From dc54db814ddf93e5750217f246bc04c3a414aab2 Mon Sep 17 00:00:00 2001 From: dennyverbeeck Date: Tue, 22 Nov 2016 14:48:21 +0100 Subject: [PATCH 001/136] Fix for ui autocomplete --- grails-app/views/RWG/_extSearchField.gsp | 2 +- grails-app/views/RWG/_extTagSearchField.gsp | 2 +- grails-app/views/uploadData/_extDiseaseSearchField.gsp | 2 +- grails-app/views/uploadData/_extSearchField.gsp | 2 +- web-app/js/datasetExplorer/omicsFilter.js | 2 +- web-app/js/rwgsearch.js | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/grails-app/views/RWG/_extSearchField.gsp b/grails-app/views/RWG/_extSearchField.gsp index a2926503d..f36e93cac 100644 --- a/grails-app/views/RWG/_extSearchField.gsp +++ b/grails-app/views/RWG/_extSearchField.gsp @@ -12,7 +12,7 @@ jQuery(document).ready(function() { jQuery("#" + escapedFieldName).val(id); return false; } - }).data("uiAutocomplete")._renderItem = function( ul, item ) { + }).data("ui-autocomplete")._renderItem = function( ul, item ) { return jQuery('
  • ') .data("item.autocomplete", item ) .append('' + item.category + '> ' + item.label + ' ' + item.synonyms + '') diff --git a/grails-app/views/RWG/_extTagSearchField.gsp b/grails-app/views/RWG/_extTagSearchField.gsp index a4079dd61..990f00c72 100644 --- a/grails-app/views/RWG/_extTagSearchField.gsp +++ b/grails-app/views/RWG/_extTagSearchField.gsp @@ -21,7 +21,7 @@ jQuery(document).ready(function() { newTag.hide().fadeIn('slow'); return false; } - }).data("uiAutocomplete")._renderItem = function( ul, item ) { + }).data("ui-autocomplete")._renderItem = function( ul, item ) { return jQuery('
  • ') .data("item.autocomplete", item ) .append('' + item.category + '> ' + item.label + ' ' + item.synonyms + '') diff --git a/grails-app/views/uploadData/_extDiseaseSearchField.gsp b/grails-app/views/uploadData/_extDiseaseSearchField.gsp index 1d1c94d97..21a19796d 100644 --- a/grails-app/views/uploadData/_extDiseaseSearchField.gsp +++ b/grails-app/views/uploadData/_extDiseaseSearchField.gsp @@ -67,7 +67,7 @@ jQuery(document).ready(function() { addObservationTag(diseaseName, sourceAndCode, escapedFieldName); } } - }).data("uiAutocomplete")._renderItem = function( ul, item ) { + }).data("ui-autocomplete")._renderItem = function( ul, item ) { return jQuery('
  • ') .data("item.autocomplete", item ) .append('' + item.category + '> ' + item.keyword + '') diff --git a/grails-app/views/uploadData/_extSearchField.gsp b/grails-app/views/uploadData/_extSearchField.gsp index f335ca0c9..0c78065ac 100644 --- a/grails-app/views/uploadData/_extSearchField.gsp +++ b/grails-app/views/uploadData/_extSearchField.gsp @@ -21,7 +21,7 @@ jQuery(document).ready(function() { updateStudyTable(studyId); return false; } - }).data("uiAutocomplete")._renderItem = function( ul, item ) { + }).data("ui-autocomplete")._renderItem = function( ul, item ) { return jQuery('
  • ') .data("item.autocomplete", item ) .append('' + item.category + '> ' + item.keyword + '') diff --git a/web-app/js/datasetExplorer/omicsFilter.js b/web-app/js/datasetExplorer/omicsFilter.js index a67072deb..c0d656d56 100644 --- a/web-app/js/datasetExplorer/omicsFilter.js +++ b/web-app/js/datasetExplorer/omicsFilter.js @@ -157,7 +157,7 @@ function addOmicsFilterAutocomplete() { response: function(event, ui) { omicsAutoCompleteList = ui.content.map(function(item) {return item.label;}); } - }).data("uiAutocomplete")._renderItem = function( ul, item ) { + }).data("ui-autocomplete")._renderItem = function( ul, item ) { var resulta = '' + item.label + ''; if (item.synonyms != null) { resulta += (item.synonyms + ''); diff --git a/web-app/js/rwgsearch.js b/web-app/js/rwgsearch.js index e806ad093..ae0f1e489 100644 --- a/web-app/js/rwgsearch.js +++ b/web-app/js/rwgsearch.js @@ -96,7 +96,7 @@ function addSearchAutoComplete() { var category = jQuery("#search-categories").val(); return false; } - }).data("uiAutocomplete")._renderItem = function( ul, item ) { + }).data("ui-autocomplete")._renderItem = function( ul, item ) { var resulta = '' + item.category + '> ' + item.label + ' '; if (item.synonyms != null) { resulta += (item.synonyms + ''); From 04e906ff834cb54a8a56c4a1d38ba2bb84aaf82d Mon Sep 17 00:00:00 2001 From: Peter Rice Date: Mon, 12 Dec 2016 19:21:58 +0000 Subject: [PATCH 002/136] version release 16.2 --- grails-app/conf/BuildConfig.groovy | 38 +++++++++++++++--------------- 1 file changed, 19 insertions(+), 19 deletions(-) diff --git a/grails-app/conf/BuildConfig.groovy b/grails-app/conf/BuildConfig.groovy index b92c2f3ab..344c26295 100644 --- a/grails-app/conf/BuildConfig.groovy +++ b/grails-app/conf/BuildConfig.groovy @@ -58,7 +58,7 @@ grails.project.dependency.resolution = { runtime 'org.javassist:javassist:3.16.1-GA' - compile 'org.transmartproject:transmart-core-api:16.2-SNAPSHOT' + compile 'org.transmartproject:transmart-core-api:16.2' compile 'antlr:antlr:2.7.7' compile 'net.sf.opencsv:opencsv:2.3' @@ -134,30 +134,30 @@ grails.project.dependency.resolution = { compile ":codenarc:0.21" if (!dm) { - runtime ':smart-r:1.1-STABLE-SNAPSHOT' - compile ':rdc-rmodules:16.2-SNAPSHOT' - runtime ':transmart-core:16.2-SNAPSHOT' - compile ':transmart-gwas:16.2-SNAPSHOT' + runtime ':smart-r:16.2-STABLE' + compile ':rdc-rmodules:16.2' + runtime ':transmart-core:16.2' + compile ':transmart-gwas:16.2' //// already included in transmart-gwas - //compile ':transmart-legacy-db:16.2-SNAPSHOT' + //compile ':transmart-legacy-db:16.2' //// already included in transmart-gwas - //compile ':folder-management:16.2-SNAPSHOT' + //compile ':folder-management:16.2' //// already included in transmart-gwas, folder-management - //compile ':search-domain:16.2-SNAPSHOT' + //compile ':search-domain:16.2' //// already included in search-domain, transmart-gwas, // folder-management - //compile ':biomart-domain:16.2-SNAPSHOT' + //compile ':biomart-domain:16.2' //// already included in biomart-domain - //compile ':transmart-java:16.2-SNAPSHOT' - runtime ':dalliance-plugin:16.2-SNAPSHOT' - runtime ':transmart-mydas:16.2-SNAPSHOT' - runtime ':transmart-rest-api:16.2-SNAPSHOT' - runtime ':blend4j-plugin:16.2-SNAPSHOT' - runtime ':transmart-metacore-plugin:16.2-SNAPSHOT' - runtime ':transmart-xnat-importer:16.2-SNAPSHOT' - runtime ':xnat-viewer:16.2-SNAPSHOT' - - test ':transmart-core-db-tests:16.2-SNAPSHOT' + //compile ':transmart-java:16.2' + runtime ':dalliance-plugin:16.2' + runtime ':transmart-mydas:16.2' + runtime ':transmart-rest-api:16.2' + runtime ':blend4j-plugin:16.2' + runtime ':transmart-metacore-plugin:16.2' + runtime ':transmart-xnat-importer:16.2' + runtime ':xnat-viewer:16.2' + + test ':transmart-core-db-tests:16.2' } else { dm.internalDependencies delegate } From b66ea481f421e96edd24223eaa8ce49d18c580ac Mon Sep 17 00:00:00 2001 From: Peter Rice Date: Tue, 13 Dec 2016 11:27:11 +0000 Subject: [PATCH 003/136] application version 16.2 --- application.properties | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/application.properties b/application.properties index 716d01e84..75d77d03f 100644 --- a/application.properties +++ b/application.properties @@ -3,4 +3,4 @@ app.grails.version=2.3.11 app.name=transmart app.servlet.version=2.5 -app.version=tranSMART 16.2 CI +app.version=tranSMART 16.2 From ed40d7716892989db71b8734bab3cdf4a534eea7 Mon Sep 17 00:00:00 2001 From: Peter Rice Date: Wed, 14 Dec 2016 14:38:07 +0000 Subject: [PATCH 004/136] updated browse delete study/program with children messages --- web-app/js/rwgsearch.js | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/web-app/js/rwgsearch.js b/web-app/js/rwgsearch.js index 935993e02..6cd529614 100644 --- a/web-app/js/rwgsearch.js +++ b/web-app/js/rwgsearch.js @@ -856,7 +856,7 @@ jQuery(document).ready(function() { var id = jQuery(this).attr('name'); var parent = jQuery(this).data('parent'); - if (confirm("Are you sure you want to delete this folder and the files and folders beneath it?")) { + if (confirm("Are you sure you want to delete this folder and the files and folders below it?")) { jQuery.ajax({ url:deleteFolderURL, data: {id: id}, @@ -905,7 +905,7 @@ jQuery(document).ready(function() { if (confirm("Are you sure you want to delete this study?")) { findChildByParent(id, function (hasChildren) { if (hasChildren) { - if (!confirm("This study contain beneath some elements it. Are you sure?")) { + if (!confirm("This study contains some elements below it. Are you sure?")) { return; } } @@ -933,7 +933,7 @@ jQuery(document).ready(function() { if (confirm("Are you sure you want to delete this program?")) { findChildByParent(id, function (hasChildren) { if (hasChildren) { - if (!confirm("This program contain beneath some elements it. Are you sure?")) { + if (!confirm("This program contains some elements below it. Are you sure?")) { return; } } @@ -1388,4 +1388,4 @@ function findChildByParent(parent, callFunc){ callFunc(hasChildred); } }); -} \ No newline at end of file +} From 39c15bb25d26495c898b818802e5f72ce437b6d2 Mon Sep 17 00:00:00 2001 From: Peter Rice Date: Wed, 14 Dec 2016 14:38:54 +0000 Subject: [PATCH 005/136] include GWAS-plink plugin --- grails-app/conf/BuildConfig.groovy | 2 ++ 1 file changed, 2 insertions(+) diff --git a/grails-app/conf/BuildConfig.groovy b/grails-app/conf/BuildConfig.groovy index 344c26295..c28cb86f0 100644 --- a/grails-app/conf/BuildConfig.groovy +++ b/grails-app/conf/BuildConfig.groovy @@ -138,6 +138,7 @@ grails.project.dependency.resolution = { compile ':rdc-rmodules:16.2' runtime ':transmart-core:16.2' compile ':transmart-gwas:16.2' + compile ':transmart-gwas-plink:16.2' //// already included in transmart-gwas //compile ':transmart-legacy-db:16.2' //// already included in transmart-gwas @@ -172,6 +173,7 @@ dm?.with { configureInternalPlugin 'runtime', 'transmart-core' configureInternalPlugin 'test', 'transmart-core-db-tests' configureInternalPlugin 'compile', 'transmart-gwas' + configureInternalPlugin 'compile', 'transmart-gwas-plink' configureInternalPlugin 'compile', 'transmart-java' configureInternalPlugin 'compile', 'biomart-domain' configureInternalPlugin 'compile', 'search-domain' From 9b481cc770cc7e089b649500f6e9aac2116d8c04 Mon Sep 17 00:00:00 2001 From: Peter Rice Date: Wed, 14 Dec 2016 15:11:34 +0000 Subject: [PATCH 006/136] simple version number --- application.properties | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/application.properties b/application.properties index 75d77d03f..a313c2cc7 100644 --- a/application.properties +++ b/application.properties @@ -3,4 +3,4 @@ app.grails.version=2.3.11 app.name=transmart app.servlet.version=2.5 -app.version=tranSMART 16.2 +app.version=16.2 From fbf6ab3aef1c93c1f38e3fb3511bb5284c97c7c5 Mon Sep 17 00:00:00 2001 From: Ruslan Forostianov Date: Thu, 15 Dec 2016 21:22:35 +0100 Subject: [PATCH 007/136] Escape collision of jq versions on the qurypanel. JQuery -> $j --- web-app/js/datasetExplorer/querypanels.js | 186 +++++++++++----------- 1 file changed, 93 insertions(+), 93 deletions(-) diff --git a/web-app/js/datasetExplorer/querypanels.js b/web-app/js/datasetExplorer/querypanels.js index 0d812d87b..ed27f1cb9 100644 --- a/web-app/js/datasetExplorer/querypanels.js +++ b/web-app/js/datasetExplorer/querypanels.js @@ -5,7 +5,7 @@ */ function prepareQueryPanels() { - var table = jQuery("#queryTable tr:last-of-type td") + var table = $j("#queryTable tr:last-of-type td") window.queryPanelNumber = 0 for (var i = 0; i < table.size(); i++) { @@ -13,7 +13,7 @@ function prepareQueryPanels() { appendQueryPanelInto(i + 1) } - jQuery("#queryPanel").click(function () { + $j("#queryPanel").click(function () { resetSelected() }) } @@ -26,12 +26,12 @@ function prepareQueryPanels() { */ function appendQueryPanelInto(subset) { - var clone = jQuery("#panelModel").clone().removeAttr('id').each(function () { - jQuery(this).html(this.innerHTML.replace(/\$n/g, window.queryPanelNumber++)).find("input[id^='panelInclude']").attr("checked", "checked") + var clone = $j("#panelModel").clone().removeAttr('id').each(function () { + $j(this).html(this.innerHTML.replace(/\$n/g, window.queryPanelNumber++)).find("input[id^='panelInclude']").attr("checked", "checked") }).attr('subset', subset) // Subsets are inflated by 1 - jQuery(jQuery("#queryTable tr:last-of-type td")[subset - 1]).append(clone) + $j($j("#queryTable tr:last-of-type td")[subset - 1]).append(clone) setupQueryPanelClone(clone) removeUselessPanels() } @@ -48,9 +48,9 @@ function appendItemFromConceptInto(destination, concept, invert) { var _panel = null if (typeof destination == "number") - _panel = jQuery(jQuery("#queryTable tr:last-of-type td")[destination - 1]).find('div[id^=panelBoxList]').last() + _panel = $j($j("#queryTable tr:last-of-type td")[destination - 1]).find('div[id^=panelBoxList]').last() else - _panel = jQuery(destination) + _panel = $j(destination) var _invert = typeof invert !