gCubeSystem
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species-discovery
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Projet merged with private version at revision 83976 

git-svn-id: http://svn.research-infrastructures.eu/public/d4science/gcube/trunk/portlets/user/speciesdiscovery@83979 82a268e6-3cf1-43bd-a215-b396298e98cf
This commit is contained in:
Francesco Mangiacrapa 2013-10-24 10:52:34 +00:00
parent cf85009708
commit c234e93a19
32 changed files with 2815 additions and 722 deletions
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2
distro/README
View File

@ -17,7 +17,7 @@ Authors
Version and Release Date
------------------------
v. 3.3.0
v. 3.5.0
Description
-----------

12
distro/changelog.xml
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@ -1,4 +1,16 @@
<ReleaseNotes>
<Changeset
component="org.gcube.application.speciesmanagement.speciesdiscovery.3-5-0"
date="24-10-2013">
<Change>Portlet updated to support GWT 2.5.1</Change>
<Change>Ticket 2224: was implemented</Change>
</Changeset>
<Changeset
component="org.gcube.application.speciesmanagement.speciesdiscovery.3-4-0"
date="06-09-2013">
<Change>Enhancements on GUI of SPD portlet was realized (view last query, new expand button are available)</Change>
<Change>The functionalities was updated in order to fit the changes in the service client. New advanced options are now available: "Expand with synonyms", "Unfold the taxa group by".</Change>
</Changeset>
<Changeset
component="org.gcube.application.speciesmanagement.speciesdiscovery.3-3-0"
date="09-07-2013">

16
pom.xml
View File

@ -67,6 +67,14 @@
<scope>provided</scope>
</dependency>
<dependency>
<groupId>com.sencha.gxt</groupId>
<artifactId>gxt</artifactId>
<version>2.2.5</version>
<scope>provided</scope>
</dependency>
<!-- SPD service dependecies -->
<dependency>
<groupId>org.gcube.data.spd</groupId>
@ -185,12 +193,10 @@
<!-- <scope>provided</scope> -->
</dependency>
<!-- ACCESS-LOGGER -->
<dependency>
<groupId>com.sencha.gxt</groupId>
<artifactId>gxt</artifactId>
<version>2.2.5</version>
<scope>provided</scope>
<groupId>org.gcube.applicationsupportlayer</groupId>
<artifactId>accesslogger</artifactId>
</dependency>
<!-- FWS -->

7
src/main/java/org/gcube/portlets/user/speciesdiscovery/client/ConstantsSpeciesDiscovery.java
View File

@ -73,7 +73,8 @@ public final class ConstantsSpeciesDiscovery {
public static final String NULL = "null";
public static final String UNDEFINED = "Undefined";
public static final String NOT_FOUND = "not found";
public static int LIMIT_ITEM_DETAILS = 100;
public static int RESULT_ROW_LIMIT_ITEM_DETAILS = 250;
public static int TAXONOMY_LIMIT_ITEMS_DETAILS = 100;
//USED IN VIEW DETAILSWINDOW
public static final String THE_MAX_NUMBER_OF_ITEMS_DISPLAYABLE_IS = "The max number of items displayable is ";
@ -111,5 +112,9 @@ public final class ConstantsSpeciesDiscovery {
public static final String DARWIN_CORE_ARCHIVE = "Darwin Core Archive";
public static final String SAVES_TAXONOMY_CHILDREN_FROM_RESULT = "Saves taxonomy children from result.";
public static final String SAVE_TAXONOMY_CHILDREN = "Save Taxonomy Children";
//SERVLETS
public static final String RESULT_ROW_TABLE = "ResultRowTable";
public static final String TAXONOMY_ROW_TABLE = "TaxonomyRowTable";
}

14
src/main/java/org/gcube/portlets/user/speciesdiscovery/client/SearchController.java
View File

@ -82,6 +82,7 @@ import org.gcube.portlets.user.speciesdiscovery.shared.DataSourceModel;
import org.gcube.portlets.user.speciesdiscovery.shared.DownloadState;
import org.gcube.portlets.user.speciesdiscovery.shared.JobOccurrencesModel;
import org.gcube.portlets.user.speciesdiscovery.shared.JobTaxonomyModel;
import org.gcube.portlets.user.speciesdiscovery.shared.LightTaxonomyRow;
import org.gcube.portlets.user.speciesdiscovery.shared.OccurrencesSaveEnum;
import org.gcube.portlets.user.speciesdiscovery.shared.OccurrencesStatus;
import org.gcube.portlets.user.speciesdiscovery.shared.ResultRow;
@ -91,7 +92,6 @@ import org.gcube.portlets.user.speciesdiscovery.shared.SearchFilters;
import org.gcube.portlets.user.speciesdiscovery.shared.SearchResultType;
import org.gcube.portlets.user.speciesdiscovery.shared.SearchType;
import org.gcube.portlets.user.speciesdiscovery.shared.SpeciesCapability;
import org.gcube.portlets.user.speciesdiscovery.shared.TaxonomyRow;
import org.gcube.portlets.user.speciesdiscovery.shared.filter.ResultFilter;
import org.gcube.portlets.user.speciesdiscovery.shared.util.SearchTermValidator;
import org.gcube.portlets.widgets.lighttree.client.ItemType;
@ -222,11 +222,11 @@ public class SearchController {
boolean selected = updateAllRowSelectionEvent.getSelectionValue();
String msgRow = result.intValue()==1?"row":"rows";
String msgRow = result.intValue()==1?"row was":"rows were";
String msgSel = selected==true?"selected":"deselected";
Info.display("Info", result.intValue()+" "+msgRow+" was "+msgSel);
Info.display("Info", result.intValue()+" "+msgRow+" "+msgSel);
if(updateAllRowSelectionEvent.getSearchType().equals(SearchResultType.SPECIES_PRODUCT))
searchBorderLayoutPanel.getSpeciesCenterPanel().getResultRowPanel().selectAllRows(selected);
@ -362,8 +362,10 @@ public class SearchController {
public void onSuccess(List<JobOccurrencesModel> result) {
if(result!=null){
if(result.size()>0){
Info.display("Species Occurrence Job", result.size() + " occurrence job was submitted");
int jobs = result.size();
if(jobs>0){
String msg = jobs==1? "was":"were";
Info.display("Species Occurrence Job", result.size() + " occurrence job "+msg+" submitted");
excecuteGetJobs(SearchResultType.OCCURRENCE_POINT, false);
searchBorderLayoutPanel.getSpeciesSouthPanel().setIconOccurrenceByCounter(result.size());
}
@ -428,7 +430,7 @@ public class SearchController {
case BYCHILDREN:
TaxonomyRow taxonomy = createSpeciesJobEvent.getTaxonomy();
LightTaxonomyRow taxonomy = createSpeciesJobEvent.getTaxonomy();
SpeciesDiscovery.taxonomySearchService.createTaxonomyJobByChildren(taxonomy.getServiceId(), taxonomy.getName(), taxonomy.getRank(), createSpeciesJobEvent.getDataSourceName(), new AsyncCallback<JobTaxonomyModel>() {

807
src/main/java/org/gcube/portlets/user/speciesdiscovery/client/cluster/TabItemForTaxonomyRow.java
View File

