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source: trunk/grails-app/controllers/nl/tno/massSequencing/RunController.groovy @ 71

Last change on this file since 71 was 71, checked in by robert@…, 12 years ago
Made some textual changes
File size: 28.6 KB

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1	package nl.tno.massSequencing
2
3	import java.util.Date;
4	import grails.converters.JSON
5	import nl.tno.massSequencing.auth.*
6	import nl.tno.massSequencing.classification.*;
7
8	import org.codehaus.groovy.grails.commons.ConfigurationHolder
9
10	class RunController {
11	def fileService
12	def synchronizationService
13	def sampleExcelService
14	def fastaService
15	def dataTablesService
16	def classificationService
17
18	def index = {
19	[runs: Run.list(), user: session.user]
20	}
21
22	/**
23	* Returns JSON data for the datatable with runs
24	* @see http://www.datatables.net/usage/server-side
25	* @see DataTablesService.retrieveData
26	*/
27	def showRunList = {
28	// Determine the total number of assaysamples for this run
29	def ids = Run.executeQuery( "SELECT r.id FROM Run r" );
30	def total = ids.size();
31
32	// Which columns are shown on screen and should be retrieved from the database
33	def columns = [
34	"r.id",
35	"r.name",
36	"COUNT( DISTINCT a )",
37	"SUM( a.numSequences )",
38	"(SELECT SUM( c.unclassified ) FROM Classification c WHERE c.assaySample.run = r)"
39	]
40
41	def groupColumns = columns[0..1];
42	def orderByMapping = null; // Meaning: order by column 2 on screen = order by column 1 in the table (screen starts at column 0, table starts at column 1 )
43
44	// Retrieve data from assaySample table
45	def from = "Run r LEFT JOIN r.assaySamples a"
46
47	// This closure determines what to do with a row that is retrieved from the database.
48	def convertClosure = {
49	def runId = it[ 0 ];
50	def runName = it[ 1 ];
51	def numSamples = it[ 2 ];
52	def numSequences = it[ 3 ];
53	def numClassified = it[ 4 ];
54
55	// Create buttons in the last three columns
56	def editButton = g.link( controller: "run", action: "show", id: it[ 0 ], "title": "View run" ) { '<img src="' + fam.icon( name: 'application_form_magnify' ) + '" title="View run" />' };
57	def deleteButton = '';
58	def chartButton = '';
59
60	if( numSequences > 0 ) {
61	chartButton = g.link( controller: "run", action: "sequenceLengthHistogram", id: runId, title: "Sequence length histogram" ) { '<img src="' + fam.icon( name: 'chart_bar' ) + '" alt="Sequence length histogram" title="Sequence length histogram" />' }
62	} else {
63	chartButton = '<img src="' + fam.icon( name: 'chart_bar' ) + '" class="disabled" alt="No histogram available because no sequences are uploaded." title="No histogram available because no sequences are uploaded." />'
64	}
65
66	if( numSequences > 0 \|\| Run.hasNonWritableAssays( runId, session.user.id ) ) {
67	deleteButton = '<img src="' + fam.icon( name: 'delete' ) + '" class="disabled" alt="Run can not be deleted because data is associated with it." title="Run can not be deleted because data is associated with it." />'
68	} else {
69	deleteButton = g.link( title:"Delete run", onClick:"return confirm( 'Are you sure you want to delete this run?' );", controller:"run", action:"deleteRun", id: runId ) { '<img src="' + fam.icon( name: 'delete' ) + '" alt="Delete run" title="Delete run" />' }
70	}
71
72	[
73	g.checkBox( name: "ids", value: runId, checked: false, onClick: "updateCheckAll(this);" ),
