1 | <html> |
---|
2 | <head> |
---|
3 | <meta name="layout" content="main" /> |
---|
4 | <title>Show run ${run.name} | Mass Sequencing | dbNP</title> |
---|
5 | |
---|
6 | <link rel="stylesheet" href="<g:resource dir="css" file="showAssay.css" />" type="text/css"/> |
---|
7 | <link rel="stylesheet" href="<g:resource dir="css" file="fileuploader.new.css" />" type="text/css"/> |
---|
8 | |
---|
9 | <g:javascript src="jquery.ui.tabbeddialog.js" /> |
---|
10 | <g:javascript src="addFilesDialog.js" /> |
---|
11 | <g:javascript src="editSampleDialog.js" /> |
---|
12 | <g:javascript src="enterTagsDialog.js" /> |
---|
13 | |
---|
14 | <g:javascript src="run.show.enterTagsDialog.js" /> |
---|
15 | <g:javascript src="run.show.assayDialog.js" /> |
---|
16 | <g:javascript src="run.show.runDialog.js" /> |
---|
17 | <g:javascript src="run.show.addSamplesDialog.js" /> |
---|
18 | <g:javascript src="showSampleDialogUniversal.js" /> |
---|
19 | |
---|
20 | <g:javascript src="assay.show.showRunDialog.js" /> |
---|
21 | |
---|
22 | <g:javascript src="fileuploads.new.js" /> |
---|
23 | |
---|
24 | <script> |
---|
25 | var runId = ${run.id}; |
---|
26 | var numOtherAssays = ${otherAssays.size()}; |
---|
27 | |
---|
28 | // Create a variable with assay names to check for existing names |
---|
29 | var runNames = []; |
---|
30 | <g:each in="${allRuns}" var="currentrun"> |
---|
31 | runNames[ runNames.length ] = {id: ${currentrun.id}, name: '${currentrun.name}', alreadyAdded: false }; |
---|
32 | </g:each> |
---|
33 | |
---|
34 | function initializeUploadedFiles( selector ) { |
---|
35 | if( selector == undefined ) |
---|
36 | selector = ""; |
---|
37 | |
---|
38 | $( selector + ' .uploadedFile').each( function( idx, el ) { |
---|
39 | $(el).html( createFileHTML( $(el).text(), 'getPermanent' ) ); |
---|
40 | }); |
---|
41 | } |
---|
42 | |
---|
43 | // Initializefiles on load |
---|
44 | $(function() { initializeUploadedFiles(); }); |
---|
45 | </script> |
---|
46 | </head> |
---|
47 | <body> |
---|
48 | <h1> |
---|
49 | Run ${run.name} |
---|
50 | </h1> |
---|
51 | |
---|
52 | <div id="editRunDialog" class="dialog"></div> |
---|
53 | <div id="editSampleDialog" class="dialog"></div> |
---|
54 | |
---|
55 | <div class="blok_data"> |
---|
56 | <label>Run</label>: ${run.name}<br /> |
---|
57 | <label>Date</label>: <g:formatDate format="dd-MM-yyyy" date="${run.date}"/><br /> |
---|
58 | <label>Supplier</label>: ${run.supplier}<br /> |
---|
59 | <label>Machine</label>: ${run.machine}<br /> |
---|
60 | <label>Parameters</label>: <g:uploadedFile value="${run.parameterFile}" /><br /> |
---|
61 | </div> |
---|
62 | <div class="blok_data"> |
---|
63 | <label># assays</label>: ${run.assays?.size()} |
---|
64 | <% def numHidden = run.assays?.findAll { !it.study.canRead( session.user ) }.size() ; %> |
---|
65 | <g:if test="${numHidden}"> |
---|
66 | (${numHidden} |
---|
67 | <a href="#" onClick="alert( '${numHidden} assay(s) from this run are hidden because you don\'t have the right permissions to view them.' ); return false;"> |
---|
68 | hidden</a>) |
---|
69 | </g:if> |
---|
70 | <br /> |
---|
71 | |
---|
72 | <label># samples</label>: ${run.assaySamples?.size()} |
---|
73 | <% numHidden = run.assaySamples?.findAll { !it.assay?.study.canRead( session.user ) }.size() ; %> |
---|
74 | <g:if test="${numHidden}"> |
---|
75 | (${numHidden} |
---|
76 | <a href="#" onClick="alert( '${numHidden} sample(s) from this run are hidden because you don\'t have the right permissions to view them.' ); return false;"> |
---|
77 | hidden</a>) |
---|
78 | </g:if> |
---|
