gCubeSystem
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species-discovery
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Working on Task #7001 

git-svn-id: http://svn.research-infrastructures.eu/public/d4science/gcube/trunk/portlets/user/speciesdiscovery@142466 82a268e6-3cf1-43bd-a215-b396298e98cf
This commit is contained in:
Francesco Mangiacrapa 2017-02-10 17:04:01 +00:00
parent 6f0417e86e
commit 4e5b889342
14 changed files with 224 additions and 171 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
src/main/java/org/gcube/portlets/user/speciesdiscovery/client/SearchBorderLayoutPanel.java
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@ -115,6 +115,7 @@ public class SearchBorderLayoutPanel extends ContentPanel {
SearchController.excecuteGetJobs(SearchResultType.TAXONOMY_ITEM, false);
SearchController.excecuteGetJobs(SearchResultType.OCCURRENCE_POINT, false);
SearchController.excecuteGetJobs(SearchResultType.GIS_LAYER_POINT, false);
pollSpeciesJobs(ConstantsSpeciesDiscovery.JOBPOLLINGMILLISECONDS);
@ -132,6 +133,7 @@ public class SearchBorderLayoutPanel extends ContentPanel {
SearchController.excecuteGetJobs(SearchResultType.TAXONOMY_ITEM, false);
SearchController.excecuteGetJobs(SearchResultType.OCCURRENCE_POINT, false);
SearchController.excecuteGetJobs(SearchResultType.GIS_LAYER_POINT, false);
}
};

36
src/main/java/org/gcube/portlets/user/speciesdiscovery/client/SearchController.java
View File

@ -286,9 +286,9 @@ public class SearchController {
}
@Override
public void onSuccess(JobGisLayerModel jobId) {
Info.display("Gis Layer Occurrence Job", "Generating Gis layer: "+jobId.getJobName()+" submitted");
public void onSuccess(JobGisLayerModel gisJob) {
GWT.log("Returned gis job: "+gisJob);
Info.display("Gis Layer Occurrence Job", "Generating Gis layer: "+gisJob.getJobName()+" submitted");
excecuteGetJobs(SearchResultType.GIS_LAYER_POINT, false);
searchBorderLayoutPanel.getSpeciesSouthPanel().setIconGisLayerByCounter(1);
@ -297,35 +297,6 @@ public class SearchController {
// showMap(layerName);
}
});
// SpeciesDiscovery.taxonomySearchService.createOccurrencesJob(listJobOccurrenceModel, createOccurrenceJobEvent.getFileFormat(), createOccurrenceJobEvent.getSaveEnum(), createOccurrenceJobEvent.isByDataSource(), createOccurrenceJobEvent.getExpectedOccurrences(), new AsyncCallback<List<JobOccurrencesModel>>() {
//
// @Override
// public void onFailure(Throwable caught) {
// Info.display("Error", "Sorry, An error occurred on create job. Please try again later");
// Log.error("Error on loading", "An error occurred on create job, retry." +caught.getMessage());
//
// }
//
// @Override
// public void onSuccess(List<JobOccurrencesModel> result) {
//
// if(result!=null){
// int jobs = result.size();
// if(jobs>0){
// String msg = jobs==1? "was":"were";
// Info.display("Species Occurrence Job", result.size() + " occurrence job "+msg+" submitted");
// excecuteGetJobs(SearchResultType.OCCURRENCE_POINT, false);
// searchBorderLayoutPanel.getSpeciesSouthPanel().setIconOccurrenceByCounter(result.size());
// }
// else{
// Info.display("Species Occurrence Job","An error occurred on submit job, retry");
// }
//
// }
// }
// });
}
});
@ -1719,6 +1690,7 @@ public class SearchController {
if(resetStructures)
GisLayerJobSpeciesPanel.getInstance(eventBus).getGridJob().mask("Loading", ConstantsSpeciesDiscovery.LOADINGSTYLE);
//TODO
SpeciesDiscovery.taxonomySearchService.getListGisLayerJob(new AsyncCallback<List<JobGisLayerModel>>() {

2
src/main/java/org/gcube/portlets/user/speciesdiscovery/client/job/gislayer/GisLayerGridJob.java
View File

@ -518,7 +518,7 @@ public class GisLayerGridJob extends ContentPanel{
public void handleEvent(BaseEvent be) {
// resetStore();
eventBus.fireEvent(new ReLoadListJobEvent(SearchResultType.OCCURRENCE_POINT));
eventBus.fireEvent(new ReLoadListJobEvent(SearchResultType.GIS_LAYER_POINT));
}
});

