grnsight 4.0.0 → 6.0.0

package/web-client/views/upload.jade

@@ -1,464 +0,0 @@
-doctype html
-html
-  head
-    title GRNsight
-    link(href="//netdna.bootstrapcdn.com/bootstrap/3.1.1/css/bootstrap.min.css", rel="stylesheet")
-    link(href="stylesheets/grnsight.css", rel="stylesheet")
-    link(href="stylesheets/print.css", rel="stylesheet", media="print")
-    link(href="//code.jquery.com/ui/1.10.1/themes/base/jquery-ui.css", rel="stylesheet")
-    script(src="//code.jquery.com/jquery-1.9.1.js")
-    script(src="//code.jquery.com/ui/1.10.1/jquery-ui.js")
-    script.
-      (function(i,s,o,g,r,a,m){i["GoogleAnalyticsObject"]=r;i[r]=i[r]||function(){
-          (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
-          m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
-      })(window,document,"script","//www.google-analytics.com/analytics.js","ga");
-      ga("create", "UA-54882218-1", "auto");
-
-  body
-    nav(class='navbar navbar-default' role='navigation')
-      div(class='container-fluid')
-        div(class='navbar-header')
-          button(type='button' class='navbar-toggle' data-toggle='collapse' data-target='#header-nav')
-            span(class='sr-only') Toggle Navigation
-            span(class='icon-bar')
-            span(class='icon-bar')
-            span(class='icon-bar')
-        div(class='collapse navbar-collapse' id='header-nav')
-          ul(class='nav navbar-nav')
-            li(class='dropdown')
-              a(href='#' class='dropdown-toggle' data-toggle='dropdown') File
-              ul(class='dropdown-menu' role='menu')
-                li
-                  a(class='upload' href='#' id='open-item')
-                    label(for='upload' id='open')
-                      span(class='glyphicon glyphicon-folder-open')
-                      |   Open
-                    input(type='file' name='upload' id='upload' accept='application/vnd.openxmlformats-officedocument.spreadsheetml.sheet')
-                    input(type='hidden' id='service-root' value='#{serviceRoot}')
-                li(class='startDisabled disabled')
-                  a(href='#' id='reload')
-                    span(class='glyphicon glyphicon-repeat')
-                    |   Reload
-                li(class='divider')
-                li(class='dropdown-submenu')
-                  a(href='#')
-                    span(class='glyphicon glyphicon-import')
-                    |   Import
-                  ul(class='dropdown-menu')
-                    li
-                      a(class='upload' href='#' id='importSif')
-                        label(for='upload-sif' id='import-sif') SIF…
-                        input(type='file' name='upload-sif' id='upload-sif' accept='.sif')
-                    li
-                      a(class='upload' href='#' id='importGraphMl')
-                        label(for='upload-graphml' id='import-graphml') GraphML…
-                        input(type='file' name='upload-graphml' id='upload-graphml' accept='.graphml')
-                    li(class='disabled not-yet-implemented')
-                      a(class='upload' href='#' id='importGml')
-                        label(for='upload-gml' id='import-gml') GML…
-                li(class='dropdown-submenu')
-                  a(href='#')
-                    span(class='glyphicon glyphicon-export')
-                    |   Export Data
-                  ul(class='dropdown-menu')
-                    //- Temporary hardcoded display: none pending further testing of the Excel export feature.
-                    li(class='startDisabled disabled unweighted export' style='display: none')
-                      a(href='#' id='exportAsExcelWkbk') To Excel Workbook
-                    //- Need to omit the divider too.
