Fixes #122. Solved the synchronization issues with the GePiDataService.

All data now has a unique state associated with it. This dataSessionId is given around into the client to use as request context to identify the data to request. This circumvents the timing issues caused by synchronizing with respect to the Tapestry Session.
JULIELab · Aug 28, 2020 · 1edfd4e · 1edfd4e
1 parent cf7f6de
commit 1edfd4e
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Showing 22 changed files with 349 additions and 216 deletions.
diff --git a/gepi/gepi-core/src/main/java/de/julielab/gepi/core/retrieval/data/GePiData.java b/gepi/gepi-core/src/main/java/de/julielab/gepi/core/retrieval/data/GePiData.java
@@ -0,0 +1,51 @@
+package de.julielab.gepi.core.retrieval.data;
+
+import java.util.concurrent.CompletableFuture;
+import java.util.concurrent.Future;
+
+/**
+ * A single class to hold the input and result data of a GePi request.
+ */
+public class GePiData {
+    public static final GePiData EMPTY = new GePiData();
+    private long sessionId;
+    private Future<AggregatedEventsRetrievalResult> aggregatedResult;
+    private Future<EventRetrievalResult> unrolledResult;
+    private Future<IdConversionResult> listAIdConversionResult;
+    private Future<IdConversionResult> listBIdConversionResult;
+
+    public GePiData(Future<AggregatedEventsRetrievalResult> aggregatedResult, Future<EventRetrievalResult> unrolledResult, Future<IdConversionResult> listAIdConversionResult, Future<IdConversionResult> listBIdConversionResult) {
+        this.aggregatedResult = aggregatedResult;
+        this.unrolledResult = unrolledResult;
+        this.listAIdConversionResult = listAIdConversionResult;
+        this.listBIdConversionResult = listBIdConversionResult;
+    }
+
+    private GePiData() {
+        // for the EMPTY constant
+    }
+
+    public long getSessionId() {
+        return sessionId;
+    }
+
+    public void setSessionId(long sessionId) {
+        this.sessionId = sessionId;
+    }
+
+    public Future<AggregatedEventsRetrievalResult> getAggregatedResult() {
+        return aggregatedResult;
+    }
+
+    public Future<EventRetrievalResult> getUnrolledResult() {
+        return unrolledResult;
+    }
+
+    public Future<IdConversionResult> getListAIdConversionResult() {
+        return listAIdConversionResult;
+    }
+
+    public Future<IdConversionResult> getListBIdConversionResult() {
+        return listBIdConversionResult;
+    }
+}
diff --git a/...gepi/core/services/ChartsDataManager.java → ...b/gepi/core/services/GePiDataService.java b/...gepi/core/services/ChartsDataManager.java → ...b/gepi/core/services/GePiDataService.java
@@ -5,7 +5,10 @@
 import java.util.function.Function;
 import java.util.stream.Collectors;
 
+import com.google.common.cache.Cache;
+import com.google.common.cache.CacheBuilder;
 import de.julielab.gepi.core.retrieval.data.AggregatedEventsRetrievalResult;
+import de.julielab.gepi.core.retrieval.data.GePiData;
 import org.apache.commons.collections.CollectionUtils;
 import org.apache.tapestry5.json.JSONArray;
 import org.apache.tapestry5.json.JSONObject;
@@ -16,9 +19,42 @@
 import de.julielab.gepi.core.retrieval.data.Argument.ComparisonMode;
 import de.julielab.gepi.core.retrieval.data.Event;
 
-public class ChartsDataManager implements IChartsDataManager {
+public class GePiDataService implements IGePiDataService {
 
