org.jbei.ice.storage.hibernate.search

Class HibernateSearch

java.lang.Object

org.jbei.ice.storage.hibernate.search.HibernateSearch

public class HibernateSearch
extends Object

Apache Lucene full text library functionality in Hibernate. Implemented as a singleton

Author:

Hector Plahar, Elena Aravina

Method Summary

Modifier and Type	Method and Description
protected void	checkEnableHasAttribute(org.hibernate.search.FullTextQuery fullTextQuery, SearchQuery.Parameters parameters)
protected org.hibernate.search.FullTextQuery	checkEnableSecurityFilter(String userId, org.hibernate.search.FullTextQuery fullTextQuery) Enables the security filter if the account does not have administrative privileges
protected static String	cleanQuery(String query)
protected void	createBlastFilterQuery(org.hibernate.search.FullTextSession fullTextSession, HashMap<String,SearchResult> blastResults, org.apache.lucene.search.BooleanQuery.Builder builder)
SearchResults	executeSearch(String userId, HashMap<String,QueryType> terms, SearchQuery searchQuery, HashMap<String,SearchResult> blastResults)
SearchResults	executeSearchNoTerms(String userId, HashMap<String,SearchResult> blastResults, SearchQuery searchQuery)
SearchResults	filterBlastResults(String userId, int start, int count, SearchQuery searchQuery, HashMap<String,SearchResult> blastResults) Intended to be called after running a blast search to filter the results.
protected org.apache.lucene.search.BooleanQuery.Builder	generateQueriesForType(org.hibernate.search.FullTextSession fullTextSession, HashSet<String> fields, org.apache.lucene.search.BooleanQuery.Builder builder, String term, QueryType type, BioSafetyOption option)
static HibernateSearch	getInstance() Retrieve the singleton instance of this class.
protected org.apache.lucene.search.Sort	getSort(boolean asc, ColumnField sortField)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Detail

getInstance

public static HibernateSearch getInstance()

Retrieve the singleton instance of this class.

Returns:

HibernateSearch instance.

executeSearchNoTerms

public SearchResults executeSearchNoTerms(String userId,
                                          HashMap<String,SearchResult> blastResults,
                                          SearchQuery searchQuery)

filterBlastResults

public SearchResults filterBlastResults(String userId,
                                        int start,
                                        int count,
                                        SearchQuery searchQuery,
                                        HashMap<String,SearchResult> blastResults)

Intended to be called after running a blast search to filter the results. Blast search runs on a fasta file which contains all the sequences. Hibernate search has a security filter for permissions and is therefore used to filter out the blast results, as well as to filter based on the entry attributes not handled by blast; such as "has sequence" and "bio-safety level"

Parameters:

userId - identifier for account of user performing search

start - paging start

count - maximum number of results to return

blastResults - raw results of the blast search

Returns:

wrapper around list of filtered results

executeSearch

public SearchResults executeSearch(String userId,
                                   HashMap<String,QueryType> terms,
                                   SearchQuery searchQuery,
                                   HashMap<String,SearchResult> blastResults)

generateQueriesForType

protected org.apache.lucene.search.BooleanQuery.Builder generateQueriesForType(org.hibernate.search.FullTextSession fullTextSession,
                                                                               HashSet<String> fields,
                                                                               org.apache.lucene.search.BooleanQuery.Builder builder,
                                                                               String term,
                                                                               QueryType type,
                                                                               BioSafetyOption option)

getSort

protected org.apache.lucene.search.Sort getSort(boolean asc,
                                                ColumnField sortField)

createBlastFilterQuery

protected void createBlastFilterQuery(org.hibernate.search.FullTextSession fullTextSession,
                                      HashMap<String,SearchResult> blastResults,
                                      org.apache.lucene.search.BooleanQuery.Builder builder)

checkEnableSecurityFilter

protected org.hibernate.search.FullTextQuery checkEnableSecurityFilter(String userId,
                                                                       org.hibernate.search.FullTextQuery fullTextQuery)

Enables the security filter if the account does not have administrative privileges

Parameters:

userId - identifier for account which is checked for administrative privs

fullTextQuery - search fulltextquery for which filter is enabled

checkEnableHasAttribute

protected void checkEnableHasAttribute(org.hibernate.search.FullTextQuery fullTextQuery,
                                       SearchQuery.Parameters parameters)

cleanQuery

protected static String cleanQuery(String query)