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source: trunk/grails-app/controllers/dbnp/studycapturing/AssayController.groovy @ 2053

Last change on this file since 2053 was 2053, checked in by s.h.sikkema@…, 7 years ago
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1	package dbnp.studycapturing
2
3	import grails.plugins.springsecurity.Secured
4
5	@Secured(['IS_AUTHENTICATED_REMEMBERED'])
6	class AssayController {
7
8	def assayService
9	def authenticationService
10	def fileService
11
12	static allowedMethods = [save: "POST", update: "POST", delete: "POST"]
13
14	def index = {
15	redirect(action: "list", params: params)
16	}
17
18	def list = {
19	params.max = Math.min(params.max ? params.int('max') : 10, 100)
20	[assayInstanceList: Assay.list(params), assayInstanceTotal: Assay.count()]
21	}
22
23	def create = {
24	def assayInstance = new Assay()
25	assayInstance.properties = params
26	return [assayInstance: assayInstance]
27	}
28
29	def save = {
30	def assayInstance = new Assay(params)
31
32	// The following lines deviate from the generate-all generated code.
33	// See http://jira.codehaus.org/browse/GRAILS-3783 for why we have this shameful workaround...
34	def study = assayInstance.parent
35	study.addToAssays(assayInstance)
36
37	if (assayInstance.save(flush: true)) {
38	flash.message = "${message(code: 'default.created.message', args: [message(code: 'assay.label', default: 'Assay'), assayInstance.id])}"
39	redirect(action: "show", id: assayInstance.id)
40	}
41	else {
42	render(view: "create", model: [assayInstance: assayInstance])
43	}
44	}
45
46	def show = {
47	def assayInstance = Assay.get(params.id)
48	if (!assayInstance) {
49	flash.message = "${message(code: 'default.not.found.message', args: [message(code: 'assay.label', default: 'Assay'), params.id])}"
50	redirect(action: "list")
51	}
52	else {
53	[assayInstance: assayInstance]
54	}
55	}
56
57	def showByToken = {
58	def assayInstance = Assay.findByAssayUUID(params.id)
59	if (!assayInstance) {
60	flash.message = "${message(code: 'default.not.found.message', args: [message(code: 'assay.label', default: 'Assay'), params.id])}"
61	redirect(action: "list")
62	}
63	else {
64	redirect(action: "show", id: assayInstance.id)
65	}
66	}
67
68	def edit = {
69	def assayInstance = Assay.get(params.id)
70	if (!assayInstance) {
71	flash.message = "${message(code: 'default.not.found.message', args: [message(code: 'assay.label', default: 'Assay'), params.id])}"
72	redirect(action: "list")
73	}
74	else {
75	return [assayInstance: assayInstance]
76	}
77	}
78
79	def update = {
80	def assayInstance = Assay.get(params.id)
81	if (assayInstance) {
82	if (params.version) {
83	def version = params.version.toLong()
84	if (assayInstance.version > version) {
85
86	assayInstance.errors.rejectValue("version", "default.optimistic.locking.failure", [message(code: 'assay.label', default: 'Assay')] as Object[], "Another user has updated this Assay while you were editing")
87	render(view: "edit", model: [assayInstance: assayInstance])
88	return
89	}
90	}
91	assayInstance.properties = params
92	if (!assayInstance.hasErrors() && assayInstance.save(flush: true)) {
93	flash.message = "${message(code: 'default.updated.message', args: [message(code: 'assay.label', default: 'Assay'), assayInstance.id])}"
94	redirect(action: "show", id: assayInstance.id)
95	}
96	else {
97	render(view: "edit", model: [assayInstance: assayInstance])
98	}
99	}
100	else {
101	flash.message = "${message(code: 'default.not.found.message', args: [message(code: 'assay.label', default: 'Assay'), params.id])}"
102	redirect(action: "list")
103	}
104	}
105
106	def delete = {
107	def assayInstance = Assay.get(params.id)
108	if (assayInstance) {
109	try {
110	assayInstance.delete(flush: true)
111	flash.message = "${message(code: 'default.deleted.message', args: [message(code: 'assay.label', default: 'Assay'), params.id])}"
112	redirect(action: "list")
113	}
114	catch (org.springframework.dao.DataIntegrityViolationException e) {
