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

grnsight 4.0.0 → 6.0.0

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Files changed (458) hide show

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

@@ -0,0 +1,716 @@
+<!doctype html>
+<html lang="en">
+<head>
+    <title>Code coverage report for controllers/importers/graphml.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> graphml.js
+    </h1>
+    <div class='clearfix'>
+      <div class='fl pad1y space-right2'>
+        <span class="strong">97.67% </span>
+        <span class="quiet">Statements</span>
+        <span class='fraction'>84/86</span>
+      </div>
+      <div class='fl pad1y space-right2'>
+        <span class="strong">86.9% </span>
+        <span class="quiet">Branches</span>
+        <span class='fraction'>73/84</span>
+      </div>
+      <div class='fl pad1y space-right2'>
+        <span class="strong">100% </span>
+        <span class="quiet">Functions</span>
+        <span class='fraction'>18/18</span>
+      </div>
+      <div class='fl pad1y space-right2'>
+        <span class="strong">97.67% </span>
+        <span class="quiet">Lines</span>
+        <span class='fraction'>84/86</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 parseString = require("xml2js").parseString;
+var semanticChecker = require(__dirname + "/../semantic-checker");
+&nbsp;
+/*
+var graphmlWarnings = {
+    EDGES_WITHOUT_WEIGHTS: {
+        warningCode: "EDGES_WITHOUT_WEIGHTS",
+        errorDescription: "GRNsight has detected that one or more edges in your network are missing numerical weight" +
+                          " values. Because the algorithm GRNsight uses for determining the arrowhead type and the" +
+                          " color and thickness of the edges requires numerical weight values, your graph will" +
+                          " display as an unweighted graph with black edges and pointed arrowheads. If you want to" +
+                          " display the network as a weighted graph, please modify your input file to include weight" +
+                          " values for all edges."
+    },
+&nbsp;
+    EDGE_DEFAULT_NOT_DIRECTED: {
+        warningCode: "EDGE_DEFAULT_NOT_DIRECTED",
+        errorDescription: "GRNsight interprets the graph as directed unconditionally."
+    }
+};
+&nbsp;
+*/
+&nbsp;
+var graphmlErrors = {
+    GRAPHML_GENERAL_SYNTAX_ERROR: function (error) {
+        return {
+            errorCode: "GRAPHML_GENERAL_SYNTAX_ERROR",
+            possibleCause: "There are a number of things that could've triggered this error, but the general gist" +
+                           " is that there is something syntactically wrong with your file. The parcer we are using" +
+                           " has associated your syntax error with this message: " + error + ".",
+            suggestedFix:  "Please check the format of your file and make sure that it is in line with our" +
+                           " Documentation page. Some common errors to check for are missing start/end tags, missing" +
+                           " quotation marks, and proper spelling of all attribute names."
+        };
+    }
+};
+&nbsp;
+module.exports = function (graphml) {
+    var graph;
+    var key;
+&nbsp;
+    var network = {
+        genes: [],
+        links: [],
+        errors: [],
+        warnings: [],
+        positiveWeights: [],
+        negativeWeights: [],
+        sheetType: constants.UNWEIGHTED
+    };
+&nbsp;
+    var readErrorFromErr = function (err) {
+        var isolatedError = (err + "").split(": ")[1];
+        isolatedError = isolatedError.substring(0, isolatedError.length - 5);
+        return isolatedError;
+    };
+&nbsp;
+    var pushRelevantError = function (err) {
+        var parseError = readErrorFromErr(err);
+        network.errors.push(graphmlErrors.GRAPHML_GENERAL_SYNTAX_ERROR(parseError));
+&nbsp;
+        // TODO Ask Dondi about how to do this in a more data-driven manner.
+&nbsp;
+        // switch(parseError) {
+        //   case "Invalid attribute name":
+        //     network.errors.push(graphmlErrors.UNKNOWN_ERROR);
+        //     break;
+        //   default:
+        //     network.errors.push(graphmlErrors.GRAPHML_GENERAL_SYNTAX_ERROR);
+        // }
+    };
+&nbsp;
+    // Note this relies on sync execution being the default, *not* async.
+    //
+    // Limitation is due to the way the import function is expected to return its result.
+    // To address this later on, import functions should accept a callback instead.
+    parseString(graphml, function (err, result) {
+        if (err) {
+            pushRelevantError(err);
+        } else {
+            // Quick fix to handle completely empty GraphML file. #428
+            <span class="missing-if-branch" title="if path not taken" >I</span>if (!result) {
+<span class="cstat-no" title="statement not covered" >                return semanticChecker(network);</span>
+            }
+            key = result.graphml &amp;&amp; result.graphml.key;
+            graph = result.graphml &amp;&amp; result.graphml.graph &amp;&amp; result.graphml.graph[0];
+        }
+    });
+&nbsp;
+    if (network.errors.length &gt; 0) {
+        return network;
+    }
+&nbsp;
+    var findKeyId = function (attrName, attrFor) {
+        return key &amp;&amp; key.reduce(function (keyId, keyElement) {
+            return keyId || (keyElement.$["attr.name"] === attrName &amp;&amp;