-    private static final Logger log = LoggerFactory.getLogger(ChartsDataManager.class);
+    private static final Logger log = LoggerFactory.getLogger(GePiDataService.class);
+
+    private Cache<Long, GePiData> dataCache;
+
+    public GePiDataService() {
+        // We use weak keys and values. So when a user session is evicted,
+        // its GePi data can also be removed as soon as possible.
+        dataCache = CacheBuilder.newBuilder().weakValues().build();
+    }
+
+
+    @Override
+    public void putData(long dataSessionId, GePiData data) {
+        data.setSessionId(dataSessionId);
+        dataCache.put(dataSessionId, data);
+    }
+
+    @Override
+    public long newSession() {
+        long id;
+        synchronized (dataCache) {
+            do {
+                id = System.currentTimeMillis();
+            } while (dataCache.getIfPresent(id) != null);
+        }
+        return id;
+    }
+
+    @Override
+    public GePiData getData(long sessionId) {
+        GePiData data = dataCache.getIfPresent(sessionId);
+        log.trace("Data for dataSessionId {} was {}.", sessionId, data != null ? "found" : "not found");
+        return data != null ? data : GePiData.EMPTY;
+    }
 
     /**
      * sets json formated input list for google charts that accept one entry

diff --git a/gepi/gepi-core/src/main/java/de/julielab/gepi/core/services/GepiCoreModule.java b/gepi/gepi-core/src/main/java/de/julielab/gepi/core/services/GepiCoreModule.java
@@ -14,6 +14,6 @@ public static void bind (ServiceBinder binder) {
 		binder.bind(IEventResponseProcessingService.class, EventResponseProcessingService.class);
 		binder.bind(IEventPostProcessingService.class, EventPostProcessingService.class);
 		binder.bind(IGeneIdService.class, GeneIdService.class);
-		binder.bind(IChartsDataManager.class, ChartsDataManager.class);
+		binder.bind(IGePiDataService.class, GePiDataService.class);
 	}
 }
diff --git a/gepi/gepi-core/src/main/java/de/julielab/gepi/core/services/IChartsDataManager.java b/gepi/gepi-core/src/main/java/de/julielab/gepi/core/services/IChartsDataManager.java
diff --git a/gepi/gepi-core/src/main/java/de/julielab/gepi/core/services/IGePiDataService.java b/gepi/gepi-core/src/main/java/de/julielab/gepi/core/services/IGePiDataService.java
@@ -0,0 +1,58 @@
+package de.julielab.gepi.core.services;
+
+import java.util.List;
+
+import de.julielab.gepi.core.retrieval.data.AggregatedEventsRetrievalResult;
+import de.julielab.gepi.core.retrieval.data.GePiData;
+import org.apache.tapestry5.json.JSONArray;
+
+import de.julielab.gepi.core.retrieval.data.Event;
+import org.apache.tapestry5.json.JSONObject;
+
+public interface IGePiDataService {
+
+    /**
+     * <p>Puts data to the data cache. If the data already has a session ID, the respective cache entry will be updated.
+     * Otherwise, a new ID will be generated and set to <tt>data</tt>. The final session ID is returned.</p>
+     *
+     *
+     * @param dataSessionId
+     * @param data The data of a new session.
+     */
+    void putData(long dataSessionId, GePiData data);
+
+    /**
+     * <p>Generates a new ID for a data session that can be used in {@link #getData(long)}}.</p>
+     *
+     * @return A new data session ID.
+     */
+    long newSession();
+
+    /**
+     * <p>Returns the data associated with the given session ID.</p>
+     *
+     * @param sessionId The session ID for which the data should be retrieved.
+     * @return The data of the session or {@link GePiData#EMPTY} if no such data exists.
+     */
+    GePiData getData(long sessionId);
+
+    /**
+     * input structure for pie chart and bar chart
+     *
+     * @return JSONArray - json array of tuples (itself realised as an json array)
+     */
+    JSONArray getTargetArgCount(List<Event> e);
+
+    /**
+     * input structure required for sankey graph
+     *
+     * @return JSONArray - array of triplets ([<from, <to>, count])
+     */
+    JSONObject getPairedArgsCount(List<Event> e);
+
+    JSONObject getPairedArgsCount(AggregatedEventsRetrievalResult aggregatedEvents);
+
+    JSONObject getPairsWithCommonTarget(List<Event> evtList);
+
+    JSONArray convertToJson(List<Event> eventList);
+}
diff --git a/gepi/gepi-core/src/test/java/de/julielab/gepi/core/services/ChartsDataManagerTest.java b/gepi/gepi-core/src/test/java/de/julielab/gepi/core/services/ChartsDataManagerTest.java
@@ -81,7 +81,7 @@ public void testGetPairesWithCommonTarget() {
         for (int i = 0; i < 10; i++)
             events.add(e6);
 
