gCubeSystem
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species-discovery
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Porting to spd-client-library 4.0 

Fixced bug #6156
Updated pom version at 3.9.0

git-svn-id: http://svn.research-infrastructures.eu/public/d4science/gcube/trunk/portlets/user/speciesdiscovery@141521 82a268e6-3cf1-43bd-a215-b396298e98cf
This commit is contained in:
Francesco Mangiacrapa 2017-01-11 17:39:11 +00:00
parent 630ddcb9b2
commit 76f12eebdd
33 changed files with 2145 additions and 1463 deletions
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4
.classpath
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@ -1,7 +1,7 @@
<?xml version="1.0" encoding="UTF-8"?>
<classpath>
<classpathentry kind="lib" path="/home/francesco-mangiacrapa/libraries/asm-5.0.3/lib/asm-5.0.3.jar"/>
<classpathentry kind="src" output="target/species-discovery-3.8.0-SNAPSHOT/WEB-INF/classes" path="src/main/java">
<classpathentry kind="src" output="target/species-discovery-3.8.2-SNAPSHOT/WEB-INF/classes" path="src/main/java">
<attributes>
<attribute name="optional" value="true"/>
<attribute name="maven.pomderived" value="true"/>
@ -31,5 +31,5 @@
<attribute name="org.eclipse.jst.component.dependency" value="/WEB-INF/lib"/>
</attributes>
</classpathentry>
<classpathentry kind="output" path="target/species-discovery-3.8.0-SNAPSHOT/WEB-INF/classes"/>
<classpathentry kind="output" path="target/species-discovery-3.8.2-SNAPSHOT/WEB-INF/classes"/>
</classpath>

5
.settings/org.eclipse.wst.common.project.facet.core.prefs.xml
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@ -4,4 +4,9 @@
<attribute name="provider-id" value="jpa-no-op-library-provider"/>
</node>
</facet>
<facet id="jst.jaxrs">
<node name="libprov">
<attribute name="provider-id" value="jaxrs-no-op-library-provider"/>
</node>
</facet>
</root>

1
.settings/org.eclipse.wst.common.project.facet.core.xml
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@ -6,4 +6,5 @@
<installed facet="jpt.jpa" version="2.0"/>
<installed facet="liferay.portlet" version="6.0"/>
<installed facet="jst.web" version="3.0"/>
<installed facet="jst.jaxrs" version="2.0"/>
</faceted-project>

7
distro/changelog.xml
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@ -1,5 +1,10 @@
<ReleaseNotes>
<Changeset component="org.gcube.portlets-user.species-discovery.3-8-1" date="15-09-2016">
<Changeset component="org.gcube.portlets-user.species-discovery.3-9-0"
date="11-01-2016">
<Change>[Feature #6313] SPD portlet upgrade: porting to spd-client-library 4.0.0 </Change>
</Changeset>
<Changeset component="org.gcube.portlets-user.species-discovery.3-8-1"
date="15-09-2016">
<Change>Removed Gis -viewer dependency</Change>
</Changeset>
<Changeset component="org.gcube.portlets-user.species-discovery.3-8-0"

15
pom.xml
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@ -19,7 +19,7 @@
<groupId>org.gcube.portlets.user</groupId>
<artifactId>species-discovery</artifactId>
<packaging>war</packaging>
<version>3.8.1-SNAPSHOT</version>
<version>3.9.0-SNAPSHOT</version>
<name>gCube Species Discovery</name>
<description>
gCube Species Discovery Portlet lets the users discovery species information from the Species Service.
@ -31,7 +31,7 @@
</scm>
<properties>
<!-- Convenience property to set the GWT version -->
<gwtVersion>2.6.1</gwtVersion>
<gwtVersion>2.7.0</gwtVersion>
<distroDirectory>distro</distroDirectory>
<!-- GWT needs at least java 1.6 -->
<maven.compiler.source>1.7</maven.compiler.source>
@ -82,7 +82,7 @@
<dependency>
<groupId>org.gcube.data.spd</groupId>
<artifactId>spd-client-library</artifactId>
<version>[3.0.0-SNAPSHOT, 4.0.0-SNAPSHOT)</version>
<version>[4.0.0-SNAPSHOT, 5.0.0-SNAPSHOT)</version>
<scope>compile</scope>
</dependency>
@ -93,6 +93,13 @@
<scope>compile</scope>
</dependency>
<!-- USED TO SHOW A LAYER VIA GISVIEWER -->
<!-- <dependency> -->
<!-- <groupId>org.gcube.portlets.user</groupId> -->
<!-- <artifactId>gcube-gis-viewer</artifactId> -->
<!-- <version>[2.0.0-SNAPSHOT, 3.0.0-SNAPSHOT)</version> -->
<!-- </dependency> -->
<dependency>
<groupId>org.gcube.common</groupId>
<artifactId>csv4j</artifactId>
@ -106,8 +113,6 @@
<scope>provided</scope>
</dependency>
<!-- Eclipselink dependencies -->
<dependency>
<groupId>org.eclipse.persistence</groupId>

2
src/main/java/org/gcube/portlets/user/speciesdiscovery/client/SpeciesDiscovery.java
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@ -1,7 +1,7 @@
package org.gcube.portlets.user.speciesdiscovery.client;
import org.gcube.portlets.user.speciesdiscovery.client.rpc.GISInfoServiceAsync;
import org.gcube.portlets.user.speciesdiscovery.client.rpc.GISInfoService;
import org.gcube.portlets.user.speciesdiscovery.client.rpc.GISInfoServiceAsync;
import org.gcube.portlets.user.speciesdiscovery.client.rpc.TaxonomySearchService;
import org.gcube.portlets.user.speciesdiscovery.client.rpc.TaxonomySearchServiceAsync;

30
src/main/java/org/gcube/portlets/user/speciesdiscovery/server/GisInfoServiceImpl.java
View File

@ -1,5 +1,10 @@
package org.gcube.portlets.user.speciesdiscovery.server;
import it.geosolutions.geonetwork.util.GNSearchRequest;
import it.geosolutions.geonetwork.util.GNSearchRequest.Config;
import it.geosolutions.geonetwork.util.GNSearchRequest.Param;
import it.geosolutions.geonetwork.util.GNSearchResponse;
import java.util.HashMap;
import java.util.Map;
@ -16,20 +21,15 @@ import org.gcube.spatial.data.geonetwork.LoginLevel;
import com.google.gwt.user.server.rpc.RemoteServiceServlet;
import it.geosolutions.geonetwork.util.GNSearchRequest;
import it.geosolutions.geonetwork.util.GNSearchResponse;
import it.geosolutions.geonetwork.util.GNSearchRequest.Config;
import it.geosolutions.geonetwork.util.GNSearchRequest.Param;
public class GisInfoServiceImpl extends RemoteServiceServlet implements GISInfoService{
/**
*
*
*/
private static final long serialVersionUID = -1137730151475571288L;
protected static Logger logger = Logger.getLogger(GisInfoServiceImpl.class);
@Override
public String getGisLinkByLayerName(String layername) throws Exception {
try{
@ -46,19 +46,17 @@ public class GisInfoServiceImpl extends RemoteServiceServlet implements GISInfoS
}
}
private static String getPublicLink(String uuid) throws UriResolverMapException, IllegalArgumentException{
UriResolverManager resolver = new UriResolverManager("GIS");
Map<String, String> params = new HashMap<String, String>();
params.put("gis-UUID", uuid);
params.put("scope", ScopeProvider.instance.get());
return resolver.getLink(params, true);
}
private static String getUUIDbyGSId(String gsID) throws Exception{
GeoNetworkReader reader=GeoNetwork.get();
reader.login(LoginLevel.ADMIN);
@ -67,8 +65,8 @@ public class GisInfoServiceImpl extends RemoteServiceServlet implements GISInfoS
GNSearchRequest req=new GNSearchRequest();
req.addParam(Param.any, gsID);
req.addConfig(Config.similarity, "1");
GNSearchResponse resp=reader.query(req);
GNSearchResponse resp=reader.query(req);
return resp.getMetadata(0).getUUID();
}
}

177
src/main/java/org/gcube/portlets/user/speciesdiscovery/server/TaxonomyRowTable.java
View File

@ -27,7 +27,6 @@ import org.gcube.portlets.user.speciesdiscovery.server.persistence.dao.TaxonomyR
import org.gcube.portlets.user.speciesdiscovery.server.service.SpeciesService;
import org.gcube.portlets.user.speciesdiscovery.server.service.TaxonomyItemConverter;
import org.gcube.portlets.user.speciesdiscovery.server.stream.CloseableIterator;
import org.gcube.portlets.user.speciesdiscovery.server.stream.StreamExtend;
import org.gcube.portlets.user.speciesdiscovery.shared.CommonName;
import org.gcube.portlets.user.speciesdiscovery.shared.ItemParameter;
import org.gcube.portlets.user.speciesdiscovery.shared.SearchServiceException;
@ -35,7 +34,7 @@ import org.gcube.portlets.user.speciesdiscovery.shared.TaxonomyRow;
/**
*
*
* @author Francesco Mangiacrapa francesco.mangiacrapa@isti.cnr.it
* @Sep 6, 2013
*
@ -43,37 +42,37 @@ import org.gcube.portlets.user.speciesdiscovery.shared.TaxonomyRow;
public class TaxonomyRowTable extends HttpServlet {
/**
*
*
*/
protected static final String UTF_8 = "UTF-8";
/**
*
*
*/
private static final long serialVersionUID = 9157876104914505028L;
/**
*
*
*/
public static final String TEXT_HTML = "text/html; charset=UTF-8";
public static final String DOCTYPE = "<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\">";
public static final String HTML = "<HTML>";
public static final String HTMLCLOSE = "</HTML>";
public static final String HEAD = "<HEAD>";
public static final String HEADCLOSE = "</HEAD>";
public static final String TITLE = "<TITLE>";
public static final String TITLECLOSE = "</TITLE>";
public static final String TITLECLOSE = "</TITLE>";
public static final String BODY = "<BODY>";
public static final String BODYCLOSE = "</BODY>";
public static String headWithTitle(String title) {
// return (DOCTYPE + "\n" + HTML+"\n<link type=\"text/css\" rel=\"stylesheet\" href=\"SpeciesDiscovery.css\">" + HEAD+TITLE + title + TITLECLOSE+HEADCLOSE+"\n");
return (DOCTYPE + "\n" + HTML+ "\n"+HEAD + "\n"+TITLE + title + TITLECLOSE+"\n"+HEADCLOSE+"\n");
return DOCTYPE + "\n" + HTML+ "\n"+HEAD + "\n"+TITLE + title + TITLECLOSE+"\n"+HEADCLOSE+"\n";
}
protected Logger logger = Logger.getLogger(TaxonomyRowTable.class);
@ -89,96 +88,92 @@ public class TaxonomyRowTable extends HttpServlet {
protected void doGet(HttpServletRequest req, HttpServletResponse resp) throws ServletException, IOException {
retrieveTaxonomyRowAsHtmlTable(req, resp);
}
@Override
protected void doPost(HttpServletRequest req, HttpServletResponse resp) throws ServletException, IOException {
retrieveTaxonomyRowAsHtmlTable(req, resp);
}
/**
* @param req
* @param resp
* @throws IOException
* @throws IOException
*/
private void retrieveTaxonomyRowAsHtmlTable(HttpServletRequest req, HttpServletResponse resp) {
String taxonomyServiceRowID = "";
// resp.setCharacterEncoding(UTF_8);
resp.setContentType(TEXT_HTML);
resp.setContentType(TEXT_HTML);
TaxonomyRow row = null;
PrintWriter out = null;
try {
out = new PrintWriter(new OutputStreamWriter(resp.getOutputStream(), UTF_8), true);
out.println(headWithTitle(""));
out.println(BODY);
// get parameters
taxonomyServiceRowID = req.getParameter("oid");
ASLSession aslSession = getASLSession(req);
//IS VALID RR ID?
if(taxonomyServiceRowID==null || taxonomyServiceRowID.isEmpty()){
out.println(error("Parameter oid not found"));
}else{
}else{
logger.trace("doGet found oid "+taxonomyServiceRowID);
try {
TaxonomyRowPersistence persistence = SessionUtil.getCurrentEJBTaxonomyItem(aslSession);
if(persistence==null){
logger.trace("TaxonomyRowPersistence not found in session, creating it");
persistence = new TaxonomyRowPersistence(DaoSession.getEntityManagerFactory(aslSession));
}
CriteriaBuilder queryBuilder = persistence.getCriteriaBuilder();
CriteriaQuery<Object> cq = queryBuilder.createQuery();
Predicate pr1 = queryBuilder.equal(persistence.rootFrom(cq).get(TaxonomyRow.SERVICE_ID_FIELD), taxonomyServiceRowID);
cq.where(pr1);
Iterator<TaxonomyRow> iterator = persistence.executeCriteriaQuery(cq).iterator();
while(iterator.hasNext()){
row = iterator.next();
break;
}
if(row==null){
logger.trace("Taxonomy Row with id "+taxonomyServiceRowID+" not found in database");
row = findingTaxonomyInCaches(taxonomyServiceRowID, getASLSession(req));
if(row!=null){
logger.trace("Taxonomy Row with id "+taxonomyServiceRowID+" found into hash map caches");
//ROW was found into database or by service
logger.trace("converting taxonomy row to html table");
String table = getHTMLTableForTaxonomy(row);
logger.trace("table for ResultRowPersistence is empty? "+table.isEmpty());
out.println(table);
out.close();
return;
}else
logger.trace("Taxonomy Row with id "+taxonomyServiceRowID+" doesn't found into hash map caches");
logger.trace("Tentative recovering taxonomy with id "+taxonomyServiceRowID+" from service");
SpeciesService service = getSpeciesService(req);
StreamExtend<String> streamIds = new StreamExtend<String>(Arrays.asList(taxonomyServiceRowID).iterator());
CloseableIterator<TaxonomyItem> streamIterator = service.retrieveTaxonomyById(streamIds);
//StreamExtend<String> streamIds = new StreamExtend<String>(Arrays.asList(taxonomyServiceRowID).iterator());
CloseableIterator<TaxonomyItem> streamIterator = service.retrieveTaxonomyById(Arrays.asList(taxonomyServiceRowID));
TaxonomyItemConverter taxonomyItemConverter = new TaxonomyItemConverter(aslSession);
// int i = 1;
while (streamIterator.hasNext()) {
TaxonomyItem tax = streamIterator.next();
@ -189,7 +184,7 @@ public class TaxonomyRowTable extends HttpServlet {
}
streamIterator.close();
if(row==null){
out.println(error("Sorry, taxonomy with "+taxonomyServiceRowID+" doesn't found in service"));
out.close();
@ -203,9 +198,9 @@ public class TaxonomyRowTable extends HttpServlet {
logger.trace("table for ResultRowPersistence is empty? "+table.isEmpty());
out.println(table);
} catch (Exception e) {
logger.error("Error in TaxonomyRowTable servlet ",e);
throw new Exception("Error in ResultRowTable servlet ", e);
}
@ -213,10 +208,10 @@ public class TaxonomyRowTable extends HttpServlet {
out.println(BODYCLOSE);
out.println(HTMLCLOSE);
out.close(); //CLOSE STREAM
}catch (Exception e) {
String error = "Sorry an error occurred when creating the table for taxonomy row with id: "+taxonomyServiceRowID;
if(out==null){
try{
out = resp.getWriter();
@ -229,56 +224,52 @@ public class TaxonomyRowTable extends HttpServlet {
out.println(HTMLCLOSE);
out.close(); //CLOSE STREAM
}
}
protected TaxonomyRow findingTaxonomyInCaches(String taxonomyServiceRowID, ASLSession session){
HashMap<String, TaxonomyRow> hashChildrenTaxa = SessionUtil.getHashMapChildrenTaxonomyCache(session);
if(hashChildrenTaxa!=null){
logger.trace("Finding Taxonomy Row with id "+taxonomyServiceRowID+" into hash map children");
TaxonomyRow row = hashChildrenTaxa.get(taxonomyServiceRowID);
if(row!=null){
logger.trace("Taxonomy Row with id "+taxonomyServiceRowID+" found into hash map children");
return row;
}
}
hashChildrenTaxa = SessionUtil.getHashMapSynonymsTaxonomyCache(session);
if(hashChildrenTaxa!=null){
logger.trace("Finding Taxonomy Row with id "+taxonomyServiceRowID+" into hash map synonyms");
TaxonomyRow row = hashChildrenTaxa.get(taxonomyServiceRowID);
if(row!=null){
logger.trace("Taxonomy Row with id "+taxonomyServiceRowID+" found into hash map synonyms");
return row;
}
}
hashChildrenTaxa = SessionUtil.getHashMapTaxonomyByIdsCache(session);
if(hashChildrenTaxa!=null){
logger.trace("Finding Taxonomy Row with id "+taxonomyServiceRowID+" into hash map ByIds");
TaxonomyRow row = hashChildrenTaxa.get(taxonomyServiceRowID);
if(row!=null){
logger.trace("Taxonomy Row with id "+taxonomyServiceRowID+" found into hash map ByIds");
return row;
}
}
return null;
}
protected SpeciesService getSpeciesService(HttpServletRequest req) throws SearchServiceException
{
@ -292,83 +283,83 @@ public class TaxonomyRowTable extends HttpServlet {
throw new SearchServiceException("contacting the species service.");
}
}
public String error(String message){
String errorPage = "";
errorPage +=("<p>Error: "+message+"</p>");
errorPage +="<p>Error: "+message+"</p>";
return errorPage;
}
public String getHTMLTableForTaxonomy(TaxonomyRow row){
//Init values
String dataProviderName = "";
String dataSetCitation= "";
String matchingAccordionTo= "";
String rank= "";
// String matchingCredits= "";
String statusName = "";
String dateModified = "";
String statusRemark = "";
String scientificNameAuthorship = "";
String lsid = "";
String credits = "";
String propertiesHtml = "";
if(row.getDataProviderName()!=null) dataProviderName = row.getDataProviderName();
if(row.getStatusName()!=null) statusName = row.getStatusName();
if(row.getDateModified()!=null) dateModified = row.getDateModified();
if(row.getDataSetCitation()!=null) dataSetCitation = row.getDataSetCitation();
if(row.getRank()!=null) rank = row.getRank();
if(row.getAccordingTo()!=null) matchingAccordionTo = row.getAccordingTo();
if(row.getStatusRemarks()!=null) statusRemark = row.getStatusRemarks();
if(row.getScientificNameAuthorship()!=null) scientificNameAuthorship = row.getScientificNameAuthorship();
if(row.getLsid()!=null) lsid = row.getLsid();
if(row.getCredits()!=null) credits = row.getCredits();
//BUILD TABLES PROPERTIES
if(row.getProperties()!=null){
List<ItemParameter> hashProperties = row.getProperties();
Collections.sort(hashProperties, ItemParameter.COMPARATOR);
propertiesHtml+="<table class=\"parameters\">";
for (ItemParameter itemParameter : hashProperties) {
propertiesHtml+=
"<tr>" +
" <td class=\"title\">"+itemParameter.getKey()+"</td>" +
" <td>"+itemParameter.getValue()+"</td>" +
"</tr>";
}
propertiesHtml+="</table>";
}
//Create list common name
String commonNames = "";
if(row.getCommonNames()!=null){
for (CommonName comName : row.getCommonNames()) {
commonNames+= "<b>"+comName.getName()+"</b>" +" ("+comName.getLanguage()+") - ";
}
}
String table = "<table class=\"imagetable\">";
// if(isNewTab)
table+=
"<tr>" +
@ -385,8 +376,8 @@ public class TaxonomyRowTable extends HttpServlet {
// " <td class=\"title\">"+TaxonomyGridField.STATUS_REMARKS.getName()+"</td>" +
// " <td>"+statusRemark+"</td>" +
// "</tr>" +
table +="<tr>" +
" <td class=\"title\">"+TaxonomyGridField.DATASOURCE.getName()+"</td>" +
" <td>"+dataProviderName+"</td>" +
@ -415,19 +406,19 @@ public class TaxonomyRowTable extends HttpServlet {
" <td class=\"title\">"+TaxonomyGridField.CREDITS.getName()+"</td>" +
" <td>"+credits+"</td>" +
"</tr>" +
"<tr>" +
" <td class=\"title\">"+TaxonomyGridField.PROPERTIES.getName()+"</td>" +
" <td>"+propertiesHtml+"</td>" +
"</tr>" +
"</table>";
//DEBUG
// System.out.println("Table: "+table);
return table;
}
}