== 'undefined' ? invert : false; if (_invert) @@ -72,10 +72,10 @@ function setupQueryPanelClone(clone) { clone.find(".panelRadio").buttonset() clone.find(".panelDate").button().click(function() { - if (jQuery(this).attr('checked') == 'checked') - jQuery(this).closest(".panelBox").addClass("withDates") + if ($j(this).attr('checked') == 'checked') + $j(this).closest(".panelBox").addClass("withDates") else - jQuery(this).closest(".panelBox").removeClass("withDates") + $j(this).closest(".panelBox").removeClass("withDates") adjustPanelSize() }) @@ -92,11 +92,11 @@ function setupQueryPanelClone(clone) { var dtrg = new Ext.dd.DropTarget(exto, { ddGroup : 'makeQuery' }) dtrg.notifyEnter = function (source, e, data) { - jQuery("#" + e.target.id).parent().find(".holder").addClass('overed') + $j("#" + e.target.id).parent().find(".holder").addClass('overed') } dtrg.notifyOut = function (source, e, data) { - jQuery(".panelBoxListPlaceholder .holder").removeClass('overed') + $j(".panelBoxListPlaceholder .holder").removeClass('overed') } dtrg.notifyDrop = function (source, e, data) { @@ -138,8 +138,8 @@ function setupQueryPanelClone(clone) { */ function clearQueryPanels() { - jQuery(".panelModel").each(function (){ - clearQueryPanel(jQuery(this)) + $j(".panelModel").each(function (){ + clearQueryPanel($j(this)) }) } @@ -160,10 +160,10 @@ function clearQueryPanel(clone) */ function removeUselessPanels() { - jQuery("#queryTable tr:last-of-type td").each(function() { - jQuery("div[id^='panelBoxList']:not(:last)", this).each(function() { - if (jQuery(this).html().trim() == '') - jQuery(this).closest(".panelModel").remove() + $j("#queryTable tr:last-of-type td").each(function() { + $j("div[id^='panelBoxList']:not(:last)", this).each(function() { + if ($j(this).html().trim() == '') + $j(this).closest(".panelModel").remove() }) }) @@ -176,13 +176,13 @@ function removeUselessPanels() */ function adjustPanelSize() { - jQuery(".panelBox").each(function() { + $j(".panelBox").each(function() { - var _itemNumber = jQuery(".panelBoxListItem", jQuery(this)).size() - var _totalHeight = (_itemNumber + 0.5) * jQuery(".panelBoxListItem:first").outerHeight() + var _itemNumber = $j(".panelBoxListItem", $j(this)).size() + var _totalHeight = (_itemNumber + 0.5) * $j(".panelBoxListItem:first").outerHeight() - _totalHeight += parseInt(jQuery(".panelBoxList", jQuery(this)).css('padding-top')) - jQuery(this).css('height', _totalHeight) + _totalHeight += parseInt($j(".panelBoxList", $j(this)).css('padding-top')) + $j(this).css('height', _totalHeight) }) } @@ -199,13 +199,13 @@ function refillQueryPanels(subsets) { clearQueryPanels() // Looping through subsets - jQuery.each(subsets, function (subset, query) { + $j.each(subsets, function (subset, query) { - jQuery(query).find("panel").each(function () { + $j(query).find("panel").each(function () { //This is dangerous, but time efficient - var _panel = jQuery(this) - var _panelDOM = jQuery(".panelModel", jQuery("#queryTable tr:last-of-type td")[parseInt(subset) - 1]).last() + var _panel = $j(this) + var _panelDOM = $j(".panelModel", $j("#queryTable tr:last-of-type td")[parseInt(subset) - 1]).last() _panelDOM.find(".panelBoxListPlaceholder").hide() @@ -235,7 +235,7 @@ function refillQueryPanels(subsets) { */ function getConceptFromQueryItem(item) { - var _item = jQuery(item) + var _item = $j(item) var _concept = {} _concept["conceptid"] = _item.find("item_key").text() @@ -311,7 +311,7 @@ function getConceptFromQueryItem(item) { } }) - jQuery.each(_concept, function(key, value) { + $j.each(_concept, function(key, value) { if (_concept[key] == undefined) _concept[key] = "" }) @@ -325,7 +325,7 @@ function getConceptFromQueryItem(item) { */ function getPanelItemFromConcept(concept) { - var _item = jQuery("
    ") + var _item = $j("
    ") var _valueText = getSetValueText( concept["setvaluemode"], concept["setvalueoperator"], @@ -335,16 +335,16 @@ function getPanelItemFromConcept(concept) { concept["setvalueunits"]).trim() // We try to infer the type when possible to match the icon - jQuery.get(pageInfo.basePath + "/concepts/getResource", { concept_key: concept["conceptid"] }, function() {}, 'json') + $j.get(pageInfo.basePath + "/concepts/getResource", { concept_key: concept["conceptid"] }, function() {}, 'json') .success(function (data) { - jQuery("span:first", _item).addClass(getClassForNodeResource(data)) + $j("span:first", _item).addClass(getClassForNodeResource(data)) }) _item - .append(jQuery("").addClass("x-tree-node-icon")) - .append(jQuery("").addClass("concept-text").html(concept.conceptname + _valueText)) + .append($j("").addClass("x-tree-node-icon")) + .append($j("").addClass("concept-text").html(concept.conceptname + _valueText)) - jQuery.each(concept, function(key, value) { + $j.each(concept, function(key, value) { _item.attr(key, value) }) @@ -375,7 +375,7 @@ function getClassForNodeResource(node) { if (_OKToUseValue) _iconClass = "valueicon"; - jQuery.each(_visualAttributes, function (index, value) { + $j.each(_visualAttributes, function (index, value) { if (!_OKToUseValue && (value.toUpperCase() == "LEAF" || value.toUpperCase() == "MULTIPLE")) _iconClass = "alphaicon"; if (value.toUpperCase() == "HIGH_DIMENSIONAL") @@ -401,9 +401,9 @@ function getClassForNodeResource(node) { function getSubsetQuery (subset) { var _query = '' - jQuery(".panelModel[subset='" + subset + "']").each(function () { - if (jQuery(this).find(".panelBoxList").html().trim() != '') - _query += getQueryPanel(jQuery(this)).html() + $j(".panelModel[subset='" + subset + "']").each(function () { + if ($j(this).find(".panelBoxList").html().trim() != '') + _query += getQueryPanel($j(this)).html() }) return _query; @@ -416,17 +416,17 @@ function getSubsetQuery (subset) { */ function getQuery(subset) { - var _query = jQuery("") + var _query = $j("") _query.attr('xmlns:ns4', 'http://www.i2b2.org/xsd/cell/crc/psm/1.1/') _query - .append(jQuery("").html("0")) + .append($j("").html("0")) .append(getQueryPanels(subset)) - if (jQuery('#queryEncounter_' + subset).attr('checked') == 'checked') - _query.append(jQuery('').html('SAMEVISIT')) + if ($j('#queryEncounter_' + subset).attr('checked') == 'checked') + _query.append($j('').html('SAMEVISIT')) else - _query.append(jQuery('').html('ANY')) + _query.append($j('').html('ANY')) return _query } @@ -438,12 +438,12 @@ function getQuery(subset) { */ function getQueryPanels(subset) { - var _panels = jQuery() + var _panels = $j() - jQuery(".panelModel[subset='" + subset + "']").each(function () { + $j(".panelModel[subset='" + subset + "']").each(function () { - if (jQuery(this).find(".panelBoxList").html().trim() != '') - _panels = _panels.add(getQueryPanel(jQuery(this))) + if ($j(this).find(".panelBoxList").html().trim() != '') + _panels = _panels.add(getQueryPanel($j(this))) }) @@ -458,7 +458,7 @@ function getQueryPanels(subset) { */ function getQueryPanel(panel) { - var _panel = jQuery("") + var _panel = $j("") var _number = panel.find("div[id^='panelBoxList']").attr('id') var _invert = panel.find("input[name^=panelRadio]:checked").val() var _occurrence = 1 @@ -466,9 +466,9 @@ function getQueryPanel(panel) { _number = _number ? _number.substring(_number.indexOf('_') + 1) : new Date().getTime() _invert = _invert != undefined ? _invert : 0 _panel - .append(jQuery("").html(_number)) - .append(jQuery("").html(_invert)) - .append(jQuery("").html(_occurrence)) + .append($j("").html(_number)) + .append($j("").html(_invert)) + .append($j("").html(_occurrence)) .append(getQueryPanelItems(panel)) if (panel.find(".panelDate").attr('checked') == 'checked') { @@ -480,15 +480,15 @@ function getQueryPanel(panel) { _offset = 'T00:00:00.000' + _offset.slice(0, 3) + ':' +_offset.slice(3) if (_from != '') - _panel.append(jQuery("").html(_from + _offset)) + _panel.append($j("").html(_from + _offset)) if (_to != '') - _panel.append(jQuery("").html(_to + _offset)) + _panel.append($j("").html(_to + _offset)) } - if (jQuery('#queryEncounter_' + panel.attr('subset')).attr('checked') == 'checked') - _panel.append(jQuery('').html('SAMEVISIT')) + if ($j('#queryEncounter_' + panel.attr('subset')).attr('checked') == 'checked') + _panel.append($j('').html('SAMEVISIT')) else - _panel.append(jQuery('').html('ANY')) + _panel.append($j('').html('ANY')) return _panel } @@ -501,11 +501,11 @@ function getQueryPanel(panel) { function getQueryPanelItems(panel) { - var _items = jQuery() + var _items = $j() - jQuery(".panelBoxListItem", panel).each(function () { + $j(".panelBoxListItem", panel).each(function () { - _items = _items.add(getQueryPanelItem(jQuery(this))) + _items = _items.add(getQueryPanelItem($j(this))) }) @@ -519,8 +519,8 @@ function getQueryPanelItems(panel) { */ function getQueryPanelItem(item) { - var _item = jQuery("") - var _constrainValue = jQuery('') + var _item = $j("") + var _constrainValue = $j('') var _value = '' switch (item.attr('setvaluemode').toLowerCase()) { @@ -531,63 +531,63 @@ function getQueryPanelItem(item) { _value += ' AND ' + item.attr('setvaluehighvalue') _constrainValue - .append(jQuery("").html(item.attr('setvalueoperator'))) - .append(jQuery("").html(_value)) - .append(jQuery("").html(item.attr('setvalueunits'))) - .append(jQuery("").html("NUMBER")) + .append($j("").html(item.attr('setvalueoperator'))) + .append($j("").html(_value)) + .append($j("").html(item.attr('setvalueunits'))) + .append($j("").html("NUMBER")) break; case 'highlow' : _constrainValue - .append(jQuery("").html("EQ")) - .append(jQuery("").html(item.attr('setvaluehighlowselect').substring(0, 1).toUpperCase())) - .append(jQuery("").html(item.attr('setvalueunits'))) - .append(jQuery("").html("FLAG")) + .append($j("").html("EQ")) + .append($j("").html(item.attr('setvaluehighlowselect').substring(0, 1).toUpperCase())) + .append($j("").html(item.attr('setvalueunits'))) + .append($j("").html("FLAG")) break; case 'text' : _constrainValue - .append(jQuery("").html('LIKE[' + item.attr('setvalueoperator') + ']')) - .append(jQuery("").html('')) - .append(jQuery("").html("TEXT")) + .append($j("").html('LIKE[' + item.attr('setvalueoperator') + ']')) + .append($j("").html('')) + .append($j("").html("TEXT")) break; case 'list' : _constrainValue - .append(jQuery("").html("IN")) - .append(jQuery("").html(item.attr('***'))) - .append(jQuery("").html("TEXT")) + .append($j("").html("IN")) + .append($j("").html(item.attr('***'))) + .append($j("").html("TEXT")) break; case 'omics_value' : - _constrainValue = jQuery("") + _constrainValue = $j("") _constrainValue - .append(jQuery("").html(item.attr('omicsoperator'))) - .append(jQuery("").html(item.attr('omicsvalue'))) - .append(jQuery("").html(item.attr('omicsvaluetype'))) - .append(jQuery("").html(item.attr('omicsproperty'))) - .append(jQuery("").html(item.attr('omicsselector'))) - .append(jQuery("").html(item.attr('omicsprojection'))) + .append($j("").html(item.attr('omicsoperator'))) + .append($j("").html(item.attr('omicsvalue'))) + .append($j("").html(item.attr('omicsvaluetype'))) + .append($j("").html(item.attr('omicsproperty'))) + .append($j("").html(item.attr('omicsselector'))) + .append($j("").html(item.attr('omicsprojection'))) } _item - .append(jQuery("").html(item.attr('conceptname').legacyI2B2Escape())) - .append(jQuery("").html(item.attr('conceptid').legacyI2B2Escape())) - .append(jQuery("").html(item.attr('concepttooltip').legacyI2B2Escape())) - .append(jQuery("").html(item.attr('conceptlevel'))) - .append(jQuery("").html("ENC")) + .append($j("").html(item.attr('conceptname').legacyI2B2Escape())) + .append($j("").html(item.attr('conceptid').legacyI2B2Escape())) + .append($j("").html(item.attr('concepttooltip').legacyI2B2Escape())) + .append($j("").html(item.attr('conceptlevel'))) + .append($j("").html("ENC")) if (item.attr('ismodifier')) { - var _constrainModifier = jQuery('') + var _constrainModifier = $j('') _constrainModifier - .append(jQuery("").html(item.attr('conceptname'))) - .append(jQuery("").html(item.attr('applied_path'))) - .append(jQuery("").html(item.attr('conceptid'))) + .append($j("").html(item.attr('conceptname'))) + .append($j("").html(item.attr('applied_path'))) + .append($j("").html(item.attr('conceptid'))) if (_constrainValue.html().length) _constrainModifier.append(_constrainValue) @@ -611,7 +611,7 @@ function getSubsetQuerySummary(subset) { _panels.each(function() { - var _e = jQuery(this) + var _e = $j(this) var _item = "" if (_summary.trim() != '') From 872abace4127f23af8d22787e53ad7fb3906b3f9 Mon Sep 17 00:00:00 2001 From: Peter Rice Date: Thu, 22 Dec 2016 10:58:25 +0000 Subject: [PATCH 008/136] Fix TRANSREL-153: ignore empty string variable values --- .../transmart/asynchronous/job/AsyncJobController.groovy | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/grails-app/controllers/com/recomdata/transmart/asynchronous/job/AsyncJobController.groovy b/grails-app/controllers/com/recomdata/transmart/asynchronous/job/AsyncJobController.groovy index dd2e41fa6..bff682bff 100644 --- a/grails-app/controllers/com/recomdata/transmart/asynchronous/job/AsyncJobController.groovy +++ b/grails-app/controllers/com/recomdata/transmart/asynchronous/job/AsyncJobController.groovy @@ -181,19 +181,19 @@ class AsyncJobController { // for concept paths we have to make sure they start with \\top node // note the string is escaped so we are adding a double backslash at the start - if (params.independentVariable != null) { + if (params.independentVariable != null && params.independentVariable != "") { concept_key = params.independentVariable.split("\\|")[0] concept_table = concept_key.split("\\\\")[1] studyIds += studyIdService.getStudyIdForConceptKey('\\\\' + concept_table + concept_key) } - if (params.dependentVariable != null) { + if (params.dependentVariable != null && params.dependentVariable != "") { concept_key = params.dependentVariable.split("\\|")[0] concept_table = concept_key.split("\\\\")[1] studyIds += studyIdService.getStudyIdForConceptKey('\\\\' + concept_table + concept_key) } - if (params.variablesConceptPaths != null) { + if (params.variablesConceptPaths != null && params.variablesConceptPaths != "") { concept_key = params.variablesConceptPaths.split("\\|")[0] concept_table = concept_key.split("\\\\")[1] studyIds += studyIdService.getStudyIdForConceptKey('\\\\' + concept_table + concept_key) From d8533e67ce1f7c3e6a493a882481b5b650f2a4c7 Mon Sep 17 00:00:00 2001 From: Sascha Herzinger Date: Mon, 2 Jan 2017 08:54:59 +0100 Subject: [PATCH 009/136] updated SmartR version --- grails-app/conf/BuildConfig.groovy | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/grails-app/conf/BuildConfig.groovy b/grails-app/conf/BuildConfig.groovy index f301f5850..b030ed7cd 100644 --- a/grails-app/conf/BuildConfig.groovy +++ b/grails-app/conf/BuildConfig.groovy @@ -135,7 +135,7 @@ grails.project.dependency.resolution = { compile ":codenarc:0.21" if (!dm) { - runtime ':smart-r:1.0-STABLE-SNAPSHOT' + runtime ':smart-r:16.2-SNAPSHOT' compile ':rdc-rmodules:16.2-SNAPSHOT' runtime ':transmart-core:16.2-SNAPSHOT' compile ':transmart-gwas:16.2-SNAPSHOT' From 48fe62ac5b51ba747ae15dabe66efa0049a57ba8 Mon Sep 17 00:00:00 2001 From: Peter Rice Date: Tue, 3 Jan 2017 15:50:15 +0000 Subject: [PATCH 010/136] use standard email contact for uploadData --- grails-app/views/uploadData/uploadData.gsp | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/grails-app/views/uploadData/uploadData.gsp b/grails-app/views/uploadData/uploadData.gsp index d533a3a8a..1c0fdbf10 100644 --- a/grails-app/views/uploadData/uploadData.gsp +++ b/grails-app/views/uploadData/uploadData.gsp @@ -80,7 +80,7 @@ var buildVer = 'Build Version: -
    - Email administrator + Email administrator  
    If you are unable to locate the relevant study, email the administrator by clicking the button above.
