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source: trunk/src/groovy/dbnp/query/Search.groovy @ 1902

Last change on this file since 1902 was 1902, checked in by robert@…, 9 years ago
Resolving issues with searching (#446)
Property svn:keywords set to `Rev Author Date`
File size: 30.6 KB

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1	/**
2	* Search Domain Class
3	*
4	* Abstract class containing search criteria and search results when querying.
5	* Should be subclassed in order to enable searching for different entities.
6	*
7	* @author Robert Horlings (robert@isdat.nl)
8	* @since 20110118
9	* @package dbnp.query
10	*
11	* Revision information:
12	* $Rev: 1902 $
13	* $Author: robert@isdat.nl $
14	* $Date: 2011-05-31 08:09:18 +0000 (di, 31 mei 2011) $
15	*/
16	package dbnp.query
17
18	import org.dbnp.gdt.*
19	import java.util.List;
20	import java.text.DateFormat;
21	import java.text.SimpleDateFormat
22	import java.util.List;
23
24	import org.springframework.context.ApplicationContext
25	import org.springframework.web.context.request.RequestContextHolder;
26	import org.codehaus.groovy.grails.commons.ApplicationHolder;
27
28	import dbnp.authentication.*
29
30	/**
31	* Available boolean operators for searches
32	* @author robert
33	*
34	*/
35	enum SearchMode {
36	and, or
37	}
38
39	class Search {
40	/**
41	* User that is performing this search. This has impact on the search results returned.
42	*/
43	public SecUser user;
44
45	/**
46	* Date of execution of this search
47	*/
48	public Date executionDate;
49
50	/**
51	* Public identifier of this search. Is only used when this query is saved in session
52	*/
53	public int id;
54
55	/**
56	* Human readable entity name of the entities that can be found using this search
57	*/
58	public String entity;
59
60	/**
61	* Mode to search: OR or AND.
62	* @see SearchMode
63	*/
64	public SearchMode searchMode = SearchMode.and
65
66	protected List criteria;
67	protected List results;
68	protected Map resultFields = [:];
69
70	/**
71	* Constructor of this search object. Sets the user field to the
72	* currently logged in user
73	* @see #user
74	*/
75	public Search() {
76	def ctx = ApplicationHolder.getApplication().getMainContext();
77	def authenticationService = ctx.getBean("authenticationService");
78	def sessionUser = authenticationService?.getLoggedInUser();
79
80	if( sessionUser )
81	this.user = sessionUser;
82	else
83	this.user = null
84	}
85
86	/**
87	* Returns the number of results found by this search
88	* @return
89	*/
90	public int getNumResults() {
91	if( results )
92	return results.size();
93
94	return 0;
95	}
96
97	/**
98	* Executes a search based on the given criteria. Should be filled in by
99	* subclasses searching for a specific entity
100	*
101	* @param c List with criteria to search on
102	*/
103	public void execute( List c ) {
104	setCriteria( c );
105	execute();
106	}
107
108	/**
109	* Executes a search based on the given criteria.
110	*/
111	public void execute() {
112	this.executionDate = new Date();
113
114	// Execute the search
115	executeSearch();
116
117	// Save the value of this results for later use
118	saveResultFields();
119	}
120
121	/**
122	* Executes a query
123	*/
124	protected void executeSearch() {
125	// Create HQL query for criteria for the entity being sought
126	def selectClause = ""
127	def fullHQL = createHQLForEntity( this.entity );
128
129	// Create SQL for other entities, by executing a subquery first, and
130	// afterwards selecting the study based on the entities found
131	def resultsFound
132
133	def entityNames = [ "Study", "Subject", "Sample", "Assay", "Event", "SamplingEvent" ];
134	for( entityToSearch in entityNames ) {
135	// Add conditions for all criteria for the given entity. However,
136	// the conditions for the 'main' entity (the entity being sought) are already added
137	if( entity != entityToSearch ) {
138	resultsFound = addEntityConditions(
139	entityToSearch, // Name of the entity to search in
140	TemplateEntity.parseEntity( 'dbnp.studycapturing.' + entityToSearch ), // Class of the entity to search in
141	elementName( entityToSearch ), // HQL name of the collection to search in
142	entityToSearch[0].toLowerCase() + entityToSearch[1..-1], // Alias for the entity to search in
143	fullHQL // Current HQL statement
144	)
145
146	// If no results are found, and we are searching 'inclusive', there will be no
147	// results whatsoever. So we can quit this method now.
