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/exporters/sif.js.html ADDED Viewed

@@ -0,0 +1,150 @@
+<!doctype html>
+<html lang="en">
+<head>
+    <title>Code coverage report for controllers/exporters/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/exporters</a> sif.js
+    </h1>
+    <div class='clearfix'>
+      <div class='fl pad1y space-right2'>
+        <span class="strong">25% </span>
+        <span class="quiet">Statements</span>
+        <span class='fraction'>3/12</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'>0/4</span>
+      </div>
+      <div class='fl pad1y space-right2'>
+        <span class="strong">25% </span>
+        <span class="quiet">Lines</span>
+        <span class='fraction'>3/12</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></td><td class="line-coverage quiet"><span class="cline-any cline-yes">1x</span>
+<span class="cline-any cline-neutral">&nbsp;</span>
+<span class="cline-any cline-yes">1x</span>
+<span class="cline-any cline-no">&nbsp;</span>
+<span class="cline-any cline-neutral">&nbsp;</span>
+<span class="cline-any cline-no">&nbsp;</span>
+<span class="cline-any cline-no">&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-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>
+<span class="cline-any cline-yes">1x</span>
+<span class="cline-any cline-no">&nbsp;</span>
+<span class="cline-any cline-neutral">&nbsp;</span>
+<span class="cline-any cline-no">&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-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">var constants = require(__dirname + "/../constants");
+&nbsp;
+var exportEdges = <span class="fstat-no" title="function not covered" >fu</span>nction (network, gene, geneIndex) {
+    var result = <span class="cstat-no" title="statement not covered" >"";</span>
+&nbsp;
+<span class="cstat-no" title="statement not covered" >    network.links.forEach(<span class="fstat-no" title="function not covered" >fu</span>nction (link) {</span>
+<span class="cstat-no" title="statement not covered" >        if (link.source === geneIndex) {</span>
+<span class="cstat-no" title="statement not covered" >            result += [</span>
+                gene.name,
+                network.sheetType === constants.UNWEIGHTED ? "pd" : link.value,
+                network.genes[link.target].name
+            ].join("\t") + "\n";
+        }
+    });
+&nbsp;
+<span class="cstat-no" title="statement not covered" >    return result || (gene.name + "\t\t\n");</span>
+};
+&nbsp;
+module.exports = <span class="fstat-no" title="function not covered" >fu</span>nction (network) {
+    var result = <span class="cstat-no" title="statement not covered" >"";</span>
+&nbsp;
+<span class="cstat-no" title="statement not covered" >    network.genes.forEach(<span class="fstat-no" title="function not covered" >fu</span>nction (gene, geneIndex) {</span>
+<span class="cstat-no" title="statement not covered" >        result += exportEdges(network, gene, geneIndex);</span>
+    });
+&nbsp;
+<span class="cstat-no" title="statement not covered" >    return result;</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 15:29:17 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/controllers/helpers.js.html ADDED Viewed

@@ -0,0 +1,114 @@
+<!doctype html>
+<html lang="en">
+<head>
+    <title>Code coverage report for controllers/helpers.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</a> helpers.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'>2/6</span>
+      </div>
+      <div class='fl pad1y space-right2'>
+        <span class="strong">100% </span>
+        <span class="quiet">Branches</span>
+        <span class='fraction'>0/0</span>
+      </div>
+      <div class='fl pad1y space-right2'>
+        <span class="strong">0% </span>
+        <span class="quiet">Functions</span>
+        <span class='fraction'>0/2</span>
+      </div>
+      <div class='fl pad1y space-right2'>
+        <span class="strong">33.33% </span>
+        <span class="quiet">Lines</span>
+        <span class='fraction'>2/6</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></td><td class="line-coverage quiet"><span class="cline-any cline-yes">1x</span>
+<span class="cline-any cline-neutral">&nbsp;</span>
+<span class="cline-any cline-yes">1x</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-no">&nbsp;</span>
+<span class="cline-any cline-no">&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-neutral">&nbsp;</span></td><td class="text"><pre class="prettyprint lang-js">var constants = require(__dirname + "/constants");
+&nbsp;
+module.exports = {
+&nbsp;
+    attachCorsHeader: <span class="fstat-no" title="function not covered" >fu</span>nction (res, app) {
+<span class="cstat-no" title="statement not covered" >        res.header("Access-Control-Allow-Origin", app.get("corsOrigin"));</span>
+    },
+&nbsp;
+    attachFileHeaders: <span class="fstat-no" title="function not covered" >fu</span>nction (res, path) {
+<span class="cstat-no" title="statement not covered" >        res.header("Access-Control-Allow-Methods", "POST, GET");</span>
+<span class="cstat-no" title="statement not covered" >        res.header("Access-Control-Expose-Headers", constants.GRNSIGHT_FILENAME_HEADER);</span>
+<span class="cstat-no" title="statement not covered" >        res.header(constants.GRNSIGHT_FILENAME_HEADER, path.split("/").pop());</span>
+    }
+&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="https://istanbul.js.org/" target="_blank">istanbul</a> at Thu May 31 2018 15:29:17 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/controllers/import-controller.js.html ADDED Viewed

