[697] | 1 | package dbnp.studycapturing |
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| 2 | |
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| 3 | class AssayController { |
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| 4 | |
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[1261] | 5 | def assayService |
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| 6 | def authenticationService |
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| 7 | |
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[697] | 8 | static allowedMethods = [save: "POST", update: "POST", delete: "POST"] |
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| 9 | |
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| 10 | def index = { |
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| 11 | redirect(action: "list", params: params) |
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| 12 | } |
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| 13 | |
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| 14 | def list = { |
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| 15 | params.max = Math.min(params.max ? params.int('max') : 10, 100) |
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| 16 | [assayInstanceList: Assay.list(params), assayInstanceTotal: Assay.count()] |
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| 17 | } |
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| 18 | |
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| 19 | def create = { |
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| 20 | def assayInstance = new Assay() |
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| 21 | assayInstance.properties = params |
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| 22 | return [assayInstance: assayInstance] |
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| 23 | } |
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| 24 | |
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| 25 | def save = { |
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| 26 | def assayInstance = new Assay(params) |
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| 27 | |
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| 28 | // The following lines deviate from the generate-all generated code. |
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| 29 | // See http://jira.codehaus.org/browse/GRAILS-3783 for why we have this shameful workaround... |
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| 30 | def study = assayInstance.parent |
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| 31 | study.addToAssays(assayInstance) |
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| 32 | |
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| 33 | if (assayInstance.save(flush: true)) { |
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| 34 | flash.message = "${message(code: 'default.created.message', args: [message(code: 'assay.label', default: 'Assay'), assayInstance.id])}" |
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| 35 | redirect(action: "show", id: assayInstance.id) |
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| 36 | } |
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| 37 | else { |
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| 38 | render(view: "create", model: [assayInstance: assayInstance]) |
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| 39 | } |
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| 40 | } |
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| 41 | |
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| 42 | def show = { |
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| 43 | def assayInstance = Assay.get(params.id) |
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| 44 | if (!assayInstance) { |
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| 45 | flash.message = "${message(code: 'default.not.found.message', args: [message(code: 'assay.label', default: 'Assay'), params.id])}" |
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| 46 | redirect(action: "list") |
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| 47 | } |
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| 48 | else { |
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| 49 | [assayInstance: assayInstance] |
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| 50 | } |
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| 51 | } |
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| 52 | |
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[942] | 53 | def showByToken = { |
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[1440] | 54 | def assayInstance = Assay.findByAssayUUID(params.id) |
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[942] | 55 | if (!assayInstance) { |
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| 56 | flash.message = "${message(code: 'default.not.found.message', args: [message(code: 'assay.label', default: 'Assay'), params.id])}" |
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| 57 | redirect(action: "list") |
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| 58 | } |
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| 59 | else { |
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| 60 | redirect(action: "show", id: assayInstance.id) |
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| 61 | } |
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| 62 | } |
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| 63 | |
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[697] | 64 | def edit = { |
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| 65 | def assayInstance = Assay.get(params.id) |
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| 66 | if (!assayInstance) { |
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| 67 | flash.message = "${message(code: 'default.not.found.message', args: [message(code: 'assay.label', default: 'Assay'), params.id])}" |
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| 68 | redirect(action: "list") |
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| 69 | } |
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| 70 | else { |
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| 71 | return [assayInstance: assayInstance] |
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| 72 | } |
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| 73 | } |
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| 74 | |
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| 75 | def update = { |
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| 76 | def assayInstance = Assay.get(params.id) |
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| 77 | if (assayInstance) { |
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| 78 | if (params.version) { |
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| 79 | def version = params.version.toLong() |
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| 80 | if (assayInstance.version > version) { |
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| 81 | |
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| 82 | 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") |
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| 83 | render(view: "edit", model: [assayInstance: assayInstance]) |
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| 84 | return |
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| 85 | } |