148	if( !resultsFound && searchMode == SearchMode.and ) {
149	return
150	}
151	}
152	}
153
154	// Search in all entities
155	resultsFound = addWildcardConditions( fullHQL, entityNames )
156	if( !resultsFound && searchMode == SearchMode.and ) {
157	return
158	}
159
160	// Combine all parts to generate a full HQL query
161	def hqlQuery = selectClause + " " + fullHQL.from + ( fullHQL.where ? " WHERE " + fullHQL.where.join( " " + searchMode.toString() + " " ) : "" );
162
163	// Find all objects
164	def entities = entityClass().findAll( hqlQuery, fullHQL.parameters );
165
166	// Find criteria that match one or more 'complex' fields
167	// These criteria must be checked extra, since they are not correctly handled
168	// by the HQL criteria. See also Criterion.manyToManyWhereCondition and
169	// http://opensource.atlassian.com/projects/hibernate/browse/HHH-4615
170	entities = filterForComplexCriteria( entities, getEntityCriteria( this.entity ) );
171
172	// Filter on module criteria. If the search is 'and', only the entities found until now
173	// should be queried in the module. Otherwise, all entities are sent, in order to retrieve
174	// data (to show on screen) for all entities
175	if( hasModuleCriteria() ) {
176	if( searchMode == SearchMode.and ) {
177	entities = filterOnModuleCriteria( entities );
178	} else {
179	entities = filterOnModuleCriteria( entityClass().list().findAll { this.isAccessible( it ) } )
180	}
181	}
182
183	// Determine which studies can be read
184	results = entities;
185
186	}
187
188	/************************************************************************
189	*
190	* These methods are used in querying and can be overridden by subclasses
191	* in order to provide custom searching
192	*
193	************************************************************************/
194
195	/**
196	* Returns a closure for the given entitytype that determines the value for a criterion
197	* on the given object. The closure receives two parameters: the object and a criterion.
198	*
199	* For example: when searching for studies, the object given to the closure is a Study.
200	* Also, when searching for samples, the object given is a Sample. When you have the criterion
201	*
202	* sample.name equals 'sample 1'
203	*
204	* and searching for samples, it is easy to determine the value of the object for this criterion:
205	*
206	* object.getFieldValue( "name" )
207	*
208	*
209	* However, when searching for samples with the criterion
210	*
211	* study.title contains 'nbic'
212	*
213	* this determination is more complex:
214	*
215	* object.parent.getFieldValue( "title" )
216	*
217	*
218	* The other way around, when searching for studies with
219	*
220	* sample.name equals 'sample 1'
221	*
222	* the value of the 'sample.name' property is a list:
223	*
224	* object.samples*.getFieldValue( "name" )
225	*
226	* The other search methods will handle the list and see whether any of the values
227	* matches the criterion.
228	*
229	* NB. The Criterion object has a convenience method to retrieve the field value on a
230	* specific (TemplateEntity) object: getFieldValue. This method also handles
231	* non-existing fields and casts the value to the correct type.
232	*
233	* This method should be overridden by all searches
234	*
235	* @see Criterion.getFieldValue()
236	*
237	* @return Closure having 2 parameters: object and criterion
238	*/
239	protected Closure valueCallback( String entity ) {
240	switch( entity ) {
241	case "Study":
242	case "Subject":
243	case "Sample":
244	case "Event":
245	case "SamplingEvent":
246	case "Assay":
247	return { object, criterion -> return criterion.getFieldValue( object ); }
248	default:
249	return null;
250	}
251	}
252
253	/**
254	* Returns the HQL name for the element or collections to be searched in, for the given entity name
255	* For example: when searching for Subject.age > 50 with Study results, the system must search in all study.subjects for age > 50.
