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source: trunk/grails-app/controllers/dbnp/studycapturing/SimpleWizardController.groovy @ 1608

Last change on this file since 1608 was 1608, checked in by robert@…, 7 years ago
Fixed bug with hibernate and transactional services in the simple wizard
Property svn:keywords set to `Rev Author Date`
File size: 34.1 KB

Line
1	/**
2	* SimpleWizardController Controler
3	*
4	* Description of my controller
5	*
6	* @author your email (+name?)
7	* @since 2010mmdd
8	* @package ???
9	*
10	* Revision information:
11	* $Rev: 1608 $
12	* $Author: robert@isdat.nl $
13	* $Date: 2011-03-09 14:56:26 +0000 (wo, 09 mrt 2011) $
14	*/
15	package dbnp.studycapturing
16
17	import org.apache.poi.ss.usermodel.DataFormatter
18	import org.dbnp.gdt.*
19	import grails.plugins.springsecurity.Secured
20	import dbnp.authentication.SecUser
21	import dbnp.importer.ImportCell
22	import dbnp.importer.ImportRecord
23	import dbnp.importer.MappingColumn
24
25	@Secured(['IS_AUTHENTICATED_REMEMBERED'])
26	class SimpleWizardController extends StudyWizardController {
27	def authenticationService
28	def fileService
29	def importerService
30	def gdtService = new GdtService()
31
32	/**
33	* index closure
34	*/
35	def index = {
36	if( params.id )
37	redirect( action: "simpleWizard", id: params.id );
38	else
39	redirect( action: "simpleWizard" );
40	}
41
42	def simpleWizardFlow = {
43	entry {
44	action{
45	flow.study = getStudyFromRequest( params )
46	if (!flow.study) retrievalError()
47	}
48	on("retrievalError").to "handleError"
49	on("success").to "study"
50	}
51
52	study {
53	on("next") {
54	handleStudy( flow.study, params )
55	if( !validateObject( flow.study ) )
56	error()
57	}.to "decisionState"
58	on("refresh") { handleStudy( flow.study, params ); }.to "study"
59	on( "success" ) { handleStudy( flow.study, params ) }.to "study"
60	}
61
62	decisionState {
63	action {
64	// Create data in the flow
65	flow.templates = [
66	'Sample': Template.findAllByEntity( Sample.class ),
67	'Subject': Template.findAllByEntity( Subject.class ),
68	'Event': Template.findAllByEntity( Event.class ),
69	'SamplingEvent': Template.findAllByEntity( SamplingEvent.class )
70	];
71	flow.encodedEntity = [
72	'Sample': gdtService.encryptEntity( Sample.class.name ),
73	'Subject': gdtService.encryptEntity( Subject.class.name ),
74	'Event': gdtService.encryptEntity( Event.class.name ),
75	'SamplingEvent': gdtService.encryptEntity( SamplingEvent.class.name )
76	]
77
78	if (flow.study.samples)
79	checkStudySimplicity(flow.study) ? existingSamples() : complexStudy()
80	else
81	samples()
82	}
83	on ("existingSamples").to "startExistingSamples"
84	on ("complexStudy").to "complexStudy"
85	on ("samples").to "samples"
86	}
87
88	startExistingSamples {
89	action {
90	def records = importerService.getRecords( flow.study );
91	flow.records = records
92	flow.templateCombinations = records.templateCombination.unique()
93	success();
94	}
95	on( "success" ).to "existingSamples"
96	}
97
98	existingSamples {
99	on("next") {
100	handleExistingSamples( flow.study, params, flow ) ? success() : error()
101	}.to "startAssays"
102	on("previous").to "study"
103	on("update") {
104	handleExistingSamples( flow.study, params, flow ) ? success() : error()
105	}.to "samples"
106
107	on("skip").to "startAssays"
108	}
109
110	complexStudy {
111	on("save").to "save"
112	on("previous").to "study"
113	}
114
115	samples {
116	on("next") {
117	handleSamples( flow.study, params, flow ) ? success() : error ()
118
119	// Add domain fields for all entities
120	flow.domainFields = [:]
121
122	flow.templates.each {
123	if( it.value ) {
124	flow.domainFields[ it.key ] = it.value[0].entity.giveDomainFields();
125	}
126	}
127
128	}.to "columns"
129	on("previous").to "returnFromSamples"
130	on("study").to "study"
131	on("skip").to "startAssays"
132	}
133
134	returnFromSamples {
135	action {
136	flow.study.samples ? existingSamples() : study();
137	}
138	on( "existingSamples" ).to "startExistingSamples"
139	on( "study" ).to "study"
140	}
141
142	columns {
143	on( "next" ) {
144	handleColumns( flow.study, params, flow ) ? success() : error()
145	}.to "checkImportedEntities"
146	on( "previous" ).to "samples"
147	}
148
149	checkImportedEntities {
150	action {
151	// Only continue to the next page if the information entered is correct
152	if( flow.imported.numInvalidEntities > 0 ) {
153	missingFields();
154	} else {
155	// The import of the excel file has finished. Now delete the excelfile
156	if( flow.excel.filename )
157	fileService.delete( flow.excel.filename );
158
159	flow.sampleForm = null
160
161	assays();
162	}
163	}
164	on( "missingFields" ).to "missingFields"
165	on( "assays" ).to "startAssays"
166	}
167
168	missingFields {
169	on( "next" ) {
170	if( !handleMissingFields( flow.study, params, flow ) ) {
171	return error();
172	}
173
174	// The import of the excel file has finished. Now delete the excelfile
175	if( flow.excel.filename )
176	fileService.delete( flow.excel.filename );
177
178	flow.sampleForm = null
179
180	success();
181	}.to "startAssays"
182	on( "previous" ) {
183	// The user goes back to the previous page, so the already imported entities
184	// (of which some gave an error) should be removed again.
