diff --git a/distro/README b/distro/README index f15ca84..6c1dd11 100644 --- a/distro/README +++ b/distro/README @@ -17,7 +17,7 @@ Authors Version and Release Date ------------------------ -v. 3.3.0 +v. 3.5.0 Description ----------- diff --git a/distro/changelog.xml b/distro/changelog.xml index 78f0eaa..ef8b408 100644 --- a/distro/changelog.xml +++ b/distro/changelog.xml @@ -1,4 +1,16 @@ + + Portlet updated to support GWT 2.5.1 + Ticket 2224: was implemented + + + Enhancements on GUI of SPD portlet was realized (view last query, new expand button are available) + 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". + diff --git a/pom.xml b/pom.xml index 600a586..a6ae81d 100644 --- a/pom.xml +++ b/pom.xml @@ -67,6 +67,14 @@ provided + + com.sencha.gxt + gxt + 2.2.5 + provided + + + org.gcube.data.spd @@ -185,12 +193,10 @@ - + - com.sencha.gxt - gxt - 2.2.5 - provided + org.gcube.applicationsupportlayer + accesslogger diff --git a/src/main/java/org/gcube/portlets/user/speciesdiscovery/client/ConstantsSpeciesDiscovery.java b/src/main/java/org/gcube/portlets/user/speciesdiscovery/client/ConstantsSpeciesDiscovery.java index 00e2c56..53cead1 100644 --- a/src/main/java/org/gcube/portlets/user/speciesdiscovery/client/ConstantsSpeciesDiscovery.java +++ b/src/main/java/org/gcube/portlets/user/speciesdiscovery/client/ConstantsSpeciesDiscovery.java @@ -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"; } diff --git a/src/main/java/org/gcube/portlets/user/speciesdiscovery/client/SearchController.java b/src/main/java/org/gcube/portlets/user/speciesdiscovery/client/SearchController.java index 31b8e74..f42824f 100644 --- a/src/main/java/org/gcube/portlets/user/speciesdiscovery/client/SearchController.java +++ b/src/main/java/org/gcube/portlets/user/speciesdiscovery/client/SearchController.java @@ -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 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() { diff --git a/src/main/java/org/gcube/portlets/user/speciesdiscovery/client/cluster/TabItemForTaxonomyRow.java b/src/main/java/org/gcube/portlets/user/speciesdiscovery/client/cluster/TabItemForTaxonomyRow.java index 4109b3b..731599a 100644 --- a/src/main/java/org/gcube/portlets/user/speciesdiscovery/client/cluster/TabItemForTaxonomyRow.java +++ b/src/main/java/org/gcube/portlets/user/speciesdiscovery/client/cluster/TabItemForTaxonomyRow.java @@ -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 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>() { + SpeciesDiscovery.taxonomySearchService.loadListChildrenByParentId(taxonomyItem.getServiceId(), new AsyncCallback>() { @Override - public void onSuccess(ArrayList result) { + public void onSuccess(ArrayList 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 list = new ArrayList(); + List list = new ArrayList(); 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 hashProperties = row.getProperties(); - Collections.sort(hashProperties, ItemParameter.COMPARATOR); - - propertiesHtml+=""; - - for (ItemParameter itemParameter : hashProperties) { - - propertiesHtml+= - "" + - " " + - " " + - ""; - } - - propertiesHtml+="
"+itemParameter.getKey()+""+itemParameter.getValue()+"
"; - } - - - //Create list common name - String commonNames = ""; - -// if(isNewTab){ - if(row.getCommonNames()!=null){ - for (CommonName comName : row.getCommonNames()) { - commonNames+= ""+comName.getName()+"" +" ("+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 hashProperties = row.getProperties(); +// Collections.sort(hashProperties, ItemParameter.COMPARATOR); +// +// propertiesHtml+=""; +// +// for (ItemParameter itemParameter : hashProperties) { +// +// propertiesHtml+= +// "" + +// " " + +// " " + +// ""; +// } +// +// propertiesHtml+="
"+itemParameter.getKey()+""+itemParameter.getValue()+"
"; // } - - - String table = ""; - -// if(isNewTab) - table+= - "" + - " " + - " " + - ""; - - - table+="" + - " " + - " " + - "" + - "" + - " " + - " " + - "" + - "" + - " " + - " " + - "" + - "" + - " " + - " " + - "" + - "" + - " " + - " " + - "" + - "" + - " " + - " " + - "" + -// "" + -// " " + -// " " + +// +// +// //Create list common name +// String commonNames = ""; +// +//// if(isNewTab){ +// if(row.getCommonNames()!=null){ +// for (CommonName comName : row.getCommonNames()) { +// commonNames+= ""+comName.getName()+"" +" ("+comName.getLanguage()+") - "; +// } +// } +//// } +// +// +// String table = "
"+TaxonomyGridField.COMMON_NAMES.getName()+" (Language)"+commonNames+"
"+TaxonomyGridField.STATUSREFNAME.getName()+""+statusName+"
"+TaxonomyGridField.STATUS_REMARKS.getName()+""+statusRemark+"