79 | <br /> |
---|
80 | <label># sequences</label>: ${run.numSequences()}<br /> |
---|
81 | <label># files</label>: ${run.numFiles()}<br /> |
---|
82 | </div> |
---|
83 | <p class="options"> |
---|
84 | <a class="edit" href="#" onClick="showEditRunDialog( ${run.id} ); return false;">Edit run</a> |
---|
85 | </p> |
---|
86 | |
---|
87 | <!-- Samples --> |
---|
88 | <h2>Samples</h2> |
---|
89 | <% def assaySamples = run.assaySamples ? run.assaySamples.findAll { it.assay?.study.canRead( session.user ) }.toList().sort { it.sample.name } : []; %> |
---|
90 | <g:if test="${assaySamples.size() == 0}"> |
---|
91 | No samples found in run. |
---|
92 | </g:if> |
---|
93 | <g:else> |
---|
94 | <form id="sampleForm"><input type="hidden" name="runId" value="${run.id}" /></form> |
---|
95 | <table class="paginate" id="samples"> |
---|
96 | <thead> |
---|
97 | <tr> |
---|
98 | <th width="5" class="nonsortable"><input type="checkbox" id="checkAll" onClick="checkAllPaginated(this);" /></th> |
---|
99 | <th nowrap>name</th> |
---|
100 | <th nowrap>study</th> |
---|
101 | <th nowrap>assay</th> |
---|
102 | <th nowrap>Forward mid</th> |
---|
103 | <th nowrap># sequences</th> |
---|
104 | <th nowrap># qual</th> |
---|
105 | <th class="nonsortable"></th> |
---|
106 | <th class="nonsortable"></th> |
---|
107 | <th class="nonsortable"></th> |
---|
108 | </tr> |
---|
109 | </thead> |
---|
110 | <tbody> |
---|
111 | <g:each in="${assaySamples}" var="assaySample"> |
---|
112 | <tr> |
---|
113 | <td><g:checkBox name="ids" value="${assaySample.id}" checked="${false}" onClick="updateCheckAll(this);" /></td> |
---|
114 | <td><a href="#" onClick="showSample(${assaySample.id}, 'run'); return false;">${assaySample.sample.name}</a></td> |
---|
115 | <td>${assaySample.assay.study.name}</td> |
---|
116 | <td>${assaySample.assay.name}</td> |
---|
117 | <td>${assaySample.fwMidName}</td> |
---|
118 | <td> |
---|
119 | <g:if test="${assaySample.numSequenceFiles() > 0}"> |
---|
120 | ${assaySample.numSequences()} |
---|
121 | </g:if> |
---|
122 | <g:else> |
---|
123 | - |
---|
124 | </g:else> |
---|
125 | </td> |
---|
126 | <td> |
---|
127 | <g:if test="${assaySample.numQualityFiles() > 0}"> |
---|
128 | ${assaySample.numQualScores()} |
---|
129 | </g:if> |
---|
130 | <g:else> |
---|
131 | - |
---|
132 | </g:else> |
---|
133 | </td> |
---|
134 | <td class="button"> |
---|
135 | <g:if test="${!assaySample.assay.study.canWrite(session.user)}"> |
---|
136 | <img src="${fam.icon(name: 'pencil')}" class="disabled" title="You can't edit this sample because you don't have sufficient privileges." /> |
---|
137 | </g:if> |
---|
138 | <g:else> |
---|
139 | <a onClick="showEditSampleDialog(${assaySample.id}, 'run', ${run.id});" href="#"><img src="${fam.icon(name: 'pencil')}" /></a> |
---|
140 | </g:else> |
---|
141 | </td> |
---|
142 | <td class="button"> |
---|
143 | <g:if test="${!assaySample.assay.study.canWrite(session.user)}"> |
---|
144 | <img src="${fam.icon(name: 'application_delete')}" class="disabled" title="You can't remove this sample because you don't have sufficient privileges." /> |
---|
145 | </g:if> |
---|
146 | <g:else> |
---|
147 | <g:link onClick="return confirm( 'Are you sure you want to remove the selected sample from this run?' );" controller="run" action="removeSample" id="${run.id}" params="${[assaySampleId: assaySample.id]}" ><img src="${fam.icon(name: 'application_delete')}" /></g:link> |
---|
148 | </g:else> |
---|
149 | </td> |
---|
150 | <td class="button"> |
---|
151 | <g:if test="${assaySample.numSequences() > 0}"> |
---|
