| 1 | <html> |
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| 2 | <head> |
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| 3 | <title>Generic Study Capture Framework</title> |
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| 4 | <meta property="og:title" content="Generic Study Capture Framework"/> |
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| 5 | <meta property="og:description" content="A generic tool for planning scientific studies, and capturing study meta-data, integrating with analysis platform(s) / LIMS systems and searching relevant studies."/> |
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| 6 | <meta name="layout" content="main"/> |
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| 7 | <g:if test="${showstats}"><script type="text/javascript" src="${resource(dir: 'js', file: 'highcharts.js')}"></script></g:if> |
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| 8 | <script type="text/javascript" src="${resource(dir: 'js', file: 'jquery.ui.autocomplete.html.js', plugin: 'gdt')}"></script> |
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| 9 | <script type="text/javascript"> |
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| 10 | $(document).ready(function() { |
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| 11 | <g:if test="${showstats}"> |
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| 12 | Highcharts.theme = { colors: ['#4572A7'] }; |
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| 13 | var highchartsOptions = Highcharts.getOptions(); |
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| 14 | var studiesPieChart, dailyStatistics; |
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| 15 | |
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| 16 | studiesPieChart = new Highcharts.Chart({ |
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| 17 | chart: { |
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| 18 | renderTo: 'studies-pie', |
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| 19 | plotBackgroundColor: null, |
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| 20 | plotBorderWidth: null, |
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| 21 | plotShadow: false |
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| 22 | }, |
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| 23 | title: { |
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| 24 | text: '${studyCount} Studies' |
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| 25 | }, |
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| 26 | tooltip: { |
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| 27 | formatter: function() { |
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| 28 | return '<b>' + this.point.name + '</b>: ' + this.y + ' ' + ((this.y == 1) ? 'study' : 'studies'); |
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| 29 | } |
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| 30 | }, |
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| 31 | plotOptions: { |
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| 32 | pie: { |
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| 33 | allowPointSelect: true, |
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| 34 | cursor: 'pointer', |
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| 35 | dataLabels: { |
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| 36 | enabled: true, |
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| 37 | color: Highcharts.theme.textColor || '#000000', |
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| 38 | connectorColor: Highcharts.theme.textColor || '#000000', |
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| 39 | formatter: function() { |
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| 40 | return '<b>' + this.point.name + '</b>: ' + this.y + ' ' + ((this.y == 1) ? 'study' : 'studies'); |
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| 41 | } |
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| 42 | } |
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| 43 | } |
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| 44 | }, |
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| 45 | series: [ |
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| 46 | { |
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| 47 | type: 'pie', |
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| 48 | name: 'Your statistics',<sec:ifLoggedIn> |
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| 49 | size: '45%', |
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| 50 | innerSize: '25%', |
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| 51 | </sec:ifLoggedIn><sec:ifNotLoggedIn> |
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| 52 | innerSize: '45%', |
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| 53 | </sec:ifNotLoggedIn> |
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| 54 | data: [ |
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| 55 | { name: 'Public', y: ${publicStudyCount}, color: '#89A54E' }, |
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| 56 | { name: 'Private', y: ${privateStudyCount}, color: '#AA4643' } |
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| 57 | ], |
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| 58 | dataLabels: { |
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| 59 | enabled: <sec:ifLoggedIn>false</sec:ifLoggedIn><sec:ifNotLoggedIn>true</sec:ifNotLoggedIn>, |
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| 60 | } |
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| 61 | }, |
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| 62 | { |
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| 63 | type: 'pie', |
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| 64 | name: 'Your statistics',<sec:ifLoggedIn> |
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| 65 | size: '25%', |
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| 66 | innerSize: '10%', |
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| 67 | </sec:ifLoggedIn><sec:ifNotLoggedIn> |
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| 68 | size: '45%', |
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| 69 | </sec:ifNotLoggedIn> |
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| 70 | data: [ |
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| 71 | { name: 'Published public', y: ${publishedPublicStudyCount}, color: '#89A54E' }, |
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| 72 | { name: 'Unpublished Public', y: ${unPublishedPublicStudyCount}, color: '#bbc695' }, |
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| 73 | { name: 'Published Private', y: ${publishedPrivateStudyCount}, color: '#AA4643' }, |
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| 74 | { name: 'Unpublished Private', y: ${unPublishedPrivateStudyCount}, color: '#ae6e6c' } |
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| 75 | ], |
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| 76 | dataLabels: { |
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| 77 | enabled: false |
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| 78 | } |
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| 79 | } |
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| 80 | <sec:ifLoggedIn> |
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| 81 | , |
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| 82 | { |
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| 83 | type: 'pie', |
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| 84 | name: 'Total statistics', |
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| 85 | |
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| 86 | innerSize: '45%', |
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| 87 | data: [ |
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| 88 | { name: 'Read only', y: ${readOnlyStudyCount}, color: '#80699B' }, |
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| 89 | { name: 'Readable & writable', y: ${readWriteStudyCount}, color: '#89A54E' }, |
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| 90 | { name: 'Not accessible', y: ${noAccessStudyCount}, color: '#AA4643' } |
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| 91 | ], |
