grnsight 4.0.0 → 6.0.0

package/_gh_pages/coverage/lcov-report/base.css

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package/_gh_pages/coverage/lcov-report/block-navigation.js

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+var jumpToCode = (function init () {
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+
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+  var selector = notSelector + missingCoverageClasses.join(', ' + notSelector); // becomes `:not(a):not(b) > a, :not(a):not(b) > b`
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+
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+  };
+}());
+window.addEventListener('keydown', jumpToCode);

package/_gh_pages/coverage/lcov-report/controllers/additional-sheet-parser.js.html

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+<!doctype html>
+<html lang="en">
+<head>
+    <title>Code coverage report for controllers/additional-sheet-parser.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 {
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+        }
+    </style>
+</head>
+<body>
+<div class='wrapper'>
+  <div class='pad1'>
+    <h1>
+      <a href="../index.html">All files</a> / <a href="index.html">controllers</a> additional-sheet-parser.js
+    </h1>
+    <div class='clearfix'>
+      <div class='fl pad1y space-right2'>
+        <span class="strong">17.39% </span>
+        <span class="quiet">Statements</span>
+        <span class='fraction'>8/46</span>
+      </div>
+      <div class='fl pad1y space-right2'>
+        <span class="strong">0% </span>
+        <span class="quiet">Branches</span>
+        <span class='fraction'>0/16</span>
+      </div>
+      <div class='fl pad1y space-right2'>
+        <span class="strong">0% </span>
+        <span class="quiet">Functions</span>
+        <span class='fraction'>0/11</span>
+      </div>
+      <div class='fl pad1y space-right2'>
+        <span class="strong">17.39% </span>
+        <span class="quiet">Lines</span>
+        <span class='fraction'>8/46</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>
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+<span class="cline-any cline-neutral">&nbsp;</span></td><td class="text"><pre class="prettyprint lang-js">// Parses "optimization_paramters," expression data sheets, and 2-column sheets
+// from GRNmap input or output workbook
+&nbsp;
+var TWO_COL_SHEET_NAMES = [
+    "production_rates",
+    "degradation_rates",
+    "threshold_b",
+    "optimized_production_rates",
+    "optimized_threshold_b"];
+&nbsp;
+var EXPRESSION_SHEET_SUFFIXES = ["_expression", "_optimized_expression", "_sigmas"];
+&nbsp;
+var isExpressionSheet = <span class="fstat-no" title="function not covered" >fu</span>nction (sheetName) {
+<span class="cstat-no" title="statement not covered" >    return EXPRESSION_SHEET_SUFFIXES.some(<span class="fstat-no" title="function not covered" >fu</span>nction (suffix) {</span>
+<span class="cstat-no" title="statement not covered" >        return sheetName.includes(suffix);</span>
+    });
+};
+&nbsp;
+var fillArray = <span class="fstat-no" title="function not covered" >fu</span>nction (value, array, length) { // mutator
+<span class="cstat-no" title="statement not covered" >    while (array.length &lt; length) {</span>
+<span class="cstat-no" title="statement not covered" >        array.push(value);</span>
+    }
+<span class="cstat-no" title="statement not covered" >    return array;</span>
+};
+&nbsp;
+var parseMetaDataSheet = <span class="fstat-no" title="function not covered" >fu</span>nction (sheet) {
+    var meta = <span class="cstat-no" title="statement not covered" >{};</span>
+<span class="cstat-no" title="statement not covered" >    sheet.data.forEach(<span class="fstat-no" title="function not covered" >fu</span>nction (element, index) {</span>
+<span class="cstat-no" title="statement not covered" >        if (index !== 0) {</span>
+            var value = <span class="cstat-no" title="statement not covered" >element.slice(1);</span>
+            // Extract element from array if array contains only 1 value
+<span class="cstat-no" title="statement not covered" >            meta[element[0]] = value.length &gt; 1 ? value : value[0];</span>
+        }
+    });
+<span class="cstat-no" title="statement not covered" >    return meta;</span>