540
src/main/java/org/gcube/portlets/user/speciesdiscovery/server/TaxonomySearchServiceImpl.java
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File diff suppressed because it is too large Load Diff

333
src/main/java/org/gcube/portlets/user/speciesdiscovery/server/job/OccurrenceJobUtil.java
View File

@ -15,7 +15,8 @@ import javax.persistence.criteria.Predicate;
import org.apache.log4j.Logger;
import org.gcube.application.framework.core.session.ASLSession;
import org.gcube.data.spd.stubs.types.Status;
import org.gcube.data.spd.model.service.types.CompleteJobStatus;
import org.gcube.data.spd.model.service.types.JobStatus;
import org.gcube.portlets.user.speciesdiscovery.server.persistence.DaoSession;
import org.gcube.portlets.user.speciesdiscovery.server.persistence.dao.OccurrenceJobPersistence;
import org.gcube.portlets.user.speciesdiscovery.server.persistence.dao.ResultRowPersistence;
@ -33,6 +34,13 @@ import org.gcube.portlets.user.speciesdiscovery.shared.OccurrencesSaveEnum;
import org.gcube.portlets.user.speciesdiscovery.shared.ResultRow;
import org.gcube.portlets.user.speciesdiscovery.shared.SaveFileFormat;
/**
* The Class OccurrenceJobUtil.
*
* @author Francesco Mangiacrapa francesco.mangiacrapa@isti.cnr.it
* Jan 10, 2017
*/
public class OccurrenceJobUtil {
//STATE RETURNED BY STATUS RESPONSE
@ -40,24 +48,32 @@ public class OccurrenceJobUtil {
public static final String FAILED = "FAILED";
public static final String RUNNING = "RUNNING";
public static final String PENDING = "PENDING";
private static final String ALIASKEY = "key";
protected static Logger logger = Logger.getLogger(OccurrenceJobUtil.class);
public static JobOccurrencesModel convertJob(OccurrencesJob job, Status statusResponse, OccurrenceJobPersistence occurrencesJobDao) {
//TODO SET END TIME
/**
* Convert job.
*
* @param job the job
* @param statusResponse the status response
* @param occurrencesJobDao the occurrences job dao
* @return the job occurrences model
*/
public static JobOccurrencesModel convertJob(OccurrencesJob job, CompleteJobStatus statusResponse, OccurrenceJobPersistence occurrencesJobDao) {
//TODO SET END TIME
JobOccurrencesModel jobOccurrenceModel;
DownloadState downloadState = null;
long endTime = 0;
String status = statusResponse.getStatus();
JobStatus status = statusResponse.getStatus();
downloadState = getDownloadState(status);
logger.trace("jobId: "+job.getId() +" download state: " + downloadState);
//FOR DEBUG
// System.out.println("jobId: "+job.getId() +" download state: " + downloadState);
if(downloadState==null) //Case with exception
return null;
@ -65,13 +81,13 @@ public class OccurrenceJobUtil {
long submitTime = job.getSubmitTime();
Date submit = DateUtil.millisecondsToDate(submitTime);
// jobSpeciesModel.setStartTime(DateUtil.dateToDateFormatString(start));
int completedEntry = 0;
if(statusResponse.getCompletedEntries()>0)
completedEntry = statusResponse.getCompletedEntries();
boolean changeStatus = false;
//if status is completed and job was saved, update status as saved
if(downloadState.equals(DownloadState.COMPLETED)){
if(job.getState().compareTo(DownloadState.SAVED.toString())==0){
@ -79,18 +95,18 @@ public class OccurrenceJobUtil {
changeStatus = true;
}
}
jobOccurrenceModel = new JobOccurrencesModel(job.getId(), job.getName(), job.getDescription(), downloadState, job.getScientificName(), job.getDataSources(), submit, null,completedEntry, job.getExpectedOccurrence());
try{
boolean changeEndTime = false;
//UPDATE END TIME
if(downloadState.equals(DownloadState.FAILED) || downloadState.equals(DownloadState.COMPLETED)){
// if(job.getEndTime()==0){ //UPDATE end time first time only
//
//
// logger.trace("UPDATE end time first time only - " + downloadState);
// endTime = Calendar.getInstance().getTimeInMillis();
// job.setEndTime(endTime);
@ -99,22 +115,22 @@ public class OccurrenceJobUtil {
// System.out.println("job "+job);
// System.out.println("statusResponse.getEndDate() "+statusResponse.getEndDate());
// System.out.println("job.getEndTime() "+job.getEndTime());
if(statusResponse.getEndDate()!=null && job.getEndTime()==0){ //UPDATE end time first time only
logger.trace("UPDATE end time first time only - " + downloadState);
// endTime = Calendar.getInstance().getTimeInMillis();
endTime = statusResponse.getEndDate().getTimeInMillis();
job.setEndTime(endTime);
changeEndTime = true;
// speciesJobDao.update(job);
}
}
boolean changeStartTime = false;
//SET START TIME
long startTime = job.getStartTime();
if(statusResponse.getStartDate()!=null && startTime==0){ //UPDATE start time first time only
@ -124,7 +140,7 @@ public class OccurrenceJobUtil {
changeStartTime = true;
}
//UPDATE DAO
if(changeStatus || changeEndTime || changeStartTime){
job.setState(downloadState.toString());
@ -134,11 +150,11 @@ public class OccurrenceJobUtil {
}catch (Exception e) {
logger.error("An error occurred on update the occurrencesJobDao ", e);
}
endTime = job.getEndTime();
long elapsedTime = 0;
//SET END TIME, BECAUSE IT IS CHANGED
if(endTime!=0){
Date end = DateUtil.millisecondsToDate(endTime);
@ -147,39 +163,54 @@ public class OccurrenceJobUtil {
}
else
elapsedTime = Calendar.getInstance().getTimeInMillis();
//SET ELAPSED TIME
jobOccurrenceModel.setElapsedTime(DateUtil.getDifference(submitTime, elapsedTime));
//OTHERS SET
jobOccurrenceModel.setFileFormat(converFileFormat(job.getFileFormat()));
jobOccurrenceModel.setCsvType(convertCsvType(job.getCsvType()));
jobOccurrenceModel.setByDataSource(job.isByDataSource());
return jobOccurrenceModel;
}
public static DownloadState getDownloadState(String status){
if(status!=null){
if(status.compareToIgnoreCase(PENDING)==0){
return DownloadState.PENDING;
}else if(status.compareToIgnoreCase(RUNNING)==0){
return DownloadState.ONGOING;
}else if(status.compareToIgnoreCase(FAILED)==0){
return DownloadState.FAILED;
}else if(status.compareToIgnoreCase(COMPLETED)==0){
/**
* Gets the download state.
*
* @param status the status
* @return the download state
*/
public static DownloadState getDownloadState(JobStatus status){
if(status!=null){
switch (status) {
case COMPLETED:
return DownloadState.COMPLETED;
case FAILED:
return DownloadState.FAILED;
case PENDING:
return DownloadState.PENDING;
case RUNNING:
return DownloadState.ONGOING;
default:
return null;
}
}
return null;
}
/**
* Convert csv type.
*
* @param csvType the csv type
* @return the occurrences save enum
*/
public static OccurrencesSaveEnum convertCsvType(String csvType) {
if(csvType!=null){
if(csvType.compareToIgnoreCase(OccurrencesSaveEnum.STANDARD.toString())==0){
return OccurrencesSaveEnum.STANDARD;
@ -191,8 +222,14 @@ public class OccurrenceJobUtil {
}
/**
* Conver file format.
*
* @param fileFormat the file format
* @return the save file format
*/
public static SaveFileFormat converFileFormat(String fileFormat) {
if(fileFormat!=null){
if(fileFormat.compareToIgnoreCase(SaveFileFormat.CSV.toString())==0){
return SaveFileFormat.CSV;
@ -205,6 +242,13 @@ public class OccurrenceJobUtil {
}
/**
* Delete occurrence job by id.
*
* @param jobIdentifier the job identifier
* @param occurrencesJobDao the occurrences job dao
* @return the int
*/
public static int deleteOccurrenceJobById(String jobIdentifier, OccurrenceJobPersistence occurrencesJobDao){
logger.trace("Delete occurrence job id: " + jobIdentifier);
@ -214,55 +258,70 @@ public class OccurrenceJobUtil {
}catch (Exception e) {
logger.error("An error occured deleteOccurrenceJobById jobId: " + jobIdentifier + " exception: "+e, e);
}
logger.trace("job not exists : " +jobIdentifier);
return 0;
}
/**
* Change status occurrence job by id.
*
* @param jobIdentifier the job identifier
* @param state the state
* @param occurrencesJobDao the occurrences job dao
* @return the int
*/
public static int changeStatusOccurrenceJobById(String jobIdentifier, DownloadState state, OccurrenceJobPersistence occurrencesJobDao){
logger.trace("Change status occurrence job id: " + jobIdentifier);
// System.out.println("Delete job id: " + jobIdentifier);
int result = 0;
try{
CriteriaBuilder queryBuilder = occurrencesJobDao.getCriteriaBuilder();
CriteriaQuery<Object> cq = queryBuilder.createQuery();
Predicate pr1 = queryBuilder.equal(occurrencesJobDao.rootFrom(cq).get(OccurrencesJob.ID_FIELD), jobIdentifier);
cq.where(pr1);
Iterator<OccurrencesJob> iterator = occurrencesJobDao.executeCriteriaQuery(cq).iterator();
OccurrencesJob job;
if(iterator.hasNext())
job = iterator.next();
else
return 0;
job.setState(state.toString());
occurrencesJobDao.update(job);
}catch (Exception e) {
logger.error("An error occured in change status jobId: " + jobIdentifier + " exception: "+e, e );
}
return result;
}
/**
* Gets the list of selected key.
*
* @param searchSession the search session
* @return the list of selected key
* @throws Exception the exception
*/
public static List<String> getListOfSelectedKey(FetchingSession<ResultRow> searchSession) throws Exception{
Collection<ResultRow> selectedRows = ((SelectableFetchingBuffer<ResultRow>) searchSession.getBuffer()).getSelected();
logger.trace("found "+selectedRows.size()+" selected rows");
int count = 0;
List<String> keys = new ArrayList<String>(selectedRows.size());
for (ResultRow row:selectedRows) {
@ -272,45 +331,52 @@ public class OccurrenceJobUtil {
count += row.getOccurencesCount();
}
}
logger.trace("found "+count+" occurrence points");
return keys;
}
/**
* Gets the list of selected key by data source.
*
* @param dataSource the data source
* @param session the session
* @return the list of selected key by data source
*/
public static OccurrenceKeys getListOfSelectedKeyByDataSource(String dataSource, ASLSession session) {
logger.trace("getListOfSelectedKeyByDataSource...");
OccurrenceKeys occurrenceKeys = new OccurrenceKeys();
List<String> keys = new ArrayList<String>();
Iterator<ResultRow> resulRowIt = null;
int count = 0;
try{
// System.out.println("dasource name: "+dataSource);
logger.trace("datasource name: "+dataSource);
ResultRowPersistence resultRowDao = DaoSession.getResultRowDAO(session);
/*CriteriaBuilder cb = resultRowDao.getCriteriaBuilder();
CriteriaQuery<Object> cq = cb.createQuery();
Predicate pr1 = cb.equal(resultRowDao.rootFrom(cq).get(ResultRow.DATASOURCE_NAME), dataSource);
Predicate pr2 = cb.equal(resultRowDao.rootFrom(cq).get(ResultRow.SELECTED), true);
cq.where(cb.and(pr1,pr2));
Iterator<ResultRow> resulRowIt = resultRowDao.executeCriteriaQuery(cq).iterator();
*/
EntityManager em = resultRowDao.createNewManager();
try {
@ -318,7 +384,7 @@ public class OccurrenceJobUtil {
resulRowIt = query.getResultList().iterator();
} catch (Exception e) {
logger.error("Error in update: "+e.getMessage(), e);
return null;
@ -328,59 +394,72 @@ public class OccurrenceJobUtil {
}
while(resulRowIt.hasNext()){
ResultRow row = resulRowIt.next();
if(row.getOccurencesKey()!=null && row.getOccurencesKey().length()>0){
keys.add(row.getOccurencesKey());
count += row.getOccurencesCount();
}
}
occurrenceKeys.setListKey(keys);
occurrenceKeys.setTotalOccurrence(count);
}catch (Exception e) {
logger.error("error in getListOfSelectedKeyByDataSource "+ e);
}
logger.trace("found "+count+" occurrence points");
return occurrenceKeys;
}
/**
* Creates the occurrence job on service by keys.
*
* @param jobModel the job model
* @param taxonomyService the taxonomy service
* @param occurrencesJobDao the occurrences job dao
* @param keys the keys
* @param dataSources the data sources
* @param saveFileFormat the save file format
* @param csvType the csv type
* @param expectedOccurrence the expected occurrence
* @return the job occurrences model
*/
public static JobOccurrencesModel createOccurrenceJobOnServiceByKeys(JobOccurrencesModel jobModel,SpeciesService taxonomyService, OccurrenceJobPersistence occurrencesJobDao, List<String> keys, List<DataSource> dataSources, SaveFileFormat saveFileFormat, OccurrencesSaveEnum csvType, int expectedOccurrence) {
String serviceJobId = null;
StreamExtend<String> streamKeys = new StreamExtend<String>(keys.iterator()); //convert
String csvTypeString = null;
try {
switch (saveFileFormat) {
case CSV:
if(csvType.equals(OccurrencesSaveEnum.STANDARD))
serviceJobId = taxonomyService.createOccurrenceCSVJob(streamKeys);
else if(csvType.equals(OccurrencesSaveEnum.OPENMODELLER))
serviceJobId = taxonomyService.createOccurrenceCSVOpenModellerJob(streamKeys);
if(jobModel.getCsvType()!=null)
csvTypeString = jobModel.getCsvType().toString(); //CASE CSV
break;
case DARWIN_CORE:
serviceJobId = taxonomyService.createOccurrenceDARWINCOREJob(streamKeys);
csvTypeString = "";
break;
default:
@ -391,23 +470,23 @@ public class OccurrenceJobUtil {
logger.error("An error occured in create new occurrences job on server ",e);
return null;
}
long submitTimeInMillis = Calendar.getInstance().getTimeInMillis();
try {
//STORE INTO DAO
OccurrencesJob occurrenceJob = new OccurrencesJob(serviceJobId, jobModel.getJobName(), jobModel.getDescription(), jobModel.getScientificName(), dataSources, DownloadState.PENDING.toString(), "", submitTimeInMillis, 0, 0, jobModel.getFileFormat().toString(),csvTypeString, jobModel.isByDataSource(), convertListKeyIntoStoreXMLString(keys), expectedOccurrence);
//for debug
// System.out.println("INTO createOccurrenceJobOnServiceByKeys " + occurrenceJob);
occurrencesJobDao.insert(occurrenceJob);
Date start = DateUtil.millisecondsToDate(submitTimeInMillis);
jobModel.setSubmitTime(start);
//FILL MODEL WITH OTHER DATA
jobModel.setId(serviceJobId);
jobModel.setState(DownloadState.PENDING);
@ -416,25 +495,31 @@ public class OccurrenceJobUtil {
}catch (Exception e) {
logger.error("An error occured in create new occurrences job on dao object " +e,e);
}
return jobModel;
}
/**
* Convert list key into store xml string.
*
* @param keys the keys
* @return the string
*/
public static String convertListKeyIntoStoreXMLString(List<String> keys){
String storeKeys = "";
KeyStringList keyStringList = new KeyStringList();
XStreamUtil<KeyStringList> xstreamUtil = new XStreamUtil<KeyStringList>(ALIASKEY,KeyStringList.class);
for (String key : keys) {
// System.out.println("key :"+ key);
logger.info("key converted: "+key);
keyStringList.addKey(key);
}
storeKeys = xstreamUtil.toXML(keyStringList);
//FOR DEBUG
@ -442,15 +527,21 @@ public class OccurrenceJobUtil {
return storeKeys;
}
/**
* Revert list key from stored xml string.
*
* @param storedKeysAsXml the stored keys as xml
* @return the list
*/
public static List<String> revertListKeyFromStoredXMLString(String storedKeysAsXml){
List<String> listKey = new ArrayList<String>();
XStreamUtil<KeyStringList> xstreamUtil = new XStreamUtil<KeyStringList>(ALIASKEY,KeyStringList.class);
KeyStringList keyStringList = (KeyStringList) xstreamUtil.fromXML(storedKeysAsXml);
for (String key : keyStringList.getListKeys()) {
// for debug
// System.out.println("key :"+ key);

