Merge pull request #279 from JULIELab/api

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]", ":")