@ -2,20 +2,16 @@ package org.gcube.portlets.user.speciesdiscovery.client.cluster;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.List;
import org.gcube.portlets.user.speciesdiscovery.client.SpeciesDiscovery;
import org.gcube.portlets.user.speciesdiscovery.client.resources.Resources;
import org.gcube.portlets.user.speciesdiscovery.client.util.TaxonomyGridField;
import org.gcube.portlets.user.speciesdiscovery.shared.CommonName;
import org.gcube.portlets.user.speciesdiscovery.shared.ItemParameter;
import org.gcube.portlets.user.speciesdiscovery.shared.LightTaxonomyRow;
import org.gcube.portlets.user.speciesdiscovery.shared.TaxonomyRow;
import org.gcube.portlets.user.speciesdiscovery.shared.util.NormalizeString;
import com.allen_sauer.gwt.log.client.Log;
import com.extjs.gxt.ui.client.widget.ContentPanel;
import com.extjs.gxt.ui.client.widget.Html;
import com.extjs.gxt.ui.client.widget.Info;
import com.extjs.gxt.ui.client.widget.LayoutContainer;
import com.extjs.gxt.ui.client.widget.TabPanel;
@ -47,9 +43,9 @@ public class TabItemForTaxonomyRow {
// private List<TaxonomyRow> parents = null;
private TablesForTaxonomyRow tablesForTaxonomyRow;
private TaxonomyRow currentTaxonomy;
private LightTaxonomyRow currentTaxonomy;
public void setCurrentTaxonomy(TaxonomyRow taxonomy){
public void setCurrentTaxonomy(LightTaxonomyRow taxonomy){
this.currentTaxonomy = taxonomy;
}
@ -68,7 +64,7 @@ public class TabItemForTaxonomyRow {
* @return
*/
public VerticalPanel getPanelClassificationForTaxonomy(TaxonomyRow taxonomy, String dataSource, boolean isNewTab){
public VerticalPanel getPanelClassificationForTaxonomy(LightTaxonomyRow taxonomy, String dataSource, boolean isNewTab){
VerticalPanel vpClassification = new VerticalPanel();
vpClassification.setSpacing(5);
@ -97,7 +93,7 @@ public class TabItemForTaxonomyRow {
* @param isNewTab
* @param parentIndex
*/
public void createPanelForParentTaxonomy(TaxonomyRow taxon, VerticalPanel vpClassification, String taxonomyServiceId, boolean isNewTab, String dataSource, int parentIndex){
public void createPanelForParentTaxonomy(LightTaxonomyRow taxon, VerticalPanel vpClassification, String taxonomyServiceId, boolean isNewTab, String dataSource, int parentIndex){
if(taxon==null)
return;
@ -128,7 +124,7 @@ public class TabItemForTaxonomyRow {
}
}
private void loadChildrenListOfItem(final VerticalPanel vpClassification, final TaxonomyRow taxonomyItem, final String dataSource, final String parentName, final int parentIndex){
private void loadChildrenListOfItem(final VerticalPanel vpClassification, final LightTaxonomyRow taxonomyItem, final String dataSource, final String parentName, final int parentIndex){
final ContentPanel cp = new ContentPanel();
cp.setId("cp" + taxonomyItem.getId());
@ -146,10 +142,10 @@ public class TabItemForTaxonomyRow {
// printParent = printParent.getParent();
// }
SpeciesDiscovery.taxonomySearchService.loadListChildByParentId(taxonomyItem.getServiceId(), new AsyncCallback<ArrayList<TaxonomyRow>>() {
SpeciesDiscovery.taxonomySearchService.loadListChildrenByParentId(taxonomyItem.getServiceId(), new AsyncCallback<ArrayList<LightTaxonomyRow>>() {
@Override
public void onSuccess(ArrayList<TaxonomyRow> result) {
public void onSuccess(ArrayList<LightTaxonomyRow> result) {
Log.trace("Children returned in client: " + result.size() + " for parentName " +parentName);
LayoutContainer lc = new LayoutContainer();
@ -166,7 +162,7 @@ public class TabItemForTaxonomyRow {
if(result.size()>0){
for (int i=0; i<result.size()-1; i++) {
TaxonomyRow taxonomy = result.get(i);
LightTaxonomyRow taxonomy = result.get(i);
// //FOR DEBUG
// System.out.println("child "+taxonomy);
@ -184,7 +180,7 @@ public class TabItemForTaxonomyRow {
lc.add(comma);
}
TaxonomyRow taxonomy = result.get(result.size()-1);
LightTaxonomyRow taxonomy = result.get(result.size()-1);
if(!setRank)
setRank = replaceLabelRank(hp, labelRank, taxonomy.getRank());
@ -252,7 +248,7 @@ public class TabItemForTaxonomyRow {
* @return
*/
private Anchor getAnchorByTaxonomy(final TaxonomyRow taxon, final String dataSource, final int parentIndex)
private Anchor getAnchorByTaxonomy(final LightTaxonomyRow taxon, final String dataSource, final int parentIndex)
{
Anchor anchor = null;
@ -273,11 +269,11 @@ public class TabItemForTaxonomyRow {
}
else if(parentIndex == -1){ //items loaded from get children - the current Taxonomy item is the parent
List<TaxonomyRow> list = new ArrayList<TaxonomyRow>();
List<LightTaxonomyRow> list = new ArrayList<LightTaxonomyRow>();
list.add(currentTaxonomy);
list.addAll(currentTaxonomy.getParents());
System.out.println("parentIndex == -1");
// System.out.println("parentIndex == -1");
printParents(taxon);
taxon.setParent(list);
}
@ -295,11 +291,11 @@ public class TabItemForTaxonomyRow {
}
void printParents(TaxonomyRow taxon){
void printParents(LightTaxonomyRow taxon){
System.out.println("principal "+taxon.getName());
int i = 0;
for (TaxonomyRow tax : taxon.getParents()) {
for (LightTaxonomyRow tax : taxon.getParents()) {
System.out.println(++i + " parent name " + tax.getName());
}
}
@ -318,346 +314,346 @@ public class TabItemForTaxonomyRow {
return label;
}
public Html getHTMLTableForTaxonomy(TaxonomyRow row, boolean isNewTab){
//Init values
String dataProviderName = "";
String dataSetCitation= "";
String matchingAccordionTo= "";
String rank= "";
// String matchingCredits= "";
String statusName = "";
String dateModified = "";
String statusRemark = "";
String author = "";
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.getAuthor()!=null) author = row.getAuthor();
if(row.getLsid()!=null) lsid = row.getLsid();
if(row.getCredits()!=null) credits = row.getCredits();
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(isNewTab){
if(row.getCommonNames()!=null){
for (CommonName comName : row.getCommonNames()) {
commonNames+= "<b>"+comName.getName()+"</b>" +" ("+comName.getLanguage()+") - ";
}
}
// public Html getHTMLTableForTaxonomy(TaxonomyRow row, boolean isNewTab){
//
// //Init values
// String dataProviderName = "";
// String dataSetCitation= "";
// String matchingAccordionTo= "";
// String rank= "";
//// String matchingCredits= "";
//
// String statusName = "";
// String dateModified = "";
// String statusRemark = "";
//
// String author = "";
// 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.getAuthor()!=null) author = row.getAuthor();
//
// if(row.getLsid()!=null) lsid = row.getLsid();
//
// if(row.getCredits()!=null) credits = row.getCredits();
//
//
// 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>";
// }
String table = "<table class=\"imagetable\">";
// if(isNewTab)
table+=
"<tr>" +
" <td class=\"title\">"+TaxonomyGridField.COMMON_NAMES.getName()+" (Language)</td>" +
" <td>"+commonNames+"</td>" +
"</tr>";
table+="<tr>" +
" <td class=\"title\">"+TaxonomyGridField.STATUSREFNAME.getName()+"</td>" +
" <td>"+statusName+"</td>" +
"</tr>" +
"<tr>" +
" <td class=\"title\">"+TaxonomyGridField.STATUS_REMARKS.getName()+"</td>" +
" <td>"+statusRemark+"</td>" +
"</tr>" +
"<tr>" +
" <td class=\"title\">"+TaxonomyGridField.DATASOURCE.getName()+"</td>" +
" <td>"+dataProviderName+"</td>" +
"</tr>" +
"<tr>" +
" <td class=\"title\">"+TaxonomyGridField.DATEMODIFIED.getName()+"</td>" +
" <td>"+dateModified+"</td>" +
"</tr>" +
"<tr>" +
" <td class=\"title\">"+TaxonomyGridField.MATCHING_RANK.getName()+"</td>" +
" <td>"+rank+"</td>" +
"</tr>" +
"<tr>" +
" <td class=\"title\">"+TaxonomyGridField.CITATION.getName()+"</td>" +
" <td>"+dataSetCitation+"</td>" +
"</tr>" +
// "<tr>" +
// " <td class=\"title\">"+TaxonomyGridField.MATCHING_AUTHOR.getName()+"</td>" +
// " <td>"+matchingAccordionTo+"</td>" +
//
//
// //Create list common name
// String commonNames = "";
//
//// if(isNewTab){
// 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>" +
// " <td class=\"title\">"+TaxonomyGridField.COMMON_NAMES.getName()+" (Language)</td>" +
// " <td>"+commonNames+"</td>" +
// "</tr>";
//
//
// table+="<tr>" +
// " <td class=\"title\">"+TaxonomyGridField.STATUSREFNAME.getName()+"</td>" +
// " <td>"+statusName+"</td>" +
// "</tr>" +
"<tr>" +
" <td class=\"title\">"+TaxonomyGridField.LSID.getName()+"</td>" +
" <td>"+lsid+"</td>" +
"</tr>" +
"<tr>" +
" <td class=\"title\">"+TaxonomyGridField.AUTHOR.getName()+"</td>" +
" <td>"+author+"</td>" +
"</tr>" +
"<tr>" +
" <td class=\"title\">"+TaxonomyGridField.CREDITS.getName()+"</td>" +
" <td>"+credits+"</td>" +
"</tr>" +
"<tr>" +
" <td class=\"title\">"+TaxonomyGridField.PROPERTIES.getName()+"</td>" +
" <td>"+propertiesHtml+"</td>" +
"</tr>" +
"</table>";
return new Html(table);
}
// "<tr>" +
// " <td class=\"title\">"+TaxonomyGridField.STATUS_REMARKS.getName()+"</td>" +
// " <td>"+statusRemark+"</td>" +
// "</tr>" +
// "<tr>" +
// " <td class=\"title\">"+TaxonomyGridField.DATASOURCE.getName()+"</td>" +
// " <td>"+dataProviderName+"</td>" +
// "</tr>" +
// "<tr>" +
// " <td class=\"title\">"+TaxonomyGridField.DATEMODIFIED.getName()+"</td>" +
// " <td>"+dateModified+"</td>" +
// "</tr>" +
// "<tr>" +
// " <td class=\"title\">"+TaxonomyGridField.MATCHING_RANK.getName()+"</td>" +
// " <td>"+rank+"</td>" +
// "</tr>" +
// "<tr>" +
// " <td class=\"title\">"+TaxonomyGridField.CITATION.getName()+"</td>" +
// " <td>"+dataSetCitation+"</td>" +
// "</tr>" +
//// "<tr>" +
//// " <td class=\"title\">"+TaxonomyGridField.MATCHING_AUTHOR.getName()+"</td>" +
//// " <td>"+matchingAccordionTo+"</td>" +
//// "</tr>" +
// "<tr>" +
// " <td class=\"title\">"+TaxonomyGridField.LSID.getName()+"</td>" +
// " <td>"+lsid+"</td>" +
// "</tr>" +
// "<tr>" +
// " <td class=\"title\">"+TaxonomyGridField.AUTHOR.getName()+"</td>" +
// " <td>"+author+"</td>" +
// "</tr>" +
// "<tr>" +
// " <td class=\"title\">"+TaxonomyGridField.CREDITS.getName()+"</td>" +
// " <td>"+credits+"</td>" +
// "</tr>" +
//
// "<tr>" +
// " <td class=\"title\">"+TaxonomyGridField.PROPERTIES.getName()+"</td>" +
// " <td>"+propertiesHtml+"</td>" +
// "</tr>" +
//
// "</table>";
// return new Html(table);
//
// }
//
// public FlexTable getHTMLTableForTaxonomyWithRef(final LightTaxonomyRow row,boolean isNewTab, final String dataSource) {
//
// // Init values
// String dataProviderName = "";
// String dataSetCitation = "";
// String matchingAccordionTo = "";
// String rank = "";
// // String matchingCredits= "";
//
// String statusName = "";
// String dateModified = "";
// String statusRemark = "";
//
// String author = "";
// String lsid = "";
// String credits = "";
//
// String refId = null;
//
// 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.getAuthor() != null)
// author = row.getAuthor();
//
// if (row.getLsid() != null)
// lsid = row.getLsid();
//
// if (row.getCredits() != null)
// credits = row.getCredits();
//
// if (row.getStatusRefId() != null && !row.getStatusRefId().isEmpty())
// refId = row.getStatusRefId();
//
// 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(isNewTab){
// if (row.getCommonNames() != null) {
// for (CommonName comName : row.getCommonNames()) {
// commonNames += "<b>" + comName.getName() + "</b>" + " ("
// + comName.getLanguage() + ") - ";
// }
// }
// // }
//
// final FlexTable flexTable = new FlexTable();
//
// flexTable.setStyleName("imagetable");
//
// flexTable.setWidget(0, 0,new Label(TaxonomyGridField.COMMON_NAMES.getName()));
// flexTable.setWidget(0, 1, new Html(commonNames));
//
// flexTable.setWidget(1, 0,new Label(TaxonomyGridField.STATUSREFNAME.getName()));
// flexTable.setWidget(1, 1, new Label(statusName));
//
// if (refId != null) {
//
// final String status;
//
// if(!statusRemark.isEmpty())
// status = statusRemark;
// else
// status = statusName;
//
// final String referenceId = refId;
//
// flexTable.setWidget(2, 0, new Label(TaxonomyGridField.STATUS_REMARKS.getName()));
//
// AbstractImagePrototype synonyms = AbstractImagePrototype.create(Resources.INSTANCE.getSearch());
//
// final Image imageStatusRemark = synonyms.createImage();
// imageStatusRemark.setStyleName("image-load-synonyms");
// imageStatusRemark.setAltText("show accepted name");
// imageStatusRemark.setTitle("show accepted name");
// final LayoutContainer layoutContainer = new LayoutContainer();
//
// final Label labelStatusRemark = new Label(statusRemark);
// labelStatusRemark.addStyleName("status-of");
// layoutContainer.add(labelStatusRemark);
//
// imageStatusRemark.addClickHandler(new ClickHandler() {
//
// @Override
// public void onClick(ClickEvent event) {
// flexTable.remove(layoutContainer);
// if(row.getParents().size()>0)
// getTaxonomyByReferenceId(flexTable, 2, 1, status, referenceId, dataSource, row.getParents());
//
// }
// });
//
// layoutContainer.add(labelStatusRemark);
// layoutContainer.add(imageStatusRemark);
//
// flexTable.setWidget(2, 1, layoutContainer);
//
// } else {
// flexTable.setWidget(2, 0, new Label(TaxonomyGridField.STATUS_REMARKS.getName()));
// flexTable.setWidget(2, 1, new Label(statusRemark));
// }
//
//
// //Create row get synonyms
// flexTable.setWidget(3, 0,new Label(TaxonomyGridField.SYNONYMS.getName()));
//
// AbstractImagePrototype synonyms = AbstractImagePrototype.create(Resources.INSTANCE.getSearch());
//
// final Image imageSynonyms = synonyms.createImage();
// imageSynonyms.setStyleName("image-load-synonyms");
// imageSynonyms.setAltText("show synonyms");
// imageSynonyms.setTitle("show synonyms");
//
// imageSynonyms.addClickHandler(new ClickHandler() {
//
// @Override
// public void onClick(ClickEvent event) {
// flexTable.remove(imageSynonyms);
//
//// DEBUG
//// System.out.println("getSynonyms of "+row.getName() + " serviceId "+row.getServiceId());
//
//
// if(row.getParents().size()>0){
//
//
// //TODO
// getSynonymsByReferenceId(flexTable, 3, 1, row.getServiceId(),dataSource, row.getParents());
//
//
//
// }
// }
// });
//
// flexTable.setWidget(3, 1, imageSynonyms);
//
//
// flexTable.setWidget(4, 0,new Label(TaxonomyGridField.DATASOURCE.getName()));
// flexTable.setWidget(4, 1, new Label(dataProviderName));
//
// flexTable.setWidget(5, 0,new Label(TaxonomyGridField.DATEMODIFIED.getName()));
// flexTable.setWidget(5, 1, new Label(dateModified));
//
// flexTable.setWidget(6, 0,
// new Label(TaxonomyGridField.MATCHING_RANK.getName()));
// flexTable.setWidget(6, 1, new Label(rank));
//
// flexTable.setWidget(7, 0,
// new Label(TaxonomyGridField.CITATION.getName()));
// flexTable.setWidget(7, 1, new Label(dataSetCitation));
//
// flexTable.setWidget(8, 0, new Label(TaxonomyGridField.LSID.getName()));
// flexTable.setWidget(8, 1, new Label(lsid));
//
// flexTable
// .setWidget(9, 0, new Label(TaxonomyGridField.AUTHOR.getName()));
// flexTable.setWidget(9, 1, new Label(author));
//
// flexTable.setWidget(10, 0,
// new Label(TaxonomyGridField.CREDITS.getName()));
// flexTable.setWidget(10, 1, new Label(credits));
//
// flexTable.setWidget(11, 0,
// new Label(TaxonomyGridField.PROPERTIES.getName()));
// flexTable.setWidget(11, 1, new Html(propertiesHtml));
//
// for (int i = 0; i < flexTable.getRowCount(); i++) {
// flexTable.getFlexCellFormatter().setStyleName(i, 0, "title");
// }
//
// return flexTable;
//
// }
public FlexTable getHTMLTableForTaxonomyWithRef(final TaxonomyRow row,boolean isNewTab, final String dataSource) {
// Init values
String dataProviderName = "";
String dataSetCitation = "";
String matchingAccordionTo = "";
String rank = "";
// String matchingCredits= "";
String statusName = "";
String dateModified = "";
String statusRemark = "";
String author = "";
String lsid = "";
String credits = "";
String refId = null;
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.getAuthor() != null)
author = row.getAuthor();
if (row.getLsid() != null)
lsid = row.getLsid();
if (row.getCredits() != null)
credits = row.getCredits();
if (row.getStatusRefId() != null && !row.getStatusRefId().isEmpty())
refId = row.getStatusRefId();
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(isNewTab){
if (row.getCommonNames() != null) {
for (CommonName comName : row.getCommonNames()) {
commonNames += "<b>" + comName.getName() + "</b>" + " ("
+ comName.getLanguage() + ") - ";
}
}
// }
final FlexTable flexTable = new FlexTable();
flexTable.setStyleName("imagetable");
flexTable.setWidget(0, 0,new Label(TaxonomyGridField.COMMON_NAMES.getName()));
flexTable.setWidget(0, 1, new Html(commonNames));
flexTable.setWidget(1, 0,new Label(TaxonomyGridField.STATUSREFNAME.getName()));
flexTable.setWidget(1, 1, new Label(statusName));
if (refId != null) {
final String status;
if(!statusRemark.isEmpty())
status = statusRemark;
else
status = statusName;
final String referenceId = refId;
flexTable.setWidget(2, 0, new Label(TaxonomyGridField.STATUS_REMARKS.getName()));
AbstractImagePrototype synonyms = AbstractImagePrototype.create(Resources.INSTANCE.getSearch());
final Image imageStatusRemark = synonyms.createImage();
imageStatusRemark.setStyleName("image-load-synonyms");
imageStatusRemark.setAltText("show accepted name");
imageStatusRemark.setTitle("show accepted name");
final LayoutContainer layoutContainer = new LayoutContainer();
final Label labelStatusRemark = new Label(statusRemark);
labelStatusRemark.addStyleName("status-of");
layoutContainer.add(labelStatusRemark);
imageStatusRemark.addClickHandler(new ClickHandler() {
@Override
public void onClick(ClickEvent event) {
flexTable.remove(layoutContainer);
if(row.getParents().size()>0)
getTaxonomyByReferenceId(flexTable, 2, 1, status, referenceId, dataSource, row.getParents());
}
});
layoutContainer.add(labelStatusRemark);
layoutContainer.add(imageStatusRemark);
flexTable.setWidget(2, 1, layoutContainer);
} else {
flexTable.setWidget(2, 0, new Label(TaxonomyGridField.STATUS_REMARKS.getName()));
flexTable.setWidget(2, 1, new Label(statusRemark));
}
//Create row get synonyms
flexTable.setWidget(3, 0,new Label(TaxonomyGridField.SYNONYMS.getName()));
AbstractImagePrototype synonyms = AbstractImagePrototype.create(Resources.INSTANCE.getSearch());
final Image imageSynonyms = synonyms.createImage();
imageSynonyms.setStyleName("image-load-synonyms");
imageSynonyms.setAltText("show synonyms");
imageSynonyms.setTitle("show synonyms");
imageSynonyms.addClickHandler(new ClickHandler() {
@Override
public void onClick(ClickEvent event) {
flexTable.remove(imageSynonyms);
// DEBUG
// System.out.println("getSynonyms of "+row.getName() + " serviceId "+row.getServiceId());
if(row.getParents().size()>0){
//TODO
getSynonymsByReferenceId(flexTable, 3, 1, row.getServiceId(),dataSource, row.getParents());
}
}
});
flexTable.setWidget(3, 1, imageSynonyms);
flexTable.setWidget(4, 0,new Label(TaxonomyGridField.DATASOURCE.getName()));
flexTable.setWidget(4, 1, new Label(dataProviderName));
flexTable.setWidget(5, 0,new Label(TaxonomyGridField.DATEMODIFIED.getName()));
flexTable.setWidget(5, 1, new Label(dateModified));
flexTable.setWidget(6, 0,
new Label(TaxonomyGridField.MATCHING_RANK.getName()));
flexTable.setWidget(6, 1, new Label(rank));
flexTable.setWidget(7, 0,
new Label(TaxonomyGridField.CITATION.getName()));
flexTable.setWidget(7, 1, new Label(dataSetCitation));
flexTable.setWidget(8, 0, new Label(TaxonomyGridField.LSID.getName()));
flexTable.setWidget(8, 1, new Label(lsid));
flexTable
.setWidget(9, 0, new Label(TaxonomyGridField.AUTHOR.getName()));
flexTable.setWidget(9, 1, new Label(author));
flexTable.setWidget(10, 0,
new Label(TaxonomyGridField.CREDITS.getName()));
flexTable.setWidget(10, 1, new Label(credits));
flexTable.setWidget(11, 0,
new Label(TaxonomyGridField.PROPERTIES.getName()));
flexTable.setWidget(11, 1, new Html(propertiesHtml));
for (int i = 0; i < flexTable.getRowCount(); i++) {
flexTable.getFlexCellFormatter().setStyleName(i, 0, "title");
}
return flexTable;
}
public void getSynonymsByReferenceId(FlexTable flexTable, int row, int col, String refId, final String dataSource, final List<TaxonomyRow> parents){
public void getSynonymsByReferenceId(FlexTable flexTable, int row, int col, String refId, final String dataSource, final List<LightTaxonomyRow> parents){
final LayoutContainer layoutContainer = new LayoutContainer();
final Image loading = AbstractImagePrototype.create(Resources.INSTANCE.loadingBalls()).createImage();
@ -665,7 +661,7 @@ public class TabItemForTaxonomyRow {
flexTable.setWidget(row, col, layoutContainer);
SpeciesDiscovery.taxonomySearchService.retrieveSynonymsByRefId(refId, new AsyncCallback<List<TaxonomyRow>>() {
SpeciesDiscovery.taxonomySearchService.retrieveSynonymsByRefId(refId, new AsyncCallback<List<LightTaxonomyRow>>() {
@Override
public void onFailure(Throwable caught) {
@ -675,7 +671,7 @@ public class TabItemForTaxonomyRow {
}
@Override
public void onSuccess(List<TaxonomyRow> result) {
public void onSuccess(List<LightTaxonomyRow> result) {
Log.trace("getReferenceById return " +result.size() + " items");
// System.out.println("getReferenceById return " +result.size() + " items");
@ -687,7 +683,7 @@ public class TabItemForTaxonomyRow {
if(result.size()>0){
for (int i=0; i<result.size()-1; i++) {
TaxonomyRow taxonomy = result.get(i);
LightTaxonomyRow taxonomy = result.get(i);
// System.out.println("child "+taxonomy);
//SET PARENTS
@ -704,7 +700,7 @@ public class TabItemForTaxonomyRow {
lc.add(comma);
}
TaxonomyRow taxonomy = result.get(result.size()-1);
LightTaxonomyRow taxonomy = result.get(result.size()-1);
// System.out.println("child "+taxonomy);
//SET PARENTS
@ -727,7 +723,7 @@ public class TabItemForTaxonomyRow {
}
public void getTaxonomyByReferenceId(FlexTable flexTable, int row, int col, final String statusRemark, String refId, final String dataSource, final List<TaxonomyRow> parents){
public void getTaxonomyByReferenceId(FlexTable flexTable, int row, int col, final String statusRemark, String refId, final String dataSource, final List<LightTaxonomyRow> parents){
final LayoutContainer layoutContainer = new LayoutContainer();
// hp.getElement().getStyle().setBorderStyle(BorderStyle.NONE);
@ -744,7 +740,7 @@ public class TabItemForTaxonomyRow {
List<String> listId = new ArrayList<String>();
listId.add(refId);
SpeciesDiscovery.taxonomySearchService.retrieveTaxonomyByIds(listId, new AsyncCallback<List<TaxonomyRow>>() {
SpeciesDiscovery.taxonomySearchService.retrieveTaxonomyByIds(listId, new AsyncCallback<List<LightTaxonomyRow>>() {
@Override
public void onFailure(Throwable caught) {
@ -754,7 +750,7 @@ public class TabItemForTaxonomyRow {
}
@Override
public void onSuccess(List<TaxonomyRow> result) {
public void onSuccess(List<LightTaxonomyRow> result) {
Log.trace("getReferenceById return " +result.size() + " items");
// System.out.println("getReferenceById return " +result.size() + " items");
@ -770,7 +766,7 @@ public class TabItemForTaxonomyRow {
if(result.size()>0){
for (int i=0; i<result.size()-1; i++) {
TaxonomyRow taxonomy = result.get(i);
LightTaxonomyRow taxonomy = result.get(i);
// System.out.println("child "+taxonomy);
//SET PARENTS
@ -782,21 +778,16 @@ public class TabItemForTaxonomyRow {
lc.add(comma);
}
TaxonomyRow taxonomy = result.get(result.size()-1);
LightTaxonomyRow taxonomy = result.get(result.size()-1);
//FOR DEBUG
// System.out.println("child "+taxonomy);
//SET PARENTS
taxonomy.setParent(parents);
//TODO
lc.add(getAnchorByTaxonomy(taxonomy, dataSource, -2));
}
layoutContainer.add(lc);
@ -807,80 +798,4 @@ public class TabItemForTaxonomyRow {
});
}
// protected ContentPanel getPanelForTaxonomy(TaxonomyRow taxon, String dataSource, boolean isNewTab, final int parentIndex) {
//
// ContentPanel contentPanel = new ContentPanel();
//// contentPanel.setLayout(new FitLayout());
// contentPanel.setHeaderVisible(false);
// contentPanel.setBodyBorder(false);
//
// contentPanel.setStyleAttribute("padding", "5px");
// contentPanel.setStyleAttribute("margin", "5px");
//
// VerticalPanel verticaPanel = new VerticalPanel();
// verticaPanel.setSize("100%", "100%");
//
// contentPanel.add(new Html("<br/><br/><p style=\"font-size:18px;\"><b>" + taxon.getName() + "</b></p><hr>"));
// contentPanel.add(new Html("<br/><br/><p style=\"font-size:12px;\"><b>Scientific Classification</b></p><br/>"));
//
// contentPanel.add(getPanelClassificationForTaxonomy(taxon, dataSource, isNewTab));
//
// contentPanel.add(getHTMLTableForTaxonomyWithRef(taxon, isNewTab, dataSource,parentIndex));
//
// return contentPanel;
//
// }
// protected void addTabItem(final TaxonomyRow taxon, final String dataSource, final int parentIndex){
//
//
// TabItem tabItem = new TabItem();
//// tabItem.setLayout(new FitLayout());
// tabItem.setScrollMode(Scroll.AUTO);
// tabItem.setClosable(true);
//
//
// ContentPanel cp = new ContentPanel();
// cp.setHeaderVisible(false);
// ToolBar toolbar = new ToolBar();
//
//
// Button btnSaveTaxonomyChildren = new Button(ConstantsSpeciesDiscovery.SAVE_TAXONOMY_CHILDREN);
// Menu formatSubMenu = new Menu();
// btnSaveTaxonomyChildren.setMenu(formatSubMenu);
// btnSaveTaxonomyChildren.setScale(ButtonScale.SMALL);
// btnSaveTaxonomyChildren.setIconAlign(IconAlign.TOP);
// btnSaveTaxonomyChildren.setIcon(AbstractImagePrototype.create(Resources.INSTANCE.getSaveProducts()));
// btnSaveTaxonomyChildren.setToolTip(new ToolTipConfig(ConstantsSpeciesDiscovery.SAVE_TAXONOMY_CHILDREN, ConstantsSpeciesDiscovery.SAVES_TAXONOMY_CHILDREN_FROM_RESULT));
//
// MenuItem darwinCoreArchiveItem = new MenuItem(ConstantsSpeciesDiscovery.DARWIN_CORE_ARCHIVE);
// darwinCoreArchiveItem.setToolTip(new ToolTipConfig(ConstantsSpeciesDiscovery.SAVES_IN_DARWIN_CORE_ARCHIVE_FORMAT));
// darwinCoreArchiveItem.addSelectionListener(new SelectionListener<MenuEvent>() {
//
// @Override
// public void componentSelected(MenuEvent ce) {
// eventBus.fireEvent(new CreateTaxonomyJobEvent(taxon, dataSource, TaxonomyJobType.BYCHILDREN));
// }
// });
//
// formatSubMenu.add(darwinCoreArchiveItem);
// toolbar.add(btnSaveTaxonomyChildren);
//
// cp.setTopComponent(toolbar);
// cp.setBodyBorder(false);
//// cp.setScrollMode(Scroll.AUTOY);
//
// String tabName = taxon.getName() + " ("+ dataSource + ")";
// tabItem.setText(tabName);
//
// cp.add(getPanelForTaxonomy(taxon, dataSource, true, parentIndex));
//
// tabItem.add(cp);
//
// tabPanel.add(tabItem);
//
// }
}

211
src/main/java/org/gcube/portlets/user/speciesdiscovery/client/cluster/TablesForTaxonomyRow.java
View File