-        final ChartsDataManager manager = new ChartsDataManager();
+        final GePiDataService manager = new GePiDataService();
         final JSONObject nodesNLinks = manager.getPairsWithCommonTarget(events);
         final JSONArray pairs = nodesNLinks.getJSONArray("links");
         System.out.println(pairs);

diff --git a/gepi/gepi-webapp/src/main/java/de/julielab/gepi/webapp/components/BarChartWidget.java b/gepi/gepi-webapp/src/main/java/de/julielab/gepi/webapp/components/BarChartWidget.java
@@ -7,15 +7,15 @@
 import org.apache.tapestry5.json.JSONArray;
 import org.apache.tapestry5.services.javascript.JavaScriptSupport;
 
-import de.julielab.gepi.core.services.IChartsDataManager;
+import de.julielab.gepi.core.services.IGePiDataService;
 
 public class BarChartWidget extends GepiWidget {
 
 	@Inject
     private JavaScriptSupport javaScriptSupport;
 
 	@Inject
-	private IChartsDataManager gChartMnger;
+	private IGePiDataService gChartMnger;
 
 	@Property
 	private JSONArray eventsJSON;

diff --git a/gepi/gepi-webapp/src/main/java/de/julielab/gepi/webapp/components/CircleWidget.java b/gepi/gepi-webapp/src/main/java/de/julielab/gepi/webapp/components/CircleWidget.java
@@ -1,15 +1,11 @@
 package de.julielab.gepi.webapp.components;
 
-import de.julielab.gepi.core.services.IChartsDataManager;
 import org.apache.tapestry5.BindingConstants;
 import org.apache.tapestry5.annotations.Parameter;
 import org.apache.tapestry5.annotations.Property;
 import org.apache.tapestry5.ioc.annotations.Inject;
-import org.apache.tapestry5.json.JSONArray;
 import org.apache.tapestry5.services.javascript.JavaScriptSupport;
 
-import java.util.concurrent.ExecutionException;
-
 public class CircleWidget extends GepiWidget {
 
     @Inject

diff --git a/gepi/gepi-webapp/src/main/java/de/julielab/gepi/webapp/components/GepiInput.java b/gepi/gepi-webapp/src/main/java/de/julielab/gepi/webapp/components/GepiInput.java
@@ -9,15 +9,15 @@
 import java.util.stream.Stream;
 
 import de.julielab.gepi.core.retrieval.data.AggregatedEventsRetrievalResult;
+import de.julielab.gepi.core.retrieval.data.GePiData;
 import de.julielab.gepi.core.retrieval.services.IAggregatedEventsRetrievalService;
 import de.julielab.gepi.core.retrieval.data.IdConversionResult;
-import org.apache.tapestry5.ComponentResources;
-import org.apache.tapestry5.PersistenceConstants;
-import org.apache.tapestry5.SelectModel;
-import org.apache.tapestry5.ValueEncoder;
+import de.julielab.gepi.core.services.IGePiDataService;
+import org.apache.tapestry5.*;
 import org.apache.tapestry5.annotations.*;
 import org.apache.tapestry5.corelib.components.Form;
 import org.apache.tapestry5.corelib.components.TextArea;
+import org.apache.tapestry5.corelib.components.TextField;
 import org.apache.tapestry5.internal.OptionModelImpl;
 import org.apache.tapestry5.internal.SelectModelImpl;
 import org.apache.tapestry5.internal.services.StringValueEncoder;
@@ -60,6 +60,9 @@ public class GepiInput {
     @InjectComponent
     private TextArea listb;
 
+    @InjectComponent
+    private TextField dataSessionIdField;
+
     @Property
     @Persist
     private String listATextAreaValue;
@@ -80,6 +83,9 @@ public class GepiInput {
     @Inject
     private IGeneIdService geneIdService;
 
+    @Inject
+    private IGePiDataService dataService;
+
     @Parameter
     private CompletableFuture<EventRetrievalResult> esResult;
 