74	g.link( title:"View run", controller:"run", action:"show", id: runId ) { runName }, // it.name
75	numSamples > 0 ? g.formatNumber( number: numSamples, format: "###,###,##0" ) : "-", // it.numSequences(),
76	numSequences > 0 ? g.formatNumber( number: numSequences, format: "###,###,##0" ) : "-", // it.numQualScores(),
77	numClassified > 0 ? g.formatNumber( number: numClassified, format: "###,###,##0" ) : "-", // it.percentageClassified
78	editButton,
79	deleteButton,
80	chartButton
81	]
82	}
83
84	// Send the data to the user
85	render dataTablesService.retrieveData(
86	params,
87	Run.class,
88	convertClosure,
89	columns,
90	groupColumns,
91	from,
92	total,
93	ids,
94	orderByMapping
95	) as JSON
96	}
97
98	def show = {
99	// load run with id specified by param.id
100	def run = getRun( params.id );
101
102	if (!run) {
103	redirect(controller: 'study', action: 'index')
104	return
105	}
106
107	// Find statistics for all assaySamples in order to improve performance
108	AssaySample.initStats( run.assaySamples?.toList() )
109
110	// Determine runs not used in this assay
111	def otherAssays = Assay.list( sort: "name" ).findAll { !it.runs.contains( run ) && it.study.canRead( session.user ) }
112
113	// Determine several parameters to show on screen
114	def numClassified = Classification.executeQuery( "SELECT SUM( c.unclassified ) FROM Classification c WHERE c.assaySample IN (:assaySamples)", [ "assaySamples": run.assaySamples ] );
115
116	// Send the assay information to the view
117	[run: run, allRuns: Run.list(), otherAssays: otherAssays, editable: true, "numClassified": numClassified ? ( numClassified[ 0 ] ?: 0 ) : 0 ]
118	}
119
120	/**
121	* Returns JSON data for the datatable with assaysamples
122	* @see http://www.datatables.net/usage/server-side
123	* @see DataTablesService.retrieveData
124	*/
125	def showSampleData = {
126	// load run with id specified by params.id
127	def run = getRun( params.id );
128
129	if (!run) {
130	response.sendError(404, "Run not found" )
131	return
132	}
133
134	// Determine the total number of assaysamples for this run
135	def ids = AssaySample.executeQuery( "SELECT s.id FROM AssaySample s WHERE s.run.id = :runId AND EXISTS( FROM Auth a3 WHERE s.assay.study = a3.study AND a3.user = :user AND a3.canRead = true )", [ "runId": run.id, "user": session.user ] );
136	def total = ids.size();
137
138	// Which columns are shown on screen and should be retrieved from the database
139	def columns = [
140	"s.id",
141	"s.sample.name",
142	"s.assay.study.name",
143	"s.assay.name",
144	"s.fwMidName",
145	"SUM( sd.numSequences )",
146	"SUM( CASE WHEN sd.qualityFile IS NULL THEN 0 ELSE sd.numSequences END )",
147	's.run.id',
148	's.assay.id',
149	's.assay.study.id',
150	]
151
152	def groupColumns = columns[0..4] + columns[7..9];
153	def orderByMapping = null; // Meaning: order by column 2 on screen = order by column 1 in the table (screen starts at column 0, table starts at column 1 )
154
155	// Retrieve data from assaySample table
156	def from = "AssaySample s LEFT JOIN s.sequenceData as sd"
157
158	// And filter by runId
159	def where = "s.run.id = :runId AND EXISTS( FROM Auth a3 WHERE s.assay.study = a3.study AND a3.user = :user AND a3.canRead = true )"
160	def parameters = [ "runId": run.id, "user": session.user ];
161
162	// This closure determines what to do with a row that is retrieved from the database.