@ -6,7 +6,8 @@ import org.gcube.portlets.user.speciesdiscovery.client.ConstantsSpeciesDiscovery
import org.gcube.portlets.user.speciesdiscovery.client.event.CreateTaxonomyJobEvent;
import org.gcube.portlets.user.speciesdiscovery.client.event.CreateTaxonomyJobEvent.TaxonomyJobType;
import org.gcube.portlets.user.speciesdiscovery.client.resources.Resources;
import org.gcube.portlets.user.speciesdiscovery.shared.TaxonomyRow;
import org.gcube.portlets.user.speciesdiscovery.client.util.TaxonomyGridField;
import org.gcube.portlets.user.speciesdiscovery.shared.LightTaxonomyRow;
import com.extjs.gxt.ui.client.Style.ButtonScale;
import com.extjs.gxt.ui.client.Style.IconAlign;
@ -15,6 +16,7 @@ import com.extjs.gxt.ui.client.event.MenuEvent;
import com.extjs.gxt.ui.client.event.SelectionListener;
import com.extjs.gxt.ui.client.widget.ContentPanel;
import com.extjs.gxt.ui.client.widget.Html;
import com.extjs.gxt.ui.client.widget.LayoutContainer;
import com.extjs.gxt.ui.client.widget.TabItem;
import com.extjs.gxt.ui.client.widget.TabPanel;
import com.extjs.gxt.ui.client.widget.VerticalPanel;
@ -23,9 +25,19 @@ import com.extjs.gxt.ui.client.widget.menu.Menu;
import com.extjs.gxt.ui.client.widget.menu.MenuItem;
import com.extjs.gxt.ui.client.widget.tips.ToolTipConfig;
import com.extjs.gxt.ui.client.widget.toolbar.ToolBar;
import com.google.gwt.core.client.GWT;
import com.google.gwt.event.dom.client.ClickEvent;
import com.google.gwt.event.dom.client.ClickHandler;
import com.google.gwt.event.shared.EventBus;
import com.google.gwt.http.client.Request;
import com.google.gwt.http.client.RequestBuilder;
import com.google.gwt.http.client.RequestCallback;
import com.google.gwt.http.client.RequestException;
import com.google.gwt.http.client.Response;
import com.google.gwt.user.client.ui.AbstractImagePrototype;
import com.google.gwt.user.client.ui.FlexTable;
import com.google.gwt.user.client.ui.Image;
import com.google.gwt.user.client.ui.Label;
/**
*
@ -37,17 +49,19 @@ public class TablesForTaxonomyRow {
private TabPanel tabPanel;
private EventBus eventBus;
private List<TaxonomyRow> parents = null;
private List<LightTaxonomyRow> parents = null;
private TabItemForTaxonomyRow tabTR;
private AbstractImagePrototype imageLoading = AbstractImagePrototype.create(Resources.INSTANCE.loadingBalls());
// private HashMap<String, TabItemForTaxonomyRow> hashTR = new HashMap<String, TabItemForTaxonomyRow>();
public List<TaxonomyRow> getParents() {
public List<LightTaxonomyRow> getParents() {
return parents;
}
public void setParents(List<TaxonomyRow> parents) {
public void setParents(List<LightTaxonomyRow> parents) {
this.parents = parents;
}
@ -67,39 +81,39 @@ public class TablesForTaxonomyRow {
* @return
*/
public VerticalPanel getPanelClassificationForTaxonomy(TaxonomyRow taxonomy, String dataSource, boolean isNewTab){
public VerticalPanel getPanelClassificationForTaxonomy(LightTaxonomyRow taxonomy, String dataSource, boolean isNewTab){
// hashTR.put(taxonomy.getIdToString(),tabTR);
tabTR.setCurrentTaxonomy(taxonomy);
//DEBUG
System.out.println("in getPanelClassificationForTaxonomy...");
System.out.println("principal "+taxonomy.getName() + " id " + taxonomy.getServiceId()+" parents");
int i=0;
for (TaxonomyRow tax : taxonomy.getParents()) {
System.out.println(++i + " parent name " + tax.getName());
}
// System.out.println("in getPanelClassificationForTaxonomy...");
// System.out.println("principal "+taxonomy.getName() + " id " + taxonomy.getServiceId()+" parents");
// int i=0;
// for (TaxonomyRow tax : taxonomy.getParents()) {
// System.out.println(++i + " parent name " + tax.getName());
// }
return tabTR.getPanelClassificationForTaxonomy(taxonomy, dataSource, isNewTab);
}
/**
*
* @param row
* @param isNewTab
* @param dataSource
* @param parentIndex
* @return
*/
public FlexTable getHTMLTableForTaxonomyWithRef(final TaxonomyRow row,boolean isNewTab, final String dataSource) {
return tabTR.getHTMLTableForTaxonomyWithRef(row, isNewTab, dataSource);
}
// /**
// *
// * @param row
// * @param isNewTab
// * @param dataSource
// * @param parentIndex
// * @return
// */
// public FlexTable getHTMLTableForTaxonomyWithRef(final LightTaxonomyRow row,boolean isNewTab, final String dataSource) {
//
// return tabTR.getHTMLTableForTaxonomyWithRef(row, isNewTab, dataSource);
// }
//
protected ContentPanel getPanelForTaxonomy(TaxonomyRow taxon, String dataSource, boolean isNewTab) {
protected ContentPanel getPanelForTaxonomy(final LightTaxonomyRow taxon, final String dataSource, boolean isNewTab) {
ContentPanel contentPanel = new ContentPanel();
// contentPanel.setLayout(new FitLayout());
@ -117,13 +131,58 @@ public class TablesForTaxonomyRow {
contentPanel.add(getPanelClassificationForTaxonomy(taxon, dataSource, isNewTab));
contentPanel.add(getHTMLTableForTaxonomyWithRef(taxon, isNewTab, dataSource));
contentPanel.add(new Html("<p style=\"font-size:11px; margin-top:10px;\"><b>Status and Synonyms</b></p>"));
contentPanel.add(getStatusAndSynonyms(taxon, dataSource));
contentPanel.add(new Html("<p style=\"font-size:11px; margin-top:10px;\"><b>Other Information</b></p"));
// HorizontalPanel hp = new HorizontalPanel();
// contentPanel.add(getHTMLTableForTaxonomyWithRef(taxon, isNewTab, dataSource));
final LayoutContainer lcRRTables = new LayoutContainer();
lcRRTables.setStyleAttribute("width", "99%");
// lcRRTables.setLayout(new FitLayout());
lcRRTables.setStyleAttribute("margin", "5px");
lcRRTables.setStyleAttribute("padding", "5px");
lcRRTables.setStyleAttribute("font-size", "12px");
contentPanel.add(lcRRTables);
final Image loading = imageLoading.createImage();
lcRRTables.add(loading);
String urlRequest = GWT.getModuleBaseURL() + ConstantsSpeciesDiscovery.TAXONOMY_ROW_TABLE + "?" +"oid=" + taxon.getServiceId();
RequestBuilder requestBuilder = new RequestBuilder(RequestBuilder.POST, urlRequest);
requestBuilder.setHeader("Content-Type", "application/x-www-form-urlencoded");
try {
requestBuilder.sendRequest("", new RequestCallback() {
@Override
public void onResponseReceived(Request request, Response response) {
lcRRTables.remove(loading);
Html respHtml = new Html(response.getText());
lcRRTables.add(respHtml);
lcRRTables.layout();
}
@Override
public void onError(Request request, Throwable exception) {
lcRRTables.remove(loading);
lcRRTables.add(new Html("Sorry, an error occurred while contacting server, try again"));
}
});
} catch (RequestException e) {
lcRRTables.remove(loading);
lcRRTables.add(new Html("Sorry, an error occurred while contacting server, try again"));
}
return contentPanel;
}
protected void addTabItem(final TaxonomyRow taxon, final String dataSource){
protected void addTabItem(final LightTaxonomyRow taxon, final String dataSource){
this.tabTR = new TabItemForTaxonomyRow(this, this.tabPanel, this.eventBus);
@ -174,5 +233,103 @@ public class TablesForTaxonomyRow {
}
public FlexTable getStatusAndSynonyms(final LightTaxonomyRow taxon, final String dataSource){
String refId = null;
String statusRemark="";
String statusName="";
if (taxon.getStatusRefId() != null && !taxon.getStatusRefId().isEmpty())
refId = taxon.getStatusRefId();
if (taxon.getStatusRemarks() != null)
statusRemark = taxon.getStatusRemarks();
if (taxon.getStatusName() != null)
statusName = taxon.getStatusName();
//BUILD TABLE WITH STATUS REF ID; STATUS REMARK AND SYNONYMS
final FlexTable flexTable = new FlexTable();
flexTable.setStyleName("imagetable-status");
flexTable.setWidget(0, 0, new Label(TaxonomyGridField.STATUSREFNAME.getName()));
flexTable.setWidget(0, 1, new Label(statusName));
if (refId != null) {
final String status;
if(!statusRemark.isEmpty())
status = statusRemark;
else
status = statusName;
final String referenceId = refId;
flexTable.setWidget(1, 0, new Label(TaxonomyGridField.STATUS_REMARKS.getName()));
AbstractImagePrototype synonyms = AbstractImagePrototype.create(Resources.INSTANCE.getSearch());
final Image imageStatusRemark = synonyms.createImage();
imageStatusRemark.setStyleName("image-load-synonyms");
imageStatusRemark.setAltText("show accepted name");
imageStatusRemark.setTitle("show accepted name");
final LayoutContainer layoutContainer = new LayoutContainer();
final Label labelStatusRemark = new Label(statusRemark);
labelStatusRemark.addStyleName("status-of");
layoutContainer.add(labelStatusRemark);
imageStatusRemark.addClickHandler(new ClickHandler() {
@Override
public void onClick(ClickEvent event) {
flexTable.remove(layoutContainer);
if(taxon.getParents().size()>0)
tabTR.getTaxonomyByReferenceId(flexTable, 1, 1, status, referenceId, dataSource, taxon.getParents());
// getTaxonomyByReferenceId(flexTable, 2, 1, status, referenceId, dataSource, taxon.getParents());
}
});
layoutContainer.add(labelStatusRemark);
layoutContainer.add(imageStatusRemark);
flexTable.setWidget(1, 1, layoutContainer);
} else {
flexTable.setWidget(1, 0, new Label(TaxonomyGridField.STATUS_REMARKS.getName()));
flexTable.setWidget(1, 1, new Label(statusRemark));
}
//Create row get synonyms
flexTable.setWidget(2, 0,new Label(TaxonomyGridField.SYNONYMS.getName()));
AbstractImagePrototype synonyms = AbstractImagePrototype.create(Resources.INSTANCE.getSearch());
final Image imageSynonyms = synonyms.createImage();
imageSynonyms.setStyleName("image-load-synonyms");
imageSynonyms.setAltText("show synonyms");
imageSynonyms.setTitle("show synonyms");
imageSynonyms.addClickHandler(new ClickHandler() {
@Override
public void onClick(ClickEvent event) {
flexTable.remove(imageSynonyms);
if(taxon.getParents().size()>0){
tabTR.getSynonymsByReferenceId(flexTable, 2, 1, taxon.getServiceId(),dataSource, taxon.getParents());
}
}
});
flexTable.setWidget(2, 1, imageSynonyms);
return flexTable;
}
}

10
src/main/java/org/gcube/portlets/user/speciesdiscovery/client/event/CreateTaxonomyJobEvent.java
View File

@ -3,7 +3,7 @@
*/
package org.gcube.portlets.user.speciesdiscovery.client.event;
import org.gcube.portlets.user.speciesdiscovery.shared.TaxonomyRow;
import org.gcube.portlets.user.speciesdiscovery.shared.LightTaxonomyRow;
import com.google.gwt.event.shared.GwtEvent;
@ -15,7 +15,7 @@ import com.google.gwt.event.shared.GwtEvent;
public class CreateTaxonomyJobEvent extends GwtEvent<CreateTaxonomyJobEventHandler> {
public static final GwtEvent.Type<CreateTaxonomyJobEventHandler> TYPE = new Type<CreateTaxonomyJobEventHandler>();
private TaxonomyRow taxonomy;
private LightTaxonomyRow taxonomy;
private String dataSourceName;
public enum TaxonomyJobType {BYCHILDREN, BYIDS};
private TaxonomyJobType jobType;
@ -37,7 +37,7 @@ public class CreateTaxonomyJobEvent extends GwtEvent<CreateTaxonomyJobEventHandl
* @param type
* @param rank
*/
public CreateTaxonomyJobEvent(TaxonomyRow taxonomy, String dataSourceName, TaxonomyJobType jobType) {
public CreateTaxonomyJobEvent(LightTaxonomyRow taxonomy, String dataSourceName, TaxonomyJobType jobType) {
this.taxonomy = taxonomy;
this.dataSourceName = dataSourceName;
this.jobType = jobType;
@ -55,11 +55,11 @@ public class CreateTaxonomyJobEvent extends GwtEvent<CreateTaxonomyJobEventHandl
return jobType;
}
public TaxonomyRow getTaxonomy() {
public LightTaxonomyRow getTaxonomy() {
return taxonomy;
}
public void setTaxonomy(TaxonomyRow taxonomy) {
public void setTaxonomy(LightTaxonomyRow taxonomy) {
this.taxonomy = taxonomy;
}

23
src/main/java/org/gcube/portlets/user/speciesdiscovery/client/rpc/TaxonomySearchService.java
View File

@ -12,6 +12,7 @@ import org.gcube.portlets.user.speciesdiscovery.shared.DataSourceModel;
import org.gcube.portlets.user.speciesdiscovery.shared.DownloadState;
import org.gcube.portlets.user.speciesdiscovery.shared.JobOccurrencesModel;
import org.gcube.portlets.user.speciesdiscovery.shared.JobTaxonomyModel;
import org.gcube.portlets.user.speciesdiscovery.shared.LightTaxonomyRow;
import org.gcube.portlets.user.speciesdiscovery.shared.OccurrenceBatch;
import org.gcube.portlets.user.speciesdiscovery.shared.OccurrencesSaveEnum;
import org.gcube.portlets.user.speciesdiscovery.shared.OccurrencesStatus;
@ -24,6 +25,8 @@ import org.gcube.portlets.user.speciesdiscovery.shared.SearchServiceException;
import org.gcube.portlets.user.speciesdiscovery.shared.SearchStatus;
import org.gcube.portlets.user.speciesdiscovery.shared.Taxon;
import org.gcube.portlets.user.speciesdiscovery.shared.TaxonomyRow;
import org.gcube.portlets.user.speciesdiscovery.shared.cluster.ClusterCommonNameDataSourceForResultRow;
import org.gcube.portlets.user.speciesdiscovery.shared.cluster.ClusterCommonNameDataSourceForTaxonomyRow;
import org.gcube.portlets.user.speciesdiscovery.shared.cluster.ClusterStructuresForResultRow;
import org.gcube.portlets.user.speciesdiscovery.shared.cluster.ClusterStructuresForTaxonomyRow;
import org.gcube.portlets.user.speciesdiscovery.shared.filter.ResultFilter;
@ -93,8 +96,7 @@ public interface TaxonomySearchService extends RemoteService {
ResultFilter activeFiltersObject, boolean showOnlySelected)
throws SearchServiceException;
public ArrayList<TaxonomyRow> loadListChildByParentId(String parentId)
throws Exception;
ArrayList<LightTaxonomyRow> loadListChildrenByParentId(String parentId) throws Exception;
void saveSelectedTaxonomyPoints(String destinationFolderId,
String fileName, SaveFileFormat fileFormat)
@ -114,11 +116,9 @@ public interface TaxonomySearchService extends RemoteService {
String destinationFolderId, String fileName, String scientificName,
String dataSourceName) throws Exception;
public List<TaxonomyRow> retrieveTaxonomyByIds(List<String> ids)
throws Exception;
public List<LightTaxonomyRow> retrieveTaxonomyByIds(List<String> ids) throws Exception;
public List<TaxonomyRow> retrieveSynonymsByRefId(String refId)
throws Exception;
public List<LightTaxonomyRow> retrieveSynonymsByRefId(String refId) throws Exception;
public List<JobOccurrencesModel> createOccurrencesJob(
List<JobOccurrencesModel> listJobOccurrenceModel,
@ -193,5 +193,16 @@ public interface TaxonomySearchService extends RemoteService {
* @return
*/
String getLastQuery();
/**
* @param scientificName
* @return
* @throws Exception
*/
ClusterCommonNameDataSourceForResultRow loadClusterCommonNameForResultRowByScientificName(
String scientificName) throws Exception;
ClusterCommonNameDataSourceForTaxonomyRow loadClusterCommonNameForTaxonomyRowByScientificName(
String scientificName);
}

17
src/main/java/org/gcube/portlets/user/speciesdiscovery/client/rpc/TaxonomySearchServiceAsync.java
View File

@ -12,6 +12,7 @@ import org.gcube.portlets.user.speciesdiscovery.shared.DataSourceModel;
import org.gcube.portlets.user.speciesdiscovery.shared.DownloadState;
import org.gcube.portlets.user.speciesdiscovery.shared.JobOccurrencesModel;
import org.gcube.portlets.user.speciesdiscovery.shared.JobTaxonomyModel;
import org.gcube.portlets.user.speciesdiscovery.shared.LightTaxonomyRow;
import org.gcube.portlets.user.speciesdiscovery.shared.OccurrenceBatch;
import org.gcube.portlets.user.speciesdiscovery.shared.OccurrencesSaveEnum;
import org.gcube.portlets.user.speciesdiscovery.shared.OccurrencesStatus;
@ -23,6 +24,8 @@ import org.gcube.portlets.user.speciesdiscovery.shared.SearchResult;
import org.gcube.portlets.user.speciesdiscovery.shared.SearchStatus;
import org.gcube.portlets.user.speciesdiscovery.shared.Taxon;
import org.gcube.portlets.user.speciesdiscovery.shared.TaxonomyRow;
import org.gcube.portlets.user.speciesdiscovery.shared.cluster.ClusterCommonNameDataSourceForResultRow;
import org.gcube.portlets.user.speciesdiscovery.shared.cluster.ClusterCommonNameDataSourceForTaxonomyRow;
import org.gcube.portlets.user.speciesdiscovery.shared.cluster.ClusterStructuresForResultRow;
import org.gcube.portlets.user.speciesdiscovery.shared.cluster.ClusterStructuresForTaxonomyRow;
import org.gcube.portlets.user.speciesdiscovery.shared.filter.ResultFilter;
@ -86,7 +89,7 @@ public interface TaxonomySearchServiceAsync {
boolean showOnlySelected,
AsyncCallback<SearchResult<TaxonomyRow>> asyncCallback);
void loadListChildByParentId(String parentId, AsyncCallback<ArrayList<TaxonomyRow>> callback);
void loadListChildrenByParentId(String parentId, AsyncCallback<ArrayList<LightTaxonomyRow>> asyncCallback);
void saveSelectedTaxonomyPoints(String destinationFolderId, String fileName, SaveFileFormat fileFormat, AsyncCallback<Void> callback);
@ -101,9 +104,9 @@ public interface TaxonomySearchServiceAsync {
void saveTaxonomyJob(String jobIdentifier, String destinationFolderId, String fileName, String scientificName, String dataSourceName, AsyncCallback<Boolean> callback);
void retrieveTaxonomyByIds(List<String> ids, AsyncCallback<List<TaxonomyRow>> callback);
void retrieveTaxonomyByIds(List<String> ids, AsyncCallback<List<LightTaxonomyRow>> asyncCallback);
void retrieveSynonymsByRefId(String refId, AsyncCallback<List<TaxonomyRow>> callback);
void retrieveSynonymsByRefId(String refId, AsyncCallback<List<LightTaxonomyRow>> asyncCallback);
void createOccurrencesJob(List<JobOccurrencesModel> listJobOccurrenceModel, SaveFileFormat saveFileFormat, OccurrencesSaveEnum csvType, boolean isByDataSource, int expectedOccurrence, AsyncCallback<List<JobOccurrencesModel>> callback);
@ -156,5 +159,13 @@ public interface TaxonomySearchServiceAsync {
AsyncCallback<Boolean> callback);
void getLastQuery(AsyncCallback<String> callback);
void loadClusterCommonNameForResultRowByScientificName(
String scientificName,
AsyncCallback<ClusterCommonNameDataSourceForResultRow> callback);
void loadClusterCommonNameForTaxonomyRowByScientificName(
String scientificName,
AsyncCallback<ClusterCommonNameDataSourceForTaxonomyRow> callback);
}

176
src/main/java/org/gcube/portlets/user/speciesdiscovery/client/windowdetail/ResultRowDetailsFiller.java
View File