-                    li(class='divider' style='display: none')
-                    li(class='startDisabled disabled unweighted export')
-                      a(href='#' id='exportAsUnweightedSif') To Unweighted SIF
-                    li(class='startDisabled disabled weighted export')
-                      a(href='#' id='exportAsWeightedSif') To Weighted SIF
-                    li(class='divider')
-                    li(class='startDisabled disabled unweighted export')
-                      a(href='#' id='exportAsUnweightedGraphMl') To Unweighted GraphML
-                    li(class='startDisabled disabled weighted export')
-                      a(href='#' id='exportAsWeightedGraphMl') To Weighted GraphML
-                    li(class='divider not-yet-implemented')
-                    li(class='startDisabled disabled not-yet-implemented unweighted export')
-                      a(href='#' id='exportAsUnweightedGml') To Unweighted GML
-                    li(class='startDisabled disabled not-yet-implemented weighted export')
-                      a(href='#' id='exportAsWeightedGml') To Weighted GML
-                li(class='dropdown-submenu disabled not-yet-implemented')
-                  a(href='#')
-                    span(class='glyphicon glyphicon-picture')
-                    |   Export Image
-                  ul(class='dropdown-menu')
-                    li(class='disabled')
-                      a(href='#' id='exportAsJpg') To JPEG
-                    li(class='disabled')
-                      a(href='#' id='exportAsPdf') To PDF
-                    li(class='disabled')
-                      a(href='#' id='exportAsSvg') To SVG
-                li(class='divider')
-                li(class=' startDisabled disabled')
-                  a(href='#' id='printGraph')
-                    span(class='glyphicon glyphicon-print')
-                    |   Print
-
-            li(class='dropdown')
-              a(href='#' class='dropdown-toggle' data-toggle='dropdown') View
-              ul(class='dropdown-menu' role='menu')
-                span(class='menu-subheader') Viewport Size
-                li
-                  a(href='#' id='viewport-size-s' class='viewportOption active')
-                    span(class='glyphicon')
-                    |   Small (1104 x 648 pixels)
-                li
-                  a(href='#' id='viewport-size-m' class='viewportOption')
-                    span(class='glyphicon glyphicon-ok')
-                    |   Medium (1414 x 840 pixels)
-                li
-                  a(href='#' id='viewport-size-l' class='viewportOption')
-                    span(class='glyphicon')
-                    |   Large (1920 x 1080 pixels)
-                li
-                  a(href='#' id='viewport-size-fit' class='viewportOption')
-                    span(class='glyphicon')
-                    |   Fit To Window
-                li(class='divider')
-                li
-                  a(href='#' id='restrict-graph-to-viewport' class='viewportOption')
-                    span(class='glyphicon')
-                    |   Restrict Graph to Viewport
-                li(class='divider')
-                li(class='startDisabled disabled')
-                  a(href='#' id='zoom')
-                    span(class='glyphicon invisible')
-                    |   Zoom (1 - 200%)  
-                    input(type='number' id='zoomInput' min='1' max='200' value='100' class='zoom keepopen' aria-describedby='basic-addon1' disabled="true")
-                    span
-                    |   %
-
-            li(class='dropdown')
-              a(href='#' class='dropdown-toggle', data-toggle='dropdown') Layout
-              ul(class='dropdown-menu' role='menu')
-                span(class='menu-subheader') Graph Options
-                li
-                  a(href='#' id='gridLayout' class='layout')
-                    span(class='glyphicon')
-                    |   Grid Layout
-                  a(href='#' id='forceGraph' class='layout' checked)
-                    span(class='glyphicon glyphicon-ok')
-                    |   Force Graph
-                li(class='divider')
-                li
-                  a(href='#' id='lockSlidersMenu' class="lockSliders")
-                    span(class='glyphicon invisible')
-                    |   Lock Force Graph Parameters
-                li
-                  a(href='#' id='resetSlidersMenu' class="resetSliders")
-                    span(class='glyphicon invisible')
-                    |   Reset Force Graph Parameters