256	* But when searching for Sample results, the system must search in sample.parentSubject for age > 50
257	*
258	* This method should be overridden in child classes
259	*
260	* @param entity Name of the entity of the criterion
261	* @return HQL name for this element or collection of elements
262	*/
263	protected String elementName( String entity ) {
264	switch( entity ) {
265	case "Study":
266	case "Subject":
267	case "Sample":
268	case "Event":
269	case "SamplingEvent":
270	case "Assay":
271	return entity[ 0 ].toLowerCase() + entity[ 1 .. -1 ]
272	default: return null;
273	}
274	}
275
276	/**
277	* Returns the a where clause for the given entity name
278	* For example: when searching for Subject.age > 50 with Study results, the system must search
279	*
280	* WHERE EXISTS( FROM study.subjects subject WHERE subject IN (...)
281	*
282	* The returned string is fed to sprintf with 3 string parameters:
283	* from (in this case 'study.subjects'
284	* alias (in this case 'subject'
285	* paramName (in this case '...')
286	*
287	* This method can be overridden in child classes to enable specific behaviour
288	*
289	* @param entity Name of the entity of the criterion
290	* @return HQL where clause for this element or collection of elements
291	*/
292	protected String entityClause( String entity ) {
293	return ' EXISTS( FROM %1$s %2$s WHERE %2$s IN (:%3$s) )'
294	}
295
296	/**
297	* Returns true iff the given entity is accessible by the user currently logged in
298	*
299	* This method should be overridden in child classes, since the check is different for every type of search
300	*
301	* @param entity Entity to determine accessibility for. The entity is of the type 'this.entity'
302	* @return True iff the user is allowed to access this entity
303	*/
304	protected boolean isAccessible( def entity ) {
305	return false
306	}
307
308	/****************************************************
309	*
310	* Helper methods for generating HQL statements
311	*
312	****************************************************/
313
314	/**
315	* Add all conditions for criteria for a specific entity
316	*
317	* @param entityName Name of the entity to search in
318	* @param entityClass Class of the entity to search
319	* @param from Name of the HQL collection to search in (e.g. study.subjects)
320	* @param alias Alias of the HQL collection objects (e.g. 'subject')
321	* @param fullHQL Original HQL map to be extended (fields 'from', 'where' and 'parameters')
322	* @param determineParentId Closure to determine the id of the final entity to search, based on these objects
323	* @param entityCriteria (optional) list of criteria to create the HQL for. If no criteria are given, all criteria for the entity are found
324	* @return True if one ore more entities are found, false otherwise
325	*/
326	protected boolean addEntityConditions( String entityName, def entityClass, String from, String alias, def fullHQL, def entityCriteria = null ) {
327	if( entityCriteria == null )
328	entityCriteria = getEntityCriteria( entityName )
329
330	// Create HQL for these criteria
331	def entityHQL = createHQLForEntity( entityName, entityCriteria );
332
333	// If any clauses are generated for these criteria, find entities that match these criteria
334	def whereClauses = entityHQL.where?.findAll { it && it?.trim() != "" }
335	if( whereClauses ) {
336	// First find all entities that match these criteria
337	def hqlQuery = entityHQL.from + " WHERE " + whereClauses.join( searchMode == SearchMode.and ? " AND " : " OR " );
338	def entities = entityClass.findAll( hqlQuery, entityHQL.parameters )
339
340	// If there are entities matching these criteria, put a where clause in the full HQL query
341	if( entities && entities.findAll { it } ) {
342	// Find criteria that match one or more 'complex' fields
343	// These criteria must be checked extra, since they are not correctly handled
344	// by the HQL criteria. See also Criterion.manyToManyWhereCondition and
345	// http://opensource.atlassian.com/projects/hibernate/browse/HHH-4615