185	// Add all samples
186	flow.imported.data.each { record ->
187	record.each { entity ->
188	if( entity ) {
189	switch( entity.class ) {
190	case Sample: flow.study.removeFromSamples( entity ); break;
191	case Subject: flow.study.removeFromSubjects( entity ); break;
192	case Event: flow.study.removeFromEvents( entity ); break;
193	case SamplingEvent: flow.study.removeFromSamplingEvents( entity ); break;
194	}
195	}
196	}
197	}
198
199	success();
200	}.to "columns"
201	}
202
203	startAssays {
204	action {
205	if( !flow.assay )
206	flow.assay = new Assay( parent: flow.study );
207
208	success();
209	}
210	on( "success" ).to "assays"
211	}
212
213	assays {
214	on( "next" ) {
215	handleAssays( flow.assay, params, flow );
216	if( !validateObject( flow.assay ) )
217	error();
218	}.to "overview"
219	on( "skip" ) {
220	// In case the user has created an assay before he clicked 'skip', it should only be kept if it
221	// existed before this step
222	if( flow.assay != null && !flow.assay.id ) {
223	flow.remove( "assay" )
224	}
225
226	}.to "overview"
227	on( "previous" ).to "returnFromAssays"
228	on("refresh") { handleAssays( flow.assay, params, flow ); success() }.to "assays"
229	}
230
231	returnFromAssays {
232	action {
233	flow.study.samples ? existingSamples() : samples();
234	}
235	on( "existingSamples" ).to "existingSamples"
236	on( "samples" ).to "samples"
237	}
238
239	overview {
240	on( "save" ).to "saveStudy"
241	on( "previous" ).to "startAssays"
242	}
243
244	saveStudy {
245	action {
246	if( flow.assay && !flow.study.assays?.contains( flow.assay ) ) {
247	flow.study.addToAssays( flow.assay );
248	}
249
250	if( flow.study.save( flush: true ) ) {
251	// Make sure all samples are attached to all assays
252	flow.study.assays.each { assay ->
253	def l = []+ assay.samples;
254	l.each { sample ->
255	if( sample )
256	assay.removeFromSamples( sample );
257	}
258	assay.samples?.clear();
259
260	flow.study.samples.each { sample ->
261	assay.addToSamples( sample )
262	}
263	}
264
265	flash.message = "Your study is succesfully saved.";
266
267	finish();
268	} else {
269	flash.error = "An error occurred while saving your study: <br />"
270	flow.study.getErrors().each { flash.error += it.toString() + "<br />"}
271
272	// Remove the assay from the study again, since it is still available
273	// in the session
274	if( flow.assay ) {
275	flow.study.removeFromAssays( flow.assay );
276	flow.assay.parent = flow.study;
277	}
278
279	overview();
280	}
281	}
282	on( "finish" ).to "finish"
283	on( "overview" ).to "overview"
284	}
285
286	finish()
287
288	handleError{
289	redirect action: "errorPage"
290	}
291	}
292
293	/**
294	* Retrieves the required study from the database or return an empty Study object if
295	* no id is given
296	*
297	* @param params Request parameters with params.id being the ID of the study to be retrieved
298	* @return A study from the database or an empty study if no id was given
299	*/
300	protected Study getStudyFromRequest( def params ) {
301	int id = params.int( "id" );
302
303	if( !id ) {
304	return new Study( title: "New study", owner: authenticationService.getLoggedInUser() );
305	}
306
307	Study s = Study.get( id );
308
309	if( !s ) {
310	flash.error = "No study found with given id";
311	return null;
312	}
313	if( !s.canWrite( authenticationService.getLoggedInUser() ) ) {
314	flash.error = "No authorization to edit this study."
