org.gcube.portlets.user.speciesdiscovery.server
Class TaxonomySearchServiceImpl

java.lang.Object
  extended by javax.servlet.GenericServlet
      extended by javax.servlet.http.HttpServlet
          extended by com.google.gwt.user.server.rpc.AbstractRemoteServiceServlet
              extended by com.google.gwt.user.server.rpc.RemoteServiceServlet
                  extended by org.gcube.portlets.user.speciesdiscovery.server.TaxonomySearchServiceImpl
All Implemented Interfaces:
com.google.gwt.user.client.rpc.RemoteService, com.google.gwt.user.server.rpc.SerializationPolicyProvider, Serializable, javax.servlet.Servlet, javax.servlet.ServletConfig, TaxonomySearchService

public class TaxonomySearchServiceImpl
extends com.google.gwt.user.server.rpc.RemoteServiceServlet
implements TaxonomySearchService

The server side implementation of the RPC service.

Author:
"Federico De Faveri defaveri@isti.cnr.it" -, "Francesco Mangiacrapa francesco.mangiacrapa@isti.cnr.it"
See Also:
Serialized Form

Field Summary
static String BASETAXONOMY
           
protected static long BUFFER_LIMIT
           
protected  org.apache.log4j.Logger logger
           
protected static long MAX_BUFFERING_ELEMENTS
           
protected static String RESUBMIT
           
protected static String SAVE_CHILDREN_OF
           
static String TAXONOMYUNKNOWN
           
static String UNK
           
 
Fields inherited from class com.google.gwt.user.server.rpc.AbstractRemoteServiceServlet
perThreadRequest, perThreadResponse
 
Constructor Summary
TaxonomySearchServiceImpl()
           
 
Method Summary
 boolean cancelOccurrenceJob(String jobIdentifier)
           
 boolean cancelTaxonomyJob(String jobIdentifier)
           
 boolean changeStatusOccurrenceJob(String jobIdentifier, DownloadState state)
           
 boolean changeStatusTaxonomyJob(String jobIdentifier, DownloadState state)
           
 int countOfSelectedRow()
          
 List<JobOccurrencesModel> createOccurrencesJob(List<JobOccurrencesModel> listJobOccurrenceModel, SaveFileFormat saveFileFormat, OccurrencesSaveEnum csvType, boolean isByDataSource, int expectedOccurrence)
          
 JobTaxonomyModel createTaxonomyJobByChildren(String taxonomyServiceId, String taxonomyName, String taxonomyRank, String dataSourceName)
           
 JobTaxonomyModel createTaxonomyJobByIds(String search, List<DataSourceModel> dataSources)
           
protected  File generateCSVFile(List<String> ids, OccurrencesSaveEnum csvType)
           
 String generateMapFromSelectedOccurrencePoints()
          
protected  org.gcube.application.framework.core.session.ASLSession getASLSession()
           
 OccurrencesStatus getCountOfOccurrencesBatch()
           
 HashMap<String,Integer> getFilterCounterById(GridField field)
          
 HashMap<String,ClassificationModel> getFilterCounterForClassification(String rankLabel)
           
protected  Iterator<Occurrence> getIteratorSelectedOccurrenceIds()
           
 String getLastQuery()
           
 List<JobOccurrencesModel> getListOccurrencesJob()
           
 List<JobTaxonomyModel> getListTaxonomyJobs()
           
 OccurrenceBatch getOccurrencesBatch(int start, int limit)
           
protected  FetchingSession<Occurrence> getOccurrenceSession()
           
 List<Taxon> getParentsList(Taxon taxon)
           
 SearchResult<ResultRow> getSearchResultRows(int start, int limit, ResultFilter activeFiltersObject, boolean onlySelected)
          
protected  FetchingSession<? extends FetchingElement> getSearchSession()
           
 SearchStatus getSearchStatus(boolean onlySelected, boolean isActiveFilterOnResult)
          
 SearchResult<TaxonomyRow> getSearchTaxonomyRow(int start, int limit, ResultFilter activeFiltersObject, boolean onlySelected)
           
protected  List<String> getSelectedOccurrenceIds()
           
protected  List<String> getSelectedOccurrenceKeys()
           
protected  List<String> getSelectedResultRowId()
           
protected  Map<String,String> getSelectedTaxonomyIdAndDataSource()
           
protected  SpeciesService getSpeciesService()
           
 boolean isAvailableOccurrenceJobReportError(String jobIdentifier)
           
 boolean isAvailableTaxonomyJobReportError(String jobIdentifier)
           