169
src/main/java/org/gcube/portlets/user/speciesdiscovery/server/job/TaxonomyJobUtil.java
View File

@ -12,14 +12,21 @@ import javax.persistence.criteria.CriteriaQuery;
import javax.persistence.criteria.Predicate;
import org.apache.log4j.Logger;
import org.gcube.data.spd.stubs.types.NodeStatus;
import org.gcube.data.spd.stubs.types.Status;
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.NodeStatus;
import org.gcube.portlets.user.speciesdiscovery.server.persistence.dao.TaxonomyJobPersistence;
import org.gcube.portlets.user.speciesdiscovery.server.util.DateUtil;
import org.gcube.portlets.user.speciesdiscovery.shared.DownloadState;
import org.gcube.portlets.user.speciesdiscovery.shared.JobTaxonomyModel;
import org.gcube.portlets.user.speciesdiscovery.shared.TaxonomyJob;
/**
* The Class TaxonomyJobUtil.
*
* @author Francesco Mangiacrapa francesco.mangiacrapa@isti.cnr.it
* Jan 10, 2017
*/
public class TaxonomyJobUtil {
//STATE RETURNED BY STATUS RESPONSE
@ -31,40 +38,50 @@ public class TaxonomyJobUtil {
protected static Logger logger = Logger.getLogger(TaxonomyJobUtil.class);
public static JobTaxonomyModel convertJob(TaxonomyJob job, Status statusResponse, TaxonomyJobPersistence speciesJobDao) throws SQLException{
//TODO SET END TIME
/**
* Convert job.
*
* @param job the job
* @param statusResponse the status response
* @param speciesJobDao the species job dao
* @return the job taxonomy model
* @throws SQLException the SQL exception
*/
public static JobTaxonomyModel convertJob(TaxonomyJob job, CompleteJobStatus statusResponse, TaxonomyJobPersistence speciesJobDao) throws SQLException{
//TODO SET END TIME
JobTaxonomyModel jobSpeciesModel;
String status = statusResponse.getStatus();
JobStatus status = statusResponse.getStatus();
DownloadState downloadState = null;
long endTime = 0;
downloadState = getDownloadState(status);
logger.trace("download state: " + downloadState);
if(downloadState==null){ //Case with exception
logger.warn("download state is null, returning");
return null;
}
boolean onSaving = true;
//GET CHILDREN
ArrayList<JobTaxonomyModel> listChildJob = new ArrayList<JobTaxonomyModel>();
logger.trace("status response subnodes is != null? " + (statusResponse.getSubNodes()!=null));
if(statusResponse.getSubNodes()!=null){
logger.trace("subNodes size is: " + statusResponse.getSubNodes().size());
for (NodeStatus nodeStatus : statusResponse.getSubNodes()){
logger.trace("node status " + nodeStatus);
DownloadState downloadStateChildren = getDownloadState(nodeStatus.getStatus());
if(!downloadStateChildren.equals(DownloadState.COMPLETED))
onSaving=false;
listChildJob.add(new JobTaxonomyModel(UUID.randomUUID().toString(), nodeStatus.getScientificName(),downloadStateChildren));
}
}else{
@ -72,12 +89,12 @@ public class TaxonomyJobUtil {
onSaving=false;
}
boolean changeStatus = false;
//If status of children is completed and job status is not completed (the file is generated) or failed, set download state on saving
if(onSaving &&(!downloadState.equals(DownloadState.COMPLETED) && !downloadState.equals(DownloadState.FAILED))){
if(onSaving &&!downloadState.equals(DownloadState.COMPLETED) && !downloadState.equals(DownloadState.FAILED)){
downloadState = DownloadState.SAVING;
changeStatus = true;
//if status is completed and job was saved, update status as saved
}else if(downloadState.equals(DownloadState.COMPLETED)){
if(job.getState().compareTo(DownloadState.SAVED.toString())==0){
@ -85,65 +102,65 @@ public class TaxonomyJobUtil {
changeStatus = true;
}
}
jobSpeciesModel = new JobTaxonomyModel(job.getId(), job.getDescriptiveName(), downloadState, null, job.getScientificName(), job.getDataSourceName(), job.getRank());
jobSpeciesModel.setListChildJobs(listChildJob);
boolean changeEndTime = false;
//UPDATE END TIME
if(downloadState.equals(DownloadState.FAILED) || downloadState.equals(DownloadState.COMPLETED)){
// if(job.getEndTime()==0){ //UPDATE end time first time only
//
//
// logger.trace("UPDATE end time first time only - " + downloadState);
// endTime = Calendar.getInstance().getTimeInMillis();
// job.setEndTime(endTime);
// changeEndTime = true;
//// speciesJobDao.update(job);
//
//
// }
// System.out.println("job "+job);
// System.out.println("statusResponse.getEndDate() "+statusResponse.getEndDate());
// System.out.println("job.getEndTime() "+job.getEndTime());
if(statusResponse.getEndDate()!=null && job.getEndTime()==0){ //UPDATE end time first time only
logger.trace("UPDATE end time first time only - " + downloadState);
// endTime = Calendar.getInstance().getTimeInMillis();
endTime = statusResponse.getEndDate().getTimeInMillis();
job.setEndTime(endTime);
changeEndTime = true;
// speciesJobDao.update(job);
}
}
boolean changeStartTime = false;
//SET START TIME
long startTime = job.getStartTime();
// System.out.println("statusResponse.getStartDate(): "+statusResponse.getStartDate());
// System.out.println("startTime: "+startTime);
if(statusResponse.getStartDate()!=null && startTime==0){ //UPDATE start time first time only
Date start = DateUtil.millisecondsToDate(statusResponse.getStartDate().getTimeInMillis());
// jobSpeciesModel.setStartTime(DateUtil.dateToDateFormatString(start));
jobSpeciesModel.setStartTime(start);
changeStartTime = true;
}
try{
//UPDATE DAO
if(changeStatus || changeEndTime || changeStartTime){
job.setState(downloadState.toString());
speciesJobDao.update(job);
}
}
}catch (Exception e) {
logger.trace("An error occurred when update dao: ",e);
}
@ -154,10 +171,10 @@ public class TaxonomyJobUtil {
// jobSpeciesModel.setStartTime(DateUtil.dateToDateFormatString(start));
jobSpeciesModel.setSubmitTime(submit);
endTime = job.getEndTime();
long elapsedTime = 0;
//SET END TIME, BECAUSE IT IS CHANGED
if(endTime!=0){
Date end = DateUtil.millisecondsToDate(endTime);
@ -167,31 +184,49 @@ public class TaxonomyJobUtil {
}
else
elapsedTime = Calendar.getInstance().getTimeInMillis();
//SET ELAPSED TIME
jobSpeciesModel.setElapsedTime(DateUtil.getDifference(submitTime, elapsedTime));
return jobSpeciesModel;
}
public static DownloadState getDownloadState(String status){
/**
* Gets the download state.
*
* @param status the status
* @return the download state
*/
public static DownloadState getDownloadState(JobStatus status){
if(status!=null){
if(status.compareToIgnoreCase(PENDING)==0){
return DownloadState.PENDING;
}else if(status.compareToIgnoreCase(RUNNING)==0){
return DownloadState.ONGOING;
}else if(status.compareToIgnoreCase(FAILED)==0){
return DownloadState.FAILED;
}else if(status.compareToIgnoreCase(COMPLETED)==0){
switch (status) {
case COMPLETED:
return DownloadState.COMPLETED;
case FAILED:
return DownloadState.FAILED;
case PENDING:
return DownloadState.PENDING;
case RUNNING:
return DownloadState.ONGOING;
default:
return null;
}
}
return null;
}
/**
* Delete taxonomy job by id.
*
* @param jobIdentifier the job identifier
* @param taxonomyJobDao the taxonomy job dao
* @return the int
* @throws SQLException the SQL exception
*/
public static int deleteTaxonomyJobById(String jobIdentifier, TaxonomyJobPersistence taxonomyJobDao) throws SQLException{
logger.trace("Delete taxonomy job id: " + jobIdentifier);
try{
@ -203,41 +238,49 @@ public class TaxonomyJobUtil {
logger.error("An error occured deleteTaxonomyJobById " + jobIdentifier + " exception: "+e, e);
e.printStackTrace();
}
return 0;
}
/**
* Change status taxonomy job by id.
*
* @param jobIdentifier the job identifier
* @param state the state
* @param taxonomyJobDAO the taxonomy job dao
* @return the int
*/
public static int changeStatusTaxonomyJobById(String jobIdentifier,DownloadState state, TaxonomyJobPersistence taxonomyJobDAO) {
logger.trace("Change status taxonomy job id: " + jobIdentifier);
// System.out.println("Delete job id: " + jobIdentifier);
int result = 0;
try{
CriteriaBuilder queryBuilder = taxonomyJobDAO.getCriteriaBuilder();
CriteriaQuery<Object> cq = queryBuilder.createQuery();
Predicate pr1 = queryBuilder.equal(taxonomyJobDAO.rootFrom(cq).get(TaxonomyJob.ID_FIELD), jobIdentifier);
cq.where(pr1);
Iterator<TaxonomyJob> iterator = taxonomyJobDAO.executeCriteriaQuery(cq).iterator();
TaxonomyJob job;
if(iterator.hasNext())
job = iterator.next();
else
return 0;
job.setState(state.toString());
taxonomyJobDAO.update(job);
}catch (Exception e) {
logger.error("An error occured in change status jobId: " + jobIdentifier + " exception: "+e, e );
}
return result;
}
}

139
src/main/java/org/gcube/portlets/user/speciesdiscovery/server/persistence/ResultRowBuffer.java
View File