-                li(class='disabled')
-                  a(href='#' id='undoResetMenu' class="undoSliderReset")
-                    span(class='glyphicon invisible')
-                    |   Undo Reset
-                li
-                  a(href='#' id='link-distance')
-                    span(class='glyphicon invisible')
-                    |   Link Distance (1 - 1000)  
-                    input(type='number' id='link-distance-menu' class='keepopen' value='500' aria-describedby='basic-addon1')
-                  a(href='#' id='charge')
-                    span(class='glyphicon invisible')
-                    |   Charge (-2000 - 0)  
-                    input(type='number' id='charge-menu' class='keepopen' value='-50' aria-describedby='basic-addon1')
-
-
-            li(class='dropdown')
-              a(href='#' class='dropdown-toggle' data-toggle='dropdown') Node
-              ul(class='dropdown-menu' role='menu')
-                li(class='node-coloring-menu disabled')
-                  a(href='#' id='node-coloring-toggle-menu' class='nodeColoringToggle')
-                    span(class='glyphicon')
-                    |   Disable Node Coloring
-                li(class='divider')
-                li(class='node-coloring-menu dropdown-submenu disabled')
-                  a(href='#')
-                    span(class='glyphicon invisible')
-                    |   Select Top Dataset
-                  ul(class='dropdown-menu' id='topDatasetDropdownMenu')
-                li(class='node-coloring-menu disabled')
-                  a(href='#' id='averageDataTopMenu' class='nodeColoring')
-                    span(class='glyphicon')
-                    |   Average Replicate Values for Top Dataset
-                li(class='divider')
-                li(class='node-coloring-menu dropdown-submenu disabled')
-                  a(href='#')
-                    span(class='glyphicon invisible')
-                    |   Select Bottom Dataset
-                  ul(class='dropdown-menu' id='bottomDatasetDropdownMenu')
-                li(class='node-coloring-menu disabled')
-                  a(href='#' id='averageDataBottomMenu' class='viewportOption')
-                    span(class='glyphicon')
-                    |   Average Replicate Values for Bottom Dataset
-                li(class='divider')
-                li(class='node-coloring-menu disabled')
-                  a(href='#' class='nodeOptions')
-                    span(class='glyphicon invisible')
-                    |   Log Fold Change Max Value (0.01 - 100):  
-                    input(type='number' min="0.01" max="100" id='log-fold-change-max-value-menu' class='logFoldChangeMaxValue keepopen' aria-describedby='basic-addon1')
-
-            li(class='dropdown')
-              a(href='#' class='dropdown-toggle' data-toggle='dropdown') Edge
-              ul(class='dropdown-menu')
-                li
-                  a(href='#' id='colorEdges' class='colorEdges active')
-                    span(class='glyphicon glyphicon-ok')
-                    |   Enable Formatting of Edges Based on Weight Values
-                li
-                  a(href='#' id='blackEdges' class='blackEdges')
-                    span(class='glyphicon')
-                    |   Disable Formatting of Edges Based on Weight Values
-                li(class='divider')
-                li
-                  a(href='#' id='weightsMouseOverMenu' class='weightsMouseOver' class='selected')
-                    span(class='glyphicon glyphicon-ok')
-                    |   Only Show Edge Weights With Mouse Over
-                li
-                  a(href='#' id='weightsAlwaysMenu' class='weightsAlways')
-                    span(class='glyphicon')
-                    |   Always Show Edge Weights
-                li
-                  a(href='#' id='weightsNeverMenu' class='weightsNever')
-                    span(class='glyphicon')
-                    |   Never Show Edge Weights
-                li(class='divider')
-                li(class='weightedGraphOptionsMenu disabled')
-                  a(href='#')
-                    span(class='glyphicon invisible')
-                    |   Edge Weight Normalization Factor (0.0001 - 1000)  
-                    input(type='number' id='edge-weight-normalization-factor-menu' class='keepopen' placeholder='' aria-describedby='basic-addon1')
-                  a(href='#' id='reset-normalization-factor-menu')
-                    span(class='glyphicon invisible')
-                    |   Reset Edge Weight Normalization Factor
-                li(class='divider')