315	return null;
316	}
317
318	return s
319	}
320
321	/**
322	* Handles study input
323	* @param study Study to update
324	* @param params Request parameter map
325	* @return True if everything went OK, false otherwise. An error message is put in flash.error
326	*/
327	def handleStudy( study, params ) {
328	// did the study template change?
329	if (params.get('template') && study.template?.name != params.get('template')) {
330	// set the template
331	study.template = Template.findByName(params.remove('template'))
332	}
333
334	// does the study have a template set?
335	if (study.template && study.template instanceof Template) {
336	// yes, iterate through template fields
337	study.giveFields().each() {
338	// and set their values
339	study.setFieldValue(it.name, params.get(it.escapedName()))
340	}
341	}
342
343	// handle public checkbox
344	if (params.get("publicstudy")) {
345	study.publicstudy = params.get("publicstudy")
346	}
347
348	// handle publications
349	handleStudyPublications(study, params)
350
351	// handle contacts
352	handleStudyContacts(study, params)
353
354	// handle users (readers, writers)
355	handleStudyUsers(study, params, 'readers')
356	handleStudyUsers(study, params, 'writers')
357
358	return true
359	}
360
361	/**
362	* Handles the editing of existing samples
363	* @param study Study to update
364	* @param params Request parameter map
365	* @return True if everything went OK, false otherwise. An error message is put in flash.error
366	*/
367	def handleExistingSamples( study, params, flow ) {
368	flash.validationErrors = [];
369
370	def errors = false;
371
372	// iterate through objects; set field values and validate the object
373	def eventgroups = study.samples.parentEventGroup.findAll { it }
374	def events;
375	if( !eventgroups )
376	events = []
377	else
378	events = eventgroups.events?.getAt(0);
379
380	def objects = [
381	'Sample': study.samples,
382	'Subject': study.samples.parentSubject.findAll { it },
383	'SamplingEvent': study.samples.parentEvent.findAll { it },
384	'Event': events.flatten().findAll { it }
385	];
386	objects.each {
387	def type = it.key;
388	def entities = it.value;
389
390	entities.each { entity ->
391	// iterate through entity fields
392	entity.giveFields().each() { field ->
393	def value = params.get( type.toLowerCase() + '_' + entity.getIdentifier() + '_' + field.escapedName())
394
395	// set field value; name cannot be set to an empty value
396	if (field.name != 'name' \|\| value) {
397	log.info "setting "+field.name+" to "+value
398	entity.setFieldValue(field.name, value)
399	}
400	}
401
402	// has the template changed?
403	def templateName = params.get(type.toLowerCase() + '_' + entity.getIdentifier() + '_template')
404	if (templateName && entity.template?.name != templateName) {
405	entity.template = Template.findByName(templateName)
406	}
407
408	// validate sample
409	if (!entity.validate()) {
410	errors = true;
411
412	def entityName = entity.class.name[ entity.class.name.lastIndexOf( "." ) + 1 .. -1 ]
413	getHumanReadableErrors( entity ).each {
414	flash.validationErrors << [ key: it.key, value: "(" + entityName + ") " + it.value ];
415	}
416	}
417	}
418	}
419
420	return !errors
421	}
422
423	/**
424	* Handles the upload of sample data
425	* @param study Study to update
426	* @param params Request parameter map
427	* @return True if everything went OK, false otherwise. An error message is put in flash.error
428	*/
429	def handleSamples( study, params, flow ) {
430	def filename = params.get( 'importfile' );
431
432	// Handle 'existing*' in front of the filename. This is put in front to make a distinction between
433	// an already uploaded file test.txt (maybe moved to some other directory) and a newly uploaded file test.txt
434	// still being in the temporary directory.
435	// This import step doesn't have to make that distinction, since all files remain in the temporary directory.
436	if( filename == 'existing*' )
437	filename = '';
438	else if( filename[0..8] == 'existing*' )
439	filename = filename[9..-1]
440
441	def sampleTemplateId = params.long( 'sample_template_id' )
442	def subjectTemplateId = params.long( 'subject_template_id' )
443	def eventTemplateId = params.long( 'event_template_id' )
444	def samplingEventTemplateId = params.long( 'samplingEvent_template_id' )
445
446	// These fields have been removed from the form, so will always contain
447	// their default value. The code however remains like this for future use.
