Advanced search

pom.xml

@@ -79,7 +79,7 @@
                 <enabled>false</enabled>
             </releases>
             <name>Cytoscape Snapshots</name>
-            <url>http://code.cytoscape.org/nexus/content/repositories/snapshots/</url>
+            <url>https://code.cytoscape.org/nexus/content/repositories/snapshots/</url>
         </repository>
         <repository>
             <id>cytoscape_releases</id>
@@ -90,7 +90,7 @@
                 <enabled>true</enabled>
             </releases>
             <name>Cytoscape Releases</name>
-            <url>http://code.cytoscape.org/nexus/content/repositories/releases/</url>
+            <url>https://code.cytoscape.org/nexus/content/repositories/releases/</url>
         </repository>
         <repository>
             <id>apache-repo-releases</id>
@@ -106,6 +106,7 @@
                 <enabled>true</enabled>
             </releases>
         </repository>
+
     </repositories>
 
     <dependencies>
@@ -249,6 +250,39 @@
             <version>${osgi.api.version}</version>
             <scope>provided</scope>
         </dependency>
+        <dependency>
+            <groupId>org.projectlombok</groupId>
+            <artifactId>lombok</artifactId>
+            <version>1.18.34</version>
+            <scope>provided</scope>
+        </dependency>
+
+        <dependency>
+            <groupId>org.junit.jupiter</groupId>
+            <artifactId>junit-jupiter-api</artifactId>
+            <version>5.8.2</version>
+            <scope>test</scope>
+        </dependency>
+
+        <dependency>
+            <groupId>org.junit.jupiter</groupId>
+            <artifactId>junit-jupiter-engine</artifactId>
+            <version>5.8.2</version>
+            <scope>test</scope>
+        </dependency>
+
+        <dependency>
+            <groupId>org.junit.platform</groupId>
+            <artifactId>junit-platform-runner</artifactId>
+            <version>1.8.2</version>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>org.testng</groupId>
+            <artifactId>testng</artifactId>
+            <version>RELEASE</version>
+            <scope>test</scope>
+        </dependency>
     </dependencies>
 
 </project>

src/main/java/uk/ac/ebi/intact/app/internal/CyActivator.java

@@ -18,6 +18,7 @@
 import uk.ac.ebi.intact.app.internal.tasks.query.NoGUIQueryTask;
 import uk.ac.ebi.intact.app.internal.tasks.query.factories.ExactQueryTaskFactory;
 import uk.ac.ebi.intact.app.internal.tasks.query.factories.FuzzySearchTaskFactory;
+import uk.ac.ebi.intact.app.internal.tasks.query.factories.AdvancedSearchTaskFactory;
 import uk.ac.ebi.intact.app.internal.tasks.settings.SettingsTask;
 import uk.ac.ebi.intact.app.internal.tasks.version.factories.VersionTaskFactory;
 import uk.ac.ebi.intact.app.internal.tasks.view.extract.ExtractNetworkViewTaskFactory;
@@ -222,6 +223,11 @@ public TaskIterator createTaskIterator() {
             Properties propsSearch = new Properties();
             registerService(bc, intactSearch, NetworkSearchTaskFactory.class, propsSearch);
         }
+        {
+            AdvancedSearchTaskFactory advancedSearchTaskFactory = new AdvancedSearchTaskFactory(manager);
+            Properties propsSearch = new Properties();
+            registerService(bc, advancedSearchTaskFactory, NetworkSearchTaskFactory.class, propsSearch);
+        }
 
         manager.utils.info("Intact App initialized");
     }

src/main/java/uk/ac/ebi/intact/app/internal/io/HttpUtils.java

@@ -1,11 +1,17 @@
 package uk.ac.ebi.intact.app.internal.io;
 
 import com.fasterxml.jackson.core.JsonProcessingException;
+import com.fasterxml.jackson.databind.DeserializationFeature;
 import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.databind.MapperFeature;
 import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.databind.json.JsonMapper;
 import com.fasterxml.jackson.databind.node.NullNode;
 import org.cytoscape.io.util.StreamUtil;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import uk.ac.ebi.intact.app.internal.model.managers.Manager;
+import uk.ac.ebi.intact.app.internal.ui.components.query.advanced.Field;
 
 import java.io.*;
 import java.net.*;
@@ -19,11 +25,53 @@
 import java.util.concurrent.CompletableFuture;
 import java.util.function.Supplier;
 