152 | <g:link controller="assaySample" action="sequenceLengthHistogram" id="${assaySample.id}"><img src="${fam.icon( name: 'chart_bar' )}" alt="Sequence length histogram" title="Sequence length histogram" /></g:link> |
---|
153 | </g:if> |
---|
154 | <g:else> |
---|
155 | <img src="${fam.icon( name: 'chart_bar' )}" class="disabled" alt="No histogram available because no sequences are uploaded." title="No histogram available because no sequences are uploaded." /> |
---|
156 | </g:else> |
---|
157 | </td> |
---|
158 | </tr> |
---|
159 | </g:each> |
---|
160 | </tbody> |
---|
161 | </table> |
---|
162 | <div id="showSampleDialog" class="dialog"></div> |
---|
163 | </g:else> |
---|
164 | <g:if test="${editable}"> |
---|
165 | <p class="options multiple"> |
---|
166 | <% def writableAssaySamples = assaySamples.findAll { it.assay.study.canWrite( session.user ) } %> |
---|
167 | <a class="addAssociation" onClick="showAddSamplesDialog(); return false;" href="#">Add samples</a><br /> |
---|
168 | |
---|
169 | <g:if test="${writableAssaySamples.size() > 0}"> |
---|
170 | <a class="editAssociation" onClick="showEnterTagsDialog(); return false;" href="#">Edit sample data</a> |
---|
171 | </g:if> |
---|
172 | <g:else> |
---|
173 | <a class="editAssociation disabled" onClick="return false;" href="#">Edit sample data</a> |
---|
174 | </g:else> |
---|
175 | |
---|
176 | <br /> |
---|
177 | |
---|
178 | <g:if test="${writableAssaySamples.size() > 0}"> |
---|
179 | <a class="removeAssociation" href="#" onClick="if( confirm( 'Are you sure you want to remove selected samples from this run?' ) ) { submitPaginatedForm( $( '#sampleForm' ), '<g:createLink controller="run" action="removeSamples" />', '#samples', 'Please select one or more samples to remove from this run' ); } return false;">Remove selected samples</a> |
---|
180 | </g:if> |
---|
181 | <g:else> |
---|
182 | <a class="removeAssociation disabled" onClick="return false;" href="#">Remove selected samples</a> |
---|
183 | </g:else> |
---|
184 | </p> |
---|
185 | <p class="options multiple"> |
---|
186 | <g:if test="${writableAssaySamples.size() == 0 || !run.assays?.size()}"> |
---|
187 | <a class="addSequences disabled" onClick="return false;" href="#">Add sequence files</a> |
---|
188 | </g:if> |
---|
189 | <g:else> |
---|
190 | <a class="addSequences" onClick="showAddFilesDialog(); return false;" href="#">Add sequence files</a> |
---|
191 | </g:else> |
---|
192 | |
---|
193 | <br /> |
---|
194 | |
---|
195 | <g:if test="${writableAssaySamples.size() > 0 && run.numFiles() > 0 }"> |
---|
196 | <a class="removeSequences" href="#" onClick="if( confirm( 'Are you sure you want to remove all sequence data from this run? Only sequences are removed from samples you have write access to.' ) ) { submitPaginatedForm( $( '#sampleForm' ), '<g:createLink controller="run" action="deleteSequenceData" />', '#samples', 'Please select one or more samples to remove sequences from.' ); } return false;">Delete selected sequences</a> |
---|
197 | </g:if> |
---|
198 | <g:else> |
---|
199 | <a class="removeSequences disabled" onClick="return false;" href="#">Delete selected sequences</a> |
---|
200 | </g:else> |
---|
201 | </p> |
---|
202 | |
---|
203 | <p class="options multiple"> |
---|
204 | <a class="fasta" href="#" onClick="submitPaginatedForm( $( '#sampleForm' ), '<g:createLink controller="assaySample" action="exportAsFasta" />', '#samples', 'Please select one or more samples to export' ); return false;">Export as fasta</a><br /> |
---|
205 | </p> |
---|
206 | |
---|
207 | <br clear="all" /> |
---|
208 | <g:if test="${writableAssaySamples.size() > 0}"> |