@ -1,5 +1,5 @@
/**
*
*
*/
package org.gcube.portlets.user.speciesdiscovery.server.persistence;
@ -27,41 +27,41 @@ import org.gcube.portlets.user.speciesdiscovery.shared.util.NormalizeString;
/**
*
*
* @author Francesco Mangiacrapa francesco.mangiacrapa@isti.cnr.it
* @May 20, 2013
*
*/
public class ResultRowBuffer extends AbstractSelectableDaoBuffer<ResultRow> implements FilterableFetchingBuffer<ResultRow> {
protected Logger logger = Logger.getLogger(ResultRowBuffer.class);
private AbstractPersistence<Taxon> taxonDao;
private int filteredListSize = 0;
public ResultRowBuffer(AbstractPersistence<ResultRow> dao, AbstractPersistence<Taxon> taxonDao)
{
super(dao, ResultRow.ID_FIELD, ResultRow.SELECTED);
this.taxonDao = taxonDao;
}
/**
* {@inheritDoc}
* @throws Exception
* @throws Exception
*/
@Override
public void add(ResultRow row) throws Exception{
//FOR DEBUG
// logger.trace("Add item "+ row.getId() + " service id: " +row.getServiceId());
super.add(row);
}
public int getFilteredListSize() throws SQLException
{
return filteredListSize;
}
//TODO MODIFIED
@Override
@ -71,22 +71,18 @@ public class ResultRowBuffer extends AbstractSelectableDaoBuffer<ResultRow> impl
List<ResultRow> list = new ArrayList<ResultRow>();
Iterator<ResultRow> iterator = null;
String value;
if(activeFiltersObject!=null){
//FILTER BY CLASSIFICATION
if(activeFiltersObject.isByClassification()){
// List<Integer> listId = activeFiltersObject.getListByClassification();
int counter = activeFiltersObject.getNumberOfData();
logger.trace("in classification filter - counter: "+counter);
logger.trace("in classification filter - rank: "+activeFiltersObject.getRankClassification());
logger.trace("in classification filter - classification id: "+activeFiltersObject.getClassificationId());
String columName = null;
if(activeFiltersObject.getRankClassification().compareTo(MainTaxonomicRankEnum.KINGDOM.getLabel())==0)
columName = ResultRow.KINGDOM_ID;
else if(activeFiltersObject.getRankClassification().compareTo(MainTaxonomicRankEnum.FAMILY.getLabel())==0)
@ -101,121 +97,103 @@ public class ResultRowBuffer extends AbstractSelectableDaoBuffer<ResultRow> impl
columName = ResultRow.PHYLUM_ID;
else if(activeFiltersObject.getRankClassification().compareTo(MainTaxonomicRankEnum.SPECIES.getLabel())==0)
columName = ResultRow.SPECIES_ID;
// logger.trace("in classification filter - columName: "+columName);
try {
CriteriaBuilder queryBuilder = dao.getCriteriaBuilder();
Query query = dao.createNewManager().createQuery("select r FROM ResultRow r where r."+columName+ "='"+activeFiltersObject.getClassificationId()+"'");
//
query.setMaxResults(counter);
iterator = query.getResultList().iterator();
// logger.trace("in classification filter - statement: "+queryBuilder.where().eq(columName, activeFiltersObject.getClassificationId()).getStatement());
} catch (Exception e) {
logger.error("Error in activeFiltersObject.isByClassification(): "+e, e);
}
//FILTER BY DATA PROVIDER
}else if(activeFiltersObject.isByDataProvider()){
try {
CriteriaBuilder queryBuilder = dao.getCriteriaBuilder();
value = activeFiltersObject.getDataProviderName();
CriteriaQuery<Object> cq = queryBuilder.createQuery();
Predicate pr1 = queryBuilder.equal(dao.rootFrom(cq).get(ResultRow.DATAPROVIDER_NAME), value);
cq.where(pr1);
//TODO FIXME empty value
logger.trace("FILTER BY DATA PROVIDER: "+ value );
iterator = dao.executeCriteriaQuery(cq).iterator();
} catch (Exception e) {
logger.error("Error in activeFiltersObject.isByDataProvider(): "+e, e);
e.printStackTrace();
}
//FILTER BY DATA SOURCE
}else if(activeFiltersObject.isByDataSourceName()){
try {
CriteriaBuilder queryBuilder = dao.getCriteriaBuilder();
value = activeFiltersObject.getDataSourceName();
CriteriaQuery<Object> cq = queryBuilder.createQuery();
Predicate pr1 = queryBuilder.equal(dao.rootFrom(cq).get(ResultRow.DATASOURCE_NAME), NormalizeString.validateUndefined(value));
cq.where(pr1);
logger.trace("FILTER BY DATA DATA SOURCE NAME: "+ value );
iterator = dao.executeCriteriaQuery(cq).iterator();
} catch (Exception e) {
logger.error("Error in activeFiltersObject.isByDataSourceName(): "+e, e);
e.printStackTrace();
}
//FILTER BY RANK
}else if(activeFiltersObject.isByRank()){
try {
CriteriaBuilder queryBuilder = taxonDao.getCriteriaBuilder();
value = activeFiltersObject.getRankName();
// value = NormalizeString.lowerCaseUpFirstChar(activeFiltersObject.getRankName());
CriteriaQuery<Object> cq = queryBuilder.createQuery();
Predicate pr1 = queryBuilder.equal(taxonDao.rootFrom(cq).get(Taxon.RANK), NormalizeString.validateUndefined(value));
cq.where(pr1);
Iterator<Taxon> iteratorTaxon = taxonDao.executeCriteriaQuery(cq).iterator();
logger.trace("in rank filter - value: "+value);
List<Integer> listTaxonId = new ArrayList<Integer>();
if(iteratorTaxon!=null){
while(iteratorTaxon.hasNext()){
Taxon tax = iteratorTaxon.next();
listTaxonId.add(tax.getId());
}
try {
value = activeFiltersObject.getRankName();
EntityManager em = dao.createNewManager();
String queryString = "select *" +
" FROM "+ResultRow.class.getSimpleName()+" r" +
" INNER JOIN RESULTROW_TAXON rt on r.ID=rt.RESULTROW_ID" +
" INNER JOIN "+Taxon.class.getSimpleName()+" t on t.INTERNALID=rt.MATCHINGTAXON_INTERNALID" +
" where t.RANK = '"+value+"' and t.ID IN" +
" (select MIN(tax.ID) from TAXON tax)";
Query query = em.createNativeQuery(queryString, ResultRow.class);
List<ResultRow> listResultRow = new ArrayList<ResultRow>();
try {
listResultRow = query.getResultList();
} catch (Exception e) {
logger.error("Error in ResultRow - executeCriteriaQuery: " + e.getMessage(), e);
} finally {
em.close();
}
logger.trace("in rank filter - listTaxonId size: "+listTaxonId.size());
queryBuilder = dao.getCriteriaBuilder();
cq = queryBuilder.createQuery();
pr1 = dao.rootFrom(cq).get(ResultRow.PARENT_FOREIGN_KEY_TAXON).in(listTaxonId);
cq.where(pr1);
iterator = dao.executeCriteriaQuery(cq).iterator();
iterator = listResultRow.iterator();
} catch (Exception e) {
logger.error("Error in activeFiltersObject.isByRank(): "+e, e);
e.printStackTrace();
}
}
if(iterator!=null){
while(iterator.hasNext()){
ResultRow row = iterator.next();
list.add(row);
}
filteredListSize = list.size();
filteredListSize = list.size();
}
}
logger.trace("RETURNED List size " + list.size());
return list;
}
@ -225,14 +203,11 @@ public class ResultRowBuffer extends AbstractSelectableDaoBuffer<ResultRow> impl
EntityManager em = dao.createNewManager();
//TODO use filterMap
try {
em.getTransaction().begin();
int updateCount = em.createQuery("UPDATE ResultRow SET " + ResultRow.SELECTED + " = "+ selection).executeUpdate();
logger.trace("Updated " + updateCount + " item");
em.getTransaction().commit();
} finally {
if (em.getTransaction().isActive())
@ -248,22 +223,22 @@ public class ResultRowBuffer extends AbstractSelectableDaoBuffer<ResultRow> impl
@Override
public void updateAllSelectionByIds(boolean selection, List<String> listIds)
throws Exception {
EntityManager em = dao.createNewManager();
String queryString = "UPDATE ResultRow t SET "
String queryString = "UPDATE ResultRow t SET "
+ ResultRow.SELECTED + " = "+ selection +" where "
+ ResultRow.ID_FIELD+" IN :inclList";
try {
em.getTransaction().begin();
TypedQuery<ResultRow> query = em.createQuery(queryString, ResultRow.class);
query.setParameter("inclList", listIds);
int updateCount = query.executeUpdate();
logger.trace("Updated " + updateCount + " item");
em.getTransaction().commit();

77
src/main/java/org/gcube/portlets/user/speciesdiscovery/server/persistence/TaxonomyRowBuffer.java
View File

@ -1,5 +1,5 @@
/**
*
*
*/
package org.gcube.portlets.user.speciesdiscovery.server.persistence;
@ -25,7 +25,7 @@ import org.gcube.portlets.user.speciesdiscovery.shared.filter.ResultFilter;
import org.gcube.portlets.user.speciesdiscovery.shared.util.NormalizeString;
/**
*
*
* @author Francesco Mangiacrapa francesco.mangiacrapa@isti.cnr.it
* @May 20, 2013
*
@ -37,17 +37,17 @@ public class TaxonomyRowBuffer extends AbstractSelectableDaoBuffer<TaxonomyRow>
public TaxonomyRowBuffer(AbstractPersistence<TaxonomyRow> dao) {
super(dao, TaxonomyRow.ID_FIELD, TaxonomyRow.SELECTED);
}
/**
* {@inheritDoc}
* @throws Exception
* @throws Exception
*/
@Override
public void add(TaxonomyRow row) throws Exception
{
//DEBUG
// logger.trace("Add item "+ row.getId() + " service id: " +row.getServiceId());
super.add(row);
}
@ -58,14 +58,14 @@ public class TaxonomyRowBuffer extends AbstractSelectableDaoBuffer<TaxonomyRow>
Iterator<TaxonomyRow> iterator = null;
// QueryBuilder<TaxonomyRow, Integer> queryBuilder = dao.queryBuilder();
String value;
if(activeFiltersObject!=null){
if(activeFiltersObject!=null){
//FILTER BY CLASSIFICATION
if(activeFiltersObject.isByClassification()){
int counter = activeFiltersObject.getNumberOfData();
String columName = null;
if(activeFiltersObject.getRankClassification().compareTo(MainTaxonomicRankEnum.KINGDOM.getLabel())==0)
columName = TaxonomyRow.KINGDOM_ID;
else if(activeFiltersObject.getRankClassification().compareTo(MainTaxonomicRankEnum.FAMILY.getLabel())==0)
@ -80,17 +80,14 @@ public class TaxonomyRowBuffer extends AbstractSelectableDaoBuffer<TaxonomyRow>
columName = TaxonomyRow.PHYLUM_ID;
else if(activeFiltersObject.getRankClassification().compareTo(MainTaxonomicRankEnum.SPECIES.getLabel())==0)
columName = TaxonomyRow.SPECIES_ID;
//
//
// logger.trace("in classification filter - columName: "+columName);
try {
CriteriaBuilder queryBuilder = dao.getCriteriaBuilder();
Query query = dao.createNewManager().createQuery("select r FROM TaxonomyRow r where r."+columName+ "='"+activeFiltersObject.getClassificationId()+"'");
//
query.setMaxResults(counter);
iterator = query.getResultList().iterator();
// logger.trace("in classification filter - statement: "+queryBuilder.where().eq(columName, activeFiltersObject.getClassificationId()).getStatement());
@ -98,22 +95,21 @@ public class TaxonomyRowBuffer extends AbstractSelectableDaoBuffer<TaxonomyRow>
logger.error("Error in activeFiltersObject.isByClassification(): "+e, e);
e.printStackTrace();
}
//FILTER BY DATA PROVIDER
}else if(activeFiltersObject.isByDataProvider()){
try {
CriteriaBuilder queryBuilder = dao.getCriteriaBuilder();
value = activeFiltersObject.getDataProviderName();
CriteriaQuery<Object> cq = queryBuilder.createQuery();
Predicate pr1 = queryBuilder.equal(dao.rootFrom(cq).get(TaxonomyRow.DATAPROVIDER_NAME), value);
cq.where(pr1);
//TODO FIXME empty value
logger.trace("FILTER BY DATA PROVIDER: "+ value );
iterator = dao.executeCriteriaQuery(cq).iterator();
} catch (Exception e) {
logger.error("Error in activeFiltersObject.isByDataProvider(): "+e, e);
e.printStackTrace();
@ -121,30 +117,27 @@ public class TaxonomyRowBuffer extends AbstractSelectableDaoBuffer<TaxonomyRow>
//FILTER BY DATA SOURCE
}else if(activeFiltersObject.isByDataSourceName()){
try {
CriteriaBuilder queryBuilder = dao.getCriteriaBuilder();
value = activeFiltersObject.getDataSourceName();
CriteriaQuery<Object> cq = queryBuilder.createQuery();
Predicate pr1 = queryBuilder.equal(dao.rootFrom(cq).get(TaxonomyRow.DATAPROVIDER_NAME), value);
cq.where(pr1);
//TODO FIXME empty value
logger.trace("FILTER BY DATA SOURCE: "+ value );
iterator = dao.executeCriteriaQuery(cq).iterator();
} catch (Exception e) {
logger.error("Error in activeFiltersObject.isByDataProvider(): "+e, e);
e.printStackTrace();
}
// //FILTER BY RANK
}else if(activeFiltersObject.isByRank()){
try {
CriteriaBuilder queryBuilder = dao.getCriteriaBuilder();
value = activeFiltersObject.getRankName();
// value = NormalizeString.lowerCaseUpFirstChar(activeFiltersObject.getRankName());
@ -152,33 +145,25 @@ public class TaxonomyRowBuffer extends AbstractSelectableDaoBuffer<TaxonomyRow>
CriteriaQuery<Object> cq = queryBuilder.createQuery();
Predicate pr1 = queryBuilder.equal(dao.rootFrom(cq).get(TaxonomyRow.RANK), NormalizeString.validateUndefined(value));
cq.where(pr1);
logger.trace("FILTER BY RANK: "+ value );
iterator = dao.executeCriteriaQuery(cq).iterator();
} catch (Exception e) {
logger.error("Error in activeFiltersObject.isByRank(): "+e, e);
}
}
if(iterator!=null){
while(iterator.hasNext()){
TaxonomyRow row = iterator.next();
list.add(row);
}
filteredListSize = list.size();
filteredListSize = list.size();
}
}
logger.trace("RETURNED List size " + list.size());
return list;
}
@ -194,8 +179,8 @@ public class TaxonomyRowBuffer extends AbstractSelectableDaoBuffer<TaxonomyRow>
EntityManager em = dao.createNewManager();
//TODO generalize?
String queryString = "UPDATE TaxonomyRow SET "
+ ResultRow.SELECTED + " = "+ selection
String queryString = "UPDATE TaxonomyRow SET "
+ ResultRow.SELECTED + " = "+ selection
+" where "+TaxonomyRow.IS_PARENT +"=false";
try {
@ -210,7 +195,7 @@ public class TaxonomyRowBuffer extends AbstractSelectableDaoBuffer<TaxonomyRow>
if (em.getTransaction().isActive())
em.getTransaction().rollback();
em.close();
}
}
}
/* (non-Javadoc)
@ -218,12 +203,12 @@ public class TaxonomyRowBuffer extends AbstractSelectableDaoBuffer<TaxonomyRow>
*/
@Override
public void updateAllSelectionByIds(boolean selection, List<String> listIds) throws Exception {
EntityManager em = dao.createNewManager();
//TODO generalize?
String queryString = "UPDATE TaxonomyRow SET "
+ ResultRow.SELECTED + " = "+ selection
String queryString = "UPDATE TaxonomyRow SET "
+ ResultRow.SELECTED + " = "+ selection
+" where "+TaxonomyRow.IS_PARENT +"=false AND "
+ResultRow.ID_FIELD+" IN :inclList";
@ -231,9 +216,9 @@ public class TaxonomyRowBuffer extends AbstractSelectableDaoBuffer<TaxonomyRow>
em.getTransaction().begin();
TypedQuery<TaxonomyRow> query = em.createQuery(queryString, TaxonomyRow.class);
query.setParameter("inclList", listIds);
int updateCount = query.executeUpdate();
logger.trace("Updated " + updateCount + " item");
@ -243,8 +228,8 @@ public class TaxonomyRowBuffer extends AbstractSelectableDaoBuffer<TaxonomyRow>
if (em.getTransaction().isActive())
em.getTransaction().rollback();
em.close();
}
}
}

40
src/main/java/org/gcube/portlets/user/speciesdiscovery/server/persistence/dao/OccurrenceJobPersistence.java
View File

@ -23,7 +23,7 @@ public class OccurrenceJobPersistence extends AbstractPersistence<OccurrencesJob
@Override
public int removeAll() throws DatabaseServiceException {
EntityManager em = super.createNewManager();
int removed = 0;
try {
@ -31,7 +31,7 @@ public class OccurrenceJobPersistence extends AbstractPersistence<OccurrencesJob
em.getTransaction().begin();
removed = em.createQuery("DELETE FROM OccurrencesJob").executeUpdate();
em.getTransaction().commit();
logger.trace("DELETE FROM OccurrenceJob " + removed +" items");
logger.trace("DELETED FROM OccurrenceJob " + removed +" items");
} catch (Exception e) {
logger.error("Error in removeAll: " + e.getMessage(), e);
@ -51,10 +51,10 @@ public class OccurrenceJobPersistence extends AbstractPersistence<OccurrencesJob
Query query = em.createQuery("select t from OccurrencesJob t");
listOccurrencesJob = query.getResultList();
} catch (Exception e) {
logger.error("Error in OccurrencesJob - getList: " + e.getMessage(), e);
} finally {
em.close();
}
@ -73,7 +73,7 @@ public class OccurrenceJobPersistence extends AbstractPersistence<OccurrencesJob
OccurrencesJob occurrencesJob = null;
try {
occurrencesJob = em.getReference(OccurrencesJob.class, id);
} finally {
em.close();
}
@ -81,10 +81,10 @@ public class OccurrenceJobPersistence extends AbstractPersistence<OccurrencesJob
logger.trace("getItemByKey return row: "+occurrencesJob.getId());
else
logger.trace("getItemByKey return null");
//FOR DEBUG
// System.out.println("getItemByKey return: "+row );
return occurrencesJob;
}
@ -123,21 +123,21 @@ public class OccurrenceJobPersistence extends AbstractPersistence<OccurrencesJob
query.setFirstResult(startIndex);
query.setMaxResults(offset);
listOJ = query.getResultList();
} finally {
em.close();
}
return listOJ;
}
@Override
public List<OccurrencesJob> getList(Map<String, String> filterMap, int startIndex, int offset) throws DatabaseServiceException{
EntityManager em = super.createNewManager();
List<OccurrencesJob> listOJ = new ArrayList<OccurrencesJob>();
try {
String queryString = "select t from OccurrencesJob t";
if(filterMap!=null && filterMap.size()>0){
queryString+=" where ";
for (String param : filterMap.keySet()) {
@ -145,11 +145,11 @@ public class OccurrenceJobPersistence extends AbstractPersistence<OccurrencesJob
queryString+=" t."+param+"="+value;
queryString+=AND;
}
queryString = queryString.substring(0, queryString.lastIndexOf(AND));
}
Query query = em.createQuery(queryString);
if(startIndex>-1)
query.setFirstResult(startIndex);
if(offset>-1)
@ -164,24 +164,24 @@ public class OccurrenceJobPersistence extends AbstractPersistence<OccurrencesJob
@Override
public List<OccurrencesJob> executeTypedQuery(CriteriaQuery<Object> cq, int startIndex, int offset) throws DatabaseServiceException {
EntityManager em = super.createNewManager();
List<OccurrencesJob> listOJ = new ArrayList<OccurrencesJob>();
try {
TypedQuery typedQuery = em.createQuery(cq);
if(startIndex>-1)
typedQuery.setFirstResult(startIndex);
if(offset>-1)
typedQuery.setMaxResults(offset);
listOJ = typedQuery.getResultList();
} finally {
em.close();
}
return listOJ;
}
@ -190,13 +190,13 @@ public class OccurrenceJobPersistence extends AbstractPersistence<OccurrencesJob
public int deleteItemByIdField(String idField) throws DatabaseServiceException{
EntityManager em = super.createNewManager();
int removed = 0;
try {
em.getTransaction().begin();
removed = em.createQuery("DELETE FROM OccurrencesJob t WHERE t."+OccurrencesJob.ID_FIELD+"='"+idField+"'").executeUpdate();
em.getTransaction().commit();
logger.trace("Item "+ idField + " was deleted from OccurrencesJob");
} catch (Exception e) {
logger.error("Error in OccurrencesJob deleteItemByIdField: " + e.getMessage(), e);
e.printStackTrace();
@ -208,5 +208,5 @@ public class OccurrenceJobPersistence extends AbstractPersistence<OccurrencesJob
return removed;
}
}