448	int sheetIndex = (params.int( 'sheetindex' ) ?: 1 )
449	int dataMatrixStart = (params.int( 'datamatrix_start' ) ?: 2 )
450	int headerRow = (params.int( 'headerrow' ) ?: 1 )
451
452	// Save form data in session
453	flow.sampleForm = [
454	importFile: filename,
455	templateId: [
456	'Sample': sampleTemplateId,
457	'Subject': subjectTemplateId,
458	'Event': eventTemplateId,
459	'SampingEvent': samplingEventTemplateId
460	],
461	template: [
462	'Sample': sampleTemplateId ? Template.get( sampleTemplateId ) : null,
463	'Subject': subjectTemplateId ? Template.get( subjectTemplateId ) : null,
464	'Event': eventTemplateId ? Template.get( eventTemplateId ) : null,
465	'SampingEvent': samplingEventTemplateId ? Template.get( samplingEventTemplateId ) : null
466	],
467	sheetIndex: sheetIndex,
468	dataMatrixStart: dataMatrixStart,
469	headerRow: headerRow
470	];
471
472	// Check whether the template exists
473	if (!sampleTemplateId \|\| !Template.get( sampleTemplateId ) ){
474	log.error ".simple study wizard not all fields are filled in: " + sampleTemplateId
475	flash.error = "No template was chosen. Please choose a template for the samples you provided."
476	return false
477	}
478
479	def importedfile = fileService.get( filename )
480	def workbook
481	if (importedfile.exists()) {
482	try {
483	workbook = importerService.getWorkbook(new FileInputStream(importedfile))
484	} catch (Exception e) {
485	log.error ".simple study wizard could not load file: " + e
486	flash.error = "The given file doesn't seem to be an excel file. Please provide an excel file for entering samples.";
487	return false
488	}
489	} else {
490	log.error ".simple study wizard no file given";
491	flash.error = "No file was given. Please provide an excel file for entering samples.";
492	return false;
493	}
494
495	if( !workbook ) {
496	log.error ".simple study wizard could not load file into a workbook"
497	flash.error = "The given file doesn't seem to be an excel file. Please provide an excel file for entering samples.";
498	return false
499	}
500
501	def selectedentities = []
502
503	if( !excelChecks( workbook, sheetIndex, headerRow, dataMatrixStart ) )
504	return false;
505
506	// Get the header from the Excel file using the arguments given in the first step of the wizard
507	def importerHeader;
508	def importerDataMatrix;
509
510	try {
511	importerHeader = importerService.getHeader(workbook,
512	sheetIndex - 1, // 0 == first sheet
513	headerRow, // 1 == first row :s
514	dataMatrixStart - 1, // 0 == first row
515	Sample.class)
516
517	importerDataMatrix = importerService.getDatamatrix(
518	workbook,
519	importerHeader,
520	sheetIndex - 1, // 0 == first sheet
521	dataMatrixStart - 1, // 0 == first row
522	5)
523	} catch( Exception e ) {
524	// An error occurred while reading the excel file.
525	log.error ".simple study wizard error while reading the excel file";
526	e.printStackTrace();
527
528	// Show a message to the user
529	flash.error = "An error occurred while reading the excel file. Have you provided the right sheet number and row numbers. Contact your system administrator if this problem persists.";
530	return false;
531	}
532
533	// Match excel columns with template fields
534	def fieldNames = [];
535	flow.sampleForm.template.each { template ->
536	if( template.value ) {
537	def fields = template.value.entity.giveDomainFields() + template.value.getFields();
538	fields.each { field ->
539	if( !field.entity )
540	field.entity = template.value.entity
541
542	fieldNames << field
543	}
544	}
545	}
546	importerHeader.each { mc ->
547	def bestfit = importerService.mostSimilar( mc.name, fieldNames, 0.8);
548	if( bestfit ) {
549	// Remove this fit from the list
550	fieldNames.remove( bestfit );
551
552	mc.entityclass = bestfit.entity
553	mc.property = bestfit.name
554	}
555	}
556
557	// Save read excel data into session
558	def dataMatrix = [];
559	def df = new DataFormatter();
560	importerDataMatrix.each {
561	dataMatrix << it.collect{ it ? df.formatCellValue(it) : "" }
562	}
563
564	flow.excel = [
565	filename: filename,
566	sheetIndex: sheetIndex,
567	dataMatrixStart: dataMatrixStart,
568	headerRow: headerRow,
569	data: [
570	header: importerHeader,
571	dataMatrix: dataMatrix
572	]
573	]
574
575	return true
576	}
577
578
579	/**
580	* Handles the matching of template fields with excel columns by the user
581	* @param study Study to update
582	* @param params Request parameter map
583	* @return True if everything went OK, false otherwise. An error message is put in flash.error
584	* The field session.simpleWizard.imported.numInvalidEntities reflects the number of