115	flash.message = "${message(code: 'default.not.deleted.message', args: [message(code: 'assay.label', default: 'Assay'), params.id])}"
116	redirect(action: "show", id: params.id)
117	}
118	}
119	else {
120	flash.message = "${message(code: 'default.not.found.message', args: [message(code: 'assay.label', default: 'Assay'), params.id])}"
121	redirect(action: "list")
122	}
123	}
124
125	def assayExportFlow = {
126	entry {
127	action{
128	def user = authenticationService.getLoggedInUser()
129	flow.userStudies = Study.giveReadableStudies(user)
130	}
131	on("success").to "selectAssay"
132	}
133
134	selectAssay {
135	on ("submit"){
136	flow.assay = Assay.get(params.assayId)
137
138	// check if assay exists
139	if (!flow.assay) throw new Exception("No assay found with id: ${params.assayId}")
140
141	// obtain fields for each category
142	flow.fieldMap = assayService.collectAssayTemplateFields(flow.assay, null)
143
144	flash.errorMessage = flow.fieldMap.remove('Module Error')
145	flow.measurementTokens = flow.fieldMap.remove('Module Measurement Data')
146	}.to "selectFields"
147
148	on(Exception).to "handleError"
149	}
150
151	selectFields {
152	on ("submit"){
153
154	def fieldMapSelection = [:]
155
156	flow.fieldMap.eachWithIndex { cat, cat_i ->
157
158	if (params."cat_$cat_i" == 'on') {
159	fieldMapSelection[cat.key] = []
160
161	cat.value.eachWithIndex { field, field_i ->
162
163	if (params."cat_${cat_i}_${field_i}" == 'on')
164	fieldMapSelection[cat.key] += field
165	}
166
167	if (fieldMapSelection[cat.key] == [])
168	fieldMapSelection.remove(cat.key)
169	}
170	}
171
172	def measurementTokens = []
173
174	if (params."cat_4" == 'on') {
175	measurementTokens = params.list( "measurementToken" )
176	}
177
178	// collect the assay data according to user selecting
179	def assayData = assayService.collectAssayData(flow.assay, fieldMapSelection, measurementTokens)
180
181	flash.errorMessage = assayData.remove('Module Error')
182
183	flow.rowData = assayService.convertColumnToRowStructure(assayData)
184
185	// prepare the assay data preview
186	def previewRows = Math.min(flow.rowData.size() as int, 5) - 1
187	def previewCols = Math.min(flow.rowData[0].size() as int, 5) - 1
188
189	flow.assayDataPreview = flow.rowData[0..previewRows].collect{ it[0..previewCols] as ArrayList }
190
191	// store the selected file type in the flow
192	flow.exportFileType = params.exportFileType
193
194	}.to "compileExportData"
195
196	on(Exception).to "handleError"
197	}
198
199	compileExportData {
200	on ("ok"){
201	session.rowData = flow.rowData
202	session.exportFileType = flow.exportFileType
203	}.to "export"
204	on ("cancel").to "selectAssay"
205	}
206
207	export {
208	redirect(action: 'doExport')
209	}
210
211	handleError() {
212	render(view: 'errorPage')
213	}
214	}
215
216	/**
217	* This method is called when a user wants to fetch data from GSCF
218	*/
219	def galaxyExport = {
220	def galaxy_url = params.get( "GALAXY_URL" );
221	def tool_id = params.get( "tool_id" );
222
223	// Without galaxy url, we can't do anything
224	if( !galaxy_url \|\| !tool_id ) {
225	redirect( action: "assayExport" );
226	}
227
228	def user = authenticationService.getLoggedInUser()
229	def userStudies = Study.giveReadableStudies(user)
230
231	[ galaxy_url: galaxy_url, tool_id: tool_id, userStudies: userStudies ]
232	}
233
234	def sendToGalaxy = {
235	// Generate the url to redirect the user to
236	def galaxy_url = params.get( "GALAXY_URL" );
237	def tool_id = params.get( "tool_id" );
238
239	// Without galaxy url, we can't do anything
240	if( !galaxy_url \|\| !tool_id ) {
241	redirect( action: "assayExport" );
242	}
243
244	def assayId = params.long( "assayId" );
245	def assay = assayId ? Assay.get( assayId ) : null;
246
247	// If no assay is given, return to galaxyExport screen
248	if( !assay ) {
249	redirect( action: "galaxyExport", params: [ "GALAXY_URL": galaxy_url ] );
250	}
251
252	// create a random session token that will be used to allow to module to