42
src/main/java/org/gcube/portlets/user/speciesdiscovery/server/persistence/dao/OccurrenceRowPersistence.java
View File

@ -22,12 +22,12 @@ public class OccurrenceRowPersistence extends AbstractPersistence<Occurrence>{
protected CriteriaQuery<Object> criteriaQuery;
protected Root<Occurrence> rootFrom;
protected Logger logger = Logger.getLogger(OccurrenceRowPersistence.class);
public OccurrenceRowPersistence(EntityManagerFactory factory) throws DatabaseServiceException{
super(factory);
criteriaBuilder = super.createNewManager().getCriteriaBuilder();
}
@Override
public Root<Occurrence> rootFrom(CriteriaQuery<Object> cq){
return cq.from(Occurrence.class);
@ -78,7 +78,7 @@ public class OccurrenceRowPersistence extends AbstractPersistence<Occurrence>{
Occurrence row = null;
try {
row = em.getReference(Occurrence.class, id);
} finally {
em.close();
}
@ -86,10 +86,10 @@ public class OccurrenceRowPersistence extends AbstractPersistence<Occurrence>{
logger.trace("getItemByKey return row: "+row.getId() + ", service id: " + row.getServiceId());
else
logger.trace("getItemByKey return null");
//FOR DEBUG
// System.out.println("getItemByKey return: "+row );
return row;
}
@ -99,7 +99,7 @@ public class OccurrenceRowPersistence extends AbstractPersistence<Occurrence>{
}
/**
*
*
* @return
*/
public int removeAll() throws DatabaseServiceException{
@ -110,7 +110,7 @@ public class OccurrenceRowPersistence extends AbstractPersistence<Occurrence>{
em.getTransaction().begin();
removed = em.createQuery("DELETE FROM Occurrence").executeUpdate();
em.getTransaction().commit();
logger.trace("DELETE FROM Occurrence " + removed +" items");
logger.trace("DELETED FROM Occurrence " + removed +" items");
} catch (Exception e) {
logger.error("Error in removeAll: " + e.getMessage(), e);
@ -124,7 +124,7 @@ public class OccurrenceRowPersistence extends AbstractPersistence<Occurrence>{
@Override
public List<Occurrence> getList(int startIndex, int offset) throws DatabaseServiceException {
EntityManager em = super.createNewManager();
List<Occurrence> listOccurrence = new ArrayList<Occurrence>();
try {
@ -132,7 +132,7 @@ public class OccurrenceRowPersistence extends AbstractPersistence<Occurrence>{
query.setFirstResult(startIndex);
query.setMaxResults(offset);
listOccurrence = query.getResultList();
} finally {
em.close();
}
@ -141,12 +141,12 @@ public class OccurrenceRowPersistence extends AbstractPersistence<Occurrence>{
@Override
public List<Occurrence> getList(Map<String, String> filterMap, int startIndex, int offset) throws DatabaseServiceException{
EntityManager em = super.createNewManager();
List<Occurrence> listOccurrence = new ArrayList<Occurrence>();
try {
String queryString = "select t from Occurrence t";
if(filterMap!=null && filterMap.size()>0){
queryString+=" where ";
for (String param : filterMap.keySet()) {
@ -154,11 +154,11 @@ public class OccurrenceRowPersistence extends AbstractPersistence<Occurrence>{
queryString+=" t."+param+"="+value;
queryString+=AND;
}
queryString = queryString.substring(0, queryString.lastIndexOf(AND));
}
Query query = em.createQuery(queryString);
if(startIndex>-1)
query.setFirstResult(startIndex);
if(offset>-1)
@ -170,28 +170,28 @@ public class OccurrenceRowPersistence extends AbstractPersistence<Occurrence>{
}
return listOccurrence;
}
@Override
public List<Occurrence> executeTypedQuery(CriteriaQuery<Object> cq, int startIndex, int offset) throws DatabaseServiceException{
EntityManager em = super.createNewManager();
List<Occurrence> listOJ = new ArrayList<Occurrence>();
try {
TypedQuery typedQuery = em.createQuery(cq);
if(startIndex>-1)
typedQuery.setFirstResult(startIndex);
if(offset>-1)
typedQuery.setMaxResults(offset);
listOJ = typedQuery.getResultList();
} finally {
em.close();
}
return listOJ;
}
@ -200,13 +200,13 @@ public class OccurrenceRowPersistence extends AbstractPersistence<Occurrence>{
public int deleteItemByIdField(String idField) throws DatabaseServiceException{
EntityManager em = super.createNewManager();
int removed = 0;
try {
em.getTransaction().begin();
removed = em.createQuery("DELETE FROM Occurrence t WHERE t."+Occurrence.ID_FIELD+"='"+idField+"'").executeUpdate();
em.getTransaction().commit();
logger.trace("Item "+ idField + " was deleted from Occurrence");
} catch (Exception e) {
logger.error("Error in Occurrence deleteJobById: " + e.getMessage(), e);

56
src/main/java/org/gcube/portlets/user/speciesdiscovery/server/persistence/dao/ResultRowPersistence.java
View File

@ -23,14 +23,14 @@ public class ResultRowPersistence extends AbstractPersistence<ResultRow>{
protected CriteriaQuery<Object> criteriaQuery;
protected Root<ResultRow> rootFrom;
protected Logger logger = Logger.getLogger(ResultRowPersistence.class);
public ResultRowPersistence(EntityManagerFactory factory) throws DatabaseServiceException{
super(factory);
criteriaBuilder = super.createNewManager().getCriteriaBuilder();
// CriteriaQuery<Object> cq = criteriaBuilder.createQuery();
// Root<ResultRow> rootFrom = cq.from(ResultRow.class);
}
@Override
public Root<ResultRow> rootFrom(CriteriaQuery<Object> cq){
return cq.from(ResultRow.class);
@ -46,7 +46,7 @@ public class ResultRowPersistence extends AbstractPersistence<ResultRow>{
listResultRow = query.getResultList();
} catch (Exception e) {
logger.error("Error in ResultRow - getList: " + e.getMessage(), e);
logger.error("Error in ResultRow - getList: " + e.getMessage(), e);
} finally {
em.close();
}
@ -70,7 +70,7 @@ public class ResultRowPersistence extends AbstractPersistence<ResultRow>{
listResultRow = query.getResultList();
} catch (Exception e) {
logger.error("Error in ResultRow - executeCriteriaQuery: " + e.getMessage(), e);
logger.error("Error in ResultRow - executeCriteriaQuery: " + e.getMessage(), e);
} finally {
em.close();
}
@ -85,9 +85,9 @@ public class ResultRowPersistence extends AbstractPersistence<ResultRow>{
ResultRow row = null;
try {
row = em.getReference(ResultRow.class, id);
} catch (Exception e) {
logger.error("Error in ResultRow - getItemByKey: " + e.getMessage(), e);
logger.error("Error in ResultRow - getItemByKey: " + e.getMessage(), e);
} finally {
em.close();
}
@ -95,21 +95,21 @@ public class ResultRowPersistence extends AbstractPersistence<ResultRow>{
logger.trace("getItemByKey return row: "+row.getId() + ", service id: " + row.getServiceId());
else
logger.trace("getItemByKey return null");
//FOR DEBUG
// System.out.println("getItemByKey return: "+row );
return row;
}
@Override
public CriteriaBuilder getCriteriaBuilder() throws DatabaseServiceException{
return createNewManager().getCriteriaBuilder();
}
/**
*
*
* @return
*/
public int removeAll() throws DatabaseServiceException{
@ -120,10 +120,10 @@ public class ResultRowPersistence extends AbstractPersistence<ResultRow>{
em.getTransaction().begin();
removed = em.createQuery("DELETE FROM ResultRow").executeUpdate();
em.getTransaction().commit();
logger.trace("DELETE FROM ResultRow " + removed +" items");
logger.trace("DELETED FROM ResultRow " + removed +" items");
} catch (Exception e) {
logger.error("Error in ResultRow - removeAll: " + e.getMessage(), e);
logger.error("Error in ResultRow - removeAll: " + e.getMessage(), e);
} finally {
em.close();
}
@ -133,7 +133,7 @@ public class ResultRowPersistence extends AbstractPersistence<ResultRow>{
@Override
public List<ResultRow> getList(int startIndex, int offset) throws DatabaseServiceException{
EntityManager em = super.createNewManager();
List<ResultRow> listResultRow = new ArrayList<ResultRow>();
try {
@ -141,23 +141,23 @@ public class ResultRowPersistence extends AbstractPersistence<ResultRow>{
query.setFirstResult(startIndex);
query.setMaxResults(offset);
listResultRow = query.getResultList();
} catch (Exception e) {
logger.error("Error in ResultRow - getList: " + e.getMessage(), e);
logger.error("Error in ResultRow - getList: " + e.getMessage(), e);
} finally {
em.close();
}
return listResultRow;
}
@Override
public List<ResultRow> getList(Map<String, String> filterMap, int startIndex, int offset) throws DatabaseServiceException{
EntityManager em = super.createNewManager();
List<ResultRow> listResultRow = new ArrayList<ResultRow>();
try {
String queryString = "select t from ResultRow t";
if(filterMap!=null && filterMap.size()>0){
queryString+=" where ";
for (String param : filterMap.keySet()) {
@ -165,42 +165,42 @@ public class ResultRowPersistence extends AbstractPersistence<ResultRow>{
queryString+=" t."+param+"="+value;
queryString+=AND;
}
queryString = queryString.substring(0, queryString.lastIndexOf(AND));
}
Query query = em.createQuery(queryString);
listResultRow = query.getResultList();
} catch (Exception e) {
logger.error("Error in ResultRow - getList: " + e.getMessage(), e);
logger.error("Error in ResultRow - getList: " + e.getMessage(), e);
} finally {
em.close();
}
return listResultRow;
}
@Override
public List<ResultRow> executeTypedQuery(CriteriaQuery<Object> cq, int startIndex, int offset) throws DatabaseServiceException{
EntityManager em = super.createNewManager();
List<ResultRow> listOJ = new ArrayList<ResultRow>();
try {
TypedQuery typedQuery = em.createQuery(cq);
if(startIndex>-1)
typedQuery.setFirstResult(startIndex);
if(offset>-1)
typedQuery.setMaxResults(offset);
listOJ = typedQuery.getResultList();
} catch (Exception e) {
logger.error("Error in ResultRow - executeTypedQuery: " + e.getMessage(), e);
logger.error("Error in ResultRow - executeTypedQuery: " + e.getMessage(), e);
} finally {
em.close();
}
return listOJ;
}
@ -209,13 +209,13 @@ public class ResultRowPersistence extends AbstractPersistence<ResultRow>{
public int deleteItemByIdField(String idField) throws DatabaseServiceException{
EntityManager em = super.createNewManager();
int removed = 0;
try {
em.getTransaction().begin();
removed = em.createQuery("DELETE FROM ResultRow t WHERE t."+ResultRow.ID_FIELD+"='"+idField+"'").executeUpdate();
em.getTransaction().commit();
logger.trace("Item "+ idField + " was deleted from ResultRow");
} catch (Exception e) {
logger.error("Error in ResultRow - deleteJobById: " + e.getMessage(), e);

28
src/main/java/org/gcube/portlets/user/speciesdiscovery/server/persistence/dao/TaxonRowPersistence.java
View File

@ -31,7 +31,7 @@ public class TaxonRowPersistence extends AbstractPersistence<Taxon>{
em.getTransaction().begin();
removed = em.createQuery("DELETE FROM Taxon").executeUpdate();
em.getTransaction().commit();
logger.trace("DELETE FROM Taxon " + removed +" items");
logger.trace("DELETED FROM Taxon " + removed +" items");
} catch (Exception e) {
logger.error("Error in removeAll: " + e.getMessage(), e);
@ -51,7 +51,7 @@ public class TaxonRowPersistence extends AbstractPersistence<Taxon>{
Query query = em.createQuery("select t from Taxon t");
listTaxon = query.getResultList();
} catch (Exception e) {
logger.error("Error in Taxon - removeAll: " + e.getMessage(), e);
@ -63,7 +63,7 @@ public class TaxonRowPersistence extends AbstractPersistence<Taxon>{
@Override
public List<Taxon> getList(int startIndex, int offset) throws DatabaseServiceException {
EntityManager em = super.createNewManager();
List<Taxon> listTaxon = new ArrayList<Taxon>();
try {
@ -71,7 +71,7 @@ public class TaxonRowPersistence extends AbstractPersistence<Taxon>{
query.setFirstResult(startIndex);
query.setMaxResults(offset);
listTaxon = query.getResultList();
} catch (Exception e) {
logger.error("Error in Taxon - getList: " + e.getMessage(), e);
@ -93,7 +93,7 @@ public class TaxonRowPersistence extends AbstractPersistence<Taxon>{
Taxon row = null;
try {
row = em.getReference(Taxon.class, id);
} catch (Exception e) {
logger.error("Error in Taxon - getItemByKey: " + e.getMessage(), e);
@ -104,10 +104,10 @@ public class TaxonRowPersistence extends AbstractPersistence<Taxon>{
logger.trace("getItemByKey return row id: "+row.getId());
else
logger.trace("getItemByKey return null");
//FOR DEBUG
// System.out.println("getItemByKey return: "+row );
return row;
}
@ -146,7 +146,7 @@ public class TaxonRowPersistence extends AbstractPersistence<Taxon>{
List<Taxon> listTaxon = new ArrayList<Taxon>();
try {
String queryString = "select t from Taxon t";
if(filterMap!=null && filterMap.size()>0){
queryString+=" where ";
for (String param : filterMap.keySet()) {
@ -154,7 +154,7 @@ public class TaxonRowPersistence extends AbstractPersistence<Taxon>{
queryString+=" t."+param+"="+value;
queryString+=AND;
}
queryString = queryString.substring(0, queryString.lastIndexOf(AND));
}
Query query = em.createQuery(queryString);
@ -176,21 +176,21 @@ public class TaxonRowPersistence extends AbstractPersistence<Taxon>{
try {
TypedQuery typedQuery = em.createQuery(cq);
if(startIndex>-1)
typedQuery.setFirstResult(startIndex);
if(offset>-1)
typedQuery.setMaxResults(offset);
listTaxon = typedQuery.getResultList();
} catch (Exception e) {
logger.error("Error in Taxon - executeTypedQuery: " + e.getMessage(), e);
}finally {
em.close();
}
return listTaxon;
}
@ -198,13 +198,13 @@ public class TaxonRowPersistence extends AbstractPersistence<Taxon>{
public int deleteItemByIdField(String idField) throws DatabaseServiceException{
EntityManager em = super.createNewManager();
int removed = 0;
try {
em.getTransaction().begin();
removed = em.createQuery("DELETE FROM Taxon t WHERE t."+Taxon.ID_FIELD+"='"+idField+"'").executeUpdate();
em.getTransaction().commit();
logger.trace("Item "+ idField + " was deleted from Taxon");
} catch (Exception e) {
logger.error("Error in Taxon deleteJobById: " + e.getMessage(), e);