    @@ -200,7 +200,7 @@ var buildVer = 'Build Version: - Upload Data
    - Email administrator + Email administrator  
    If you are unable to locate the relevant autocomplete fields, email the administrator by clicking the button above.
    From 03c0a770da84049149cc25f074a641d90c8497c9 Mon Sep 17 00:00:00 2001 From: Peter Rice Date: Tue, 3 Jan 2017 15:56:13 +0000 Subject: [PATCH 011/136] unique name for activateTab in datasetExplorer --- web-app/js/datasetExplorer/datasetExplorer.js | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/web-app/js/datasetExplorer/datasetExplorer.js b/web-app/js/datasetExplorer/datasetExplorer.js index 31dda7e46..8daeb5534 100644 --- a/web-app/js/datasetExplorer/datasetExplorer.js +++ b/web-app/js/datasetExplorer/datasetExplorer.js @@ -406,7 +406,7 @@ Ext.onReady(function () { activate: function (p) { if (isSubsetQueriesChanged(p.subsetQueries) || !Ext.get('analysisGridPanel')) { runAllQueries(getSummaryGridData, p); - activateTab(); + activateTabResults(); onWindowResize(); } else { getSummaryGridData(); @@ -437,7 +437,7 @@ Ext.onReady(function () { if (isSubsetQueriesChanged(p.subsetQueries) || !Ext.get('analysis_title')) { p.body.mask("Loading...", 'x-mask-loading'); runAllQueries(getSummaryStatistics, p); - activateTab(); + activateTabResults(); onWindowResize(); } }, @@ -532,7 +532,7 @@ Ext.onReady(function () { * @private */ var _activateAdvancedWorkflow = function () { - activateTab(); + activateTabResults(); GLOBAL.Analysis="dataAssociation"; renderCohortSummary(); onWindowResize(); @@ -2870,7 +2870,7 @@ function getExportButtonSecurityComplete(result) { } } -function activateTab(tab) { +function activateTabResults(tab) { resultsTabPanel.tools.help.dom.style.display = "none"; } From b134ab865b91bbad596e80e19ad4eee1257aac2d Mon Sep 17 00:00:00 2001 From: Peter Rice Date: Tue, 3 Jan 2017 17:27:16 +0000 Subject: [PATCH 012/136] browserDetect script in case of future version issues --- web-app/js/browserDetect.js | 139 ++++++++++++++++++++++++++++++++++++ 1 file changed, 139 insertions(+) create mode 100644 web-app/js/browserDetect.js diff --git a/web-app/js/browserDetect.js b/web-app/js/browserDetect.js new file mode 100644 index 000000000..e3cceb95a --- /dev/null +++ b/web-app/js/browserDetect.js @@ -0,0 +1,139 @@ +/************************************************************************* + * tranSMART - translational medicine data mart + * + * Copyright 2008-2012 Janssen Research & Development, LLC. + * + * This product includes software developed at Janssen Research & Development, LLC. + * + * This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License + * as published by the Free Software * Foundation, either version 3 of the License, or (at your option) any later version, along with the following terms: + * 1. You may convey a work based on this program in accordance with section 5, provided that you retain the above notices. + * 2. You may convey verbatim copies of this program code as you receive it, in any medium, provided that you retain the above notices. + * + * This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS * FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License along with this program. If not, see . + * + * + ******************************************************************/ + + +var BrowserDetect = { + // Code to detect whether IE 6 or IE 7 are being used (and thus, + // whether we need to display static heatmap images). Code is + // from http://www.quirksmode.org/js/detect.html + init: function () { + this.browser = this.searchString(this.dataBrowser) || "An unknown browser"; + this.version = this.searchVersion(navigator.userAgent) + || this.searchVersion(navigator.appVersion) + || "an unknown version"; + this.OS = this.searchString(this.dataOS) || "an unknown OS"; + }, + searchString: function (data) { + for (var i=0;i Date: Wed, 4 Jan 2017 10:22:36 +0100 Subject: [PATCH 013/136] Update BuildConfig.groovy --- grails-app/conf/BuildConfig.groovy | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/grails-app/conf/BuildConfig.groovy b/grails-app/conf/BuildConfig.groovy index b030ed7cd..f79e5649d 100644 --- a/grails-app/conf/BuildConfig.groovy +++ b/grails-app/conf/BuildConfig.groovy @@ -135,7 +135,7 @@ grails.project.dependency.resolution = { compile ":codenarc:0.21" if (!dm) { - runtime ':smart-r:16.2-SNAPSHOT' + runtime ':smart-r:1.1-STABLE-SNAPSHOT' compile ':rdc-rmodules:16.2-SNAPSHOT' runtime ':transmart-core:16.2-SNAPSHOT' compile ':transmart-gwas:16.2-SNAPSHOT' From e1645c3116f149247429b43960b9a61c23ab7e4d Mon Sep 17 00:00:00 2001 From: Peter Rice Date: Mon, 23 Jan 2017 13:16:08 +0000 Subject: [PATCH 014/136] rename activateTab to be unique --- web-app/js/datasetExplorer/datasetExplorer.js | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/web-app/js/datasetExplorer/datasetExplorer.js b/web-app/js/datasetExplorer/datasetExplorer.js index 31dda7e46..8daeb5534 100644 --- a/web-app/js/datasetExplorer/datasetExplorer.js +++ b/web-app/js/datasetExplorer/datasetExplorer.js @@ -406,7 +406,7 @@ Ext.onReady(function () { activate: function (p) { if (isSubsetQueriesChanged(p.subsetQueries) || !Ext.get('analysisGridPanel')) { runAllQueries(getSummaryGridData, p); - activateTab(); + activateTabResults(); onWindowResize(); } else { getSummaryGridData(); @@ -437,7 +437,7 @@ Ext.onReady(function () { if (isSubsetQueriesChanged(p.subsetQueries) || !Ext.get('analysis_title')) { p.body.mask("Loading...", 'x-mask-loading'); runAllQueries(getSummaryStatistics, p); - activateTab(); + activateTabResults(); onWindowResize(); } }, @@ -532,7 +532,7 @@ Ext.onReady(function () { * @private */ var _activateAdvancedWorkflow = function () { - activateTab(); + activateTabResults(); GLOBAL.Analysis="dataAssociation"; renderCohortSummary(); onWindowResize(); @@ -2870,7 +2870,7 @@ function getExportButtonSecurityComplete(result) { } } -function activateTab(tab) { +function activateTabResults(tab) { resultsTabPanel.tools.help.dom.style.display = "none"; } From 37359c70d305a0bf787d3e520c8347504bb1b2ff Mon Sep 17 00:00:00 2001 From: Peter Rice Date: Mon, 23 Jan 2017 13:18:08 +0000 Subject: [PATCH 015/136] Catch null and empty variable params --- .../transmart/asynchronous/job/AsyncJobController.groovy | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/grails-app/controllers/com/recomdata/transmart/asynchronous/job/AsyncJobController.groovy b/grails-app/controllers/com/recomdata/transmart/asynchronous/job/AsyncJobController.groovy index dd2e41fa6..bff682bff 100644 --- a/grails-app/controllers/com/recomdata/transmart/asynchronous/job/AsyncJobController.groovy +++ b/grails-app/controllers/com/recomdata/transmart/asynchronous/job/AsyncJobController.groovy @@ -181,19 +181,19 @@ class AsyncJobController { // for concept paths we have to make sure they start with \\top node // note the string is escaped so we are adding a double backslash at the start - if (params.independentVariable != null) { + if (params.independentVariable != null && params.independentVariable != "") { concept_key = params.independentVariable.split("\\|")[0] concept_table = concept_key.split("\\\\")[1] studyIds += studyIdService.getStudyIdForConceptKey('\\\\' + concept_table + concept_key) } - if (params.dependentVariable != null) { + if (params.dependentVariable != null && params.dependentVariable != "") { concept_key = params.dependentVariable.split("\\|")[0] concept_table = concept_key.split("\\\\")[1] studyIds += studyIdService.getStudyIdForConceptKey('\\\\' + concept_table + concept_key) } - if (params.variablesConceptPaths != null) { + if (params.variablesConceptPaths != null && params.variablesConceptPaths != "") { concept_key = params.variablesConceptPaths.split("\\|")[0] concept_table = concept_key.split("\\\\")[1] studyIds += studyIdService.getStudyIdForConceptKey('\\\\' + concept_table + concept_key) From f9b2cb1ab45a25386830a7332d609ef0428c5f5c Mon Sep 17 00:00:00 2001 From: Peter Rice Date: Mon, 23 Jan 2017 13:21:15 +0000 Subject: [PATCH 016/136] browser version detect code in case of need --- web-app/js/browserDetect.js | 139 ++++++++++++++++++++++++++++++++++++ 1 file changed, 139 insertions(+) create mode 100644 web-app/js/browserDetect.js diff --git a/web-app/js/browserDetect.js b/web-app/js/browserDetect.js new file mode 100644 index 000000000..e3cceb95a --- /dev/null +++ b/web-app/js/browserDetect.js @@ -0,0 +1,139 @@ +/************************************************************************* + * tranSMART - translational medicine data mart + * + * Copyright 2008-2012 Janssen Research & Development, LLC. + * + * This product includes software developed at Janssen Research & Development, LLC. + * + * This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License + * as published by the Free Software * Foundation, either version 3 of the License, or (at your option) any later version, along with the following terms: + * 1. You may convey a work based on this program in accordance with section 5, provided that you retain the above notices. + * 2. You may convey verbatim copies of this program code as you receive it, in any medium, provided that you retain the above notices. + * + * This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS * FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License along with this program. If not, see . + * + * + ******************************************************************/ + + +var BrowserDetect = { + // Code to detect whether IE 6 or IE 7 are being used (and thus, + // whether we need to display static heatmap images). Code is + // from http://www.quirksmode.org/js/detect.html + init: function () { + this.browser = this.searchString(this.dataBrowser) || "An unknown browser"; + this.version = this.searchVersion(navigator.userAgent) + || this.searchVersion(navigator.appVersion) + || "an unknown version"; + this.OS = this.searchString(this.dataOS) || "an unknown OS"; + }, + searchString: function (data) { + for (var i=0;i Date: Thu, 2 Feb 2017 20:56:47 +0100 Subject: [PATCH 017/136] Fixed restore comparison from workspace, for clinical and highdimensional concepts. --- web-app/js/datasetExplorer/omicsFilter.js | 4 ++- web-app/js/datasetExplorer/querypanels.js | 43 ++++++++++++++++++----- 2 files changed, 38 insertions(+), 9 deletions(-) diff --git a/web-app/js/datasetExplorer/omicsFilter.js b/web-app/js/datasetExplorer/omicsFilter.js index 38437cdce..3ccf793a3 100644 --- a/web-app/js/datasetExplorer/omicsFilter.js +++ b/web-app/js/datasetExplorer/omicsFilter.js @@ -92,6 +92,8 @@ function repopulateFilterWindow() { jQuery("#highdimension-filter-selector").val(omicsFilterRepopulateWindow.omicsselector.nodeValue); jQuery("#highdimension-filter-projection").val(omicsFilterRepopulateWindow.omicsprojection.nodeValue); + omicsAutoCompleteList = [omicsFilterRepopulateWindow.omicsselector.nodeValue]; + showConceptDistributionHistogramForOmicsFilterComplete(null); showConceptDistributionHistogramForOmicsFilter(getOmicsFilterParams()); } @@ -104,8 +106,8 @@ function repopulateOmicsFilterRange() { var maxbox = jQuery("#highdimension-amount-max"); var values = omicsFilterRepopulateWindow.omicsvalue.nodeValue.split(":"); minbox.val(values[0]); - minbox.blur(); maxbox.val(values[1]); + minbox.blur(); maxbox.blur(); } } diff --git a/web-app/js/datasetExplorer/querypanels.js b/web-app/js/datasetExplorer/querypanels.js index 0d812d87b..e055159ca 100644 --- a/web-app/js/datasetExplorer/querypanels.js +++ b/web-app/js/datasetExplorer/querypanels.js @@ -213,7 +213,11 @@ function refillQueryPanels(subsets) { if (_inversion) _panelDOM.find("input[id^=panelExclude]").attr("checked", "checked") - _panelDOM.find(".panelRadio").buttonset("refresh") + var panelRadio = _panelDOM.find(".panelRadio"); + if (panelRadio.data("buttonset") == null) { + panelRadio.buttonset(); + } + panelRadio.buttonset("refresh") _panel.find("item").each(function () { _panelDOM.find(".panelBoxList").append(getPanelItemFromConcept(getConceptFromQueryItem(this))) @@ -269,6 +273,17 @@ function getConceptFromQueryItem(item) { _concept["conceptid"] = _item.find("modifier_key").text() }) + _item.find("constrain_by_omics_value").each(function() { + _concept["setvaluemode"] = "omics_value"; + _concept["oktousevalues"] = "H"; + _concept["omicsproperty"] = _item.find("omics_property").text(); + _concept["omicsselector"] = _item.find("omics_selector").text(); + _concept["omicsoperator"] = _item.find("omics_value_operator").text(); + _concept["omicsvalue"] = _item.find("omics_value_constraint").text(); + _concept["omicsprojection"] = _item.find("omics_projection_type").text(); + _concept["omicsvaluetype"] = _item.find("omics_value_type").text(); + }) + _item.find("constrain_by_value").each(function () { switch (_item.find("value_type").text().toLowerCase()) { case 'number' : @@ -326,13 +341,25 @@ function getConceptFromQueryItem(item) { function getPanelItemFromConcept(concept) { var _item = jQuery("
