grnsight 4.0.0 → 6.0.0

package/_gh_pages/coverage/lcov-report/sorter.js

@@ -0,0 +1,158 @@
+var addSorting = (function () {
+    "use strict";
+    var cols,
+        currentSort = {
+            index: 0,
+            desc: false
+        };
+
+    // returns the summary table element
+    function getTable() { return document.querySelector('.coverage-summary'); }
+    // returns the thead element of the summary table
+    function getTableHeader() { return getTable().querySelector('thead tr'); }
+    // returns the tbody element of the summary table
+    function getTableBody() { return getTable().querySelector('tbody'); }
+    // returns the th element for nth column
+    function getNthColumn(n) { return getTableHeader().querySelectorAll('th')[n]; }
+
+    // loads all columns
+    function loadColumns() {
+        var colNodes = getTableHeader().querySelectorAll('th'),
+            colNode,
+            cols = [],
+            col,
+            i;
+
+        for (i = 0; i < colNodes.length; i += 1) {
+            colNode = colNodes[i];
+            col = {
+                key: colNode.getAttribute('data-col'),
+                sortable: !colNode.getAttribute('data-nosort'),
+                type: colNode.getAttribute('data-type') || 'string'
+            };
+            cols.push(col);
+            if (col.sortable) {
+                col.defaultDescSort = col.type === 'number';
+                colNode.innerHTML = colNode.innerHTML + '<span class="sorter"></span>';
+            }
+        }
+        return cols;
+    }
+    // attaches a data attribute to every tr element with an object
+    // of data values keyed by column name
+    function loadRowData(tableRow) {
+        var tableCols = tableRow.querySelectorAll('td'),
+            colNode,
+            col,
+            data = {},
+            i,
+            val;
+        for (i = 0; i < tableCols.length; i += 1) {
+            colNode = tableCols[i];
+            col = cols[i];
+            val = colNode.getAttribute('data-value');
+            if (col.type === 'number') {
+                val = Number(val);
+            }
+            data[col.key] = val;
+        }
+        return data;
+    }
+    // loads all row data
+    function loadData() {
+        var rows = getTableBody().querySelectorAll('tr'),
+            i;
+
+        for (i = 0; i < rows.length; i += 1) {
+            rows[i].data = loadRowData(rows[i]);
+        }
+    }
+    // sorts the table using the data for the ith column
+    function sortByIndex(index, desc) {
+        var key = cols[index].key,
+            sorter = function (a, b) {
+                a = a.data[key];
+                b = b.data[key];
+                return a < b ? -1 : a > b ? 1 : 0;
+            },
+            finalSorter = sorter,
+            tableBody = document.querySelector('.coverage-summary tbody'),
+            rowNodes = tableBody.querySelectorAll('tr'),
+            rows = [],
+            i;
+
+        if (desc) {
+            finalSorter = function (a, b) {
+                return -1 * sorter(a, b);
+            };
+        }
+
+        for (i = 0; i < rowNodes.length; i += 1) {
+            rows.push(rowNodes[i]);
+            tableBody.removeChild(rowNodes[i]);
+        }
+
+        rows.sort(finalSorter);
+
+        for (i = 0; i < rows.length; i += 1) {
+            tableBody.appendChild(rows[i]);
+        }
+    }
+    // removes sort indicators for current column being sorted
+    function removeSortIndicators() {
+        var col = getNthColumn(currentSort.index),
+            cls = col.className;
+
+        cls = cls.replace(/ sorted$/, '').replace(/ sorted-desc$/, '');
+        col.className = cls;
+    }