"+TaxonomyGridField.DATASOURCE.getName()+""+dataProviderName+"
"+TaxonomyGridField.DATEMODIFIED.getName()+""+dateModified+"
"+TaxonomyGridField.MATCHING_RANK.getName()+""+rank+"
"+TaxonomyGridField.CITATION.getName()+""+dataSetCitation+"
"+TaxonomyGridField.MATCHING_AUTHOR.getName()+""+matchingAccordionTo+"
"; +// +//// if(isNewTab) +// table+= +// "" + +// " " + +// " " + +// ""; +// +// +// table+="" + +// " " + +// " " + // "" + - "" + - " " + - " " + - "" + - "" + - " " + - " " + - "" + - "" + - " " + - " " + - "" + - - "" + - " " + - " " + - "" + - - "
"+TaxonomyGridField.COMMON_NAMES.getName()+" (Language)"+commonNames+"
"+TaxonomyGridField.STATUSREFNAME.getName()+""+statusName+"
"+TaxonomyGridField.LSID.getName()+""+lsid+"
"+TaxonomyGridField.AUTHOR.getName()+""+author+"
"+TaxonomyGridField.CREDITS.getName()+""+credits+"
"+TaxonomyGridField.PROPERTIES.getName()+""+propertiesHtml+"
"; - return new Html(table); - - } +// "" + +// " "+TaxonomyGridField.STATUS_REMARKS.getName()+"" + +// " "+statusRemark+"" + +// "" + +// "" + +// " "+TaxonomyGridField.DATASOURCE.getName()+"" + +// " "+dataProviderName+"" + +// "" + +// "" + +// " "+TaxonomyGridField.DATEMODIFIED.getName()+"" + +// " "+dateModified+"" + +// "" + +// "" + +// " "+TaxonomyGridField.MATCHING_RANK.getName()+"" + +// " "+rank+"" + +// "" + +// "" + +// " "+TaxonomyGridField.CITATION.getName()+"" + +// " "+dataSetCitation+"" + +// "" + +//// "" + +//// " "+TaxonomyGridField.MATCHING_AUTHOR.getName()+"" + +//// " "+matchingAccordionTo+"" + +//// "" + +// "" + +// " "+TaxonomyGridField.LSID.getName()+"" + +// " "+lsid+"" + +// "" + +// "" + +// " "+TaxonomyGridField.AUTHOR.getName()+"" + +// " "+author+"" + +// "" + +// "" + +// " "+TaxonomyGridField.CREDITS.getName()+"" + +// " "+credits+"" + +// "" + +// +// "" + +// " "+TaxonomyGridField.PROPERTIES.getName()+"" + +// " "+propertiesHtml+"" + +// "" + +// +// ""; +// 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 hashProperties = row.getProperties(); +// Collections.sort(hashProperties, +// ItemParameter.COMPARATOR); +// +// propertiesHtml += ""; +// +// for (ItemParameter itemParameter : hashProperties) { +// +// propertiesHtml += "" + " " + " " + ""; +// } +// +// propertiesHtml += "
" +// + itemParameter.getKey() + "" +// + itemParameter.getValue() + "
"; +// } +// +// // Create list common name +// String commonNames = ""; +// +// // if(isNewTab){ +// if (row.getCommonNames() != null) { +// for (CommonName comName : row.getCommonNames()) { +// commonNames += "" + comName.getName() + "" + " (" +// + 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 hashProperties = row.getProperties(); - Collections.sort(hashProperties, - ItemParameter.COMPARATOR); - - propertiesHtml += ""; - - for (ItemParameter itemParameter : hashProperties) { - - propertiesHtml += "" + " " + " " + ""; - } - - propertiesHtml += "
" - + itemParameter.getKey() + "" - + itemParameter.getValue() + "
"; - } - - // Create list common name - String commonNames = ""; - - // if(isNewTab){ - if (row.getCommonNames() != null) { - for (CommonName comName : row.getCommonNames()) { - commonNames += "" + comName.getName() + "" + " (" - + 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 parents){ + public void getSynonymsByReferenceId(FlexTable flexTable, int row, int col, String refId, final String dataSource, final List 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>() { + SpeciesDiscovery.taxonomySearchService.retrieveSynonymsByRefId(refId, new AsyncCallback>() { @Override public void onFailure(Throwable caught) { @@ -675,7 +671,7 @@ public class TabItemForTaxonomyRow { } @Override - public void onSuccess(List result) { + public void onSuccess(List 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 parents){ + public void getTaxonomyByReferenceId(FlexTable flexTable, int row, int col, final String statusRemark, String refId, final String dataSource, final List parents){ final LayoutContainer layoutContainer = new LayoutContainer(); // hp.getElement().getStyle().setBorderStyle(BorderStyle.NONE); @@ -744,7 +740,7 @@ public class TabItemForTaxonomyRow { List listId = new ArrayList(); listId.add(refId); - SpeciesDiscovery.taxonomySearchService.retrieveTaxonomyByIds(listId, new AsyncCallback>() { + SpeciesDiscovery.taxonomySearchService.retrieveTaxonomyByIds(listId, new AsyncCallback>() { @Override public void onFailure(Throwable caught) { @@ -754,7 +750,7 @@ public class TabItemForTaxonomyRow { } @Override - public void onSuccess(List result) { + public void onSuccess(List 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