 List<DataSource> loadDataSourceForResultRow(boolean selected, boolean distinct)
           
 List<DataSourceModel> loadDataSourceList()
           
 ArrayList<TaxonomyRow> loadListChildByParentId(String parentId)
           
 ArrayList<CommonName> loadListCommonNameByRowId(String resultRowId)
           
 ClusterStructuresForResultRow loadStructuresForResultRowClustering()
           
 ClusterStructuresForTaxonomyRow loadStructuresForTaxonomyClustering()
           
 TaxonomyRow loadTaxonomyParentByParentId(String parentID)
           
protected  void printId(List<String> listId)
           
 List<JobOccurrencesModel> resubmitOccurrencesJob(String jobIdentifier)
           
 JobTaxonomyModel resubmitTaxonomyJob(String jobIdentifier)
           
 int retrieveOccurencesFromSelection()
          
 List<TaxonomyRow> retrieveSynonymsByRefId(String refId)
           
 List<TaxonomyRow> retrieveTaxonomyByIds(List<String> ids)
           
 boolean saveOccurrenceJob(JobOccurrencesModel jobModel, String destinationFolderId, String fileName, String scientificName, String dataSourceName)
           
 boolean saveOccurrenceJobError(JobOccurrencesModel jobModel, String destinationFolderId, String fileName, String scientificName, String dataSourceName)
           
 void saveSelectedOccurrencePoints(String destinationFolderId, String fileName, SaveFileFormat fileFormat, OccurrencesSaveEnum typeCSV)
           
 void saveSelectedTaxonomyPoints(String destinationFolderId, String fileName, SaveFileFormat fileFormat)
           
 boolean saveTaxonomyJob(String jobIdentifier, String destinationFolderId, String fileName, String scientificName, String dataSourceName)
           
 boolean saveTaxonomyJobError(String jobIdentifier, String destinationFolderId, String fileName, String scientificName, String dataSourceName)
           
protected  SearchResultType search(String searchTerm, SearchType searchType, SearchFilters searchFilters)
           
 void searchByCommonName(String searchTerm, SearchFilters searchFilters)
          
 SearchByQueryParameter searchByQuery(String query)
           
 void searchByScientificName(String searchTerm, SearchFilters searchFilters)
          
 void stopRetrievingOccurrences()
          
 void stopSearch()
          
 void stopSearchWithoutRemove()
          
 void updateRowSelection(int rowId, boolean selection)
          
 Integer updateRowSelections(boolean selection, ResultFilter activeFiltersObject)
          
 
Methods inherited from class com.google.gwt.user.server.rpc.RemoteServiceServlet
checkPermutationStrongName, doGetSerializationPolicy, getSerializationPolicy, onAfterResponseSerialized, onBeforeRequestDeserialized, processCall, processPost, shouldCompressResponse
 
Methods inherited from class com.google.gwt.user.server.rpc.AbstractRemoteServiceServlet
doPost, doUnexpectedFailure, getPermutationStrongName, getThreadLocalRequest, getThreadLocalResponse, onAfterRequestDeserialized, readContent
 
Methods inherited from class javax.servlet.http.HttpServlet
doDelete, doGet, doHead, doOptions, doPut, doTrace, getLastModified, service, service
 
Methods inherited from class javax.servlet.GenericServlet
destroy, getInitParameter, getInitParameterNames, getServletConfig, getServletContext, getServletInfo, getServletName, init, init, log, log
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

SAVE_CHILDREN_OF

protected static final String SAVE_CHILDREN_OF
See Also:
Constant Field Values

RESUBMIT

protected static final String RESUBMIT
See Also:
Constant Field Values

MAX_BUFFERING_ELEMENTS

protected static final long MAX_BUFFERING_ELEMENTS
See Also:
Constant Field Values

BUFFER_LIMIT

protected static final long BUFFER_LIMIT
See Also:
Constant Field Values

logger

protected org.apache.log4j.Logger logger

TAXONOMYUNKNOWN

public static final String TAXONOMYUNKNOWN
See Also:
Constant Field Values

BASETAXONOMY

public static final String BASETAXONOMY
See Also:
Constant Field Values

UNK

public static final String UNK
See Also:
Constant Field Values
Constructor Detail