2
src/main/java/org/gcube/portlets/user/speciesdiscovery/client/job/gislayer/GisLayerJobSpeciesPanel.java
View File

@ -36,7 +36,7 @@ public class GisLayerJobSpeciesPanel extends ContentPanel {
private static String LASTOPERATION = "Last Operation: ";
private Html lastOperation = new Html(LASTOPERATION);
private LayoutContainer lc;
private static String WINDOWTITLE = "Species Occurrence Jobs";
private static String WINDOWTITLE = "Gis Layer Jobs";
private static final String FAILED = "failed";
private static final String COMPLETED = "completed";
private static final String LOADING = "loading";

4
src/main/java/org/gcube/portlets/user/speciesdiscovery/client/windowdetail/ViewDetailsWindow.java
View File

@ -334,7 +334,7 @@ public class ViewDetailsWindow extends Window {
Button btnShowInGisViewer = new Button(ConstantsSpeciesDiscovery.CREATE_GIS_LAYER);
btnShowInGisViewer.setIcon(AbstractImagePrototype.create(Resources.INSTANCE.getGisProducts()));
btnShowInGisViewer.setToolTip(new ToolTipConfig(ConstantsSpeciesDiscovery.CREATE_GIS_LAYER, "Create a Gis Layer from selected occurences points in a Gis Viewer Map"));
btnShowInGisViewer.setToolTip(new ToolTipConfig(ConstantsSpeciesDiscovery.CREATE_GIS_LAYER, "Create a Gis Layer from selected occurences points."));
btnShowInGisViewer.setScale(ButtonScale.SMALL);
btnShowInGisViewer.setIconAlign(IconAlign.TOP);
btnShowInGisViewer.setArrowAlign(ButtonArrowAlign.BOTTOM);
@ -342,7 +342,7 @@ public class ViewDetailsWindow extends Window {
@Override
public void componentSelected(ButtonEvent ce) {
SearchController.eventBus.fireEvent(new CreateGisLayerJobEvent(lastSearchEvent.getSearchTerm() +" Occurrences layer", "Gis Layer generated from SPD Portlet by gCube Framework", count));
SearchController.eventBus.fireEvent(new CreateGisLayerJobEvent("Gis Layer by: "+lastSearchEvent.getSearchTerm(), "Gis Layer generated from SPD Portlet by gCube Framework", count));
}
});

9
src/main/java/org/gcube/portlets/user/speciesdiscovery/server/TaxonomySearchServiceImpl.java
View File

@ -858,6 +858,7 @@ public class TaxonomySearchServiceImpl extends RemoteServiceServlet implements T
String author = getASLSession().getUsername();
String credits = "";
GisLayerJobPersistence gisLayerJob = DaoSession.getGisLayersJobDAO(getASLSession());
logger.trace("GisLayerJobPersistence found");
return GisLayerJobUtil.createGisLayerJobByOccurrenceKeys(occurrenceKeys, taxonomyService, layerTitle, layerDescr, author, credits, totalPoints, gisLayerJob);
} catch (Exception e) {
logger.error("An error occurred creating the map", e);
@ -1712,12 +1713,17 @@ public class TaxonomySearchServiceImpl extends RemoteServiceServlet implements T
try {
GisLayerJobPersistence gisLayerJobDao = DaoSession.getGisLayersJobDAO(getASLSession());
Iterator<GisLayerJob> iterator = gisLayerJobDao.getList().iterator();
SpeciesService taxonomyService = getSpeciesService();
while (iterator!=null && iterator.hasNext()) {
GisLayerJob job = iterator.next();
CompleteJobStatus statusResponse = taxonomyService.getOccurrenceJobById(job.getId());
if(job.getId()==null || job.getId().isEmpty()){
logger.warn("Gis job has an id null or empty, skipping");
}else{
CompleteJobStatus statusResponse = taxonomyService.getGisLayerByJobId(job.getId());
logger.info("get occurrence job "+job.getId()+ " from service");
try{
@ -1743,6 +1749,7 @@ public class TaxonomySearchServiceImpl extends RemoteServiceServlet implements T
throw new Exception("Error on getListGisLayerJob", e);
}
}
}
} catch (Exception e) {
logger.error("Error on get iterator "+e, e);

4
src/main/java/org/gcube/portlets/user/speciesdiscovery/server/job/GisLayerJobUtil.java
View File