" + taxon.getName() + "

")); -// contentPanel.add(new Html("

Scientific Classification


")); -// -// 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() { -// -// @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); -// -// } - } diff --git a/src/main/java/org/gcube/portlets/user/speciesdiscovery/client/cluster/TablesForTaxonomyRow.java b/src/main/java/org/gcube/portlets/user/speciesdiscovery/client/cluster/TablesForTaxonomyRow.java index 2eec5ab..2c1b072 100644 --- a/src/main/java/org/gcube/portlets/user/speciesdiscovery/client/cluster/TablesForTaxonomyRow.java +++ b/src/main/java/org/gcube/portlets/user/speciesdiscovery/client/cluster/TablesForTaxonomyRow.java @@ -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 parents = null; + private List parents = null; private TabItemForTaxonomyRow tabTR; + private AbstractImagePrototype imageLoading = AbstractImagePrototype.create(Resources.INSTANCE.loadingBalls()); + // private HashMap hashTR = new HashMap(); - public List getParents() { + public List getParents() { return parents; } - public void setParents(List parents) { + public void setParents(List 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("

Status and Synonyms

")); + contentPanel.add(getStatusAndSynonyms(taxon, dataSource)); + contentPanel.add(new Html("

Other Information0) + 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; + } } diff --git a/src/main/java/org/gcube/portlets/user/speciesdiscovery/client/event/CreateTaxonomyJobEvent.java b/src/main/java/org/gcube/portlets/user/speciesdiscovery/client/event/CreateTaxonomyJobEvent.java index ee808da..4dcf93c 100644 --- a/src/main/java/org/gcube/portlets/user/speciesdiscovery/client/event/CreateTaxonomyJobEvent.java +++ b/src/main/java/org/gcube/portlets/user/speciesdiscovery/client/event/CreateTaxonomyJobEvent.java @@ -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 { public static final GwtEvent.Type TYPE = new Type(); - 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 loadListChildByParentId(String parentId) - throws Exception; + ArrayList 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 retrieveTaxonomyByIds(List ids) - throws Exception; + public List retrieveTaxonomyByIds(List ids) throws Exception; - public List retrieveSynonymsByRefId(String refId) - throws Exception; + public List retrieveSynonymsByRefId(String refId) throws Exception; public List createOccurrencesJob( List 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); } diff --git a/src/main/java/org/gcube/portlets/user/speciesdiscovery/client/rpc/TaxonomySearchServiceAsync.java b/src/main/java/org/gcube/portlets/user/speciesdiscovery/client/rpc/TaxonomySearchServiceAsync.java index 3ff4f9a..520020b 100644 --- a/src/main/java/org/gcube/portlets/user/speciesdiscovery/client/rpc/TaxonomySearchServiceAsync.java +++ b/src/main/java/org/gcube/portlets/user/speciesdiscovery/client/rpc/TaxonomySearchServiceAsync.java @@ -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> asyncCallback); - void loadListChildByParentId(String parentId, AsyncCallback> callback); + void loadListChildrenByParentId(String parentId, AsyncCallback> asyncCallback); void saveSelectedTaxonomyPoints(String destinationFolderId, String fileName, SaveFileFormat fileFormat, AsyncCallback callback); @@ -101,9 +104,9 @@ public interface TaxonomySearchServiceAsync { void saveTaxonomyJob(String jobIdentifier, String destinationFolderId, String fileName, String scientificName, String dataSourceName, AsyncCallback callback); - void retrieveTaxonomyByIds(List ids, AsyncCallback> callback); + void retrieveTaxonomyByIds(List ids, AsyncCallback> asyncCallback); - void retrieveSynonymsByRefId(String refId, AsyncCallback> callback); + void retrieveSynonymsByRefId(String refId, AsyncCallback> asyncCallback); void createOccurrencesJob(List listJobOccurrenceModel, SaveFileFormat saveFileFormat, OccurrencesSaveEnum csvType, boolean isByDataSource, int expectedOccurrence, AsyncCallback> callback); @@ -156,5 +159,13 @@ public interface TaxonomySearchServiceAsync { AsyncCallback callback); void getLastQuery(AsyncCallback callback); + + void loadClusterCommonNameForResultRowByScientificName( + String scientificName, + AsyncCallback callback); + + void loadClusterCommonNameForTaxonomyRowByScientificName( + String scientificName, + AsyncCallback callback); } diff --git a/src/main/java/org/gcube/portlets/user/speciesdiscovery/client/windowdetail/ResultRowDetailsFiller.java b/src/main/java/org/gcube/portlets/user/speciesdiscovery/client/windowdetail/ResultRowDetailsFiller.java index f088582..14353d6 100644 --- a/src/main/java/org/gcube/portlets/user/speciesdiscovery/client/windowdetail/ResultRowDetailsFiller.java +++ b/src/main/java/org/gcube/portlets/user/speciesdiscovery/client/windowdetail/ResultRowDetailsFiller.java @@ -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 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> hashResultRowIdTables = result.getHashClusterScientificNameResultRowID(); - HashMap> hashClusterCommonNamesDataSources = result.getHashClusterCommonNamesDataSources(); + HashMap> hashResultRowIdTables = result.getHashClusterScientificNameResultRowServiceID(); + + +// HashMap> hashClusterCommonNamesDataSources = result.getHashClusterCommonNamesDataSources(); String title = common.getSearchTitle(); @@ -187,25 +200,150 @@ public class ResultRowDetailsFiller implements DetailsFiller { panelDetails.add(common.createExternalLinks(scientificName)); + String commonNamesTitle = "

Common Names (Data Source/s)

"; panelDetails.add(new Html(commonNamesTitle)); - - ClusterCommonNameDataSource cluster = hashClusterCommonNamesDataSources.get(scientificName); - - String tableCommonName = common.createTableWithCheckCommonNameDataSource(cluster.getHashMapCommonNameDataSources(), cluster.getListDataSourcesFound()); - panelDetails.add(new Html("
"+tableCommonName+"

")); + 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() { + + @Override + public void onFailure(Throwable caught) { + Html htmlTableResult = new Html(); + htmlTableResult.setHtml("
Error on retrieving data

"); + + } + + @Override + public void onSuccess(ClusterCommonNameDataSourceForResultRow result) { + + + Html htmlTableResult = new Html(); + htmlTableResult.setHtml("
Not Found

"); + + if(result !=null){ + + if(result.getCluster()!=null){ + String tableCommonName = common.createTableWithCheckCommonNameDataSource(result.getCluster().getHashMapCommonNameDataSources(), result.getCluster().getListDataSourcesFound()); + htmlTableResult.setHtml("
"+tableCommonName+"

"); + } + else + htmlTableResult.setHtml("
Error on retrieving data

"); + }else + htmlTableResult.setHtml("
Error on retrieving data

"); + + + lcCommonName.remove(loading); + lcCommonName.add(htmlTableResult); + + panelDetails.layout(); + } + + + }); + + + } + }); + + lcCommonName.add(anchorCommon); + + panelDetails.add(lcCommonName); +// ClusterCommonNameDataSource cluster = hashClusterCommonNamesDataSources.get(scientificName); + + +// String tableCommonName = common.createTableWithCheckCommonNameDataSource(cluster.getHashMapCommonNameDataSources(), cluster.getListDataSourcesFound()); +// panelDetails.add(new Html("
"+tableCommonName+"