253	// sync with gscf prior to presenting the measurement data
254	def sessionToken = UUID.randomUUID().toString()
255	def consumer = "galaxy";
256
257	// put the session token to work
258	authenticationService.logInRemotely( consumer, sessionToken, authenticationService.getLoggedInUser() )
259
260	// Create a url where the data can be fetched
261	def fetchUrl = g.createLink( absolute: true, controller: "assay", action: "fetchGalaxyData", params: [ assayToken: assay.assayUUID, sessionToken: sessionToken ] );
262
263	// Generate url to redirect the user to
264	def url = galaxy_url + "?tool_id=" + URLEncoder.encode( tool_id.toString(), "UTF-8" ) + "&URL=" + URLEncoder.encode( fetchUrl.toString(), "UTF-8" )
265
266	log.trace "Redirecting galaxy user back to " + url;
267
268	redirect( url: url );
269	}
270
271	// This method is accessible for each user. However, he should return with a valid
272	// session token
273	@Secured(['true'])
274	def fetchGalaxyData = {
275	// Check accessibility
276	def consumer = "galaxy";
277	def remoteUser = authenticationService.getRemotelyLoggedInUser( consumer, params.sessionToken );
278	if( !remoteUser ) {
279	response.status = 401;
280	render "You must be logged in";
281	return
282	}
283
284	// retrieve assay
285	def assay = Assay.findByAssayUUID( params.assayToken );
286
287	if( !assay ) {
288	response.status = 404;
289	render "No assay found";
290	return
291	}
292
293	// Return assay data
294	def fieldMap = assayService.collectAssayTemplateFields( assay, null, remoteUser )
295
296	def measurementTokens = fieldMap.remove('Module Measurement Data');
297	def assayData = assayService.collectAssayData(assay, fieldMap, measurementTokens, null, remoteUser)
298
299	def rowData = assayService.convertColumnToRowStructure(assayData)
300
301	// Invalidate session token
302	authenticationService.logOffRemotely( consumer, params.sessionToken );
303
304	def outputDelimiter = '\t'
305	def outputFileExtension = 'txt'
306
307	def filename = "export.$outputFileExtension"
308	response.setHeader("Content-disposition", "attachment;filename=\"${filename}\"")
309	response.setContentType("application/octet-stream")
310	try {
311	// Skip first row for now to support the current PLS tool in Galaxy, will change in the future
312	assayService.exportRowWiseDataToCSVFile(rowData[1..-1], response.outputStream, outputDelimiter, java.util.Locale.US)
313	} catch (Exception e) {
314	flash.errorMessage = e.message
315	redirect action: 'errorPage'
316	}
317	}
318
319	/**
320	* Export the row data in session.rowData to the outputStream of the http
321	* response.
322	*/
323	def doExport = {
324
325	// make sure we're coming from the export flow, otherwise redirect there
326	if (!(session.rowData && session.exportFileType))
327	redirect(action: 'assayExportFlow')
328
329	// process requested output file type
330	def outputDelimiter, outputFileExtension, locale = java.util.Locale.US
331
332	switch(session.exportFileType) {
333	case '2': // Comma delimited csv
334	outputDelimiter = ','
335	outputFileExtension = 'csv'
336	break
337	case '3': // Semicolon delimited csv
338	outputDelimiter = ';'
339	outputFileExtension = 'csv'
340	locale = java.util.Locale.GERMAN // force use of comma as decimal separator
341	break
342	default: // Tab delimited with .txt extension
343	outputDelimiter = '\t'
344	outputFileExtension = 'txt'
345	}
346
347	def filename = "export.$outputFileExtension"
348	response.setHeader("Content-disposition", "attachment;filename=\"${filename}\"")
349	response.setContentType("application/octet-stream")
350	try {
351
352	assayService.exportRowWiseDataToCSVFile(session.rowData, response.outputStream, outputDelimiter, locale)
353
354	// clear the data from the session
355	session.removeAttribute('rowData')
356	session.removeAttribute('exportFileType')
357
358	} catch (Exception e) {
359
360	flash.errorMessage = e.message
361	redirect action: 'errorPage'
362
363	}
364	}
365
366	/**
367	* Method to export one or more assays to excel in separate sheets.