585	* entities that have errors, and should be fixed before saving. The errors for those entities
586	* are saved into session.simpleWizard.imported.errors
587	*/
588	def handleColumns( study, params, flow ) {
589	// Find actual Template object from the chosen template name
590	def templates = [:];
591	flow.sampleForm.templateId.each {
592	templates[ it.key ] = it.value ? Template.get( it.value ) : null;
593	}
594
595	def headers = flow.excel.data.header;
596
597	if( !params.matches ) {
598	log.error( ".simple study wizard no column matches given" );
599	flash.error = "No column matches given";
600	return false;
601	}
602
603	// Retrieve the chosen matches from the request parameters and put them into
604	// the headers-structure, for later reference
605	params.matches.index.each { columnindex, value ->
606	// Determine the entity and property by splitting it
607	def parts = value.toString().tokenize( "\|\|" );
608
609	def property
610	def entityName
611	if( parts.size() > 1 ) {
612	property = parts[ 1 ];
613	entityName = "dbnp.studycapturing." + parts[ 0 ];
614	} else if( parts.size() == 1 ) {
615	property = parts[ 0 ];
616	entityName = headers[columnindex.toInteger()].entityclass.getName();
617	}
618
619	// Create an actual class instance of the selected entity with the selected template
620	// This should be inside the closure because in some cases in the advanced importer, the fields can have different target entities
621	def entityClass = Class.forName( entityName, true, this.getClass().getClassLoader())
622	def entityObj = entityClass.newInstance(template: templates[ entityName[entityName.lastIndexOf( '.' ) + 1..-1] ])
623
624	headers[ columnindex.toInteger() ].entityclass = entityClass
625
626	// Store the selected property for this column into the column map for the ImporterService
627	headers[columnindex.toInteger()].property = property
628
629	// Look up the template field type of the target TemplateField and store it also in the map
630	headers[columnindex.toInteger()].templatefieldtype = entityObj.giveFieldType(property)
631
632	// Is a "Don't import" property assigned to the column?
633	headers[columnindex.toInteger()].dontimport = (property == "dontimport") ? true : false
634
635	//if it's an identifier set the mapping column true or false
636	entityClass.giveDomainFields().each {
637	headers[columnindex.toInteger()].identifier = ( it.preferredIdentifier && (it.name == property) )
638	}
639	}
640
641	// Import the workbook and store the table with entity records and store the failed cells
642	println "Importing samples for study " + study + " (" + study.id + ")";
643
644	def importedfile = fileService.get( flow.excel.filename )
645	def workbook
646	if (importedfile.exists()) {
647	try {
648	workbook = importerService.getWorkbook(new FileInputStream(importedfile))
649	} catch (Exception e) {
650	log.error ".simple study wizard could not load file: " + e
651	flash.error = "The given file doesn't seem to be an excel file. Please provide an excel file for entering samples.";
652	return false
653	}
654	} else {
655	log.error ".simple study wizard no file given";
656	flash.error = "No file was given. Please provide an excel file for entering samples.";
657	return false;
658	}
659
660	if( !workbook ) {
661	log.error ".simple study wizard could not load file into a workbook"
662	flash.error = "The given file doesn't seem to be an excel file. Please provide an excel file for entering samples.";
663	return false
664	}
665
666
667	def imported = importerService.importOrUpdateDataBySampleIdentifier(templates,
668	workbook,
669	flow.excel.sheetIndex - 1,
670	flow.excel.dataMatrixStart - 1,
671	flow.excel.data.header,
672	flow.study,
673	true // Also create entities for which no data is imported but where templates were chosen
674	);
675
676	def table = imported.table
677	def failedcells = imported.failedCells
678
679	flow.imported = [
680	data: table,
681	failedCells: failedcells
682	];
683
684	// loop through all entities to validate them and add them to failedcells if an error occurs
685	def numInvalidEntities = 0;
686	def errors = [];
687
688	// Add all samples
689	table.each { record ->
690	record.each { entity ->
691	if( entity ) {
692	// Determine entity class and add a parent. Add the entity to the study
693	def preferredIdentifier = importerService.givePreferredIdentifier( entity.class );
694	def equalClosure = { it.getFieldValue( preferredIdentifier.name ) == entity.getFieldValue( preferredIdentifier.name ) }
695	def entityName = entity.class.name[ entity.class.name.lastIndexOf( "." ) + 1 .. -1 ]
696