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| 92 | dataLabels: { |
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| 93 | enabled: true |
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| 94 | } |
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| 95 | }, |
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| 96 | </sec:ifLoggedIn> |
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| 97 | ] |
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| 98 | }); |
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| 99 | |
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| 100 | <g:if test="${startDate && dailyStatistics?.size()}"> |
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| 101 | dailyStatistics = new Highcharts.Chart({ |
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| 102 | chart: { |
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| 103 | renderTo: 'daily-statistics', |
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| 104 | zoomType: 'x', |
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| 105 | spacingRight: 20 |
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| 106 | }, |
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| 107 | title: { |
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| 108 | text: 'Users, studies and templates' |
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| 109 | }, |
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| 110 | subtitle: { |
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| 111 | text: document.ontouchstart === undefined ? |
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| 112 | 'Click and drag in the plot area to zoom in' : |
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| 113 | 'Drag your finger over the plot to zoom in' |
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| 114 | }, |
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| 115 | xAxis: { |
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| 116 | type: 'datetime', |
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| 117 | maxZoom: 14 * 24 * 3600000, // fourteen days |
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| 118 | title: { |
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| 119 | text: null |
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| 120 | } |
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| 121 | }, |
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| 122 | yAxis: { |
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| 123 | title: { |
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| 124 | text: 'Total' |
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| 125 | }, |
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| 126 | min: 0, |
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| 127 | startOnTick: false, |
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| 128 | showFirstLabel: false |
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| 129 | }, |
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| 130 | tooltip: { |
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| 131 | shared: true |
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| 132 | }, |
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| 133 | legend: { |
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| 134 | enabled: false |
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| 135 | }, |
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| 136 | plotOptions: { |
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| 137 | area: { |
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| 138 | |
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| 139 | lineWidth: 1, |
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| 140 | marker: { |
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| 141 | enabled: false, |
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| 142 | states: { |
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| 143 | hover: { |
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| 144 | enabled: true, |
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| 145 | radius: 5 |
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| 146 | } |
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| 147 | } |
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| 148 | }, |
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| 149 | shadow: false, |
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| 150 | states: { |
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| 151 | hover: { |
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| 152 | lineWidth: 1 |
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| 153 | } |
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| 154 | } |
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| 155 | } |
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| 156 | }, |
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| 157 | |
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| 158 | series: [ |
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| 159 | { |
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| 160 | type: 'area', |
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| 161 | name: 'Studies', |
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| 162 | pointInterval: 24 * 3600 * 1000, |
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| 163 | pointStart: Date.UTC(${startDate.year+1900}, ${startDate.month}, ${startDate.date}), |
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| 164 | data: [ |
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| 165 | <g:each var="day" in="${dailyStatistics}">${day.value.studyTotal},</g:each> |
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| 166 | ] |
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| 167 | }, |
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| 168 | { |
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| 169 | type: 'area', |
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| 170 | name: 'Templates', |
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| 171 | pointInterval: 24 * 3600 * 1000, |
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| 172 | pointStart: Date.UTC(${startDate.year+1900}, ${startDate.month}, ${startDate.date}), |
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| 173 | data: [ |
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| 174 | <g:each var="day" in="${dailyStatistics}">${day.value.templateTotal},</g:each> |
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| 175 | ] |
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| 176 | }, |
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| 177 | { |
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| 178 | type: 'area', |
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| 179 | name: 'Users', |
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| 180 | pointInterval: 24 * 3600 * 1000, |
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| 181 | pointStart: Date.UTC(${startDate.year+1900}, ${startDate.month}, ${startDate.date}), |
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| 182 | data: [ |
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| 183 | <g:each var="day" in="${dailyStatistics}">${day.value.userTotal},</g:each> |
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| 184 | ] |
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| 185 | } |
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| 186 | ] |
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| 187 | }); |
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| 188 | </g:if> |
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| 189 | </g:if> |
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| 190 | var quickSearch = $("#search_term"); |
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| 191 | quickSearch.autocomplete({ |
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| 192 | minLength: 2, |
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| 193 | delay: 300, |
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| 194 | search: function(event, ui) { |
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| 195 | quickSearch.css({ 'background': 'url(${resource(dir: 'images', file: 'spinner.gif')}) no-repeat left top' }); |