368	*
369	* @param params.ids One or more assay IDs to export
370	* @param params.format "list" in order to export all assays in one big excel sheet
371	* "sheets" in order to export every assay on its own sheet (default)
372	*/
373	def exportToExcel = {
374	def format = params.get( 'format', 'sheets' );
375	if( format == 'list' ) {
376	exportToExcelAsList( params );
377	} else {
378	exportToExcelAsSheets( params );
379	}
380	}
381
382	/**
383	* Method to export one or more assays to excel in separate sheets.
384	*
385	* @param params.ids One or more assay IDs to export
386	*/
387	def exportToExcelAsSheets = {
388	def assays = getAssaysFromParams( params );
389
390	if( !assays )
391	return;
392
393	// Send headers to the browser so the user can download the file
394	def filename = 'export.xlsx'
395	response.setHeader("Content-disposition", "attachment;filename=\"${filename}\"")
396	response.setContentType("application/octet-stream")
397
398	try {
399	// Loop through all assays to collect the data
400	def rowWiseAssayData = [];
401
402	assays.each { assay ->
403	// Determine which fields should be exported for this assay
404	def fieldMap = assayService.collectAssayTemplateFields(assay, null)
405	def measurementTokens = fieldMap.remove('Module Measurement Data')
406
407	// Retrieve row based data for this assay
408	def assayData = assayService.collectAssayData( assay, fieldMap, measurementTokens );
409	def rowData = assayService.convertColumnToRowStructure(assayData)
410
411	// Put each assay on another sheet
412	rowWiseAssayData << rowData;
413	}
414
415	assayService.exportRowWiseDataForMultipleAssaysToExcelFile( rowWiseAssayData, response.getOutputStream() )
416
417	response.outputStream.flush()
418
419	} catch (Exception e) {
420	throw e;
421	}
422	}
423
424	/**
425	* Method to export one or more assays to excel.
426	*
427	* @param params.ids One or more assay IDs to export
428	*/
429	def exportToExcelAsList = {
430	def assays = getAssaysFromParams( params );
431
432	if( !assays )
433	return;
434
435	// Send headers to the browser so the user can download the file
436	def filename = 'export.csv'
437	response.setHeader("Content-disposition", "attachment;filename=\"${filename}\"")
438	response.setContentType("application/octet-stream")
439
440	try {
441	// Loop through all assays to collect the data
442	def columnWiseAssayData = [];
443
444	assays.each { assay ->
445	// Determine which fields should be exported for this assay
446	def fieldMap = assayService.collectAssayTemplateFields(assay, null)
447	def measurementTokens = fieldMap.remove('Module Measurement Data')
448
449	// Retrieve row based data for this assay
450	def assayData = assayService.collectAssayData( assay, fieldMap, measurementTokens );
451
452	// Prepend study and assay data to the list
453	assayData = assayService.prependAssayData( assayData, assay, assay.samples?.size() )
454	assayData = assayService.prependStudyData( assayData, assay, assay.samples?.size() )
455
456	// Put each assay on another sheet
457	columnWiseAssayData << assayData;
458	}
459
460	// Merge data from all assays
461	def mergedColumnWiseData = assayService.mergeColumnWiseDataOfMultipleStudies( columnWiseAssayData );
462
463	def rowData = assayService.convertColumnToRowStructure(mergedColumnWiseData)
464	assayService.exportRowWiseDataToCSVFile( rowData, response.getOutputStream() )
465
466	response.outputStream.flush()
467
468	} catch (Exception e) {
469	throw e;
470	}
471	}
472
473	/**
474	* Method to export one or more samples to csv in separate sheets.