@ -51,7 +51,9 @@ public class GisLayerJobUtil {
Date submitTime = DateUtil.getDateFormat(Calendar.getInstance());
GisLayerJob gisLJ = new GisLayerJob(jobId, layerTitle, 0, submitTime.getTime(), 0, 0, layerDescr, DownloadState.PENDING.toString(), totalPoints);
gisLayerJob.insert(gisLJ);
return new JobGisLayerModel(jobId, layerTitle, DownloadState.PENDING,null, submitTime, null, null, layerDescr, 0, totalPoints);
JobGisLayerModel jobModel = new JobGisLayerModel(jobId, layerTitle, DownloadState.PENDING,null, submitTime, null, null, layerDescr, 0, totalPoints);
logger.info("Returning job: "+jobModel);
return jobModel;
} catch (Exception e) {
logger.error("An error occurred creating the map", e);
throw new Exception(e.getMessage());

6
src/main/java/org/gcube/portlets/user/speciesdiscovery/server/service/SpeciesService.java
View File

@ -489,10 +489,8 @@ public class SpeciesService {
return creator.createLayer(keyStream, details);
}
catch (Exception e) {
logger.error(
"Error calling the Species Service: " + e.getMessage(), e);
throw new SearchServiceException(
"Error calling the Species Service: " + e.getMessage());
logger.error("Error calling the Species Service: " + e.getMessage(), e);
throw new SearchServiceException("Error calling the Species Service: " + e.getMessage());
}
}

15
src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/DefaultJob.java
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@ -5,19 +5,22 @@ package org.gcube.portlets.user.speciesdiscovery.shared;
import java.io.Serializable;
import javax.persistence.MappedSuperclass;
/**
*
* @author Francesco Mangiacrapa francesco.mangiacrapa@isti.cnr.it
* Feb 9, 2017
*/
@MappedSuperclass
public class DefaultJob implements Serializable{
/**
*
*/
private static final long serialVersionUID = -4448201743475516557L;
private static final long serialVersionUID = 5677419614560436596L;
public final static String ID_FIELD = "id";
public final static String NAME = "name";
public final static String DESCRIPTION = "description";
@ -44,8 +47,6 @@ public class DefaultJob implements Serializable{
}
/**
* @param id
* @param name
@ -56,11 +57,7 @@ public class DefaultJob implements Serializable{
* @param state
* @param elapsedTime
*/
public DefaultJob(
String id, String name, long startTime, long submitTime, long endTime,
String description, String state, long elapsedTime) {
super();
public DefaultJob(String id, String name, long startTime, long submitTime, long endTime, String description, String state, long elapsedTime) {
this.id = id;
this.name = name;
this.startTime = startTime;

31
src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/GisLayerJob.java
View File

@ -4,6 +4,9 @@
package org.gcube.portlets.user.speciesdiscovery.shared;
import javax.persistence.Entity;
import javax.persistence.GeneratedValue;
import javax.persistence.GenerationType;
import javax.persistence.Id;
/**
@ -21,6 +24,9 @@ public class GisLayerJob extends DefaultJob{
private static final long serialVersionUID = 2604265579184366453L;
private long totalPoints;
@Id
@GeneratedValue(strategy = GenerationType.IDENTITY)
protected int internalId;
/**
* Instantiates a new gis layer job.
@ -28,8 +34,6 @@ public class GisLayerJob extends DefaultJob{
public GisLayerJob() {
}
/**
* Instantiates a new gis layer job.
*
@ -41,16 +45,11 @@ public class GisLayerJob extends DefaultJob{
* @param description the description
* @param state the state
*/
public GisLayerJob(
String id, String name, long startTime, long submitTime, long endTime,
long elapsedTime, String description, String state, long totalPoints) {
public GisLayerJob(String id, String name, long startTime, long submitTime, long endTime,long elapsedTime, String description, String state, long totalPoints) {
super(id, name, startTime, submitTime, endTime, description, state, elapsedTime);
this.totalPoints = totalPoints;
}
/**
* @return the totalPoints
*/
@ -60,8 +59,6 @@ public class GisLayerJob extends DefaultJob{
}
/**
* @param totalPoints the totalPoints to set
*/
@ -72,6 +69,16 @@ public class GisLayerJob extends DefaultJob{
/**
* @return the internalId
*/
public int getInternalId() {
return internalId;
}
/* (non-Javadoc)
* @see java.lang.Object#toString()
*/
@ -81,6 +88,8 @@ public class GisLayerJob extends DefaultJob{
StringBuilder builder = new StringBuilder();
builder.append("GisLayerJob [totalPoints=");
builder.append(totalPoints);
builder.append(", internalId=");
builder.append(internalId);
builder.append(", id=");
builder.append(id);
builder.append(", name=");
@ -101,6 +110,4 @@ public class GisLayerJob extends DefaultJob{
return builder.toString();
}
}