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| 196 | }, |
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| 197 | source: function(request, response) { |
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| 198 | quickSearch.css({ 'background': 'none' }); |
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| 199 | |
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| 200 | $.ajax({ |
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| 201 | //url: "http://ws.geonames.org/searchJSON", |
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| 202 | url: "${createLink(action:'ajaxQuickSearch')}", |
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| 203 | dataType: "jsonp", |
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| 204 | data: { |
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| 205 | featureClass: "P", |
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| 206 | style: "full", |
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| 207 | maxRows: 12, |
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| 208 | name_startsWith: request.term |
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| 209 | }, |
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| 210 | success: function(data) { |
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| 211 | response($.map(data.data, function(item) { |
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| 212 | return { |
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| 213 | label : '<span class="about">'+item.category+'</div> <span class="from">'+item.name+'</span>', |
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| 214 | value : item.link |
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| 215 | } |
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| 216 | })); |
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| 217 | } |
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| 218 | }); |
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| 219 | }, |
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| 220 | minLength: 2, |
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| 221 | select: function(event, ui) { |
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| 222 | // redirect ? |
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| 223 | if (ui.item.value) { |
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| 224 | // hide, so the URL does not show in the input field |
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| 225 | quickSearch.css( { 'display': 'none' } ); |
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| 226 | |
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| 227 | // and redirect |
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| 228 | window.location = ui.item.value; |
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| 229 | } |
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| 230 | }, |
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| 231 | open: function() { |
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| 232 | $(this).removeClass("ui-corner-all").addClass("ui-corner-top"); |
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| 233 | }, |
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| 234 | close: function() { |
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| 235 | $(this).removeClass("ui-corner-top").addClass("ui-corner-all"); |
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| 236 | }, |
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| 237 | html: true |
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| 238 | }); |
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| 239 | }); |
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| 240 | </script> |
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| 241 | <style type="text/css"> |
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| 242 | #simpleQuery { |
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| 243 | } |
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| 244 | |
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| 245 | #simpleQuery .search { |
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| 246 | display: block; |
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| 247 | height: 30px; |
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| 248 | margin-bottom: 10px; |
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| 249 | zoom: 1; /* IE 6 & 7 hack */ |
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| 250 | *display: inline; /* IE 6 & 7 hack */ |
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| 251 | } |
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| 252 | |
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| 253 | #simpleQuery .search .begin { |
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| 254 | margin: 0px; |
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| 255 | padding: 0px; |
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| 256 | display: inline-block; |
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| 257 | background-image: url(${resource(dir: 'images', file: 'simpleQuery/spotlight-begin.png')}); |
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| 258 | height: 30px; |
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| 259 | width: 140px; |
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| 260 | vertical-align: top; |
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| 261 | text-align: right; |
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| 262 | zoom: 1; /* IE 6 & 7 hack */ |
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| 263 | *display: inline; /* IE 6 & 7 hack */ |
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| 264 | } |
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| 265 | |
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| 266 | #simpleQuery .search .begin .label { |
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| 267 | color: #fff; |
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| 268 | font-face: Arial; |
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| 269 | line-height: 30px; |
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| 270 | text-shadow: 0px 0px 1px #006DBA; |
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| 271 | font-size: 12px; |
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| 272 | margin-right: 23px; |
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| 273 | } |
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| 274 | |
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| 275 | #simpleQuery .search .middle { |
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| 276 | margin: 0px 0px -20px 0px; |
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| 277 | padding: 0; |
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| 278 | display: inline-block; |
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| 279 | background-image: url(${resource(dir: 'images', file: 'simpleQuery/spotlight-middle.png')}); |
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| 280 | height: 30px; |
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| 281 | width: 300px; |
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| 282 | vertical-align: top; |
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| 283 | zoom: 1; /* IE 6 & 7 hack */ |
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| 284 | *display: inline; /* IE 6 & 7 hack */ |
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| 285 | } |
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| 286 | |
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| 287 | #simpleQuery .search .searchfield { |
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| 288 | vertical-align: middle; |
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| 289 | width: 100%; |
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| 290 | height: 100%; |
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| 291 | color: #006DBA; |
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| 292 | border-width: 0px; |
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| 293 | border: none; |
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| 294 | background-color: Transparent; |
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| 295 | zoom: 1; /* IE 6 & 7 hack */ |