163	def convertClosure = {
164	def sampleId = it[ 0 ];
165	def sampleName = it[ 1 ];
166	def runId = it[ 7 ];
167	def assayId = it[ 8 ];
168	def studyId = it[ 9 ];
169	def numSequences = it[ 5 ];
170
171	// TODO: Rewrite this authorization part in a more efficient way
172	def auth = Auth.executeQuery( "SELECT a.canWrite FROM Auth a WHERE a.study.id = :studyId AND a.user.id = :userId", [ 'studyId': studyId, 'userId': session.user?.id ] );
173	def canWrite = auth ? auth[ 0 ] : false;
174
175	// Create buttons in the last three columns
176	def editButton = '';
177	def deleteButton = '';
178	def chartButton = '';
179
180	if( canWrite ) {
181	editButton = g.link( url: '#', title: "Edit sample", onClick: "showEditSampleDialog(" + sampleId + ", 'run', " + runId + ");" ) { '<img src="' + fam.icon( name: 'pencil' ) + '" title="Edit sample" />' };
182	deleteButton = g.link( controller: 'run', action: 'removeSample', id: it[ 7 ], params: [ 'assaySampleId': sampleId ], title: "Remove sample from run", onClick: "return confirm( 'Are you sure you want to remove the selected sample from this run?' );" ) { '<img src="' + fam.icon( name: 'application_delete' ) + '" title="Remove sample from run" />' };
183	} else {
184	editButton = '<img src="' + fam.icon( name: 'pencil' ) + '" title="You can\'t edit this sample because you don\'t have sufficient privileges." class="disabled" />';
185	deleteButton = '<img src="' + fam.icon( name: 'application_delete' ) + '" title="You can\'t remove this sample because you don\'t have sufficient privileges." class="disabled" />';
186	}
187
188	if( numSequences > 0 ) {
189	chartButton = g.link( controller: "assaySample", action: "sequenceLengthHistogram", id: sampleId, title: "Sequence length histogram" ) { '<img src="' + fam.icon( name: 'chart_bar' ) + '" alt="Sequence length histogram" title="Sequence length histogram" />' }
190	} else {
191	chartButton = '<img src="' + fam.icon( name: 'chart_bar' ) + '" class="disabled" alt="No histogram available because no sequences are uploaded." title="No histogram available because no sequences are uploaded." />'
192	}
193
194	[
195	g.checkBox( name: "ids", value: sampleId, checked: false, onClick: "updateCheckAll(this);" ),
196	g.link( url: "#", onClick:"showSample( " + sampleId + ", 'run' );", title: "Show sample details" ) { sampleName }, // it.sample.name
197	it[ 2 ], // it.assay.study.name
198	it[ 3 ], // it.assay.name
199	it[ 4 ], // it.fwMidName
200	it[ 5 ] > 0 ? g.formatNumber( number: it[ 5 ], format: "###,###,##0" ) : "-", // it.numSequences(),
201	it[ 6 ] > 0 ? g.formatNumber( number: it[ 6 ], format: "###,###,##0" ) : "-", // it.numQualScores(),
202	editButton,
203	deleteButton,
204	chartButton
205	]
206	}
207
208	// Send the data to the user
209	render dataTablesService.retrieveData(
210	params,
211	AssaySample.class,
212	convertClosure,
213	columns,
214	groupColumns,
215	from,
216	total,
217	ids,
218	orderByMapping,
219	where,
220	parameters
221	) as JSON
222
223	}
224
225	/**
226	* Shows a form to edit the specified run in dialog mode
227	*/
228	def editForm = {
229	// load run with id specified by param.id
230	Run run = getRun( params.id );
231
232	if (!run) {
233	render flash.error
234	return
235	}
236
237	Assay assay = null
238	if( params.assayId ) {
239	assay = getAssay( params.assayId )
240
241	if( !assay ) {
242	render flash.error;
243	return
244	}
245	}
246
247	[assay: assay, run: run]
248	}
249
250	def create = {
251	// Retrieve the assay from the database, but don't exit with an error if no assay is found
252	Assay a = getAssay(params.id);
253	flash.error = "";
254
255	// Create run based on given parameters
256	Run run = new Run();
257
258	run.setPropertiesFromForm( params );
259
260	if( a )
261	a.addToRuns( run );
262
263	if( !run.save() ) {
264	flash.message = "Run could not be saved: " + run.getErrors();
265	} else {
266	flash.message = "Run " + run.name + " has been added to the system."