5
src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/JobGisLayerModel.java
View File

@ -6,6 +6,8 @@ package org.gcube.portlets.user.speciesdiscovery.shared;
import java.io.Serializable;
import java.util.Date;
import com.google.gwt.user.client.rpc.IsSerializable;
@ -15,7 +17,7 @@ import java.util.Date;
* @author Francesco Mangiacrapa francesco.mangiacrapa@isti.cnr.it
* Feb 9, 2017
*/
public class JobGisLayerModel implements Serializable{
public class JobGisLayerModel implements Serializable, IsSerializable{
/**
*
@ -92,7 +94,6 @@ public class JobGisLayerModel implements Serializable{
String layerDescription, long completedPoints,
long totalPoints) {
super();
this.jobIdentifier = jobIdentifier;
this.jobName = jobName;
this.downloadState = downloadState;

5
src/main/resources/META-INF/orm.xml Normal file
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@ -0,0 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
<entity-mappings version="2.0" xmlns="http://java.sun.com/xml/ns/persistence/orm" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://java.sun.com/xml/ns/persistence/orm http://java.sun.com/xml/ns/persistence/orm_2_0.xsd">
<mapped-superclass class="DefaultJob">
</mapped-superclass>
</entity-mappings>

4
src/main/resources/META-INF/persistence.xml
View File

@ -2,8 +2,7 @@
<persistence xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://java.sun.com/xml/ns/persistence http://java.sun.com/xml/ns/persistence/persistence_2_0.xsd"
version="2.0" xmlns="http://java.sun.com/xml/ns/persistence">
<persistence-unit name="SPD_PERSISTENCE_FACTORY"
transaction-type="RESOURCE_LOCAL">
<persistence-unit name="SPD_PERSISTENCE_FACTORY" transaction-type="RESOURCE_LOCAL">
<class>org.gcube.portlets.user.speciesdiscovery.shared.CommonName</class>
<class>org.gcube.portlets.user.speciesdiscovery.shared.Taxon</class>
<class>org.gcube.portlets.user.speciesdiscovery.shared.ResultRow</class>
@ -12,6 +11,7 @@
<class>org.gcube.portlets.user.speciesdiscovery.shared.TaxonomyRow</class>
<class>org.gcube.portlets.user.speciesdiscovery.shared.OccurrencesJob</class>
<class>org.gcube.portlets.user.speciesdiscovery.shared.TaxonomyJob</class>
<class>org.gcube.portlets.user.speciesdiscovery.shared.GisLayerJob</class>
<properties>
<property name="javax.persistence.jdbc.driver" value="org.h2.Driver" />
<property name="eclipselink.ddl-generation" value="create-tables" />

62
src/test/java/org/gcube/portlets/user/speciesdiscovery/client/GisJob.java Normal file
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@ -0,0 +1,62 @@
/**
*
*/
package org.gcube.portlets.user.speciesdiscovery.client;
import java.util.ArrayList;
import java.util.List;
import org.gcube.common.scope.api.ScopeProvider;
import org.gcube.data.spd.client.plugins.AbstractPlugin;
import org.gcube.data.spd.client.proxies.ExecutorClient;
import org.gcube.data.spd.model.service.types.CompleteJobStatus;
import org.gcube.data.spd.model.service.types.JobStatus;
import org.gcube.data.spd.model.service.types.MetadataDetails;
import org.gcube.data.streams.Stream;
import org.gcube.data.streams.dsl.Streams;
/**
*
* @author Francesco Mangiacrapa francesco.mangiacrapa@isti.cnr.it
* Feb 10, 2017
*/
public class GisJob {
static List<String> keys = new ArrayList<String>();
public static void main(String[] args) {
try {
ScopeProvider.instance.set("/gcube/devsec");
keys.add("OBIS:161||666236");
ExecutorClient creator = AbstractPlugin.executor().build();
Stream<String> keyStream = Streams.convert(keys);
System.out.println("keys are: "+keys.toString());
MetadataDetails details= new MetadataDetails("title", "descr", "tile", "author", "credits");
System.out.println("submittings job...");
String jobId = creator.createLayer(keyStream, details);
System.out.println("The job id is: "+jobId);
CompleteJobStatus status = creator.getStatus(jobId);
JobStatus sta = status.getStatus();
while(sta!=JobStatus.COMPLETED && sta!=JobStatus.FAILED){
Thread.sleep(1000);
sta = creator.getStatus(jobId).getStatus();
System.out.println("checking status.."+sta);
}
System.out.println("job terminated");
}catch (Exception e) {
e.printStackTrace();
}
}
}