@ -7,13 +7,10 @@ import java.util.List;
import org.gcube.portlets.user.speciesdiscovery.client.ConstantsSpeciesDiscovery;
import org.gcube.portlets.user.speciesdiscovery.client.SpeciesDiscovery;
import org.gcube.portlets.user.speciesdiscovery.client.cluster.TablesForResultRow;
import org.gcube.portlets.user.speciesdiscovery.client.event.SearchEvent;
import org.gcube.portlets.user.speciesdiscovery.client.resources.Resources;
import org.gcube.portlets.user.speciesdiscovery.client.util.stream.ResultRowDataSource;
import org.gcube.portlets.user.speciesdiscovery.shared.ResultRow;
import org.gcube.portlets.user.speciesdiscovery.shared.SpeciesCapability;
import org.gcube.portlets.user.speciesdiscovery.shared.cluster.ClusterCommonNameDataSource;
import org.gcube.portlets.user.speciesdiscovery.shared.cluster.ClusterCommonNameDataSourceForResultRow;
import org.gcube.portlets.user.speciesdiscovery.shared.cluster.ClusterStructuresForResultRow;
import com.allen_sauer.gwt.log.client.Log;
@ -30,18 +27,30 @@ import com.extjs.gxt.ui.client.widget.layout.ColumnLayout;
import com.extjs.gxt.ui.client.widget.layout.FormLayout;
import com.extjs.gxt.ui.client.widget.layout.TableData;
import com.extjs.gxt.ui.client.widget.toolbar.ToolBar;
import com.google.gwt.core.client.GWT;
import com.google.gwt.event.dom.client.ClickEvent;
import com.google.gwt.event.dom.client.ClickHandler;
import com.google.gwt.http.client.Request;
import com.google.gwt.http.client.RequestBuilder;
import com.google.gwt.http.client.RequestCallback;
import com.google.gwt.http.client.RequestException;
import com.google.gwt.http.client.Response;
import com.google.gwt.user.client.rpc.AsyncCallback;
import com.google.gwt.user.client.ui.AbstractImagePrototype;
import com.google.gwt.user.client.ui.Anchor;
import com.google.gwt.user.client.ui.Image;
public class ResultRowDetailsFiller implements DetailsFiller {
/**
*
*/
private TabItem tabItemDetails;
private ToolBar toolbarOccurrences;
private AbstractImagePrototype imgAttention = AbstractImagePrototype.create(Resources.INSTANCE.getAttention());
private AbstractImagePrototype imageLoading = AbstractImagePrototype.create(Resources.INSTANCE.loadingBalls());
private ContentPanel panelDetails;
private int width = 900;
private List<String> lastlistDataSourceFound;
@ -77,7 +86,9 @@ public class ResultRowDetailsFiller implements DetailsFiller {
@Override
public void onSuccess(ClusterStructuresForResultRow result) {
int size = result.getResult().size();
// int size = result.getResult().size();
int size = result.getResultSize();
long returnedTime = System.currentTimeMillis();
@ -89,10 +100,10 @@ public class ResultRowDetailsFiller implements DetailsFiller {
String msg = "";
if(result.getTotalRow()>size){
if(result.getAllResultRowSize()>size){
msg = ConstantsSpeciesDiscovery.ROW_LIMIT_REACHED + " - ";
tabItemDetails.setIcon(imgAttention);
tabItemDetails.setToolTip(ConstantsSpeciesDiscovery.THE_MAX_NUMBER_OF_ITEMS_DISPLAYABLE_IS+ConstantsSpeciesDiscovery.LIMIT_ITEM_DETAILS);
tabItemDetails.setToolTip(ConstantsSpeciesDiscovery.THE_MAX_NUMBER_OF_ITEMS_DISPLAYABLE_IS+ConstantsSpeciesDiscovery.RESULT_ROW_LIMIT_ITEM_DETAILS);
}
msg+= tabItemDetails.getText() + " ("+size +" "+ items+")";
@ -116,8 +127,10 @@ public class ResultRowDetailsFiller implements DetailsFiller {
private void createCommonNameDetailsPageForResultRow(ClusterStructuresForResultRow result) {
HashMap<String, ArrayList<String>> hashResultRowIdTables = result.getHashClusterScientificNameResultRowID();
HashMap<String, ClusterCommonNameDataSource<ResultRow>> hashClusterCommonNamesDataSources = result.getHashClusterCommonNamesDataSources();
HashMap<String, ArrayList<String>> hashResultRowIdTables = result.getHashClusterScientificNameResultRowServiceID();
// HashMap<String, ClusterCommonNameDataSource<ResultRow>> hashClusterCommonNamesDataSources = result.getHashClusterCommonNamesDataSources();
String title = common.getSearchTitle();
@ -187,25 +200,150 @@ public class ResultRowDetailsFiller implements DetailsFiller {
panelDetails.add(common.createExternalLinks(scientificName));
String commonNamesTitle = "<p style=\"font-size:12px;\"><b>Common Names (Data Source/s)</b></p>";
panelDetails.add(new Html(commonNamesTitle));
ClusterCommonNameDataSource<ResultRow> cluster = hashClusterCommonNamesDataSources.get(scientificName);
String tableCommonName = common.createTableWithCheckCommonNameDataSource(cluster.getHashMapCommonNameDataSources(), cluster.getListDataSourcesFound());
panelDetails.add(new Html("<br/>"+tableCommonName+"<br/><br/>"));
final LayoutContainer lcCommonName = new LayoutContainer();
lcCommonName.setStyleAttribute("width", "99%");
lcCommonName.setStyleAttribute("margin", "5px");
lcCommonName.setStyleAttribute("padding", "5px");
lcCommonName.setStyleAttribute("font-size", "12px");
// lcCommonName.setLayout(new FitLayout());
final Anchor anchorCommon = new Anchor("Compare Common Names for "+scientificName);
anchorCommon.addClickHandler(new ClickHandler() {
@Override
public void onClick(ClickEvent event) {
lcCommonName.remove(anchorCommon);
final Image loading = imageLoading.createImage();
lcCommonName.add(loading);
lcCommonName.layout();
SpeciesDiscovery.taxonomySearchService.loadClusterCommonNameForResultRowByScientificName(scientificName, new AsyncCallback<ClusterCommonNameDataSourceForResultRow>() {
@Override
public void onFailure(Throwable caught) {
Html htmlTableResult = new Html();
htmlTableResult.setHtml("<br/>Error on retrieving data<br/><br/>");
}
@Override
public void onSuccess(ClusterCommonNameDataSourceForResultRow result) {
Html htmlTableResult = new Html();
htmlTableResult.setHtml("<br/>Not Found<br/><br/>");
if(result !=null){
if(result.getCluster()!=null){
String tableCommonName = common.createTableWithCheckCommonNameDataSource(result.getCluster().getHashMapCommonNameDataSources(), result.getCluster().getListDataSourcesFound());
htmlTableResult.setHtml("<br/>"+tableCommonName+"<br/><br/>");
}
else
htmlTableResult.setHtml("<br/>Error on retrieving data<br/><br/>");
}else
htmlTableResult.setHtml("<br/>Error on retrieving data<br/><br/>");
lcCommonName.remove(loading);
lcCommonName.add(htmlTableResult);
panelDetails.layout();
}
});
}
});
lcCommonName.add(anchorCommon);
panelDetails.add(lcCommonName);
// ClusterCommonNameDataSource<ResultRow> cluster = hashClusterCommonNamesDataSources.get(scientificName);
// String tableCommonName = common.createTableWithCheckCommonNameDataSource(cluster.getHashMapCommonNameDataSources(), cluster.getListDataSourcesFound());
// panelDetails.add(new Html("<br/>"+tableCommonName+"<br/><br/>"));
ArrayList<String> arrayRowID = hashResultRowIdTables.get(scientificName);
// for(int i=0; i<arrayRowID.size(); i++ ){
// ResultRow row = result.getResultRowByRowID(arrayRowID.get(i));
// Html table = TablesForResultRow.getTableForResultRow(row, ResultRowDataSource.getClassification(row.getParents()));
// panelDetails.add(table);
// }
for(int i=0; i<arrayRowID.size(); i++ ){
ResultRow row = result.getResultRowByRowID(arrayRowID.get(i));
Html table = TablesForResultRow.getTableForResultRow(row, ResultRowDataSource.getClassification(row.getParents()));
panelDetails.add(table);
final LayoutContainer lcRRTables = new LayoutContainer();
lcRRTables.setStyleAttribute("width", "99%");
// lcRRTables.setLayout(new FitLayout());
lcRRTables.setStyleAttribute("margin", "5px");
lcRRTables.setStyleAttribute("padding", "5px");
lcRRTables.setStyleAttribute("font-size", "12px");
panelDetails.add(lcRRTables);
final Image loading = imageLoading.createImage();
lcRRTables.add(loading);
String urlRequest = GWT.getModuleBaseURL() + ConstantsSpeciesDiscovery.RESULT_ROW_TABLE + "?" +"oid=" + arrayRowID.get(i);
RequestBuilder requestBuilder = new RequestBuilder(RequestBuilder.GET, urlRequest);
try {
requestBuilder.sendRequest("", new RequestCallback() {
@Override
public void onResponseReceived(Request request, Response response) {
// int status = response.getStatusCode();
// System.out.println("status: "+status);
lcRRTables.remove(loading);
// lcRRTables.setLayout(new FitLayout());
Html respHtml = new Html(response.getText());
// respHtml.setId("respHtml"+respHtml.getId());
// respHtml.setStyleAttribute("width", "99%");
// System.out.println("response text is: "+response.getText());
lcRRTables.add(respHtml);
lcRRTables.layout();
// panelDetails.layout();
// if(status==200){
// lcRRTables.add(new Html(response.getText()));
// }else{ //OK STATUS
//
// }
}
@Override
public void onError(Request request, Throwable exception) {
lcRRTables.remove(loading);
lcRRTables.add(new Html("Sorry, an error occurred while contacting server, try again"));
}
});
} catch (RequestException e) {
lcRRTables.remove(loading);
lcRRTables.add(new Html("Sorry, an error occurred while contacting server, try again"));
}
// panelDetails.add(lcRRTables);
}
}
panelDetails.layout(true);
// panelDetails.layout(true);
panelDetails.layout();
}
@Override

143
src/main/java/org/gcube/portlets/user/speciesdiscovery/client/windowdetail/TaxonomyRowDetailsFiller.java
View File

@ -13,9 +13,9 @@ import org.gcube.portlets.user.speciesdiscovery.client.cluster.TablesForTaxonomy
import org.gcube.portlets.user.speciesdiscovery.client.event.SearchEvent;
import org.gcube.portlets.user.speciesdiscovery.client.resources.Resources;
import org.gcube.portlets.user.speciesdiscovery.shared.DataSourceModel;
import org.gcube.portlets.user.speciesdiscovery.shared.LightTaxonomyRow;
import org.gcube.portlets.user.speciesdiscovery.shared.SpeciesCapability;
import org.gcube.portlets.user.speciesdiscovery.shared.TaxonomyRow;
import org.gcube.portlets.user.speciesdiscovery.shared.cluster.ClusterCommonNameDataSource;
import org.gcube.portlets.user.speciesdiscovery.shared.cluster.ClusterCommonNameDataSourceForTaxonomyRow;
import org.gcube.portlets.user.speciesdiscovery.shared.cluster.ClusterStructuresForTaxonomyRow;
import com.allen_sauer.gwt.log.client.Log;
@ -34,18 +34,26 @@ import com.extjs.gxt.ui.client.widget.layout.ColumnLayout;
import com.extjs.gxt.ui.client.widget.layout.FormLayout;
import com.extjs.gxt.ui.client.widget.layout.TableData;
import com.extjs.gxt.ui.client.widget.toolbar.ToolBar;
import com.google.gwt.core.client.GWT;
import com.google.gwt.dom.client.Style.Unit;
import com.google.gwt.event.dom.client.ClickEvent;
import com.google.gwt.event.dom.client.ClickHandler;
import com.google.gwt.http.client.Request;
import com.google.gwt.http.client.RequestBuilder;
import com.google.gwt.http.client.RequestCallback;
import com.google.gwt.http.client.RequestException;
import com.google.gwt.http.client.Response;
import com.google.gwt.user.client.rpc.AsyncCallback;
import com.google.gwt.user.client.ui.AbstractImagePrototype;
import com.google.gwt.user.client.ui.Anchor;
import com.google.gwt.user.client.ui.Image;
public class TaxonomyRowDetailsFiller implements DetailsFiller {
private TabItem tabItemDetails;
private ToolBar toolbarTaxonomy;
private AbstractImagePrototype imgAttention = AbstractImagePrototype.create(Resources.INSTANCE.getAttention());
private AbstractImagePrototype imageLoading = AbstractImagePrototype.create(Resources.INSTANCE.loadingBalls());
private ContentPanel panelDetails;
private int width = 900;
private List<String> lastlistDataSourceFound;
@ -100,7 +108,7 @@ public class TaxonomyRowDetailsFiller implements DetailsFiller {
if(result.getTotalRow()>size){
msg = ConstantsSpeciesDiscovery.ROW_LIMIT_REACHED + " - ";
tabItemDetails.setIcon(imgAttention);
tabItemDetails.setToolTip(ConstantsSpeciesDiscovery.THE_MAX_NUMBER_OF_ITEMS_DISPLAYABLE_IS+ConstantsSpeciesDiscovery.LIMIT_ITEM_DETAILS);
tabItemDetails.setToolTip(ConstantsSpeciesDiscovery.THE_MAX_NUMBER_OF_ITEMS_DISPLAYABLE_IS+ConstantsSpeciesDiscovery.TAXONOMY_LIMIT_ITEMS_DETAILS);
}
msg+= tabItemDetails.getText() + " ("+size +" "+ items+")";
@ -122,9 +130,10 @@ public class TaxonomyRowDetailsFiller implements DetailsFiller {
}
private void createCommonNameDetailsPageForTaxonomyRow(ClusterStructuresForTaxonomyRow result) {
HashMap<String, ArrayList<String>> hashTaxonomyRowID = result.getHashClusterScientificNameTaxonomyRowID();
HashMap<String, ArrayList<String>> hashTaxonomyRowServiceID = result.getHashClusterScientificNameTaxonomyRowServiceID();
// ArrayList<String> listDataSourceFound = tableClassification.getListFoundDataSources();
HashMap<String,ClusterCommonNameDataSource<TaxonomyRow>> hashClusterCommonNamesDataSources = result.getHashClusterCommonNamesDataSources();
// HashMap<String,ClusterCommonNameDataSource<TaxonomyRow>> hashClusterCommonNamesDataSources = result.getHashClusterCommonNamesDataSources();
// HashMap<String, ArrayList<GxtClassificationModel>> hashHTMLTables = result.getHashClassificationTables();
@ -135,7 +144,7 @@ public class TaxonomyRowDetailsFiller implements DetailsFiller {
// System.out.println("############# Data Source found " + dataSource);
// }
List<String> listKey = new ArrayList<String>(hashTaxonomyRowID.keySet());
List<String> listKey = new ArrayList<String>(hashTaxonomyRowServiceID.keySet());
Collections.sort(listKey);
@ -204,16 +213,76 @@ public class TaxonomyRowDetailsFiller implements DetailsFiller {
String commonNamesTitle = "<p style=\"font-size:12px;\"><b>Common Names (Data Source/s)</b></p>";
panelDetails.add(new Html(commonNamesTitle));
ClusterCommonNameDataSource<TaxonomyRow> cluster = hashClusterCommonNamesDataSources.get(scientificName);
final LayoutContainer lcCommonName = new LayoutContainer();
lcCommonName.setStyleAttribute("width", "99%");
lcCommonName.setStyleAttribute("margin", "5px");
lcCommonName.setStyleAttribute("padding", "5px");
lcCommonName.setStyleAttribute("font-size", "12px");
String tableCommonName = common.createTableWithCheckCommonNameDataSource(cluster.getHashMapCommonNameDataSources(), cluster.getListDataSourcesFound());
panelDetails.add(new Html("<br/>"+tableCommonName+"<br/>"));
// lcCommonName.setLayout(new FitLayout());
ArrayList<String> arrayTaxonomyID = hashTaxonomyRowID.get(scientificName);
final Anchor anchorCommon = new Anchor("Compare Common Names for "+scientificName);
anchorCommon.addClickHandler(new ClickHandler() {
@Override
public void onClick(ClickEvent event) {
lcCommonName.remove(anchorCommon);
final Image loading = imageLoading.createImage();
lcCommonName.add(loading);
lcCommonName.layout();
SpeciesDiscovery.taxonomySearchService.loadClusterCommonNameForTaxonomyRowByScientificName(scientificName, new AsyncCallback<ClusterCommonNameDataSourceForTaxonomyRow>() {
@Override
public void onFailure(Throwable caught) {
Html htmlTableResult = new Html();
htmlTableResult.setHtml("<br/>Error on retrieving data<br/><br/>");
}
@Override
public void onSuccess(ClusterCommonNameDataSourceForTaxonomyRow result) {
Html htmlTableResult = new Html();
htmlTableResult.setHtml("<br/>Not Found<br/><br/>");
if(result !=null){
if(result.getCluster()!=null){
String tableCommonName = common.createTableWithCheckCommonNameDataSource(result.getCluster().getHashMapCommonNameDataSources(), result.getCluster().getListDataSourcesFound());
htmlTableResult.setHtml("<br/>"+tableCommonName+"<br/><br/>");
}
else
htmlTableResult.setHtml("<br/>Error on retrieving data<br/><br/>");
}else
htmlTableResult.setHtml("<br/>Error on retrieving data<br/><br/>");
lcCommonName.remove(loading);
lcCommonName.add(htmlTableResult);
panelDetails.layout();
}
});
}
});
lcCommonName.add(anchorCommon);
panelDetails.add(lcCommonName);
ArrayList<String> arrayTaxonomyID = hashTaxonomyRowServiceID.get(scientificName);
for(int i=0; i<arrayTaxonomyID.size(); i++ ){
TaxonomyRow taxonomy = result.getTaxonomyRowByKey(arrayTaxonomyID.get(i));
String dataSource = taxonomy.getDataProviderName();
LightTaxonomyRow lightTaxonomy = result.getLightTaxonomyRowByKey(arrayTaxonomyID.get(i));
String dataSource = lightTaxonomy.getDataProviderName();
TablesForTaxonomyRow tables = new TablesForTaxonomyRow(tabPanel, SearchController.eventBus);
@ -228,12 +297,54 @@ public class TaxonomyRowDetailsFiller implements DetailsFiller {
createAbout.getElement().getStyle().setMarginLeft(25, Unit.PX);
horizontalPanel.add(createAbout);
}
panelDetails.add(horizontalPanel);
panelDetails.add(tables.getPanelClassificationForTaxonomy(taxonomy, dataSource, false));
panelDetails.add(tables.getPanelClassificationForTaxonomy(lightTaxonomy, dataSource, false));
panelDetails.add(new Html("<p style=\"font-size:11px; margin-top:10px;\"><b>Status and Synonyms</b></p>"));
panelDetails.add(tables.getStatusAndSynonyms(lightTaxonomy, dataSource));
tables.setParents(lightTaxonomy.getParents());
tables.setParents(taxonomy.getParents());
panelDetails.add(tables.getHTMLTableForTaxonomyWithRef(taxonomy, false, dataSource));
panelDetails.add(new Html("<p style=\"font-size:11px; margin-top:10px;\"><b>Other Information</b></p>"));
final LayoutContainer lcRRTables = new LayoutContainer();
lcRRTables.setStyleAttribute("width", "99%");
// lcRRTables.setLayout(new FitLayout());
lcRRTables.setStyleAttribute("margin", "5px");
lcRRTables.setStyleAttribute("padding", "5px");
lcRRTables.setStyleAttribute("font-size", "12px");
panelDetails.add(lcRRTables);
final Image loading = imageLoading.createImage();
lcRRTables.add(loading);
String urlRequest = GWT.getModuleBaseURL() + ConstantsSpeciesDiscovery.TAXONOMY_ROW_TABLE + "?" +"oid=" + arrayTaxonomyID.get(i);
RequestBuilder requestBuilder = new RequestBuilder(RequestBuilder.GET, urlRequest);
try {
requestBuilder.sendRequest("", new RequestCallback() {
@Override
public void onResponseReceived(Request request, Response response) {
lcRRTables.remove(loading);
Html respHtml = new Html(response.getText());
lcRRTables.add(respHtml);
lcRRTables.layout();
}
@Override
public void onError(Request request, Throwable exception) {
lcRRTables.remove(loading);
lcRRTables.add(new Html("Sorry, an error occurred while contacting server, try again"));
}
});
} catch (RequestException e) {
lcRRTables.remove(loading);
lcRRTables.add(new Html("Sorry, an error occurred while contacting server, try again"));
}
}
}

313
src/main/java/org/gcube/portlets/user/speciesdiscovery/server/ResultRowTable.java Normal file
View File