@@ -0,0 +1,233 @@
+<!doctype html>
+<html lang="en">
+<head>
+    <title>Code coverage report for controllers/import-controller.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/</a> import-controller.js
+    </h1>
+    <div class='clearfix'>
+      <div class='fl pad1y space-right2'>
+        <span class="strong">20% </span>
+        <span class="quiet">Statements</span>
+        <span class='fraction'>6/30</span>
+      </div>
+      <div class='fl pad1y space-right2'>
+        <span class="strong">10% </span>
+        <span class="quiet">Branches</span>
+        <span class='fraction'>1/10</span>
+      </div>
+      <div class='fl pad1y space-right2'>
+        <span class="strong">16.67% </span>
+        <span class="quiet">Functions</span>
+        <span class='fraction'>1/6</span>
+      </div>
+      <div class='fl pad1y space-right2'>
+        <span class="strong">20% </span>
+        <span class="quiet">Lines</span>
+        <span class='fraction'>6/30</span>
+      </div>
+    </div>
+  </div>
+  <div class='status-line low'></div>
+<pre><table class="coverage">
+<tr><td class="line-count quiet">1
+2
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+57</td><td class="line-coverage quiet"><span class="cline-any cline-yes">1×</span>
+<span class="cline-any cline-neutral">&nbsp;</span>
+<span class="cline-any cline-yes">1×</span>
+<span class="cline-any cline-yes">1×</span>
+<span class="cline-any cline-neutral">&nbsp;</span>
+<span class="cline-any cline-yes">1×</span>
+<span class="cline-any cline-yes">2×</span>
+<span class="cline-any cline-no">&nbsp;</span>
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+<span class="cline-any cline-neutral">&nbsp;</span>
+<span class="cline-any cline-no">&nbsp;</span>
+<span class="cline-any cline-no">&nbsp;</span>
+<span class="cline-any cline-no">&nbsp;</span>
+<span class="cline-any cline-neutral">&nbsp;</span>
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+<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-no">&nbsp;</span>
+<span class="cline-any cline-no">&nbsp;</span>
+<span class="cline-any cline-no">&nbsp;</span>
+<span class="cline-any cline-neutral">&nbsp;</span>
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+<span class="cline-any cline-no">&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-neutral">&nbsp;</span>
+<span class="cline-any cline-neutral">&nbsp;</span>
+<span class="cline-any cline-no">&nbsp;</span>
+<span class="cline-any cline-no">&nbsp;</span>
+<span class="cline-any cline-neutral">&nbsp;</span>
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+<span class="cline-any cline-no">&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">2×</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-neutral">&nbsp;</span></td><td class="text"><pre class="prettyprint lang-js">var helpers = require(__dirname + "/helpers");
+&nbsp;
+var sifToGrnsight = require(__dirname + "/importers/sif");
+var graphMlToGrnsight = require(__dirname + "/importers/graphml");
+&nbsp;
+module.exports = function (app) {
+    <span class="missing-if-branch" title="if path not taken" >I</span>if (app) {
+<span class="cstat-no" title="statement not covered" >        var multiparty = require("multiparty");</span>
+<span class="cstat-no" title="statement not covered" >        var path = require("path");</span>
+<span class="cstat-no" title="statement not covered" >        var fs = require("fs");</span>
+&nbsp;
+<span class="cstat-no" title="statement not covered" >        var performUpload = <span class="fstat-no" title="function not covered" >function (req, res, extension, importer) {</span></span>
+<span class="cstat-no" title="statement not covered" >            helpers.attachCorsHeader(res, app);</span>
+&nbsp;
+<span class="cstat-no" title="statement not covered" >            (new multiparty.Form()).parse(req, <span class="fstat-no" title="function not covered" >function (error, fields, files) {</span></span>
+<span class="cstat-no" title="statement not covered" >                if (error) {</span>
+<span class="cstat-no" title="statement not covered" >                    return res.send(400, "There was a problem uploading your file. Please try again.");</span>
+                }
+&nbsp;
+<span class="cstat-no" title="statement not covered" >                var input;</span>
+<span class="cstat-no" title="statement not covered" >                try {</span>
+<span class="cstat-no" title="statement not covered" >                    input = files.file[0].path;</span>
+                } catch (error) {
+<span class="cstat-no" title="statement not covered" >                    return res.send(400, "No import file selected.");</span>
+                }
+&nbsp;
+<span class="cstat-no" title="statement not covered" >                if (path.extname(input) !== "." + extension) {</span>
+<span class="cstat-no" title="statement not covered" >                    return res.send(400, "The filename does not end in ." + extension + ".");</span>
+                }
+&nbsp;
+<span class="cstat-no" title="statement not covered" >                fs.readFile(input, { encoding: "utf-8" }, <span class="fstat-no" title="function not covered" >function (error, data) {</span></span>
+<span class="cstat-no" title="statement not covered" >                    if (error) {</span>
+<span class="cstat-no" title="statement not covered" >                        throw error;</span>
+                    } else {
+<span class="cstat-no" title="statement not covered" >                        helpers.attachFileHeaders(res, input);</span>
+<span class="cstat-no" title="statement not covered" >                        var network = importer(data);</span>
+<span class="cstat-no" title="statement not covered" >                        return res.json((network.errors.length === 0) ? 200 : 400, network);</span>
+                    }
+                });
+            });
+        };
+&nbsp;
+<span class="cstat-no" title="statement not covered" >        app.post("/upload-sif", <span class="fstat-no" title="function not covered" >function (req, res) {</span></span>
+<span class="cstat-no" title="statement not covered" >            performUpload(req, res, "sif", sifToGrnsight);</span>
+        });
+&nbsp;
+<span class="cstat-no" title="statement not covered" >        app.post("/upload-graphml", <span class="fstat-no" title="function not covered" >function (req, res) {</span></span>
+<span class="cstat-no" title="statement not covered" >            performUpload(req, res, "graphml", graphMlToGrnsight);</span>
+        });
+    }
+&nbsp;
+    return {
+        sifToGrnsight: sifToGrnsight,
+        graphMlToGrnsight: graphMlToGrnsight
+    };
+};
+&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>