    ") - var _valueText = getSetValueText( - concept["setvaluemode"], - concept["setvalueoperator"], - concept["setvaluehighlowselect"], - concept["setvaluehighvalue"], - concept["setvaluelowvalue"], - concept["setvalueunits"]).trim() + var _valueText = ""; + if (concept["setvaluemode"] == "omics_value") { + var valueparams = {}; + valueparams["operator"] = concept["omicsoperator"]; + valueparams["type"] = concept["omicsvaluetype"]; + valueparams["value"] = concept["omicsvalue"]; + valueparams["selector"] = concept["omicsselector"]; + valueparams["projection_pretty_name"] = concept["omicsprojection"]; + _valueText = getOmicsFilterValueText(valueparams); + } + else { + _valueText = getSetValueText( + concept["setvaluemode"], + concept["setvalueoperator"], + concept["setvaluehighlowselect"], + concept["setvaluehighvalue"], + concept["setvaluelowvalue"], + concept["setvalueunits"]).trim() + } // We try to infer the type when possible to match the icon jQuery.get(pageInfo.basePath + "/concepts/getResource", { concept_key: concept["conceptid"] }, function() {}, 'json') From 2eed6775a39176d07eb185a4a4ea8987d0444137 Mon Sep 17 00:00:00 2001 From: Anthony O Date: Wed, 1 Feb 2017 16:10:07 +0100 Subject: [PATCH 018/136] Fixing an issue linked with SmartR importation of another version of jQuery: after a click on "Advanced Workflow", we could no more use the "Clear" button of "Active Filters", nor click on the result of an auto-completing search in the top left search text box. --- web-app/js/rwgsearch.js | 563 ++++++++++++++++++++-------------------- 1 file changed, 283 insertions(+), 280 deletions(-) diff --git a/web-app/js/rwgsearch.js b/web-app/js/rwgsearch.js index ae0f1e489..200a2b2da 100644 --- a/web-app/js/rwgsearch.js +++ b/web-app/js/rwgsearch.js @@ -15,74 +15,77 @@ var nodesBeforeSelect = new Array(); // will still fire but is stopped immediately); and set this flag back to true at the end of the event so it can be triggered again. var allowOnSelectEvent = true; var uploader; + +var $j = jQuery.noConflict(); + // Method to add the categories for the select box function addSelectCategories() { if (sessionSearchCategory == "") { sessionSearchCategory = "ALL"; } - jQuery("#search-categories").append(jQuery("").attr("value", "ALL").text("All").attr('id', 'allCategory')); + $j("#search-categories").append($j("").attr("value", "ALL").text("All").attr('id', 'allCategory')); - jQuery("#search-categories").change(function() { - jQuery('#search-ac').autocomplete('option', 'source', sourceURL + "?category=" + this.options[this.selectedIndex].value); - jQuery.ajax({ + $j("#search-categories").change(function() { + $j('#search-ac').autocomplete('option', 'source', sourceURL + "?category=" + this.options[this.selectedIndex].value); + $j.ajax({ url:updateSearchCategoryURL, - data: {id: jQuery("#search-categories").val()} + data: {id: $j("#search-categories").val()} }); }); - jQuery.getJSON(getCategoriesURL, function(json) { + $j.getJSON(getCategoriesURL, function(json) { for (var i=0; i").attr("value", category).text(catText)); + $j("#search-categories").append($j("").attr("value", category).text(catText)); } - jQuery("#search-categories").html(jQuery("option", jQuery("#search-categories")).sort(function(a, b) { + $j("#search-categories").html($j("option", $j("#search-categories")).sort(function(a, b) { return a.text == b.text ? 0 : a.text < b.text ? -1 : 1; })); - jQuery("#allCategory").after(jQuery("").attr("value", "text").text("Free Text")); + $j("#allCategory").after($j("").attr("value", "text").text("Free Text")); - jQuery("#search-categories").val(sessionSearchCategory); - jQuery('#search-ac').autocomplete('option', 'source', sourceURL + "?category=" + jQuery('#search-categories').val()); + $j("#search-categories").val(sessionSearchCategory); + $j('#search-ac').autocomplete('option', 'source', sourceURL + "?category=" + $j('#search-categories').val()); }); } function addFilterCategories() { - jQuery.getJSON(getFilterCategoriesURL, function(json) { + $j.getJSON(getFilterCategoriesURL, function(json) { for (var i=0; i
    ").addClass("filtertitle").attr("name", category.category).text(category.displayName); - var contentDiv = jQuery("
    ").addClass("filtercontent").attr("name", category.category).attr("style", "display: none"); + var titleDiv = $j("
    ").addClass("filtertitle").attr("name", category.category).text(category.displayName); + var contentDiv = $j("
    ").addClass("filtercontent").attr("name", category.category).attr("style", "display: none"); for (var j=0; j < choices.length; j++) { var choice = choices[j]; - var newItem = jQuery("
    ").addClass("filteritem").attr("name", category.category).attr("id", choice.uid).text(choice.name); + var newItem = $j("
    ").addClass("filteritem").attr("name", category.category).attr("id", choice.uid).text(choice.name); //If this has been selected, highlight it var idString = '[id="' + category.displayName + "|" + category.category + ";" + choice.name + ";" + choice.uid + '"]'; idString = idString.replace(/,/g, "%44").replace(/&/g, "%26"); //Replace commas and ampersands - var element = jQuery(idString); + var element = $j(idString); if (element.size() > 0) { newItem.addClass("selected"); } contentDiv.append(newItem); } - jQuery("#filter-browser").append(titleDiv); - jQuery("#filter-browser").append(contentDiv); + $j("#filter-browser").append(titleDiv); + $j("#filter-browser").append(contentDiv); } - jQuery("#filter-browser").removeClass("ajaxloading"); + $j("#filter-browser").removeClass("ajaxloading"); }); } //Method to add the autocomplete for the search keywords function addSearchAutoComplete() { - jQuery("#search-ac").autocomplete({ + $j("#search-ac").autocomplete({ position:{my:"left top",at:"left bottom",collision:"none"}, source: sourceURL, minLength:1, @@ -91,9 +94,9 @@ function addSearchAutoComplete() { searchParam={id:ui.item.id,display:ui.item.category,keyword:ui.item.label,category:ui.item.categoryId}; addSearchTerm(searchParam); } - + //If category is ALL, add this as free text as well - var category = jQuery("#search-categories").val(); + var category = $j("#search-categories").val(); return false; } }).data("ui-autocomplete")._renderItem = function( ul, item ) { @@ -105,28 +108,28 @@ function addSearchAutoComplete() { resulta += ''; } - return jQuery('
  • ') + return $j('
  • ') .data("item.autocomplete", item ) .append(resulta) .appendTo(ul); }; // Capture the enter key on the slider and fire off the search event on the autocomplete - jQuery("#search-categories").keypress(function(event) { + $j("#search-categories").keypress(function(event) { if (event.which == 13) { - jQuery("#search-ac").autocomplete('search'); + $j("#search-ac").autocomplete('search'); } }); - jQuery('#search-ac').keypress(function(event) { - var category = jQuery("#search-categories").val(); - var categoryText = jQuery('#search-categories option:selected').text(); + $j('#search-ac').keypress(function(event) { + var category = $j("#search-categories").val(); + var categoryText = $j('#search-categories option:selected').text(); if (event.which == 13 && (category == 'DATANODE' || category == 'text' || category == 'ALL')) { - var val = jQuery('#search-ac').val(); + var val = $j('#search-ac').val(); if (category == 'ALL') {category = 'text'; categoryText = 'Free Text';} searchParam={id:val,display:categoryText,keyword:val,category:category}; addSearchTerm(searchParam); - jQuery('#search-ac').empty(); + $j('#search-ac').empty(); return false; } }); @@ -165,13 +168,13 @@ function addSearchTerm(searchTerm, noUpdate, openInAnalyze,datasetExplorerPath) } // clear the search text box - jQuery("#search-ac").val(""); + $j("#search-ac").val(""); // only refresh results if the tree was not updated (the onSelect also fires these event, so don't want to do 2x) if (!noUpdate) { if(!openInAnalyze){ - jQuery.ajax({ + $j.ajax({ url:resetNodesRwgURL }); showSearchTemplate(); @@ -191,7 +194,7 @@ function showSearchTemplate() { var geneTerms = 0; var globalLogicOperator = "AND"; - if (jQuery('#globaloperator').hasClass("or")) { globalLogicOperator = "OR"; } + if ($j('#globaloperator').hasClass("or")) { globalLogicOperator = "OR"; } // iterate through categories array and move all the "gene" categories together at the top var newCategories = new Array(); @@ -304,9 +307,9 @@ function showSearchResults(openInAnalyze, datasetExplorerPath) { analysisProbeIds = new Array(); // clear stored analysis results - jQuery('body').removeData(); + $j('body').removeData(); - jQuery('#results-div').empty(); + $j('#results-div').empty(); // call method which retrieves facet counts and search results showFacetResults(openInAnalyze, datasetExplorerPath); @@ -322,7 +325,7 @@ function showFacetResults(openInAnalyze, datasetExplorerPath) { openInAnalyze = false; } var globalLogicOperator = "AND"; - if (jQuery('#globaloperator').hasClass("or")) { globalLogicOperator = "OR" } + if ($j('#globaloperator').hasClass("or")) { globalLogicOperator = "OR" } var savedSearchTermsArray; var savedSearchTerms; @@ -383,7 +386,7 @@ function showFacetResults(openInAnalyze, datasetExplorerPath) { facetSearch.push(queryType + "=" + categories[i] + ":" + encodeURIComponent(terms[i]) + "::" + operators[i]); } - jQuery("#results-div").addClass('ajaxloading').empty(); + $j("#results-div").addClass('ajaxloading').empty(); var queryString = facetSearch.join("&"); @@ -400,11 +403,11 @@ function showFacetResults(openInAnalyze, datasetExplorerPath) { if(!openInAnalyze){ if (searchPage == 'RWG') { - jQuery.ajax({ + $j.ajax({ url:facetResultsURL, data: queryString + "&page=RWG", success: function(response) { - jQuery('#results-div').removeClass('ajaxloading').html(response); + $j('#results-div').removeClass('ajaxloading').html(response); checkSearchLog(); updateAnalysisData(null, false); displayResultsNumber(); @@ -418,12 +421,12 @@ function showFacetResults(openInAnalyze, datasetExplorerPath) { //If there are no search terms, pass responsibility on to getCategories - if not, do our custom search if (savedSearchTermsArray.length == 0) { //Need to silently clear the search map here as well - jQuery.ajax({url:clearSearchFilterURL}); + $j.ajax({url:clearSearchFilterURL}); GLOBAL.PathToExpand = ''; getCategories(); } else { - jQuery.ajax({ + $j.ajax({ url:facetResultsURL, data: queryString + "&page=datasetExplorer", success: function(response) { @@ -437,7 +440,7 @@ function showFacetResults(openInAnalyze, datasetExplorerPath) { } } }else{ - jQuery.ajax({ + $j.ajax({ url:saveSearchURL, data: queryString + "&page=RWG", success: function(response) { @@ -477,7 +480,7 @@ function getSearchKeywordList() { //Remove the search term that the user has clicked. function removeSearchTerm(ctrl) { - jQuery.ajax({ + $j.ajax({ url:resetNodesRwgURL }); var currentSearchTermID = ctrl.id.replace(/\%20/g, " ").replace(/\%44/g, ",").replace(/\%26/g, "&"); @@ -493,7 +496,7 @@ function removeSearchTerm(ctrl) { } // Call back to the server to clear the search filter (session scope) - jQuery.ajax({ + $j.ajax({ type:"POST", url:newSearchURL }); @@ -515,14 +518,14 @@ function removeSearchTerm(ctrl) { //Clear the tree, results along with emptying the two arrays that store categories and search terms. function clearSearch() { goWelcome(); - jQuery.ajax({ + $j.ajax({ url:resetNodesRwgURL }); openAnalyses = []; //all analyses will be closed, so clear this array - jQuery("#search-ac").val(""); + $j("#search-ac").val(""); currentSearchTerms = new Array(); currentCategories = new Array(); @@ -530,7 +533,7 @@ function clearSearch() { // Change the category picker back to ALL and set autocomplete to not have a category (ALL by default) document.getElementById("search-categories").selectedIndex = 0; - jQuery('#search-ac').autocomplete('option', 'source', sourceURL); + $j('#search-ac').autocomplete('option', 'source', sourceURL); showSearchTemplate(); showSearchResults(); //reload the full search results @@ -579,17 +582,17 @@ function clearCategoryIfNoTerms(category) { function unselectFilterItem(id) { //Longhand as may contain : characters - jQuery("[id='" + id + "']").removeClass('selected'); + $j("[id='" + id + "']").removeClass('selected'); } // --- function toggleSidebar() { - element = jQuery('#sidebar')[0] || jQuery('#westPanel')[0]; + element = $j('#sidebar')[0] || $j('#westPanel')[0]; element = '#' + element.id; - var leftPointingArrow = (jQuery('#sidebartoggle').css('background-image').indexOf("-right") < 0); - var sidebarIsVisible = (jQuery(element + ':visible').size() > 0); + var leftPointingArrow = ($j('#sidebartoggle').css('background-image').indexOf("-right") < 0); + var sidebarIsVisible = ($j(element + ':visible').size() > 0); //console.log("toggleSidebar: leftPointingArrow = " + leftPointingArrow + ", sidebarIsVisible = " + sidebarIsVisible); // This fixes problems with ExtJS in case of rapid consecutive clicks, double-click. JIRA TRANSREL-18. @@ -615,38 +618,38 @@ function toggleSidebar() { } }; if (sidebarIsVisible) { - jQuery(element).fadeOut(500, func); - var bgimg = jQuery('#sidebartoggle').css('background-image').replace('-left', '-right'); - jQuery('#sidebartoggle').css('background-image', bgimg); + $j(element).fadeOut(500, func); + var bgimg = $j('#sidebartoggle').css('background-image').replace('-left', '-right'); + $j('#sidebartoggle').css('background-image', bgimg); } else { - jQuery(element).fadeIn(); + $j(element).fadeIn(); if (func) func(); //Not a callback here - resize as soon as it starts appearing. - var bgimg = jQuery('#sidebartoggle').css('background-image').replace('-right', '-left'); - jQuery('#sidebartoggle').css('background-image', bgimg); + var bgimg = $j('#sidebartoggle').css('background-image').replace('-right', '-left'); + $j('#sidebartoggle').css('background-image', bgimg); } } -jQuery(document).ready(function() { - jQuery('#sidebartoggle').click(function() { +$j(document).ready(function() { + $j('#sidebartoggle').click(function() { toggleSidebar(); }); - jQuery('#filter-browser').on('click', '.filtertitle', function () { - jQuery('.filtercontent[name="' + jQuery(this).attr('name') + '"]').toggle('fast'); + $j('#filter-browser').on('click', '.filtertitle', function () { + $j('.filtercontent[name="' + $j(this).attr('name') + '"]').toggle('fast'); }); - jQuery('#filter-browser').on('click', '.filteritem', function () { - var selecting = !jQuery(this).hasClass('selected'); - jQuery(this).toggleClass('selected'); + $j('#filter-browser').on('click', '.filteritem', function () { + var selecting = !