267	}
268
269	if( a )
270	redirect( controller: "assay", action: "show", id: a.id )
271	else
272	redirect( controller: 'run' );
273	}
274
275	def update = {
276	Run run = getRun( params.id );
277
278	if( !run ) {
279	redirect(controller: 'assay', action: 'show', id: params.assayId)
280	return
281	}
282
283	// Set properties to the run
284	params.parameterFile = params.editParameterFile
285
286	run.setPropertiesFromForm( params );
287
288	if( run.save() ) {
289	flash.message = "Run succesfully saved";
290	} else {
291	flash.error = "Run could not be saved: " + run.getErrors();
292	}
293
294	Assay assay = getAssay(params.assayId);
295	flash.error = "";
296
297	if( assay ) {
298	redirect( controller: 'assay', action: 'show', id: assay.id)
299	} else {
300	redirect( controller: 'run', action: 'show', id: run.id )
301	}
302	}
303
304	def delete = {
305	Run run = getRun( params.id );
306
307	if( !run ) {
308	redirect(controller: 'assay', action: 'show', id: params.assayId)
309	return
310	}
311
312	// Don't remove runs for which data exists
313	if( run.assaySamples*.sequenceData.flatten().size() ) {
314	flash.message = "Run could not be deleted because samples with data are associated with it.";
315	redirect( controller: "assay", action: "show", id: params.assayId )
316	}
317
318	// Check whether the user has sufficient privileges to remove the run from all assays
319	def hasPrivileges = true;
320	run.assay.each {
321	if( !it.study.canWrite( session.user ) )
322	hasPrivileges = false
323	}
324
325	if( !hasPrivileges ) {
326	flash.message = "Run could not be deleted because you don't have sufficient privileges to remove the run from all assays.";
327	redirect( controller: "assay", action: "show", id: params.assayId )
328	}
329
330	// Remove all associations
331	def a = [] + run.assays
332	a.each {
333	run.removeFromAssays( it );
334	}
335
336	def name = run.name
337	run.delete();
338	flash.message = "Run " + name + " has been deleted from the system."
339
340	redirect( controller: "assay", action: "show", id: params.assayId )
341	}
342
343	def deleteRun = {
344	Run run = getRun( params.id );
345
346	if( !run ) {
347	redirect(controller: 'run', action: 'index')
348	return
349	}
350
351	// Don't remove runs for which data exists
352	if( run.assaySamples*.sequenceData.flatten().size() ) {
353	flash.message = "Run could not be deleted because samples with data are associated with it.";
354	redirect(controller: 'run', action: 'index')
355	}
356
357	// Check whether the user has sufficient privileges to remove the run from all assays
358	def hasPrivileges = true;
359	run.assays.each {
360	if( !it.study.canWrite( session.user ) )
361	hasPrivileges = false
362	}
363
364	if( !hasPrivileges ) {
365	flash.message = "Run could not be deleted because you don't have sufficient privileges to remove the run from all assays.";
366	redirect(controller: 'run', action: 'index')
367	}
368
369	// Remove all associations
370	def a = [] + run.assays
371	a.each {
372	run.removeFromAssays( it );
373	}
374
375	def name = run.name
376	run.delete();
377	flash.message = "Run " + name + " has been deleted from the system."
378
379	redirect(controller: 'run', action: 'index')
380	}
381
382	/**************************************************************************
383	*
384	* Methods for handling data about the samples in this run
385	*
386	*************************************************************************/
387
388	/**
389	* Downloads an excel sheet with data about the assay samples, to enter data in excel
390	*/
391	def downloadTagsExcel = {
392	Run run = getRun( params.id );
393
394	if( !run ) {
395	redirect(controller: 'run')
396	return
397	}
398
399	// Make it only possible to update samples writable by the user
400	def assaySamples = run.assaySamples.findAll { it.assay.study.canWrite( session.user ) }
401
402	def filename = "Run " + run.name + "_tags.xls"
403	def wb = sampleExcelService.downloadSampleExcel( assaySamples, false );
404
405	// Make file downloadable
406	log.trace( "Creation for downloading the file " + filename )
407	sampleExcelService.excelService.downloadFile( wb, filename, response )
408	}
409
410	/**
411	* Downloads an example excel sheet to describe the format of a file-matching sheet. This
412	* file is used when uploading sequence files.