+    // adds sort indicators for current column being sorted
+    function addSortIndicators() {
+        getNthColumn(currentSort.index).className += currentSort.desc ? ' sorted-desc' : ' sorted';
+    }
+    // adds event listeners for all sorter widgets
+    function enableUI() {
+        var i,
+            el,
+            ithSorter = function ithSorter(i) {
+                var col = cols[i];
+
+                return function () {
+                    var desc = col.defaultDescSort;
+
+                    if (currentSort.index === i) {
+                        desc = !currentSort.desc;
+                    }
+                    sortByIndex(i, desc);
+                    removeSortIndicators();
+                    currentSort.index = i;
+                    currentSort.desc = desc;
+                    addSortIndicators();
+                };
+            };
+        for (i =0 ; i < cols.length; i += 1) {
+            if (cols[i].sortable) {
+                // add the click event handler on the th so users
+                // dont have to click on those tiny arrows
+                el = getNthColumn(i).querySelector('.sorter').parentElement;
+                if (el.addEventListener) {
+                    el.addEventListener('click', ithSorter(i));
+                } else {
+                    el.attachEvent('onclick', ithSorter(i));
+                }
+            }
+        }
+    }
+    // adds sorting functionality to the UI
+    return function () {
+        if (!getTable()) {
+            return;
+        }
+        cols = loadColumns();
+        loadData(cols);
+        addSortIndicators();
+        enableUI();
+    };
+})();
+
+window.addEventListener('load', addSorting);

package/_gh_pages/coverage/lcov-report/web-client/public/js/grnstate.js.html

@@ -0,0 +1,225 @@
+<!doctype html>
+<html lang="en">
+<head>
+    <title>Code coverage report for web-client/public/js/grnstate.js</title>
+    <meta charset="utf-8" />
+    <link rel="stylesheet" href="../../../prettify.css" />
+    <link rel="stylesheet" href="../../../base.css" />
+    <meta name="viewport" content="width=device-width, initial-scale=1">
+    <style type='text/css'>
+        .coverage-summary .sorter {
+            background-image: url(../../../sort-arrow-sprite.png);
+        }
+    </style>
+</head>
+<body>
+<div class='wrapper'>
+  <div class='pad1'>
+    <h1>
+      <a href="../../../index.html">All files</a> / <a href="index.html">web-client/public/js</a> grnstate.js
+    </h1>
+    <div class='clearfix'>
+      <div class='fl pad1y space-right2'>
+        <span class="strong">33.33% </span>
+        <span class="quiet">Statements</span>
+        <span class='fraction'>7/21</span>
+      </div>
+      <div class='fl pad1y space-right2'>
+        <span class="strong">0% </span>
+        <span class="quiet">Branches</span>
+        <span class='fraction'>0/6</span>
+      </div>
+      <div class='fl pad1y space-right2'>
+        <span class="strong">0% </span>
+        <span class="quiet">Functions</span>
+        <span class='fraction'>0/3</span>
+      </div>
+      <div class='fl pad1y space-right2'>
+        <span class="strong">33.33% </span>
+        <span class="quiet">Lines</span>
+        <span class='fraction'>7/21</span>
+      </div>
+    </div>
+    <p class="quiet">
+      Press <em>n</em> or <em>j</em> to go to the next uncovered block, <em>b</em>, <em>p</em> or <em>k</em> for the previous block.
+    </p>
+  </div>
+  <div class='status-line low'></div>
+<pre><table class="coverage">
+<tr><td class="line-count quiet"><a name='L1'></a><a href='#L1'>1</a>
+<a name='L2'></a><a href='#L2'>2</a>
+<a name='L3'></a><a href='#L3'>3</a>
+<a name='L4'></a><a href='#L4'>4</a>
+<a name='L5'></a><a href='#L5'>5</a>