@ -0,0 +1,313 @@
package org.gcube.portlets.user.speciesdiscovery.server;
import java.io.IOException;
import java.io.PrintWriter;
import java.util.Collections;
import java.util.Iterator;
import java.util.List;
import javax.persistence.criteria.CriteriaBuilder;
import javax.persistence.criteria.CriteriaQuery;
import javax.persistence.criteria.Predicate;
import javax.servlet.ServletException;
import javax.servlet.http.HttpServlet;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
import org.apache.log4j.Logger;
import org.gcube.application.framework.core.session.ASLSession;
import org.gcube.portlets.user.speciesdiscovery.client.util.SpeciesGridFields;
import org.gcube.portlets.user.speciesdiscovery.server.asl.SessionUtil;
import org.gcube.portlets.user.speciesdiscovery.server.persistence.dao.ResultRowPersistence;
import org.gcube.portlets.user.speciesdiscovery.shared.CommonName;
import org.gcube.portlets.user.speciesdiscovery.shared.ItemParameter;
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
* @Sep 6, 2013
*
*/
public class ResultRowTable extends HttpServlet {
/**
*
*/
public static final String TEXT_HTML = "text/html";
/**
*
*/
private static final long serialVersionUID = -9006347088111602996L;
protected Logger logger = Logger.getLogger(ResultRowTable.class);
protected ASLSession getASLSession(HttpServletRequest req)
{
return SessionUtil.getAslSession(req.getSession());
}
/* (non-Javadoc)
* @see javax.servlet.http.HttpServlet#doGet(javax.servlet.http.HttpServletRequest, javax.servlet.http.HttpServletResponse)
*/
@Override
protected void doGet(HttpServletRequest req, HttpServletResponse resp) throws ServletException, IOException {
String resultServiceRowID = "";
PrintWriter out = resp.getWriter();
resp.setContentType(TEXT_HTML);
try {
// get parameters
resultServiceRowID = req.getParameter("oid");
//IS VALID RR ID?
if(resultServiceRowID==null || resultServiceRowID.isEmpty()){
out.println(error("Parameter oid not found"));
}else{
logger.trace("found oid "+resultServiceRowID);
try {
ResultRowPersistence persistence = SessionUtil.getCurrentEJBResultRow(getASLSession(req));
if(persistence==null){
logger.trace("ResultRowPersistence not found in database");
out.println(error("Row id not found in database"));
out.close();
return;
}
CriteriaBuilder queryBuilder = persistence.getCriteriaBuilder();
CriteriaQuery<Object> cq = queryBuilder.createQuery();
Predicate pr1 = queryBuilder.equal(persistence.rootFrom(cq).get(ResultRow.SERVICE_ID_FIELD), resultServiceRowID);
cq.where(pr1);
Iterator<ResultRow> iterator = persistence.executeCriteriaQuery(cq).iterator();
ResultRow row = null;
while(iterator.hasNext()){
row = iterator.next();
break;
}
if(row==null){
logger.trace("Service Row id not found in database");
out.println(error("Service Row id not found in database"));
out.close();
return;
}
String table = getTableForResultRow(row, getClassification(row.getParents()));
logger.trace("table for ResultRowPersistence is empty "+table.isEmpty());
out.println(table);
} catch (Exception e) {
logger.error("Error in ResultRowTable servlet ",e);
throw new Exception("Error in ResultRowTable servlet ", e);
}
}
out.close(); //CLOSE STREAM
}catch (Exception e) {
String error = "Sorry an error occurred when creating the table for result row with id: "+resultServiceRowID;
if(out!=null)
out.println(error);
// else
// throw new ServletException(error);
// logger.error(error, e);
out.close(); //CLOSE STREAM
}
}
public String error(String message){
String errorPage = "";
errorPage +=("<p>Error: "+message+"</p>");
return errorPage;
}
//TODO modified
public static String getClassification(List<Taxon> listTaxon)
{
StringBuilder sb = new StringBuilder();
for (int i = listTaxon.size()-1; i >= 0; i--) {
Taxon taxon = listTaxon.get(i);
sb.append("<b>");
if(!NormalizeString.isUndefined(taxon.getRank()))
sb.append(taxon.getRank());
else
sb.append("Rank not found");
sb.append("</b>: ");
if(!NormalizeString.isUndefined(taxon.getName()))
sb.append(taxon.getName());
else
sb.append("Name not found");
if(i!=0)
sb.append(" -> ");
}
return sb.toString();
}
public String getTableForResultRow(ResultRow row, String classification){
//Init values
String dataSourceName = "";
String dataProviderName = "";
String dataSetName = "";
String dataSetCitation= "";
String matchingTaxonName= "";
String matchingAccordionTo= "";
String matchingRank= "";
String matchingCredits= "";
int occurencesCount = 0;
String author = "";
String lsid = "";
String credits = "";
String propertiesHtml = "";
//Validate values
if(row.getParents()!=null){
if(row.getParents().get(0).getName()!=null) matchingTaxonName = row.getParents().get(0).getName();
if(row.getParents().get(0).getAccordingTo()!=null) matchingAccordionTo = row.getParents().get(0).getAccordingTo();
if(row.getParents().get(0).getRank()!=null) matchingRank = row.getParents().get(0).getRank();
}
if(row.getDataSourceName()!=null) dataSourceName = row.getDataSourceName();
if(row.getDataProviderName()!=null) dataProviderName = row.getDataProviderName();
if(row.getDataSetName()!=null) dataSetName = row.getDataSetName();
if(row.getDataSetCitation()!=null) dataSetCitation = row.getDataSetCitation();
if(row.getMatchingCredits()!=null) matchingCredits = row.getMatchingCredits();
if(row.getOccurencesCount()!=0) occurencesCount = row.getOccurencesCount();
String commonNames = "";
if(row.getCommonNames()!=null){
for (CommonName comName : row.getCommonNames()) {
commonNames+= "<b>"+comName.getName()+"</b>" +" ("+comName.getLanguage()+") - ";
}
}
if(row.getAuthor()!=null) author = row.getAuthor();
if(row.getLsid()!=null) lsid = row.getLsid();
if(row.getCredits()!=null) credits = row.getCredits();
if(row.getProperties()!=null){
List<ItemParameter> listProperties = row.getProperties();
Collections.sort(listProperties, ItemParameter.COMPARATOR);
propertiesHtml+="<table class=\"parameters\">";
for (ItemParameter itemParameter : listProperties) {
propertiesHtml+=
"<tr>" +
" <td class=\"title\">"+itemParameter.getKey()+"</td>" +
" <td>"+itemParameter.getValue()+"</td>" +
"</tr>";
}
propertiesHtml+="</table>";
}
String table = "<table class=\"imagetable\">" +
"<tr>" +
" <th>"+matchingTaxonName+"</th>" +
"</tr>" +
"<tr>" +
" <td class=\"title\">"+SpeciesGridFields.CLASSIFICATION_STRING.getName()+"</td>" +
" <td>"+classification+"</td>" +
"</tr>" +
"<tr>" +
" <td class=\"title\">"+SpeciesGridFields.COMMON_NAMES.getName()+" (Language)</td>" +
" <td>"+commonNames+"</td>" +
"</tr>" +
"<tr>" +
" <td class=\"title\">"+SpeciesGridFields.DATASOURCE.getName()+"</td>" +
" <td>"+dataSourceName+"</td>" +
"</tr>" +
"<tr>" +
" <td class=\"title\">"+SpeciesGridFields.DATAPROVIDER.getName()+"</td>" +
" <td>"+dataProviderName+"</td>" +
"</tr>" +
"<tr>" +
" <td class=\"title\">"+SpeciesGridFields.DATASET.getName()+"</td>" +
" <td>"+dataSetName+"</td>" +
"</tr>" +
// "<tr>" +
// " <td class=\"title\">"+SpeciesGridFields.MATCHING_AUTHOR.getName()+"</td>" +
// " <td>"+matchingAccordionTo+"</td>" +
// "</tr>" +
"<tr>" +
" <td class=\"title\">"+SpeciesGridFields.MATCHING_RANK.getName()+"</td>" +
" <td>"+matchingRank+"</td>" +
"</tr>" +
"<tr>" +
" <td class=\"title\">"+SpeciesGridFields.DATASET_CITATION.getName()+"</td>" +
" <td>"+dataSetCitation+"</td>" +
"</tr>" +
// "<tr>" +
// " <td class=\"title\">"+SpeciesGridFields.MATCHING_CREDITS.getName()+"</td>" +
// " <td>"+matchingCredits+"</td>" +
// "</tr>" +
"<tr>" +
" <td class=\"title\">"+SpeciesGridFields.PRODUCT_OCCURRENCES.getName()+"</td>" +
" <td>"+occurencesCount+"</td>" +
"</tr>" +
"<tr>" +
" <td class=\"title\">"+SpeciesGridFields.LSID.getName()+"</td>" +
" <td>"+lsid+"</td>" +
"</tr>" +
"<tr>" +
" <td class=\"title\">"+SpeciesGridFields.AUTHOR.getName()+"</td>" +
" <td>"+author+"</td>" +
"</tr>" +
"<tr>" +
" <td class=\"title\">"+SpeciesGridFields.CREDITS.getName()+"</td>" +
" <td>"+credits+"</td>" +
"</tr>" +
"<tr>" +
" <td class=\"title\">"+SpeciesGridFields.PROPERTIES.getName()+"</td>" +
" <td>"+propertiesHtml+"</td>" +
"</tr>" +
"</table>";
return table;
}
}

406
src/main/java/org/gcube/portlets/user/speciesdiscovery/server/TaxonomyRowTable.java Normal file
View File

@ -0,0 +1,406 @@
package org.gcube.portlets.user.speciesdiscovery.server;
import java.io.IOException;
import java.io.PrintWriter;
import java.util.Arrays;
import java.util.Collections;
import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
import javax.persistence.criteria.CriteriaBuilder;
import javax.persistence.criteria.CriteriaQuery;
import javax.persistence.criteria.Predicate;
import javax.servlet.ServletException;
import javax.servlet.http.HttpServlet;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
import org.apache.log4j.Logger;
import org.gcube.application.framework.core.session.ASLSession;
import org.gcube.data.spd.model.products.TaxonomyItem;
import org.gcube.portlets.user.speciesdiscovery.client.util.TaxonomyGridField;
import org.gcube.portlets.user.speciesdiscovery.server.asl.SessionUtil;
import org.gcube.portlets.user.speciesdiscovery.server.persistence.DaoSession;
import org.gcube.portlets.user.speciesdiscovery.server.persistence.dao.TaxonomyRowPersistence;
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;
import org.gcube.portlets.user.speciesdiscovery.shared.TaxonomyRow;
/**
*
* @author Francesco Mangiacrapa francesco.mangiacrapa@isti.cnr.it
* @Sep 6, 2013
*
*/
public class TaxonomyRowTable extends HttpServlet {
/**
*
*/
private static final long serialVersionUID = 9157876104914505028L;
/**
*
*/
public static final String TEXT_HTML = "text/html";
protected Logger logger = Logger.getLogger(TaxonomyRowTable.class);
protected ASLSession getASLSession(HttpServletRequest req)
{
return SessionUtil.getAslSession(req.getSession());
}
/* (non-Javadoc)
* @see javax.servlet.http.HttpServlet#doGet(javax.servlet.http.HttpServletRequest, javax.servlet.http.HttpServletResponse)
*/
@Override
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
*/
private void retrieveTaxonomyRowAsHtmlTable(HttpServletRequest req, HttpServletResponse resp) {
String taxonomyServiceRowID = "";
resp.setContentType(TEXT_HTML);
resp.setCharacterEncoding("UTF-8");
TaxonomyRow row = null;
PrintWriter out = null;
try {
out = resp.getWriter();
// 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{
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);
TaxonomyItemConverter taxonomyItemConverter = new TaxonomyItemConverter(aslSession);
// int i = 1;
while (streamIterator.hasNext()) {
TaxonomyItem tax = streamIterator.next();
logger.trace("Taxonomy with id "+taxonomyServiceRowID+" found on service, converting");
// from TaxonomyItem to LightTaxonomyRow
row = taxonomyItemConverter.convert(tax);
break;
}
streamIterator.close();
if(row==null){
out.println(error("Sorry, taxonomy with "+taxonomyServiceRowID+" doesn't found in service"));
out.close();
return;
}
}
//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);
} catch (Exception e) {
logger.error("Error in TaxonomyRowTable servlet ",e);
throw new Exception("Error in ResultRowTable servlet ", e);
}
}
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();
} catch (IOException e1) {
logger.error("Error on get Writer into servlet ",e);
}
}
out.println(error);
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
{
try {
ASLSession session = getASLSession(req);
return SessionUtil.getService(session);
} catch (Exception e) {
e.printStackTrace();
logger.error("An error occurred when contacting the species service", e);
// System.out.println("An error occurred retrieving the service" +e);
throw new SearchServiceException("contacting the species service.");
}
}
public String error(String message){
String errorPage = "";
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 author = "";
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.getAuthor()!=null) author = row.getAuthor();
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>" +
" <td class=\"title\">"+TaxonomyGridField.COMMON_NAMES.getName()+" (Language)</td>" +
" <td>"+commonNames+"</td>" +
"</tr>";
// table+="<tr>" +
// " <td class=\"title\">"+TaxonomyGridField.STATUSREFNAME.getName()+"</td>" +
// " <td>"+statusName+"</td>" +
// "</tr>" +
// "<tr>" +
// " <td class=\"title\">"+TaxonomyGridField.STATUS_REMARKS.getName()+"</td>" +
// " <td>"+statusRemark+"</td>" +
// "</tr>" +
table +="<tr>" +
" <td class=\"title\">"+TaxonomyGridField.DATASOURCE.getName()+"</td>" +
" <td>"+dataProviderName+"</td>" +
"</tr>" +
"<tr>" +
" <td class=\"title\">"+TaxonomyGridField.DATEMODIFIED.getName()+"</td>" +
" <td>"+dateModified+"</td>" +
"</tr>" +
"<tr>" +
" <td class=\"title\">"+TaxonomyGridField.MATCHING_RANK.getName()+"</td>" +
" <td>"+rank+"</td>" +
"</tr>" +
"<tr>" +
" <td class=\"title\">"+TaxonomyGridField.CITATION.getName()+"</td>" +
" <td>"+dataSetCitation+"</td>" +
"</tr>" +
"<tr>" +
" <td class=\"title\">"+TaxonomyGridField.LSID.getName()+"</td>" +
" <td>"+lsid+"</td>" +
"</tr>" +
"<tr>" +
" <td class=\"title\">"+TaxonomyGridField.AUTHOR.getName()+"</td>" +
" <td>"+author+"</td>" +
"</tr>" +
"<tr>" +
" <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;
}
}

251
src/main/java/org/gcube/portlets/user/speciesdiscovery/server/TaxonomySearchServiceImpl.java
View File