413	*/
414	def downloadMatchExcel = {
415	Run run = getRun( params.id );
416
417	if( !run ) {
418	redirect(controller: 'run')
419	return
420	}
421
422	// Make it only possible to update samples writable by the user
423	def assaySamples = run.assaySamples.findAll { it.assay.study.canWrite( session.user ) }
424
425	def filename = "Run " + run.name + "_filenames.xls"
426	def wb = sampleExcelService.downloadMatchExcel( assaySamples );
427
428	// Make file downloadable
429	log.trace( "Creation for downloading the file " + filename )
430	sampleExcelService.excelService.downloadFile( wb, filename, response )
431	}
432
433	/**
434	* Parses an uploaded excel file and shows a form to match columns
435	*/
436	def parseTagExcel = {
437	Run run = getRun( params.id );
438
439	if( !run ) {
440	redirect(controller: 'study')
441	return
442	}
443
444	def filename = params.filename
445
446	// Security check to prevent accessing files in other directories
447	if( !filename \|\| filename.contains( '..' ) ) {
448	response.status = 500;
449	response.setContentType( "text/plain" );
450	render "Invalid filename given";
451	return;
452	}
453
454	// Check for existence and readability
455	File file = new File( fileService.getUploadDir(), filename)
456
457	if( !file.exists() \|\| !file.canRead() ) {
458	response.status = 404;
459	response.setContentType( "text/plain" );
460	render "The uploaded file doesn't exist or doesn't work as expected.";
461	return;
462	}
463
464	// Save the filename in session for later use
465	session.filename = filename;
466	def excelData;
467	try {
468	excelData = sampleExcelService.parseTagsExcel( file, false );
469	} catch( Throwable e ) { // Catch a throwable here instead of an exception, since the apache poi stuff gives an Error on failure
470	e.printStackTrace()
471	// Couldn't create a workbook from this file.
472	response.status = 400 // Bad request
473	response.setContentType( "text/plain" );
474	render "Uploaded file is not a valid excel file: " + e.getMessage()
475	return
476	}
477	session.possibleFields = excelData.possibleFields
478
479	[run: run, headers: excelData.headers, exampleData: excelData.exampleData, filename: filename, possibleFields: [ "Don't import" ] + excelData.possibleFields, bestMatches: excelData.bestMatches]
480	}
481
482	/**
483	* Updates the assay samples based on the given excel file and the column matches
484	*/
485	def updateTagsByExcel = {
486	Run run = getRun( params.id );
487
488	if( !run ) {
489	// Now delete the file, since we don't need it anymore
490	_deleteUploadedFileFromSession()
491
492	redirect(controller: 'study')
493	return
494	}
495
496	if( !session.filename ) {
497	// Now delete the file, since we don't need it anymore
498	_deleteUploadedFileFromSession()
499
500	flash.error = "No excel file found because session timed out. Please try again."
501	redirect( action: 'show', id: params.id)
502	return
503	}
504
505	// Determine the match-columns
506	def matchColumns = params[ 'matches'];
507
508	// Now loop through the excel sheet and update all samples with the specified data
509	File file = new File( fileService.getUploadDir(), session.filename );
510
511	if( !file.exists() \|\| !file.canRead() ) {
512	flash.error = "Excel file has been removed since previous step. Please try again."
513	redirect( action: 'show', id: params.id)
514	return
515	}
516
517	// Make it only possible to update samples writable by the user
518	def assaySamples = run.assaySamples.findAll { it.assay.study.canWrite( session.user ) }
519
520	def excelData = sampleExcelService.updateTagsByExcel( matchColumns, session.possibleFields, file, assaySamples );
521
522	// Return a message to the user
523	if( !excelData.success ) {
524	flash.error = excelData.message
525	} else if( excelData.numSuccesful == 0 ) {
526	flash.error = "None of the " + excelData.failedRows.size() + " row(s) could be imported, because none of the sample names matched or no samples are writable. Have you provided the right excel file?"
527	} else {
528	flash.message = excelData.numSuccesful + " samples have been updated. "
529
530	if( excelData.failedRows.size() > 0 )
531	flash.message += excelData.failedRows.size() + " row(s) could not be imported, because the sample names could not be found in the database or you don't have the proper permissions to change them."