346	entities = filterForComplexCriteria( entities, entityCriteria );
347
348	def paramName = from.replaceAll( /\W/, '' );
349	fullHQL.where << sprintf( entityClause( entityName ), from, alias, paramName );
350	fullHQL.parameters[ paramName ] = entities
351	return true;
352	} else {
353	results = [];
354	return false
355	}
356	}
357
358	return true;
359	}
360
361	/**
362	* Add all conditions for a wildcard search (all fields in a given entity)
363	* @param fullHQL Original HQL map to be extended (fields 'from', 'where' and 'parameters')
364	* @return True if the addition worked
365	*/
366	protected boolean addWildcardConditions( def fullHQL, def entities) {
367	// Append study criteria
368	def entityCriteria = getEntityCriteria( "*" );
369
370	// If no wildcard criteria are found, return immediately
371	if( !entityCriteria )
372	return true
373
374	// Wildcards should be checked within each entity
375	def wildcardHQL = createHQLForEntity( this.entity, null, false );
376
377	// Create SQL for other entities, by executing a subquery first, and
378	// afterwards selecting the study based on the entities found
379	entities.each { entityToSearch ->
380	// Add conditions for all criteria for the given entity. However,
381	// the conditions for the 'main' entity (the entity being sought) are already added
382	if( entity != entityToSearch ) {
383	addEntityConditions(
384	entityToSearch, // Name of the entity to search in
385	TemplateEntity.parseEntity( 'dbnp.studycapturing.' + entityToSearch ), // Class of the entity to search in
386	elementName( entityToSearch ), // HQL name of the collection to search in
387	entityToSearch[0].toLowerCase() + entityToSearch[1..-1], // Alias for the entity to search in
388	wildcardHQL, // Current HQL statement
389	entityCriteria // Only create HQL for these criteria
390	)
391	}
392	}
393
394	// Add these clauses to the full HQL statement
395	def whereClauses = wildcardHQL.where.findAll { it };
396
397	if( whereClauses ) {
398	fullHQL.from += wildcardHQL.from
399	fullHQL.where << whereClauses.join( " OR " )
400
401	wildcardHQL[ "parameters" ].each {
402	fullHQL.parameters[ it.key ] = it.value
403	}
404	}
405
406	return true;
407	}
408
409	/**
410	* Create HQL statement for the given criteria and a specific entity
411	* @param entityName Name of the entity
412	* @param entityCriteria (optional) list of criteria to create the HQL for. If no criteria are given, all criteria for the entity are found
413	* @param includeFrom (optional) If set to true, the 'FROM entity' is prepended to the from clause. Defaults to true
414	* @return
415	*/
416	def createHQLForEntity( String entityName, def entityCriteria = null, includeFrom = true ) {
417	def fromClause = includeFrom ? "FROM " + entityName + " " + entityName.toLowerCase() : ""
418	def whereClause = []
419	def parameters = [:]
420	def criterionNum = 0;
421
422	// Append study criteria
423	if( entityCriteria == null )
424	entityCriteria = getEntityCriteria( entityName );
425
426	entityCriteria.each {
427	def criteriaHQL = it.toHQL( "criterion" +entityName + criterionNum++, entityName.toLowerCase() );
428	fromClause += " " + criteriaHQL[ "join" ]
429	whereClause << criteriaHQL[ "where" ]
430	criteriaHQL[ "parameters" ].each {
431	parameters[ it.key ] = it.value
432	}
433	}
434
435	// Add a filter such that only readable studies are returned
436	if( entityName == "Study" ) {
437
438	if( this.user == null ) {
439	// Anonymous readers are only given access when published and public
440	whereClause << "( study.publicstudy = true AND study.published = true )"
441	} else if( !this.user.hasAdminRights() ) {
442	// Administrators are allowed to read every study
443
444	// Owners and writers are allowed to read this study
445	// Readers are allowed to read this study when it is published
446	whereClause << "( study.owner = :sessionUser OR :sessionUser member of study.writers OR ( :sessionUser member of study.readers AND study.published = true ) )"