TaxonomySearchServiceImpl

public TaxonomySearchServiceImpl()
Method Detail

getASLSession

protected org.gcube.application.framework.core.session.ASLSession getASLSession()

getSpeciesService

protected SpeciesService getSpeciesService()
                                    throws SearchServiceException
Throws:
SearchServiceException

getSearchSession

protected FetchingSession<? extends FetchingElement> getSearchSession()
                                                               throws SearchServiceException
Throws:
SearchServiceException

getOccurrenceSession

protected FetchingSession<Occurrence> getOccurrenceSession()
                                                    throws SearchServiceException
Throws:
SearchServiceException

searchByScientificName

public void searchByScientificName(String searchTerm,
                                   SearchFilters searchFilters)
                            throws SearchServiceException

Specified by:
searchByScientificName in interface TaxonomySearchService
Throws:
SearchServiceException

searchByCommonName

public void searchByCommonName(String searchTerm,
                               SearchFilters searchFilters)
                        throws SearchServiceException

Specified by:
searchByCommonName in interface TaxonomySearchService
Throws:
SearchServiceException

search

protected SearchResultType search(String searchTerm,
                                  SearchType searchType,
                                  SearchFilters searchFilters)
                           throws SearchServiceException
Throws:
SearchServiceException

searchByQuery

public SearchByQueryParameter searchByQuery(String query)
                                     throws SearchServiceException
Specified by:
searchByQuery in interface TaxonomySearchService
Throws:
SearchServiceException

getSearchResultRows

public SearchResult<ResultRow> getSearchResultRows(int start,
                                                   int limit,
                                                   ResultFilter activeFiltersObject,
                                                   boolean onlySelected)
                                            throws SearchServiceException

Specified by:
getSearchResultRows in interface TaxonomySearchService
Throws:
SearchServiceException

getSearchTaxonomyRow

public SearchResult<TaxonomyRow> getSearchTaxonomyRow(int start,
                                                      int limit,
                                                      ResultFilter activeFiltersObject,
                                                      boolean onlySelected)
                                               throws SearchServiceException
Specified by:
getSearchTaxonomyRow in interface TaxonomySearchService
Throws:
SearchServiceException

loadTaxonomyParentByParentId

public TaxonomyRow loadTaxonomyParentByParentId(String parentID)
                                         throws Exception
Throws:
Exception

getFilterCounterById

public HashMap<String,Integer> getFilterCounterById(GridField field)
                                             throws Exception

Specified by:
getFilterCounterById in interface TaxonomySearchService
Throws:
Exception

getFilterCounterForClassification

public HashMap<String,ClassificationModel> getFilterCounterForClassification(String rankLabel)
                                                                      throws Exception
Specified by:
getFilterCounterForClassification in interface TaxonomySearchService
Throws:
Exception

getSearchStatus

public SearchStatus getSearchStatus(boolean onlySelected,
                                    boolean isActiveFilterOnResult)
                             throws SearchServiceException

Specified by:
getSearchStatus in interface TaxonomySearchService
Throws:
SearchServiceException

stopSearchWithoutRemove

public void stopSearchWithoutRemove()
                             throws SearchServiceException

Throws:
SearchServiceException

stopSearch

public void stopSearch()
                throws SearchServiceException

Specified by:
stopSearch in interface TaxonomySearchService
Throws:
SearchServiceException

updateRowSelection

public void updateRowSelection(int rowId,
                               boolean selection)
                        throws SearchServiceException

Specified by:
updateRowSelection in interface TaxonomySearchService
Throws:
SearchServiceException

updateRowSelections

public Integer updateRowSelections(boolean selection,
                                   ResultFilter activeFiltersObject)
                            throws SearchServiceException

Specified by:
updateRowSelections in interface TaxonomySearchService
Throws:
SearchServiceException

countOfSelectedRow

public int countOfSelectedRow()
                       throws SearchServiceException

Specified by:
countOfSelectedRow in interface TaxonomySearchService
Throws:
SearchServiceException

retrieveOccurencesFromSelection

public int retrieveOccurencesFromSelection()
                                    throws SearchServiceException

Specified by:
retrieveOccurencesFromSelection in interface TaxonomySearchService
Throws:
SearchServiceException

getOccurrencesBatch

public OccurrenceBatch getOccurrencesBatch(int start,
                                           int limit)
                                    throws SearchServiceException
Specified by:
getOccurrencesBatch in interface TaxonomySearchService
Throws:
SearchServiceException

getCountOfOccurrencesBatch

public OccurrencesStatus getCountOfOccurrencesBatch()
                                             throws SearchServiceException
Specified by:
getCountOfOccurrencesBatch in interface TaxonomySearchService
Throws:
SearchServiceException

stopRetrievingOccurrences

public void stopRetrievingOccurrences()
                               throws SearchServiceException