")); + + ArrayList arrayRowID = hashResultRowIdTables.get(scientificName); +// for(int i=0; i 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> hashTaxonomyRowID = result.getHashClusterScientificNameTaxonomyRowID(); + + HashMap> hashTaxonomyRowServiceID = result.getHashClusterScientificNameTaxonomyRowServiceID(); // ArrayList listDataSourceFound = tableClassification.getListFoundDataSources(); - HashMap> hashClusterCommonNamesDataSources = result.getHashClusterCommonNamesDataSources(); +// HashMap> hashClusterCommonNamesDataSources = result.getHashClusterCommonNamesDataSources(); // HashMap> hashHTMLTables = result.getHashClassificationTables(); @@ -135,7 +144,7 @@ public class TaxonomyRowDetailsFiller implements DetailsFiller { // System.out.println("############# Data Source found " + dataSource); // } - List listKey = new ArrayList(hashTaxonomyRowID.keySet()); + List listKey = new ArrayList(hashTaxonomyRowServiceID.keySet()); Collections.sort(listKey); @@ -204,16 +213,76 @@ public class TaxonomyRowDetailsFiller implements DetailsFiller { String commonNamesTitle = "

Common Names (Data Source/s)

"; panelDetails.add(new Html(commonNamesTitle)); - ClusterCommonNameDataSource 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("
"+tableCommonName+"
")); +// lcCommonName.setLayout(new FitLayout()); - ArrayList 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() { + + @Override + public void onFailure(Throwable caught) { + Html htmlTableResult = new Html(); + htmlTableResult.setHtml("
Error on retrieving data

"); + + } + + @Override + public void onSuccess(ClusterCommonNameDataSourceForTaxonomyRow result) { + + + Html htmlTableResult = new Html(); + htmlTableResult.setHtml("
Not Found

"); + + if(result !=null){ + + if(result.getCluster()!=null){ + String tableCommonName = common.createTableWithCheckCommonNameDataSource(result.getCluster().getHashMapCommonNameDataSources(), result.getCluster().getListDataSourcesFound()); + htmlTableResult.setHtml("
"+tableCommonName+"

"); + } + else + htmlTableResult.setHtml("
Error on retrieving data

"); + }else + htmlTableResult.setHtml("
Error on retrieving data

"); + + + lcCommonName.remove(loading); + lcCommonName.add(htmlTableResult); + + panelDetails.layout(); + } + + + }); + + + } + }); + + lcCommonName.add(anchorCommon); + + panelDetails.add(lcCommonName); + + ArrayList arrayTaxonomyID = hashTaxonomyRowServiceID.get(scientificName); for(int i=0; iStatus and Synonyms

")); + 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("

Other Information

")); + + 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")); + } } } diff --git a/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/ResultRowTable.java b/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/ResultRowTable.java new file mode 100644 index 0000000..6ee84dd --- /dev/null +++ b/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/ResultRowTable.java @@ -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 cq = queryBuilder.createQuery(); + Predicate pr1 = queryBuilder.equal(persistence.rootFrom(cq).get(ResultRow.SERVICE_ID_FIELD), resultServiceRowID); + cq.where(pr1); + + Iterator 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 +=("

Error: "+message+"

"); + return errorPage; + } + + //TODO modified + public static String getClassification(List listTaxon) + { + StringBuilder sb = new StringBuilder(); + + for (int i = listTaxon.size()-1; i >= 0; i--) { + Taxon taxon = listTaxon.get(i); + + sb.append(""); + + if(!NormalizeString.isUndefined(taxon.getRank())) + sb.append(taxon.getRank()); + else + sb.append("Rank not found"); + + sb.append(": "); + + 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+= ""+comName.getName()+"" +" ("+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 listProperties = row.getProperties(); + Collections.sort(listProperties, ItemParameter.COMPARATOR); + + propertiesHtml+=""; + + for (ItemParameter itemParameter : listProperties) { + + propertiesHtml+= + "" + + " " + + " " + + ""; + } + + propertiesHtml+="
"+itemParameter.getKey()+""+itemParameter.getValue()+"
"; + } + + String table = "" + + "" + + " " + + "" + + "" + + " " + + " " + + "" + + "" + + " " + + " " + + "" + + + "" + + " " + + " " + + "" + + "" + + " " + + " " + + "" + + "" + + " " + + " " + + "" + +// "" + +// " " + +// " " + +// "" + + "" + + " " + + " " + + "" + + "" + + " " + + " " + + "" + +// "" + +// " " + +// " " + +// "" + + "" + + " " + + " " + + "" + + + "" + + " " + + " " + + "" + + "" + + " " + + " " + + "" + + "" + + " " + + " " + + "" + + + "" + + " " + + " " + + "" + + + "
"+matchingTaxonName+"
"+SpeciesGridFields.CLASSIFICATION_STRING.getName()+""+classification+"
"+SpeciesGridFields.COMMON_NAMES.getName()+" (Language)"+commonNames+"
"+SpeciesGridFields.DATASOURCE.getName()+""+dataSourceName+"
"+SpeciesGridFields.DATAPROVIDER.getName()+""+dataProviderName+"
"+SpeciesGridFields.DATASET.getName()+""+dataSetName+"
"+SpeciesGridFields.MATCHING_AUTHOR.getName()+""+matchingAccordionTo+"
"+SpeciesGridFields.MATCHING_RANK.getName()+""+matchingRank+"
"+SpeciesGridFields.DATASET_CITATION.getName()+""+dataSetCitation+"
"+SpeciesGridFields.MATCHING_CREDITS.getName()+""+matchingCredits+"
"+SpeciesGridFields.PRODUCT_OCCURRENCES.getName()+""+occurencesCount+"
"+SpeciesGridFields.LSID.getName()+""+lsid+"
"+SpeciesGridFields.AUTHOR.getName()+""+author+"
"+SpeciesGridFields.CREDITS.getName()+""+credits+"
"+SpeciesGridFields.PROPERTIES.getName()+""+propertiesHtml+"
"; + return table; + + } + +} \ No newline at end of file diff --git a/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/TaxonomyRowTable.java b/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/TaxonomyRowTable.java new file mode 100644 index 0000000..df1798c --- /dev/null +++ b/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/TaxonomyRowTable.java @@ -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 cq = queryBuilder.createQuery(); + Predicate pr1 = queryBuilder.equal(persistence.rootFrom(cq).get(TaxonomyRow.SERVICE_ID_FIELD), taxonomyServiceRowID); + cq.where(pr1); + + Iterator 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 streamIds = new StreamExtend(Arrays.asList(taxonomyServiceRowID).iterator()); + + CloseableIterator 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 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 +=("

