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Merge pull request #279 from JULIELab/api
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Api
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@khituras
khituras authored Sep 20, 2024
2 parents 7af800a + cb4fa94 commit 59d03f7
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Showing 12 changed files with 349 additions and 225 deletions.
10 changes: 7 additions & 3 deletions ...rc/main/java/de/julielab/gepi/core/retrieval/services/EventResponseProcessingService.java
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Expand Up @@ -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);
Expand Down Expand Up @@ -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())
Expand Down
3 changes: 3 additions & 0 deletions ...pi-core/src/main/java/de/julielab/gepi/core/retrieval/services/EventRetrievalService.java
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Expand Up @@ -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
*/
Expand All @@ -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,
Expand Down
54 changes: 34 additions & 20 deletions gepi/gepi-webapp/pom.xml
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Expand Up @@ -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>-->
Expand Down Expand Up @@ -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>
Expand Down Expand Up @@ -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>
Expand Down
5 changes: 5 additions & 0 deletions gepi/gepi-webapp/src/main/java/de/julielab/gepi/webapp/components/GepiInput.java
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Original file line number Diff line number Diff line change
Expand Up @@ -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.
*/
Expand Down
69 changes: 6 additions & 63 deletions gepi/gepi-webapp/src/main/java/de/julielab/gepi/webapp/components/TableResultWidget.java
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Original file line number Diff line number Diff line change
Expand Up @@ -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;
Expand All @@ -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;

Expand Down Expand Up @@ -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");
Expand All @@ -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
Expand All @@ -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.");

}
Expand Down Expand Up @@ -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());

Expand Down Expand Up @@ -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");
}
Expand Down
14 changes: 11 additions & 3 deletions gepi/gepi-webapp/src/main/java/de/julielab/gepi/webapp/data/GepiQueryParameters.java
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Original file line number Diff line number Diff line change
Expand Up @@ -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);
Expand Down Expand Up @@ -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) {
Expand All @@ -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]", ":")
Expand Down
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