Specified by:
stopRetrievingOccurrences in interface TaxonomySearchService
Throws:
SearchServiceException

generateMapFromSelectedOccurrencePoints

public String generateMapFromSelectedOccurrencePoints()
                                               throws SearchServiceException

Specified by:
generateMapFromSelectedOccurrencePoints in interface TaxonomySearchService
Throws:
SearchServiceException

printId

protected void printId(List<String> listId)

getSelectedOccurrenceIds

protected List<String> getSelectedOccurrenceIds()
                                         throws SearchServiceException
Throws:
SearchServiceException

getIteratorSelectedOccurrenceIds

protected Iterator<Occurrence> getIteratorSelectedOccurrenceIds()
                                                         throws SearchServiceException
Throws:
SearchServiceException

saveSelectedOccurrencePoints

public void saveSelectedOccurrencePoints(String destinationFolderId,
                                         String fileName,
                                         SaveFileFormat fileFormat,
                                         OccurrencesSaveEnum typeCSV)
                                  throws SearchServiceException
Specified by:
saveSelectedOccurrencePoints in interface TaxonomySearchService
Throws:
SearchServiceException

saveSelectedTaxonomyPoints

public void saveSelectedTaxonomyPoints(String destinationFolderId,
                                       String fileName,
                                       SaveFileFormat fileFormat)
                                throws SearchServiceException
Specified by:
saveSelectedTaxonomyPoints in interface TaxonomySearchService
Throws:
SearchServiceException

getSelectedOccurrenceKeys

protected List<String> getSelectedOccurrenceKeys()
                                          throws SearchServiceException
Throws:
SearchServiceException

getSelectedResultRowId

protected List<String> getSelectedResultRowId()
                                       throws SearchServiceException
Throws:
SearchServiceException

getSelectedTaxonomyIdAndDataSource

protected Map<String,String> getSelectedTaxonomyIdAndDataSource()
                                                         throws SearchServiceException
Throws:
SearchServiceException

generateCSVFile

protected File generateCSVFile(List<String> ids,
                               OccurrencesSaveEnum csvType)
                        throws Exception
Throws:
Exception

loadDataSourceList

public List<DataSourceModel> loadDataSourceList()
                                         throws SearchServiceException
Specified by:
loadDataSourceList in interface TaxonomySearchService
Throws:
SearchServiceException

loadListCommonNameByRowId

public ArrayList<CommonName> loadListCommonNameByRowId(String resultRowId)
                                                throws Exception
Specified by:
loadListCommonNameByRowId in interface TaxonomySearchService
Throws:
Exception

getParentsList

public List<Taxon> getParentsList(Taxon taxon)
                           throws Exception
Specified by:
getParentsList in interface TaxonomySearchService
Throws:
Exception

loadListChildByParentId

public ArrayList<TaxonomyRow> loadListChildByParentId(String parentId)
                                               throws Exception
Specified by:
loadListChildByParentId in interface TaxonomySearchService
Throws:
Exception

getListTaxonomyJobs

public List<JobTaxonomyModel> getListTaxonomyJobs()
                                           throws Exception
Specified by:
getListTaxonomyJobs in interface TaxonomySearchService
Throws:
Exception

createTaxonomyJobByChildren

public JobTaxonomyModel createTaxonomyJobByChildren(String taxonomyServiceId,
                                                    String taxonomyName,
                                                    String taxonomyRank,
                                                    String dataSourceName)
                                             throws Exception
Specified by:
createTaxonomyJobByChildren in interface TaxonomySearchService
Parameters:
taxonomyServiceId -
taxonomyName -
taxonomyRank -
dataSourceName -
Returns:
Throws:
Exception

createTaxonomyJobByIds

public JobTaxonomyModel createTaxonomyJobByIds(String search,
                                               List<DataSourceModel> dataSources)
                                        throws Exception
Specified by:
createTaxonomyJobByIds in interface TaxonomySearchService
Throws:
Exception

resubmitTaxonomyJob

public JobTaxonomyModel resubmitTaxonomyJob(String jobIdentifier)
                                     throws Exception
Specified by:
resubmitTaxonomyJob in interface TaxonomySearchService
Throws:
Exception

cancelTaxonomyJob

public boolean cancelTaxonomyJob(String jobIdentifier)
                          throws Exception
Specified by:
cancelTaxonomyJob in interface TaxonomySearchService
Throws:
Exception

saveTaxonomyJob

public boolean saveTaxonomyJob(String jobIdentifier,
                               String destinationFolderId,
                               String fileName,
                               String scientificName,
                               String dataSourceName)
                        throws Exception
Specified by:
saveTaxonomyJob in interface TaxonomySearchService
Throws:
Exception