@ -64,6 +64,7 @@ import org.gcube.portlets.user.speciesdiscovery.server.stream.StreamExtend;
import org.gcube.portlets.user.speciesdiscovery.server.stream.aggregation.FieldAggregator;
import org.gcube.portlets.user.speciesdiscovery.server.stream.aggregation.TaxonomyClassificationAggregator;
import org.gcube.portlets.user.speciesdiscovery.server.util.DateUtil;
import org.gcube.portlets.user.speciesdiscovery.server.util.GetWorkspaceUtil;
import org.gcube.portlets.user.speciesdiscovery.server.util.QueryUtil;
import org.gcube.portlets.user.speciesdiscovery.shared.CommonName;
import org.gcube.portlets.user.speciesdiscovery.shared.DataSource;
@ -74,6 +75,7 @@ import org.gcube.portlets.user.speciesdiscovery.shared.FetchingElement;
import org.gcube.portlets.user.speciesdiscovery.shared.ItemParameter;
import org.gcube.portlets.user.speciesdiscovery.shared.JobOccurrencesModel;
import org.gcube.portlets.user.speciesdiscovery.shared.JobTaxonomyModel;
import org.gcube.portlets.user.speciesdiscovery.shared.LightTaxonomyRow;
import org.gcube.portlets.user.speciesdiscovery.shared.MainTaxonomicRankEnum;
import org.gcube.portlets.user.speciesdiscovery.shared.Occurrence;
import org.gcube.portlets.user.speciesdiscovery.shared.OccurrenceBatch;
@ -92,8 +94,12 @@ import org.gcube.portlets.user.speciesdiscovery.shared.SearchType;
import org.gcube.portlets.user.speciesdiscovery.shared.Taxon;
import org.gcube.portlets.user.speciesdiscovery.shared.TaxonomyJob;
import org.gcube.portlets.user.speciesdiscovery.shared.TaxonomyRow;
import org.gcube.portlets.user.speciesdiscovery.shared.cluster.ClusterCommonNameDataSourceForResultRow;
import org.gcube.portlets.user.speciesdiscovery.shared.cluster.ClusterCommonNameDataSourceForTaxonomyRow;
import org.gcube.portlets.user.speciesdiscovery.shared.cluster.ClusterStructuresForResultRow;
import org.gcube.portlets.user.speciesdiscovery.shared.cluster.ClusterStructuresForTaxonomyRow;
import org.gcube.portlets.user.speciesdiscovery.shared.cluster.ManagerClusterCommonNameDataSourceForResultRow;
import org.gcube.portlets.user.speciesdiscovery.shared.cluster.ManagerClusterCommonNameDataSourceForTaxonomyRow;
import org.gcube.portlets.user.speciesdiscovery.shared.filter.ResultFilter;
import org.gcube.portlets.user.speciesdiscovery.shared.util.NormalizeString;
@ -360,7 +366,8 @@ public class TaxonomySearchServiceImpl extends RemoteServiceServlet implements T
resultRow.setProperties(null);
}
System.out.println("################### ResultRow parents: "+resultRow.getParents());
//FOR DEBUG
// System.out.println("################### ResultRow parents: "+resultRow.getParents());
chunk.add(resultRow);
@ -1245,27 +1252,47 @@ public class TaxonomySearchServiceImpl extends RemoteServiceServlet implements T
@Override
public ArrayList<TaxonomyRow> loadListChildByParentId(String parentId) throws Exception {
public ArrayList<LightTaxonomyRow> loadListChildrenByParentId(String parentId) throws Exception {
logger.trace("Load List Children By ParentId: " + parentId);
//FOR DEBUG
// System.out.println("Load List Children By ParentId: " + parentId);
ArrayList<TaxonomyRow> listTaxonomyRow = new ArrayList<TaxonomyRow>();
ArrayList<LightTaxonomyRow> listLightTaxonomyRow = new ArrayList<LightTaxonomyRow>();
if(parentId==null || parentId.isEmpty()){
logger.warn("parentId is null or empty ");
return listLightTaxonomyRow;
}
try {
SpeciesService taxonomyService = getSpeciesService();
CloseableIterator<TaxonomyItem> streamIterator = taxonomyService.getTaxonChildrenByParentId(parentId);
ASLSession session = getASLSession();
TaxonomyItemConverter converter = new TaxonomyItemConverter(getASLSession());
int i = 0;
Map<String, TaxonomyRow> mapChildren = SessionUtil.getHashMapChildrenTaxonomyCache(session);
if(mapChildren==null){
logger.trace("Cache taxa children doesn't exists into session, creating..");
mapChildren = new HashMap<String, TaxonomyRow>();
}
// int i = 0;
while (streamIterator.hasNext()) {
TaxonomyItem tax = streamIterator.next();
// from TaxonomyItem to TaxonomyRow
TaxonomyRow taxonomyRow = converter.convert(tax);
listTaxonomyRow.add(taxonomyRow);
logger.trace(i + ") taxonomyRow: " + taxonomyRow);
i++;
TaxonomyRow taxonomy = converter.convert(tax);
if(mapChildren.get(taxonomy.getServiceId())==null){
logger.trace("Taxonomy with service id: "+taxonomy.getServiceId()+" doesn't exists into Map Children, adding..");
mapChildren.put(taxonomy.getServiceId(),taxonomy);
}
LightTaxonomyRow lightTaxRow = ClusterStructuresForTaxonomyRow.convetTaxonomyRowToLigthTaxonomyRow(taxonomy);
listLightTaxonomyRow.add(lightTaxRow);
}
SessionUtil.setHashMapChildrenTaxonomyCache(session, mapChildren);
streamIterator.close();
} catch (Exception e) {
@ -1273,9 +1300,9 @@ public class TaxonomySearchServiceImpl extends RemoteServiceServlet implements T
throw new Exception("Error on loadListChildByParentId", e);
}
logger.trace("Return list children By ParentId - size"+ listTaxonomyRow.size());
logger.trace("Return list children By ParentId "+parentId+"- with size: "+ listLightTaxonomyRow.size());
return listTaxonomyRow;
return listLightTaxonomyRow;
}
@Override
@ -1540,7 +1567,7 @@ public class TaxonomySearchServiceImpl extends RemoteServiceServlet implements T
InputStream inputStream = taxonomyService.getTaxonomyJobFileById(jobIdentifier);
if(inputStream!=null){
Workspace workspace = org.gcube.portlets.user.speciesdiscovery.server.util.GetWorkspaceUtil.getWorskspace(getASLSession());
Workspace workspace = GetWorkspaceUtil.getWorskspace(getASLSession());
logger.trace("input stream is not null");
// System.out.println("input stream is not null");
@ -1580,7 +1607,7 @@ public class TaxonomySearchServiceImpl extends RemoteServiceServlet implements T
InputStream inputStream = taxonomyService.getTaxonomyJobErrorFileById(jobIdentifier);
if(inputStream!=null){
Workspace workspace = org.gcube.portlets.user.speciesdiscovery.server.util.GetWorkspaceUtil.getWorskspace(getASLSession());
Workspace workspace = GetWorkspaceUtil.getWorskspace(getASLSession());
logger.trace("input stream is not null");
// System.out.println("input stream is not null");
@ -1607,12 +1634,12 @@ public class TaxonomySearchServiceImpl extends RemoteServiceServlet implements T
}
@Override
public List<TaxonomyRow> retrieveTaxonomyByIds(List<String> ids) throws Exception{
public List<LightTaxonomyRow> retrieveTaxonomyByIds(List<String> ids) throws Exception{
logger.trace("retrieveTaxonomyByIds ids size: " + ids.size());
// System.out.println("retrieveTaxonomyByIds ids size: " + ids.size() + " first id " + ids.get(0));
List<TaxonomyRow> listTaxonomyRow = new ArrayList<TaxonomyRow>();
List<LightTaxonomyRow> listLightTaxonomyRow = new ArrayList<LightTaxonomyRow>();
try {
SpeciesService taxonomyService = getSpeciesService();
@ -1620,19 +1647,32 @@ public class TaxonomySearchServiceImpl extends RemoteServiceServlet implements T
CloseableIterator<TaxonomyItem> streamIterator = taxonomyService.retrieveTaxonomyById(convert);
TaxonomyItemConverter taxonomyItemConverter = new TaxonomyItemConverter(getASLSession());
ASLSession session = getASLSession();
TaxonomyItemConverter taxonomyItemConverter = new TaxonomyItemConverter(session);
Map<String, TaxonomyRow> mapTaxonomyIds = SessionUtil.getHashMapTaxonomyByIdsCache(session);
if(mapTaxonomyIds==null){
logger.trace("Cache taxa ByIds doesn't exists into session, creating..");
mapTaxonomyIds = new HashMap<String, TaxonomyRow>();
}
int i = 1;
while (streamIterator.hasNext()) {
TaxonomyItem tax = streamIterator.next();
// from TaxonomyItem to TaxonomyRow
TaxonomyRow taxonomyRow = taxonomyItemConverter.convert(tax);
listTaxonomyRow.add(taxonomyRow);
logger.trace(i + ") retrieveTaxonomyById: " + taxonomyRow);
// System.out.println(i + ") retrieveTaxonomyById: " + taxonomyRow);
i++;
TaxonomyRow taxonomy = taxonomyItemConverter.convert(tax);
if(mapTaxonomyIds.get(taxonomy.getServiceId())==null){
logger.trace("Taxonomy with service id: "+taxonomy.getServiceId()+" doesn't exists into Map Taxonomy Ids, adding..");
mapTaxonomyIds.put(taxonomy.getServiceId(),taxonomy);
}
LightTaxonomyRow lightTaxRow = ClusterStructuresForTaxonomyRow.convetTaxonomyRowToLigthTaxonomyRow(taxonomy);
listLightTaxonomyRow.add(lightTaxRow);
}
SessionUtil.setHashMapTaxonomyByIdsCache(session, mapTaxonomyIds);
streamIterator.close();
} catch (Exception e) {
@ -1642,47 +1682,60 @@ public class TaxonomySearchServiceImpl extends RemoteServiceServlet implements T
// throw new Exception(e.getMessage());
}
return listTaxonomyRow;
return listLightTaxonomyRow;
}
@Override
public List<TaxonomyRow> retrieveSynonymsByRefId(String refId) throws Exception{
public List<LightTaxonomyRow> retrieveSynonymsByRefId(String refId) throws Exception{
logger.trace("retrieveSynonymsById id: " + refId);
//FOR DEBUG
// System.out.println("retrieveSynonymsById id: " + refId);
List<TaxonomyRow> listTaxonomyRow = new ArrayList<TaxonomyRow>();
List<LightTaxonomyRow> listLightTaxonomyRow = new ArrayList<LightTaxonomyRow>();
try {
SpeciesService taxonomyService = getSpeciesService();
CloseableIterator<TaxonomyItem> streamIterator = taxonomyService.retrieveSynonymsById(refId);
ASLSession session = getASLSession();
TaxonomyItemConverter taxonomyItemConverter = new TaxonomyItemConverter(getASLSession());
int i = 1;
Map<String, TaxonomyRow> mapSysnosyms = SessionUtil.getHashMapSynonymsTaxonomyCache(getASLSession());
if(mapSysnosyms==null){
logger.trace("Cache synonyms doesn't exists into session, creating..");
mapSysnosyms = new HashMap<String, TaxonomyRow>();
}
// int i = 1;
while (streamIterator.hasNext()) {
TaxonomyItem tax = streamIterator.next();
// from TaxonomyItem to TaxonomyRow
TaxonomyRow taxonomyRow = taxonomyItemConverter.convert(tax);
listTaxonomyRow.add(taxonomyRow);
logger.trace(i + ") retrieveSynonymsById: " + taxonomyRow);
// System.out.println(i + ") retrieveSynonymsById: " + taxonomyRow);
i++;
TaxonomyRow taxonomy = taxonomyItemConverter.convert(tax);
if(mapSysnosyms.get(taxonomy.getServiceId())==null){
logger.trace("Taxonomy with service id: "+taxonomy.getServiceId()+" doesn't exists into Map Synonyms, adding..");
mapSysnosyms.put(taxonomy.getServiceId(),taxonomy);
}
LightTaxonomyRow lightTaxRow = ClusterStructuresForTaxonomyRow.convetTaxonomyRowToLigthTaxonomyRow(taxonomy);
listLightTaxonomyRow.add(lightTaxRow);
}
SessionUtil.setHashMapSynonymsTaxonomyCache(session, mapSysnosyms);
streamIterator.close();
} catch (Exception e) {
e.printStackTrace();
logger.error("An error retrieve synonyms by Id",e);
// throw new Exception(e.getMessage());
}
return listTaxonomyRow;
return listLightTaxonomyRow;
}
@ -1909,7 +1962,7 @@ public class TaxonomySearchServiceImpl extends RemoteServiceServlet implements T
InputStream inputStream = taxonomyService.getOccurrenceJobFileById(jobModel.getJobIdentifier());
if(inputStream!=null){
Workspace workspace = org.gcube.portlets.user.speciesdiscovery.server.util.GetWorkspaceUtil.getWorskspace(getASLSession());
Workspace workspace = GetWorkspaceUtil.getWorskspace(getASLSession());
logger.trace("input stream is not null");
// System.out.println("input stream is not null");
@ -1960,7 +2013,7 @@ public class TaxonomySearchServiceImpl extends RemoteServiceServlet implements T
InputStream inputStream = taxonomyService.getOccurrenceJobErrorFileById(jobModel.getJobIdentifier());
if(inputStream!=null){
Workspace workspace = org.gcube.portlets.user.speciesdiscovery.server.util.GetWorkspaceUtil.getWorskspace(getASLSession());
Workspace workspace = GetWorkspaceUtil.getWorskspace(getASLSession());
logger.trace("input stream is not null");
// System.out.println("input stream is not null");
@ -2018,16 +2071,60 @@ public class TaxonomySearchServiceImpl extends RemoteServiceServlet implements T
boolean isReduced = false;
int totalRow = countSelectedRow;
ASLSession session = getASLSession();
HashMap<String, ClusterCommonNameDataSourceForResultRow> hashCluster = SessionUtil.getCurrentClusterCommonNameForResultRow(session);
//Reset cluster for common name
if(hashCluster!=null)
SessionUtil.setCurrentClusterCommonNameForResultRow(session, null);
//LIMIT NUMBER OF ITEMS TO ConstantsSpeciesDiscovery.LIMIT_ITEM_DETAILS
if(countSelectedRow>ConstantsSpeciesDiscovery.LIMIT_ITEM_DETAILS)
countSelectedRow = ConstantsSpeciesDiscovery.LIMIT_ITEM_DETAILS;
if(countSelectedRow>ConstantsSpeciesDiscovery.RESULT_ROW_LIMIT_ITEM_DETAILS)
countSelectedRow = ConstantsSpeciesDiscovery.RESULT_ROW_LIMIT_ITEM_DETAILS;
ResultFilter filter = new ResultFilter(false, true, true);
SearchResult<ResultRow> searchResults = getSearchResultRows(0, countSelectedRow, filter, true);
return new ClusterStructuresForResultRow(searchResults,isReduced, totalRow);
ClusterStructuresForResultRow cluster = new ClusterStructuresForResultRow(searchResults,isReduced, totalRow);
//TODO USE THREAD?
ManagerClusterCommonNameDataSourceForResultRow manager = new ManagerClusterCommonNameDataSourceForResultRow(cluster.getHashClusterScientificNameResultRowServiceID(), cluster.getHashResult());
SessionUtil.setCurrentClusterCommonNameForResultRow(getASLSession(), manager.getHashClusterCommonNameDataSource());
//THIS OBJECT IS NOT USED ON CLIENT
cluster.setHashResult(null);
return cluster;
}
@Override
public ClusterCommonNameDataSourceForResultRow loadClusterCommonNameForResultRowByScientificName(String scientificName) throws Exception {
logger.trace("loadClusterCommonNameForResultRowByScientificName for scientific name: "+scientificName);
HashMap<String, ClusterCommonNameDataSourceForResultRow> hashCluster = SessionUtil.getCurrentClusterCommonNameForResultRow(getASLSession());
if(hashCluster==null){
logger.warn("Error in loadClusterCommonNameForResultRowByScientificName, hashCluster was not found in session");
return null;
}
ClusterCommonNameDataSourceForResultRow cluster = hashCluster.get(scientificName);
if(cluster==null){
logger.warn("Error in loadClusterCommonNameForResultRowByScientificName, cluster was not found in session");
return null;
}
return cluster;
}
@ -2081,9 +2178,35 @@ public class TaxonomySearchServiceImpl extends RemoteServiceServlet implements T
boolean isReduced = false;
int totalRow = countSelectedRow;
ASLSession session = getASLSession();
HashMap<String, ClusterCommonNameDataSourceForTaxonomyRow> hashCluster = SessionUtil.getCurrentClusterCommonNameForTaxonomyRow(session);
//Reset cluster for common name
if(hashCluster!=null)
SessionUtil.setCurrentClusterCommonNameForTaxonomyRow(session, null);
HashMap<String, TaxonomyRow> mapOldChildren = SessionUtil.getHashMapChildrenTaxonomyCache(session);
//Reset list children to last clustering
if(mapOldChildren!=null)
SessionUtil.setHashMapChildrenTaxonomyCache(session, null);
HashMap<String, TaxonomyRow> mapSynonyms = SessionUtil.getHashMapSynonymsTaxonomyCache(session);
//Reset list synonyms to last clustering
if(mapSynonyms!=null)
SessionUtil.setHashMapSynonymsTaxonomyCache(session, null);
HashMap<String, TaxonomyRow> mapTaxonomyIds = SessionUtil.getHashMapTaxonomyByIdsCache(session);
//Reset list synonyms to last clustering
if(mapTaxonomyIds!=null)
SessionUtil.setHashMapTaxonomyByIdsCache(session, null);
//LIMIT NUMBER OF ITEMS TO ConstantsSpeciesDiscovery.LIMIT_ITEM_DETAILS
if(countSelectedRow>ConstantsSpeciesDiscovery.LIMIT_ITEM_DETAILS){
countSelectedRow = ConstantsSpeciesDiscovery.LIMIT_ITEM_DETAILS;
if(countSelectedRow>ConstantsSpeciesDiscovery.TAXONOMY_LIMIT_ITEMS_DETAILS){
countSelectedRow = ConstantsSpeciesDiscovery.TAXONOMY_LIMIT_ITEMS_DETAILS;
isReduced = true;
}
@ -2091,7 +2214,18 @@ public class TaxonomySearchServiceImpl extends RemoteServiceServlet implements T
SearchResult<TaxonomyRow> searchResults = getSearchTaxonomyRow(0, countSelectedRow, filter, true);
return new ClusterStructuresForTaxonomyRow(searchResults, isReduced, totalRow);
ClusterStructuresForTaxonomyRow cluster = new ClusterStructuresForTaxonomyRow(searchResults,isReduced, totalRow);
//TODO USE THREAD?
ManagerClusterCommonNameDataSourceForTaxonomyRow manager = new ManagerClusterCommonNameDataSourceForTaxonomyRow(cluster.getHashClusterScientificNameTaxonomyRowServiceID(), cluster.getHashResult());
SessionUtil.setCurrentClusterCommonNameForTaxonomyRow(session, manager.getHashClusterCommonNameDataSource());
//THIS OBJECT IS NOT USED ON CLIENT
cluster.setHashResult(null);
return cluster;
}
@ -2167,4 +2301,33 @@ public class TaxonomySearchServiceImpl extends RemoteServiceServlet implements T
ASLSession session = getASLSession();
return SessionUtil.getCurrentQuery(session);
}
/* (non-Javadoc)
* @see org.gcube.portlets.user.speciesdiscovery.client.rpc.TaxonomySearchService#loadClusterCommonNameForTaxonomyRowByScientificName(java.lang.String)
*/
@Override
public ClusterCommonNameDataSourceForTaxonomyRow loadClusterCommonNameForTaxonomyRowByScientificName(String scientificName) {
System.out.println("loadClusterCommonNameForTaxonomyRowByScientificName for scientific name: "+scientificName);
logger.trace("loadClusterCommonNameForTaxonomyRowByScientificName for scientific name: "+scientificName);
HashMap<String, ClusterCommonNameDataSourceForTaxonomyRow> hashCluster = SessionUtil.getCurrentClusterCommonNameForTaxonomyRow(getASLSession());
if(hashCluster==null){
logger.warn("Error in loadClusterCommonNameForTaxonomyRowByScientificName, hashCluster was not found in session");
return null;
}
ClusterCommonNameDataSourceForTaxonomyRow cluster = hashCluster.get(scientificName);
if(cluster==null){
logger.warn("Error in loadClusterCommonNameForTaxonomyRowByScientificName, cluster was not found in session");
return null;
}
return cluster;
}
}

104
src/main/java/org/gcube/portlets/user/speciesdiscovery/server/asl/SessionUtil.java
View File

@ -3,6 +3,9 @@
*/
package org.gcube.portlets.user.speciesdiscovery.server.asl;
import java.util.HashMap;
import java.util.Map;
import javax.persistence.EntityManagerFactory;
import javax.servlet.http.HttpSession;
@ -19,6 +22,9 @@ import org.gcube.portlets.user.speciesdiscovery.server.service.SpeciesService;
import org.gcube.portlets.user.speciesdiscovery.server.session.FetchingSession;
import org.gcube.portlets.user.speciesdiscovery.shared.FetchingElement;
import org.gcube.portlets.user.speciesdiscovery.shared.Occurrence;
import org.gcube.portlets.user.speciesdiscovery.shared.TaxonomyRow;
import org.gcube.portlets.user.speciesdiscovery.shared.cluster.ClusterCommonNameDataSourceForResultRow;
import org.gcube.portlets.user.speciesdiscovery.shared.cluster.ClusterCommonNameDataSourceForTaxonomyRow;
/**
*
@ -40,6 +46,11 @@ public class SessionUtil {
public static final String EJB_OCCURRENCES_JOB = "EJB_OCCURRENCES_JOB";
public static final String EJB_TAXONOMY_JOB = "EJB_TAXONOMY_JOB";
public static final String CURRENT_SPD_QUERY = "CURRENT_SPD_QUERY";
private static final String CLUSTER_COMMONNAME_FOR_RESULTROW = "CLUSTER_COMMONNAME_FOR_RESULTROW";
private static final String CLUSTER_COMMONNAME_FOR_TAXONOMYROW = "CLUSTER_COMMONNAME_FOR_TAXONOMYROW";
private static final String CACHE_HASH_MAP_CHILDREN_TAXONOMY = "CACHE_HASH_MAP_CHILDREN_TAXONOMY";
private static final String CACHE_HASH_MAP_SYNONYMS_TAXONOMY = "CACHE_HASH_MAP_SYNONYMS_TAXONOMY";
private static final String CACHE_HASH_MAP_TAXONOMYID_TAXONOMY = "CACHE_HASH_MAP_TAXONOMYID_TAXONOMY";
protected static Logger logger = Logger.getLogger(SessionUtil.class);
@ -110,7 +121,7 @@ public class SessionUtil {
httpSession.setAttribute(USERNAME_ATTRIBUTE, user);
ASLSession session = SessionManager.getInstance().getASLSession(sessionID, user);
session.setScope(scope);
logger.warn("TaxonomySearchServiceImpl STARTING IN TEST MODE - NO USER FOUND");
logger.warn("Created fake Asl session for user "+user + " with scope "+scope);
// session.setScope("/gcube/devsec");
@ -196,4 +207,95 @@ public class SessionUtil {
return (String) aslSession.getAttribute(CURRENT_SPD_QUERY);
}
/**
* @param hashClusterCommonNameDataSource
*/
public static void setCurrentClusterCommonNameForResultRow(ASLSession session, HashMap<String, ClusterCommonNameDataSourceForResultRow> hashClusterCommonNameDataSource) {
session.setAttribute(CLUSTER_COMMONNAME_FOR_RESULTROW, hashClusterCommonNameDataSource);
}
/**
* @param hashClusterCommonNameDataSource
* @return
*/
public static HashMap<String, ClusterCommonNameDataSourceForResultRow> getCurrentClusterCommonNameForResultRow(ASLSession session) {
return (HashMap<String, ClusterCommonNameDataSourceForResultRow>) session.getAttribute(CLUSTER_COMMONNAME_FOR_RESULTROW);
}
/**
* @param hashClusterCommonNameDataSource
*/
public static void setCurrentClusterCommonNameForTaxonomyRow(ASLSession session, HashMap<String, ClusterCommonNameDataSourceForTaxonomyRow> hashClusterCommonNameDataSource) {
session.setAttribute(CLUSTER_COMMONNAME_FOR_TAXONOMYROW, hashClusterCommonNameDataSource);
}
/**
* @param hashClusterCommonNameDataSource
* @return
*/
public static HashMap<String, ClusterCommonNameDataSourceForTaxonomyRow> getCurrentClusterCommonNameForTaxonomyRow(ASLSession session) {
return (HashMap<String, ClusterCommonNameDataSourceForTaxonomyRow>) session.getAttribute(CLUSTER_COMMONNAME_FOR_TAXONOMYROW);
}
/**
* @return
*
*/
public static HashMap<String, TaxonomyRow> getHashMapChildrenTaxonomyCache(ASLSession session) {
return (HashMap<String, TaxonomyRow>) session.getAttribute(CACHE_HASH_MAP_CHILDREN_TAXONOMY);
}
/**
* @return
*
*/
public static void setHashMapChildrenTaxonomyCache(ASLSession session, Map<String, TaxonomyRow> list) {
session.setAttribute(CACHE_HASH_MAP_CHILDREN_TAXONOMY, list);
}
/**
* @return
*
*/
public static HashMap<String, TaxonomyRow> getHashMapSynonymsTaxonomyCache(ASLSession session) {
return (HashMap<String, TaxonomyRow>) session.getAttribute(CACHE_HASH_MAP_SYNONYMS_TAXONOMY);
}
/**
* @return
*
*/
public static void setHashMapSynonymsTaxonomyCache(ASLSession session, Map<String, TaxonomyRow> list) {
session.setAttribute(CACHE_HASH_MAP_SYNONYMS_TAXONOMY, list);
}
/**
* @return
*
*/
public static HashMap<String, TaxonomyRow> getHashMapTaxonomyByIdsCache(ASLSession session) {
return (HashMap<String, TaxonomyRow>) session.getAttribute(CACHE_HASH_MAP_TAXONOMYID_TAXONOMY);
}
/**
* @return
*
*/
public static void setHashMapTaxonomyByIdsCache(ASLSession session, Map<String, TaxonomyRow> list) {
session.setAttribute(CACHE_HASH_MAP_TAXONOMYID_TAXONOMY, list);
}
}

1
src/main/java/org/gcube/portlets/user/speciesdiscovery/server/persistence/AbstractDaoBuffer.java
View File

@ -72,5 +72,4 @@ public abstract class AbstractDaoBuffer<T extends FetchingElement> implements Fe
public List<T> getList(Map<String, String> filterANDMap, int startIndex, int offset) throws Exception{
return dao.getList(filterANDMap, startIndex, offset);
}
}

1
src/main/java/org/gcube/portlets/user/speciesdiscovery/server/persistence/AbstractSelectableDaoBuffer.java
View File

@ -74,5 +74,4 @@ public abstract class AbstractSelectableDaoBuffer<T extends SelectableElement> e
return getSelected().size();
}
}

6
src/main/java/org/gcube/portlets/user/speciesdiscovery/server/persistence/DaoSession.java
View File