+<a name='L6'></a><a href='#L6'>6</a>
+<a name='L7'></a><a href='#L7'>7</a>
+<a name='L8'></a><a href='#L8'>8</a>
+<a name='L9'></a><a href='#L9'>9</a>
+<a name='L10'></a><a href='#L10'>10</a>
+<a name='L11'></a><a href='#L11'>11</a>
+<a name='L12'></a><a href='#L12'>12</a>
+<a name='L13'></a><a href='#L13'>13</a>
+<a name='L14'></a><a href='#L14'>14</a>
+<a name='L15'></a><a href='#L15'>15</a>
+<a name='L16'></a><a href='#L16'>16</a>
+<a name='L17'></a><a href='#L17'>17</a>
+<a name='L18'></a><a href='#L18'>18</a>
+<a name='L19'></a><a href='#L19'>19</a>
+<a name='L20'></a><a href='#L20'>20</a>
+<a name='L21'></a><a href='#L21'>21</a>
+<a name='L22'></a><a href='#L22'>22</a>
+<a name='L23'></a><a href='#L23'>23</a>
+<a name='L24'></a><a href='#L24'>24</a>
+<a name='L25'></a><a href='#L25'>25</a>
+<a name='L26'></a><a href='#L26'>26</a>
+<a name='L27'></a><a href='#L27'>27</a>
+<a name='L28'></a><a href='#L28'>28</a>
+<a name='L29'></a><a href='#L29'>29</a>
+<a name='L30'></a><a href='#L30'>30</a>
+<a name='L31'></a><a href='#L31'>31</a>
+<a name='L32'></a><a href='#L32'>32</a>
+<a name='L33'></a><a href='#L33'>33</a>
+<a name='L34'></a><a href='#L34'>34</a>
+<a name='L35'></a><a href='#L35'>35</a>
+<a name='L36'></a><a href='#L36'>36</a>
+<a name='L37'></a><a href='#L37'>37</a>
+<a name='L38'></a><a href='#L38'>38</a>
+<a name='L39'></a><a href='#L39'>39</a>
+<a name='L40'></a><a href='#L40'>40</a>
+<a name='L41'></a><a href='#L41'>41</a>
+<a name='L42'></a><a href='#L42'>42</a>
+<a name='L43'></a><a href='#L43'>43</a>
+<a name='L44'></a><a href='#L44'>44</a>
+<a name='L45'></a><a href='#L45'>45</a>
+<a name='L46'></a><a href='#L46'>46</a>
+<a name='L47'></a><a href='#L47'>47</a>
+<a name='L48'></a><a href='#L48'>48</a>
+<a name='L49'></a><a href='#L49'>49</a>
+<a name='L50'></a><a href='#L50'>50</a>
+<a name='L51'></a><a href='#L51'>51</a>
+<a name='L52'></a><a href='#L52'>52</a>
+<a name='L53'></a><a href='#L53'>53</a></td><td class="line-coverage quiet"><span class="cline-any cline-yes">1x</span>
+<span class="cline-any cline-yes">1x</span>
+<span class="cline-any cline-neutral">&nbsp;</span>
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+<span class="cline-any cline-yes">1x</span>
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+<span class="cline-any cline-neutral">&nbsp;</span>
+<span class="cline-any cline-neutral">&nbsp;</span>
+<span class="cline-any cline-neutral">&nbsp;</span>
+<span class="cline-any cline-no">&nbsp;</span>
+<span class="cline-any cline-neutral">&nbsp;</span>
+<span class="cline-any cline-neutral">&nbsp;</span>
+<span class="cline-any cline-neutral">&nbsp;</span>
+<span class="cline-any cline-yes">2x</span>
+<span class="cline-any cline-neutral">&nbsp;</span>
+<span class="cline-any cline-yes">2x</span>
+<span class="cline-any cline-yes">2x</span>
+<span class="cline-any cline-neutral">&nbsp;</span>
+<span class="cline-any cline-neutral">&nbsp;</span>
+<span class="cline-any cline-neutral">&nbsp;</span>
+<span class="cline-any cline-neutral">&nbsp;</span>
+<span class="cline-any cline-no">&nbsp;</span>
+<span class="cline-any cline-neutral">&nbsp;</span>
+<span class="cline-any cline-neutral">&nbsp;</span></td><td class="text"><pre class="prettyprint lang-js">import { max } from "d3-array";
+let currentNetwork = null;
+&nbsp;
+const <span class="fstat-no" title="function not covered" >annotateLinks = n</span>etwork =&gt; {
+    // TODO This duplicates logic that is done on the server side for an .xlsx spreadsheet.
+    //      Think of a way to consolidate it. Having discovered this, it seems like this should
+    //      be done on the client side because it rearranges data redundantly, for ease of display.