-                li(class='weightedGraphOptionsMenu disabled')
-                  a(href='#')
-                    span(class='glyphicon invisible')
-                    |   Gray Edge Threshold (0 - 100%)  
-                    input(type='number' id='gray-edge-threshold-menu' class='keepopen' value='5' aria-describedby='basic-addon1')
-                    |   %
-                li(class='weightedGraphOptionsMenu disabled')
-                  a(href='#' id='grey-edges-dashed-menu')
-                    span(class='glyphicon')
-                    |   Show Gray Edges as Dashed
-
-            li(class='dropdown')
-              a(href='#' class='dropdown-toggle' data-toggle='dropdown') Help
-              ul(class='dropdown-menu' role='menu')
-                li
-                  a(href='//dondi.github.io/GRNsight/documentation.html#gettingStarted', target='_blank') Getting Started
-                li
-                  a(href='https://github.com/dondi/GRNsight/wiki', target='_blank') GRNsight Wiki
-                li
-                  a(href='//dondi.github.io/GRNsight/about.html', target='_blank') About GRNsight
-
-            li(class='dropdown')
-              a(href='#' class='dropdown-toggle' data-toggle='dropdown') Demo
-              ul(class='dropdown-menu' role='menu')
-                li
-                  a(href='#' id='unweighted') Demo #1: Unweighted GRN (15 genes, 28 edges, Dahlquist Lab unpublished data)
-                li
-                  a(href='#' id='weighted') Demo #2: Weighted GRN (15 genes, 28 edges, Dahlquist Lab unpublished data)
-                li
-                  a(href='#' id='schadeInput') Demo #3: Unweighted GRN (21 genes, 31 edges)
-                li
-                  a(href='#' id='schadeOutput') Demo #4: Weighted GRN (21 genes, 31 edges, Schade et al. 2004 data)
-            li
-              a(href='#' id='fileName')
-          ul(class='nav navbar-nav navbar-right graph-metadata-container')
-            li(class='navbar-text text-right')
-              small(id='graph-metadata')
-
-    div(class='container')
-      div(class='grnsight-container')
-        div(class='scale-and-scroll')
-          table(class='scrollTable')
-            tr
-              td
-              td(class='scrollBtn scrollUp')
-                  p(class='movementArrow') ↑
-              td
-            tr
-              td(class='scrollBtn scrollLeft')
-                p(class='movementArrow') ←
-              td(class='scrollBtn center')
-                p(class='movementArrow') ☼
-              td(class='scrollBtn scrollRight')
-                p(class='movementArrow') →
-            tr
-              td
-              td(class='scrollBtn scrollDown')
-                p(class='movementArrow') ↓
-              td
-
-          span(class="pull-left zoomLabel")
-            b
-              | Zoom (1 - 200%): 
-          span(class="pull-right zoomLabel" id="zoomPercent") 100%
-          br
-          table(class='zoomTable')
-            tr
-              td
-                div(class="zoomCenter")
-                input(id="zoomSlider" class="zoom" type="range" min="0" max="8" value="4" step="0.25" disabled="true")
-
-    div(class='sidebar')
-        //- Sliders should have the ID convention of -Name-Val and -Name-Input in order to work properly in the javascript
-        div(id="layout")
-          form
-            //- Value is set to empty to ensure that the MVC cycle takes care of the button’s label.
-            input(id='gridLayoutButton' type='button' class='btn btn-default btnSidebar' value='')
-        div(class="node-coloring hidden")
-            p(class='sideHeader') Node Coloring
-            input(id='nodeColoringToggle' type='button' class='btn btn-default btnSidebar nodeColoringToggle' value='Disable Node Coloring')
-            label(class='info', data-toggle='tooltip') Top Dataset
-            select(id="dataset-top")
-            form
-              input(id='averageDataTop', type='checkbox' checked)
-              label(for='averageDataTop' style='font-weight:normal') Average Replicate Values
-            label(class='info', data-toggle='tooltip') Bottom Dataset
-            select(id="dataset-bottom")
-            form
-              input(id='averageDataBottom', type='checkbox' checked)
-              label(for='averageDataBottom' style='font-weight:normal') Average Replicate Values
-            p(class='sideHeader' id="logFoldChangeMaxValue") Log Fold Change Max Value
-            p(class='sideHeader' id="logFoldChangeMaxValueRange") (0.01 - 100):  
