npm - grnsight - Versions diffs - 4.0.0 → 6.0.0 - Mend

grnsight 4.0.0 → 6.0.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (458) hide show

package/_gh_pages/coverage/lcov-report/controllers/importers/index.html ADDED Viewed

@@ -0,0 +1,106 @@
+<!doctype html>
+<html lang="en">
+<head>
+    <title>Code coverage report for controllers/importers/</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> controllers/importers/
+    </h1>
+    <div class='clearfix'>
+      <div class='fl pad1y space-right2'>
+        <span class="strong">98.09% </span>
+        <span class="quiet">Statements</span>
+        <span class='fraction'>154/157</span>
+      </div>
+      <div class='fl pad1y space-right2'>
+        <span class="strong">90.23% </span>
+        <span class="quiet">Branches</span>
+        <span class='fraction'>120/133</span>
+      </div>
+      <div class='fl pad1y space-right2'>
+        <span class="strong">100% </span>
+        <span class="quiet">Functions</span>
+        <span class='fraction'>29/29</span>
+      </div>
+      <div class='fl pad1y space-right2'>
+        <span class="strong">98.09% </span>
+        <span class="quiet">Lines</span>
+        <span class='fraction'>154/157</span>
+      </div>
+    </div>
+  </div>
+  <div class='status-line high'></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 high" data-value="graphml.js"><a href="graphml.js.html">graphml.js</a></td>
+	<td data-value="97.67" class="pic high"><div class="chart"><div class="cover-fill" style="width: 97%;"></div><div class="cover-empty" style="width:3%;"></div></div></td>
+	<td data-value="97.67" class="pct high">97.67%</td>
+	<td data-value="86" class="abs high">84/86</td>
+	<td data-value="86.9" class="pct high">86.9%</td>
+	<td data-value="84" class="abs high">73/84</td>
+	<td data-value="100" class="pct high">100%</td>
+	<td data-value="18" class="abs high">18/18</td>
+	<td data-value="97.67" class="pct high">97.67%</td>
+	<td data-value="86" class="abs high">84/86</td>
+	</tr>
+<tr>
+	<td class="file high" data-value="sif.js"><a href="sif.js.html">sif.js</a></td>
+	<td data-value="98.59" class="pic high"><div class="chart"><div class="cover-fill" style="width: 98%;"></div><div class="cover-empty" style="width:2%;"></div></div></td>
+	<td data-value="98.59" class="pct high">98.59%</td>
+	<td data-value="71" class="abs high">70/71</td>
+	<td data-value="95.92" class="pct high">95.92%</td>
+	<td data-value="49" class="abs high">47/49</td>
+	<td data-value="100" class="pct high">100%</td>
+	<td data-value="11" class="abs high">11/11</td>
+	<td data-value="98.59" class="pct high">98.59%</td>
+	<td data-value="71" class="abs high">70/71</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="http://istanbul-js.org/" target="_blank">istanbul</a> at Fri Sep 29 2017 00:22:47 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>
+</body>
+</html>

package/_gh_pages/coverage/lcov-report/controllers/importers/sif.js.html ADDED Viewed

