Handle timeout

pom.xml

@@ -83,18 +83,23 @@
 			<version>${powermock.version}</version>
 			<scope>test</scope>
 		</dependency>
+		<!-- Be aware that the UniProt japi dependency
+		will include google's guice 4.0
+		which does not play nicely with Java 9+.
+		I have not found a way to resolve this yet
+		other than running this code in a Java 8 docker
+		container. -->
 		<dependency>
 			<groupId>uk.ac.ebi.uniprot</groupId>
 			<artifactId>japi</artifactId>
-			<version>1.0.31</version>
+			<version>1.0.38</version>
 		</dependency>
 		<dependency>
 			<groupId>org.hamcrest</groupId>
 			<artifactId>hamcrest</artifactId>
 			<version>2.1</version>
 			<scope>test</scope>
 		</dependency>
-
 	</dependencies>
 
 	<repositories>

src/main/java/org/reactome/release/orthopairs/Main.java

@@ -47,7 +47,7 @@ public static void main( String[] args ) throws IOException, ParseException, Ser
         String pathToSpeciesConfig = props.getProperty("pathToSpeciesConfig", "src/main/resources/Species.json");
         String pantherQfOFilename = props.getProperty("pantherQfOFilename", "QfO_Genome_Orthologs.tar.gz");
         String pantherHCOPFilename = props.getProperty("pantherHCOPFilename", "Orthologs_HCOP.tar.gz");
-
+//        String uniprotQueryBatchSize = props.getProperty("uniprotQueryBatchSize", "100");
         if (releaseNumber.isEmpty()) {
             logger.fatal("Please populate config.properties file with releaseNumber");
             throw new IllegalStateException("No releaseNumber attribute in config.properties");

src/main/java/org/reactome/release/orthopairs/UniProtGeneNamesRetriever.java

@@ -12,17 +12,22 @@
 import uk.ac.ebi.uniprot.dataservice.client.uniprot.UniProtService;
 import uk.ac.ebi.uniprot.dataservice.query.Query;
 
+import java.net.SocketTimeoutException;
+
 import java.io.IOException;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.Paths;
 import java.nio.file.StandardOpenOption;
+import java.time.Duration;
 import java.util.*;
 
 public class UniProtGeneNamesRetriever {
 
+	private static final int MAX_NUM_ATTEMPTS = 10;
     private static final Logger logger = LogManager.getLogger();
-    private static final int MAX_UNIPROT_BATCH_QUERY_SIZE = 250;
+    // TODO: Make this value configurable.
+    private static final int MAX_UNIPROT_BATCH_QUERY_SIZE = 100;
 
     /**
      * Queries the UniProt mapping service through their Java API library. All Uniprot accession IDs are taken from the Panther
@@ -129,25 +134,58 @@ public static Set<String> retrieveGeneNamesFromUniProt(List<Set<String>> partiti
         int count = 0;
         Set<String> uniprotAccessionsToGeneNames = new HashSet<>();
         for (Set<String> uniprotIdentifierPartition : partitionedUniProtIds) {
+            int currentAttemptNum = 0;
             // Build UniProt API query from Set of 250 UniProt identifiers.
             Query query = UniProtQueryBuilder.accessions(uniprotIdentifierPartition);
             // Perform UniProt API query to retrieve gene names associated with identifiers.
-            QueryResult<UniProtComponent<Gene>> uniprotEntries = uniprotService.getGenes(query);
-
-            while (uniprotEntries.hasNext()) {
-                count++;
-                // Get Gene object returned from UniProt.
-                UniProtComponent<Gene> geneObject = uniprotEntries.next();
-                if (!geneObject.getComponent().isEmpty()) {
-                    // Iterate through all Gene components in the response.
-                    for (Gene geneComponent : geneObject.getComponent()) {
-                        // Tab-separate UniProt accession ID and its associated gene name, and then store these in the Set that will be returned.
-                        uniprotAccessionsToGeneNames.add(geneObject.getAccession().toString() + "\t" + geneComponent.getGeneName().toString() + "\n");
+            QueryResult<UniProtComponent<Gene>> uniprotEntries = null;
+            while (currentAttemptNum < MAX_NUM_ATTEMPTS && uniprotEntries == null)
+            {
+                try
+                {
+                    currentAttemptNum++;
+                    uniprotEntries = uniprotService.getGenes(query);
+                    while (uniprotEntries.hasNext()) {
+                        count++;
+                        // Get Gene object returned from UniProt.
+                        UniProtComponent<Gene> geneObject = uniprotEntries.next();
+                        if (!geneObject.getComponent().isEmpty()) {
+                            // Iterate through all Gene components in the response.
+                            for (Gene geneComponent : geneObject.getComponent()) {
+                                // Tab-separate UniProt accession ID and its associated gene name, and then store these in the Set that will be returned.
+                                uniprotAccessionsToGeneNames.add(geneObject.getAccession().toString() + "\t" + geneComponent.getGeneName().toString() + "\n");
+                            }
+                        }
+
+                        if (count % 1000 == 0) {
+                            logger.info(count + " UniProt identifiers have been queried for gene names");
+                        }
                     }
                 }
-
-                if (count % 1000 == 0) {
-                    logger.info(count + " UniProt identifiers have been queried for gene names");
+                catch (ServiceException e)
+                {
+                    // Log the exception right away, just in case any code in the exception handler fails and we don't get a chance to log it later.
+                    logger.error(e);
+                    // If the exception was caused by a Timeout, then we want to retry.
+                    boolean timeoutFound = false;
+                    int i = 0;
+                    while (!timeoutFound && i < e.getStackTrace().length)
+                    {
+                        // don't be too specific - there are other classes for timeouts. ANY type timeout should trigger a wait-retry.
+                        timeoutFound = e.getStackTrace()[i].getClassName().toUpperCase().contains("TIMEOUT");
+                        i++;
+                    }
+                    // If a timeout was found, sleep for a bit and then retry.
+                    if (timeoutFound)
+                    {
+                        long sleepAmt = Duration.ofSeconds(currentAttemptNum * 2L).toMillis();
+                        logger.warn("A timeout exception was caught while trying to connect to the UniProt service after {} attempts. A retry will be performed after {} milliseconds", currentAttemptNum, sleepAmt);
+                        Thread.sleep(sleepAmt);
+                    }
+                    else
+                    {
+                        logger.error("ServiceException caught while trying to communicate with UniProt: " + e.getMessage(), e);
+                    }
                 }
             }
         }