-            input(type='number' min='1' max='100' step='1' id='log-fold-change-max-value-sidebar' class='logFoldChangeMaxValue' aria-describedby='basic-addon1')
-            span  
-            button(type="button" class='btn btn-default s' id="log-fold-change-button") Set
-            div(class="node-coloring-legend")
-        div(id="force-graph")
-          form
-            label(for='linkDistInput', class='info', data-toggle='tooltip', title='Increases/decreases the length of the edges that connect the nodes.') Link Distance (1 - 1000):
-            span(id='linkDistVal' class='forceVal') 500
-            input(class='form-control', type='range', min='1', max='1000', value='500', step='1', id='linkDistInput', name='linkDistInput')
-            label(for='chargeInput', class='info', data-toggle='tooltip', title='Increases/decreases the strength of the force that causes the nodes to repel each other.') Charge (-2000 - 0):
-            span(id='chargeVal' class='forceVal') -50
-            input(class='form-control', type='range', min='-2000', max='0', value='-50', step='1', id='chargeInput', name='chargeInput')
-          form
-            input(id='lockSlidersButton', type='checkbox', value='lockSliders' class="lockSliders")
-            label(for='lockSlidersButton' style='font-weight:normal') Lock Force Graph Parameters
-          form
-            input(id='resetSlidersButton' type='button' class='btn btn-default btnSidebar resetSliders' value='Reset Force Graph Parameters')
-            input(id='undoResetButton' type='button' class='btn btn-default btnSidebar undoSliderReset' value='Undo Reset' disabled)
-          p(id='warningMessage' data-toggle='modal' data-target='#warningsModal')
-        div(class='input-group')
-          form
-            input(type='checkbox' id='viewport' class='viewport' name='viewport' value='viewport')
-            label(for='viewport' style='font-weight:normal' class='sideLabel') Restrict graph to viewport
-            br
-            p(class='sideHeader') Viewport Size
-            input(type='radio' id='boundBoxS' class='boundBoxSize' name='size' value='containerS')
-            label(for='boundBoxS' style='font-weight:normal' class='sideLabel') Small
-            small (1104 X 648 pixels)
-            br
-            input(type='radio' id='boundBoxM' class='boundBoxSize' name='size' value='containerM')
-            label(for='boundBoxM' style='font-weight:normal' class='sideLabel') Medium
-            small (1414 X 840 pixels)
-            br
-            input(type='radio' id='boundBoxL' class='boundBoxSize' name='size' value='containerL')
-            label(for='boundBoxL' style='font-weight:normal' class='sideLabel') Large
-            small (1920 X 1080 pixels)
-            br
-            input(type='radio' id='boundBoxFit' class='boundBoxSize' name='size' value='containerFit')
-            label(for='boundBoxFit' style='font-weight:normal' class='sideLabel') Fit to window
-            br
-          form(class='weightedGraphOptions hidden')
-            p(class='sideHeader') Hide/Show Edge Weights
-            input(type='radio' id='weightsMouseOverSide' class='weightsMouseOver' name='size' class='selected' checked)
-            label(for='weightsMouseOverSide' style='font-weight:normal' class='sideLabel') Show With Mouse Over
-            <br>
-            input(type='radio' id='weightsAlwaysSide' class='weightsAlways' name='size')
-            label(for='weightsAlwaysSide' style='font-weight:normal' class='sideLabel') Always Show Edge Weights
-            <br>
-            input(type='radio' id='weightsNeverSide' class='weightsNever' name='size')
-            label(for='weightsNeverSide' style='font-weight:normal' class='sideLabel') Never Show Edge Weights
-          div(class='weightedGraphOptions hidden')
-            p(class='sideHeader' id="normLabel") Edge Weight Normalization Factor
-            p(class='sideHeader' id="normLabel") (0.0001 - 1000): &nbsp;
-            input(type='number' class='normalization-form' id='normalization-max' placeholder='maximum' aria-describedby='basic-addon1')
-            div(id='btn-side')
-              button(type="button" class='btn btn-default s' id="normalization-button") Set Factor
-              button(type='button' class='btn btn-default btn-norm' id='resetNormalizationButton') Reset Factor
-          div(class='weightedGraphOptions hidden')
-            label(id='grayLabel' for='grayThresholdInput', class='info', data-toggle='tooltip', title='Increases/decreases the threshold at which edges appear gray. Edges with normalized weight values below this percentage are shown as gray.') Gray Threshold (0 - 100%): &nbsp; &nbsp;