$j(this).hasClass('selected'); + $j(this).toggleClass('selected'); - var name = jQuery(this).attr('name'); - var id = jQuery(this).attr('id'); - var category = jQuery('.filtertitle[name="' + name + '"]').text(); - var value = jQuery(this).text(); + var name = $j(this).attr('name'); + var id = $j(this).attr('id'); + var category = $j('.filtertitle[name="' + name + '"]').text(); + var value = $j(this).text(); //If selecting this filter, add it to the list of current filters if (selecting) { @@ -660,70 +663,70 @@ jQuery(document).ready(function() { else { var idString = '[id="' + category + "|" + name + ";" + value + ";" + id + '"]'; idString = idString.replace(/,/g, "%44").replace(/&/g, "%26"); //Replace special characters! - var element = jQuery(idString); + var element = $j(idString); removeSearchTerm(element[0]); } }); - jQuery('body').on('mouseenter', '.folderheader', function() { - jQuery(this).find('.foldericonwrapper').fadeIn(150); + $j('body').on('mouseenter', '.folderheader', function() { + $j(this).find('.foldericonwrapper').fadeIn(150); }); - jQuery('body').on('mouseleave', '.folderheader', function() { - jQuery(this).find('.foldericonwrapper').fadeOut(150); + $j('body').on('mouseleave', '.folderheader', function() { + $j(this).find('.foldericonwrapper').fadeOut(150); }); - jQuery('body').on('click', '.foldericon.addcart', function() { - var id = jQuery(this).attr('name'); - jQuery(this).removeClass("foldericon").removeClass("addcart").removeClass("link").text("Added to cart"); - jQuery('#cartcount').hide(); + $j('body').on('click', '.foldericon.addcart', function() { + var id = $j(this).attr('name'); + $j(this).removeClass("foldericon").removeClass("addcart").removeClass("link").text("Added to cart"); + $j('#cartcount').hide(); - jQuery.ajax({ + $j.ajax({ url:exportAddURL, data: {id: id}, success: function(response) { - jQuery('#cartcount').show().text(response); + $j('#cartcount').show().text(response); }, error: function(xhr) { - jQuery('#cartcount').show(); + $j('#cartcount').show(); } }); }); - jQuery('body').on('click', '.foldericon.addall', function() { - var nameelements = jQuery(this).closest('table').find('.foldericon.addcart'); + $j('body').on('click', '.foldericon.addall', function() { + var nameelements = $j(this).closest('table').find('.foldericon.addcart'); var ids = []; for (i = 0; i < nameelements.size(); i++) { - ids.push(jQuery(nameelements[i]).attr('name')); - jQuery(nameelements[i]).removeClass("foldericon").removeClass("addcart").removeClass("link").text("Added to cart"); + ids.push($j(nameelements[i]).attr('name')); + $j(nameelements[i]).removeClass("foldericon").removeClass("addcart").removeClass("link").text("Added to cart"); } - jQuery('#cartcount').hide(); + $j('#cartcount').hide(); - jQuery.ajax({ + $j.ajax({ url:exportAddURL, data: {id: ids.join(",")}, success: function(response) { - jQuery('#cartcount').show().text(response); + $j('#cartcount').show().text(response); }, error: function(xhr) { - jQuery('#cartcount').show(); + $j('#cartcount').show(); } }); }); - jQuery('body').on('click', '.foldericon.deletefile', function() { - var id = jQuery(this).attr('name'); + $j('body').on('click', '.foldericon.deletefile', function() { + var id = $j(this).attr('name'); if (confirm("Are you sure you want to delete this file?")) { - jQuery.ajax({ + $j.ajax({ url:deleteFileURL, data: {id: id}, success: function(response) { - jQuery('#files-table').html(response); + $j('#files-table').html(response); //Get document count and reduce by 1 - var folderId = jQuery('#file-list-table').attr('name'); - var documentCount = jQuery('#folder-header-' + folderId + ' .document-count'); + var folderId = $j('#file-list-table').attr('name'); + var documentCount = $j('#folder-header-' + folderId + ' .document-count'); if (documentCount.size() > 0) { var currentValue = documentCount.text(); documentCount.text(currentValue - 1); @@ -736,51 +739,51 @@ jQuery(document).ready(function() { } }); - jQuery('body').on('click', '.foldericon.view', function() { - var id = jQuery(this).closest(".folderheader").attr('name'); + $j('body').on('click', '.foldericon.view', function() { + var id = $j(this).closest(".folderheader").attr('name'); showDetailDialog(id); }); - jQuery('#metadata-viewer').on('click', '.editmetadata', function() { + $j('#metadata-viewer').on('click', '.editmetadata', function() { - var id = jQuery(this).attr('name'); + var id = $j(this).attr('name'); - jQuery('#editMetadataOverlay').fadeIn(); - jQuery('#editMetadata').empty().addClass('ajaxloading'); + $j('#editMetadataOverlay').fadeIn(); + $j('#editMetadata').empty().addClass('ajaxloading'); - jQuery.ajax({ + $j.ajax({ url:editMetaDataURL, data: {folderId: id}, success: function(response) { - jQuery('#editMetadata').html(response).removeClass('ajaxloading'); + $j('#editMetadata').html(response).removeClass('ajaxloading'); }, error: function(xhr) { alert(xhr.responseText); - jQuery('#editMetadata').html(response).removeClass('ajaxloading'); + $j('#editMetadata').html(response).removeClass('ajaxloading'); } }); }); - jQuery('#box-search').on('click', '.andor', function() { + $j('#box-search').on('click', '.andor', function() { - if (jQuery(this).attr('id') == 'globaloperator') { + if ($j(this).attr('id') == 'globaloperator') { //For global switch, just alter the class - this is picked up later - if (jQuery(this).hasClass("or")) { - jQuery(this).removeClass("or").addClass("and"); + if ($j(this).hasClass("or")) { + $j(this).removeClass("or").addClass("and"); } else { - jQuery(this).removeClass("and").addClass("or"); + $j(this).removeClass("and").addClass("or"); } showSearchTemplate(); showSearchResults(); } else { //For individual categories, alter this index of the current search operators, then redisplay - if (jQuery(this).hasClass("or")) { - currentSearchOperators[jQuery(this).attr('name')] = 'and'; + if ($j(this).hasClass("or")) { + currentSearchOperators[$j(this).attr('name')] = 'and'; } else { - currentSearchOperators[jQuery(this).attr('name')] = 'or'; + currentSearchOperators[$j(this).attr('name')] = 'or'; } showSearchTemplate(); showSearchResults(); @@ -788,83 +791,83 @@ jQuery(document).ready(function() { }); - jQuery('#metadata-viewer').on('click', '.addassay', function() { + $j('#metadata-viewer').on('click', '.addassay', function() { - var id = jQuery(this).attr('name'); + var id = $j(this).attr('name'); - jQuery('#createAssayOverlay').fadeIn(); - jQuery('#createAssay').empty().addClass('ajaxloading'); - jQuery('#editMetadata').empty(); + $j('#createAssayOverlay').fadeIn(); + $j('#createAssay').empty().addClass('ajaxloading'); + $j('#editMetadata').empty(); - jQuery.ajax({ + $j.ajax({ url:createAssayURL, data: {folderId: id}, success: function(response) { - jQuery('#createAssay').html(response).removeClass('ajaxloading'); + $j('#createAssay').html(response).removeClass('ajaxloading'); }, error: function(xhr) { alert(xhr); - jQuery('#createAssay').html(response).removeClass('ajaxloading'); + $j('#createAssay').html(response).removeClass('ajaxloading'); } }); }); - jQuery('#metadata-viewer').on('click', '.addanalysis', function() { + $j('#metadata-viewer').on('click', '.addanalysis', function() { - var id = jQuery(this).attr('name'); + var id = $j(this).attr('name'); - jQuery('#createAnalysisOverlay').fadeIn(); - jQuery('#createAnalysis').empty().addClass('ajaxloading'); - jQuery('#editMetadata').empty(); + $j('#createAnalysisOverlay').fadeIn(); + $j('#createAnalysis').empty().addClass('ajaxloading'); + $j('#editMetadata').empty(); - jQuery.ajax({ + $j.ajax({ url:createAnalysisURL, data: {folderId: id}, success: function(response) { - jQuery('#createAnalysis').html(response).removeClass('ajaxloading'); + $j('#createAnalysis').html(response).removeClass('ajaxloading'); }, error: function(xhr) { alert(xhr); - jQuery('#createAnalysis').html(response).removeClass('ajaxloading'); + $j('#createAnalysis').html(response).removeClass('ajaxloading'); } }); }); - jQuery('#metadata-viewer').on('click', '.addfolder', function() { + $j('#metadata-viewer').on('click', '.addfolder', function() { - var id = jQuery(this).attr('name'); + var id = $j(this).attr('name'); - jQuery('#createFolderOverlay').fadeIn(); - jQuery('#createFolder').empty().addClass('ajaxloading'); - jQuery('#editMetadata').empty(); + $j('#createFolderOverlay').fadeIn(); + $j('#createFolder').empty().addClass('ajaxloading'); + $j('#editMetadata').empty(); - jQuery.ajax({ + $j.ajax({ url:createFolderURL + "?", data: {folderId: id}, success: function(response) { - jQuery('#createFolder').html(response).removeClass('ajaxloading'); + $j('#createFolder').html(response).removeClass('ajaxloading'); }, error: function(xhr) { alert(xhr); - jQuery('#createFolder').html(response).removeClass('ajaxloading'); + $j('#createFolder').html(response).removeClass('ajaxloading'); } }); }); - jQuery('#metadata-viewer').on('click', '.deletefolder', function() { + $j('#metadata-viewer').on('click', '.deletefolder', function() { - var id = jQuery(this).attr('name'); - var parent = jQuery(this).data('parent'); + var id = $j(this).attr('name'); + var parent = $j(this).data('parent'); if (confirm("Are you sure you want to delete this folder and the files and folders beneath it?")) { - jQuery.ajax({ + $j.ajax({ url:deleteFolderURL, data: {id: id}, success: function(response) { updateFolder(parent); showDetailDialog(parent); - jQuery('.result-folder-name').removeClass('selected'); - jQuery('#result-folder-name-' + parent).addClass('selected'); + $j('.result-folder-name').removeClass('selected'); + $j('#result-folder-name-' + parent).addClass('selected'); }, error: function(xhr) { alert(xhr.message); @@ -872,17 +875,17 @@ jQuery(document).ready(function() { }); } }); - jQuery('#metadata-viewer').on('click', '.uploadfiles', function() { - var id = jQuery(this).attr('name'); - jQuery('#uploadtitle').html("

    Upload files into folder "+jQuery('#parentFolderName').val()+"

    "); - jQuery('#parentFolderId').val(id); - jQuery('#uploadFilesOverlay').fadeIn(); - if (jQuery('#existingfiles').val()!="yes"){ - jQuery.ajax({ + $j('#metadata-viewer').on('click', '.uploadfiles', function() { + var id = $j(this).attr('name'); + $j('#uploadtitle').html("

    Upload files into folder "+$j('#parentFolderName').val()+"

    "); + $j('#parentFolderId').val(id); + $j('#uploadFilesOverlay').fadeIn(); + if ($j('#existingfiles').val()!="yes"){ + $j.ajax({ url:uploadFilesURL + "?", data: {folderId: id}, success: function(response) { - jQuery('#uploadFiles').html(response).removeClass('ajaxloading'); + $j('#uploadFiles').html(response).removeClass('ajaxloading'); createUploader(); }, error: function(xhr) { @@ -894,185 +897,185 @@ jQuery(document).ready(function() { } }); - jQuery('body').on('click', '#closeupload', function() { - jQuery('#uploadFilesOverlay').fadeOut(); + $j('body').on('click', '#closeupload', function() { + $j('#uploadFilesOverlay').fadeOut(); }); - jQuery('#metadata-viewer').on('click', '.addstudy', function() { + $j('#metadata-viewer').on('click', '.addstudy', function() { - var id = jQuery(this).attr('name'); + var id = $j(this).attr('name'); - jQuery('#createStudyOverlay').fadeIn(); - jQuery('#createStudy').empty().addClass('ajaxloading'); - jQuery('#editMetadata').empty(); + $j('#createStudyOverlay').fadeIn(); + $j('#createStudy').empty().addClass('ajaxloading'); + $j('#editMetadata').empty(); - jQuery.ajax({ + $j.ajax({ url:createStudyURL, data: {folderId: id}, success: function(response) { - jQuery('#createStudy').html(response).removeClass('ajaxloading'); + $j('#createStudy').html(response).removeClass('ajaxloading'); }, error: function(xhr) { alert(xhr); - jQuery('#createStudy').html(response).removeClass('ajaxloading'); + $j('#createStudy').html(response).removeClass('ajaxloading'); } }); }); - jQuery('#welcome-viewer').on('click', '.addprogram', function() { + $j('#welcome-viewer').on('click', '.addprogram', function() { - var id = jQuery(this).attr('name'); + var id = $j(this).attr('name'); - jQuery('#createProgramOverlay').fadeIn(); - jQuery('#createProgram').empty().addClass('ajaxloading'); - jQuery('#editMetadata').empty(); + $j('#createProgramOverlay').fadeIn(); + $j('#createProgram').empty().addClass('ajaxloading'); + $j('#editMetadata').empty(); - jQuery.ajax({ + $j.ajax({ url:createProgramURL, data: {folderId: id}, success: function(response) { - jQuery('#createProgram').html(response).removeClass('ajaxloading'); + $j('#createProgram').html(response).removeClass('ajaxloading'); }, error: function(xhr) { alert(xhr); - jQuery('#createProgram').html(response).removeClass('ajaxloading'); + $j('#createProgram').html(response).removeClass('ajaxloading'); } }); }); - jQuery('#exportOverlay').on('click', '.greybutton.remove', function() { + $j('#exportOverlay').on('click', '.greybutton.remove', function() { - var row = jQuery(this).closest("tr"); + var row = $j(this).closest("tr"); var id = row.attr('name'); - jQuery('#cartcount').hide(); + $j('#cartcount').hide(); - jQuery.ajax({ + $j.ajax({ url:exportRemoveURL, data: {id: id}, success: function(response) { row.remove(); - jQuery('#cartcount').show().text(response); + $j('#cartcount').show().text(response); updateExportCount(); - jQuery('#metadata-viewer').find(".exportaddspan[name='" + id + "']").addClass("foldericon").addClass("addcart").addClass("link").text('Add to export'); + $j('#metadata-viewer').find(".exportaddspan[name='" + id + "']").addClass("foldericon").addClass("addcart").addClass("link").text('Add to export'); }, error: function(xhr) { - jQuery('#cartcount').show(); + $j('#cartcount').show(); } }); }); - jQuery('#exportOverlay').on('click', '.greybutton.export', function() { + $j('#exportOverlay').on('click', '.greybutton.export', function() { - var checkboxes = jQuery('#exporttable input:checked'); + var checkboxes = $j('#exporttable input:checked'); var ids = []; for (i = 0; i < checkboxes.size(); i++) { - ids.push(jQuery(checkboxes[i]).attr('name')); + ids.push($j(checkboxes[i]).attr('name')); } if (ids.length == 0) {return false;} window.location = exportURL + "?id=" + ids.join(','); - jQuery('#cartcount').hide(); + $j('#cartcount').hide(); - jQuery.ajax({ + $j.ajax({ url:exportRemoveURL, data: {id: ids.join(',')}, success: function(response) { for(j=0; j 0) { var currentValue = documentCount.text(); documentCount.text(parseInt(currentValue) + 1); }else{ - jQuery('#folder-header-'+folderId).html(jQuery('#folder-header-'+folderId).html()+ + $j('#folder-header-'+folderId).html($j('#folder-header-'+folderId).html()+ ''+ 'Documents (1)'); } @@ -1131,20 +1134,20 @@ function loadSearchFromSession() { function updateFolder(id) { var imgExpand = "#imgExpand_" + id; - var src = jQuery(imgExpand).attr('src').replace('folderplus.png', 'ajax-loader-flat.gif').replace('folderminus.png', 'ajax-loader-flat.gif'); - jQuery(imgExpand).attr('src',src); + var src = $j(imgExpand).attr('src').replace('folderplus.png', 'ajax-loader-flat.gif').replace('folderminus.png', 'ajax-loader-flat.gif'); + $j(imgExpand).attr('src',src); - jQuery.ajax({ + $j.ajax({ url:folderContentsURL, data: {id: id, auto: false}, success: function(response) { - jQuery('#' + id + '_detail').html(response).addClass('gtb1').addClass('analysesopen').attr('data', true); + $j('#' + id + '_detail').html(response).addClass('gtb1').addClass('analysesopen').attr('data', true); //check if the object has children - if(jQuery('#' + id + '_detail .search-results-table .folderheader').size() > 0){ - jQuery(imgExpand).attr('src', jQuery(imgExpand).attr('src').replace('ajax-loader-flat.gif', 'folderminus.png')); + if($j('#' + id + '_detail .search-results-table .folderheader').size() > 0){ + $j(imgExpand).attr('src', $j(imgExpand).attr('src').replace('ajax-loader-flat.gif', 'folderminus.png')); }else{ - jQuery(imgExpand).attr('src', jQuery(imgExpand).attr('src').replace('ajax-loader-flat.gif', 'folderleaf.png')); + $j(imgExpand).attr('src', $j(imgExpand).attr('src').replace('ajax-loader-flat.gif', 'folderleaf.png')); } }, error: function(xhr) { @@ -1155,11 +1158,11 @@ function updateFolder(id) { function checkSearchLog() { - if (jQuery('#searchlog').size() > 0) { - jQuery.ajax({ + if ($j('#searchlog').size() > 0) { + $j.ajax({ url:searchLogURL, success: function(response) { - var searchLog = jQuery('#searchlog').empty(); + var searchLog = $j('#searchlog').empty(); searchLog.append("
