grnsight 4.0.0 → 6.0.0

package/server/controllers/semantic-checker.js

@@ -6,171 +6,35 @@
 //
 // var helpers = require(__dirname + "/helpers");
 
-var numbersToLetters = {
-    0:"A", 1:"B", 2:"C", 3:"D", 4:"E", 5:"F", 6:"G", 7:"H", 8: "I", 9:"J", 10:"K", 11:"L", 12:"M", 13:"N",
-    14:"O", 15:"P", 16:"Q", 17:"R", 18:"S", 19:"T", 20:"U", 21:"V", 22:"W", 23:"X", 24:"Y", 25:"Z", 26:"AA",
-    27:"AB", 28:"AC", 29:"AD", 30:"AE", 31:"AF", 32:"AG", 33:"AH", 34:"AI", 35:"AJ", 36:"AK", 37:"AL", 38:"AM",
-    39:"AN", 40:"AO", 41:"AP", 42:"AQ", 43:"AR", 44:"AS", 45:"AT", 46:"AU", 47:"AV", 48:"AW", 49:"AX", 50:"AY",
-    51:"AZ", 52:"BA", 53:"BB", 54:"BC", 55:"BD", 56:"BE", 57:"BF", 58:"BG", 59:"BH", 60:"BI", 61:"BJ", 62:"BK",
-    63:"BL", 64:"BM", 65:"BN", 66:"BO", 67:"BP", 68:"BQ", 69:"BR", 70:"BS", 71:"BT", 72:"BU", 73:"BV", 74:"BW",
-    75:"BX", 76:"BY"
-};
-
-var warningsList = {
-    missingSourceGeneWarning: function (row, column) {
-        var colLetter = numbersToLetters[column];
-        var rowNum = row + 1;
-        return {
-            warningCode: "MISSING_SOURCE",
-            errorDescription: "A source gene name is missing in cell " + colLetter + rowNum + "."
-        };
-    },
-
-    missingTargetGeneWarning: function (row, column) {
-        var colLetter = numbersToLetters[column];
-        var rowNum = row + 1;
-        return {
-            warningCode: "MISSING_TARGET",
-            errorDescription: "A target gene name is missing in cell " + colLetter + rowNum + "."
-        };
-    },
-
-    invalidMatrixDataWarning: function (row, column) {
-        var colLetter = numbersToLetters[column];
-        var rowNum = row + 1;
-        return {
-            warningCode: "INVALID_DATA",
-            errorDescription: "The value in cell " + colLetter + rowNum + ", is undefined."
-        };
-    },
-
-    randomDataWarning: function (type, row, column) {
-        var colLetter = numbersToLetters[column];
-        var rowNum = row + 1;
-        return {
-            warningCode: "RANDOM_DATA",
-            errorDescription: "The value in cell " + colLetter + rowNum + ", has a corresponding source" +
-            " and/or target gene that is detected as " + type + "."
-        };
-    },
-
-    emptyRowWarning: function (row) {
-        var rowNum = row + 1;
-        return {
-            warningCode: "EMPTY_ROW",
-            errorDescription: "Row " + rowNum + " was found to contain no data."
-        };
-    },
-
-    networkSizeWarning: function (genesLength, edgesLength) {
-        return {
-            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."
-        };
-    },
-};
-
-var errorList = {
-
-    emptyNetworkError: function () {
-        return {
-            errorCode: "EMPTY_NETWORK_ERROR",
-            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."
-        };
-    },
-
-    semanticDuplicateGeneError: function (geneName) {
-        return {
-            errorCode: "SEMANTIC_DUPLICATE_GENE",
-            possibleCause: "There exists a duplicate for " + geneName + ".",
-            suggestedFix: "Please remove the duplicate gene and submit again."
-        };
-    },
-
-    geneLengthError: function (geneName) {
-        return {
-            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" +
-                " shorten the name and submit again."
-        };
-    },
-
-    networkSizeError: function (genesLength, edgesLength) {
-        return {
-            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" +
-            " of your network and try again."
-        };
-    },
-
-    specialCharacterError: function (geneName) {
-        return {
-            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" +
-            " except for '-' and '_'."
-        };
-    },
-
-    errorsCountError: {
-        errorCode: "ERRORS_OVERLOAD",
-        possibleCause: "This network has over 20 errors.",
-        suggestedFix: "Please check the format of your spreadsheet with the guidlines outlined on the" +
-        "Documentation page and try again. If you fix these errors and try to upload again, there may be " +
-        "further errors detected. As a general approach for fixing the errors, consider copying and " +
-        "pasting just your adjacency matrix into a fresh Excel Workbook and saving it."
-    },
-
-    warningsCountError: {
-        errorCode: "WARNINGS_OVERLOAD",
-        possibleCause: "This network has over 75 warnings.",
-        suggestedFix: "Please check the format of your spreadsheet with the guidlines outlined on the" +
-        "Documentation page and try again. If you fix these errors and try to upload again, there may be " +
-        "further errors detected. As a general approach for fixing the errors, consider copying and " +
-        "pasting just your adjacency matrix into a fresh Excel Workbook and saving it."
-    },
-
-    unknownError: {
-        errorCode: "UNKNOWN_ERROR",
-        possibleCause: "An unexpected error occurred.",
-        suggestedFix: "Please contact the GRNsight team at kdahlquist@lmu.edu, and attach the spreadsheet you" +
-        " attempted to upload."
-    }
-
-};
+var constants = require(__dirname + "/workbook-constants");
 
