Api

gepi/gepi-core/src/main/java/de/julielab/gepi/core/retrieval/services/EventResponseProcessingService.java

@@ -113,6 +113,7 @@ private Stream<Event> resultDocuments2Events(Stream<ISearchServerDocument> docum
             Optional<Integer> likelihood = eventDocument.get(FIELD_EVENT_LIKELIHOOD);
             Optional<String> sentence = eventDocument.get(FIELD_EVENT_SENTENCE_TEXT);
             Optional<String> paragraph = eventDocument.get(FIELD_EVENT_PARAGRAPH_TEXT);
+            String source = (String)eventDocument.get(FIELD_SOURCE).get(); // pubmed or pmc
             List<String> sentenceArgumentHl = eventDocument.getHighlights().get(FIELD_EVENT_SENTENCE_TEXT_ARGUMENTS);
             List<String> sentenceTriggerHl = eventDocument.getHighlights().get(FIELD_EVENT_SENTENCE_TEXT_TRIGGER);
             List<String> sentenceFilterHl = eventDocument.getHighlights().get(FIELD_EVENT_SENTENCE_TEXT);
@@ -170,9 +171,12 @@ private Stream<Event> resultDocuments2Events(Stream<ISearchServerDocument> docum
 
             Event event = new Event();
             event.setArity(eventArity);
-            // Only one ID is present currently
-            pmid.ifPresent(event::setDocId);
-            pmcid.ifPresent(event::setDocId);
+
+            if (source.equals("pubmed") && pmid.isPresent())
+                event.setDocId(pmid.get());
+            else if (source.equals("pmc") && pmcid.isPresent())
+                event.setDocId(pmcid.get());
+
             event.setEventId(eventId);
             event.setArguments(arguments);
             if (likelihood.isPresent())

gepi/gepi-core/src/main/java/de/julielab/gepi/core/retrieval/services/EventRetrievalService.java

@@ -117,6 +117,8 @@ public class EventRetrievalService implements IEventRetrievalService {
 
     public static final String FIELD_AGGREGATION_VALUE = "aggregationvalue";
 
+    public static final String FIELD_SOURCE = "source";
+
     /**
      * The values in the field have the form symbol1---symbol2
      */
@@ -131,6 +133,7 @@ public class EventRetrievalService implements IEventRetrievalService {
     public static final List<String> FIELDS_FOR_TABLE = Arrays.asList(
             FIELD_PMID,
             FIELD_PMCID,
+            FIELD_SOURCE,
             FIELD_EVENT_LIKELIHOOD,
             FIELD_EVENT_SENTENCE_TEXT,
 //            FIELD_EVENT_PARAGRAPH_TEXT,

gepi/gepi-webapp/pom.xml

@@ -35,6 +35,12 @@
             <version>${tapestry-release-version}</version>
         </dependency>
 
+        <dependency>
+            <groupId>org.apache.tapestry</groupId>
+            <artifactId>tapestry-rest-jackson</artifactId>
+            <version>${tapestry-release-version}</version>
+        </dependency>
+
         <!-- EF 10-2020: required for the built-in less compiler. However, the last time I wanted to include this, the less compiler library was not loaded
         by intellij. Since I didn't need it, I just removed the dependency. -->
         <!--        <dependency>-->
@@ -90,6 +96,14 @@ of testing facilities designed for use with TestNG (http://testng.org/), so it's
             <!--            <scope>provided</scope>-->
         </dependency>
 
