grnsight 3.0.0 → 5.1.0

package/coverage/lcov-report/controllers/semantic-checker.js.html

@@ -16,298 +16,302 @@
 <div class='wrapper'>
   <div class='pad1'>
     <h1>
-      <a href="../index.html">all files</a> / <a href="index.html">controllers/</a> semantic-checker.js
+      <a href="../index.html">All files</a> / <a href="index.html">controllers</a> semantic-checker.js
     </h1>
     <div class='clearfix'>
       <div class='fl pad1y space-right2'>
-        <span class="strong">76.12% </span>
+        <span class="strong">14.93% </span>
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+        <span class='fraction'>10/67</span>
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-        <span class="strong">95.45% </span>
+        <span class="strong">0% </span>
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+        <span class='fraction'>0/22</span>
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+        <span class="strong">0% </span>
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+        <span class='fraction'>0/18</span>
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+        <span class="strong">14.93% </span>
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+        <span class='fraction'>10/67</span>
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+    <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 medium'></div>
+  <div class='status-line low'></div>
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+<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-neutral">&nbsp;</span>
+<span class="cline-any cline-neutral">&nbsp;</span>
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 <span class="cline-any cline-neutral">&nbsp;</span>
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@@ -354,7 +358,7 @@
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-<span class="cline-any cline-yes">2×</span>
+<span class="cline-any cline-no">&nbsp;</span>
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@@ -362,10 +366,11 @@
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-<span class="cline-any cline-yes">1×</span>
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+<span class="cline-any cline-no">&nbsp;</span>
+<span class="cline-any cline-neutral">&nbsp;</span>
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@@ -381,7 +386,7 @@
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-<span class="cline-any cline-yes">2×</span>
+<span class="cline-any cline-no">&nbsp;</span>
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@@ -390,7 +395,7 @@
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-<span class="cline-any cline-yes">2×</span>
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@@ -399,7 +404,7 @@
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-<span class="cline-any cline-yes">125×</span>
+<span class="cline-any cline-no">&nbsp;</span>
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@@ -460,80 +465,80 @@
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+<span class="cline-any cline-no">&nbsp;</span>
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+<span class="cline-any cline-yes">1x</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>
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 <span class="cline-any cline-neutral">&nbsp;</span></td><td class="text"><pre class="prettyprint lang-js">// var multiparty = require("multiparty");
 // var xlsx = require("node-xlsx");
@@ -554,36 +559,36 @@ var numbersToLetters = {
 };
 &nbsp;
 var warningsList = {
-    missingSourceGeneWarning: <span class="fstat-no" title="function not covered" >function (row, column) {</span>
-<span class="cstat-no" title="statement not covered" >        var colLetter = numbersToLetters[column];</span>
-<span class="cstat-no" title="statement not covered" >        var rowNum = row + 1;</span>
+    missingSourceGeneWarning: <span class="fstat-no" title="function not covered" >fu</span>nction (row, column) {
+        var colLetter = <span class="cstat-no" title="statement not covered" >numbersToLetters[column];</span>
+        var rowNum = <span class="cstat-no" title="statement not covered" >row + 1;</span>
 <span class="cstat-no" title="statement not covered" >        return {</span>
             warningCode: "MISSING_SOURCE",
             errorDescription: "A source gene name is missing in cell " + colLetter + rowNum + "."
         };
     },
 &nbsp;
-    missingTargetGeneWarning: <span class="fstat-no" title="function not covered" >function (row, column) {</span>
-<span class="cstat-no" title="statement not covered" >        var colLetter = numbersToLetters[column];</span>
-<span class="cstat-no" title="statement not covered" >        var rowNum = row + 1;</span>
+    missingTargetGeneWarning: <span class="fstat-no" title="function not covered" >fu</span>nction (row, column) {
+        var colLetter = <span class="cstat-no" title="statement not covered" >numbersToLetters[column];</span>
+        var rowNum = <span class="cstat-no" title="statement not covered" >row + 1;</span>
 <span class="cstat-no" title="statement not covered" >        return {</span>
             warningCode: "MISSING_TARGET",
             errorDescription: "A target gene name is missing in cell " + colLetter + rowNum + "."
         };
     },
 &nbsp;
-    invalidMatrixDataWarning: <span class="fstat-no" title="function not covered" >function (row, column) {</span>
-<span class="cstat-no" title="statement not covered" >        var colLetter = numbersToLetters[column];</span>
-<span class="cstat-no" title="statement not covered" >        var rowNum = row + 1;</span>
+    invalidMatrixDataWarning: <span class="fstat-no" title="function not covered" >fu</span>nction (row, column) {
+        var colLetter = <span class="cstat-no" title="statement not covered" >numbersToLetters[column];</span>
+        var rowNum = <span class="cstat-no" title="statement not covered" >row + 1;</span>
 <span class="cstat-no" title="statement not covered" >        return {</span>
             warningCode: "INVALID_DATA",
             errorDescription: "The value in cell " + colLetter + rowNum + ", is undefined."