 /*
 var addMessageToArray = function (messageArray, message) {
     messageArray.push(message);
 };
-var addError = function (network, message) {
-    var errorsCount = network.errors.length;
+var addError = function (workbook, message) {
+    var errorsCount = workbook.errors.length;
     var MAX_ERRORS = 20;
     if (errorsCount < MAX_ERRORS) {
-        addMessageToArray(network.errors, message);
+        addMessageToArray(workbook.errors, message);
     } else {
-        addMessageToArray(network.errors, errorList.errorsCountError);
+        addMessageToArray(workbook.errors, constants.errors.errorsCountError);
         return false;
     }
 };
-var addWarning = function (network, message) {
-    var warningsCount = network.warnings.length;
+var addWarning = function (workbook, message) {
+    var warningsCount = workbook.warnings.length;
     var MAX_WARNINGS = 75;
     if (warningsCount < MAX_WARNINGS) {
-        addMessageToArray(network.warnings, message);
+        addMessageToArray(workbook.warnings, message);
     } else {
-        addMessageToArray(network.errors, errorList.warningsCountError);
+        addMessageToArray(workbook.errors, constants.errors.warningsCountError);
         return false;
     }
 };
 */
 
-var checkNetworkSize = function (errorArray, warningArray, genesList, positiveWeights, negativeWeights) {
+var checkWorkbookSize = function (errorArray, warningArray, genesList, positiveWeights, negativeWeights) {
     var genesLength = genesList.length;
     var edgesLength = positiveWeights.length + negativeWeights.length;
     var GENE_MAX_WARNING = 50;
@@ -180,9 +44,9 @@ var checkNetworkSize = function (errorArray, warningArray, genesList, positiveWe
 
     if ((genesLength >= GENE_MAX_WARNING && genesLength < GENE_MAX_ERROR) ||
       (edgesLength >= EDGE_MAX_WARNING && edgesLength < EDGE_MAX_ERROR)) {
-        warningArray.push(warningsList.networkSizeWarning(genesLength, edgesLength));
+        warningArray.push(constants.warnings.workbookSizeWarning(genesLength, edgesLength));
     } else if (genesLength >= GENE_MAX_ERROR || edgesLength >= EDGE_MAX_ERROR) {
-        errorArray.push(errorList.networkSizeError(genesLength, edgesLength));
+        errorArray.push(constants.errors.workbookSizeError(genesLength, edgesLength));
     }
 };
 