Error: "+message+"

"); + 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 hashProperties = row.getProperties(); + Collections.sort(hashProperties, ItemParameter.COMPARATOR); + + propertiesHtml+=""; + + for (ItemParameter itemParameter : hashProperties) { + + propertiesHtml+= + "" + + " " + + " " + + ""; + } + + propertiesHtml+="
"+itemParameter.getKey()+""+itemParameter.getValue()+"
"; + } + + + //Create list common name + String commonNames = ""; + + if(row.getCommonNames()!=null){ + for (CommonName comName : row.getCommonNames()) { + commonNames+= ""+comName.getName()+"" +" ("+comName.getLanguage()+") - "; + } + } + + + String table = ""; + +// if(isNewTab) + table+= + "" + + " " + + " " + + ""; + + +// table+="" + +// " " + +// " " + +// "" + +// "" + +// " " + +// " " + +// "" + + + + table +="" + + " " + + " " + + "" + + "" + + " " + + " " + + "" + + "" + + " " + + " " + + "" + + "" + + " " + + " " + + "" + + "" + + " " + + " " + + "" + + "" + + " " + + " " + + "" + + "" + + " " + + " " + + "" + + + "" + + " " + + " " + + "" + + + "
"+TaxonomyGridField.COMMON_NAMES.getName()+" (Language)"+commonNames+"
"+TaxonomyGridField.STATUSREFNAME.getName()+""+statusName+"
"+TaxonomyGridField.STATUS_REMARKS.getName()+""+statusRemark+"
"+TaxonomyGridField.DATASOURCE.getName()+""+dataProviderName+"
"+TaxonomyGridField.DATEMODIFIED.getName()+""+dateModified+"
"+TaxonomyGridField.MATCHING_RANK.getName()+""+rank+"
"+TaxonomyGridField.CITATION.getName()+""+dataSetCitation+"
"+TaxonomyGridField.LSID.getName()+""+lsid+"
"+TaxonomyGridField.AUTHOR.getName()+""+author+"
"+TaxonomyGridField.CREDITS.getName()+""+credits+"
"+TaxonomyGridField.PROPERTIES.getName()+""+propertiesHtml+"
"; + + //DEBUG +// System.out.println("Table: "+table); + + return table; + + } + +} \ No newline at end of file diff --git a/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/TaxonomySearchServiceImpl.java b/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/TaxonomySearchServiceImpl.java index 6e50935..fdd5bef 100644 --- a/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/TaxonomySearchServiceImpl.java +++ b/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/TaxonomySearchServiceImpl.java @@ -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 loadListChildByParentId(String parentId) throws Exception { + public ArrayList 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 listTaxonomyRow = new ArrayList(); + ArrayList listLightTaxonomyRow = new ArrayList(); + + if(parentId==null || parentId.isEmpty()){ + logger.warn("parentId is null or empty "); + return listLightTaxonomyRow; + } + try { SpeciesService taxonomyService = getSpeciesService(); CloseableIterator streamIterator = taxonomyService.getTaxonChildrenByParentId(parentId); + ASLSession session = getASLSession(); TaxonomyItemConverter converter = new TaxonomyItemConverter(getASLSession()); - - int i = 0; + + Map mapChildren = SessionUtil.getHashMapChildrenTaxonomyCache(session); + + if(mapChildren==null){ + logger.trace("Cache taxa children doesn't exists into session, creating.."); + mapChildren = new HashMap(); + } +// 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 retrieveTaxonomyByIds(List ids) throws Exception{ + public List retrieveTaxonomyByIds(List ids) throws Exception{ logger.trace("retrieveTaxonomyByIds ids size: " + ids.size()); // System.out.println("retrieveTaxonomyByIds ids size: " + ids.size() + " first id " + ids.get(0)); - List listTaxonomyRow = new ArrayList(); + List listLightTaxonomyRow = new ArrayList(); try { SpeciesService taxonomyService = getSpeciesService(); @@ -1620,19 +1647,32 @@ public class TaxonomySearchServiceImpl extends RemoteServiceServlet implements T CloseableIterator streamIterator = taxonomyService.retrieveTaxonomyById(convert); - TaxonomyItemConverter taxonomyItemConverter = new TaxonomyItemConverter(getASLSession()); + ASLSession session = getASLSession(); + TaxonomyItemConverter taxonomyItemConverter = new TaxonomyItemConverter(session); + + Map mapTaxonomyIds = SessionUtil.getHashMapTaxonomyByIdsCache(session); + + if(mapTaxonomyIds==null){ + logger.trace("Cache taxa ByIds doesn't exists into session, creating.."); + mapTaxonomyIds = new HashMap(); + } - 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 retrieveSynonymsByRefId(String refId) throws Exception{ + public List retrieveSynonymsByRefId(String refId) throws Exception{ logger.trace("retrieveSynonymsById id: " + refId); //FOR DEBUG // System.out.println("retrieveSynonymsById id: " + refId); - List listTaxonomyRow = new ArrayList(); + List listLightTaxonomyRow = new ArrayList(); try { SpeciesService taxonomyService = getSpeciesService(); CloseableIterator streamIterator = taxonomyService.retrieveSynonymsById(refId); + ASLSession session = getASLSession(); TaxonomyItemConverter taxonomyItemConverter = new TaxonomyItemConverter(getASLSession()); - int i = 1; + Map mapSysnosyms = SessionUtil.getHashMapSynonymsTaxonomyCache(getASLSession()); + + if(mapSysnosyms==null){ + logger.trace("Cache synonyms doesn't exists into session, creating.."); + mapSysnosyms = new HashMap(); + } + +// 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 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 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 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 hashCluster = SessionUtil.getCurrentClusterCommonNameForTaxonomyRow(session); + + //Reset cluster for common name + if(hashCluster!=null) + SessionUtil.setCurrentClusterCommonNameForTaxonomyRow(session, null); + + + HashMap mapOldChildren = SessionUtil.getHashMapChildrenTaxonomyCache(session); + //Reset list children to last clustering + if(mapOldChildren!=null) + SessionUtil.setHashMapChildrenTaxonomyCache(session, null); + + HashMap mapSynonyms = SessionUtil.getHashMapSynonymsTaxonomyCache(session); + //Reset list synonyms to last clustering + if(mapSynonyms!