+        <!-- Required to write HttpRequestBodyConverters for the REST API -->
+        <dependency>
+            <groupId>javax.servlet</groupId>
+            <artifactId>javax.servlet-api</artifactId>
+            <version>3.1.0</version>
+            <scope>provided</scope>
+        </dependency>
+
         <!-- Provide dependency to the Tapestry javadoc taglet which replaces the Maven component report -->
         <dependency>
             <groupId>org.apache.tapestry</groupId>
@@ -171,26 +185,26 @@ of testing facilities designed for use with TestNG (http://testng.org/), so it's
                     <skip>false</skip>
                 </configuration>
             </plugin>
-<!--            <plugin>-->
-<!--                &lt;!&ndash; Run the application using "mvn jetty:run" &ndash;&gt;-->
-<!--                <groupId>org.mortbay.jetty</groupId>-->
-<!--                <artifactId>maven-jetty-plugin</artifactId>-->
-<!--                <version>6.1.16</version>-->
-<!--                <configuration>-->
-<!--                    &lt;!&ndash; Log to the console. &ndash;&gt;-->
-<!--                    <requestLog implementation="org.mortbay.jetty.NCSARequestLog">-->
-<!--                        &lt;!&ndash; This doesn't do anything for Jetty, but is a workaround for a Maven bug-->
-<!--                             that prevents the requestLog from being set. &ndash;&gt;-->
-<!--                        <append>true</append>-->
-<!--                    </requestLog>-->
-<!--                    <systemProperties>-->
-<!--                        <systemProperty>-->
-<!--                            <name>tapestry.execution-mode</name>-->
-<!--                            <value>development</value>-->
-<!--                        </systemProperty>-->
-<!--                    </systemProperties>-->
-<!--                </configuration>-->
-<!--            </plugin>-->
+            <!--            <plugin>-->
+            <!--                &lt;!&ndash; Run the application using "mvn jetty:run" &ndash;&gt;-->
+            <!--                <groupId>org.mortbay.jetty</groupId>-->
+            <!--                <artifactId>maven-jetty-plugin</artifactId>-->
+            <!--                <version>6.1.16</version>-->
+            <!--                <configuration>-->
+            <!--                    &lt;!&ndash; Log to the console. &ndash;&gt;-->
+            <!--                    <requestLog implementation="org.mortbay.jetty.NCSARequestLog">-->
+            <!--                        &lt;!&ndash; This doesn't do anything for Jetty, but is a workaround for a Maven bug-->
+            <!--                             that prevents the requestLog from being set. &ndash;&gt;-->
+            <!--                        <append>true</append>-->
+            <!--                    </requestLog>-->
+            <!--                    <systemProperties>-->
+            <!--                        <systemProperty>-->
+            <!--                            <name>tapestry.execution-mode</name>-->
+            <!--                            <value>development</value>-->
+            <!--                        </systemProperty>-->
+            <!--                    </systemProperties>-->
+            <!--                </configuration>-->
+            <!--            </plugin>-->
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-war-plugin</artifactId>

gepi/gepi-webapp/src/main/java/de/julielab/gepi/webapp/components/GepiInput.java

@@ -179,6 +179,11 @@ public class GepiInput {
      */
     @ActivationRequestParameter
     private boolean reset;
+
+    public GepiRequestData getRequestData() {
+        return requestData;
+    }
+
     /**
      * TODO This is here to allow for paging requests. It overlaps with {@link #data} which should be sorted out at some point.
      */

gepi/gepi-webapp/src/main/java/de/julielab/gepi/webapp/components/TableResultWidget.java

@@ -16,6 +16,7 @@
 import de.julielab.java.utilities.FileUtilities;
 import org.apache.tapestry5.ComponentResources;
 import org.apache.tapestry5.StreamResponse;
+import org.apache.tapestry5.SymbolConstants;
 import org.apache.tapestry5.annotations.*;
 import org.apache.tapestry5.beanmodel.BeanModel;
 import org.apache.tapestry5.beanmodel.services.BeanModelSource;
@@ -24,6 +25,7 @@
 import org.apache.tapestry5.http.services.Response;
 import org.apache.tapestry5.ioc.LoggerSource;
 import org.apache.tapestry5.ioc.annotations.Inject;
+import org.apache.tapestry5.ioc.annotations.Symbol;
 import org.apache.tapestry5.services.javascript.JavaScriptSupport;
 import org.slf4j.Logger;
 
@@ -88,58 +90,31 @@ public class TableResultWidget extends GepiWidget {
     @Persist(TabPersistentField.TAB)
     private Format contextFormat;
     @Inject
+    @Symbol(SymbolConstants.PRODUCTION_MODE)
+    private boolean productionMode;
+    @Inject
     private IEventRetrievalService eventRetrievalService;
     @Inject
     private LoggerSource loggerSource;
     @Environmental
     private JavaScriptSupport javaScriptSupport;
 