697	entity.parent = study
698
699	switch( entity.class ) {
700	case Sample:
701	if( preferredIdentifier && !study.samples?.find( equalClosure ) ) {
702	study.addToSamples( entity );
703	}
704	break;
705	case Subject:
706	if( preferredIdentifier && !study.subjects?.find( equalClosure ) ) {
707	study.addToSubjects( entity );
708	}
709	break;
710	case Event:
711	if( preferredIdentifier && !study.events?.find( equalClosure ) ) {
712	study.addToEvents( entity );
713	}
714	break;
715	case SamplingEvent:
716	if( preferredIdentifier && !study.samplingEvents?.find( equalClosure ) ) {
717	study.addToSamplingEvents( entity );
718	}
719	break;
720	}
721
722	if (!entity.validate()) {
723	numInvalidEntities++;
724
725	// Add this field to the list of failed cells, in order to give the user feedback
726	failedcells = addNonValidatingCells( failedcells, entity, flow )
727
728	// Also create a full list of errors
729	def currentErrors = getHumanReadableErrors( entity )
730	if( currentErrors ) {
731	currentErrors.each {
732	errors += "(" + entityName + ") " + it.value;
733	}
734	}
735	}
736	}
737	}
738	}
739
740	flow.imported.numInvalidEntities = numInvalidEntities + failedcells?.size();
741	flow.imported.errors = errors;
742
743	return true
744	}
745
746	/**
747	* Handles the update of the edited fields by the user
748	* @param study Study to update
749	* @param params Request parameter map
750	* @return True if everything went OK, false otherwise. An error message is put in flash.error.
751	* The field session.simpleWizard.imported.numInvalidEntities reflects the number of
752	* entities that still have errors, and should be fixed before saving. The errors for those entities
753	* are saved into session.simpleWizard.imported.errors
754	*/
755	def handleMissingFields( study, params, flow ) {
756	def numInvalidEntities = 0;
757	def errors = [];
758
759	// Check which fields failed previously
760	def failedCells = flow.imported.failedCells
761	def newFailedCells = [];
762
763	flow.imported.data.each { table ->
764	table.each { entity ->
765	def invalidFields = 0
766	def failed = new ImportRecord();
767	def entityName = entity.class.name[ entity.class.name.lastIndexOf( "." ) + 1 .. -1 ]
768
769
770	// Set the fields for this entity by retrieving values from the params
771	entity.giveFields().each { field ->
772	def fieldName = importerService.getFieldNameInTableEditor( entity, field );
773
774	if( params[ fieldName ] == "#invalidterm" ) {
775	// If the value '#invalidterm' is chosen, the user hasn't fixed anything, so this field is still incorrect
776	invalidFields++;
777
778	// store the mapping column and value which failed
779	def identifier = entityName.toLowerCase() + "_" + entity.getIdentifier() + "_" + fieldName
780	def mcInstance = new MappingColumn()
781	failed.addToImportcells(new ImportCell(mappingcolumn: mcInstance, value: params[ fieldName ], entityidentifier: identifier))
782	} else {
783	if( field.type == org.dbnp.gdt.TemplateFieldType.ONTOLOGYTERM \|\| field.type == org.dbnp.gdt.TemplateFieldType.STRINGLIST ) {
784	// If this field is an ontologyterm field or a stringlist field, the value has changed, so remove the field from
785	// the failedCells list
786	importerService.removeFailedCell( failedCells, entity, field )
787	}
788
789	// Update the field, regardless of the type of field
790	entity.setFieldValue(field.name, params[ fieldName ] )
791	}
792	}
793
794	// Try to validate the entity now all fields have been set. If it fails, return an error
795	if (!entity.validate() \|\| invalidFields) {
796	numInvalidEntities++;
797
798	// Add this field to the list of failed cells, in order to give the user feedback
799	failedCells = addNonValidatingCellsToImportRecord( failed, entity, flow )
800
801	// Also create a full list of errors
802	def currentErrors = getHumanReadableErrors( entity )
803	if( currentErrors ) {
804	currentErrors.each {
805	errors += "(" + entityName + ") " + it.value;
806	}
807	}
808
809	newFailedCells << failed;
810	} else {
811	importerService.removeFailedCell( failedCells, entity )
812	}
813	} // end of record
814	} // end of table
815
816	flow.imported.failedCells = newFailedCells
817	flow.imported.numInvalidEntities = numInvalidEntities;
818	flow.imported.errors = errors;
819
820	return numInvalidEntities == 0
821	}
822
823	/**
824	* Handles assay input
825	* @param study Study to update
826	* @param params Request parameter map
827	* @return True if everything went OK, false otherwise. An error message is put in flash.error
828	*/
829	def handleAssays( assay, params, flow ) {
830	// did the study template change?