         };
     },
 &nbsp;
-    randomDataWarning: <span class="fstat-no" title="function not covered" >function (type, row, column) {</span>
-<span class="cstat-no" title="statement not covered" >        var colLetter = numbersToLetters[column];</span>
-<span class="cstat-no" title="statement not covered" >        var rowNum = row + 1;</span>
+    randomDataWarning: <span class="fstat-no" title="function not covered" >fu</span>nction (type, row, column) {
+        var colLetter = <span class="cstat-no" title="statement not covered" >numbersToLetters[column];</span>
+        var rowNum = <span class="cstat-no" title="statement not covered" >row + 1;</span>
 <span class="cstat-no" title="statement not covered" >        return {</span>
             warningCode: "RANDOM_DATA",
             errorDescription: "The value in cell " + colLetter + rowNum + ", has a corresponding source" +
@@ -591,16 +596,16 @@ var warningsList = {
         };
     },
 &nbsp;
-    emptyRowWarning: <span class="fstat-no" title="function not covered" >function (row) {</span>
-<span class="cstat-no" title="statement not covered" >        var rowNum = row + 1;</span>
+    emptyRowWarning: <span class="fstat-no" title="function not covered" >fu</span>nction (row) {
+        var rowNum = <span class="cstat-no" title="statement not covered" >row + 1;</span>
 <span class="cstat-no" title="statement not covered" >        return {</span>
             warningCode: "EMPTY_ROW",
             errorDescription: "Row " + rowNum + " was found to contain no data."
         };
     },
 &nbsp;
-    networkSizeWarning: function (genesLength, edgesLength) {
-        return {
+    networkSizeWarning: <span class="fstat-no" title="function not covered" >fu</span>nction (genesLength, edgesLength) {
+<span class="cstat-no" title="statement not covered" >        return {</span>
             warningCode: "INVALID_NETWORK_SIZE",
             errorDescription: "Your network has " + genesLength + " genes, and " + edgesLength +
             " edges. Please note that networks are recommended to have less than 50 genes and 100 edges."
@@ -610,15 +615,16 @@ var warningsList = {
 &nbsp;
 var errorList = {
 &nbsp;
-    emptyNetworkError: function () {
-        return {
+    emptyNetworkError: <span class="fstat-no" title="function not covered" >fu</span>nction () {
+<span class="cstat-no" title="statement not covered" >        return {</span>
             errorCode: "EMPTY_NETWORK_ERROR",
-            possibleCause: "GRNsight detects that the file you uploaded is empty and does not contain any network information.",
+            possibleCause: "GRNsight detects that the file you uploaded is empty and \
+            does not contain any network information.",
             suggestedFix: "Please review the file and ensure that it specifies a network."
-        }
+        };
     },
 &nbsp;
-    semanticDuplicateGeneError: <span class="fstat-no" title="function not covered" >function(geneName) {</span>
+    semanticDuplicateGeneError: <span class="fstat-no" title="function not covered" >fu</span>nction (geneName) {
 <span class="cstat-no" title="statement not covered" >        return {</span>
             errorCode: "SEMANTIC_DUPLICATE_GENE",
             possibleCause: "There exists a duplicate for " + geneName + ".",
@@ -626,8 +632,8 @@ var errorList = {
         };
     },
 &nbsp;
-    geneLengthError: function (geneName) {
-        return {
+    geneLengthError: <span class="fstat-no" title="function not covered" >fu</span>nction (geneName) {
+<span class="cstat-no" title="statement not covered" >        return {</span>
             errorCode: "INVALID_GENE_LENGTH",
             possibleCause: "Gene " + geneName + " is more than 12 characters in length.",
             suggestedFix: "Genes may only be between 1 and 12 characters in length. Please" +
@@ -635,8 +641,8 @@ var errorList = {
         };
     },
 &nbsp;
-    networkSizeError: function (genesLength, edgesLength) {
-        return {
+    networkSizeError: <span class="fstat-no" title="function not covered" >fu</span>nction (genesLength, edgesLength) {
+<span class="cstat-no" title="statement not covered" >        return {</span>
             errorCode: "INVALID_NETWORK_SIZE",
             possibleCause: "This network has " + genesLength + " genes, and " + edgesLength + " edges.",
             suggestedFix: "Networks may not have more than 75 genes or 150 edges. Please reduce the size" +
@@ -644,8 +650,8 @@ var errorList = {
         };
     },
 &nbsp;
-    specialCharacterError: function (geneName) {
-        return {