532	}
533
534	// Now delete the file, since we don't need it anymore
535	_deleteUploadedFileFromSession()
536
537	redirect( action: 'show', id: params.id )
538	}
539
540
541	/**
542	* Update the properties of the assay samples manually
543	*/
544	def updateTagsManually = {
545	Run run = getRun( params.id );
546
547	if( !run ) {
548	redirect(controller: 'study')
549	return
550	}
551
552	// Loop through all assay samples and set data
553	def sampleParams = params.assaySample;
554
555	if( sampleParams ) {
556	run.assaySamples.findAll { it.assay.study.canWrite( session.user ) }.each { assaySample ->
557	def assaySampleParams = sampleParams.get( assaySample.id as String );
558	if( assaySampleParams ) {
559	sampleExcelService.variableFields.each { k, v ->
560	assaySample[ k ] = assaySampleParams[ k ];
561	}
562	assaySample.save()
563	}
564	}
565	}
566
567	flash.message = "Data about samples is saved."
568	redirect( action: 'show', id: params.id )
569	}
570
571	/**************************************************************************
572	*
573	* Methods for handling data about assays for this run
574	*
575	*************************************************************************/
576
577	/**
578	* Adds existing samples to this run
579	*/
580	def addSamples = {
581	Run run = getRun( params.id );
582
583	if( !run ) {
584	redirect(controller: 'run', action: 'index')
585	return
586	}
587
588	// Add checked runs to this assay
589	def assaySamples = params.assaySamples
590	if( assaySamples instanceof String ) {
591	assaySamples = [ assaySamples ]
592	}
593
594	def numAdded = 0;
595	assaySamples.each { assaySampleId ->
596	try {
597	def assaySample = AssaySample.findById( assaySampleId as Long )
598	if( !assaySample.run && assaySample.assay.study.canWrite( session.user ) ) {
599	if( run.assaySamples == null \|\| !run.assaySamples.contains( assaySample ) ) {
600	run.addToAssaySamples( assaySample );
601	numAdded++;
602	}
603	}
604	} catch( Exception e ) {}
605	}
606
607	flash.message = numAdded + " samples are added to this run."
608	redirect( action: 'show', id: params.id)
609	}
610
611	/**
612	* Removes sample from this run
613	*/
614	def removeSample = {
615	Run run = getRun( params.id );
616
617	if( !run ) {
618	redirect(controller: 'study')
619	return
620	}
621
622	if( !params.assaySampleId ) {
623	flash.error = "No sample id given"
624	redirect(action: 'show', id: params.id)
625	return
626	}
627
628	def assaySample
629
630	try {
631	assaySample = AssaySample.findById( params.assaySampleId as Long )
632	} catch( Exception e ) {
633	log.error e
634	flash.error = "Incorrect assaysample id given: " + params.assaySampleId
635	redirect(action: 'show', id: params.id)
636	return
637	}
638
639	if( !assaySample.assay.study.canWrite( session.user ) ) {
640	flash.error = "You don't have sufficient privileges to remove the specified sample from this run."
641	redirect(action: 'show', id: params.id)
642	return
643	}
644
645	if( run.assaySamples.contains( assaySample ) ) {
646	run.removeFromAssaySamples( assaySample );
647	flash.message = "The sample has been removed from this run."
648	} else {
649	flash.message = "The given sample was not associated with this run."
650	}
651
652	redirect( action: 'show', id: params.id)
653	}
654
655	/**
656	* Removes samples from this run
657	*/
658	def removeSamples = {
659	// Determine the run we are in
660	Run run = getRun( params.runId );
661
662	if( !run ) {
663	redirect(controller: 'run', action: 'list')
664	return
665	}
666
667	// Find the selected assaysamples
668	def ids = params.list( 'ids' );
669	ids = ids.findAll { it.isLong() }.collect { Long.parseLong( it ) }
670	def assaySamples = ids.collect { AssaySample.get( it ) }.findAll { it }
671
672	if( !assaySamples ) {
673	flash.message = "No samples selected for removal"
674	redirect( action: 'show', id: run.id );
675	return;
676	}
677
678	def numRemoved = 0;
679	assaySamples.each { assaySample ->
680	if( assaySample.assay.study.canWrite( session.user ) ) {
681	if( assaySample.run ) {
682	assaySample.run.removeFromAssaySamples( assaySample );
683	numRemoved++;
684	}
685	}
686	}
687
688	if( numRemoved > 0 )
689	flash.message = numRemoved + " sample(s) have been removed from this run."