447	parameters[ "sessionUser" ] = this.user
448	}
449	}
450
451	return [ "from": fromClause, "where": whereClause, "parameters": parameters ]
452	}
453
454	/*****************************************************
455	*
456	* The other methods are helper functions for the execution of queries in subclasses
457	*
458	*****************************************************/
459
460	/**
461	* Returns a list of criteria targeted on the given entity
462	* @param entity Entity to search criteria for
463	* @return List of criteria
464	*/
465	protected List getEntityCriteria( String entity ) {
466	return criteria?.findAll { it.entity == entity }
467	}
468
469
470	/**
471	* Prepares a value from a template entity for comparison, by giving it a correct type
472	*
473	* @param value Value of the field
474	* @param type TemplateFieldType Type of the specific field
475	* @return The value of the field in the correct entity
476	*/
477	public static def prepare( def value, TemplateFieldType type ) {
478	if( value == null )
479	return value
480
481	switch (type) {
482	case TemplateFieldType.DATE:
483	try {
484	return new SimpleDateFormat( "yyyy-MM-dd" ).parse( value.toString() )
485	} catch( Exception e ) {
486	return value.toString();
487	}
488	case TemplateFieldType.RELTIME:
489	try {
490	if( value instanceof Number ) {
491	return new RelTime( value );
492	} else if( value.toString().isNumber() ) {
493	return new RelTime( Long.parseLong( value.toString() ) )
494	} else {
495	return new RelTime( value );
496	}
497	} catch( Exception e ) {
498	try {
499	return Long.parseLong( value )
500	} catch( Exception e2 ) {
501	return value.toString();
502	}
503	}
504	case TemplateFieldType.DOUBLE:
505	try {
506	return Double.valueOf( value )
507	} catch( Exception e ) {
508	return value.toString();
509	}
510	case TemplateFieldType.BOOLEAN:
511	try {
512	return Boolean.valueOf( value )
513	} catch( Exception e ) {
514	return value.toString();
515	}
516	case TemplateFieldType.LONG:
517	try {
518	return Long.valueOf( value )
519	} catch( Exception e ) {
520	return value.toString();
521	}
522	case TemplateFieldType.STRING:
523	case TemplateFieldType.TEXT:
524	case TemplateFieldType.STRINGLIST:
525	case TemplateFieldType.TEMPLATE:
526	case TemplateFieldType.MODULE:
527	case TemplateFieldType.FILE:
528	case TemplateFieldType.ONTOLOGYTERM:
529	default:
530	return value.toString();
531	}
532
533	}
534
535	/*****************************************************
536	*
537	* Methods for filtering lists based on specific (GSCF) criteria
538	*
539	*****************************************************/
540
541
542	/**
543	* Filters a list with entities, based on the given criteria and a closure to check whether a criterion is matched
544	*
545	* @param entities Original list with entities to check for these criteria
546	* @param criteria List with criteria to match on
547	* @param check Closure to see whether a specific entity matches a criterion. Gets two arguments:
548	* element The element to check
549	* criterion The criterion to check on.
550	* Returns true if the criterion holds, false otherwise
551	* @return The filtered list of entities
552	*/
553	protected List filterEntityList( List entities, List<Criterion> criteria, Closure check ) {
554	if( !entities \|\| !criteria \|\| criteria.size() == 0 ) {
555	if( searchMode == SearchMode.and )
556	return entities;
557	else if( searchMode == SearchMode.or )
558	return []
559	}
560
561	return entities.findAll { entity ->
562	if( searchMode == SearchMode.and ) {
563	for( criterion in criteria ) {
564	if( !check( entity, criterion ) ) {
565	return false;
566	}
567	}
568	return true;
569	} else if( searchMode == SearchMode.or ) {
570	for( criterion in criteria ) {
571	if( check( entity, criterion ) ) {
572	return true;
573	}
574	}
575	return false;
576	}
577	}
578	}
579
580	/**
581	* Filters an entity list manually on complex criteria found in the criteria list.
582	* This method is needed because hibernate contains a bug in the HQL INDEX() function.