-            span(class='forceVal', id='grayThresholdValue') 5%
-            <br />
-            input(id='grayThresholdInput', class='form-control', type='range', min='0', max='1', value='0.05', step='0.01')
-            <br />
-            input(id='dashedGrayLineButton', type='checkbox', value='dashedGrayLine')
-            label(for='dashedGrayLineButton' style='font-weight:normal') &nbsp; Show Gray Edges as Dashed
-
-    div(class='graph-statistics-container hidden')
-      div(class='panel panel-default')
-        div(class='panel-heading' role='tab' id='graph-statistics-heading')
-          h4(class='panel-title')
-            a(role='button' data-toggle='collapse' href='#graph-statistics' aria-expanded='true') Graph Statistics
-        div(id='graph-statistics' class='panel-collapse collapse' role='tabpanel' aria-labelledby='graph-statistics-heading')
-          div(class='panel-body')
-            table(class='table table-condensed')
-              thead
-                tr
-                  th(rowspan='2')
-                  th(rowspan='2') Betweenness Centrality
-                  th(class='shortest-path-header') Shortest Path
-                tr(class='shortest-path-column-headers')
-              tbody
-
-    div(id='errorModal' class='modal fade' tab-index='-1' role='dialog' aria-labelledby='mySmallModalLabel' aria-hidden='true')
-      div(class='modal-dialog')
-        div(class='modal-content')
-          div(class='modal-header')
-            button(type='button' class='close' data-dismiss='modal' aria-label='Close')
-              span(aria-hidden='true') &times;
-            h4(class='modal-title') Error
-          div(class='modal-body')
-            p(id='error')
-          div(class='modal-footer')
-            input(type='button' class='btn btn-default' data-dismiss='modal' value='Close')
-            input(type='button' id='launchFileOpen' class='btn btn-primary' data-dismiss='modal' value='Select New File')
-
-    div(id='warningsModal' class='modal fade' tab-index='-1' role='dialog' aria-labelledby='mySmallModalLabel' aria-hidden='true')
-      div(class='modal-dialog')
-        div(class='modal-content')
-          div(class='modal-header')
-            button(type='button' class='close' data-dismiss='modal' aria-label='Close')
-              span(aria-hidden='true') &times;
-            h4(class='modal-title') Warning
-          div(class='modal-body' overflow='scroll')
-            p(id='warningIntro')
-            div(class='panel-group' id='accordion' role='tablist' aria-multiselectable='true')
-              div(class='panel panel-default')
-                div(class='panel-heading' role='tab' id='warningsHeader')
-                  h4(class='panel-title')
-                    a(data-toggle='collapse' data-parent='accordian' href='#warningsInfo' aria-expanded='true' aria-controls='warningsInfo') Warnings List
-                div(id='warningsInfo' class='panel-collapse collapse' role='tabpanel' aria-labelledby='warningsHeader')
-                  div(class='panel-body' id='list-frame')
-                    p(id='warningsList')
-
-          div(class='modal-footer')
-            input(type='button' class='btn btn-default' data-dismiss='modal' value='Close')
-            //- input(type='button' id='launchFileOpen' class='btn btn-primary' data-dismiss='modal' value='Select New File' onclick="$('#upload').click()")
-
-    div(id='importErrorModal' class='modal fade' tab-index='-1' role='dialog' aria-hidden='true')
-      div(class='modal-dialog')
-        div(class='modal-content')
-          div(class='modal-header')
-            button(type='button' class='close' data-dismiss='modal' aria-label='Close')
-              span(aria-hidden='true') &times;
-            h4(class='modal-title') Import Error
-          div(class='modal-body')
-            p The following error was encountered during the import attempt:
-            blockquote(id='importErrorMessage')
-            div Please verify that the file being imported is in the right format then try the import again.
-          div(class='modal-footer')
-            input(type='button' class='btn btn-default' data-dismiss='modal' value='Close')
-  script(src='//maxcdn.bootstrapcdn.com/bootstrap/3.2.0/js/bootstrap.min.js')
-  script(src='lib/bootstrap.file-input/bootstrap.file-input.js')
-  script(src='//cdnjs.cloudflare.com/ajax/libs/d3/4.10.2/d3.min.js')
-  script(src='//d3js.org/d3-scale-chromatic.v1.min.js')
-  script(src='js/grnsight.min.js')