690	else
691	flash.message = "No samples have been removed from this run, because you don't have the right privileges to do so."
692
693	redirect( action: 'show', id: run.id)
694	}
695
696
697	/**
698	* Adds existing assays to this run
699	*/
700	def addAssays = {
701	Run run = getRun( params.id );
702
703	if( !run ) {
704	redirect(controller: 'study')
705	return
706	}
707
708	// Add checked runs to this assay
709	def assays = params.assays
710	if( assays instanceof String ) {
711	assays = [ assays ]
712	}
713
714	def numAdded = 0;
715	assays.each { assay_id ->
716	try {
717	def assay = Assay.findById( assay_id as Long )
718	if( assay.study.canWrite( session.user ) ) {
719	if( run.assays == null \|\| !run.assays.contains( assay ) ) {
720	run.addToAssays( assay );
721	numAdded++;
722	}
723	}
724	} catch( Exception e ) {}
725	}
726
727	flash.message = numAdded + " assays are added to this run."
728	redirect( action: 'show', id: params.id)
729	}
730
731	/**
732	* Removes assay for this run
733	*/
734	def removeAssay = {
735	Run run = getRun( params.id );
736
737	if( !run ) {
738	redirect(controller: 'run', action: 'index')
739	return
740	}
741
742	if( !params.assay_id ) {
743	flash.message = "No assay id given"
744	redirect(action: 'show', id: params.id)
745	return
746	}
747
748	def assay
749
750	try {
751	assay = Assay.findById( params.assay_id as Long )
752	} catch( Exception e ) {
753	throw e
754	flash.message = "Incorrect assay id given: "
755	redirect(action: 'show', id: params.id)
756	return
757	}
758
759	if( !assay.study.canWrite( session.user ) ) {
760	flash.error = "You don't have sufficient privileges to remove the specified assay from this run."
761	redirect(action: 'show', id: params.id)
762	return
763	}
764
765	if( run.assays.contains( assay ) ) {
766	run.removeFromAssays( assay );
767	flash.message = "The assay has been removed from this run."
768	} else {
769	flash.message = "The given assay was not associated with this run."
770	}
771
772	redirect( action: 'show', id: params.id)
773	}
774
775	/**
776	* Deletes all sequences for a given run
777	*/
778	def deleteSequenceData = {
779	// Determine the run we are in
780	Run run = getRun( params.runId );
781
782	if( !run ) {
783	redirect(controller: 'run', action: 'index')
784	return
785	}
786
787	// Find the selected assaysamples
788	def ids = params.list( 'ids' );
789	ids = ids.findAll { it.isLong() }.collect { Long.parseLong( it ) }
790	def assaySamples = ids.collect { AssaySample.get( it ) }.findAll { it }
791
792	if( !assaySamples ) {
793	flash.message = "No samples selected"
794	redirect( action: 'show', id: run.id );
795	return;
796	}
797
798	def numFiles = fastaService.deleteSequenceData( assaySamples );
799
800	// Reset classification for given samples
801	classificationService.updateClassificationForAssaySample( assaySamples );
802
803	flash.message = numFiles + " files have been removed from the run.";
804	redirect( controller: 'run', action: 'show', id: run.id );
805	}
806
807	/**
808	* Exports data about one or more runs in fasta format
809	*/
810	def exportAsFasta = {
811	def assaySamples = getAssaySamples( params );
812
813	if( assaySamples == null )
814	return;
815
816	def name
817
818	if( assaySamples.size() == 0 ) {
819	flash.error = "No samples found for selected runs";
820	redirect( action: "index" );
821	return;
822	} else if( assaySamples*.run.unique().size() == 1 )
823	name = "Run_" + assaySamples[0].run?.name?.replace( ' ', '_' );
824	else
825	name = "runs";
826
827
828	// Start the export in the background
829	def returnUrl = createLink( controller: "run", action: "index" ).toString()
830	def finishUrl = createLink( controller: "assaySample", action: 'downloadFasta', params: [ processId: '%s' ] ).toString();