42
src/main/java/org/gcube/portlets/user/speciesdiscovery/server/persistence/dao/TaxonomyJobPersistence.java
View File

@ -30,7 +30,7 @@ public class TaxonomyJobPersistence extends AbstractPersistence<TaxonomyJob>{
em.getTransaction().begin();
removed = em.createQuery("DELETE FROM TaxonomyJob").executeUpdate();
em.getTransaction().commit();
logger.trace("DELETE FROM TaxonomyJob " + removed +" items");
logger.trace("DELETED FROM TaxonomyJob " + removed +" items");
} catch (Exception e) {
logger.error("Error in removeAll: " + e.getMessage(), e);
@ -41,19 +41,19 @@ public class TaxonomyJobPersistence extends AbstractPersistence<TaxonomyJob>{
return removed;
}
@Override
public int deleteItemByIdField(String idField) throws DatabaseServiceException{
EntityManager em = super.createNewManager();
int removed = 0;
try {
em.getTransaction().begin();
removed = em.createQuery("DELETE FROM TaxonomyJob t WHERE t."+TaxonomyJob.ID_FIELD+"='"+idField+"'").executeUpdate();
em.getTransaction().commit();
logger.trace("Item "+ idField + " was deleted from TaxonomyJob. removed "+ removed + " item" );
logger.trace("Item "+ idField + " was deleted from TaxonomyJob. removed "+ removed + " item" );
// System.out.println("Item "+ idField + " was deleted from TaxonomyJob. removed "+ removed + " item" );
} catch (Exception e) {
logger.error("Error in TaxonomyJob deleteJobById: " + e.getMessage(), e);
e.printStackTrace();
@ -73,7 +73,7 @@ public class TaxonomyJobPersistence extends AbstractPersistence<TaxonomyJob>{
Query query = em.createQuery("select t from TaxonomyJob t");
listTaxJob = query.getResultList();
} catch (Exception e) {
logger.error("Error in TaxonomyJob - getList: " + e.getMessage(), e);
@ -95,7 +95,7 @@ public class TaxonomyJobPersistence extends AbstractPersistence<TaxonomyJob>{
TaxonomyJob taxJob = null;
try {
taxJob = em.getReference(TaxonomyJob.class, id);
} catch (Exception e) {
logger.error("Error in TaxonomyJob - getItemByKey: " + e.getMessage(), e);
@ -106,10 +106,10 @@ public class TaxonomyJobPersistence extends AbstractPersistence<TaxonomyJob>{
logger.trace("getItemByKey return row: "+taxJob.getId());
else
logger.trace("getItemByKey return null");
//FOR DEBUG
// System.out.println("getItemByKey return: "+row );
return taxJob;
}
@ -152,7 +152,7 @@ public class TaxonomyJobPersistence extends AbstractPersistence<TaxonomyJob>{
query.setFirstResult(startIndex);
query.setMaxResults(offset);
listTaxJob = query.getResultList();
} catch (Exception e) {
logger.error("Error in TaxonomyJob - getList: " + e.getMessage(), e);
@ -161,15 +161,15 @@ public class TaxonomyJobPersistence extends AbstractPersistence<TaxonomyJob>{
}
return listTaxJob;
}
@Override
public List<TaxonomyJob> getList(Map<String, String> filterMap, int startIndex, int offset) throws DatabaseServiceException {
EntityManager em = super.createNewManager();
List<TaxonomyJob> listTaxJob = new ArrayList<TaxonomyJob>();
try {
String queryString = "select t from TaxonomyJob t";
if(filterMap!=null && filterMap.size()>0){
queryString+=" where ";
for (String param : filterMap.keySet()) {
@ -177,11 +177,11 @@ public class TaxonomyJobPersistence extends AbstractPersistence<TaxonomyJob>{
queryString+=" t."+param+"="+value;
queryString+=AND;
}
queryString = queryString.substring(0, queryString.lastIndexOf(AND));
}
Query query = em.createQuery(queryString);
if(startIndex>-1)
query.setFirstResult(startIndex);
if(offset>-1)
@ -196,33 +196,33 @@ public class TaxonomyJobPersistence extends AbstractPersistence<TaxonomyJob>{
}
return listTaxJob;
}
@Override
public List<TaxonomyJob> executeTypedQuery(CriteriaQuery<Object> cq, int startIndex, int offset) throws DatabaseServiceException {
EntityManager em = super.createNewManager();
List<TaxonomyJob> listOJ = new ArrayList<TaxonomyJob>();
try {
TypedQuery typedQuery = em.createQuery(cq);
if(startIndex>-1)
typedQuery.setFirstResult(startIndex);
if(offset>-1)
typedQuery.setMaxResults(offset);
listOJ = typedQuery.getResultList();
} catch (Exception e) {
logger.error("Error in TaxonomyJob - executeTypedQuery: " + e.getMessage(), e);
} finally {
em.close();
}
return listOJ;
}
}

38
src/main/java/org/gcube/portlets/user/speciesdiscovery/server/persistence/dao/TaxonomyRowPersistence.java
View File

@ -31,7 +31,7 @@ public class TaxonomyRowPersistence extends AbstractPersistence<TaxonomyRow>{
em.getTransaction().begin();
removed = em.createQuery("DELETE FROM TaxonomyRow").executeUpdate();
em.getTransaction().commit();
logger.trace("DELETE FROM TaxonomyRow " + removed +" items");
logger.trace("DELETED FROM TaxonomyRow " + removed +" items");
} catch (Exception e) {
logger.error("Error in TaxonomyRow - removeAll: " + e.getMessage(), e);
@ -51,7 +51,7 @@ public class TaxonomyRowPersistence extends AbstractPersistence<TaxonomyRow>{
Query query = em.createQuery("select t from TaxonomyRow t");
listTaxonomy = query.getResultList();
} catch (Exception e) {
logger.error("Error in TaxonomyRow - getList: " + e.getMessage(), e);
@ -75,10 +75,10 @@ public class TaxonomyRowPersistence extends AbstractPersistence<TaxonomyRow>{
TaxonomyRow row = null;
try {
row = em.getReference(TaxonomyRow.class, id);
}catch (Exception e) {
logger.error("An error occurred in TaxonomyRow - getItemByKey ",e);
} finally {
em.close();
}
@ -86,10 +86,10 @@ public class TaxonomyRowPersistence extends AbstractPersistence<TaxonomyRow>{
logger.trace("getItemByKey return row: "+row.getId() + ", service id: " + row.getServiceId());
else
logger.trace("getItemByKey return null");
//FOR DEBUG
// System.out.println("getItemByKey return: "+row );
return row;
}
@ -131,7 +131,7 @@ public class TaxonomyRowPersistence extends AbstractPersistence<TaxonomyRow>{
query.setFirstResult(startIndex);
query.setMaxResults(offset);
listTaxonomyRow = query.getResultList();
}catch (Exception e) {
logger.error("An error occurred in TaxonomyRow - get List ",e);
}
@ -140,15 +140,15 @@ public class TaxonomyRowPersistence extends AbstractPersistence<TaxonomyRow>{
}
return listTaxonomyRow;
}
@Override
public List<TaxonomyRow> getList(Map<String, String> filterMap, int startIndex, int offset) throws DatabaseServiceException{
EntityManager em = super.createNewManager();
List<TaxonomyRow> listTaxonomyRow = new ArrayList<TaxonomyRow>();
try {
String queryString = "select t from TaxonomyRow t";
if(filterMap!=null && filterMap.size()>0){
queryString+=" where ";
for (String param : filterMap.keySet()) {
@ -156,11 +156,11 @@ public class TaxonomyRowPersistence extends AbstractPersistence<TaxonomyRow>{
queryString+=" t."+param+"="+value;
queryString+=AND;
}
queryString = queryString.substring(0, queryString.lastIndexOf(AND));
}
Query query = em.createQuery(queryString);
if(startIndex>-1)
query.setFirstResult(startIndex);
if(offset>-1)
@ -174,16 +174,16 @@ public class TaxonomyRowPersistence extends AbstractPersistence<TaxonomyRow>{
}
return listTaxonomyRow;
}
@Override
public List<TaxonomyRow> executeTypedQuery(CriteriaQuery cq, int startIndex, int offset) throws DatabaseServiceException{
EntityManager em = super.createNewManager();
List<TaxonomyRow> listOJ = new ArrayList<TaxonomyRow>();
try {
TypedQuery typedQuery = em.createQuery(cq);
if(startIndex>-1)
typedQuery.setFirstResult(startIndex);
if(offset>-1)
@ -195,7 +195,7 @@ public class TaxonomyRowPersistence extends AbstractPersistence<TaxonomyRow>{
} finally {
em.close();
}
return listOJ;
}
@ -204,13 +204,13 @@ public class TaxonomyRowPersistence extends AbstractPersistence<TaxonomyRow>{
public int deleteItemByIdField(String idField) throws DatabaseServiceException{
EntityManager em = super.createNewManager();
int removed = 0;
try {
em.getTransaction().begin();
removed = em.createQuery("DELETE FROM TaxonomyRow t WHERE t."+TaxonomyRow.ID_FIELD+"='"+idField+"'").executeUpdate();
em.getTransaction().commit();
logger.trace("Item "+ idField + " was deleted from TaxonomyRow");
} catch (Exception e) {
logger.error("Error in TaxonomyRow deleteJobById: " + e.getMessage(), e);
@ -221,5 +221,5 @@ public class TaxonomyRowPersistence extends AbstractPersistence<TaxonomyRow>{
return removed;
}
}

84
src/main/java/org/gcube/portlets/user/speciesdiscovery/server/service/ResultItemConverter.java
View File

@ -1,5 +1,5 @@
/**
*
*
*/
package org.gcube.portlets.user.speciesdiscovery.server.service;
@ -23,37 +23,47 @@ import org.gcube.portlets.user.speciesdiscovery.shared.ResultRow;
import org.gcube.portlets.user.speciesdiscovery.shared.Taxon;
import org.gcube.portlets.user.speciesdiscovery.shared.util.NormalizeString;
/**
*
* @author Francesco Mangiacrapa francesco.mangiacrapa@isti.cnr.it
* The Class ResultItemConverter.
*
* @author Francesco Mangiacrapa francesco.mangiacrapa@isti.cnr.it
* Jan 11, 2017
*/
public class ResultItemConverter implements Converter<ResultItem, ResultRow> {
protected Logger logger = Logger.getLogger(ResultItemConverter.class);
protected int id = 0;
protected ASLSession session;
/**
* Instantiates a new result item converter.
*
* @param session the session
*/
public ResultItemConverter(ASLSession session) {
this.session = session;
}
/* (non-Javadoc)
* @see org.gcube.portlets.user.speciesdiscovery.server.stream.Converter#convert(java.lang.Object)
*/
@Override
public ResultRow convert(ResultItem input) throws Exception {
ResultRow row = new ResultRow(id++);
row.setServiceId(input.getId());
//Retrieve Properties
List<ElementProperty> listProperties = input.getProperties();
List<ElementProperty> listProperties = input.getProperties();
//Fill properties
if(listProperties!=null){
for (ElementProperty elementProperty : listProperties)
// row.getProperties().add(new ItemParameter(StringEscapeUtils.escapeSql(elementProperty.getName()), StringEscapeUtils.escapeSql(elementProperty.getValue())));
row.getProperties().add(new ItemParameter(elementProperty.getName(), elementProperty.getValue()));
row.setExistsProperties(true);
}
@ -64,7 +74,7 @@ public class ResultItemConverter implements Converter<ResultItem, ResultRow> {
}
else
row.setScientificNameAuthorship(ConstantsSpeciesDiscovery.NOT_FOUND);
//set credits
if(input.getCredits()!=null && !input.getCredits().isEmpty()){
// row.setCredits(StringEscapeUtils.escapeSql(input.getCredits()));
@ -72,7 +82,7 @@ public class ResultItemConverter implements Converter<ResultItem, ResultRow> {
}
else
row.setCredits(ConstantsSpeciesDiscovery.NOT_FOUND);
//set lsid
if(input.getLsid()!=null && !input.getLsid().isEmpty()){
// row.setLsid(StringEscapeUtils.escapeSql(input.getLsid()));
@ -80,7 +90,7 @@ public class ResultItemConverter implements Converter<ResultItem, ResultRow> {
}
else
row.setLsid(ConstantsSpeciesDiscovery.NOT_FOUND);
if(input.getProvider()!=null && !input.getProvider().isEmpty()){
// row.setDataSourceId(StringEscapeUtils.escapeSql(input.getProvider()));
@ -94,34 +104,34 @@ public class ResultItemConverter implements Converter<ResultItem, ResultRow> {
if (input.getDataSet()!=null) {
DataSet dataSet = input.getDataSet();
if(dataSet.getCitation()==null || dataSet.getCitation().isEmpty())
row.setDataSetCitation("Citation Id not found");
else
// row.setDataSetCitation(StringEscapeUtils.escapeSql(dataSet.getCitation()));
row.setDataSetCitation(dataSet.getCitation());
if(dataSet.getId()==null || dataSet.getId().isEmpty())
row.setDataSetId("Data Set Id not found");
else
row.setDataSetId(dataSet.getId());
if(dataSet.getName()==null || dataSet.getName().isEmpty())
row.setDataSetName("Data Set Name not found");
else
// row.setDataSetName(StringEscapeUtils.escapeSql(dataSet.getName()));
row.setDataSetName(dataSet.getName());
if (input.getDataSet().getDataProvider()!=null) {
DataProvider dataProvider = dataSet.getDataProvider();
if(dataProvider.getId() == null || dataProvider.getId().isEmpty())
row.setDataProviderId("Data Provider Id not found");
else
// row.setDataProviderId(StringEscapeUtils.escapeSql(dataProvider.getId()));
row.setDataProviderId(dataProvider.getId());
if(dataProvider.getName()==null || dataProvider.getName().isEmpty())
row.setDataProviderName("Data Provider not found");
else
@ -129,17 +139,17 @@ public class ResultItemConverter implements Converter<ResultItem, ResultRow> {
row.setDataProviderName(dataProvider.getName());
}
}
if(input.getCommonNames()!=null){
for (org.gcube.data.spd.model.CommonName commonName : input.getCommonNames()){
CommonName com = new CommonName(commonName.getName(), commonName.getLanguage(), row.getId());
// DaoSession.createOrUpdateCommonName(com, session);
row.getCommonNames().add(com);
row.setExistsCommonName(true);
}
}
if (input.getProducts()!=null) {
for (Product product:input.getProducts()) {
@ -152,35 +162,39 @@ public class ResultItemConverter implements Converter<ResultItem, ResultRow> {
}
}
//DEBUG
// System.out.println("Insert row id: "+row.getId());
row.setMatchingTaxon(convertTaxon(input));
row.setBaseTaxonValue(NormalizeString.lowerCaseUpFirstChar(getBaseTaxonValue(TaxonomySearchServiceImpl.BASETAXONOMY,input)));
// row.setMatchingCredits(StringEscapeUtils.escapeSql(input.getCredits()));
row.setMatchingCredits(input.getCredits());
// logger.trace("convert completed: " +row);
return row;
}
/**
* Gets the base taxon value.
*
* @param rank the rank
* @param taxon the taxon
* @return the base taxon value
*/
private String getBaseTaxonValue(String rank, TaxonomyInterface taxon){
while(taxon!=null){
if(taxon.getRank()!=null && taxon.getRank().equalsIgnoreCase(rank))
return taxon.getRank();
taxon = taxon.getParent();
}
return TaxonomySearchServiceImpl.TAXONOMYUNKNOWN;
}
/**
* Convert taxon.
*
* @param taxon the taxon
* @return the list
*/
protected List<Taxon> convertTaxon(TaxonomyInterface taxon)
{
List<Taxon> listTaxon = new ArrayList<Taxon>();
@ -190,9 +204,7 @@ public class ResultItemConverter implements Converter<ResultItem, ResultRow> {
Taxon tax = new Taxon(count++, taxon.getScientificName(), taxon.getCitation(), NormalizeString.lowerCaseUpFirstChar(taxon.getRank()));
listTaxon.add(tax);
taxon = taxon.getParent();
// System.out.println("Insert tax parent id: "+tax.getId());
}
return listTaxon;
return listTaxon;
}
}

1104
src/main/java/org/gcube/portlets/user/speciesdiscovery/server/service/SpeciesService.java
View File

File diff suppressed because it is too large Load Diff

4
src/main/java/org/gcube/portlets/user/speciesdiscovery/server/session/Fetcher.java
View File