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| 296 | *display: inline; /* IE 6 & 7 hack */ |
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| 297 | } |
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| 298 | |
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| 299 | #simpleQuery .search .end { |
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| 300 | margin: 0px; |
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| 301 | padding: 0px; |
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| 302 | display: inline-block; |
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| 303 | background-image: url(${resource(dir: 'images', file: 'simpleQuery/spotlight-end.png')}); |
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| 304 | height: 30px; |
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| 305 | width: 28px; |
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| 306 | zoom: 1; /* IE 6 & 7 hack */ |
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| 307 | *display: inline; /* IE 6 & 7 hack */ |
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| 308 | } |
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| 309 | |
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| 310 | </style> |
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| 311 | </head> |
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| 312 | <body> |
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| 313 | |
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| 314 | <div style="clear:both;display:block;"> |
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| 315 | <div style="margin:2px;width:476px;display:inline-block;float:left;zoom:1;*display:inline;"> |
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| 316 | <h1>Introduction</h1> |
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| 317 | <p> |
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| 318 | The phenotype database (dbNP) is an application that can store any biological study. It contains |
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| 319 | templates which makes it possible to customize |
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| 320 | </p> |
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| 321 | <p> |
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| 322 | In order to allow flexibility to capture all information you require within a study, <i>and</i> to |
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| 323 | make it possible to compare studies or study data, the system uses customizable templates and ontologies. |
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| 324 | It is especially designed to store complex study designs including cross-over designs and challenges. |
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| 325 | </p> |
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| 326 | <p> |
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| 327 | The application facilitates sharing of data within a research group or consortium, as the study owner can |
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| 328 | decide who can view or access the data. In addition, the application can stimulate collaborations by making |
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| 329 | study information publically visible. New studies can be based on study data within the database, as |
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| 330 | standardized storage is stimulated by the system. |
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| 331 | </p> |
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| 332 | </div> |
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| 333 | <div style="margin:2px;width:476px;display:inline-block;float:left;zoom:1;*display:inline;"> |
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| 334 | <h1>Quicksearch</h1> |
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| 335 | <div id="simpleQuery" class="simplequery"> |
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| 336 | <g:form action="pages" name="simpleQueryForm" id="simpleQueryForm"> |
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| 337 | <g:if test="${search_term}"><g:set var="preterm" value="${search_term}"/></g:if> |
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| 338 | <div class="searchContainer"> |
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| 339 | <div class="search"> |
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| 340 | <div class="begin"><span class="label">Search term</span></div><div class="middle"><g:textField name="search_term" id="search_term" class="searchfield" value="${preterm}"/></div><div class="end"><a onClick="$('#search_term').val('');"><img src="${resource(dir: 'images', file: 'simpleQuery/spotlight-end.png')}" value="Reset" alt="Reset" border="0"></a></div> |
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| 341 | </div> |
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| 342 | <span style="font-style:italic;color:#aaa;font-size:10px;">more advanced searches can be performed <g:link controller="advancedQuery">here</g:link>...</span> |
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| 343 | </div> |
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| 344 | </g:form> |
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| 345 | <h1>Quick Start</h1> |
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| 346 | <p> |
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| 347 | Through the <i>studies</i> menu you can either <i>create</i>, <i>view</i> or <i>import</i> studies |
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| 348 | (or study data). '<g:link controller="studyWizard" action="index" params="[jump:'create']">Create a new study</g:link>' will guide you through several steps to include your study |
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| 349 | into the system where question marks (<img src="${fam.icon(name: 'help')}">) will explain what information is |
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| 350 | required. You can (quick)save your study to complete it at another point in time, or use |
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| 351 | <i>import study data</i> to import large datasets (for example: many subjects) from an excel sheet |
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| 352 | into your study. Several data-types of different platforms (assays) can |
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| 353 | be linked to your study, like <i>simple assays</i> (e.g. clinical chemistry or Western blot) |
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| 354 | or <i>metabolomics</i>. |
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| 355 | </p> |
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| 356 | </div> |
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| 357 | </div> |
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| 358 | </div> |
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| 359 | |
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| 360 | <g:if test="${showstats}"> |
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| 361 | <div style="clear:both;display:block;padding-top:10px;"> |
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| 362 | <h1>Usage Statistics</h1> |
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| 363 | <div id="graphs" style="display:block;border:1px solid #6c6f70;width:100%;height:300px;"> |
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| 364 | <div id="studies-pie" style="margin:2px;width:476px;height:296px;display:inline-block;float:left;zoom:1;*display:inline;"></div> |
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| 365 | <div id="daily-statistics" style="margin:2px;width:476px;height:296px;display:inline-block;float:left;zoom:1;*display:inline;"></div> |
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| 366 | </div> |
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| 367 | </div> |
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| 368 | </g:if> |
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| 369 | |
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| 370 | </body> |
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| 371 | </html> |
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