475	*
476	* @param params.ids One or more sample ids to export
477	*/
478	def exportSamplesToCsv = {
479	def samples = getSamplesFromParams( params );
480
481	if( !samples ) {
482	return;
483	}
484
485	// Determine a list of assays these samples have been involved in. That way, we can
486	// retrieve the data for that assay once, and save precious time doing HTTP calls
487	def assays = [:];
488
489	samples.each { sample ->
490	def thisAssays = sample.getAssays();
491
492	// Loop through all assays. If it already exists, add the sample it to the list
493	thisAssays.each { assay ->
494	if( !assays[ assay.id ] ) {
495	assays[ assay.id ] = [ 'assay': assay, 'samples': [] ]
496	}
497
498	assays[ assay.id ].samples << sample
499	}
500	}
501
502	// Now collect data for all assays
503	try {
504	// Loop through all assays to collect the data
505	def columnWiseAssayData = [];
506
507	assays.each { assayInfo ->
508	def assay = assayInfo.value.assay;
509	def assaySamples = assayInfo.value.samples;
510
511	// Determine which fields should be exported for this assay
512	def fieldMap = assayService.collectAssayTemplateFields(assay, null)
513	def measurementTokens = fieldMap.remove('Module Measurement Data')
514
515	// Retrieve row based data for this assay
516	def assayData = assayService.collectAssayData( assay, fieldMap, measurementTokens, assaySamples );
517
518	// Prepend study and assay data to the list
519	assayData = assayService.prependAssayData( assayData, assay, assaySamples.size() )
520	assayData = assayService.prependStudyData( assayData, assay, assaySamples.size() )
521
522	// Make sure the assay data can be distinguished later
523	assayData.put( "Assay data - " + assay.name, assayData.remove( "Assay Data") )
524	assayData.put( "Module measurement data - " + assay.name, assayData.remove( "Module Measurement Data") )
525
526	// Add the sample IDs to the list, in order to be able to combine
527	// data for a sample that has been processed in multiple assays
528	assayData[ "Sample Data" ][ "id" ] = assaySamples*.id;
529
530	println "Assay data"
531	assayData.each { println it }
532
533	columnWiseAssayData << assayData;
534	}
535
536	def mergedColumnWiseData = assayService.mergeColumnWiseDataOfMultipleStudiesForASetOfSamples( columnWiseAssayData );
537
538	def rowData = assayService.convertColumnToRowStructure(mergedColumnWiseData)
539
540	// Send headers to the browser so the user can download the file
541	def filename = 'export.csv'
542	response.setHeader("Content-disposition", "attachment;filename=\"${filename}\"")
543	response.setContentType("application/octet-stream")
544
545	assayService.exportRowWiseDataToCSVFile( rowData, response.getOutputStream() )
546
547	response.outputStream.flush()
548
549	} catch (Exception e) {
550	throw e;
551	}
552	}
553
554
555	def getAssaysFromParams( params ) {
556	def ids = params.list( 'ids' ).findAll { it.isLong() }.collect { Long.valueOf( it ) };
557	def tokens = params.list( 'tokens' );
558
559	if( !ids && !tokens ) {
560	flash.errorMessage = "No assay ids given";
561	redirect( action: "errorPage" );
562	return [];
563	}
564
565	// Find all assays for the given ids
566	def assays = [];
567	ids.each { id ->
568	def assay = Assay.get( id );
569	if( assay )
570	assays << assay;
571	}
572
573	// Also accept tokens for defining studies
574	tokens.each { token ->
575	def assay = Assay.findByAssayUUID( token );
576	if( assay )
577	assays << assay;
578	}
579
580	if( !assays ) {
581	flash.errorMessage = "No assays found";
582	redirect( action: "errorPage" );
583	return [];
584	}
585
586	return assays.unique();
587	}
588
589	def getSamplesFromParams( params ) {
590	def ids = params.list( 'ids' ).findAll { it.isLong() }.collect { Long.valueOf( it ) };
591	def tokens = params.list( 'tokens' );
592
593	if( !ids && !tokens ) {
594	flash.errorMessage = "No sample ids given";
595	redirect( action: "errorPage" );
596	return [];
597	}
598
599	// Find all assays for the given ids
600	def samples = [];
601	ids.each { id ->
602	def sample = Sample.get( id );
603	if( sample )
604	samples << sample;
605	}
606
607	// Also accept tokens for defining studies
608	tokens.each { token ->
609	def sample = Sample.findBySampleUUID( token );
610	if( sample )
611	samples << sample;
612	}
613
614	if( !samples ) {
615	flash.errorMessage = "No assays found";
616	redirect( action: "errorPage" );
617	return [];
618	}
619
620	return samples.unique();
621	}
622
623	def errorPage = {
624	render(view: 'assayExport/errorPage')
625	}
626	}

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