+<span class="cstat-no" title="statement not covered" >    network.positiveWeights = [];</span>
+<span class="cstat-no" title="statement not covered" >    network.negativeWeights = [];</span>
+&nbsp;
+<span class="cstat-no" title="statement not covered" >    network.links.forEach(<span class="fstat-no" title="function not covered" >link =&gt; </span>{</span>
+<span class="cstat-no" title="statement not covered" >        if (network.sheetType === "unweighted" &amp;&amp; !link.value) {</span>
+<span class="cstat-no" title="statement not covered" >            link.value = 1;</span>
+        }
+&nbsp;
+<span class="cstat-no" title="statement not covered" >        if (link.value &gt; 0) {</span>
+<span class="cstat-no" title="statement not covered" >            link.type = "arrowhead";</span>
+            // link.stroke = "MediumVioletRed";   // GRNsight v1 magenta edge color
+<span class="cstat-no" title="statement not covered" >            link.stroke = "rgb(195, 61, 61)";     // Node coloring-consistent red edge color</span>
+<span class="cstat-no" title="statement not covered" >            network.positiveWeights.push(link.value);</span>
+        } else {
+<span class="cstat-no" title="statement not covered" >            link.type = "repressor";</span>
+            // link.stroke = "DarkTurquoise";     // GRNsight v1 cyan edge color
+<span class="cstat-no" title="statement not covered" >            link.stroke = "rgb(51, 124, 183)";    // Node coloring-consistent blue edge color</span>
+<span class="cstat-no" title="statement not covered" >            network.negativeWeights.push(link.value);</span>
+        }
+    });
+};
+&nbsp;
+export const grnState = {
+    name: null,
+&nbsp;
+    newNetwork: false,
+&nbsp;
+    normalizationMax: null,
+    resetNormalizationMax: null,
+&nbsp;
+    get network () {
+<span class="cstat-no" title="statement not covered" >        return currentNetwork;</span>
+    },
+&nbsp;
+    set network (network) {
+        currentNetwork = network;
+        // TODO: add colorOptimal so that the rest of the normalization code can get added
+        this.resetNormalizationMax = max(network.positiveWeights.concat(network.negativeWeights));
+        this.newNetwork = true;
+    },
+&nbsp;
+    dashedLine: false,
+&nbsp;
+    annotateLinks: <span class="cstat-no" title="statement not covered" ><span class="fstat-no" title="function not covered" >() =&gt; annotateLinks(currentNetwork),</span></span>
+};
+&nbsp;</pre></td></tr>
+</table></pre>
+<div class='push'></div><!-- for sticky footer -->
+</div><!-- /wrapper -->
+<div class='footer quiet pad2 space-top1 center small'>
+  Code coverage
+  generated by <a href="https://istanbul.js.org/" target="_blank">istanbul</a> at Thu May 31 2018 15:29:57 GMT-0700 (PDT)
+</div>
+</div>
+<script src="../../../prettify.js"></script>
+<script>
+window.onload = function () {
+        if (typeof prettyPrint === 'function') {
+            prettyPrint();
+        }
+};
+</script>
+<script src="../../../sorter.js"></script>
+<script src="../../../block-navigation.js"></script>
+</body>
+</html>

package/_gh_pages/coverage/lcov-report/web-client/public/js/index.html

@@ -0,0 +1,97 @@
+<!doctype html>
+<html lang="en">
+<head>
+    <title>Code coverage report for web-client/public/js</title>
+    <meta charset="utf-8" />
+    <link rel="stylesheet" href="../../../prettify.css" />
+    <link rel="stylesheet" href="../../../base.css" />
+    <meta name="viewport" content="width=device-width, initial-scale=1">
+    <style type='text/css'>
+        .coverage-summary .sorter {
+            background-image: url(../../../sort-arrow-sprite.png);
+        }
+    </style>
+</head>
+<body>
+<div class='wrapper'>
+  <div class='pad1'>
+    <h1>
+      <a href="../../../index.html">All files</a> web-client/public/js
+    </h1>
+    <div class='clearfix'>
+      <div class='fl pad1y space-right2'>
+        <span class="strong">33.33% </span>
+        <span class="quiet">Statements</span>
+        <span class='fraction'>7/21</span>
+      </div>
+      <div class='fl pad1y space-right2'>
+        <span class="strong">0% </span>
+        <span class="quiet">Branches</span>
+        <span class='fraction'>0/6</span>
+      </div>
+      <div class='fl pad1y space-right2'>
+        <span class="strong">0% </span>
+        <span class="quiet">Functions</span>
+        <span class='fraction'>0/3</span>
+      </div>
+      <div class='fl pad1y space-right2'>
+        <span class="strong">33.33% </span>
+        <span class="quiet">Lines</span>
+        <span class='fraction'>7/21</span>
+      </div>
+    </div>
+    <p class="quiet">
+      Press <em>n</em> or <em>j</em> to go to the next uncovered block, <em>b</em>, <em>p</em> or <em>k</em> for the previous block.
