1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 | 1 1 1 1 1 3 729 337 337 616 262 354 337 3 1 439 439 439 439 1 1 1 1 204 1 1 1 1 1 1 1 1 7 1 1 9 7 1 1 1 1 86 84 2 86 1 1 1 1 1 1 1 1 806 1 1 439 439 439 439 439 434 5 5 439 1 1 | /*jslint node: true */ /*jshint laxbreak: true */ "use strict"; var $ = require('jquery'); var _ = require('underscore'); var Evidence = require('./Evidence'); var Constants = require('./Constants'); var groupEvidencesByCode = function(features) { _.each(features, function(ft) { if (ft.evidences) { var evidences = {}; _.each(ft.evidences, function(ev) { if (evidences[ev.code]) { evidences[ev.code].push(ev.source); } else { evidences[ev.code] = [ev.source]; } }); ft.evidences = evidences; } }); return features; }; var setVariantData = function (source, d) { var datum = {}; Iif (source && (source !== Constants.getUniProtSource())) { datum.begin = d.begin; delete d.begin; datum.end = d.end; delete d.end; datum.wildType = d.wildType; delete d.wildType; datum.alternativeSequence = d.alternativeSequence; delete d.alternativeSequence; datum.sourceType = d.sourceType; delete d.sourceType; datum.type = d.type; delete d.type; datum.externalData = {}; datum.externalData[source] = d; } else { datum = d; } return datum; }; var DataLoader = function() { return { get: function(url) { return $.getJSON(url); }, groupFeaturesByCategory: function(features, sequence, source, includeVariants) { features = groupEvidencesByCode(features); var categories = _.groupBy(features, function(d) { return d.category; }); var variants; Iif (source && (source !== Constants.getUniProtSource()) && (includeVariants === true)) { variants = categories.VARIATION; delete categories.VARIATION; } else { delete categories.VARIANTS; } var orderedPairs = []; var categoriesNames = Constants.getCategoryNamesInOrder(); categoriesNames = _.pluck(categoriesNames, 'name'); var newCategoryNames = []; _.each(categories, function (catInfo, catKey) { Iif (!_.contains(categoriesNames, catKey)) { newCategoryNames.push({ name: catKey, label: Constants.convertNameToLabel(catKey), visualizationType: Constants.getVisualizationTypes().basic }); } }); Iif (newCategoryNames.length !== 0) { Constants.addCategories(newCategoryNames); categoriesNames = Constants.getCategoryNamesInOrder(); categoriesNames = _.pluck(categoriesNames, 'name'); } _.each(categoriesNames, function(catName){ if(categories[catName]){ orderedPairs.push([ catName, categories[catName] ]); } }); Iif (variants) { var orderedVariantPairs = DataLoader.processVariants(variants, sequence, source, true); orderedPairs.push(orderedVariantPairs[0]); } return orderedPairs; }, processProteomics: function(features) { features = groupEvidencesByCode(features); var types = _.map(features, function(d){ if (d.unique) { d.type = 'unique'; } else { d.type = 'non_unique'; } return d; }); return [['PROTEOMICS',types]]; }, processUngroupedFeatures: function(features) { return [[features[0].type, features]]; }, processVariants: function(variants, sequence, source, evidenceAlreadyGrouped) { Iif (source && (source !== Constants.getUniProtSource())) { _.each(variants, function(variant) { delete variant.category; }); } Eif (!evidenceAlreadyGrouped) { variants = groupEvidencesByCode(variants); } var mutationArray = []; mutationArray.push({ 'type': 'VARIANT', 'normal': '-', 'pos': 0, 'variants': [] }); var seq = sequence.split(''); _.each(seq, function(d, i) { mutationArray.push({ 'type': 'VARIANT', 'normal': seq[i], 'pos': i + 1, 'variants': [] }); }); mutationArray.push({ 'type': 'VARIANT', 'normal': '-', 'pos': seq.length + 1, 'variants': [] }); _.each(variants, function(d) { d.begin = +d.begin; d.end = d.end ? +d.end : d.begin; d.wildType = d.wildType ? d.wildType : sequence.substring(d.begin, d.end+1); d.sourceType = d.sourceType ? d.sourceType.toLowerCase() : d.sourceType; if ((1 <= d.begin) && (d.begin <= seq.length)) { mutationArray[d.begin].variants.push(setVariantData(source, d)); } else Eif ((seq.length + 1) === d.begin) { mutationArray[d.begin - 1].variants.push(setVariantData(source, d)); } Iif (d.consequence) { Constants.addConsequenceType(d.consequence); } }); return [['VARIATION', mutationArray]]; } }; }(); module.exports = DataLoader; |