=null) + SessionUtil.setHashMapSynonymsTaxonomyCache(session, null); + + HashMap 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 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 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; + } } diff --git a/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/asl/SessionUtil.java b/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/asl/SessionUtil.java index cc8cf2d..a46f66e 100644 --- a/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/asl/SessionUtil.java +++ b/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/asl/SessionUtil.java @@ -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 hashClusterCommonNameDataSource) { + session.setAttribute(CLUSTER_COMMONNAME_FOR_RESULTROW, hashClusterCommonNameDataSource); + + } + + /** + * @param hashClusterCommonNameDataSource + * @return + */ + public static HashMap getCurrentClusterCommonNameForResultRow(ASLSession session) { + return (HashMap) session.getAttribute(CLUSTER_COMMONNAME_FOR_RESULTROW); + + } + + + /** + * @param hashClusterCommonNameDataSource + */ + public static void setCurrentClusterCommonNameForTaxonomyRow(ASLSession session, HashMap hashClusterCommonNameDataSource) { + session.setAttribute(CLUSTER_COMMONNAME_FOR_TAXONOMYROW, hashClusterCommonNameDataSource); + + } + + /** + * @param hashClusterCommonNameDataSource + * @return + */ + public static HashMap getCurrentClusterCommonNameForTaxonomyRow(ASLSession session) { + return (HashMap) session.getAttribute(CLUSTER_COMMONNAME_FOR_TAXONOMYROW); + + } + + /** + * @return + * + */ + public static HashMap getHashMapChildrenTaxonomyCache(ASLSession session) { + return (HashMap) session.getAttribute(CACHE_HASH_MAP_CHILDREN_TAXONOMY); + + } + + /** + * @return + * + */ + public static void setHashMapChildrenTaxonomyCache(ASLSession session, Map list) { + session.setAttribute(CACHE_HASH_MAP_CHILDREN_TAXONOMY, list); + + } + + + /** + * @return + * + */ + public static HashMap getHashMapSynonymsTaxonomyCache(ASLSession session) { + return (HashMap) session.getAttribute(CACHE_HASH_MAP_SYNONYMS_TAXONOMY); + + } + + /** + * @return + * + */ + public static void setHashMapSynonymsTaxonomyCache(ASLSession session, Map list) { + session.setAttribute(CACHE_HASH_MAP_SYNONYMS_TAXONOMY, list); + + } + + + /** + * @return + * + */ + public static HashMap getHashMapTaxonomyByIdsCache(ASLSession session) { + return (HashMap) session.getAttribute(CACHE_HASH_MAP_TAXONOMYID_TAXONOMY); + + } + + /** + * @return + * + */ + public static void setHashMapTaxonomyByIdsCache(ASLSession session, Map list) { + session.setAttribute(CACHE_HASH_MAP_TAXONOMYID_TAXONOMY, list); + + } } diff --git a/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/persistence/AbstractDaoBuffer.java b/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/persistence/AbstractDaoBuffer.java index e2515f6..7b9d718 100644 --- a/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/persistence/AbstractDaoBuffer.java +++ b/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/persistence/AbstractDaoBuffer.java @@ -72,5 +72,4 @@ public abstract class AbstractDaoBuffer implements Fe public List getList(Map filterANDMap, int startIndex, int offset) throws Exception{ return dao.getList(filterANDMap, startIndex, offset); } - } diff --git a/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/persistence/AbstractSelectableDaoBuffer.java b/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/persistence/AbstractSelectableDaoBuffer.java index d90f1c3..83e36c4 100644 --- a/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/persistence/AbstractSelectableDaoBuffer.java +++ b/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/persistence/AbstractSelectableDaoBuffer.java @@ -74,5 +74,4 @@ public abstract class AbstractSelectableDaoBuffer e return getSelected().size(); } - } diff --git a/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/persistence/DaoSession.java b/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/persistence/DaoSession.java index f1440c7..2533add 100644 --- a/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/persistence/DaoSession.java +++ b/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/persistence/DaoSession.java @@ -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); diff --git a/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/persistence/ResultRowBuffer.java b/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/persistence/ResultRowBuffer.java index a253403..d28ef1c 100644 --- a/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/persistence/ResultRowBuffer.java +++ b/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/persistence/ResultRowBuffer.java @@ -52,8 +52,7 @@ public class ResultRowBuffer extends AbstractSelectableDaoBuffer 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); } diff --git a/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/persistence/TaxonomyRowBuffer.java b/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/persistence/TaxonomyRowBuffer.java index 3941f51..d6d7a09 100644 --- a/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/persistence/TaxonomyRowBuffer.java +++ b/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/persistence/TaxonomyRowBuffer.java @@ -46,8 +46,7 @@ public class TaxonomyRowBuffer extends AbstractSelectableDaoBuffer 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); } diff --git a/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/service/TaxonomyItemConverter.java b/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/service/TaxonomyItemConverter.java index 6e0227a..ec85e5e 100644 --- a/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/service/TaxonomyItemConverter.java +++ b/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/service/TaxonomyItemConverter.java @@ -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 Converter0) + 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 listTaxonomy = taxon.getParents(); + + for (LightTaxonomyRow taxonomyRow : listTaxonomy) { + + if(taxonomyRow.getRank().compareToIgnoreCase(rank)==0) + return taxonomyRow.getName(); + } + + return TaxonomySearchServiceImpl.TAXONOMYUNKNOWN; + } + + + protected List convertParentsLightTaxonomy(TaxonomyItem taxon) throws Exception + { + if (taxon == null) return null; + List listTaxonomy = new ArrayList(); + 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 convertParentsTaxonomy(TaxonomyItem taxon) throws Exception { if (taxon == null) return null; diff --git a/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/util/StorageUtil.java b/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/util/StorageUtil.java index c40570a..7c23ae8 100644 --- a/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/util/StorageUtil.java +++ b/src/main/java/org/gcube/portlets/user/speciesdiscovery/server/util/StorageUtil.java @@ -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=="); + + + } } diff --git a/src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/JobTaxonomyModel.java b/src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/JobTaxonomyModel.java index 55a6573..a491841 100644 --- a/src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/JobTaxonomyModel.java +++ b/src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/JobTaxonomyModel.java @@ -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() { diff --git a/src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/LightTaxonomyRow.java