+    </p>
+  </div>
+  <div class='status-line low'></div>
+<div class="pad1">
+<table class="coverage-summary">
+<thead>
+<tr>
+   <th data-col="file" data-fmt="html" data-html="true" class="file">File</th>
+   <th data-col="pic" data-type="number" data-fmt="html" data-html="true" class="pic"></th>
+   <th data-col="statements" data-type="number" data-fmt="pct" class="pct">Statements</th>
+   <th data-col="statements_raw" data-type="number" data-fmt="html" class="abs"></th>
+   <th data-col="branches" data-type="number" data-fmt="pct" class="pct">Branches</th>
+   <th data-col="branches_raw" data-type="number" data-fmt="html" class="abs"></th>
+   <th data-col="functions" data-type="number" data-fmt="pct" class="pct">Functions</th>
+   <th data-col="functions_raw" data-type="number" data-fmt="html" class="abs"></th>
+   <th data-col="lines" data-type="number" data-fmt="pct" class="pct">Lines</th>
+   <th data-col="lines_raw" data-type="number" data-fmt="html" class="abs"></th>
+</tr>
+</thead>
+<tbody><tr>
+	<td class="file low" data-value="grnstate.js"><a href="grnstate.js.html">grnstate.js</a></td>
+	<td data-value="33.33" class="pic low"><div class="chart"><div class="cover-fill" style="width: 33%;"></div><div class="cover-empty" style="width:67%;"></div></div></td>
+	<td data-value="33.33" class="pct low">33.33%</td>
+	<td data-value="21" class="abs low">7/21</td>
+	<td data-value="0" class="pct low">0%</td>
+	<td data-value="6" class="abs low">0/6</td>
+	<td data-value="0" class="pct low">0%</td>
+	<td data-value="3" class="abs low">0/3</td>
+	<td data-value="33.33" class="pct low">33.33%</td>
+	<td data-value="21" class="abs low">7/21</td>
+	</tr>
+
+</tbody>
+</table>
+</div><div class='push'></div><!-- for sticky footer -->
+</div><!-- /wrapper -->
+<div class='footer quiet pad2 space-top1 center small'>
+  Code coverage
+  generated by <a href="https://istanbul.js.org/" target="_blank">istanbul</a> at Thu May 31 2018 15:29:57 GMT-0700 (PDT)
+</div>
+</div>
+<script src="../../../prettify.js"></script>
+<script>
+window.onload = function () {
+        if (typeof prettyPrint === 'function') {
+            prettyPrint();
+        }
+};
+</script>
+<script src="../../../sorter.js"></script>
+<script src="../../../block-navigation.js"></script>
+</body>
+</html>

package/_gh_pages/coverage/lcov.info

@@ -0,0 +1,49 @@
+TN:
+SF:/Users/dondi/Documents/Main/Code/git/GRNsight/server/controllers/additional-sheet-parser.js
+FN:14,(anonymous_1)
+FN:26,(anonymous_2)
+FN:34,(anonymous_3)
+FN:39,(anonymous_4)
+FNF:4
+FNH:0
+FNDA:0,(anonymous_1)
+FNDA:0,(anonymous_2)
+FNDA:0,(anonymous_3)
+FNDA:0,(anonymous_4)
+DA:4,1
+DA:12,1
+DA:13,0
+DA:14,0
+DA:15,0
+DA:16,0
+DA:18,0
+DA:21,0
+DA:24,1
+DA:25,0
+DA:26,0
+DA:27,0
+DA:28,0
+DA:31,0
+DA:34,1
+DA:35,0
+DA:39,0
+DA:40,0
+DA:41,0
+DA:43,0
+DA:44,0
+DA:47,0
+LF:22
+LH:4
+BRDA:15,1,0,0
+BRDA:15,1,1,0
+BRDA:18,2,0,0
+BRDA:18,2,1,0
+BRDA:27,3,0,0
+BRDA:27,3,1,0
+BRDA:40,4,0,0
+BRDA:40,4,1,0
+BRDA:43,5,0,0
+BRDA:43,5,1,0
+BRF:10
+BRH:0
+end_of_record