@ -79,7 +79,7 @@ public class Fetcher<T extends FetchingElement> implements Runnable, Closeable {
}
else{
countNullItems++;
logger.warn("fetch new row is null!! It is the number: "+countNullItems);
logger.warn("fetch new row is null!! Number of null value/s: "+countNullItems);
if(MAX_CONSECUTIVE_ATTEMPTS_ON_NULL==countNullItems){
logger.warn("Fetched "+MAX_CONSECUTIVE_ATTEMPTS_ON_NULL+ " null rows, MAX ATTEMPTS reached, complete fetch true and closing stream!!");
silentClose();
@ -93,7 +93,7 @@ public class Fetcher<T extends FetchingElement> implements Runnable, Closeable {
}
} catch (Exception e) {
logger.error("Error in add row " + e.getMessage());
logger.error("Error in add row " + e.getMessage(), e);
silentClose();
}

81
src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/DataSource.java
View File

@ -1,41 +1,41 @@
package org.gcube.portlets.user.speciesdiscovery.shared;
import java.io.Serializable;
import javax.persistence.Entity;
import javax.persistence.GeneratedValue;
import javax.persistence.GenerationType;
import javax.persistence.Id;
import com.google.gwt.user.client.rpc.IsSerializable;
/**
*
* @author Francesco Mangiacrapa francesco.mangiacrapa@isti.cnr.it
* The Class DataSource.
*
* @author Francesco Mangiacrapa francesco.mangiacrapa@isti.cnr.it
* Jan 10, 2017
*/
@Entity
public class DataSource implements Serializable{
/**
*
*/
private static final long serialVersionUID = 3373136869904925484L;
public class DataSource implements IsSerializable{
@Id
@GeneratedValue(strategy = GenerationType.IDENTITY)
protected int internalId;
private String id;
private String name;
private String description;
public DataSource() {}
/**
*
* @param id
* @param name
* @param description
* Instantiates a new data source.
*/
public DataSource() {}
/**
* Instantiates a new data source.
*
* @param id the id
* @param name the name
* @param description the description
*/
public DataSource(String id, String name, String description) {
setId(id);
@ -44,38 +44,75 @@ public class DataSource implements Serializable{
}
//Used in Data Source advanced option to create the check list
/**
* Instantiates a new data source.
*
* @param id the id
* @param name the name
*/
public DataSource(String id, String name){
setId(id);
setName(name);
}
/**
* Gets the id.
*
* @return the id
*/
public String getId() {
return id;
}
/**
* Sets the id.
*
* @param id the new id
*/
public void setId(String id) {
this.id = id;
}
/**
* Gets the name.
*
* @return the name
*/
public String getName() {
return name;
}
/**
* Sets the name.
*
* @param name the new name
*/
public void setName(String name) {
this.name = name;
}
/**
* Gets the description.
*
* @return the description
*/
public String getDescription() {
return description;
}
/**
* Sets the description.
*
* @param description the new description
*/
public void setDescription(String description) {
this.description = description;
}
/* (non-Javadoc)
* @see java.lang.Object#toString()
*/
@Override
public String toString() {
StringBuilder builder = new StringBuilder();

54
src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/DataSourceCapability.java
View File

@ -1,23 +1,33 @@
package org.gcube.portlets.user.speciesdiscovery.shared;
import java.io.Serializable;
import java.util.ArrayList;
/**
*
* @author Francesco Mangiacrapa francesco.mangiacrapa@isti.cnr.it
*
*/
public class DataSourceCapability implements Serializable{
import com.google.gwt.user.client.rpc.IsSerializable;
private static final long serialVersionUID = -9083819206898794333L;
/**
* The Class DataSourceCapability.
*
* @author Francesco Mangiacrapa francesco.mangiacrapa@isti.cnr.it
* Jan 10, 2017
*/
public class DataSourceCapability implements IsSerializable{
private ArrayList<SpeciesCapability> listFilters;
private SpeciesCapability capability;
/**
* Instantiates a new data source capability.
*/
public DataSourceCapability() {}
/**
* Instantiates a new data source capability.
*
* @param capability the capability
* @param listFilters the list filters
*/
public DataSourceCapability(SpeciesCapability capability, ArrayList<SpeciesCapability> listFilters) {
super();
this.capability = capability;
@ -25,20 +35,40 @@ public class DataSourceCapability implements Serializable{
}
/**
* Gets the list filters.
*
* @return the list filters
*/
public ArrayList<SpeciesCapability> getListFilters() {
return listFilters;
}
/**
* Sets the list filters.
*
* @param listFilters the new list filters
*/
public void setListFilters(ArrayList<SpeciesCapability> listFilters) {
this.listFilters = listFilters;
}
/**
* Gets the capability.
*
* @return the capability
*/
public SpeciesCapability getCapability() {
return capability;
}
/**
* Sets the capability.
*
* @param capability the new capability
*/
public void setCapability(SpeciesCapability capability) {
this.capability = capability;
}
}

68
src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/DataSourceModel.java
View File

@ -1,57 +1,85 @@
package org.gcube.portlets.user.speciesdiscovery.shared;
import java.io.Serializable;
import java.util.ArrayList;
/**
*
* @author Francesco Mangiacrapa francesco.mangiacrapa@isti.cnr.it
* The Class DataSourceModel.
*
* @author Francesco Mangiacrapa francesco.mangiacrapa@isti.cnr.it
* Jan 10, 2017
*/
public class DataSourceModel extends DataSource {
public class DataSourceModel extends DataSource implements Serializable{
private static final long serialVersionUID = 7399231525793036218L;
private ArrayList<DataSourceCapability> listCapabilities;
private DataSourceRepositoryInfo dataSourceRepositoryInfo;
public DataSourceModel() {}
/**
*
* @param id
* @param name
* @param description
* @param listCapabilities
* @param dsInfo
* Instantiates a new data source model.
*/
public DataSourceModel() {}
/**
* Instantiates a new data source model.
*
* @param id the id
* @param name the name
* @param description the description
* @param listCapabilities the list capabilities
* @param dsInfo the ds info
*/
public DataSourceModel(String id, String name, String description, ArrayList<DataSourceCapability> listCapabilities, DataSourceRepositoryInfo dsInfo) {
super(id,name,description);
setListCapabilities(listCapabilities);
setDataSourceRepositoryInfo(dsInfo);
}
/**
* Sets the data source repository info.
*
* @param dsInfo the new data source repository info
*/
private void setDataSourceRepositoryInfo(DataSourceRepositoryInfo dsInfo) {
this.dataSourceRepositoryInfo = dsInfo;
}
//Used in Data Source advanced option to create the check list
/**
* Instantiates a new data source model.
*
* @param id the id
* @param name the name
*/
public DataSourceModel(String id, String name){
super(id,name);
}
/**
* Gets the list capabilities.
*
* @return the list capabilities
*/
public ArrayList<DataSourceCapability> getListCapabilities() {
return listCapabilities;
}
/**
* Sets the list capabilities.
*
* @param listCapabilities the new list capabilities
*/
public void setListCapabilities(ArrayList<DataSourceCapability> listCapabilities) {
this.listCapabilities = listCapabilities;
}
/**
* Gets the data source repository info.
*
* @return the data source repository info
*/
public DataSourceRepositoryInfo getDataSourceRepositoryInfo() {
return dataSourceRepositoryInfo;
}

92
src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/DataSourceRepositoryInfo.java
View File

@ -1,30 +1,37 @@
package org.gcube.portlets.user.speciesdiscovery.shared;
import java.io.Serializable;
import java.util.Map;
import com.google.gwt.user.client.rpc.IsSerializable;
/**
*
* @author Francesco Mangiacrapa francesco.mangiacrapa@isti.cnr.it
* The Class DataSourceRepositoryInfo.
*
* @author Francesco Mangiacrapa francesco.mangiacrapa@isti.cnr.it
* Jan 10, 2017
*/
public class DataSourceRepositoryInfo implements IsSerializable{
public class DataSourceRepositoryInfo implements Serializable{
/**
*
*/
private static final long serialVersionUID = -4557351371954637191L;
private String logoUrl;
private String pageUrl;
private Map<String, String> properties;
private String name;
private String description;
/**
* Instantiates a new data source repository info.
*/
public DataSourceRepositoryInfo() {}
/**
* Instantiates a new data source repository info.
*
* @param logoUrl the logo url
* @param pageUrl the page url
* @param properties the properties
* @param description the description
*/
public DataSourceRepositoryInfo(String logoUrl, String pageUrl, Map<String,String> properties, String description) {
this.logoUrl = logoUrl;
this.pageUrl = pageUrl;
@ -32,33 +39,90 @@ public class DataSourceRepositoryInfo implements Serializable{
this.description = description;
}
/**
* Gets the logo url.
*
* @return the logo url
*/
public String getLogoUrl() {
return logoUrl;
}
/**
* Sets the logo url.
*
* @param logoUrl the new logo url
*/
public void setLogoUrl(String logoUrl) {
this.logoUrl = logoUrl;
}
/**
* Gets the page url.
*
* @return the page url
*/
public String getPageUrl() {
return pageUrl;
}
/**
* Sets the page url.
*
* @param pageUrl the new page url
*/
public void setPageUrl(String pageUrl) {
this.pageUrl = pageUrl;
}
/**
* Gets the properties.
*
* @return the properties
*/
public Map<String, String> getProperties() {
return properties;
}
/**
* Sets the properties.
*
* @param properties the properties
*/
public void setProperties(Map<String, String> properties) {
this.properties = properties;
}
/**
* Gets the name.
*
* @return the name
*/
public String getName() {
return name;
}
/**
* Gets the description.
*
* @return the description
*/
public String getDescription() {
return description;
}
/**
* Sets the description.
*
* @param description the new description
*/
public void setDescription(String description) {
this.description = description;
}
/* (non-Javadoc)
* @see java.lang.Object#toString()
*/
@Override
public String toString() {
StringBuilder builder = new StringBuilder();
@ -73,5 +137,5 @@ public class DataSourceRepositoryInfo implements Serializable{
builder.append("]");
return builder.toString();
}
}

38
src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/ResultRow.java
View File

@ -1,5 +1,5 @@
/**
*
*
*/
package org.gcube.portlets.user.speciesdiscovery.shared;
@ -17,7 +17,7 @@ import javax.persistence.Id;
import javax.persistence.OneToMany;
/**
*
*
* @author Francesco Mangiacrapa francesco.mangiacrapa@isti.cnr.it
*
*/
@ -48,7 +48,7 @@ public class ResultRow implements FetchingElement, SelectableElement, Serializab
public static final String BASE_TAXON_VALUE = "baseTaxonValue";
public static final String DATAPROVIDER_ID = "dataProviderId";
public static final String DATASOURCE_ID = "dataSourceId";
public static final String KINGDOM_ID = "kingdomID";
public static final String PHYLUM_ID = "phylumID";
public static final String CLASS_ID = "classID";
@ -56,7 +56,7 @@ public class ResultRow implements FetchingElement, SelectableElement, Serializab
public static final String FAMILY_ID = "familyID";
public static final String GENUS_ID = "genusID";
public static final String SPECIES_ID = "speciesID";
public final static String SCIENTIFICNAMEAUTHORSHIP = "scientificNameAuthorship"; //USED
public final static String CREDITS = "credits"; //USED
public final static String LSID = "lsid"; //USED
@ -67,7 +67,7 @@ public class ResultRow implements FetchingElement, SelectableElement, Serializab
@Id
@GeneratedValue(strategy = GenerationType.IDENTITY)
protected int id;
protected boolean selected = false;
protected String dataSourceId;
protected String dataSourceName;
@ -82,10 +82,10 @@ public class ResultRow implements FetchingElement, SelectableElement, Serializab
@OneToMany(cascade=CascadeType.PERSIST, fetch=FetchType.EAGER)
protected List<CommonName> commonNames = new ArrayList<CommonName>();
@OneToMany(cascade=CascadeType.PERSIST, fetch=FetchType.EAGER)
protected List<Taxon> matchingTaxon = new ArrayList<Taxon>();
@OneToMany(cascade=CascadeType.PERSIST, fetch=FetchType.EAGER)
protected List<ItemParameter> properties = new ArrayList<ItemParameter>();
@ -108,17 +108,13 @@ public class ResultRow implements FetchingElement, SelectableElement, Serializab
protected String scientificNameAuthorship;
protected String credits;
protected String lsid;
// protected String propertiesAsXml;
// protected ItemParameterList properties;
protected boolean existsProperties = false;
protected ResultRow() {
}
/**
* @param id
*/
@ -140,7 +136,7 @@ public class ResultRow implements FetchingElement, SelectableElement, Serializab
return id+"";
}
/**
* @return the selected
*/
@ -162,7 +158,7 @@ public class ResultRow implements FetchingElement, SelectableElement, Serializab
public String getDataSourceId() {
return dataSourceId;
}
/**
* @param dataSourceId
@ -407,7 +403,7 @@ public class ResultRow implements FetchingElement, SelectableElement, Serializab
}
/**
*
*
* @return true if there are common names
*/
public boolean existsCommonName() {
@ -415,7 +411,7 @@ public class ResultRow implements FetchingElement, SelectableElement, Serializab
}
/**
*
*
* @param the
* boolean to set
*/
@ -486,7 +482,7 @@ public class ResultRow implements FetchingElement, SelectableElement, Serializab
public void setSpeciesID(String speciesID) {
this.speciesID = speciesID;
}
public String getServiceId() {
return serviceIdField;
}
@ -513,7 +509,7 @@ public class ResultRow implements FetchingElement, SelectableElement, Serializab
}
public void setExistsProperties(boolean b) {
this.existsProperties = b;
this.existsProperties = b;
}
public boolean existsProperties() {
@ -522,7 +518,7 @@ public class ResultRow implements FetchingElement, SelectableElement, Serializab
public List<Taxon> getParents() {
Collections.sort(matchingTaxon);
// for (Taxon t : matchingTaxon) {
// System.out.println("+++ Parent :" +t.getId() + ", name: "+t.getName() +", rank: "+t.getRank());

25
src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/SpeciesCapability.java
View File

@ -1,30 +1,31 @@
package org.gcube.portlets.user.speciesdiscovery.shared;
import com.google.gwt.user.client.rpc.IsSerializable;
public enum SpeciesCapability implements IsSerializable{
public enum SpeciesCapability {
//Filters
FROMDATE("FROMDATE", "Date From"),
TODATE("DATETO", "Date To"),
LOWERBOUND("LOWERBOUND", "Lower Bound"),
FROMDATE("FROMDATE", "Date From"),
TODATE("DATETO", "Date To"),
LOWERBOUND("LOWERBOUND", "Lower Bound"),
UPPERBOUND("UPPERBOUND", "Upper Bound"),
//Capabilities
RESULTITEM("RESULTITEM", "Occurrence"),
TAXONOMYITEM("TAXONOMYITEM", "Taxon"),
OCCURRENCESPOINTS("OCCURRENCESPOINTS", "OccurrencesPoints"),
SYNONYMS("SYNONYMS", "Synonyms"),
UNFOLD("UNFOLD", "Unfold"),
NAMESMAPPING("NAMESMAPPING", "Names Mapping"),
UNKNOWN("UNKNOWN", "unknown");
private String id;
private String name;
private SpeciesCapability(){
private SpeciesCapability(){
}

3
src/main/resources/org/gcube/portlets/user/speciesdiscovery/SpeciesDiscovery.gwt.xml
View File

@ -7,7 +7,8 @@
<!-- Other module inherits -->
<inherits name="com.extjs.gxt.ui.GXT" />
<inherits name="org.gcube.portlets.user.gcubegisviewer.GCubeGisViewer" />
<!-- Used to show a layer via GisViewer -->
<!-- <inherits name="org.gcube.portlets.user.gcubegisviewer.GCubeGisViewer" /> -->
<inherits name="com.allen_sauer.gwt.log.gwt-log-TRACE" />
<set-property name="log_DivLogger" value="DISABLED" />

