Mercurial > repos > eduardo > annotateviz

annotate static/js/app.js @ 0:7537482eed36 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty
author eduardo
date Sat, 17 Jun 2017 13:31:06 -0400
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7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty
eduardo
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1 var app = angular.module('app', ['ngTouch', 'ui.grid','ui.grid.expandable', 'ui.grid.pagination']);
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2
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3 app.service('transcriptome', [
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty
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4 '$http', 'uiGridConstants', function($http, uiGridConstants) {
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5
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6 var paginationOptions = {
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7 pageNumber: 1,
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8 pageSize: 25,
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9 sort: null
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10 };
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11 var query ={
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12 baseurl: '/api/datasets/'+hdaId+'?provider=sqlite-dict&data_type=raw_data&query=',
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13 groupby: '%20group%20by%20gene_id%20',
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty
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14 genesel: 'select%20t.gene_id,sum(e.frag_count)%20as%20e_count%20from%20expression%20e,transcript%20t%20',
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15 diffsel:"select%20feature_name as gene_id,sample_id_A||'vs'||sample_id_b%20as%20contrast,log_fold_change%20as%20logfc,p_value,fdr%20from%20diff_expression%20d%20",
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16 diffwhere: 'where%20d.feature_name=t.gene_id%20',
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17 totsel: 'select%20gene_id%20from%20',
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18 transjoin: 'transcript%20t,%20orf%20o,blastdbase%20x%20',
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty
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19 tottable: 'transcript%20t,%20orf%20o,blastdbase%20x%20,%20diff_expression%20d%20,hmmerdbase%20h%20',
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20 pfamjoin: 'transcript%20t,%20orf%20o,hmmerdbase%20h%20',
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21 genewhere: 'where%20e.feature_name=t.gene_id%20',
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22 transwhere: 'where%20t.transcript_id=o.transcript_id%20and%20x.trinityid=t.transcript_id%20',
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23 totwhere: 'where%20t.transcript_id=o.transcript_id%20and%20x.trinityid=t.transcript_id%20and%20h.queryprotid=o.orf_id%20and%20d.feature_name=t.gene_id%20',
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24 orfwhere: 'where%20t.transcript_id=o.transcript_id%20and%20x.Trinityid=o.orf_id%20',
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25 pfamwhere: 'where%20t.transcript_id=o.transcript_id%20and%20h.queryprotid=o.orf_id%20',
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26 group: 'group%20by%20gene_id%20',
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27 pfamsel: 'select%20t.gene_id,o.orf_id,h.pfam_id,h.hmmerdomain%20as%20h_domain,querystartalign,3*(queryendalign-querystartalign)/o.length%20as%20h_qcov,h.fullseqevalue%20as%20h_eval%20from%20',
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28 //transgroup: 'group%20by%20trans_id%20',
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29 //orfgroup: 'group%20by%20orf_id%20',
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30 filter: '',
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31 sorting: 'order%20by gene_id%20asc%20',
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32 paging: 'limit%20'+paginationOptions.pageSize+'%20offset%20 '+(paginationOptions.pageNumber - 1) * paginationOptions.pageSize,
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33 transsel: 'select%20distinct%20t.gene_id%20as%20gene_id,t.transcript_id%20as%20trans_id,length(sequence)%20as%20t_len,x.FullAccession%20as%20x_hit,abs(x.queryend-x.querystart)/o.length%20as%20x_qcov,x.percentidentity%20as%20x_id,x.evalue%20as%20x_eval,x.databasesource%20as%20x_source%20from%20',
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34 orfsel: 'select%20distinct%20t.gene_id%20as%20gene_id,o.orf_id%20,o.rend,o.lend,o.length%20as%20o_len,o.strand,x.FullAccession%20as%20p_hit,3*abs(x.queryend-x.querystart)/o.length%20as%20p_qcov,x.percentidentity%20as%20p_id,x.evalue%20as%20p_eval,x.databasesource%20as%20p_source%20from%20',
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35 }
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36
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37 mygridOptions = {
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38 enableHorizontalScrollbar: 0,
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39 enableVerticalScrollbar: 1,
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40 expandableRowTemplate: 'GridTemplate.html',
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41 expandableRowHeight: 180,
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42 //subGridVariable will be available in subGrid scope
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43 expandableRowScope: {
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44 subGridVariable: 'subGridScopeVariable'
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45 },
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46 // enableFiltering: true,
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47 // useExternalFiltering: true,
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48 paginationPageSizes: [25, 50],
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49 paginationPageSize: 25,
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50 useExternalPagination: true,
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51 useExternalSorting: true,
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52 columnDefs: [
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53 { name: 'gene_id', enableSorting: false },
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54 { name: 'e_count'}
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55 ],
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56 onRegisterApi: function(gridApi) {
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57 this.gridApi = gridApi;
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58 /*
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59 $scope.gridApi.core.on.sortChanged($scope, function(grid, sortColumns) {
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60 if (sortColumns.length == 0) {
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61 paginationOptions.sort = null;
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62 } else {
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63 paginationOptions.sort = sortColumns[0].sort.direction;
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64 }
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65 getPage();
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66 });
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67 */
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68 gridApi.pagination.on.paginationChanged(this, function (newPage, pageSize) {
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69 paginationOptions.pageNumber = newPage;
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70 paginationOptions.pageSize = pageSize;
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71 query.paging='limit%20'+paginationOptions.pageSize+'%20offset%20 '+(paginationOptions.pageNumber - 1) * paginationOptions.pageSize;
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72 getPage();
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73 });
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74 getPage();
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75 }
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76 };
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77
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78 var unpack = function(url) {
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79 $http.get(url)
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80 .success (function(response){
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81 return [].concat.apply([], response.data);
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82 });
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83 };
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84 var getPage = function() {
