFactory(http_config));
 		connector.setPort(conf.port);
-		connector.setRequestHeaderSize(conf.requestHeaderSize);
-		connector.setRequestBufferSize(conf.requestBufferSize);
+
 		server.addConnector(connector);
 
 		ServletContextHandler context = new ServletContextHandler(ServletContextHandler.SESSIONS);