+import static uk.ac.ebi.intact.app.internal.model.managers.Manager.INTACT_GRAPH_WS;
+
 public class HttpUtils {
+
     private static final HttpClient httpClient = HttpClient.newBuilder()
             .version(HttpClient.Version.HTTP_1_1)
             .build();
 
+    private static final HttpRequest.Builder requestBuilder = HttpRequest.newBuilder()
+            .header("Content-Type", "application/json")
+            .header("Accept", "application/json");
+
+    private static final ObjectMapper mapper = JsonMapper.builder()
+            .configure(DeserializationFeature.ACCEPT_SINGLE_VALUE_AS_ARRAY, true)
+            .configure(MapperFeature.ACCEPT_CASE_INSENSITIVE_ENUMS, true)
+            .build();
+
+    private static final Logger LOGGER = LoggerFactory.getLogger(HttpUtils.class);
+
+    public static JsonNode getJsonNetworkWithRequestBody(String query, int page) throws IOException, InterruptedException {
+        String baseUrl = INTACT_GRAPH_WS + "network/fromPagedInteractions";
+
+        Map<String, Object> params = Map.of(
+                "query", query,
+                "advancedSearch", isAdvancedSearch(query),
+                "page", page
+        );
+
+        HttpRequest request = requestBuilder
+                .uri(URI.create(baseUrl))
+                .POST(HttpRequest.BodyPublishers.ofString(mapper.writeValueAsString(params)))
+                .build();
+
+        HttpResponse<InputStream> response = httpClient.send(request, HttpResponse.BodyHandlers.ofInputStream());
+
+        return mapper.readTree(response.body());
+    }
+
+    public static boolean isAdvancedSearch(String query) {
+        for (Field field : Field.values()) {
+            if (query.contains(field.getMiqlQuery())) {
+                return true;
+            }
+        }
+        return false;
+    }
+
     public static JsonNode getJSON(String url, Map<String, String> queryMap, Manager manager) {
         URL trueURL;
         try {
@@ -48,7 +96,7 @@ public static JsonNode getJSON(String url, Map<String, String> queryMap, Manager
             entityStream.close();
 
         } catch (Exception e) {
-            e.printStackTrace();
+            logError(e.getMessage());
         }
         return jsonObject;
     }
@@ -65,11 +113,11 @@ public static JsonNode postJSON(String url, Map<Object, Object> data, Manager ma
 
             HttpResponse<String> response = httpClient.send(request, HttpResponse.BodyHandlers.ofString());
             if (response == null) {
-                manager.utils.error("No response from " + url + " with post data = " + data.toString());
+                manager.utils.error("No response from " + url + " with post data = " + data);
                 return null;
             }
             if (response.statusCode() != 200) {
-                manager.utils.error("Error " + response.statusCode() + " from " + url + " with post data = " + data.toString());
+                manager.utils.error("Error " + response.statusCode() + " from " + url + " with post data = " + data);
             }
             return new ObjectMapper().readTree(response.body());
 
@@ -80,32 +128,31 @@ public static JsonNode postJSON(String url, Map<Object, Object> data, Manager ma
         }
     }
 