583	* See also Criterion.manyToManyWhereCondition and
584	* http://opensource.atlassian.com/projects/hibernate/browse/HHH-4615
585	*
586	* @param entities List of entities
587	* @param entityCriteria List of criteria that apply to the type of entities given (e.g. Subject criteria for Subjects)
588	* @return Filtered entity list
589	*/
590	protected filterForComplexCriteria( def entities, def entityCriteria ) {
591	def complexCriteria = entityCriteria.findAll { it.isComplexCriterion() }
592
593	if( complexCriteria ) {
594	def checkCallback = { entity, criterion ->
595	def value = criterion.getFieldValue( entity )
596
597	if( value == null ) {
598	return false
599	}
600
601	if( value instanceof Collection ) {
602	return value.any { criterion.match( it ) }
603	} else {
604	return criterion.match( value );
605	}
606	}
607
608	entities = filterEntityList( entities, complexCriteria, checkCallback );
609	}
610
611	return entities;
612	}
613
614	/********************************************************************
615	*
616	* Methods for filtering object lists on module criteria
617	*
618	********************************************************************/
619
620	protected boolean hasModuleCriteria() {
621
622	return AssayModule.list().any { module ->
623	// Remove 'module' from module name
624	def moduleName = module.name.replace( 'module', '' ).trim()
625	def moduleCriteria = getEntityCriteria( moduleName );
626	return moduleCriteria?.size() > 0
627	}
628	}
629
630	/**
631	* Filters the given list of entities on the module criteria
632	* @param entities Original list of entities. Entities should expose a giveUUID() method to give the token.
633	* @return List with all entities that match the module criteria
634	*/
635	protected List filterOnModuleCriteria( List entities ) {
636	// An empty list can't be filtered more than is has been now
637	if( !entities \|\| entities.size() == 0 )
638	return [];
639
640	// Determine the moduleCommunicationService. Because this object
641	// is mocked in the tests, it can't be converted to a ApplicationContext object
642	def ctx = ApplicationHolder.getApplication().getMainContext();
643	def moduleCommunicationService = ctx.getBean("moduleCommunicationService");
644
645	switch( searchMode ) {
646	case SearchMode.and:
647	// Loop through all modules and check whether criteria have been given
648	// for that module
649	AssayModule.list().each { module ->
650	// Remove 'module' from module name
651	def moduleName = module.name.replace( 'module', '' ).trim()
652	def moduleCriteria = getEntityCriteria( moduleName );
653
654	if( moduleCriteria && moduleCriteria.size() > 0 ) {
655	def callUrl = moduleCriteriaUrl( module );
656	def callArgs = moduleCriteriaArguments( module, entities, moduleCriteria );
657
658	try {
659	def json = moduleCommunicationService.callModuleMethod( module.url, callUrl, callArgs, "POST" );
660	Closure checkClosure = moduleCriterionClosure( json );
661	entities = filterEntityList( entities, moduleCriteria, checkClosure );
662	} catch( Exception e ) {
663	//log.error( "Error while retrieving data from " + module.name + ": " + e.getMessage() )
664	e.printStackTrace()
665	throw e
666	}
667	}
668	}
669
670	return entities;
671	case SearchMode.or:
672	def resultingEntities = []
673
674	// Loop through all modules and check whether criteria have been given
675	// for that module
676	AssayModule.list().each { module ->
677	// Remove 'module' from module name
678	def moduleName = module.name.replace( 'module', '' ).trim()
679	def moduleCriteria = getEntityCriteria( moduleName );
680
681	if( moduleCriteria && moduleCriteria.size() > 0 ) {
682	def callUrl = moduleCriteriaUrl( module );
683	def callArgs = moduleCriteriaArguments( module, entities, moduleCriteria );
684
685	try {
686	def json = moduleCommunicationService.callModuleMethod( module.url, callUrl, callArgs, "POST" );
687	Closure checkClosure = moduleCriterionClosure( json );
688
689	resultingEntities += filterEntityList( entities, moduleCriteria, checkClosure );
690	resultingEntities = resultingEntities.unique();
691
692	} catch( Exception e ) {
693	//log.error( "Error while retrieving data from " + module.name + ": " + e.getMessage() )