831	if (params.get('template') && assay.template?.name != params.get('template')) {
832	// set the template
833	assay.template = Template.findByName(params.remove('template'))
834	}
835
836	// does the study have a template set?
837	if (assay.template && assay.template instanceof Template) {
838	// yes, iterate through template fields
839	assay.giveFields().each() {
840	// and set their values
841	assay.setFieldValue(it.name, params.get(it.escapedName()))
842	}
843	}
844
845	return true
846	}
847
848
849	/**
850	* Checks whether the given study is simple enough to be edited using this controller.
851	*
852	* The study is simple enough if the samples, subjects, events and samplingEvents can be
853	* edited as a flat table. That is:
854	* - Every subject belongs to 0 or 1 eventgroup
855	* - Every eventgroup belongs to 0 or 1 sample
856	* - Every eventgroup has 0 or 1 subjects, 0 or 1 event and 0 or 1 samplingEvents
857	* - If a sample belongs to an eventgroup:
858	* - If that eventgroup has a samplingEvent, that same samplingEvent must also be
859	* the sampling event that generated this sample
860	* - If that eventgroup has a subject, that same subject must also be the subject
861	* from whom the sample was taken
862	*
863	* @param study Study to check
864	* @return True if the study can be edited by this controller, false otherwise
865	*/
866	def checkStudySimplicity( study ) {
867	def simplicity = true;
868
869	if( !study )
870	return false
871
872	if( study.eventGroups ) {
873	study.eventGroups.each { eventGroup ->
874	// Check for simplicity of eventgroups: only 0 or 1 subject, 0 or 1 event and 0 or 1 samplingEvent
875	if( eventGroup.subjects?.size() > 1 \|\| eventGroup.events?.size() > 1 \|\| eventGroup.samplingEvents?.size() > 1 ) {
876	flash.message = "One or more eventgroups contain multiple subjects or events."
877	simplicity = false;
878	}
879
880	// Check whether this eventgroup only belongs to (max) 1 sample
881	def numSamples = 0;
882	study.samples.each { sample ->
883	// If no id is given for the eventGroup, it has been entered in this wizard, but
884	// not yet saved. In that case, it is always OK
885	if( eventGroup.id && sample.parentEventGroup?.id == eventGroup.id )
886	numSamples++;
887	}
888
889	if( numSamples > 1 ) {
890	flash.message = "One or more eventgroups belong to multiple samples."
891	simplicity = false;
892	}
893	}
894
895	if( !simplicity ) return false;
896
897	// Check whether subject only belong to zero or one event group
898	if( study.subjects ) {
899	study.subjects.each { subject ->
900	def numEventGroups = 0
901	study.eventGroups.each { eventGroup ->
902	// If no id is given for the subject, it has been entered in this wizard, but
903	// not yet saved. In that case, it is always OK
904	if( subject.id && eventGroup.subjects[0]?.id == subject.id )
905	numEventGroups++
906	}
907
908	if( numEventGroups > 1 ) {
909	flash.message = "One or more subjects belong to multiple eventgroups."
910	simplicity = false;
911	}
912	}
913	}
914
915	if( !simplicity ) return false;
916
917	// Check whether the samples that belong to an eventgroup have the right parentObjects
918	study.samples.each { sample ->
919	if( sample.parentEventGroup ) {
920	// If no id is given for the subject, it has been entered in this wizard, but
921	// not yet saved. In that case, it is always OK
922	if( sample.parentSubject && sample.parentSubject.id) {
923	if( !sample.parentEventGroup.subjects \|\| sample.parentEventGroup.subjects[0]?.id != sample.parentSubject.id ) {
924	flash.message = "The structure of the eventgroups of one or more samples is too complex"
925	simplicity = false;
926	}
927	}
928
929	// If no id is given for the sampling event, it has been entered in this wizard, but
930	// not yet saved. In that case, it is always OK
931	if( sample.parentEvent && sample.parentEvent.id) {
932	if( !sample.parentEventGroup.samplingEvents \|\| sample.parentEventGroup.samplingEvents[0]?.id != sample.parentEvent.id ) {
933	flash.message = "The structure of the eventgroups of one or more samples is too complex"
934	simplicity = false;
935	}
936	}
937	}
938	}
939
940	if( !simplicity ) return false;
941	}
942
943	return simplicity;
944	}
945
946
947	/**
948	* Adds all fields of this entity that have given an error when validating to the failedcells list
949	* @param failedcells Current list of ImportRecords
950	* @param entity Entity to check. The entity must have been validated before
951	* @return Updated list of ImportRecords
952	*/
