| 1 | <html> |
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| 2 | <head> |
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| 3 | <meta name="layout" content="main" /> |
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| 4 | <title>Processed files for assay ${assay.name} | Metagenomics | dbNP</title> |
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| 5 | |
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| 6 | <script> |
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| 7 | var assayId = ${assay.id}; |
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| 8 | </script> |
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| 9 | </head> |
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| 10 | <body> |
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| 11 | <h1> |
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| 12 | ${assay.study.name} - ${assay.name} |
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| 13 | </h1> |
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| 14 | <g:if test="${matchedFiles.size() > 0}"> |
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| 15 | <h2>Match files with samples</h2> |
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| 16 | <% |
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| 17 | def sortedSamples = assay.assaySamples.sort() { a,b -> a.sample.name <=> b.sample.name } |
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| 18 | def sortedRuns = assay.runs.sort() { a,b -> a.name <=> b.name } |
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| 19 | %> |
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| 20 | <g:form name="saveProcessedFiles" action="saveProcessedFiles" id="${assay.id}"> |
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| 21 | <table> |
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| 22 | <thead> |
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| 23 | <tr> |
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| 24 | <th></th> |
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| 25 | <th>Fasta file</th> |
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| 26 | <th># sequences</th> |
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| 27 | <th>Qual file</th> |
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| 28 | <th>Sample</th> |
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| 29 | <th>Run</th> |
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| 30 | </tr> |
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| 31 | </thead> |
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| 32 | |
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| 33 | <g:each in="${matchedFiles}" var="file" status="i"> |
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| 34 | <tr> |
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| 35 | <td> |
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| 36 | <g:hiddenField name="file.${i}.fasta" value="${file.fasta.filename}" /> |
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| 37 | <g:checkBox name="file.${i}.include" value="${true}" /> |
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| 38 | </td> |
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| 39 | <td class="name">${file.fasta.originalfilename}</td> |
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| 40 | <td class="sequences">${file.fasta.numSequences}</td> |
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| 41 | <td> |
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| 42 | <g:if test="${file.feasibleQuals?.size()}"> |
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| 43 | <g:select name="file.${i}.qual" from="${file.feasibleQuals}" optionKey="filename" optionValue="originalfilename" value="${file.qual?.filename}" noSelection="['': '- No qual file -']"/> |
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| 44 | </g:if> |
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| 45 | <g:else> |
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| 46 | No qual file available |
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| 47 | </g:else> |
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| 48 | </td> |
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| 49 | <td> |
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| 50 | <g:if test="${sortedSamples.size()}"> |
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| 51 | <select name="file.${i}.assaySample"> |
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| 52 | <g:each in="${sortedSamples}" var="assaySample"> |
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| 53 | <option |
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| 54 | <g:if test="${file.assaySample?.id == assaySample.id}"> |
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| 55 | selected="selected" |
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| 56 | </g:if> |
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| 57 | value="${assaySample.id}">${assaySample.sample.name}</option> |
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| 58 | </g:each> |
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| 59 | </select> |
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| 60 | </g:if> |
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| 61 | <g:else> |
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| 62 | No samples available. |
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| 63 | </g:else> |
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| 64 | </td> |
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| 65 | <td> |
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| 66 | <g:if test="${sortedRuns.size()}"> |
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| 67 | <select name="file.${i}.run"> |
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| 68 | <g:each in="${sortedRuns}" var="run"> |
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| 69 | <option |
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| 70 | <g:if test="${selectedRun?.toLong() == run.id}"> |
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| 71 | selected="selected" |
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| 72 | </g:if> |
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| 73 | value="${run.id}">${run.name}</option> |
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| 74 | </g:each> |
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| 75 | </select> |
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| 76 | </g:if> |
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| 77 | <g:else> |
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| 78 | No runs available. |
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| 79 | </g:else> |
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| 80 | </td> |
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| 81 | </tr> |
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| 82 | </g:each> |
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| 83 | |
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| 84 | </table> |
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| 85 | |
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| 86 | <input type="submit" value="Continue"> |
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| 87 | </g:form> |
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| 88 | |
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| 89 | </g:if> |
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| 90 | <g:else> |
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| 91 | <h2>Uploaded files</h2> |
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| 92 | <p> |
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| 93 | ${parsedFiles.success?.size()} files were successfully uploaded, but no FASTA file could be determined. Please |
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| 94 | upload at least one FASTA file. |
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| 95 | </p> |
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| 96 | </g:else> |
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| 97 | |
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| 98 | <g:if test="${parsedFiles.failure?.size()}"> |
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| 99 | <h2>Failure</h2> |
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| 100 | <p> |
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| 101 | The following files could not be correctly imported. The system can only interpret FASTA and QUAL files.<br /> |
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| 102 | If these files were intended to be included into the system, please check the messages below. |
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| 103 | </p> |
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| 104 | <ul> |
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| 105 | <g:each in="${parsedFiles.failure}" var="file"> |
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| 106 | <li> |
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| 107 | ${file.originalfilename}: |
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| 108 | ${file.message} |
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| 109 | </li> |
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| 110 | </g:each> |
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| 111 | </ul> |
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| 112 | </g:if> |
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| 113 | |
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| 114 | <p> |
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| 115 | <g:link controller="assay" action="show" id="${assay.id}">Return to assay</g:link> |
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| 116 | </p> |
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| 117 | </body> |
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| 118 | </html> |
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