+};
+&nbsp;
+var parseTwoColumnSheet = <span class="fstat-no" title="function not covered" >fu</span>nction (sheet) {
+    var data = <span class="cstat-no" title="statement not covered" >{};</span>
+<span class="cstat-no" title="statement not covered" >    sheet.data.forEach(<span class="fstat-no" title="function not covered" >fu</span>nction (element, index) {</span>
+<span class="cstat-no" title="statement not covered" >        if (index !== 0) {</span>
+<span class="cstat-no" title="statement not covered" >            data[element[0]] = element[1];</span>
+        }
+    });
+<span class="cstat-no" title="statement not covered" >    return data;</span>
+};
+&nbsp;
+var parseExpressionSheet = <span class="fstat-no" title="function not covered" >fu</span>nction (sheet) {
+    var expressionData = <span class="cstat-no" title="statement not covered" >{};</span>
+    var geneData = <span class="cstat-no" title="statement not covered" >{};</span>
+<span class="cstat-no" title="statement not covered" >    expressionData["time_points"] = sheet.data[0].slice(1);</span>
+    var numberOfDataPoints = <span class="cstat-no" title="statement not covered" >expressionData["time_points"].length;</span>
+<span class="cstat-no" title="statement not covered" >    sheet.data.forEach(<span class="fstat-no" title="function not covered" >fu</span>nction (sheet) {</span>
+        var geneName = <span class="cstat-no" title="statement not covered" >sheet[0];</span>
+<span class="cstat-no" title="statement not covered" >        if (geneName) {</span>
+            var rowData = <span class="cstat-no" title="statement not covered" >sheet.slice(1);</span>
+            // Sometimes, missing data is at the end of the row. In this case, pad the
+            // array with nulls
+<span class="cstat-no" title="statement not covered" >            if (rowData.length &lt; numberOfDataPoints) {</span>
+<span class="cstat-no" title="statement not covered" >                fillArray(null, rowData, numberOfDataPoints);</span>
+            }
+<span class="cstat-no" title="statement not covered" >            geneData[geneName] = rowData;</span>
+        }
+    });
+<span class="cstat-no" title="statement not covered" >    expressionData["data"] = geneData;</span>
+<span class="cstat-no" title="statement not covered" >    return expressionData;</span>
+};
+&nbsp;
+module.exports = <span class="fstat-no" title="function not covered" >fu</span>nction (workbook) {
+    var output = <span class="cstat-no" title="statement not covered" >{</span>
+        expression: {}, // expression data
+        meta: {},
+        test: {} // 2-column data
+    };
+<span class="cstat-no" title="statement not covered" >    workbook.forEach(<span class="fstat-no" title="function not covered" >fu</span>nction (sheet) {</span>
+<span class="cstat-no" title="statement not covered" >        if (sheet.name === "optimization_parameters") {</span>
+<span class="cstat-no" title="statement not covered" >            output["meta"] = parseMetaDataSheet(sheet);</span>
+        // Parse 2-column sheets
+        } else <span class="cstat-no" title="statement not covered" >if (TWO_COL_SHEET_NAMES.includes(sheet.name)) {</span>
+<span class="cstat-no" title="statement not covered" >            output["test"][sheet.name] = parseTwoColumnSheet(sheet);</span>
+        // Parse expression sheets
+        } else <span class="cstat-no" title="statement not covered" >if (isExpressionSheet(sheet.name)) {</span>
+<span class="cstat-no" title="statement not covered" >            output["expression"][sheet.name] = parseExpressionSheet(sheet);</span>
+        }
+    });
+<span class="cstat-no" title="statement not covered" >    return output;</span>
+};
+&nbsp;</pre></td></tr>
+</table></pre>
+<div class='push'></div><!-- for sticky footer -->
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+  Code coverage
+  generated by <a href="https://istanbul.js.org/" target="_blank">istanbul</a> at Thu May 31 2018 15:29:17 GMT-0700 (PDT)
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+</div>
+<script src="../prettify.js"></script>
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+        if (typeof prettyPrint === 'function') {
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