-//    @Property
-//    private List<String> selectedColumns;
     @Inject
     private IGeneIdService geneIdService;
-//    @Inject
-//    private TypeCoercer typeCoercer;
-//
-//    public ValueEncoder getColumnsEncoder() {
-//        return new StringValueEncoder();
-//    }
-//
-//    public SelectModel getColumnsModel() {
-//        return new SelectModelImpl(tableModel.getPropertyNames().stream().map(p -> new OptionModelImpl(p)).toArray(OptionModel[]::new));
-//    }
 
-//    @Inject
-//    private AjaxResponseRenderer ajaxResponseRenderer;
-//
-//    @InjectComponent
-//    private GepiWidgetLayout gepiWidgetLayout;
-//
-    // for columns selection
-//    public void onSuccessFromColumnsForm() {
-//        tableModel.include(selectedColumns.toArray(String[]::new));
-//        ajaxResponseRenderer.addRender(gepiWidgetLayout.getBodyZone());
-//    }
 
     @Log
     void setupRender() {
         getEventSource();
         List<String> availableColumns = new ArrayList<>(List.of("firstArgumentPreferredName",
                 "secondArgumentPreferredName",
-//                "firstArgumentText",
-//                "secondArgumentText",
                 "firstArgumentGeneId",
                 "secondArgumentGeneId",
-//                "firstArgumentMatchType",
-//                "secondArgumentMatchType",
                 "allEventTypes",
                 "factuality",
                 "fulltextMatchSource",
                 "docId",
-//                "eventId",
                 "context"
-//                ,
-//                "geneMappingSources"
         ));
         if (inputMode != null && !inputMode.contains(InputMode.FULLTEXT_QUERY))
             availableColumns.remove("fulltextMatchSource");
@@ -149,16 +124,10 @@ void setupRender() {
 
         tableModel.get("firstArgumentPreferredName").label("Gene A Symbol");
         tableModel.get("secondArgumentPreferredName").label("Gene B Symbol");
-//        tableModel.get("firstArgumentText").label("Gene A Text");
-//        tableModel.get("secondArgumentText").label("Gene B Text");
         tableModel.get("firstArgumentGeneId").label("Gene A Gene ID");
         tableModel.get("secondArgumentGeneId").label("Gene B Gene ID");
-//        tableModel.get("firstArgumentMatchType").label("gene A match type");
-//        tableModel.get("secondArgumentMatchType").label("gene B match type");
         tableModel.get("allEventTypes").label("Relation Types");
         tableModel.get("docId").label("Document ID");
-//        tableModel.get("eventId").label("event id");
-//        tableModel.get("geneMappingSources").label("gene tagger");
         // Disable the sorting buttons. Since we reorder the event arguments so that arguments from list A
         // always appear as the "first" argument, we cannot sort in ElasticSearch because there is no fixed
         // field we could sort on for the gene arguments. Other columns would be possible to sort on but
@@ -177,28 +146,14 @@ public Object parseObject(String source, ParsePosition pos) {
                 return source;
             }
         };
-//        selectedColumns = tableModel.getPropertyNames();
     }
 
-    /**
-     * When the form containing the filter elements is submitted, we want to re-render the table via AJAX
-     */
-//    void onValidateFromFilterCriteria() {
-//        if (request.isXHR()) {
-//            ajaxResponseRenderer.addRender(tableZone);
-//        }
-//    }
     public EventPagesDataSource getEventSource() {
-//        FilteredGepiRequestData filteredRequest = new FilteredGepiRequestData(requestData);
-//        filteredRequest.setEventTypeFilter(filterEventType);
         return new EventPagesDataSource(loggerSource.getLogger(EventPagesDataSource.class), dataService.getData(requestData.getDataSessionId()).getPagedResult(), eventRetrievalService, geneIdService, requestData);
     }
 
     void onUpdateTableData() {
         log.debug("Waiting for table data.");
-//            beanEvents = getEsResult().get().getEventList().stream()
-//                    .map(e -> new BeanModelEvent(e))
-//                    .collect(Collectors.toList());
         log.debug("Table data was loaded.");
 