@ -26,7 +26,7 @@ public class DaoSession {
protected static final String PROPERTY_CATALINA_HOME = "catalina.home";
protected static final String CATALINA_HOME = "CATALINA_HOME";
protected static final String TEMP_H2DBSPECIES_H2 = "temp/h2dbspecies/h2";
protected static final String PERSISTENCE_H2DBSPECIES_H2 = "persistence/h2dbspecies/h2";
public static Logger logger = Logger.getLogger(DaoSession.class);
private static final String JDBCDRIVER = "jdbc:h2:";
@ -63,7 +63,7 @@ public class DaoSession {
String username = session.getUsername();
String scope = session.getScopeName();
return JDBCDRIVER +getTomcatFolder()+TEMP_H2DBSPECIES_H2+getUsernameScopeValue(username,scope)+";create=true";
return JDBCDRIVER +getTomcatFolder()+PERSISTENCE_H2DBSPECIES_H2+getUsernameScopeValue(username,scope)+";create=true";
}
@ -145,7 +145,7 @@ public class DaoSession {
logger.error("error on get connection url "+e, e);
String username = session.getUsername();
String scope = session.getScopeName();
properties.put("javax.persistence.jdbc.url", JDBCDRIVER+"/temp/h2dbspecies/h2"+getUsernameScopeValue(username,scope)+";create=true");
properties.put("javax.persistence.jdbc.url", JDBCDRIVER+getTomcatFolder()+"/temp/h2dbspecies/h2"+getUsernameScopeValue(username,scope)+";create=true");
}
//emf = Persistence.createEntityManagerFactory("jpablogPUnit");
return Persistence.createEntityManagerFactory("SPD_PERSISTENCE_FACTORY",properties);

3
src/main/java/org/gcube/portlets/user/speciesdiscovery/server/persistence/ResultRowBuffer.java
View File

@ -52,8 +52,7 @@ public class ResultRowBuffer extends AbstractSelectableDaoBuffer<ResultRow> impl
@Override
public void add(ResultRow row) throws Exception{
//FOR DEBUG
// logger.trace("Add item "+ row.getServiceId());
logger.trace("Add item "+ row.getId() + " service id: " +row.getServiceId());
// logger.trace("Add item "+ row.getId() + " service id: " +row.getServiceId());
super.add(row);
}

3
src/main/java/org/gcube/portlets/user/speciesdiscovery/server/persistence/TaxonomyRowBuffer.java
View File

@ -46,8 +46,7 @@ public class TaxonomyRowBuffer extends AbstractSelectableDaoBuffer<TaxonomyRow>
public void add(TaxonomyRow row) throws Exception
{
//DEBUG
logger.trace("Add item "+ row.getId() + " service id: " +row.getServiceId());
// logger.trace("Add item "+ row);
// logger.trace("Add item "+ row.getId() + " service id: " +row.getServiceId());
super.add(row);
}

119
src/main/java/org/gcube/portlets/user/speciesdiscovery/server/service/TaxonomyItemConverter.java
View File

@ -12,6 +12,7 @@ import org.gcube.portlets.user.speciesdiscovery.server.TaxonomySearchServiceImpl
import org.gcube.portlets.user.speciesdiscovery.server.stream.Converter;
import org.gcube.portlets.user.speciesdiscovery.shared.CommonName;
import org.gcube.portlets.user.speciesdiscovery.shared.ItemParameter;
import org.gcube.portlets.user.speciesdiscovery.shared.LightTaxonomyRow;
import org.gcube.portlets.user.speciesdiscovery.shared.TaxonomyRow;
import org.gcube.portlets.user.speciesdiscovery.shared.util.NormalizeString;
@ -53,6 +54,87 @@ public class TaxonomyItemConverter implements Converter<TaxonomyItem, TaxonomyRo
return taxonomy;
}
public LightTaxonomyRow convertLightTaxonomy(TaxonomyItem input) throws Exception {
LightTaxonomyRow taxonomy = createLightTaxonomyRow(input);
//SET PARENTS
// System.out.println("Convert Taxonomy parent for: "+taxonomy.getId());
taxonomy.setParent(convertParentsLightTaxonomy(input));
//SET BASE TAXON
taxonomy.setBaseTaxonValue(NormalizeString.lowerCaseUpFirstChar(getTaxonomyValue(TaxonomySearchServiceImpl.BASETAXONOMY,taxonomy)));
if(taxonomy.getParents()!=null && taxonomy.getParents().size()>0)
taxonomy.setParentID(""+taxonomy.getParents().get(0).getId());
return taxonomy;
}
protected LightTaxonomyRow createLightTaxonomyRow(TaxonomyItem input) throws Exception{
LightTaxonomyRow tax = new LightTaxonomyRow(id++);
if(input.getId()!=null){
tax.setServiceId(input.getId());
}
if(input.getProvider()!=null && !input.getProvider().isEmpty()){
tax.setDataProviderId(input.getProvider());
tax.setDataProviderName(input.getProvider());
}else{
tax.setDataProviderId(ConstantsSpeciesDiscovery.NOT_FOUND);
tax.setDataProviderName(ConstantsSpeciesDiscovery.NOT_FOUND);
}
if(input.getRank()!=null && !input.getRank().isEmpty()){
tax.setRank(NormalizeString.lowerCaseUpFirstChar(input.getRank()));
}else{
tax.setRank(ConstantsSpeciesDiscovery.NOT_FOUND);
}
if(input.getScientificName()!=null && !input.getScientificName().isEmpty()){
tax.setName(input.getScientificName());
}else{
tax.setName(ConstantsSpeciesDiscovery.NOT_FOUND);
}
if(input.getStatus()!=null){
if(input.getStatus().getRefId()!=null && !input.getStatus().getRefId().isEmpty()){
tax.setStatusRefId(input.getStatus().getRefId());
}else{
tax.setStatusRefId("");
}
if(input.getStatus().getStatusAsString()!=null && !input.getStatus().getStatusAsString().isEmpty()){
tax.setStatusRemarks(input.getStatus().getStatusAsString());
}else{
tax.setStatusRemarks(ConstantsSpeciesDiscovery.NOT_FOUND);
}
if(input.getStatus().getStatus()!=null){
if(input.getStatus().getStatus().name()!=null && !input.getStatus().getStatus().name().isEmpty()){
tax.setStatusName(input.getStatus().getStatus().name());
}else{
tax.setStatusName(ConstantsSpeciesDiscovery.NOT_FOUND);
}
}
}
return tax;
}
protected TaxonomyRow createTaxonomyRow(TaxonomyItem input) throws Exception{
@ -177,6 +259,43 @@ public class TaxonomyItemConverter implements Converter<TaxonomyItem, TaxonomyRo
}
private String getTaxonomyValue(String rank, LightTaxonomyRow taxon){
List<LightTaxonomyRow> listTaxonomy = taxon.getParents();
for (LightTaxonomyRow taxonomyRow : listTaxonomy) {
if(taxonomyRow.getRank().compareToIgnoreCase(rank)==0)
return taxonomyRow.getName();
}
return TaxonomySearchServiceImpl.TAXONOMYUNKNOWN;
}
protected List<LightTaxonomyRow> convertParentsLightTaxonomy(TaxonomyItem taxon) throws Exception
{
if (taxon == null) return null;
List<LightTaxonomyRow> listTaxonomy = new ArrayList<LightTaxonomyRow>();
TaxonomyItem parent = taxon.getParent();
int i=0;
while(parent!=null){
LightTaxonomyRow row = createLightTaxonomyRow(parent);
row.setParent(true);
row.setParentIndex(i++);
// System.out.println("Insert Taxonomy parent id: "+row.getId() + ", row.getParentIndex: "+row.getParentIndex());
listTaxonomy.add(row);
parent = parent.getParent();
}
return listTaxonomy;
}
protected List<TaxonomyRow> convertParentsTaxonomy(TaxonomyItem taxon) throws Exception
{
if (taxon == null) return null;

10
src/main/java/org/gcube/portlets/user/speciesdiscovery/server/util/StorageUtil.java
View File

@ -14,8 +14,8 @@ import org.gcube.contentmanager.storageclient.model.protocol.smp.SMPURLConnectio
public class StorageUtil {
protected Logger logger = Logger.getLogger(StorageUtil.class);
protected static Logger logger = Logger.getLogger(StorageUtil.class);
public static InputStream getInputStreamByStorageClient(String url) throws Exception {
Handler.activateProtocol();
@ -40,11 +40,13 @@ public class StorageUtil {
InputStream is=uc.getInputStream();
return is;
}
public static void main(String[] args) throws Exception {
InputStream is = getInputStreamByStorageClient("smp:/51e1065ee4b0a159b8c25cc8?5ezvFfBOLqb2cBxvyAbVnOhbxBCSqhv+Z4BC5NS/+OwS5RYBeaUL5FS9eDyNubiTI4vSpggUgPA+jm9rQxwbisfhkOW/m6l2IYG9BKb8AEJFLgVvG3FJTk0+4xV9iM/hNQvChZjoJZna0aPXkHN4Eg==");
}
}

4
src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/JobTaxonomyModel.java
View File

@ -129,8 +129,8 @@ public class JobTaxonomyModel implements Serializable {
return submitTime;
}
public void setSubmitTime(Date submitTime) {
this.submitTime = submitTime;
public void setSubmitTime(Date startTime) {
this.submitTime = startTime;
}
public Date getEndTime() {

253
src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/LightTaxonomyRow.java Normal file
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@ -0,0 +1,253 @@
/**
*
*/
package org.gcube.portlets.user.speciesdiscovery.shared;
import java.io.Serializable;
import java.util.Collections;
import java.util.List;
/**
*
* @author Francesco Mangiacrapa francesco.mangiacrapa@isti.cnr.it
*
*/
public class LightTaxonomyRow implements FetchingElement, Serializable, Comparable<LightTaxonomyRow> {
/**
*
*/
private static final long serialVersionUID = -3303399965998066897L;
public final static String ID_FIELD = "id";
public final static String DATAPROVIDER_NAME = "dataProviderName";
public static final String DATAPROVIDER_ID = "dataProviderId";
public final static String RANK = "rank";
public static final String NAME = "name";
public static final String STATUSREFID = "statusRefId";
public static final String STATUSNAME = "statusName";
public final static String PARENT_ID = "parentID";
public final static String IS_PARENT = "isParent";
public final static String SERVICE_ID_FIELD = "serviceIdField";
public final static String STATUS_REMARKS = "statusRemarks";
public static final String BASE_TAXON_VALUE = "baseTaxonValue";
protected String name;
protected String serviceIdField;
protected String dataProviderId;
protected String dataProviderName;
protected String rank;
private String statusRefId;
private String statusName;
protected String baseTaxonValue;
protected String statusRemarks;
private boolean isParent = false;
protected List<LightTaxonomyRow> parents;
//USED FOR PARENT
protected String parentID;
protected int id;
protected int parentIndex = -1;
protected LightTaxonomyRow() {
}
/**
* @param id
*/
public LightTaxonomyRow(int id) {
this.id = id;
}
/**
* @return the id
*/
public int getId() {
return id;
}
/**
* @return the id
*/
public String getIdToString() {
return id+"";
}
public void setBaseTaxonValue(String taxonomyValue) {
this.baseTaxonValue = taxonomyValue;
}
public String getBaseTaxonValue() {
return baseTaxonValue;
}
/**
* @return the dataProviderId
*/
public String getDataProviderId() {
return dataProviderId;
}
/**
* @param dataProviderId
* the dataProviderId to set
*/
public void setDataProviderId(String dataProviderId) {
this.dataProviderId = dataProviderId;
}
/**
* @return the dataProviderName
*/
public String getDataProviderName() {
return dataProviderName;
}
/**
* @param dataProviderName
* the dataProviderName to set
*/
public void setDataProviderName(String dataProviderName) {
this.dataProviderName = dataProviderName;
}
public String getRank() {
return rank;
}
public void setRank(String rank) {
this.rank = rank;
}
public String getName() {
return name;
}
public void setName(String name) {
this.name = name;
}
public void setStatusRefId(String statusRefId) {
this.statusRefId = statusRefId;
}
public void setStatusName(String statusName) {
this.statusName = statusName;
}
public void setParent(List<LightTaxonomyRow> parent) {
this.parents = parent;
}
public List<LightTaxonomyRow> getParents() {
Collections.sort(parents);
return parents;
}
public String getStatusRefId() {
return statusRefId;
}
public String getStatusName() {
return statusName;
}
public String getTaxonId() {
return ""+id;
}
public String getParentID() {
return parentID;
}
public void setParentID(String parentID) {
this.parentID = parentID;
}
public String getServiceId() {
return serviceIdField;
}
public void setServiceId(String serviceIdField) {
this.serviceIdField = serviceIdField;
}
public String getStatusRemarks() {
return statusRemarks;
}
public void setStatusRemarks(String statusRemarks) {
this.statusRemarks = statusRemarks;
}
public boolean isParent() {
return isParent;
}
public void setParent(boolean isParent) {
this.isParent = isParent;
}
public int getParentIndex() {
return parentIndex;
}
public void setParentIndex(int parentIndex) {
this.parentIndex = parentIndex;
}
/* (non-Javadoc)
* Comparable on insertion order
* @see java.lang.Comparable#compareTo(java.lang.Object)
*/
@Override
public int compareTo(LightTaxonomyRow o) {
return parentIndex - o.getParentIndex();
}
@Override
public String toString() {
StringBuilder builder = new StringBuilder();
builder.append("MinimalTaxonomyRow [id=");
builder.append(id);
builder.append(", name=");
builder.append(name);
builder.append(", serviceIdField=");
builder.append(serviceIdField);
builder.append(", dataProviderId=");
builder.append(dataProviderId);
builder.append(", dataProviderName=");
builder.append(dataProviderName);
builder.append(", rank=");
builder.append(rank);
builder.append(", statusRefId=");
builder.append(statusRefId);
builder.append(", statusName=");
builder.append(statusName);
builder.append(", baseTaxonValue=");
builder.append(baseTaxonValue);
builder.append(", statusRemarks=");
builder.append(statusRemarks);
builder.append(", isParent=");
builder.append(isParent);
builder.append(", parents=");
builder.append(parents);
builder.append(", parentID=");
builder.append(parentID);
builder.append(", parentIndex=");
builder.append(parentIndex);
builder.append("]");
return builder.toString();
}
}

15
src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/cluster/ClusterCommonNameDataSource.java
View File

@ -11,13 +11,28 @@ import org.gcube.portlets.user.speciesdiscovery.shared.ResultRow;
import org.gcube.portlets.user.speciesdiscovery.shared.TaxonomyRow;
import org.gcube.portlets.user.speciesdiscovery.shared.util.NormalizeString;
/**
*
* @author Francesco Mangiacrapa francesco.mangiacrapa@isti.cnr.it
* @Sep 5, 2013
*
* @param <T>
*/
//@Entity
public class ClusterCommonNameDataSource<T extends FetchingElement> implements Serializable{
/**
*
*/
private static final long serialVersionUID = -4602671242562941238L;
// @Id
// @GeneratedValue(strategy = GenerationType.IDENTITY)
// private int internalId;
private HashMap<String, ArrayList<String>> hashMapCommonNameDataSources = new HashMap<String, ArrayList<String>>();
private ArrayList<String> listDataSourcesFound = new ArrayList<String>();

78
src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/cluster/ClusterCommonNameDataSourceForResultRow.java Normal file
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@ -0,0 +1,78 @@
/**
*
*/
package org.gcube.portlets.user.speciesdiscovery.shared.cluster;
import java.io.Serializable;
import org.gcube.portlets.user.speciesdiscovery.shared.ResultRow;
/**
* @author Francesco Mangiacrapa francesco.mangiacrapa@isti.cnr.it
* @Sep 5, 2013
*
*/
//@Entity
public class ClusterCommonNameDataSourceForResultRow implements Serializable{
/**
*
*/
private static final long serialVersionUID = -7566939414748687391L;
// @Id
// @GeneratedValue(strategy = GenerationType.IDENTITY)
// private int internalId;
private String scientificName; //IS THE KEY
private ClusterCommonNameDataSource<ResultRow> cluster = new ClusterCommonNameDataSource<ResultRow>(); //NEW CLUSTER
public ClusterCommonNameDataSourceForResultRow(){}
/**
* @param scientificName
* @param cluster
*/
public ClusterCommonNameDataSourceForResultRow(String scientificName, ClusterCommonNameDataSource<ResultRow> cluster) {
super();
this.scientificName = scientificName;
this.cluster = cluster;
}
public String getScientificName() {
return scientificName;
}
public void setScientificName(String scientificName) {
this.scientificName = scientificName;
}
public ClusterCommonNameDataSource<ResultRow> getCluster() {
return cluster;
}
public void setCluster(ClusterCommonNameDataSource<ResultRow> cluster) {
this.cluster = cluster;
}
// public int getInternalId() {
// return internalId;
// }
@Override
public String toString() {
StringBuilder builder = new StringBuilder();
builder.append("ClusterCommonNameDataSourceForResultRow [scientificName=");
builder.append(scientificName);
builder.append(", cluster=");
builder.append(cluster);
builder.append("]");
return builder.toString();
}
}

67
src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/cluster/ClusterCommonNameDataSourceForTaxonomyRow.java Normal file
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@ -0,0 +1,67 @@
/**
*
*/
package org.gcube.portlets.user.speciesdiscovery.shared.cluster;
import java.io.Serializable;
import org.gcube.portlets.user.speciesdiscovery.shared.TaxonomyRow;
/**
*
* @author Francesco Mangiacrapa francesco.mangiacrapa@isti.cnr.it
* @Sep 18, 2013
*
*/
public class ClusterCommonNameDataSourceForTaxonomyRow implements Serializable{
/**
*
*/
private static final long serialVersionUID = 769286880968121045L;
private String scientificName; //IS THE KEY
private ClusterCommonNameDataSource<TaxonomyRow> cluster = new ClusterCommonNameDataSource<TaxonomyRow>(); //NEW CLUSTER
public ClusterCommonNameDataSourceForTaxonomyRow(){}
/**
* @param scientificName
* @param cluster
*/
public ClusterCommonNameDataSourceForTaxonomyRow(String scientificName, ClusterCommonNameDataSource<TaxonomyRow> cluster) {
super();
this.scientificName = scientificName;
this.cluster = cluster;
}
public String getScientificName() {
return scientificName;
}
public void setScientificName(String scientificName) {
this.scientificName = scientificName;
}
public ClusterCommonNameDataSource<TaxonomyRow> getCluster() {
return cluster;
}
public void setCluster(ClusterCommonNameDataSource<TaxonomyRow> cluster) {
this.cluster = cluster;
}
@Override
public String toString() {
StringBuilder builder = new StringBuilder();
builder.append("ClusterCommonNameDataSourceForTaxonomyRow [scientificName=");
builder.append(scientificName);
builder.append(", cluster=");
builder.append(cluster);
builder.append("]");
return builder.toString();
}
}

103
src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/cluster/ClusterStructuresForResultRow.java
View File