831	def url = fastaService.startExportProcess( assaySamples, session, name, returnUrl, finishUrl )
832
833	// Show a waiting screen
834	redirect( url: url );
835	}
836
837	/**
838	* Export metadata of selected samples in excel format
839	*/
840	def exportMetaData = {
841	def assaySamples = getAssaySamples( params );
842	def name
843
844	if( assaySamples == null )
845	return;
846
847	if( assaySamples.size() == 0 ) {
848	flash.error = "No samples found for selected runs";
849	redirect( action: "index" );
850	return;
851	} else if( assaySamples*.run.unique().size() == 1 ) {
852	name = "Run_" + assaySamples[0].run?.name?.replace( ' ', '_' );
853	} else {
854	name = "runs";
855	}
856
857	// Export the metadata
858	try {
859	// The export functionality needs a assaysSample-tag list, but it
860	// should be empty when only exporting metadata
861	def tags = [];
862	assaySamples.unique().each { assaySample ->
863	tags << [assaySampleId: assaySample.id, sampleName: assaySample.sample.name, assayName: assaySample.assay.name, studyName: assaySample.assay.study.name, tag: "-"]
864	}
865	response.setHeader "Content-disposition", "attachment; filename=${name}.xls"
866
867	sampleExcelService.sessionToken = session.sessionToken
868
869	if( !sampleExcelService.exportExcelSampleData( assaySamples.unique(), tags, response.outputStream ) ) {
870	flash.error = "An error occurred while fetching sample data. Maybe the session has timed out.";
871	response.setHeader( "Content-disposition", "" );
872	redirect( action: "index" );
873	}
874	response.outputStream.flush();
875	} catch( Exception e ) {
876	log.error( "Exception occurred during export of sequences. Probably the user has cancelled the download." );
877	e.printStackTrace();
878	}
879	}
880
881	def sequenceLengthHistogram = {
882	redirect( controller: "assaySample", action: "sequenceLengthHistogramForRun", id: params.id );
883	}
884
885	protected List getAssaySamples( params ) {
886	def ids = params.list( 'ids' );
887
888	ids = ids.findAll { it.isLong() }.collect { Long.parseLong( it ) }
889
890	if( !ids ) {
891	def message = "No run ids given"
892	flash.error = message
893	redirect( action: "index" );
894	return;
895	}
896
897	def assaySamples = [];
898
899	// Determine which assaySamples to export
900	ids.each { id ->
901	def run = Run.get( id );
902	if( run )
903	assaySamples += run.assaySamples.findAll { it.assay.study.canRead( session.user ) }
904	}
905
906	return assaySamples;
907	}
908
909	/**
910	* Deletes an uploaded file for which the filename is given in the session.
911	* @return
912	*/
913	def _deleteUploadedFileFromSession() {
914	if( !session.filename )
915	return
916
917	// Now delete the file, since we don't need it anymore
918	fileService.delete( session.filename )
919	session.filename = ''
920	}
921
922	protected Run getRun(def runId) {
923	// load study with id specified by param.id
924	def run
925	try {
926	run = Run.get(runId as Long)
927	} catch( Exception e ) {
928	flash.error = "Incorrect id given: " + runId
929	return null
930	}
931
932	if (!run) {
933	flash.error = "No run found with id: " + runId
934	return null
935	}
936
937	return run
938	}
939
940	protected Assay getAssay(def assayId) {
941	// load study with id specified by param.id
942	def assay
943	try {
944	assay = Assay.get(assayId as Long)
945	} catch( Exception e ) {
946	flash.error = "Incorrect id given: " + assayId
947	return null
948	}
949
950	if (!assay) {
951	flash.error = "No assay found with id: " + assayId
952	return null
953	}
954
955	if (!assay.study.canRead( session.user ) ) {
956	flash.error = "You don't have the right authorizaton to access assay " + assay.name
957	return null
958	}
959
960	return assay
961	}
962	}

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