+    specialCharacterError: <span class="fstat-no" title="function not covered" >fu</span>nction (geneName) {
+<span class="cstat-no" title="statement not covered" >        return {</span>
             errorCode: "INVALID_CHARACTER",
             possibleCause: "The value under gene name " + geneName + " contains invalid character.",
             suggestedFix: "Please ensure all values in the data does not contain special characters" +
@@ -706,80 +712,80 @@ var addWarning = function (network, message) {
 };
 */
 &nbsp;
-var checkNetworkSize = function(errorArray, warningArray, genesList, positiveWeights, negativeWeights) {
-    var genesLength = genesList.length;
-    var edgesLength = positiveWeights.length + negativeWeights.length;
-    var GENE_MAX_WARNING = 50;
-    var EDGE_MAX_WARNING = 100;
-    var GENE_MAX_ERROR = 75;
-    var EDGE_MAX_ERROR = 150;
+var checkNetworkSize = <span class="fstat-no" title="function not covered" >fu</span>nction (errorArray, warningArray, genesList, positiveWeights, negativeWeights) {
+    var genesLength = <span class="cstat-no" title="statement not covered" >genesList.length;</span>
+    var edgesLength = <span class="cstat-no" title="statement not covered" >positiveWeights.length + negativeWeights.length;</span>
+    var GENE_MAX_WARNING = <span class="cstat-no" title="statement not covered" >50;</span>
+    var EDGE_MAX_WARNING = <span class="cstat-no" title="statement not covered" >100;</span>
+    var GENE_MAX_ERROR = <span class="cstat-no" title="statement not covered" >75;</span>
+    var EDGE_MAX_ERROR = <span class="cstat-no" title="statement not covered" >150;</span>
 &nbsp;
-    if ((genesLength &gt;= GENE_MAX_WARNING &amp;&amp; genesLength &lt; GENE_MAX_ERROR) ||
+<span class="cstat-no" title="statement not covered" >    if ((genesLength &gt;= GENE_MAX_WARNING &amp;&amp; genesLength &lt; GENE_MAX_ERROR) ||</span>
       (edgesLength &gt;= EDGE_MAX_WARNING &amp;&amp; edgesLength &lt; EDGE_MAX_ERROR)) {
-        warningArray.push(warningsList.networkSizeWarning(genesLength, edgesLength));
-    } else if (genesLength &gt;= GENE_MAX_ERROR || edgesLength &gt;= EDGE_MAX_ERROR) {
-        errorArray.push(errorList.networkSizeError(genesLength, edgesLength));
+<span class="cstat-no" title="statement not covered" >        warningArray.push(warningsList.networkSizeWarning(genesLength, edgesLength));</span>
+    } else <span class="cstat-no" title="statement not covered" >if (genesLength &gt;= GENE_MAX_ERROR || edgesLength &gt;= EDGE_MAX_ERROR) {</span>
+<span class="cstat-no" title="statement not covered" >        errorArray.push(errorList.networkSizeError(genesLength, edgesLength));</span>
     }
 };
 &nbsp;
-var checkDuplicateErrors = function (errorArray) {
-    for (var i = 0; i &lt; errorArray.length; i++) {
-        if (errorArray[i].errorCode === "DUPLICATE_GENE") {
-            return true;
+var checkDuplicateErrors = <span class="fstat-no" title="function not covered" >fu</span>nction (errorArray) {
+<span class="cstat-no" title="statement not covered" >    for (var i = 0; i &lt; errorArray.length; i++) {</span>
+<span class="cstat-no" title="statement not covered" >        if (errorArray[i].errorCode === "DUPLICATE_GENE") {</span>
+<span class="cstat-no" title="statement not covered" >            return true;</span>
         }
     }
 };
 &nbsp;
-var checkDuplicates = function(errorArray, genesList) {
-    if (!checkDuplicateErrors(errorArray)) {
-        var genesName = [];
-        for (var i = 0; i &lt; genesList.length; i++) {
-            genesName.push(genesList[i].name);
+var checkDuplicates = <span class="fstat-no" title="function not covered" >fu</span>nction (errorArray, genesList) {
+<span class="cstat-no" title="statement not covered" >    if (!checkDuplicateErrors(errorArray)) {</span>
+        var genesName = <span class="cstat-no" title="statement not covered" >[];</span>
+<span class="cstat-no" title="statement not covered" >        for (var i = 0; i &lt; genesList.length; i++) {</span>
+<span class="cstat-no" title="statement not covered" >            genesName.push(genesList[i].name);</span>
         }
 &nbsp;
-        genesName.sort();
-        for (var j = 0; j &lt; genesName.length - 1; j++) {
-            <span class="missing-if-branch" title="if path not taken" >I</span>if (genesName[j] === genesName[j + 1]) {
+<span class="cstat-no" title="statement not covered" >        genesName.sort();</span>
+<span class="cstat-no" title="statement not covered" >        for (var j = 0; j &lt; genesName.length - 1; j++) {</span>