b/src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/LightTaxonomyRow.java new file mode 100644 index 0000000..5735ae5 --- /dev/null +++ b/src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/LightTaxonomyRow.java @@ -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 { + + + /** + * + */ + 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 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 parent) { + this.parents = parent; + } + + public List 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(); + } + +} diff --git a/src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/cluster/ClusterCommonNameDataSource.java b/src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/cluster/ClusterCommonNameDataSource.java index 11c9551..0edeb32 100644 --- a/src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/cluster/ClusterCommonNameDataSource.java +++ b/src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/cluster/ClusterCommonNameDataSource.java @@ -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 + */ +//@Entity public class ClusterCommonNameDataSource implements Serializable{ /** * */ + + private static final long serialVersionUID = -4602671242562941238L; +// @Id +// @GeneratedValue(strategy = GenerationType.IDENTITY) +// private int internalId; + + private HashMap> hashMapCommonNameDataSources = new HashMap>(); private ArrayList listDataSourcesFound = new ArrayList(); diff --git a/src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/cluster/ClusterCommonNameDataSourceForResultRow.java b/src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/cluster/ClusterCommonNameDataSourceForResultRow.java new file mode 100644 index 0000000..acef75a --- /dev/null +++ b/src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/cluster/ClusterCommonNameDataSourceForResultRow.java @@ -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 cluster = new ClusterCommonNameDataSource(); //NEW CLUSTER + + + public ClusterCommonNameDataSourceForResultRow(){} + + /** + * @param scientificName + * @param cluster + */ + public ClusterCommonNameDataSourceForResultRow(String scientificName, ClusterCommonNameDataSource cluster) { + super(); + this.scientificName = scientificName; + this.cluster = cluster; + } + + public String getScientificName() { + return scientificName; + } + + public void setScientificName(String scientificName) { + this.scientificName = scientificName; + } + + public ClusterCommonNameDataSource getCluster() { + return cluster; + } + + public void setCluster(ClusterCommonNameDataSource 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(); + } + + +} diff --git a/src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/cluster/ClusterCommonNameDataSourceForTaxonomyRow.java b/src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/cluster/ClusterCommonNameDataSourceForTaxonomyRow.java new file mode 100644 index 0000000..d4ef15f --- /dev/null +++ b/src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/cluster/ClusterCommonNameDataSourceForTaxonomyRow.java @@ -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 cluster = new ClusterCommonNameDataSource(); //NEW CLUSTER + + + public ClusterCommonNameDataSourceForTaxonomyRow(){} + + /** + * @param scientificName + * @param cluster + */ + public ClusterCommonNameDataSourceForTaxonomyRow(String scientificName, ClusterCommonNameDataSource cluster) { + super(); + this.scientificName = scientificName; + this.cluster = cluster; + } + + public String getScientificName() { + return scientificName; + } + + public void setScientificName(String scientificName) { + this.scientificName = scientificName; + } + + public ClusterCommonNameDataSource getCluster() { + return cluster; + } + + public void setCluster(ClusterCommonNameDataSource 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(); + } + +} diff --git a/src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/cluster/ClusterStructuresForResultRow.java b/src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/cluster/ClusterStructuresForResultRow.java index 8baf2c2..4e82ffd 100644 --- a/src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/cluster/ClusterStructuresForResultRow.java +++ b/src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/cluster/ClusterStructuresForResultRow.java @@ -22,51 +22,36 @@ public class ClusterStructuresForResultRow implements Serializable{ * */ private static final long serialVersionUID = 1205113606387863736L; - - private ArrayList listResultRowID; - private Map hashResult = new HashMap(); + private ArrayList listResultRowServiceID; private ArrayList listFoundDataSources = new ArrayList(); - private HashMap> hashClusterCommonNamesDataSources = new HashMap>(); //HASH scientific name - cluster - private HashMap> hashScientificNameResultRowID = new HashMap>(); //HASH scientific name - result row ID + private HashMap> hashScientificNameResultRowServiceID = new HashMap>(); //HASH scientific name - result row service ID private boolean isReduced; - private int totalRow; + private int allResultRowSize; + private int resultSize; + + private Map hashResult = new HashMap(); //HASH result row service ID - result row + public ClusterStructuresForResultRow(){} public ClusterStructuresForResultRow(SearchResult 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 listResultRowServiceID = hashScientificNameResultRowID.get(scientificName); //get RR serviceID - - ClusterCommonNameDataSource cluster = new ClusterCommonNameDataSource(); //NEW CLUSTER - - for(int i=0; i 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(); //USED FOR CLUSTER COMMON NAMES + listResultRowServiceID = new ArrayList(); //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> getHashClusterScientificNameResultRowID() { - return hashScientificNameResultRowID; + public HashMap> getHashClusterScientificNameResultRowServiceID() { + return hashScientificNameResultRowServiceID; } public List getListFoundDataSources() { return listFoundDataSources; } - public HashMap> getHashClusterCommonNamesDataSources() { - return hashClusterCommonNamesDataSources; + public ArrayList getListResultRowID() { + return listResultRowServiceID; } - public List getResult() { - return new ArrayList(hashResult.values()); - } - - public ResultRow getResultRowByRowID(String key) { - return hashResult.get(key); + public void setListResultRowID(ArrayList 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 listFoundDataSources) { + this.listFoundDataSources = listFoundDataSources; + } + + public Map getHashResult() { + return hashResult; + } + + public void setHashResult(Map hashResult) { + this.hashResult = hashResult; + } } diff --git a/src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/cluster/ClusterStructuresForTaxonomyRow.java b/src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/cluster/ClusterStructuresForTaxonomyRow.java index bd28a49..b75d32f 100644 --- a/src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/cluster/ClusterStructuresForTaxonomyRow.java +++ b/src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/cluster/ClusterStructuresForTaxonomyRow.java @@ -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 hashResult = new HashMap(); - private HashMap> hashClusterCommonNamesDataSources = new HashMap>(); - private HashMap> hashClusterScientificNameTaxonomyRowID = new HashMap>(); //HASH scientific name - taxonomy row ID + //USED ON CLIENT + private Map hashLightResult = new HashMap(); + + private HashMap> hashClusterScientificNameTaxonomyRowServiceID = new HashMap>(); //HASH scientific name - taxonomy row service ID private ArrayList listFoundDataSources = new ArrayList(); - private ArrayList listTaxonomyRowID; + private ArrayList listTaxonomyRowServiceID; private boolean isReduced; private int totalRow; + + //USED ON SERVER FOR CLUSERING ON COMMON NAMES + private Map hashResult = new HashMap(); public ClusterStructuresForTaxonomyRow(){ } public ClusterStructuresForTaxonomyRow(SearchResult 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 sublistParents = new ArrayList(); -//// 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 parents = new ArrayList(); + 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 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(); //USED FOR CLUSTER COMMON NAMES + listTaxonomyRowServiceID = new ArrayList(); //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 listTaxonomyRowID = hashClusterScientificNameTaxonomyRowID.get(scientificName); - - ClusterCommonNameDataSource cluster = new ClusterCommonNameDataSource(); //NEW CLUSTER - - for(int i=0; i getListFoundDataSources() { return listFoundDataSources; } - public HashMap> getHashClusterScientificNameTaxonomyRowID() { - return hashClusterScientificNameTaxonomyRowID; + public HashMap> getHashClusterScientificNameTaxonomyRowServiceID() { + return hashClusterScientificNameTaxonomyRowServiceID; } - public HashMap> getHashClusterCommonNamesDataSources() { - return hashClusterCommonNamesDataSources; - } - - public ArrayList getResult() { - return new ArrayList(hashResult.values()); + public ArrayList getResult() { + return new ArrayList(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 getHashLightResult() { + return hashLightResult; + } + + public Map getHashResult() { + return hashResult; + } + + public void setHashResult(Map hashResult) { + this.hashResult = hashResult; + } + } diff --git a/src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/cluster/ManagerClusterCommonNameDataSourceForResultRow.java b/src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/cluster/ManagerClusterCommonNameDataSourceForResultRow.java new file mode 100644 index 0000000..9b025d6 --- /dev/null +++ b/src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/cluster/ManagerClusterCommonNameDataSourceForResultRow.java @@ -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> hashScientificNameResultRowServiceID = new HashMap>(); //HASH scientific name - result row service ID + private Map hashResult = new HashMap(); + + private HashMap hashClusterCommonNameDataSource = new HashMap(); //HASH scientific name - cluster + + + /** + * @param hashScientificNameResultRowID + * @param hashClusterCommonNameDataSource + * @param hashResult + * @throws Exception + */ + public ManagerClusterCommonNameDataSourceForResultRow(HashMap> hashScientificNameResultRowID, Map 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 listResultRowServiceID = hashScientificNameResultRowServiceID.get(scientificName); //get RR serviceID + + ClusterCommonNameDataSource cluster = new ClusterCommonNameDataSource(); //NEW CLUSTER + + for(int i=0; i> getHashScientificNameResultRowID() { + return hashScientificNameResultRowServiceID; + } + + + public void setHashScientificNameResultRowID( + HashMap> hashScientificNameResultRowID) { + this.hashScientificNameResultRowServiceID = hashScientificNameResultRowID; + } + + + public HashMap getHashClusterCommonNameDataSource() { + return hashClusterCommonNameDataSource; + } + + + public void setHashClusterCommonNameDataSource( + HashMap hashClusterCommonNameDataSource) { + this.hashClusterCommonNameDataSource = hashClusterCommonNameDataSource; + } + + + public Map getHashResult() { + return hashResult; + } + + + public void setHashResult(Map 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(); + } + +} diff --git a/src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/cluster/ManagerClusterCommonNameDataSourceForTaxonomyRow.java b/src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/cluster/ManagerClusterCommonNameDataSourceForTaxonomyRow.java new file mode 100644 index 0000000..6ff81bb --- /dev/null +++ b/src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/cluster/ManagerClusterCommonNameDataSourceForTaxonomyRow.java @@ -0,0 +1,113 @@ +/** + * + */ +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> hashScientificNameTaxonomyRowServiceID = new HashMap>(); //HASH scientific name - taxonomy row service ID + private Map hashResult = new HashMap(); + + private HashMap hashClusterCommonNameDataSource = new HashMap(); //HASH scientific name - cluster + + + /** + * @param hashScientificNameResultRowServiceID + * @param hashClusterCommonNameDataSource + * @param hashResult + * @throws Exception + */ + public ManagerClusterCommonNameDataSourceForTaxonomyRow(HashMap> hashScientificNameResultRowServiceID, Map 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 listTaxonomyRowServiceID = hashScientificNameTaxonomyRowServiceID.get(scientificName); + + ClusterCommonNameDataSource cluster = new ClusterCommonNameDataSource(); //NEW CLUSTER + + for(int i=0; i> getHashScientificNameResultRowID() { + return hashScientificNameTaxonomyRowServiceID; + } + + + public void setHashScientificNameResultRowID( + HashMap> hashScientificNameResultRowID) { + this.hashScientificNameTaxonomyRowServiceID = hashScientificNameResultRowID; + } + + + public HashMap getHashClusterCommonNameDataSource() { + return hashClusterCommonNameDataSource; + } + + + public void setHashClusterCommonNameDataSource(HashMap hashClusterCommonNameDataSource) { + this.hashClusterCommonNameDataSource = hashClusterCommonNameDataSource; + } + + + public Map getHashResult() { + return hashResult; + } + + + public void setHashResult(Map 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(); + } + +}