    " + "------"); var log = response.log for (var i = 0; i < log.length; i++) { @@ -1175,10 +1178,10 @@ function checkSearchLog() { //go back to the welcome message function goWelcome() { - jQuery('#metadata-viewer').empty(); - jQuery('#welcome-viewer').empty().addClass('ajaxloading'); - jQuery('#welcome-viewer').load(welcomeURL, {}, function() { - jQuery('#welcome-viewer').removeClass('ajaxloading'); + $j('#metadata-viewer').empty(); + $j('#welcome-viewer').empty().addClass('ajaxloading'); + $j('#welcome-viewer').load(welcomeURL, {}, function() { + $j('#welcome-viewer').removeClass('ajaxloading'); }); } @@ -1187,8 +1190,8 @@ function displayResultsNumber(){ if(resultNumber!=""){ var jsonNumbers = JSON.parse(resultNumber); - jQuery('#welcome-viewer').empty(); - jQuery('#metadata-viewer').empty(); + $j('#welcome-viewer').empty(); + $j('#metadata-viewer').empty(); var htmlResults="

    Search results by type

    "; htmlResults+=""; htmlResults+=""; @@ -1198,64 +1201,64 @@ function displayResultsNumber(){ htmlResults+=""; htmlResults+=""; htmlResults+="
    ObjectNumber of results
    Analyses"+jsonNumbers.ANALYSIS+"
    Folders"+jsonNumbers.FOLDER+"
    "; - jQuery('#metadata-viewer').html(htmlResults); + $j('#metadata-viewer').html(htmlResults); } } //Globally prevent AJAX from being cached (mostly by IE) -jQuery.ajaxSetup({ +$j.ajaxSetup({ cache: false }); function createUploader() { - $fub = jQuery('#fine-uploader-basic'); + $fub = $j('#fine-uploader-basic'); uploader = new qq.FineUploaderBasic({ button: $fub[0], multiple: true, request: { - endpoint: uploadActionURL+'?parentId='+jQuery('#parentFolderId').val() + endpoint: uploadActionURL+'?parentId='+$j('#parentFolderId').val() }, callbacks: { onSubmit: function(id, fileName) { - var folderName = jQuery('#folderName').val(); + var folderName = $j('#folderName').val(); - jQuery('#uploadtable').append(''+ + $j('#uploadtable').append(''+ ''+folderName+''+ ''+fileName+''+ 'Submitting'+ ''); }, onUpload: function(id, fileName) { - jQuery('#file-' + id + " #name").html(fileName); - jQuery('#file-' + id + " #status").html('Initializing '); + $j('#file-' + id + " #name").html(fileName); + $j('#file-' + id + " #status").html('Initializing '); }, onProgress: function(id, fileName, loaded, total) { if (loaded < total) { progress = Math.round(loaded / total * 100) + '% of ' + Math.round(total / 1024) + ' kB'; - jQuery('#file-' + id + " #status").html('Uploading '); - jQuery('#file-' + id + " #progress").html(progress); + $j('#file-' + id + " #status").html('Uploading '); + $j('#file-' + id + " #progress").html(progress); } else { - jQuery('#file-' + id + " #status").html('Saving'); - jQuery('#file-' + id + " #progress").html('100%'); + $j('#file-' + id + " #status").html('Saving'); + $j('#file-' + id + " #progress").html('100%'); } }, onComplete: function(id, fileName, responseJSON) { if (responseJSON.success) { - jQuery('#file-' + id + " #status").html('File successfully uploaded '); - jQuery('#file-' + id + " #progress").html(''); + $j('#file-' + id + " #status").html('File successfully uploaded '); + $j('#file-' + id + " #progress").html(''); var folderId=responseJSON.folderId; incrementeDocumentCount(folderId); - if(folderId == jQuery('#parentFolderId').val()){ - jQuery('#metadata-viewer').empty().addClass('ajaxloading'); - jQuery('#metadata-viewer').load(folderDetailsURL + '?id=' + folderId, {}, function() { - jQuery('#metadata-viewer').removeClass('ajaxloading'); + if(folderId == $j('#parentFolderId').val()){ + $j('#metadata-viewer').empty().addClass('ajaxloading'); + $j('#metadata-viewer').load(folderDetailsURL + '?id=' + folderId, {}, function() { + $j('#metadata-viewer').removeClass('ajaxloading'); }); } } else { - jQuery('#file-' + id + " #status").html('Error: '+responseJSON.error); - jQuery('#file-' + id + " #progress").html(''); + $j('#file-' + id + " #status").html('Error: '+responseJSON.error); + $j('#file-' + id + " #progress").html(''); } } @@ -1263,55 +1266,55 @@ function createUploader() { }); } function createUploader() { - $fub = jQuery('#fine-uploader-basic'); + $fub = $j('#fine-uploader-basic'); uploader = new qq.FineUploaderBasic({ button: $fub[0], multiple: true, request: { - endpoint: uploadActionURL+'?parentId='+jQuery('#parentFolderId').val() + endpoint: uploadActionURL+'?parentId='+$j('#parentFolderId').val() }, callbacks: { onSubmit: function(id, fileName) { - var folderName = jQuery('#parentFolderName').val(); + var folderName = $j('#parentFolderName').val(); - jQuery('#uploadtable').append(''+ + $j('#uploadtable').append(''+ ''+folderName+''+ ''+fileName+''+ 'Submitting'+ ''); }, onUpload: function(id, fileName) { - jQuery('#file-' + id + " #name").html(fileName); - jQuery('#file-' + id + " #status").html('Initializing '); + $j('#file-' + id + " #name").html(fileName); + $j('#file-' + id + " #status").html('Initializing '); }, onProgress: function(id, fileName, loaded, total) { if (loaded < total) { progress = Math.round(loaded / total * 100) + '% of ' + Math.round(total / 1024) + ' kB'; - jQuery('#file-' + id + " #status").html('Uploading '); - jQuery('#file-' + id + " #progress").html(progress); + $j('#file-' + id + " #status").html('Uploading '); + $j('#file-' + id + " #progress").html(progress); } else { - jQuery('#file-' + id + " #status").html('Saving'); - jQuery('#file-' + id + " #progress").html('100%'); + $j('#file-' + id + " #status").html('Saving'); + $j('#file-' + id + " #progress").html('100%'); } }, onComplete: function(id, fileName, responseJSON) { if (responseJSON.success) { - jQuery('#file-' + id + " #status").html('File successfully uploaded '); - jQuery('#file-' + id + " #progress").html(''); + $j('#file-' + id + " #status").html('File successfully uploaded '); + $j('#file-' + id + " #progress").html(''); var folderId=responseJSON.folderId; incrementeDocumentCount(folderId); - if(folderId == jQuery('#parentFolderId').val()){ - jQuery('#metadata-viewer').empty().addClass('ajaxloading'); - jQuery('#metadata-viewer').load(folderDetailsURL + '?id=' + folderId, {}, function() { - jQuery('#metadata-viewer').removeClass('ajaxloading'); + if(folderId == $j('#parentFolderId').val()){ + $j('#metadata-viewer').empty().addClass('ajaxloading'); + $j('#metadata-viewer').load(folderDetailsURL + '?id=' + folderId, {}, function() { + $j('#metadata-viewer').removeClass('ajaxloading'); }); } } else { - jQuery('#file-' + id + " #status").html('Error: '+responseJSON.error); - jQuery('#file-' + id + " #progress").html(''); + $j('#file-' + id + " #status").html('Error: '+responseJSON.error); + $j('#file-' + id + " #progress").html(''); } } } From acb4a7a90b60f069bd62c84f7b04a8a155facbbd Mon Sep 17 00:00:00 2001 From: dennyverbeeck Date: Fri, 3 Feb 2017 14:44:35 +0100 Subject: [PATCH 019/136] Hidome Ffature: when search term left empty, you get a 'no-value' type filter. I.e. match all subjects who have the high dimensional concept (a.k.a. the original pre-Hidome behavior) Fix: when entering numeric values manually in the min and max boxes, they are no longer compared as strings. --- web-app/js/datasetExplorer/omicsFilter.js | 92 +++++++++++++++-------- web-app/js/datasetExplorer/querypanels.js | 8 +- 2 files changed, 68 insertions(+), 32 deletions(-) diff --git a/web-app/js/datasetExplorer/omicsFilter.js b/web-app/js/datasetExplorer/omicsFilter.js index 3ccf793a3..d4f796500 100644 --- a/web-app/js/datasetExplorer/omicsFilter.js +++ b/web-app/js/datasetExplorer/omicsFilter.js @@ -88,18 +88,24 @@ function omicsFilterWindowReceived(result, request) { function repopulateFilterWindow() { if (omicsFilterRepopulateWindow == null) return; - jQuery("#highdimension-search-property").val(omicsFilterRepopulateWindow.omicsproperty.nodeValue); - jQuery("#highdimension-filter-selector").val(omicsFilterRepopulateWindow.omicsselector.nodeValue); - jQuery("#highdimension-filter-projection").val(omicsFilterRepopulateWindow.omicsprojection.nodeValue); + if (omicsFilterRepopulateWindow.omicsproperty != null) { + jQuery("#highdimension-search-property").val(omicsFilterRepopulateWindow.omicsproperty.nodeValue); + } - omicsAutoCompleteList = [omicsFilterRepopulateWindow.omicsselector.nodeValue]; + if (omicsFilterRepopulateWindow.omicsprojection != null) { + jQuery("#highdimension-filter-projection").val(omicsFilterRepopulateWindow.omicsprojection.nodeValue); + } - showConceptDistributionHistogramForOmicsFilterComplete(null); - showConceptDistributionHistogramForOmicsFilter(getOmicsFilterParams()); + if (omicsFilterRepopulateWindow.omicsselector != null) { + jQuery("#highdimension-filter-selector").val(omicsFilterRepopulateWindow.omicsselector.nodeValue); + omicsAutoCompleteList = [omicsFilterRepopulateWindow.omicsselector.nodeValue]; + showConceptDistributionHistogramForOmicsFilterComplete(null); + showConceptDistributionHistogramForOmicsFilter(getOmicsFilterParams()); + } } function repopulateOmicsFilterRange() { - if (omicsFilterRepopulateWindow == null) return; + if (omicsFilterRepopulateWindow.omicsvalue == null) return; if (omics_filter_info.filter_type == "SINGLE_NUMERIC" || omics_filter_info.filter_type == "ACGH") { var minbox = jQuery("#highdimension-amount-min"); @@ -220,45 +226,55 @@ function addOmicsFilterMinMaxInputHandlers() { minbox.blur(function(event) { var slider = jQuery("#highdimension-range"); var value = minbox.val(); + var sliderMin = parseFloat(slider.slider('option','min')); + var sliderMax = parseFloat(slider.slider('option','max')); if (!jQuery.isNumeric(value)) { - minbox.val(slider.slider('option','min')); + minbox.val(sliderMin); + } + if (!jQuery.isNumeric(maxbox.val())) { + maxbox.val(sliderMax); } - else if (value < slider.slider('option','min')) { - minbox.val(slider.slider('option','min')); + value = parseFloat(minbox.val()); + var maxboxVal = parseFloat(maxbox.val()); + if (value < sliderMin) { + minbox.val(sliderMin); } - else if (value > maxbox.val()) { - minbox.val(maxbox.val()); + else if (value > maxboxVal) { + minbox.val(maxboxVal); } - slider.slider('values',0,minbox.val()); - jQuery("#highdimension-filter-subjectcount").html(omicsFilterValues.filter(function (el, idx, array) {return el >= minbox.val();}) - .filter(function(el, idx, array) {return el <= maxbox.val();}) + slider.slider('values',0,value); + jQuery("#highdimension-filter-subjectcount").html(omicsFilterValues.filter(function (el, idx, array) {return el >= value;}) + .filter(function(el, idx, array) {return el <= maxboxVal;}) .length); - var min = slider.slider('option', 'min'); - var max = slider.slider('option', 'max'); - omicsSliderLowHandleRatio = (minbox.val() - min) / (max - min); + omicsSliderLowHandleRatio = (value - sliderMin) / (sliderMax - sliderMin); }); maxbox.blur(function(event) { var slider = jQuery("#highdimension-range"); var value = maxbox.val(); + var sliderMin = parseFloat(slider.slider('option','min')); + var sliderMax = parseFloat(slider.slider('option','max')); if (!jQuery.isNumeric(value)) { - maxbox.val(slider.slider('option','max')); + maxbox.val(sliderMax); } - else if (value > slider.slider('option','max')) { - maxbox.val(slider.slider('option','max')); + if (!jQuery.isNumeric(minbox.val())) { + minbox.val(sliderMin); } - else if (value < minbox.val()) { - maxbox.val(minbox.val()); + value = parseFloat(maxbox.val()); + var minboxVal = parseFloat(minbox.val()) + if (value > sliderMax) { + maxbox.val(sliderMax); + } + else if (value < minboxVal) { + maxbox.val(minboxVal); } - slider.slider('values',1,maxbox.val()); - jQuery("#highdimension-filter-subjectcount").html(omicsFilterValues.filter(function (el, idx, array) {return el >= minbox.val();}) - .filter(function(el, idx, array) {return el <= maxbox.val();}) + slider.slider('values',1,value); + jQuery("#highdimension-filter-subjectcount").html(omicsFilterValues.filter(function (el, idx, array) {return el >= minboxVal;}) + .filter(function(el, idx, array) {return el <= value;}) .length); - var min = slider.slider('option', 'min'); - var max = slider.slider('option', 'max'); - omicsSliderHighHandleRatio = (maxbox.val() - min) / (max - min); + omicsSliderHighHandleRatio = (value - sliderMin) / (sliderMax - sliderMin); }); // let the enter key blur the text fields, thus updating the slider and subject counts @@ -495,10 +511,26 @@ function applySingleNumericOmicsFilter(validation) { // filter if (validation) { if (params.selector == "") { - alert("You must choose a gene."); + // no gene supplied, we assume a "no value" type filter + omicsFilterValues = []; + omicsSliderLowHandleRatio = 0; + omicsSliderHighHandleRatio = 1; + document.getElementById("highdimension-filter-main").removeChild(document.getElementById("highdimension-filter-content")); + omicsfilterwin.hide(); + var concept = jQuery('#' + selectedConcept.id); + jQuery('#' + selectedConcept.id + " .concept-text").html(selectedConcept.attributes["conceptname"].nodeValue); + concept.removeAttr("omicsproperty"); + concept.removeAttr("omicsselector"); + concept.removeAttr("omicsoperator"); + concept.removeAttr("omicsvalue"); + concept.removeAttr("omicsprojection"); + concept.removeAttr("omicsvaluetype"); + concept.attr("setvaluemode",""); + moveSelectedConceptFromHoldingToTarget(); return; } + var in_list = false; for (var i = 0; i < omicsAutoCompleteList.length; i++) { if (omicsAutoCompleteList[i].toLowerCase() == params.selector.toLocaleLowerCase()) { diff --git a/web-app/js/datasetExplorer/querypanels.js b/web-app/js/datasetExplorer/querypanels.js index e055159ca..2b3b6ac27 100644 --- a/web-app/js/datasetExplorer/querypanels.js +++ b/web-app/js/datasetExplorer/querypanels.js @@ -364,12 +364,16 @@ function getPanelItemFromConcept(concept) { // We try to infer the type when possible to match the icon jQuery.get(pageInfo.basePath + "/concepts/getResource", { concept_key: concept["conceptid"] }, function() {}, 'json') .success(function (data) { - jQuery("span:first", _item).addClass(getClassForNodeResource(data)) + jQuery("span:first", _item).addClass(getClassForNodeResource(data)); + jQuery.each(data.visualAttributes, function (index, value) { + if (value.toUpperCase() == "HIGH_DIMENSIONAL") + _item.attr("oktousevalues", "H"); + }); }) _item .append(jQuery("").addClass("x-tree-node-icon")) - .append(jQuery("").addClass("concept-text").html(concept.conceptname + _valueText)) + .append(jQuery("").addClass("concept-text").html(concept.conceptname + " " + _valueText)) jQuery.each(concept, function(key, value) { _item.attr(key, value) From a3621230e4062dfb911578c086b97a6a4b0fffb6 Mon Sep 17 00:00:00 2001 From: Peter Rice Date: Fri, 3 Feb 2017 16:46:11 +0000 Subject: [PATCH 020/136] Catch empty search terms list --- web-app/js/rwgsearch.js | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/web-app/js/rwgsearch.js b/web-app/js/rwgsearch.js index 200a2b2da..ccafa5ba8 100644 --- a/web-app/js/rwgsearch.js +++ b/web-app/js/rwgsearch.js @@ -506,13 +506,14 @@ function removeSearchTerm(ctrl) { // only refresh results if the tree was not updated (the onSelect also fires these event, so don't want to do 2x) if (!treeUpdated) { - showSearchTemplate(); - showSearchResults(); + showSearchTemplate(); + showSearchResults(); } - //Remove selected status from filter browser for this item - unselectFilterItem(fields[2]); - + //Remove selected status from filter browser for this item + if(idx > -1) { + unselectFilterItem(fields[2]); + } } //Clear the tree, results along with emptying the two arrays that store categories and search terms. From 24b25dac310579afcd2f2f37d276714fb410d5e4 Mon Sep 17 00:00:00 2001 From: Peter Rice Date: Fri, 3 Feb 2017 16:46:36 +0000 Subject: [PATCH 021/136] name of xnat import enable parameter --- grails-app/views/layouts/_adminnavbar.gsp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/grails-app/views/layouts/_adminnavbar.gsp b/grails-app/views/layouts/_adminnavbar.gsp index 767065ef8..2f922867d 100644 --- a/grails-app/views/layouts/_adminnavbar.gsp +++ b/grails-app/views/layouts/_adminnavbar.gsp @@ -166,7 +166,7 @@ - +

    From 3b95368445f50f4ff1cba665b30a215685bf3584 Mon Sep 17 00:00:00 2001 From: Peter Rice Date: Fri, 3 Feb 2017 16:47:08 +0000 Subject: [PATCH 022/136] xnat import enable parameter --- grails-app/views/datasetExplorer/datasetExplorer.gsp | 1 + 1 file changed, 1 insertion(+) diff --git a/grails-app/views/datasetExplorer/datasetExplorer.gsp b/grails-app/views/datasetExplorer/datasetExplorer.gsp index 94824de51..17aea2e04 100644 --- a/grails-app/views/datasetExplorer/datasetExplorer.gsp +++ b/grails-app/views/datasetExplorer/datasetExplorer.gsp @@ -95,6 +95,7 @@ sampleExplorerEnabled: ${!!grailsApplication.config.ui.tabs.sampleExplorer.show}, metacoreAnalyticsEnabled: ${!!grailsApplication.config.com.thomsonreuters.transmart.metacoreAnalyticsEnable}, metacoreUrl: '${grailsApplication.config.com.thomsonreuters.transmart.metacoreURL}', + xnatViewerEnabled: ${!!grailsApplication.config.org.transmart.xnatViewerEnable}, AnalysisHasBeenRun: false, ResultSetRegionParams: {}, currentReportCodes: [], From 0f9a306914ccf4ba8ce3e22ab67a299d402d7f4b Mon Sep 17 00:00:00 2001 From: Peter Rice Date: Fri, 3 Feb 2017 16:47:52 +0000 Subject: [PATCH 023/136] typo in error message --- grails-app/conf/BootStrap.groovy | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/grails-app/conf/BootStrap.groovy b/grails-app/conf/BootStrap.groovy index b3f7493f4..01cfda89b 100644 --- a/grails-app/conf/BootStrap.groovy +++ b/grails-app/conf/BootStrap.groovy @@ -78,7 +78,7 @@ class BootStrap { } if (!tsAppRScriptsDir || !tsAppRScriptsDir.isDirectory()) { - throw new RuntimeException('Could not determine proper for ' + + throw new RuntimeException('Could not determine proper value for ' + 'com.recomdata.transmart.data.export.rScriptDirectory') } c.com.recomdata.transmart.data.export.rScriptDirectory = tsAppRScriptsDir.canonicalPath From 9d69e3236fa1ef1da3f43a673c062cfb76a3ce98 Mon Sep 17 00:00:00 2001 From: dennyverbeeck Date: Wed, 8 Feb 2017 10:43:58 +0100 Subject: [PATCH 024/136] Fix in repopulate filter window that caused not being able to create new high dimensional queries. Fix high dimensional filter properties not showing up in workspaces tab. --- .../controllers/SubsetController.groovy | 23 ++++++++++++++++++- web-app/js/datasetExplorer/omicsFilter.js | 2 +- 2 files changed, 23 insertions(+), 2 deletions(-) diff --git a/grails-app/controllers/SubsetController.groovy b/grails-app/controllers/SubsetController.groovy index cf0b60564..312867e46 100644 --- a/grails-app/controllers/SubsetController.groovy +++ b/grails-app/controllers/SubsetController.groovy @@ -1,6 +1,7 @@ import com.recomdata.transmart.domain.searchapp.Subset import grails.converters.JSON -import org.transmartproject.core.querytool.QueriesResource +import org.transmartproject.core.dataquery.highdim.projections.Projection +import org.transmartproject.core.querytool.ConstraintByOmicsValue class SubsetController { @@ -122,6 +123,26 @@ class SubsetController { if (i.constraint) { result += "( with constraints )" } + if (i.constraintByOmicsValue) { + result += " ( " + i.constraintByOmicsValue.selector + " " + + Projection.prettyNames.get(i.constraintByOmicsValue.projectionType, + i.constraintByOmicsValue.projectionType) + " " + + i.constraintByOmicsValue.operator.value + " " + if (i.constraintByOmicsValue.operator == ConstraintByOmicsValue.Operator.BETWEEN) { + String[] bounds = i.constraintByOmicsValue.constraint.split(':') + if (bounds.length != 2) { + log.error "BETWEEN constraint type found with values not seperated by ':'" + result += i.constraintByOmicsValue.constraint + } + else { + result += bounds.join(" and ") + } + } + else { + result += i.constraintByOmicsValue.constraint + } + result += " )" + } result += "
    " } } diff --git a/web-app/js/datasetExplorer/omicsFilter.js b/web-app/js/datasetExplorer/omicsFilter.js index d4f796500..b0f8c1c8e 100644 --- a/web-app/js/datasetExplorer/omicsFilter.js +++ b/web-app/js/datasetExplorer/omicsFilter.js @@ -105,7 +105,7 @@ function repopulateFilterWindow() { } function repopulateOmicsFilterRange() { - if (omicsFilterRepopulateWindow.omicsvalue == null) return; + if (omicsFilterRepopulateWindow == null || omicsFilterRepopulateWindow.omicsvalue == null) return; if (omics_filter_info.filter_type == "SINGLE_NUMERIC" || omics_filter_info.filter_type == "ACGH") { var minbox = jQuery("#highdimension-amount-min"); From 349727c63094fa7339250a29b312df8e2fb5f044 Mon Sep 17 00:00:00 2001 From: dennyverbeeck Date: Wed, 8 Feb 2017 11:07:32 +0100 Subject: [PATCH 025/136] Add button for 'No filter' option in high dimensional data instead of clicking ok with no filter, as this is not clear to users. --- web-app/js/datasetExplorer/datasetExplorer.js | 6 +++ web-app/js/datasetExplorer/omicsFilter.js | 37 ++++++++++--------- 2 files changed, 26 insertions(+), 17 deletions(-) diff --git a/web-app/js/datasetExplorer/datasetExplorer.js b/web-app/js/datasetExplorer/datasetExplorer.js index 8daeb5534..ee913e5dc 100644 --- a/web-app/js/datasetExplorer/datasetExplorer.js +++ b/web-app/js/datasetExplorer/datasetExplorer.js @@ -1004,6 +1004,12 @@ Ext.onReady(function () { border: false, items: [omicsfilterpanel], buttons: [ + { + text: 'No filter', + handler: function () { + applyOmicsNoFilterDialog(); + } + }, { text: 'OK', handler: function () { diff --git a/web-app/js/datasetExplorer/omicsFilter.js b/web-app/js/datasetExplorer/omicsFilter.js index b0f8c1c8e..e178c3402 100644 --- a/web-app/js/datasetExplorer/omicsFilter.js +++ b/web-app/js/datasetExplorer/omicsFilter.js @@ -505,32 +505,35 @@ function omicsValuesFailed(result) { document.getElementById("highdimension-filter-histogram").innerHTML = "An error occured while retrieving the histogram values: " + result.responseText; } +function applyOmicsNoFilterDialog() { + // no gene supplied, we assume a "no value" type filter + omicsFilterValues = []; + omicsSliderLowHandleRatio = 0; + omicsSliderHighHandleRatio = 1; + document.getElementById("highdimension-filter-main").removeChild(document.getElementById("highdimension-filter-content")); + omicsfilterwin.hide(); + var concept = jQuery('#' + selectedConcept.id); + jQuery('#' + selectedConcept.id + " .concept-text").html(selectedConcept.attributes["conceptname"].nodeValue); + concept.removeAttr("omicsproperty"); + concept.removeAttr("omicsselector"); + concept.removeAttr("omicsoperator"); + concept.removeAttr("omicsvalue"); + concept.removeAttr("omicsprojection"); + concept.removeAttr("omicsvaluetype"); + concept.attr("setvaluemode",""); + moveSelectedConceptFromHoldingToTarget(); +} + function applySingleNumericOmicsFilter(validation) { var params = getOmicsFilterParams(); if (omics_filter_info.filter) { // filter if (validation) { if (params.selector == "") { - // no gene supplied, we assume a "no value" type filter - omicsFilterValues = []; - omicsSliderLowHandleRatio = 0; - omicsSliderHighHandleRatio = 1; - document.getElementById("highdimension-filter-main").removeChild(document.getElementById("highdimension-filter-content")); - omicsfilterwin.hide(); - var concept = jQuery('#' + selectedConcept.id); - jQuery('#' + selectedConcept.id + " .concept-text").html(selectedConcept.attributes["conceptname"].nodeValue); - concept.removeAttr("omicsproperty"); - concept.removeAttr("omicsselector"); - concept.removeAttr("omicsoperator"); - concept.removeAttr("omicsvalue"); - concept.removeAttr("omicsprojection"); - concept.removeAttr("omicsvaluetype"); - concept.attr("setvaluemode",""); - moveSelectedConceptFromHoldingToTarget(); + alert("You must choose a gene."); return; } - var in_list = false; for (var i = 0; i < omicsAutoCompleteList.length; i++) { if (omicsAutoCompleteList[i].toLowerCase() == params.selector.toLocaleLowerCase()) { From d0d67b480bb5b927e24d6226c36ab96d86fa1636 Mon Sep 17 00:00:00 2001 From: dennyverbeeck Date: Wed, 8 Feb 2017 11:07:59 +0100 Subject: [PATCH 026/136] Cosmetic change to query display --- grails-app/controllers/SubsetController.groovy | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/grails-app/controllers/SubsetController.groovy b/grails-app/controllers/SubsetController.groovy index 312867e46..5e0badaed 100644 --- a/grails-app/controllers/SubsetController.groovy +++ b/grails-app/controllers/SubsetController.groovy @@ -124,7 +124,7 @@ class SubsetController { result += "( with constraints )" } if (i.constraintByOmicsValue) { - result += " ( " + i.constraintByOmicsValue.selector + " " + + result += " - " + i.constraintByOmicsValue.selector + " " + Projection.prettyNames.get(i.constraintByOmicsValue.projectionType, i.constraintByOmicsValue.projectionType) + " " + i.constraintByOmicsValue.operator.value + " " @@ -141,7 +141,6 @@ class SubsetController { else { result += i.constraintByOmicsValue.constraint } - result += " )" } result += "
    " } From 1bf36e0eafc824d81a8b33618f5d202244fd3129 Mon Sep 17 00:00:00 2001 From: dennyverbeeck Date: Thu, 9 Feb 2017 09:53:44 +0100 Subject: [PATCH 027/136] Fix for using 'No filter' when dropping high dimensional concept into summary statistics or grid view --- web-app/js/datasetExplorer/omicsFilter.js | 34 +++++++++++++++++++++-- 1 file changed, 32 insertions(+), 2 deletions(-) diff --git a/web-app/js/datasetExplorer/omicsFilter.js b/web-app/js/datasetExplorer/omicsFilter.js index e178c3402..fc0bc1225 100644 --- a/web-app/js/datasetExplorer/omicsFilter.js +++ b/web-app/js/datasetExplorer/omicsFilter.js @@ -506,7 +506,7 @@ function omicsValuesFailed(result) { } function applyOmicsNoFilterDialog() { - // no gene supplied, we assume a "no value" type filter + if (omics_filter_info.filter) { omicsFilterValues = []; omicsSliderLowHandleRatio = 0; omicsSliderHighHandleRatio = 1; @@ -520,8 +520,38 @@ function applyOmicsNoFilterDialog() { concept.removeAttr("omicsvalue"); concept.removeAttr("omicsprojection"); concept.removeAttr("omicsvaluetype"); - concept.attr("setvaluemode",""); + concept.attr("setvaluemode", ""); moveSelectedConceptFromHoldingToTarget(); + } + else { + resultsTabPanel.body.mask("Running analysis...", 'x-mask-loading'); + Ext.Ajax.request( + { + url : pageInfo.basePath+"/chart/analysis", + method : 'POST', + timeout: '600000', + params : Ext.urlEncode( + { + charttype : "analysis", + concept_key : omics_filter_info.concept_key, + result_instance_id1 : GLOBAL.CurrentSubsetIDs[1], + result_instance_id2 : GLOBAL.CurrentSubsetIDs[2] + } + ), // or a URL encoded string + success: function (result, request) { + buildAnalysisComplete(result); + resultsTabPanel.body.unmask(); + }, + failure: function (result, request) { + alert("A problem arose while trying to retrieve the results"); + resultsTabPanel.body.unmask(); + } + } + ); + getAnalysisGridData(omics_filter_info.concept_key); + document.getElementById("highdimension-filter-main").removeChild(document.getElementById("highdimension-filter-content")); + omicsfilterwin.hide(); + } } function applySingleNumericOmicsFilter(validation) { From f6931c9c32e08fb4c41581981645aed5a2dc95be Mon Sep 17 00:00:00 2001 From: dennyverbeeck Date: Wed, 1 Mar 2017 14:15:20 +0100 