-    public static JsonNode postJSON(String url, Map<Object, Object> data, Manager manager, Supplier<Boolean> isCancelled) {
+    public static JsonNode postJSON(String url, Map<Object, Object> body, Manager manager, Supplier<Boolean> isCancelled) {
         try {
             HttpRequest request = HttpRequest.newBuilder()
-                    .POST(buildFormDataFromMap(data))
                     .uri(URI.create(url))
+                    .POST(HttpRequest.BodyPublishers.ofString(mapper.writeValueAsString(body)))
                     .setHeader("User-Agent", "Java 11 HttpClient Bot") // add request header
-                    .header("Content-Type", "application/x-www-form-urlencoded")
                     .header("accept", "application/json")
                     .build();
             Instant begin = Instant.now();
-            CompletableFuture<String> body = httpClient.sendAsync(request, HttpResponse.BodyHandlers.ofString())
+            CompletableFuture<String> responseBody = httpClient.sendAsync(request, HttpResponse.BodyHandlers.ofString())
                     .thenApply(response -> {
                         if (response.statusCode() != 200) {
-                            manager.utils.error("Error " + response.statusCode() + " from " + url + " with post data = " + data.toString());
+                            manager.utils.error("Error " + response.statusCode() + " from " + url + " with post data = " + body);
                         }
                         return response;
                     }).thenApply(HttpResponse::body);
 
-            while (!body.isDone()) {
+            while (!responseBody.isDone()) {
                 if (isCancelled.get()) {
-                    body.cancel(true);
+                    responseBody.cancel(true);
                     return null;
                 }
             }
             System.out.println("Response received in " + Duration.between(begin, Instant.now()).toSeconds() + "s from " + url);
-            return new ObjectMapper().readTree(body.get());
+            return new ObjectMapper().readTree(responseBody.get());
 
         } catch (Exception e) {
             // e.printStackTrace();
@@ -114,7 +161,6 @@ public static JsonNode postJSON(String url, Map<Object, Object> data, Manager ma
         }
     }
 
-
     public static String getStringArguments(Map<String, String> args) {
         StringBuilder s = null;
         try {
@@ -125,26 +171,24 @@ public static String getStringArguments(Map<String, String> args) {
                     s.append("&").append(key).append("=").append(URLEncoder.encode(args.get(key), StandardCharsets.UTF_8.displayName()));
             }
         } catch (Exception e) {
-            e.printStackTrace();
+            logError(e.getMessage());
         }
         return s != null ? s.toString() : "";
     }
 
-
     public static String truncate(String str) {
         if (str.length() > 1000)
             return str.substring(0, 1000) + "...";
         return str;
     }
 
-
     private static URLConnection executeWithRedirect(Manager manager, String url, Map<String, String> queryMap) throws Exception {
         // Get the connection from Cytoscape
         HttpURLConnection connection = (HttpURLConnection) manager.utils.getService(StreamUtil.class).getURLConnection(new URL(url));
 
         // We want to write on the stream
         connection.setDoOutput(true);
-        // We want to deal with redirection ourself
+        // We want to deal with redirection ourselves
         connection.setInstanceFollowRedirects(false);
 
         // We write the POST arguments
@@ -178,7 +222,7 @@ private static String readStream(InputStream stream) throws Exception {
                 builder.append(line); // + "\r\n"(no need, json has no line breaks!)
             }
         }
-        System.out.println("JSON error response: " + builder.toString());
+        System.out.println("JSON error response: " + builder);
         return builder.toString();
     }
 
@@ -194,7 +238,7 @@ public static String getRequestResultForUrl(String requestURL) {
             }
             jsonText = builder.toString();
         } catch (IOException e) {
-            e.printStackTrace();
+            logError(e.getMessage());
         }
 
         return jsonText;
@@ -206,7 +250,7 @@ public static JsonNode getJsonForUrl(String jsonQuery) {
             try {
                 return new ObjectMapper().readTree(jsonText);
             } catch (JsonProcessingException e) {
-                e.printStackTrace();
+                logError(e.getMessage());
             }
         }
         return null;
@@ -235,4 +279,7 @@ private static HttpRequest.BodyPublisher buildFormDataFromMap(Map<Object, Object
         return HttpRequest.BodyPublishers.ofString(builder.toString());
     }
 