@@ -0,0 +1,488 @@
+<!doctype html>
+<html lang="en">
+<head>
+    <title>Code coverage report for controllers/importers/sif.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">controllers/importers/</a> sif.js
+    </h1>
+    <div class='clearfix'>
+      <div class='fl pad1y space-right2'>
+        <span class="strong">98.59% </span>
+        <span class="quiet">Statements</span>
+        <span class='fraction'>70/71</span>
+      </div>
+      <div class='fl pad1y space-right2'>
+        <span class="strong">95.92% </span>
+        <span class="quiet">Branches</span>
+        <span class='fraction'>47/49</span>
+      </div>
+      <div class='fl pad1y space-right2'>
+        <span class="strong">100% </span>
+        <span class="quiet">Functions</span>
+        <span class='fraction'>11/11</span>
+      </div>
+      <div class='fl pad1y space-right2'>
+        <span class="strong">98.59% </span>
+        <span class="quiet">Lines</span>
+        <span class='fraction'>70/71</span>
+      </div>
+    </div>
+  </div>
+  <div class='status-line high'></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">var constants = require(__dirname + "/../constants");
+var semanticChecker = require(__dirname + "/../semantic-checker");
+&nbsp;
+var GENE_NAME = 0;
+var RELATIONSHIP = 1;
+var TARGET = 2;
+&nbsp;
+&nbsp;
+module.exports = function (sif) {
+&nbsp;
+    var warnings = [];
+    var errors = [];
+&nbsp;
+    // Workaround for empty SIF file handling
+    var emptySifFile = sif === "";
+    sif = sif || " ";
+&nbsp;
+    // Replace any carriage return characters with new lines.
+    sif = sif.replace(/\r\n/g, "\n");
+&nbsp;
+    // Stray data detected when there are 2 or more consecutive tabs NOT followed by a newline in the SIF file.
+    // OR Stray data detected when there are 2 or more consecutive new lines
+    if (sif.match(/(?=.*[\t]{2,}?[^\n\t]).*/g) || sif.match(/[\n]{2,}/g)) {
+        errors.push(constants.errors.SIF_STRAY_DATA_ERROR);
+    }
+&nbsp;
+    // Detects comma separated SIF files
+    if (!sif.match(/[\t]+/g) &amp;&amp; sif.match(/[,]+/g)) {
+        errors.push(constants.warnings.SIF_FORMAT_WARNING);
+    }
+&nbsp;
+    var isNumber = function (relationship) {
+        return !isNaN(+relationship);
+    };
+&nbsp;
+    var sifNetworkType = function (sifEntries) {
+        var errors = [];
+        var relationships = [];
+        var numRowsWithTwoColumns = 0;
+        var unweightedRelationshipTypeErrorDetected = false;
+&nbsp;
+        sifEntries.forEach(function (entry) {
+            if (entry.length &gt; TARGET) {
+                if (!isNumber(entry[RELATIONSHIP])) {
+                    if (entry[RELATIONSHIP] !== "pd") {
+                        unweightedRelationshipTypeErrorDetected = true;
+                    }
+                }
+                relationships.push(entry[RELATIONSHIP]);
+            } else if (entry.length === 2) {
+                numRowsWithTwoColumns++;
+            }
+        });
+&nbsp;
+        if (unweightedRelationshipTypeErrorDetected) {
+            errors.push(constants.errors.SIF_UNWEIGHTED_RELATIONSHIP_TYPE_ERROR);
+        }
+&nbsp;
+        if (numRowsWithTwoColumns &gt; 0) {
+            errors.push(constants.errors.SIF_MISSING_DATA_ERROR);
+        }
+&nbsp;
+        var hasNumbers = relationships.some(isNumber);
+        var allNumbers = relationships.every(isNumber);
+        return {
+            sheetType: allNumbers ? constants.WEIGHTED : constants.UNWEIGHTED,
+            warnings: hasNumbers &amp;&amp; !allNumbers ? constants.warnings.EDGES_WITHOUT_WEIGHTS : null,
+            errors: errors
+        };
+    };
+&nbsp;
+    var entries = sif.match(/[^\r\n]+/g).map(function (line) {
+        return line.match(/[^\t]+/g);
+    });
+&nbsp;
+    var genes = [];
+    var links = [];
+    var networkType = "unweighted";
+&nbsp;
+    var nullEntries = entries.filter(function (entry) {
+        return entry === null;
+    });
+&nbsp;
+    <span class="missing-if-branch" title="if path not taken" >I</span>if (nullEntries.length &gt; 0) {
+<span class="cstat-no" title="statement not covered" >        errors.push(constants.errors.SIF_STRAY_DATA_ERROR);</span>
+    } else {
+        entries.forEach(function (entry) {
+            if (entry.length &amp;&amp; entry[GENE_NAME] &amp;&amp; genes.indexOf(entry[GENE_NAME]) === constants.NOT_FOUND) {
+                genes.push(entry[GENE_NAME]);
+            }
+        });
+&nbsp;
+        networkType = sifNetworkType(entries);
+        if (networkType.warnings) {
+            warnings.push(networkType.warnings);
+        }
+&nbsp;
+        <span class="missing-if-branch" title="else path not taken" >E</span>if (networkType.errors) {
+            networkType.errors.forEach(function (error) {
+                errors.push(error);
+            });
+        }
+&nbsp;
+        entries.forEach(function (entry) {
+            if (entry.length &gt; TARGET) {
+                var sourceIndex = genes.indexOf(entry[GENE_NAME]);
+                var targets = entry.slice(TARGET);
+                targets.forEach(function (target) {
+                    var targetIndex = genes.indexOf(target);
+                    if (targetIndex === constants.NOT_FOUND) {
+                        genes.push(target);
+                        targetIndex = genes.indexOf(target);
+                    }
+                    var link = {
+                        source: sourceIndex,
+                        target: targetIndex
+                    };
+                    if (networkType.sheetType === constants.WEIGHTED) {
+                        link.value = +entry[RELATIONSHIP];
+                    }
+                    links.push(link);
+                });
+            }
+        });
+  }
+&nbsp;
+  var network = {
+    genes: emptySifFile ? [] : genes.map(function (geneName) {
+      return { name: geneName };
+    }),
+    links: links,
+    errors: errors,
+    warnings: warnings,
+    sheetType: networkType.sheetType,
+    positiveWeights: [],
+    negativeWeights: []
+  };
+&nbsp;
+  return (network.errors.length === 0) ? semanticChecker(network) : network;
+&nbsp;
+};
+&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="http://istanbul-js.org/" target="_blank">istanbul</a> at Fri Sep 29 2017 00:22:47 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>
+</body>
+</html>