694	e.printStackTrace()
695	throw e
696	}
697	}
698	}
699
700	return resultingEntities;
701	default:
702	return [];
703	}
704	}
705
706	/**
707	* Returns a closure for determining the value of a module field
708	* @param json
709	* @return
710	*/
711	protected Closure moduleCriterionClosure( def json ) {
712	return { entity, criterion ->
713	// Find the value of the field in this sample. That value is still in the
714	// JSON object
715	def token = entity.giveUUID()
716	def value
717
718	if( criterion.field == '*' ) {
719	// Collect the values from all fields
720	value = [];
721	json[ token ].each { field ->
722	if( field.value instanceof Collection ) {
723	field.value.each { value << it }
724	} else {
725	value << field.value;
726	}
727	}
728	} else {
729	if( !json[ token ] \|\| json[ token ][ criterion.field ] == null )
730	return false;
731
732	// Check whether a list or string is given
733	value = json[ token ][ criterion.field ];
734
735	// Save the value of this entity for later use
736	saveResultField( entity.id, criterion.entity + " " + criterion.field, value )
737
738	if( !( value instanceof Collection ) ) {
739	value = [ value ];
740	}
741	}
742
743	// Convert numbers to a long or double in order to process them correctly
744	def values = value.collect { val ->
745	val = val.toString();
746	if( val.isLong() ) {
747	val = Long.parseLong( val );
748	} else if( val.isDouble() ) {
749	val = Double.parseDouble( val );
750	}
751	return val;
752	}
753
754	// Loop through all values and match any
755	for( val in values ) {
756	if( criterion.match( val ) )
757	return true;
758	}
759
760	return false;
761	}
762	}
763
764	protected String moduleCriteriaUrl( module ) {
765	def callUrl = module.url + '/rest/getQueryableFieldData'
766	return callUrl;
767	}
768
769	protected String moduleCriteriaArguments( module, entities, moduleCriteria ) {
770	// Retrieve the data from the module
771	def tokens = entities.collect { it.giveUUID() }.unique();
772	def fields = moduleCriteria.collect { it.field }.unique();
773
774	def callUrl = 'entity=' + this.entity
775	tokens.sort().each { callUrl += "&tokens=" + it.encodeAsURL() }
776
777	// If all fields are searched, all fields should be retrieved
778	if( fields.contains( '*' ) ) {
779
780	} else {
781	fields.sort().each { callUrl += "&fields=" + it.encodeAsURL() }
782	}
783
784	return callUrl;
785	}
786
787	/*********************************************************************
788	*
789	* These methods are used for saving information about the search results and showing the information later on.
790	*
791	*********************************************************************/
792
793	/**
794	* Saves data about template entities to use later on. This data is copied to a special
795	* structure to make it compatible with data fetched from other modules.
796	* @see #saveResultField()
797	*/
798	protected void saveResultFields() {
799	if( !results \|\| !criteria )
800	return
801
802	criteria.each { criterion ->
803	if( criterion.field && criterion.field != '*' ) {
804	def valueCallback = valueCallback( criterion.entity );
805
806	if( valueCallback != null ) {
807	def name = criterion.entity + ' ' + criterion.field
808
809	results.each { result ->
810	saveResultField( result.id, name, valueCallback( result, criterion ) );
811	}
812	}
813	}
814	}
815	}
816
817	/**
818	* Saves data about template entities to use later on. This data is copied to a special
819	* structure to make it compatible with data fetched from other modules.
820	* @param entities List of template entities to find data in
821	* @param criteria Criteria to search for
822	* @param valueCallback Callback to retrieve a specific field from the entity
823	* @see #saveResultField()
824	*/
825	protected void saveResultFields( entities, criteria, valueCallback ) {
826	for( criterion in criteria ) {
827	for( entity in entities ) {
828	if( criterion.field && criterion.field != '*' )
829	saveResultField( entity.id, criterion.entity + ' ' + criterion.field, valueCallback( entity, criterion ) )
830	}
831	}
832	}
833
834
835	/**
836	* Saves a specific field of an object to use later on. Especially useful when looking up data from other modules.