+              (attrFor ? keyElement.$.for === attrFor : true) ? keyElement.$.id : null);
+        }, "");
+    };
+&nbsp;
+    var findYFilesKeyId = function (yFilesType, attrFor) {
+        return key &amp;&amp; key.reduce(function (keyId, keyElement) {
+            return keyId || (keyElement.$["yfiles.type"] === yFilesType &amp;&amp;
+              (attrFor ? keyElement.$.for === attrFor : <span class="branch-1 cbranch-no" title="branch not covered" >true)</span> ? keyElement.$.id : null);
+        }, "");
+    };
+&nbsp;
+    var findKey = function (element, keyId) {
+        <span class="missing-if-branch" title="if path not taken" >I</span>if (!element.data) {
+<span class="cstat-no" title="statement not covered" >            return null;</span>
+        }
+&nbsp;
+        var keyMatch = element.data.filter(function (data) {
+            return data.$.key === keyId;
+        });
+&nbsp;
+        return keyMatch.length ? keyMatch[0]._ : <span class="branch-1 cbranch-no" title="branch not covered" >null;</span>
+    };
+&nbsp;
+    var findYFilesKey = function (element, keyId) {
+        if (!element.data) {
+            return null;
+        }
+&nbsp;
+        var keyMatch = element.data.filter(function (data) {
+            return data.$.key === keyId;
+        });
+&nbsp;
+        return keyMatch.length ? keyMatch[0] : <span class="branch-1 cbranch-no" title="branch not covered" >null;</span>
+    };
+&nbsp;
+&nbsp;
+    // We will only consider GraphML data to be weighted if:
+    // (a) A key for the weight attribute is present, AND
+    // (b) Every edge in the file has a data element with that key
+    var weightId = findKeyId("weight"/*, "edge"*/);
+    // Edge condition temporarily commented out pending Cytoscape GraphML export bug fix.
+&nbsp;
+    if (weightId &amp;&amp; graph.edge &amp;&amp; graph.edge.every(function (edge) { // What
+        return edge.data &amp;&amp; edge.data.some(function (data) {
+            return data.$.key === weightId &amp;&amp; !isNaN(+data._);
+        });
+    })) {
+        network.sheetType = constants.WEIGHTED;
+    } else if (weightId) {
+        network.warnings.push(constants.warnings.EDGES_WITHOUT_WEIGHTS);
+    }
+&nbsp;
+    if (!graph.$ || graph.$.edgedefault !== "directed") {
+        network.warnings.push(constants.warnings.EDGE_DEFAULT_NOT_DIRECTED);
+    }
+&nbsp;
+    var nameId = findKeyId("name", "node");
+    var sharedNameId = findKeyId("shared name", "node");
+    var yFilesNodeId = findYFilesKeyId("nodegraphics", "node");
+&nbsp;
+    var geneIds = [];
+    <span class="missing-if-branch" title="else path not taken" >E</span>if (graph.node) {
+        network.genes = graph.node.map(function (node) {
+            var nodeName = node.$.id;
+&nbsp;
+            if (yFilesNodeId) {
+                var yNodeGraphics = findYFilesKey(node, yFilesNodeId);
+                if (yNodeGraphics) {
+                    var yShapeNode = yNodeGraphics["y:ShapeNode"];
+                    var yNodeLabel = yShapeNode &amp;&amp; yShapeNode[0]["y:NodeLabel"];
+                    <span class="missing-if-branch" title="else path not taken" >E</span>if (yNodeLabel) {
+                        // The yNodeLabel may either be plain text or have subelements, so...
+                        nodeName = (yNodeLabel[0]._ || yNodeLabel[0]).trim();
+                    }
+                }
+            }
+&nbsp;
+            if (sharedNameId) {
+                var sharedName = findKey(node, sharedNameId);
+                <span class="missing-if-branch" title="else path not taken" >E</span>if (sharedName) {
+                    nodeName = sharedName;
+                }
+            }
+&nbsp;
+            if (nameId) {
+                var name = findKey(node, nameId);
+                <span class="missing-if-branch" title="else path not taken" >E</span>if (name) {
+                    nodeName = name;
+                }
+            }
+&nbsp;
+            geneIds.push(node.$.id);
+            return { name: nodeName };
+        });
+    }
+&nbsp;
+    <span class="missing-if-branch" title="else path not taken" >E</span>if (graph.edge) {
+        graph.edge.forEach(function (edge) {
+            var link = {
+                source: geneIds.indexOf(edge.$.source),
+                target: geneIds.indexOf(edge.$.target)
+            };
+&nbsp;
+            if (link.source === constants.NOT_FOUND || link.target === constants.NOT_FOUND) {
+                return;
+            }
+&nbsp;
+            if (network.sheetType === constants.WEIGHTED) {
+                link.value = +edge.data.filter(function (data) {
+                    return data.$.key === weightId;
+                })[0]._;
+            }
+&nbsp;
+            network.links.push(link);
+        });
+    }
+&nbsp;
+  return (network.errors.length === 0) ? semanticChecker(network) : <span class="branch-1 cbranch-no" title="branch not covered" >network;</span>
+&nbsp;
+};
+&nbsp;</pre></td></tr>
+</table></pre>
+<div class='push'></div><!-- for sticky footer -->
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+<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)
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+</div>
+<script src="../../prettify.js"></script>
+<script>
+window.onload = function () {
+        if (typeof prettyPrint === 'function') {
+            prettyPrint();
+        }
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