@@ -204,7 +68,7 @@ var checkDuplicates = function (errorArray, genesList) {
         genesName.sort();
         for (var j = 0; j < genesName.length - 1; j++) {
             if (genesName[j] === genesName[j + 1]) {
-                errorArray.push(errorList.semanticDuplicateGeneError(genesName[j]));
+                errorArray.push(constants.errors.semanticDuplicateGeneError(genesName[j]));
             }
         }
     }
@@ -215,33 +79,37 @@ var checkGeneLength = function (errorArray, genesList) {
     var maxGeneLength = 12;
     for (var i = 0; i < genesList.length; i++) {
         if (genesList[i].name.length > maxGeneLength) {
-            errorArray.push(errorList.geneLengthError(genesList[i].name));
+            errorArray.push(constants.errors.geneLengthError(genesList[i].name));
         }
     }
 };
 
-var checkSpecialCharacter = function (errorArray, genesList) {
+var checkSpecialCharacter = function (errorArray, genesList, sheetName, row) {
     var regex = /[^a-z0-9\_\-]/gi;
     for (var i = 0; i < genesList.length; i++) {
         if (genesList[i].name.match(regex) !== null) {
-            errorArray.push(errorList.specialCharacterError(genesList[i].name));
+            errorArray.push(constants.errors.specialCharacterError(sheetName, genesList[i].name, row));
         }
     }
 };
 
-var checkIfEmptyNetwork = function (errorArray, genesList) {
+var checkIfEmptyWorkbook = function (errorArray, genesList) {
     if (genesList.length === 0) {
-        errorArray.push(errorList.emptyNetworkError());
+        errorArray.push(constants.errors.emptyWorkbookError());
     }
 };
 
 // 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);
-    // We're done. Return the network.
-    return network;
+module.exports = function (workbook) {
+    // Note: checkSpecialCharacter is unused, however it does not contain all of the parameters needed to
+    //       call the specialCharacterError in rorkbook-constants.js. As it has no real impact to the current codebase,
+    //       this is being mentioned because when this is implemented, it is a good thing to be aware of.
+    checkSpecialCharacter(workbook.errors, workbook.genes);
+    checkDuplicates(workbook.errors, workbook.genes);
+    checkGeneLength(workbook.errors, workbook.genes);
+    checkWorkbookSize(workbook.errors, workbook.warnings, workbook.genes,
+                    workbook.positiveWeights, workbook.negativeWeights);
+    checkIfEmptyWorkbook(workbook.errors, workbook.genes);
+    // We're done. Return the workbook.
+    return workbook;
 };

package/server/controllers/sif-constants.js

@@ -0,0 +1,36 @@
+module.exports = {
+    warnings: {
+        SIF_FORMAT_WARNING: {
+            warningCode: "SIF_FORMAT_WARNING",
+            errorDescription: " GRNsight has detected that there are no tabs in your file. The GRNsight specification" +
+                " for SIF files states that data must be delimited by tabs. Please review your data. This warning may" +
+                " suggest that your SIF file has comma separated data or contains no data at all. Additionally, valid" +
+                " networks which consist of single source nodes may also trigger this warning."
+        },
+    },
+
+    errors: {
+        SIF_UNWEIGHTED_RELATIONSHIP_TYPE_ERROR: {
+            errorCode: "SIF_UNWEIGHTED_RELATIONSHIP_TYPE_ERROR",
+            possibleCause: "The SIF importer detects an unweighted network with an unsupported relationship type.",
+            suggestedFix: "SIF files accepted by GRNsight must use 'pd' as the text string for the relationship" +
+                " type in unweighted networks. Please review the SIF input documentation. Additionally, this" +
+                " error may be have been caused by missing data in your file, which caused the importer to" +
+                " incorrectly interpret a source or target as the relationship."
+        },
+
+        SIF_MISSING_DATA_ERROR: {
+            errorCode: "SIF_MISSING_DATA_ERROR",
+            possibleCause: "GRNsight has detected that your SIF file contains missing data. ",
+            suggestedFix: "Please review the data. In a SIF file, each entry must have a source node, relationship" +
+                " type, and at least one target node, separated by tabs. An entry with a single source node is also" +
+                " allowed."
+        },
+
+        SIF_STRAY_DATA_ERROR: {
+            errorCode: "SIF_STRAY_DATA_ERROR",
+            possibleCause: "GRNsight has detected stray data and/or extraneous blank rows in your SIF file. ",
+            suggestedFix: "Please review the data and delete extraneous data from the file."
+        },
+    },
+};