953	protected def addNonValidatingCells( failedcells, entity, flow ) {
954	// Add this entity and the fields with an error to the failedCells list
955	ImportRecord failedRecord = addNonValidatingCellsToImportRecord( new ImportRecord(), entity, flow );
956
957	failedcells.add( failedRecord );
958
959	return failedcells
960	}
961
962	/**
963	* Adds all fields of this entity that have given an error when validating to the failedcells list
964	* @param failedcells Current list of ImportRecords
965	* @param entity Entity to check. The entity must have been validated before
966	* @return Updated list of ImportRecords
967	*/
968	protected def addNonValidatingCellsToImportRecord( failedRecord, entity, flow ) {
969	entity.getErrors().getFieldErrors().each { error ->
970	String field = error.getField();
971
972	def mc = importerService.findMappingColumn( flow.excel.data.header, field );
973	def mcInstance = new MappingColumn( name: field, entityClass: Sample.class, index: -1, property: field.toLowerCase(), templateFieldType: entity.giveFieldType( field ) );
974
975	// Create a clone of the mapping column
976	if( mc ) {
977	mcInstance.properties = mc.properties
978	}
979
980	failedRecord.addToImportcells( new ImportCell(mappingcolumn: mcInstance, value: error.getRejectedValue(), entityidentifier: importerService.getFieldNameInTableEditor( entity, field ) ) )
981	}
982
983	return failedRecord
984	}
985
986
987	/**
988	* Checks an excel workbook whether the given sheetindex and rownumbers are correct
989	* @param workbook Excel workbook to read
990	* @param sheetIndex 1-based sheet index for the sheet to read (1=first sheet)
991	* @param headerRow 1-based row number for the header row (1=first row)
992	* @param dataMatrixStart 1-based row number for the first data row (1=first row)
993	* @return True if the sheet index and row numbers are correct.
994	*/
995	protected boolean excelChecks( def workbook, int sheetIndex, int headerRow, int dataMatrixStart ) {
996	// Perform some basic checks on the excel file. These checks should be performed by the importerservice
997	// in a perfect scenario.
998	if( sheetIndex > workbook.getNumberOfSheets() ) {
999	log.error ".simple study wizard Sheet index is too high: " + sheetIndex + " / " + workbook.getNumberOfSheets();
1000	flash.error = "Your excel sheet contains too few excel sheets. The provided excel sheet has only " + workbook.getNumberOfSheets() + " sheet(s).";
1001	return false
1002	}
1003
1004	def sheet = workbook.getSheetAt(sheetIndex - 1);
1005	def firstRowNum = sheet.getFirstRowNum();
1006	def lastRowNum = sheet.getLastRowNum();
1007	def numRows = lastRowNum - firstRowNum + 1;
1008
1009	if( headerRow > numRows ) {
1010	log.error ".simple study wizard Header row number is incorrect: " + headerRow + " / " + numRows;
1011	flash.error = "Your excel sheet doesn't contain enough rows (" + numRows + "). Please provide an excel sheet with one header row and data below";
1012	return false
1013	}
1014
1015	if( dataMatrixStart > numRows ) {
1016	log.error ".simple study wizard Data row number is incorrect: " + dataMatrixStart + " / " + numRows;
1017	flash.error = "Your excel sheet doesn't contain enough rows (" + numRows + "). Please provide an excel sheet with one header row and data below";
1018	return false
1019	}
1020
1021	return true;
1022	}
1023
1024	/**
1025	* Validates an object and puts human readable errors in validationErrors variable
1026	* @param entity Entity to validate
1027	* @return True iff the entity validates, false otherwise
1028	*/
1029	protected boolean validateObject( def entity ) {
1030	if( !entity.validate() ) {
1031	flash.validationErrors = getHumanReadableErrors( entity )
1032	return false;
1033	}
1034	return true;
1035	}
1036
1037	/**
1038	* transform domain class validation errors into a human readable
1039	* linked hash map
1040	* @param object validated domain class
1041	* @return object linkedHashMap
1042	*/
1043	def getHumanReadableErrors(object) {
1044	def errors = [:]
1045	object.errors.getAllErrors().each() { error ->
1046	// error.codes.each() { code -> println code }
1047
1048	// generally speaking g.message(...) should work,
1049	// however it fails in some steps of the wizard
1050	// (add event, add assay, etc) so g is not always
1051	// availably. Using our own instance of the
1052	// validationTagLib instead so it is always
1053	// available to us
1054	errors[error.getArguments()[0]] = validationTagLib.message(error: error)
1055	}
1056
1057	return errors
1058	}
1059	}

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