@ -22,51 +22,36 @@ public class ClusterStructuresForResultRow implements Serializable{
*
*/
private static final long serialVersionUID = 1205113606387863736L;
private ArrayList<String> listResultRowID;
private Map<String, ResultRow> hashResult = new HashMap<String, ResultRow>();
private ArrayList<String> listResultRowServiceID;
private ArrayList<String> listFoundDataSources = new ArrayList<String>();
private HashMap<String,ClusterCommonNameDataSource<ResultRow>> hashClusterCommonNamesDataSources = new HashMap<String,ClusterCommonNameDataSource<ResultRow>>(); //HASH scientific name - cluster
private HashMap<String, ArrayList<String>> hashScientificNameResultRowID = new HashMap<String, ArrayList<String>>(); //HASH scientific name - result row ID
private HashMap<String, ArrayList<String>> hashScientificNameResultRowServiceID = new HashMap<String, ArrayList<String>>(); //HASH scientific name - result row service ID
private boolean isReduced;
private int totalRow;
private int allResultRowSize;
private int resultSize;
private Map<String, ResultRow> hashResult = new HashMap<String, ResultRow>(); //HASH result row service ID - result row
public ClusterStructuresForResultRow(){}
public ClusterStructuresForResultRow(SearchResult<ResultRow> result, boolean isReduced, int totalRow){
//Create hashMap ID - resultRow
//Create hashMap service ID - resultRow
for (ResultRow row : result.getResults()) {
hashResult.put(row.getIdToString(), row);
// hashResult.put(row.getIdToString(), row);
hashResult.put(row.getServiceId(), row);
}
//
this.isReduced = isReduced;
this.totalRow = totalRow;
this.allResultRowSize = totalRow;
this.resultSize = result.getResults().size();
createStructures(result.getResults());
createStructuresForCommonName();
// createStructuresForCommonName();
}
public void createStructuresForCommonName(){
if(hashScientificNameResultRowID.size()>0){
for(String scientificName : hashScientificNameResultRowID.keySet()){
ArrayList<String> listResultRowServiceID = hashScientificNameResultRowID.get(scientificName); //get RR serviceID
ClusterCommonNameDataSource<ResultRow> cluster = new ClusterCommonNameDataSource<ResultRow>(); //NEW CLUSTER
for(int i=0; i<listResultRowServiceID.size(); i++){
ResultRow row = hashResult.get(listResultRowServiceID.get(i));
cluster.updateHashCommonNamesDataSources(row);
}
hashClusterCommonNamesDataSources.put(scientificName, cluster);
}
}
}
public void createStructures(ArrayList<ResultRow> arrayListRR){
@ -84,13 +69,13 @@ public class ClusterStructuresForResultRow implements Serializable{
else
keyScientificName = NormalizeString.lowerCaseUpFirstChar(keyScientificName);
if(hashScientificNameResultRowID.get(keyScientificName)==null){
if(hashScientificNameResultRowServiceID.get(keyScientificName)==null){
listResultRowID = new ArrayList<String>(); //USED FOR CLUSTER COMMON NAMES
listResultRowServiceID = new ArrayList<String>(); //USED FOR CLUSTER COMMON NAMES
}
else{
listResultRowID = hashScientificNameResultRowID.get(keyScientificName); //USED FOR CLUSTER COMMON NAMES
listResultRowServiceID = hashScientificNameResultRowServiceID.get(keyScientificName); //USED FOR CLUSTER COMMON NAMES
}
}
@ -102,31 +87,30 @@ public class ClusterStructuresForResultRow implements Serializable{
if(listFoundDataSources.indexOf(dataSource)==-1)
listFoundDataSources.add(dataSource);
listResultRowID.add(row.getIdToString()+"");
// listResultRowServiceID.add(row.getIdToString()+"");
listResultRowServiceID.add(row.getServiceId());
//USED FOR CLUSTER COMMON NAMES
hashScientificNameResultRowID.put(keyScientificName, listResultRowID);
hashScientificNameResultRowServiceID.put(keyScientificName, listResultRowServiceID);
}
}
}
public HashMap<String, ArrayList<String>> getHashClusterScientificNameResultRowID() {
return hashScientificNameResultRowID;
public HashMap<String, ArrayList<String>> getHashClusterScientificNameResultRowServiceID() {
return hashScientificNameResultRowServiceID;
}
public List<String> getListFoundDataSources() {
return listFoundDataSources;
}
public HashMap<String, ClusterCommonNameDataSource<ResultRow>> getHashClusterCommonNamesDataSources() {
return hashClusterCommonNamesDataSources;
public ArrayList<String> getListResultRowID() {
return listResultRowServiceID;
}
public List<ResultRow> getResult() {
return new ArrayList<ResultRow>(hashResult.values());
}
public ResultRow getResultRowByRowID(String key) {
return hashResult.get(key);
public void setListResultRowID(ArrayList<String> listResultRowID) {
this.listResultRowServiceID = listResultRowID;
}
public boolean isReduced() {
@ -137,12 +121,31 @@ public class ClusterStructuresForResultRow implements Serializable{
this.isReduced = isReduced;
}
public int getTotalRow() {
return totalRow;
public int getAllResultRowSize() {
return allResultRowSize;
}
public void setTotalRow(int totalRow) {
this.totalRow = totalRow;
public void setAllResultRowSize(int allResultRowSize) {
this.allResultRowSize = allResultRowSize;
}
public int getResultSize() {
return resultSize;
}
public void setResultSize(int resultSize) {
this.resultSize = resultSize;
}
public void setListFoundDataSources(ArrayList<String> listFoundDataSources) {
this.listFoundDataSources = listFoundDataSources;
}
public Map<String, ResultRow> getHashResult() {
return hashResult;
}
public void setHashResult(Map<String, ResultRow> hashResult) {
this.hashResult = hashResult;
}
}

139
src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/cluster/ClusterStructuresForTaxonomyRow.java
View File

@ -3,8 +3,10 @@ package org.gcube.portlets.user.speciesdiscovery.shared.cluster;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import org.gcube.portlets.user.speciesdiscovery.shared.LightTaxonomyRow;
import org.gcube.portlets.user.speciesdiscovery.shared.SearchResult;
import org.gcube.portlets.user.speciesdiscovery.shared.TaxonomyRow;
import org.gcube.portlets.user.speciesdiscovery.shared.util.NormalizeString;
@ -23,63 +25,62 @@ public class ClusterStructuresForTaxonomyRow implements Serializable{
*/
private static final long serialVersionUID = 2680552140187511057L;
private Map<String, TaxonomyRow> hashResult = new HashMap<String, TaxonomyRow>();
private HashMap<String,ClusterCommonNameDataSource<TaxonomyRow>> hashClusterCommonNamesDataSources = new HashMap<String,ClusterCommonNameDataSource<TaxonomyRow>>();
private HashMap<String, ArrayList<String>> hashClusterScientificNameTaxonomyRowID = new HashMap<String, ArrayList<String>>(); //HASH scientific name - taxonomy row ID
//USED ON CLIENT
private Map<String, LightTaxonomyRow> hashLightResult = new HashMap<String, LightTaxonomyRow>();
private HashMap<String, ArrayList<String>> hashClusterScientificNameTaxonomyRowServiceID = new HashMap<String, ArrayList<String>>(); //HASH scientific name - taxonomy row service ID
private ArrayList<String> listFoundDataSources = new ArrayList<String>();
private ArrayList<String> listTaxonomyRowID;
private ArrayList<String> listTaxonomyRowServiceID;
private boolean isReduced;
private int totalRow;
//USED ON SERVER FOR CLUSERING ON COMMON NAMES
private Map<String, TaxonomyRow> hashResult = new HashMap<String, TaxonomyRow>();
public ClusterStructuresForTaxonomyRow(){
}
public ClusterStructuresForTaxonomyRow(SearchResult<TaxonomyRow> result, boolean isReduced, int totalRow) {
//Create hashMap row ID - resultRow
for (TaxonomyRow row : result.getResults()) {
hashResult.put(row.getIdToString(), row);
//Create hashMap row service ID - resultRow
for (TaxonomyRow row : result.getResults()){
// int parentsSize = row.getParents().size();
//
// //FILL LIST PARENT FOR PARENTS ITEM
// for(int i=parentsSize-1; i>=0; i--){
// TaxonomyRow taxon = row.getParents().get(i);
// List<TaxonomyRow> sublistParents = new ArrayList<TaxonomyRow>();
//// for (TaxonomyRow taxon : taxonomy.getParents()) {
//
// if(i+1!=parentsSize)
// sublistParents.addAll(row.getParents().subList(i+1, parentsSize));
//
// taxon.setParent(sublistParents);
//
////// DEBUG
//// System.out.println("parent of "+taxon.getName());
//// for (TaxonomyRow tax : sublistParents) {
//// System.out.println("taxon.getName() " + tax.getName());
//// }
//// System.out.println("\n\n");
// }
LightTaxonomyRow lr = convetTaxonomyRowToLigthTaxonomyRow(row);
//DEBUG
// System.out.println("principal "+row.getName() + " id " + row.getServiceId()+" parents");
// for (TaxonomyRow tax : row.getParents()) {
// System.out.println("taxon.getName() " + tax.getName());
// System.out.println("parent of "+tax.getName());
// for (TaxonomyRow taxon : tax.getParents()) {
// System.out.println("taxon.getName() " + taxon.getName());
// }
// System.out.println("\n\n");
// }
List<LightTaxonomyRow> parents = new ArrayList<LightTaxonomyRow>();
for (TaxonomyRow txParent: row.getParents()) {
parents.add(convetTaxonomyRowToLigthTaxonomyRow(txParent));
}
lr.setParent(parents);
hashLightResult.put(row.getServiceId(), lr);
hashResult.put(row.getServiceId(), row);
}
this.isReduced = isReduced;
this.totalRow = totalRow;
createStructures(result.getResults());
createStructuresForCommonName();
}
public static LightTaxonomyRow convetTaxonomyRowToLigthTaxonomyRow(TaxonomyRow row){
LightTaxonomyRow lr = new LightTaxonomyRow(row.getId());
lr.setServiceId(row.getServiceId());
lr.setBaseTaxonValue(row.getBaseTaxonValue());
lr.setDataProviderId(row.getDataProviderId());
lr.setDataProviderName(row.getDataProviderName());
lr.setName(row.getName());
lr.setParentID(row.getParentID());
lr.setRank(row.getRank());
lr.setParentIndex(row.getParentIndex());
lr.setStatusName(row.getStatusName());
lr.setStatusRefId(row.getStatusRefId());
lr.setStatusRemarks(row.getStatusRemarks());
return lr;
}
public void createStructures(ArrayList<TaxonomyRow> arrayListTax){
@ -100,69 +101,41 @@ public class ClusterStructuresForTaxonomyRow implements Serializable{
else
keyScientificName = NormalizeString.lowerCaseUpFirstChar(keyScientificName);
if(hashClusterScientificNameTaxonomyRowID.get(keyScientificName)==null){
if(hashClusterScientificNameTaxonomyRowServiceID.get(keyScientificName)==null){
listTaxonomyRowID = new ArrayList<String>(); //USED FOR CLUSTER COMMON NAMES
listTaxonomyRowServiceID = new ArrayList<String>(); //USED FOR CLUSTER COMMON NAMES
}
else{
listTaxonomyRowID = hashClusterScientificNameTaxonomyRowID.get(keyScientificName); //USED FOR CLUSTER COMMON NAMES
listTaxonomyRowServiceID = hashClusterScientificNameTaxonomyRowServiceID.get(keyScientificName); //USED FOR CLUSTER COMMON NAMES
}
if(listFoundDataSources.indexOf(dataSource)==-1)
listFoundDataSources.add(dataSource);
listTaxonomyRowID.add(row.getIdToString());
hashClusterScientificNameTaxonomyRowID.put(keyScientificName, listTaxonomyRowID);
listTaxonomyRowServiceID.add(row.getServiceId());
hashClusterScientificNameTaxonomyRowServiceID.put(keyScientificName, listTaxonomyRowServiceID);
}
}
}
public void createStructuresForCommonName(){
if(hashClusterScientificNameTaxonomyRowID.size()>0){
for(String scientificName : hashClusterScientificNameTaxonomyRowID.keySet()){
ArrayList<String> listTaxonomyRowID = hashClusterScientificNameTaxonomyRowID.get(scientificName);
ClusterCommonNameDataSource<TaxonomyRow> cluster = new ClusterCommonNameDataSource<TaxonomyRow>(); //NEW CLUSTER
for(int i=0; i<listTaxonomyRowID.size(); i++){
TaxonomyRow row = hashResult.get(listTaxonomyRowID.get(i));
cluster.updateHashCommonNamesDataSources(row);
}
hashClusterCommonNamesDataSources.put(scientificName, cluster);
}
}
}
public ArrayList<String> getListFoundDataSources() {
return listFoundDataSources;
}
public HashMap<String, ArrayList<String>> getHashClusterScientificNameTaxonomyRowID() {
return hashClusterScientificNameTaxonomyRowID;
public HashMap<String, ArrayList<String>> getHashClusterScientificNameTaxonomyRowServiceID() {
return hashClusterScientificNameTaxonomyRowServiceID;
}
public HashMap<String, ClusterCommonNameDataSource<TaxonomyRow>> getHashClusterCommonNamesDataSources() {
return hashClusterCommonNamesDataSources;
}
public ArrayList<TaxonomyRow> getResult() {
return new ArrayList<TaxonomyRow>(hashResult.values());
public ArrayList<LightTaxonomyRow> getResult() {
return new ArrayList<LightTaxonomyRow>(hashLightResult.values());
}
public TaxonomyRow getTaxonomyRowByKey(String key) {
return hashResult.get(key);
public LightTaxonomyRow getLightTaxonomyRowByKey(String key) {
return hashLightResult.get(key);
}
public boolean isReduced() {
@ -181,4 +154,16 @@ public class ClusterStructuresForTaxonomyRow implements Serializable{
this.totalRow = totalRow;
}
public Map<String, LightTaxonomyRow> getHashLightResult() {
return hashLightResult;
}
public Map<String, TaxonomyRow> getHashResult() {
return hashResult;
}
public void setHashResult(Map<String, TaxonomyRow> hashResult) {
this.hashResult = hashResult;
}
}

110
src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/cluster/ManagerClusterCommonNameDataSourceForResultRow.java Normal file
View File

@ -0,0 +1,110 @@
/**
*
*/
package org.gcube.portlets.user.speciesdiscovery.shared.cluster;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.Map;
import org.gcube.portlets.user.speciesdiscovery.shared.ResultRow;
/**
* @author Francesco Mangiacrapa francesco.mangiacrapa@isti.cnr.it
* @Sep 5, 2013
*
* This class calculates the cluster for common names / data sources: hashClusterCommonNameDataSource
*/
public class ManagerClusterCommonNameDataSourceForResultRow {
private HashMap<String, ArrayList<String>> hashScientificNameResultRowServiceID = new HashMap<String, ArrayList<String>>(); //HASH scientific name - result row service ID
private Map<String, ResultRow> hashResult = new HashMap<String, ResultRow>();
private HashMap<String, ClusterCommonNameDataSourceForResultRow> hashClusterCommonNameDataSource = new HashMap<String, ClusterCommonNameDataSourceForResultRow>(); //HASH scientific name - cluster
/**
* @param hashScientificNameResultRowID
* @param hashClusterCommonNameDataSource
* @param hashResult
* @throws Exception
*/
public ManagerClusterCommonNameDataSourceForResultRow(HashMap<String, ArrayList<String>> hashScientificNameResultRowID, Map<String, ResultRow> hashResult) throws Exception {
this.hashScientificNameResultRowServiceID = hashScientificNameResultRowID;
this.hashResult = hashResult;
createStructuresForCommonName();
}
public void createStructuresForCommonName() throws Exception{
if(hashScientificNameResultRowServiceID.size()>0){
for(String scientificName : hashScientificNameResultRowServiceID.keySet()){
ArrayList<String> listResultRowServiceID = hashScientificNameResultRowServiceID.get(scientificName); //get RR serviceID
ClusterCommonNameDataSource<ResultRow> cluster = new ClusterCommonNameDataSource<ResultRow>(); //NEW CLUSTER
for(int i=0; i<listResultRowServiceID.size(); i++){
ResultRow row = hashResult.get(listResultRowServiceID.get(i));
cluster.updateHashCommonNamesDataSources(row);
}
hashClusterCommonNameDataSource.put(scientificName, new ClusterCommonNameDataSourceForResultRow(scientificName, cluster));
}
}
}
public HashMap<String, ArrayList<String>> getHashScientificNameResultRowID() {
return hashScientificNameResultRowServiceID;
}
public void setHashScientificNameResultRowID(
HashMap<String, ArrayList<String>> hashScientificNameResultRowID) {
this.hashScientificNameResultRowServiceID = hashScientificNameResultRowID;
}
public HashMap<String, ClusterCommonNameDataSourceForResultRow> getHashClusterCommonNameDataSource() {
return hashClusterCommonNameDataSource;
}
public void setHashClusterCommonNameDataSource(
HashMap<String, ClusterCommonNameDataSourceForResultRow> hashClusterCommonNameDataSource) {
this.hashClusterCommonNameDataSource = hashClusterCommonNameDataSource;
}
public Map<String, ResultRow> getHashResult() {
return hashResult;
}
public void setHashResult(Map<String, ResultRow> hashResult) {
this.hashResult = hashResult;
}
@Override
public String toString() {
StringBuilder builder = new StringBuilder();
builder.append("ManagerClusterCommonNameDataSource [hashScientificNameResultRowID=");
builder.append(hashScientificNameResultRowServiceID);
builder.append(", hashClusterCommonNameDataSource=");
builder.append(hashClusterCommonNameDataSource);
builder.append(", hashResult=");
builder.append(hashResult);
builder.append("]");
return builder.toString();
}
}

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src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/cluster/ManagerClusterCommonNameDataSourceForTaxonomyRow.java Normal file
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/**
*
*/
package org.gcube.portlets.user.speciesdiscovery.shared.cluster;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.Map;
import org.gcube.portlets.user.speciesdiscovery.shared.TaxonomyRow;
/**
*
* @author Francesco Mangiacrapa francesco.mangiacrapa@isti.cnr.it
* @Sep 18, 2013
*
* This class calculates the cluster for common names / data sources: hashClusterCommonNameDataSource
*
*/
public class ManagerClusterCommonNameDataSourceForTaxonomyRow {
private HashMap<String, ArrayList<String>> hashScientificNameTaxonomyRowServiceID = new HashMap<String, ArrayList<String>>(); //HASH scientific name - taxonomy row service ID
private Map<String, TaxonomyRow> hashResult = new HashMap<String, TaxonomyRow>();
private HashMap<String, ClusterCommonNameDataSourceForTaxonomyRow> hashClusterCommonNameDataSource = new HashMap<String, ClusterCommonNameDataSourceForTaxonomyRow>(); //HASH scientific name - cluster
/**
* @param hashScientificNameResultRowServiceID
* @param hashClusterCommonNameDataSource
* @param hashResult
* @throws Exception
*/
public ManagerClusterCommonNameDataSourceForTaxonomyRow(HashMap<String, ArrayList<String>> hashScientificNameResultRowServiceID, Map<String, TaxonomyRow> hashResult) throws Exception {
this.hashScientificNameTaxonomyRowServiceID = hashScientificNameResultRowServiceID;
this.hashResult = hashResult;
createStructuresForCommonName();
}
public void createStructuresForCommonName() throws Exception{
if(hashScientificNameTaxonomyRowServiceID.size()>0){
for(String scientificName : hashScientificNameTaxonomyRowServiceID.keySet()){
ArrayList<String> listTaxonomyRowServiceID = hashScientificNameTaxonomyRowServiceID.get(scientificName);
ClusterCommonNameDataSource<TaxonomyRow> cluster = new ClusterCommonNameDataSource<TaxonomyRow>(); //NEW CLUSTER
for(int i=0; i<listTaxonomyRowServiceID.size(); i++){
TaxonomyRow row = hashResult.get(listTaxonomyRowServiceID.get(i));
cluster.updateHashCommonNamesDataSources(row);
}
hashClusterCommonNameDataSource.put(scientificName, new ClusterCommonNameDataSourceForTaxonomyRow(scientificName, cluster));
}
}
}
public HashMap<String, ArrayList<String>> getHashScientificNameResultRowID() {
return hashScientificNameTaxonomyRowServiceID;
}
public void setHashScientificNameResultRowID(
HashMap<String, ArrayList<String>> hashScientificNameResultRowID) {
this.hashScientificNameTaxonomyRowServiceID = hashScientificNameResultRowID;
}
public HashMap<String, ClusterCommonNameDataSourceForTaxonomyRow> getHashClusterCommonNameDataSource() {
return hashClusterCommonNameDataSource;
}
public void setHashClusterCommonNameDataSource(HashMap<String, ClusterCommonNameDataSourceForTaxonomyRow> hashClusterCommonNameDataSource) {
this.hashClusterCommonNameDataSource = hashClusterCommonNameDataSource;
}
public Map<String, TaxonomyRow> getHashResult() {
return hashResult;
}
public void setHashResult(Map<String, TaxonomyRow> hashResult) {
this.hashResult = hashResult;
}
@Override
public String toString() {
StringBuilder builder = new StringBuilder();
builder.append("ManagerClusterCommonNameDataSourceForTaxonomyRow [hashScientificNameTaxonomyRowServiceID=");
builder.append(hashScientificNameTaxonomyRowServiceID);
builder.append(", hashResult=");
builder.append(hashResult);
builder.append(", hashClusterCommonNameDataSource=");
builder.append(hashClusterCommonNameDataSource);
builder.append("]");
return builder.toString();
}
}