     }
@@ -233,18 +188,6 @@ public StreamResponse onDownload() {
             @Override
             public void prepareResponse(Response response) {
                 try {
-//                    Future<EventRetrievalResult> unrolledResult4download = getUnrolledResult4download();
-//                    // Check if we have the download data cached. Otherwise, get it and cache it
-//                    if (unrolledResult4download == null) {
-//                        long time = System.currentTimeMillis();
-//                        log.info("[{}] Retrieving unrolled result for Excel sheet creation.", requestData.getDataSessionId());
-//                        unrolledResult4download = eventRetrievalService.getEvents(requestData, 0, Integer.MAX_VALUE, false);
-//                        // We use a weak reference for the complete data since it requires much memory because of all
-//                        // the context data. The GC should be able to evict it, if necessary.
-//                        dataService.getData(requestData.getDataSessionId()).setUnrolledResult4download(new WeakReference<>(unrolledResult4download));
-//                        time = System.currentTimeMillis() - time;
-//                        log.info("[{}] Unrolled result retrieval for Excel sheet creation took {} seconds", requestData.getDataSessionId(), time / 1000);
-//                    }
                     final Future<EventRetrievalResult> unrolledResult4download = dataService.getUnrolledResult4download(requestData, eventRetrievalService);
                     statisticsFile = dataService.getOverviewExcel(unrolledResult4download, requestData.getDataSessionId(), requestData.getInputMode(), requestData.getSentenceFilterString(), requestData.getParagraphFilterString(), requestData.getSectionNameFilterString());
 
@@ -293,7 +236,7 @@ public String getArgumentLink(int argPosition) {
 
     public void afterRender() {
         final Link downloadEventLink = resources.createEventLink("download");
-        javaScriptSupport.require("gepi/charts/tablewidget").invoke("download").with(downloadEventLink.toAbsoluteURI().replace(":80", ""));
+        javaScriptSupport.require("gepi/charts/tablewidget").invoke("download").with(downloadEventLink.toAbsoluteURI(productionMode));
         javaScriptSupport.require("gepi/charts/tablewidget").invoke("setupHighlightTooltips");
         javaScriptSupport.require("gepi/base").invoke("setuptooltips");
     }

gepi/gepi-webapp/src/main/java/de/julielab/gepi/webapp/data/GepiQueryParameters.java

@@ -117,12 +117,12 @@ private void readParameters(Request request) {
             if (listATextAreaValue == null)
                 listATextAreaValue = request.getParameter(ALIST);
             if (listATextAreaValue != null)
-                listATextAreaValue = Arrays.stream(listATextAreaValue.split("[\n,]")).map(this::decodeUrlEncoding).collect(Collectors.joining("\n"));
+                listATextAreaValue = Arrays.stream(decodeUrlEncoding(listATextAreaValue).split("[\n,]")).collect(Collectors.joining("\n"));
             listBTextAreaValue = request.getParameter(LISTB);
             if (listBTextAreaValue == null)
                 listBTextAreaValue = request.getParameter(BLIST);
             if (listBTextAreaValue != null)
-                listBTextAreaValue = Arrays.stream(listBTextAreaValue.split("[\n,]")).map(this::decodeUrlEncoding).collect(Collectors.joining("\n"));
+                listBTextAreaValue = Arrays.stream(decodeUrlEncoding(listBTextAreaValue).split("[\n,]")).collect(Collectors.joining("\n"));
             taxId = request.getParameter(TAXID);
             selectedEventTypes = new ArrayList<>(EnumSet.allOf(EventTypes.class));
             final String eventTypesString = request.getParameter(EVENTTYPES);
@@ -161,7 +161,7 @@ private void readParameters(Request request) {
             interactionRetrievalLimitForAggregations = INTERACTION_RETRIEVAL_LIMIT_FOR_AGGREGATIONS;
             format = request.getParameter(FORMAT) != null ? request.getParameter(FORMAT).toLowerCase() : null;
             if (format == null)
-                format = "web";
+                format = "tsv";
             try {
                 interactionRetrievalLimitForAggregations = Integer.parseInt(request.getParameter(INTERACTION_RETRIEVAL_LIMIT));
             } catch (NumberFormatException e) {
@@ -170,6 +170,14 @@ private void readParameters(Request request) {
         }
     }
 
+    /**
+     * This method is required for the help pages. For some reason, Tapestry converts the percent-URL-encodings
+     * in the HTML attributes into these dollar-sign encodings which are then not translated back.
+     *
+     * The API - when used with cURL, for example - works just fine.
+     * @param encodedString
+     * @return
+     */
     private String decodeUrlEncoding(String encodedString) {
         return encodedString.replaceAll("\\$002520", " ")
                 .replaceAll("\\$00253[Aa]", ":")