+    private static void logError(String message) {
+        LOGGER.error(message);
+    }
 }

src/main/java/uk/ac/ebi/intact/app/internal/model/core/elements/edges/Edge.java

@@ -24,6 +24,7 @@ public abstract class Edge implements Element {
     public final double miScore;
     public final List<String> sourceFeatureAcs;
     public final List<String> targetFeatureAcs;
+    public final boolean isNegative;
 
 
     public static Edge createEdge(Network network, CyEdge edge) {
@@ -57,6 +58,8 @@ public static Edge createEdge(Network network, CyEdge edge) {
         if (targetFeatureAcs != null) {
             targetFeatureAcs.removeIf(String::isBlank);
         }
+
+        isNegative = IS_NEGATIVE_INTERACTION.getValue(edgeRow);
     }
 
     public abstract Map<Node, List<Feature>> getFeatures() ;

src/main/java/uk/ac/ebi/intact/app/internal/model/core/elements/edges/EvidenceEdge.java

@@ -13,10 +13,7 @@
 import uk.ac.ebi.intact.app.internal.model.core.network.Network;
 import uk.ac.ebi.intact.app.internal.model.tables.fields.enums.FeatureFields;
 
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
+import java.util.*;
 
 import static uk.ac.ebi.intact.app.internal.model.managers.Manager.INTACT_GRAPH_WS;
 import static uk.ac.ebi.intact.app.internal.model.tables.fields.enums.EdgeFields.*;
@@ -36,6 +33,7 @@ public class EvidenceEdge extends Edge {
     public final CVTerm targetBiologicalRole;
     public final CVTerm targetExperimentalRole;
     private JsonNode detailsJSON;
+    public final Boolean isNegative;
 
     EvidenceEdge(Network network, CyEdge edge) {
         super(network, edge);
@@ -55,6 +53,7 @@ public class EvidenceEdge extends Edge {
         targetExperimentalRole = new CVTerm(edgeRow, EXPERIMENTAL_ROLE.TARGET);
 
         pubMedId = PUBMED_ID.getValue(edgeRow);
+        isNegative = IS_NEGATIVE_INTERACTION.getValue(edgeRow);
     }
 
     @Override
@@ -128,6 +127,7 @@ public EvidenceEdge cloneInto(Network network) {
         AFFECTED_BY_MUTATION.setValue(row, isAffectedByMutation());
 
         PUBMED_ID.setValue(row, pubMedId);
+
         return (EvidenceEdge) Edge.createEdge(network, edge);
     }
 

src/main/java/uk/ac/ebi/intact/app/internal/model/core/elements/edges/SummaryEdge.java

@@ -28,6 +28,10 @@ public Map<Node, List<Feature>> getFeatures() {
         return features;
     }
 
+    public Boolean isNegative() {
+        return getSummarizedEdges().stream().anyMatch(edge -> edge.isNegative);
+    }
+
     protected void buildFeatures(Map<Node, List<Feature>> features, List<String> featureAcs, Node participant, Set<Long> edgesSUID) {
         ArrayList<Feature> participantFeatures = new ArrayList<>();
         features.put(participant, participantFeatures);
@@ -64,6 +68,7 @@ public void updateSummary() {
                     if (summarizedCyEdge == null) return false;
                     return network.getEvidenceEdge(summarizedCyEdge) != null;
                 }).count();
+        EdgeFields.IS_NEGATIVE_INTERACTION.setValue(edgeRow, isNegative());
         EdgeFields.SUMMARY_NB_EDGES.setValue(edgeRow, nbSummarizedEdges);
     }
 

src/main/java/uk/ac/ebi/intact/app/internal/model/core/view/NetworkView.java

@@ -74,6 +74,7 @@ private void setupFilters(boolean loadData) {
         filters.add(new EdgeExpansionTypeFilter(this));
         filters.add(new EdgeTypeFilter(this));
         filters.add(new EdgeMutationFilter(this));
+        filters.add(new EdgePositiveFilter(this));
 
         filters.add(new OrphanNodeFilter(this)); // Must be after edge filters
         filters.add(new OrphanEdgeFilter(this));