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85
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86
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87 var tot_url= query.totsel +query.tottable +query.totwhere+ query.group+query.filter;
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88 var gene_url= query.baseurl + query.genesel + query.genewhere+ 'and%20t.gene_id%20in%20('+tot_url+ query.sorting+query.paging+')'+query.group;
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89 var trans_url = query.baseurl + query.transsel +query.transjoin +query.transwhere+'and%20t.gene_id%20in%20('+tot_url+ query.sorting+query.paging+')'+query.group;
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90 var orf_url = query.baseurl + query.orfsel +query.transjoin +query.orfwhere+'and%20t.gene_id%20in%20('+tot_url+ query.sorting+query.paging+')'+query.group;
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91 var pfam_url = query.baseurl + query.pfamsel +query.pfamjoin +query.pfamwhere+'and%20t.gene_id%20in%20('+tot_url+ query.sorting+query.paging+')'+query.group;
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92 var diff_url = query.baseurl + query.diffsel +'where%20feature_name%20in%20('+tot_url+ query.sorting+query.paging+')';
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93
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94 $http.get(query.baseurl+tot_url)
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95 .success (function(response){
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96
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97 mygridOptions.totalItems = ([].concat.apply([], response.data)).length;
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98
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99 });
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100
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101
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102 trans_promise=$http.get(trans_url);
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103 $http.get(orf_url)
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104 .success (function(response){
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105 orfdata = [].concat.apply([], response.data);
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106 });
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107 $http.get(pfam_url)
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108 .success (function(response){
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109 pfamdata = [].concat.apply([], response.data);
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110 });
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111 $http.get(diff_url)
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112 .success (function(response){
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113 diffdata = [].concat.apply([], response.data);
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114 });
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115 trans_promise.then(function(response){ transdata = [].concat.apply([], response.data);
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116 $http.get(gene_url)
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117 .success (function(response){
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118 mygridOptions.data = [].concat.apply([], response.data);
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119 for(i = 0; i < mygridOptions.data.length; i++){
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120
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121 mygridOptions.data[i].subGridOptions1 = {
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122 enableVerticalScrollbars: 1,
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123
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124 columnDefs: [ {name:"trans_id", field:"trans_id"},{name:"t_len", field:"t_len"},{name:"x_hit", field:"x_hit"},{name:"x_qcov", field:"x_qcov"},
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125 ,{name:"x_id", field:"x_id"},{name:"x_eval", field:"x_eval"},{name:"x_source", field:"x_source"} ],
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126 data: transdata.filter(function(trans){return trans.gene_id===mygridOptions.data[i].gene_id;})
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127 }
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128 // for(j = 0; j < this.gridOptions.data[i].subGridOptions.data.length; j++){
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129
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130 mygridOptions.data[i].subGridOptions2 = {
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131 //enableVerticalScrollbars: 0,
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132
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133 columnDefs: [ {name:"orf_id", field:"orf_id"},{name:"rend", field:"rend"},{name:"lend", field:"lend"},{name:"o_len", field:"o_len"},{name:"strand", field:"strand"},{name:"p_hit", field:"p_hit"},{name:"p_qcov", field:"p_qcov"},
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134 ,{name:"p_id", field:"p_id"},{name:"p_eval", field:"p_eval"},{name:"p_source", field:"p_source"}],
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135 data: orfdata.filter(function(orf){return orf.gene_id===mygridOptions.data[i].gene_id;})
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136 }
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137 mygridOptions.data[i].subGridOptions3 = {
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138 //enableVerticalScrollbars: 0,
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139 columnDefs: [ {name:"orf_id", field:"orf_id"}, {name:"pfam_id", field:"pfam_id"},{name:"hmmerdomain", field:"h_domain"},{name:"querystartalign", field:"QueryStartAlign"},{name:"h_qcov", field:"h_qcov"},{name:"h_eval", field:"h_eval"} ],
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140 data: pfamdata.filter(function(pfam){return pfam.gene_id===mygridOptions.data[i].gene_id;})
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141 }
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142 mygridOptions.data[i].subGridOptions0 = {
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143 //enableVerticalScrollbars: 0,
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144 columnDefs: [ {name:"contrast", field:"contrast"},{name:"logfc", field:"logfc"},{name:"p_value", field:"p_value"},{name:"fdr", field:"fdr"} ],
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145 data: diffdata.filter(function(diff){return diff.gene_id===mygridOptions.data[i].gene_id;})
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146 }
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147 // }
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148 }
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149
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150 });//end get gene_url
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151 });//end promise
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152 };
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153 // getPage();
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154 return {filter: (function() {
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155 if (this.filterValue.length>0){
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156 query.filter= 'having%20'+this.filterValue+'%20';
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157 }
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158 else {
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159 query.filter='';
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160 }
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161 getPage();
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162 console.log('filtering');
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163 }),
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164 gridOptions: mygridOptions
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165 };
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166
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167 }
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168 ]);
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169 app.controller('MainCtrl',['$scope', 'transcriptome', function($scope,transcriptome) {
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty
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170 $scope.gridOptions=transcriptome.gridOptions;
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty
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171 $scope.filter=transcriptome.filter;
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty
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172 }
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty
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173 ]);