---|
209 | <g:render template="enterTagsDialog" model="[run: run, writableAssaySamples: writableAssaySamples]" /> |
---|
210 | <g:render template="addFilesDialog" model="[run: run]" /> |
---|
211 | </g:if> |
---|
212 | |
---|
213 | <g:render template="addSamplesDialog" model="[run: run]" /> |
---|
214 | |
---|
215 | </g:if> |
---|
216 | |
---|
217 | |
---|
218 | |
---|
219 | <!-- Runs --> |
---|
220 | <h2>Assays</h2> |
---|
221 | <g:if test="${run.assays == null || run.assays.size() == 0}"> |
---|
222 | No assay found for this run |
---|
223 | </g:if> |
---|
224 | <g:else> |
---|
225 | <table class="paginate"> |
---|
226 | <thead> |
---|
227 | <tr> |
---|
228 | <th nowrap>name</th> |
---|
229 | <th nowrap>study</th> |
---|
230 | <th nowrap># samples</th> |
---|
231 | <th nowrap>other runs</th> |
---|
232 | <th class="nonsortable"></th> |
---|
233 | </tr> |
---|
234 | </thead> |
---|
235 | <tbody> |
---|
236 | <% def assays = run.assays.findAll { it.study.canRead( session.user ) }.toList().sort { it.name }; %> |
---|
237 | <g:each in="${assays}" var="assay"> |
---|
238 | <tr> |
---|
239 | <td><g:link controller="assay" action="show" id="${assay.id}">${assay.name}</g:link></td> |
---|
240 | <td>${assay.study?.name}</td> |
---|
241 | <td>${assay.assaySamples?.size()}</td> |
---|
242 | <td> |
---|
243 | <g:if test="${assay.runs?.size() == 1}"> |
---|
244 | <% /* If only 1 run is found, then it is the current one */ %> |
---|
245 | - |
---|
246 | </g:if> |
---|
247 | <g:else> |
---|
248 | <g:each in="${assay.runs - run}" var="otherRun"> |
---|
249 | <g:link action="show" id="${otherRun.id}">${otherRun.name}</g:link><br /> |
---|
250 | </g:each> |
---|
251 | </g:else> |
---|
252 | </td> |
---|
253 | <td class="button"> |
---|
254 | <g:if test="${run.samples(assay.id).size()}"> |
---|
255 | <img src="${fam.icon(name: 'application_delete')}" class="disabled" title="You can't remove this assay because sequences from this assay are coupled to this run." /> |
---|
256 | </g:if> |
---|
257 | <g:else> |
---|
258 | <g:if test="${!assay.study.canWrite(session.user)}"> |
---|
259 | <img src="${fam.icon(name: 'application_delete')}" class="disabled" title="You can't remove this assay because you don't have sufficient privileges." /> |
---|
260 | </g:if> |
---|
261 | <g:else> |
---|
262 | <g:link onClick="return confirm( 'Are you sure you want to remove the selected assay from this run?' );" controller="run" action="removeAssay" id="${run.id}" params="${[assay_id: assay.id]}" ><img src="${fam.icon(name: 'application_delete')}" /></g:link> |
---|
263 | </g:else> |
---|
264 | </g:else> |
---|
265 | </td> |
---|
266 | </tr> |
---|
267 | </g:each> |
---|
268 | </tbody> |
---|
269 | </table> |
---|
270 | </g:else> |
---|
271 | <% def writableAssays = otherAssays.findAll { it.study.canWrite( session.user ) } %> |
---|
272 | <g:if test="${editable}"> |
---|
273 | <p class="options"> |
---|
274 | <g:if test="${writableAssays.size() > 0}"> |
---|
275 | <a class="addAssociation" href="#" onClick="showAddAssayDialog(); return false;">Add assay</a> |
---|
276 | </g:if> |
---|
277 | <g:else> |
---|
278 | <a class="addAssociation disabled" href="#" onClick="return false;">Add assay</a> |
---|
279 | </g:else> |
---|
280 | </p> |
---|
281 | <g:if test="${writableAssays.size() > 0}"> |
---|
282 | <g:render template="addAssayDialog" model="[run: run, writableAssays: writableAssays]" /> |
---|
283 | </g:if> |
---|
284 | </g:if> |
---|
285 | <div id="showRunDialog" class="dialog"></div> |
---|
286 | </body> |
---|
287 | </html> |
---|