+<span class="cstat-no" title="statement not covered" >            if (genesName[j] === genesName[j + 1]) {</span>
 <span class="cstat-no" title="statement not covered" >                errorArray.push(errorList.semanticDuplicateGeneError(genesName[j]));</span>
             }
         }
     }
 };
 &nbsp;
-var checkGeneLength = function(errorArray, genesList) {
+var checkGeneLength = <span class="fstat-no" title="function not covered" >fu</span>nction (errorArray, genesList) {
     // Check if any genes are over the gene length (currently 12)
-    var maxGeneLength = 12;
-    for (var i = 0; i &lt; genesList.length; i++) {
-        if (genesList[i].name.length &gt; maxGeneLength) {
-            errorArray.push(errorList.geneLengthError(genesList[i].name));
+    var maxGeneLength = <span class="cstat-no" title="statement not covered" >12;</span>
+<span class="cstat-no" title="statement not covered" >    for (var i = 0; i &lt; genesList.length; i++) {</span>
+<span class="cstat-no" title="statement not covered" >        if (genesList[i].name.length &gt; maxGeneLength) {</span>
+<span class="cstat-no" title="statement not covered" >            errorArray.push(errorList.geneLengthError(genesList[i].name));</span>
         }
     }
 };
 &nbsp;
-var checkSpecialCharacter = function (errorArray, genesList) {
-    var regex = /[^a-z0-9\_\-]/gi;
-    for (var i = 0; i &lt; genesList.length; i++) {
-        if (genesList[i].name.match(regex) !== null) {
-            errorArray.push(errorList.specialCharacterError(genesList[i].name));
+var checkSpecialCharacter = <span class="fstat-no" title="function not covered" >fu</span>nction (errorArray, genesList) {
+    var regex = <span class="cstat-no" title="statement not covered" >/[^a-z0-9\_\-]/gi;</span>
+<span class="cstat-no" title="statement not covered" >    for (var i = 0; i &lt; genesList.length; i++) {</span>
+<span class="cstat-no" title="statement not covered" >        if (genesList[i].name.match(regex) !== null) {</span>
+<span class="cstat-no" title="statement not covered" >            errorArray.push(errorList.specialCharacterError(genesList[i].name));</span>
         }
     }
 };
 &nbsp;
-var checkIfEmptyNetwork = function (errorArray, genesList) {
-    if (genesList.length === 0) {
-        errorArray.push(errorList.emptyNetworkError());
+var checkIfEmptyNetwork = <span class="fstat-no" title="function not covered" >fu</span>nction (errorArray, genesList) {
+<span class="cstat-no" title="statement not covered" >    if (genesList.length === 0) {</span>
+<span class="cstat-no" title="statement not covered" >        errorArray.push(errorList.emptyNetworkError());</span>
     }
-}
+};
 &nbsp;
 // TODO Entry-point semantic checker function goes here.
-module.exports = function (network) {
-    checkSpecialCharacter(network.errors, network.genes);
-    checkDuplicates(network.errors, network.genes);
-    checkGeneLength(network.errors, network.genes);
-    checkNetworkSize(network.errors, network.warnings, network.genes, network.positiveWeights, network.negativeWeights);
-    checkIfEmptyNetwork(network.errors, network.genes);
+module.exports = <span class="fstat-no" title="function not covered" >fu</span>nction (network) {
+<span class="cstat-no" title="statement not covered" >    checkSpecialCharacter(network.errors, network.genes);</span>
+<span class="cstat-no" title="statement not covered" >    checkDuplicates(network.errors, network.genes);</span>
+<span class="cstat-no" title="statement not covered" >    checkGeneLength(network.errors, network.genes);</span>
+<span class="cstat-no" title="statement not covered" >    checkNetworkSize(network.errors, network.warnings, network.genes, network.positiveWeights, network.negativeWeights);</span>
+<span class="cstat-no" title="statement not covered" >    checkIfEmptyNetwork(network.errors, network.genes);</span>
     // We're done. Return the network.
-    return network;
+<span class="cstat-no" title="statement not covered" >    return network;</span>
 };
 &nbsp;</pre></td></tr>
 </table></pre>
@@ -787,7 +793,7 @@ module.exports = function (network) {
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 <div class='footer quiet pad2 space-top1 center small'>
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-  generated by <a href="http://istanbul-js.org/" target="_blank">istanbul</a> at Fri Sep 29 2017 00:22:47 GMT-0700 (PDT)
+  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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@@ -799,5 +805,6 @@ window.onload = function () {
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