grnsight 6.0.4 → 7.1.1

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

@@ -1,158 +0,0 @@
-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

@@ -1,225 +0,0 @@
-<!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'>
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-        <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">
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-<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 () {
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-            prettyPrint();
-        }
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-</html>

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

@@ -1,97 +0,0 @@
-<!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">
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-        .coverage-summary .sorter {
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-<div class='wrapper'>
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-    <h1>
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-        <span class="strong">33.33% </span>
-        <span class="quiet">Statements</span>
-        <span class='fraction'>7/21</span>
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-      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.
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-   <th data-col="branches_raw" data-type="number" data-fmt="html" class="abs"></th>
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-  generated by <a href="https://istanbul.js.org/" target="_blank">istanbul</a> at Thu May 31 2018 15:29:57 GMT-0700 (PDT)
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package/_gh_pages/coverage/lcov.info

@@ -1,49 +0,0 @@
-TN:
-SF:/Users/dondi/Documents/Main/Code/git/GRNsight/server/controllers/additional-sheet-parser.js
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