32
src/main/webapp/WEB-INF/web.xml
View File

@ -36,26 +36,26 @@
</servlet-mapping>
<!-- GisViewer Servlets -->
<servlet>
<servlet-name>GisViewerService</servlet-name>
<servlet-class>org.gcube.portlets.user.gcubegisviewer.server.GCubeGisViewerServletImpl</servlet-class>
</servlet>
<!-- <servlet> -->
<!-- <servlet-name>GisViewerService</servlet-name> -->
<!-- <servlet-class>org.gcube.portlets.user.gcubegisviewer.server.GCubeGisViewerServletImpl</servlet-class> -->
<!-- </servlet> -->
<servlet-mapping>
<servlet-name>GisViewerService</servlet-name>
<url-pattern>/speciesdiscovery/GisViewerService</url-pattern>
</servlet-mapping>
<!-- <servlet-mapping> -->
<!-- <servlet-name>GisViewerService</servlet-name> -->
<!-- <url-pattern>/speciesdiscovery/GisViewerService</url-pattern> -->
<!-- </servlet-mapping> -->
<!-- GISVIEWER MAP GENERATOR -->
<servlet>
<servlet-name>MapGenerator</servlet-name>
<servlet-class>org.gcube.portlets.user.gisviewer.server.MapGenerator</servlet-class>
</servlet>
<!-- <servlet> -->
<!-- <servlet-name>MapGenerator</servlet-name> -->
<!-- <servlet-class>org.gcube.portlets.user.gisviewer.server.MapGenerator</servlet-class> -->
<!-- </servlet> -->
<servlet-mapping>
<servlet-name>MapGenerator</servlet-name>
<url-pattern>/speciesdiscovery/MapGenerator</url-pattern>
</servlet-mapping>
<!-- <servlet-mapping> -->
<!-- <servlet-name>MapGenerator</servlet-name> -->
<!-- <url-pattern>/speciesdiscovery/MapGenerator</url-pattern> -->
<!-- </servlet-mapping> -->
<!-- Workspace Light Tree servlet -->
<!-- <servlet> -->

167
src/test/java/org/gcube/portlets/user/speciesdiscovery/client/DBTester.java
View File

@ -1,30 +1,35 @@
/**
*
*
*/
package org.gcube.portlets.user.speciesdiscovery.client;
import java.sql.Connection;
import java.sql.DriverManager;
import java.sql.ResultSet;
import java.sql.ResultSetMetaData;
import java.sql.SQLException;
import java.sql.Statement;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import javax.naming.Context;
import javax.naming.InitialContext;
import javax.naming.NamingException;
import javax.persistence.EntityManager;
import javax.persistence.EntityManagerFactory;
import javax.persistence.Persistence;
import javax.persistence.Query;
import javax.persistence.TypedQuery;
import javax.persistence.metamodel.EntityType;
import org.apache.log4j.Logger;
import org.gcube.portlets.user.speciesdiscovery.shared.ResultRow;
import org.h2.jdbcx.JdbcDataSource;
/**
* @author Francesco Mangiacrapa francesco.mangiacrapa@isti.cnr.it
* @Nov 11, 2013
*
*
*/
public class DBTester {
@ -33,74 +38,172 @@ public class DBTester {
public static Logger logger = Logger.getLogger(DBTester.class);
public static void main(String[] a) throws Exception {
/*
Class.forName("org.h2.Driver");
Connection conn = DriverManager.getConnection("jdbc:h2:/home/francesco-mangiacrapa/Portal-Bundle2.2/tomcat-6.0.29/persistence/h2dbspecies/h2testusergcubedevsec;create=true", "","");
//Class.forName("org.h2.Driver");
//Connection conn = DriverManager.getConnection("jdbc:h2:/home/francesco-mangiacrapa/Portal-Bundle-3.0.0-3.2.0/tomcat-6.0.29/persistence/h2dbspecies/h2testusergcubedevsec;create=true", "","");
// add application code here
Statement stat = conn.createStatement();
ResultSet rs = stat.executeQuery("select * from TaxonomyRow");
/* Statement stat = conn.createStatement();
ResultSet rs = stat.executeQuery("select * from ResultRow");
ResultSetMetaData meta = rs.getMetaData();
int columnCount = meta.getColumnCount();
while (rs.next())
{
System.out.println("New row");
for (int i = 1; i <= columnCount; i++) {
// System.out.println("ColumName: "+ meta.getColumnName(i));
System.out.println("ColumLabel: "+meta.getColumnLabel(i));
System.out.println(rs.getString(meta.getColumnLabel(i)));
}
System.out.println("\n\n");
}
conn.close();
*/
testJdbcDataSource();
}*/
//testJdbcDataSource();
//String queryString = "SELECT MIN(tax.id) from Taxon tax";
//
// testTypedQuery(queryString, Taxon.class);
getAllEntities();
String queryString = "SELECT *" +
" FROM "+ResultRow.class.getSimpleName()+" r" +
" LEFT OUTER JOIN RESULTROW_TAXON rt";
// " INNER JOIN "+Taxon.class.getSimpleName()+" t";
queryString = "select *" +
" from RESULTROW r JOIN RESULTROW_TAXON rt on r.ID=rt.RESULTROW_ID JOIN TAXON t on t.INTERNALID=rt.MATCHINGTAXON_INTERNALID" +
" where t.RANK = 'Genus' and t.ID IN" +
" (select MIN(tax.ID) from TAXON tax)";
//////
//
// testTypedQuery(queryString, ResultRow.class);
//testQuery(queryString);
testNativeQuery(queryString, ResultRow.class);
}
/**
* @param queryString
* @param class1
*/
private static void testNativeQuery(String queryString, Class<?> className) {
EntityManagerFactory emF = createEntityManagerFactory("/home/francesco-mangiacrapa/Portal-Bundle-3.0.0-3.2.0/tomcat-6.0.29/persistence/h2dbspecies/h2testusergcubedevsec;");
EntityManager em = emF.createEntityManager();
Query query = em.createNativeQuery(queryString, className);
List<Object> listResult = new ArrayList<Object>();
try {
listResult = query.getResultList();
for (Object object : listResult) {
System.out.println(object.toString());
}
} catch (Exception e) {
logger.error("Error in TypedQuery: " + e.getMessage(), e);
} finally {
em.close();
}
}
public static void getAllEntities(){
EntityManagerFactory emF = createEntityManagerFactory("/home/francesco-mangiacrapa/Portal-Bundle-3.0.0-3.2.0/tomcat-6.0.29/persistence/h2dbspecies/h2testusergcubedevsec;");
EntityManager em = emF.createEntityManager();
for (EntityType<?> entity : em.getMetamodel().getEntities()) {
final String className = entity.getName();
System.out.println("Trying select * from: " + className);
Query q = em.createQuery("SELECT c from " + className + " c");
q.getResultList().iterator();
System.out.println("ok: " + className);
}
}
public static void testTypedQuery(String queryString, Class classToReturn){
EntityManagerFactory emF = createEntityManagerFactory("/home/francesco-mangiacrapa/Portal-Bundle-3.0.0-3.2.0/tomcat-6.0.29/persistence/h2dbspecies/h2testusergcubedevsec;");
EntityManager em = emF.createEntityManager();
TypedQuery<Class> tQuery = em.createQuery(queryString, classToReturn);
List<Class> listResult = new ArrayList<Class>();
try {
listResult = tQuery.getResultList();
System.out.println(listResult.toString());
} catch (Exception e) {
logger.error("Error in TypedQuery: " + e.getMessage(), e);
} finally {
em.close();
}
}
public static void testQuery(String queryString){
EntityManagerFactory emF = createEntityManagerFactory("/home/francesco-mangiacrapa/Portal-Bundle-3.0.0-3.2.0/tomcat-6.0.29/persistence/h2dbspecies/h2testusergcubedevsec;");
EntityManager em = emF.createEntityManager();
Query query = em.createQuery(queryString);
List<Object> listResult = new ArrayList<Object>();
try {
listResult = query.getResultList();
System.out.println(listResult.toString());
} catch (Exception e) {
logger.error("Error in TypedQuery: " + e.getMessage(), e);
} finally {
em.close();
}
}
public static void testJdbcDataSource() throws NamingException {
JdbcDataSource ds = new JdbcDataSource();
ds.setURL("jdbc:h2:/home/francesco-mangiacrapa/Portal-Bundle2.2/tomcat-6.0.29/persistence/h2dbspecies/h2testusergcubedevsec;create=true");
Context ctx = new InitialContext();
ctx.bind("java:global/jpa-eclipselink/TaxonomyRow", ds);
// final Context context = EJBContainer.createEJBContainer(p).getContext();
//
//
// Movies movies = (Movies) context.lookup("java:global/jpa-eclipselink/Movies");
try {
Connection conn = ds.getConnection();
ResultSet rs = conn.createStatement().executeQuery("select * from TaxonomyRow");
ResultSetMetaData meta = rs.getMetaData();
int columnCount = meta.getColumnCount();
while (rs.next())
{
System.out.println("New row");
for (int i = 1; i <= columnCount; i++) {
// System.out.println("ColumName: "+ meta.getColumnName(i));
System.out.println("ColumLabel: "+meta.getColumnLabel(i));
System.out.println(rs.getString(meta.getColumnLabel(i)));
}
System.out.println("\n\n");
}
conn.close();
} catch (SQLException e) {
// TODO Auto-generated catch block
e.printStackTrace();

42
src/test/java/org/gcube/portlets/user/speciesdiscovery/client/ListPlugins.java
View File

@ -1,5 +1,5 @@
/**
*
*
*/
package org.gcube.portlets.user.speciesdiscovery.client;
@ -9,44 +9,48 @@ import java.util.List;
import java.util.concurrent.TimeUnit;
import org.gcube.common.scope.api.ScopeProvider;
import org.gcube.data.spd.client.proxies.Classification;
import org.gcube.data.spd.client.proxies.Executor;
import org.gcube.data.spd.client.proxies.Manager;
import org.gcube.data.spd.client.proxies.Occurrence;
import org.gcube.data.spd.client.proxies.ClassificationClient;
import org.gcube.data.spd.client.proxies.ExecutorClient;
import org.gcube.data.spd.client.proxies.ManagerClient;
import org.gcube.data.spd.client.proxies.OccurrenceClient;
import org.gcube.data.spd.model.PluginDescription;
/**
* @author "Federico De Faveri defaveri@isti.cnr.it"
* The Class ListPlugins.
*
* @author Francesco Mangiacrapa francesco.mangiacrapa@isti.cnr.it
* Jan 10, 2017
*/
public class ListPlugins {
protected static Manager call;
protected static Occurrence occurrencesCall;
protected static Classification classificationCall;
protected static Executor executorCall;
protected static ManagerClient call;
protected static OccurrenceClient occurrencesCall;
protected static ClassificationClient classificationCall;
protected static ExecutorClient executorCall;
/**
* @param args
* The main method.
*
* @param args the arguments
*/
public static void main(String[] args) {
String scope = "/gcube/devsec";
ScopeProvider.instance.set(scope);
// this.call = manager().at( URI.create("http://node24.d.d4science.research-infrastructures.eu:9000")).withTimeout(3, TimeUnit.MINUTES).build();
// this.occurrencesCall = occurrences().at( URI.create("http://node24.d.d4science.research-infrastructures.eu:9000")).withTimeout(3, TimeUnit.MINUTES).build();
// this.classificationCall = classification().at( URI.create("http://node24.d.d4science.research-infrastructures.eu:9000")).withTimeout(3, TimeUnit.MINUTES).build();
call = manager().withTimeout(3, TimeUnit.MINUTES).build();
// executorCall = executor().withTimeout(3, TimeUnit.MINUTES).build();
// occurrencesCall = occurrence().withTimeout(3, TimeUnit.MINUTES).build();
// classificationCall = classification().withTimeout(3, TimeUnit.MINUTES).build();
// call = manager().at(URI.create("http://node24.d.d4science.research-infrastructures.eu:9000")).withTimeout(3, TimeUnit.MINUTES).build();
//Manager call = manager().withTimeout(3, TimeUnit.MINUTES).build();
List<PluginDescription> plugins = call.getPluginsDescription();

69
src/test/java/org/gcube/portlets/user/speciesdiscovery/client/ServiceQuery.java
View File

@ -1,5 +1,5 @@
/**
*
*
*/
package org.gcube.portlets.user.speciesdiscovery.client;
@ -10,12 +10,12 @@ import java.util.concurrent.TimeUnit;
import org.gcube.application.framework.core.session.ASLSession;
import org.gcube.application.framework.core.session.SessionManager;
import org.gcube.common.scope.api.ScopeProvider;
import org.gcube.data.spd.client.proxies.Manager;
import org.gcube.data.spd.client.proxies.ManagerClient;
import org.gcube.data.spd.model.exceptions.InvalidQueryException;
import org.gcube.data.spd.model.products.ResultElement;
import org.gcube.data.spd.model.products.ResultItem;
import org.gcube.data.spd.stubs.exceptions.UnsupportedCapabilityException;
import org.gcube.data.spd.stubs.exceptions.UnsupportedPluginException;
import org.gcube.data.spd.model.service.exceptions.UnsupportedCapabilityException;
import org.gcube.data.spd.model.service.exceptions.UnsupportedPluginException;
import org.gcube.data.streams.Stream;
import org.gcube.portlets.user.speciesdiscovery.server.service.ResultItemConverter;
import org.gcube.portlets.user.speciesdiscovery.server.service.StreamIterator;
@ -24,76 +24,81 @@ import org.gcube.portlets.user.speciesdiscovery.server.stream.CloseableIterator;
import org.gcube.portlets.user.speciesdiscovery.server.stream.ConversionIterator;
import org.gcube.portlets.user.speciesdiscovery.shared.ResultRow;
/**
* @author "Federico De Faveri defaveri@isti.cnr.it"
* The Class ServiceQuery.
*
* @author Francesco Mangiacrapa francesco.mangiacrapa@isti.cnr.it
* Jan 10, 2017
*/
public class ServiceQuery {
/**
* @param args
* @throws UnsupportedPluginException
* @throws InvalidQueryException
* @throws UnsupportedCapabilityException
* @throws UnsupportedPluginException
* @throws InvalidQueryException
* @throws UnsupportedCapabilityException
*/
private static String username = "test.user";
/**
* The main method.
*
* @param args the arguments
* @throws InvalidQueryException the invalid query exception
* @throws UnsupportedPluginException the unsupported plugin exception
* @throws UnsupportedCapabilityException the unsupported capability exception
*/
public static void main(String[] args) throws InvalidQueryException, UnsupportedPluginException, UnsupportedCapabilityException {
String scope = "/gcube/devsec";
// String scope = "/d4science.research-infrastructures.eu/gCubeApps/BiodiversityResearchEnvironment"; //Production
ScopeProvider.instance.set(scope);
ASLSession session = SessionManager.getInstance().getASLSession("123", username);
Manager call = manager().withTimeout(3, TimeUnit.MINUTES).build();
ManagerClient call = manager().withTimeout(3, TimeUnit.MINUTES).build();
// Manager call = manager().at(URI.create("http://node24.d.d4science.research-infrastructures.eu:9000")).withTimeout(3, TimeUnit.MINUTES).build();
//Stream<ResultElement> results = call.search("SEARCH BY CN 'shark' RESOLVE WITH OBIS EXPAND WITH ITIS RETURN Product");
// Stream<ResultElement> results = call.search("SEARCH BY CN 'shark' RESOLVE WITH OBIS EXPAND WITH ITIS WHERE coordinate <= 15.12, 16.12 RETURN Product");
// Stream<ResultElement> results = call.search("SEARCH BY SN 'sarda sarda' RESOLVE WITH OBIS EXPAND WITH ITIS WHERE coordinate <= 15.12, 16.12 RETURN Product");
System.out.println("start query...");
Stream<ResultElement> results = call.search("SEARCH BY SN 'Latimeria chalumnae' IN GBIF RETURN Product HAVING xpath(\"//product[type='Occurrence' and count>0]\")");
// Stream<ResultElement> results = call.search("SEARCH BY SN 'Palinurus elephas' IN WoRMS RETURN Taxon");
StreamIterator<ResultElement> input = new StreamIterator<ResultElement>(results);
System.out.println("Results from service...");
int i=0;
while(results.hasNext()) {
ResultElement elem = results.next();
System.out.println(++i +") el: "+elem.getId() +" type: "+elem.getType().name());
}
System.out.println("Results from conversion...");
ConversionIterator<ResultElement, ResultItem> caster = buildCaster(input);
//from ResultItem to ResultRow
ResultItemConverter converter = new ResultItemConverter(session);
ConversionIterator<ResultItem, ResultRow> inputConverter = new ConversionIterator<ResultItem, ResultRow>(caster, converter);
while (inputConverter.hasNext()) {
ResultRow row = inputConverter.next();
System.out.println(++i +") row: "+row);
}
results.close();
System.out.println("DONE");
}
/**
* Builds the caster.
*
* @param <I> the generic type
* @param <O> the generic type
* @param input the input
* @return the conversion iterator
*/
protected static <I,O> ConversionIterator<I, O> buildCaster(CloseableIterator<I> input)
{
{
CastConverter<I, O> elementConverter = new CastConverter<I, O>();
ConversionIterator<I, O> caster = new ConversionIterator<I, O>(input, elementConverter);
return caster;