837	* @param id ID of the object
838	* @param fieldName Field name that has been searched
839	* @param value Value of the field
840	*/
841	protected void saveResultField( id, fieldName, value ) {
842	if( resultFields[ id ] == null )
843	resultFields[ id ] = [:]
844
845	// Handle special cases
846	if( value == null )
847	value = "";
848
849	if( fieldName == "*" )
850	return;
851
852	if( value instanceof Collection ) {
853	value = value.findAll { it != null }
854	}
855
856	resultFields[ id ][ fieldName ] = value;
857	}
858
859	/**
860	* Removes all data from the result field map
861	*/
862	protected void clearResultFields() {
863	resultFields = [:]
864	}
865
866	/**
867	* Returns the saved field data that could be shown on screen. This means, the data is filtered to show only data of the query results.
868	*
869	* Subclasses could filter out the fields they don't want to show on the result screen (e.g. because they are shown regardless of the
870	* query.)
871	* @return Map with the entity id as a key, and a field-value map as value
872	*/
873	public Map getShowableResultFields() {
874	def resultIds = getResults()*.id;
875	return getResultFields().findAll {
876	resultIds.contains( it.key )
877	}
878	}
879
880	/**
881	* Returns the field names that are found in the map with showable result fields
882	*
883	* @param fields Map with showable result fields
884	* @see getShowableResultFields
885	* @return
886	*/
887	public List getShowableResultFieldNames( fields ) {
888	return fields.values()*.keySet().flatten().unique();
889	}
890
891
892	/************************************************************************
893	*
894	* Getters and setters
895	*
896	************************************************************************/
897
898	/**
899	* Returns a list of Criteria
900	*/
901	public List getCriteria() { return criteria; }
902
903	/**
904	* Sets a new list of criteria
905	* @param c List with criteria objects
906	*/
907	public void setCriteria( List c ) { criteria = c; }
908
909	/**
910	* Adds a criterion to this query
911	* @param c Criterion
912	*/
913	public void addCriterion( Criterion c ) {
914	if( criteria )
915	criteria << c;
916	else
917	criteria = [c];
918	}
919
920	/**
921	* Retrieves the results found using this query. The result is empty is
922	* the query has not been executed yet.
923	*/
924	public List getResults() { return results; }
925
926	/**
927	* Returns the results found using this query, filtered by a list of ids.
928	* @param selectedIds List with ids of the entities you want to return.
929	* @return A list with only those results for which the id is in the selectedIds
930	*/
931	public List filterResults( List selectedTokens ) {
932	if( !selectedTokens \|\| !results )
933	return results
934
935	return results.findAll {
936	selectedTokens.contains( it.giveUUID() )
937	}
938	}
939
940	/**
941	* Returns a list of fields for the results of this query. The fields returned are those
942	* fields that the query searched for.
943	*/
944	public Map getResultFields() { return resultFields; }
945
946	public String toString() {
947	return ( this.entity ? this.entity + " search" : "Search" ) + " " + this.id
948	}
949
950	public boolean equals( Object o ) {
951	if( o == null )
952	return false
953
954	if( !( o instanceof Search ) )
955	return false
956
957	Search s = (Search) o;
958
959	return ( searchMode == s.searchMode &&
960	entity == s.entity &&
961	criteria.size() == s.criteria.size() &&
962	s.criteria.containsAll( criteria ) &&
963	criteria.containsAll( s.criteria ) );
964	}
965
966	/**
967	* Returns the class for the entity being searched
968	* @return
969	*/
970	public Class entityClass() {
971	if( !this.entity )
972	return null;
973
974	try {
975	return TemplateEntity.parseEntity( 'dbnp.studycapturing.' + this.entity)
976	} catch( Exception e ) {
977	throw new Exception( "Unknown entity for criterion " + this, e );
978	}
979	}
980
981	}

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