@@ -109,9 +115,32 @@ public class GepiInput {
     @Property
     private String filterString;
 
+    /**
+     * This is not an ID for the servlet session but to the current data state.
+     */
+    @Parameter
+    @Property
+    private long dataSessionId;
+
     @Persist(PersistenceConstants.FLASH)
     private boolean newSearch;
-
+    /**
+     * Do not access this field. It is only here to store the data in the session. Data access should happen through
+     * {@link de.julielab.gepi.core.services.GePiDataService}. There, the data is cached with weak keys and values.
+     * The idea is that the data is evicted when the session ends.
+     */
+    @Persist
+    private GePiData data;
+    /**
+     * This is an emergency exit against being locked in an error during development.
+     */
+    @ActivationRequestParameter
+    private boolean reset;
+    void onActivate(EventContext eventContext) {
+        if (reset) {
+            data = null;
+        }
+    }
 
     public ValueEncoder getEventTypeEncoder() {
         return new EnumValueEncoder(typeCoercer, EventTypes.class);
@@ -161,6 +190,9 @@ void onSuccessFromInputForm() {
         fetchEventsFromNeo4j(selectedEventTypeNames, isAListPresent, isABSearchRequest);
 //        }
 
+        data = new GePiData(neo4jResult, esResult, listAGePiIds, listBGePiIds);
+        log.debug("Setting newly retrieved data for dataSessionId: {}", dataSessionId);
+        dataService.putData(dataSessionId, data);
         Index indexPage = (Index) resources.getContainer();
         ajaxResponseRenderer.addRender(indexPage.getInputZone()).addRender(indexPage.getOutputZone());
         log.debug("Ajax rendering commands sent, entering the output display mode");

diff --git a/gepi/gepi-webapp/src/main/java/de/julielab/gepi/webapp/components/GepiWidget.java b/gepi/gepi-webapp/src/main/java/de/julielab/gepi/webapp/components/GepiWidget.java
@@ -2,48 +2,44 @@
 
 import de.julielab.gepi.core.retrieval.data.AggregatedEventsRetrievalResult;
 import de.julielab.gepi.core.retrieval.data.EventRetrievalResult;
+import de.julielab.gepi.core.services.GePiDataService;
+import de.julielab.gepi.core.services.IGePiDataService;
 import de.julielab.gepi.webapp.pages.Index;
 import org.apache.tapestry5.BindingConstants;
-import org.apache.tapestry5.annotations.InjectComponent;
-import org.apache.tapestry5.annotations.InjectPage;
-import org.apache.tapestry5.annotations.Parameter;
-import org.apache.tapestry5.annotations.Property;
+import org.apache.tapestry5.annotations.*;
 import org.apache.tapestry5.ioc.annotations.Inject;
 import org.slf4j.Logger;
 
-import java.util.concurrent.CompletableFuture;
+import java.util.concurrent.Future;
 
 public class GepiWidget {
 
     @Inject
     private Logger log;
 
+    @Inject
+    private IGePiDataService dataService;
+
     @Parameter(defaultPrefix = BindingConstants.LITERAL, name = "class")
     @Property
     private String classes;
 
     @InjectComponent
     private GepiWidgetLayout gepiWidgetLayout;
 
+    @Parameter
+    @Property
+    private long dataSessionId;
+
     @InjectPage
     private Index index;
 
-    public CompletableFuture<EventRetrievalResult> getEsResult() {
-        try {
-            log.debug("Trying to access index for ES result.");
-            return index.getEsResult();
-        } finally {
-            log.debug("Retrieved ES result.");
-        }
+    public Future<EventRetrievalResult> getEsResult() {
+        return dataService.getData(dataSessionId).getUnrolledResult();
     }
 
-    public CompletableFuture<AggregatedEventsRetrievalResult> getNeo4jResult() {
-        try {
-            log.debug("Trying to access index for Neo4j result.");
-            return index.getNeo4jResult();
-        } finally {
-            log.debug("Retrieved Neo4j result.");
-        }
+    public Future<AggregatedEventsRetrievalResult> getNeo4jResult() {
+        return dataService.getData(dataSessionId).getAggregatedResult();
     }
 
     public boolean isLargeView() {