saveTaxonomyJobError

public boolean saveTaxonomyJobError(String jobIdentifier,
                                    String destinationFolderId,
                                    String fileName,
                                    String scientificName,
                                    String dataSourceName)
                             throws Exception
Specified by:
saveTaxonomyJobError in interface TaxonomySearchService
Returns:
Throws:
Exception

retrieveTaxonomyByIds

public List<TaxonomyRow> retrieveTaxonomyByIds(List<String> ids)
                                        throws Exception
Specified by:
retrieveTaxonomyByIds in interface TaxonomySearchService
Throws:
Exception

retrieveSynonymsByRefId

public List<TaxonomyRow> retrieveSynonymsByRefId(String refId)
                                          throws Exception
Specified by:
retrieveSynonymsByRefId in interface TaxonomySearchService
Throws:
Exception

createOccurrencesJob

public List<JobOccurrencesModel> createOccurrencesJob(List<JobOccurrencesModel> listJobOccurrenceModel,
                                                      SaveFileFormat saveFileFormat,
                                                      OccurrencesSaveEnum csvType,
                                                      boolean isByDataSource,
                                                      int expectedOccurrence)
                                               throws Exception

Specified by:
createOccurrencesJob in interface TaxonomySearchService
Throws:
Exception

resubmitOccurrencesJob

public List<JobOccurrencesModel> resubmitOccurrencesJob(String jobIdentifier)
                                                 throws Exception
Specified by:
resubmitOccurrencesJob in interface TaxonomySearchService
Throws:
Exception

getListOccurrencesJob

public List<JobOccurrencesModel> getListOccurrencesJob()
                                                throws Exception
Specified by:
getListOccurrencesJob in interface TaxonomySearchService
Throws:
Exception

saveOccurrenceJob

public boolean saveOccurrenceJob(JobOccurrencesModel jobModel,
                                 String destinationFolderId,
                                 String fileName,
                                 String scientificName,
                                 String dataSourceName)
                          throws Exception
Specified by:
saveOccurrenceJob in interface TaxonomySearchService
Throws:
Exception

saveOccurrenceJobError

public boolean saveOccurrenceJobError(JobOccurrencesModel jobModel,
                                      String destinationFolderId,
                                      String fileName,
                                      String scientificName,
                                      String dataSourceName)
                               throws Exception
Specified by:
saveOccurrenceJobError in interface TaxonomySearchService
Returns:
Throws:
Exception

cancelOccurrenceJob

public boolean cancelOccurrenceJob(String jobIdentifier)
                            throws Exception
Specified by:
cancelOccurrenceJob in interface TaxonomySearchService
Throws:
Exception

loadStructuresForResultRowClustering

public ClusterStructuresForResultRow loadStructuresForResultRowClustering()
                                                                   throws Exception
Specified by:
loadStructuresForResultRowClustering in interface TaxonomySearchService
Throws:
Exception

loadDataSourceForResultRow

public List<DataSource> loadDataSourceForResultRow(boolean selected,
                                                   boolean distinct)
                                            throws Exception
Specified by:
loadDataSourceForResultRow in interface TaxonomySearchService
Throws:
Exception

loadStructuresForTaxonomyClustering

public ClusterStructuresForTaxonomyRow loadStructuresForTaxonomyClustering()
                                                                    throws Exception
Specified by:
loadStructuresForTaxonomyClustering in interface TaxonomySearchService
Throws:
Exception

changeStatusOccurrenceJob

public boolean changeStatusOccurrenceJob(String jobIdentifier,
                                         DownloadState state)
                                  throws Exception
Specified by:
changeStatusOccurrenceJob in interface TaxonomySearchService
Throws:
Exception

changeStatusTaxonomyJob

public boolean changeStatusTaxonomyJob(String jobIdentifier,
                                       DownloadState state)
                                throws Exception
Specified by:
changeStatusTaxonomyJob in interface TaxonomySearchService
Throws:
Exception

isAvailableTaxonomyJobReportError

public boolean isAvailableTaxonomyJobReportError(String jobIdentifier)
                                          throws Exception
Specified by:
isAvailableTaxonomyJobReportError in interface TaxonomySearchService
Throws:
Exception

isAvailableOccurrenceJobReportError

public boolean isAvailableOccurrenceJobReportError(String jobIdentifier)
                                            throws Exception
Specified by:
isAvailableOccurrenceJobReportError in interface TaxonomySearchService
Throws:
Exception

getLastQuery

public String getLastQuery()
Specified by:
getLastQuery in interface TaxonomySearchService
Returns:


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