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| 86 | } |
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| 87 | assayInstance.properties = params |
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| 88 | if (!assayInstance.hasErrors() && assayInstance.save(flush: true)) { |
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| 89 | flash.message = "${message(code: 'default.updated.message', args: [message(code: 'assay.label', default: 'Assay'), assayInstance.id])}" |
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| 90 | redirect(action: "show", id: assayInstance.id) |
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| 91 | } |
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| 92 | else { |
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| 93 | render(view: "edit", model: [assayInstance: assayInstance]) |
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| 94 | } |
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| 95 | } |
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| 96 | else { |
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| 97 | flash.message = "${message(code: 'default.not.found.message', args: [message(code: 'assay.label', default: 'Assay'), params.id])}" |
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| 98 | redirect(action: "list") |
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| 99 | } |
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| 100 | } |
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| 101 | |
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| 102 | def delete = { |
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| 103 | def assayInstance = Assay.get(params.id) |
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| 104 | if (assayInstance) { |
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| 105 | try { |
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| 106 | assayInstance.delete(flush: true) |
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| 107 | flash.message = "${message(code: 'default.deleted.message', args: [message(code: 'assay.label', default: 'Assay'), params.id])}" |
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| 108 | redirect(action: "list") |
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| 109 | } |
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| 110 | catch (org.springframework.dao.DataIntegrityViolationException e) { |
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| 111 | flash.message = "${message(code: 'default.not.deleted.message', args: [message(code: 'assay.label', default: 'Assay'), params.id])}" |
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| 112 | redirect(action: "show", id: params.id) |
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| 113 | } |
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| 114 | } |
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| 115 | else { |
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| 116 | flash.message = "${message(code: 'default.not.found.message', args: [message(code: 'assay.label', default: 'Assay'), params.id])}" |
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| 117 | redirect(action: "list") |
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| 118 | } |
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| 119 | } |
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[1261] | 120 | |
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| 121 | /** |
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| 122 | * Shows a page where an assay from a study can be selected |
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| 123 | * |
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| 124 | * @param none |
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| 125 | */ |
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| 126 | def selectAssay = { |
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| 127 | def user = authenticationService.getLoggedInUser() |
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| 128 | def studies = Study.findAllByOwner(user) |
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| 129 | def assays = Assay.findAllByParent(studies[0]) |
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| 130 | |
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| 131 | [userStudies: studies, assays: assays] |
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| 132 | } |
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| 133 | |
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| 134 | /** |
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| 135 | * Exports all assay information as an Excel file. |
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| 136 | * |
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| 137 | * @param params.id Assay id |
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| 138 | */ |
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| 139 | def exportAssayAsExcel = { |
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| 140 | |
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[1425] | 141 | Assay assay = Assay.get(params.assayId) |
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| 142 | |
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[1261] | 143 | if (!assay) { |
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[1425] | 144 | flash.errorMessage = "No assay found with id: $params.assayId." |
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[1261] | 145 | redirect action: 'selectAssay' |
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| 146 | return |
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| 147 | } |
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| 148 | |
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[1425] | 149 | try { |
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[1261] | 150 | |
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[1425] | 151 | def assayData = assayService.collectAssayData(assay, grailsApplication.config.modules.metabolomics.url) |
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[1261] | 152 | |
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[1425] | 153 | def filename = 'export.xlsx' |
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| 154 | response.setHeader("Content-disposition", "attachment;filename=\"${filename}\"") |
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| 155 | response.setContentType("application/octet-stream") |
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[1261] | 156 | |
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[1425] | 157 | assayService.exportColumnWiseDataToExcelFile(assayData, response.outputStream) |
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[1261] | 158 | |
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[1425] | 159 | } catch (Exception e) { |
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[1261] | 160 | |
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[1425] | 161 | flash.errorMessage = e.toString() |
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| 162 | redirect action: 'selectAssay' |
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[1261] | 163 | |
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| 164 | } |
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| 165 | } |
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[697] | 166 | } |
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