Subject: [PATCH 028/136] Fixes for HiDome Fix dialog behavior for VCF datatype: dragging into a panel leads to the 'No filter' behavior. Right-clicking and choosing Set filter shows the not supported yet message. Fix concept count bar charts not showing up in summary statistics when using the 'No filter' dialog option. Fix grid view columns for high dimensional nodes not appearing when using the 'No filter' dialog option Fix uncaught exceptions when specifying constraints that lead to an empty patient set. Fix bug related to using only Subset 2 with high dimensional data --- grails-app/controllers/ChartController.groovy | 4 +- .../HighDimensionFilterController.groovy | 27 ++++--- grails-app/services/ChartService.groovy | 27 ++++--- .../services/HighDimensionQueryService.groovy | 21 +++--- grails-app/services/I2b2HelperService.groovy | 14 +++- web-app/js/datasetExplorer/omicsFilter.js | 72 ++++++++++++++----- 6 files changed, 114 insertions(+), 51 deletions(-) diff --git a/grails-app/controllers/ChartController.groovy b/grails-app/controllers/ChartController.groovy index 05478e1c6..7bb972129 100644 --- a/grails-app/controllers/ChartController.groovy +++ b/grails-app/controllers/ChartController.groovy @@ -272,8 +272,6 @@ class ChartController { PrintWriter pw = new PrintWriter(response.getOutputStream()); if (concept_key && !concept_key.isEmpty()) { - - // We retrieve the highdimension parameters from the client, if they were passed def omics_params = [:] params.findAll { k, v -> @@ -281,7 +279,7 @@ class ChartController { }.each { k, v -> omics_params[k] = v } - if (omics_params) { // empty maps are coerced to false by groovy + if (omics_params) { omics_params.concept_key = concept_key if (s1) highDimensionQueryService.addHighDimConceptDataToTable(table, omics_params, result_instance_id1) if (s2) highDimensionQueryService.addHighDimConceptDataToTable(table, omics_params, result_instance_id2) diff --git a/grails-app/controllers/HighDimensionFilterController.groovy b/grails-app/controllers/HighDimensionFilterController.groovy index ec9bf2d38..9ad4ced44 100644 --- a/grails-app/controllers/HighDimensionFilterController.groovy +++ b/grails-app/controllers/HighDimensionFilterController.groovy @@ -1,9 +1,7 @@ import grails.converters.JSON import org.transmartproject.core.dataquery.highdim.projections.Projection -import org.transmartproject.core.querytool.ConstraintByOmicsValue import org.transmartproject.db.dataquery.highdim.DeGplInfo import org.transmartproject.db.dataquery.highdim.DeSubjectSampleMapping - /** * Author: Denny Verbeeck (dverbeec@its.jnj.com) */ @@ -43,14 +41,23 @@ class HighDimensionFilterController { def resource = highDimensionResourceService.getHighDimDataTypeResourceFromConcept(concept_key) - def model = [gpl_id: platform.id, - marker_type: platform.markerType, - filter_type: resource.getHighDimensionFilterType(), - searchable_properties: resource.getSearchableAnnotationProperties().collectEntries {[it, searchableAnnotationPropertiesDictionary.get(it, it)]}, - filter: filter, - projections: resource.getSearchableProjections().collectEntries {[it, Projection.prettyNames.get(it, it)]}] - - render(template: template, model: model) + if (resource.dataTypeName == 'vcf') { + render "Small Variant data is not supperted yet, stay tuned!" + } + else { + def model = [gpl_id : platform.id, + marker_type : platform.markerType, + filter_type : resource.getHighDimensionFilterType(), + searchable_properties: resource.getSearchableAnnotationProperties().collectEntries { + [it, searchableAnnotationPropertiesDictionary.get(it, it)] + }, + filter : filter, + projections : resource.getSearchableProjections().collectEntries { + [it, Projection.prettyNames.get(it, it)] + }] + + render(template: template, model: model) + } } /** diff --git a/grails-app/services/ChartService.groovy b/grails-app/services/ChartService.groovy index 7c1bf733a..a8ce345e3 100644 --- a/grails-app/services/ChartService.groovy +++ b/grails-app/services/ChartService.groovy @@ -22,6 +22,7 @@ import org.jfree.graphics2d.svg.SVGGraphics2D import org.jfree.ui.RectangleInsets import org.jfree.util.ShapeUtilities import org.transmartproject.core.dataquery.highdim.projections.Projection +import org.transmartproject.core.exceptions.EmptySetException import org.transmartproject.core.querytool.ConstraintByOmicsValue import java.awt.* @@ -217,7 +218,7 @@ class ChartService { } } - } else if (i2b2HelperService.isHighDimensionalConceptCode(result.commons.conceptCode) && result.commons.omics_params) { + } else if (i2b2HelperService.isHighDimensionalConceptCode(result.commons.conceptCode) && i2b2HelperService.isValidOmicsParams(result.commons.omics_params)) { result.commons.type = 'value' result.commons.conceptName = result.commons.omics_params.omics_selector + " in " + result.commons.conceptName @@ -233,13 +234,19 @@ class ChartService { }.each { n, p -> // Getting the concept data - p.conceptData = - resource.getDistribution( - new ConstraintByOmicsValue(projectionType: result.commons.omics_params.omics_projection_type, - property : result.commons.omics_params.omics_property, - selector : result.commons.omics_params.omics_selector), - concept, - (p.instance == "" ? null : p.instance as Long)).collect {k, v -> v} + try { + p.conceptData = + resource.getDistribution( + new ConstraintByOmicsValue(projectionType: result.commons.omics_params.omics_projection_type, + property: result.commons.omics_params.omics_property, + selector: result.commons.omics_params.omics_selector), + concept, + (p.instance == "" ? null : p.instance as Long)).collect { k, v -> v } + } + catch (EmptySetException ese) { + log.warn("No assays satisfy the provided criteria in result_instance_id " + p.instance) + p.conceptData = [] + } if (p.instance != "") p.patientCount = i2b2HelperService.getPatientSetSize(p.instance) @@ -258,7 +265,7 @@ class ChartService { result.commons.conceptPlot = getSVGChart(type: 'boxplot-and-points', data: conceptHistogramHandle, boxplotdata: conceptPlotHandle, size: chartSize) // Lets calculate the T test if possible - if (result[2].exists) { + if (result[1].exists && result[2].exists) { if (result[1].conceptData.toArray() == result[2].conceptData.toArray()) result.commons.testmessage = 'No T-test calculated: these are the same subsets' @@ -301,7 +308,7 @@ class ChartService { } // Let's calculate the χ² test if possible - if (result[2].exists) { + if (result[1].exists && result[2].exists) { def junction = false diff --git a/grails-app/services/HighDimensionQueryService.groovy b/grails-app/services/HighDimensionQueryService.groovy index 53a3cb256..8277c7dcf 100644 --- a/grails-app/services/HighDimensionQueryService.groovy +++ b/grails-app/services/HighDimensionQueryService.groovy @@ -47,8 +47,8 @@ class HighDimensionQueryService { } xml.panel.each { p -> p.item.each { i -> - if (i.constrain_by_omics_value.size()) { - def constraint_params = [:] + def constraint_params = [:] + if (i.constrain_by_omics_value?.size()) { constraint_params.concept_key = i.item_key.toString() constraint_params.omics_selector = i.constrain_by_omics_value.omics_selector.toString() constraint_params.omics_value_type = i.constrain_by_omics_value.omics_value_type.toString() @@ -56,8 +56,12 @@ class HighDimensionQueryService { constraint_params.omics_value_constraint = i.constrain_by_omics_value.omics_value_constraint.toString() constraint_params.omics_projection_type = i.constrain_by_omics_value.omics_projection_type.toString() constraint_params.omics_property = i.constrain_by_omics_value.omics_property.toString() - concepts.add(constraint_params) } + else if (i.item_key) { + // high dimensional concept but no value filter + constraint_params.concept_key = i.item_key.toString() + } + concepts.add(constraint_params) } } }) @@ -71,6 +75,10 @@ class HighDimensionQueryService { def ExportTableNew addHighDimConceptDataToTable(ExportTableNew tablein, omics_constraint, String result_instance_id) { checkQueryResultAccess result_instance_id + if (!i2b2HelperService.isValidOmicsParams(omics_constraint)) { + return i2b2HelperService.addConceptDataToTable(tablein, omics_constraint.concept_key, result_instance_id) + } + def concept_key = omics_constraint.concept_key def selector = omics_constraint.omics_selector String columnid = (concept_key + selector + omics_constraint.omics_projection_type).encodeAsSHA1() @@ -109,13 +117,6 @@ class HighDimensionQueryService { tablein.putRow(subject, newrow); } } - - //pad all the empty values for this column - for (ExportRowNew row : tablein.getRows()) { - if (!row.containsColumn(columnid)) { - row.put(columnid, "NULL"); - } - } } return tablein; diff --git a/grails-app/services/I2b2HelperService.groovy b/grails-app/services/I2b2HelperService.groovy index c2c012da2..e3807c2f8 100644 --- a/grails-app/services/I2b2HelperService.groovy +++ b/grails-app/services/I2b2HelperService.groovy @@ -603,6 +603,15 @@ class I2b2HelperService { return res; } + /** + * Check if a map contains all the keys an omics_params map should contain + * @param params the map to check + * @return True if the map contains all necessary keys, false otherwise + */ + def Boolean isValidOmicsParams(Map params) { + ['omics_selector', 'omics_projection_type', 'omics_property', 'omics_selector'].every {params?.containsKey(it)} + } + def Boolean nodeXmlRepresentsValueConcept(String xml) { Boolean res = false; @@ -636,11 +645,12 @@ class I2b2HelperService { def xTrialsCaseFlag = isXTrialsConcept(concept_key) def leafNodeFlag = isLeafConceptKey(concept_key) + def highDimNodeFlag = isHighDimensionalConceptKey(concept_key) def HashMap results = new LinkedHashMap() log.trace "input concept_key = " + concept_key - if (leafNodeFlag) { + if (leafNodeFlag && !highDimNodeFlag) { concept_key = getParentConceptKey(concept_key) } log.trace "lookup concept_key = " + concept_key @@ -656,7 +666,7 @@ class I2b2HelperService { } else { String fullname = concept_key.substring(concept_key.indexOf("\\", 2), concept_key.length()); - int i = getLevelFromKey(concept_key) + 1; + int i = getLevelFromKey(concept_key) + (highDimNodeFlag ? 0 : 1); Sql sql = new Sql(dataSource); String sqlt = """ SELECT DISTINCT c_name, c_fullname diff --git a/web-app/js/datasetExplorer/omicsFilter.js b/web-app/js/datasetExplorer/omicsFilter.js index e178c3402..577fb8ebf 100644 --- a/web-app/js/datasetExplorer/omicsFilter.js +++ b/web-app/js/datasetExplorer/omicsFilter.js @@ -39,20 +39,29 @@ function highDimensionalConceptDropped(node, filter) { function omicsFilterInfoReceived(result, request) { omics_filter_info = JSON.parse(result.responseText); omics_filter_info.filter = (omics_filter_info.filter == "true"); - Ext.Ajax.request({ - url: pageInfo.basePath + "/highDimensionFilter/filterDialog", - method: 'GET', - timeout: '60000', - params: Ext.urlEncode({ - gpl_id: omics_filter_info.platform.id, - filter: omics_filter_info.filter, - concept_key: omics_filter_info.concept_key - }), - success: omicsFilterWindowReceived, - failure: function (result, request) { - alert("Could not retrieve filter info for " + node.id + ": " + result.statusText); + if (omics_filter_info.filter_type != 'VCF') { + Ext.Ajax.request({ + url: pageInfo.basePath + "/highDimensionFilter/filterDialog", + method: 'GET', + timeout: '60000', + params: Ext.urlEncode({ + gpl_id: omics_filter_info.platform.id, + filter: omics_filter_info.filter, + concept_key: omics_filter_info.concept_key + }), + success: omicsFilterWindowReceived, + failure: function (result, request) { + alert("Could not retrieve filter info for " + node.id + ": " + result.statusText); + } + }); + } + else { + if (omicsFilterRepopulateWindow != null) { + // We did a right click -> set filter on a vcf concept, let's inform the user it's not ready yet + Ext.Msg.alert('VCF','Filtering on VCF data is not supported yet, stay tuned!'); } - }); + applyOmicsNoFilterDialog(); + } } function omicsFilterWindowReceived(result, request) { @@ -506,11 +515,15 @@ function omicsValuesFailed(result) { } function applyOmicsNoFilterDialog() { - // no gene supplied, we assume a "no value" type filter + // Just add the high dimensional concept as a criterion, no constraints on the data itself + if (omics_filter_info.filter) { omicsFilterValues = []; omicsSliderLowHandleRatio = 0; omicsSliderHighHandleRatio = 1; - document.getElementById("highdimension-filter-main").removeChild(document.getElementById("highdimension-filter-content")); + var mainpanel = document.getElementById("highdimension-filter-main"); + if (mainpanel != null && mainpanel.children.length > 0) { + mainpanel.removeChild(document.getElementById("highdimension-filter-content")); + } omicsfilterwin.hide(); var concept = jQuery('#' + selectedConcept.id); jQuery('#' + selectedConcept.id + " .concept-text").html(selectedConcept.attributes["conceptname"].nodeValue); @@ -520,8 +533,35 @@ function applyOmicsNoFilterDialog() { concept.removeAttr("omicsvalue"); concept.removeAttr("omicsprojection"); concept.removeAttr("omicsvaluetype"); - concept.attr("setvaluemode",""); + concept.attr("setvaluemode", ""); moveSelectedConceptFromHoldingToTarget(); + omicsFilterRepopulateWindow = null; + } + else { + resultsTabPanel.body.mask("Running analysis...", 'x-mask-loading'); + + Ext.Ajax.request({ + url: pageInfo.basePath + "/chart/analysis", + method: 'POST', + timeout: '600000', + params: Ext.urlEncode({ + charttype: "analysis", + concept_key: omics_filter_info.concept_key, + result_instance_id1: GLOBAL.CurrentSubsetIDs[1], + result_instance_id2: GLOBAL.CurrentSubsetIDs[2] + }), // or a URL encoded string + success: function (result, request) { + buildAnalysisComplete(result); + resultsTabPanel.body.unmask(); + }, + failure: function (result, request) { + alert("A problem arose while trying to retrieve the results"); + resultsTabPanel.body.unmask(); + } + }); + getAnalysisGridData(omics_filter_info.concept_key); + omicsfilterwin.hide(); + } } function applySingleNumericOmicsFilter(validation) { From c69d19ea67033aca564581101c2b4e97f6bc7e82 Mon Sep 17 00:00:00 2001 From: dennyverbeeck Date: Wed, 1 Mar 2017 17:33:44 +0100 Subject: [PATCH 029/136] Fix an issue in Workspace (saved queries) Fix issue when hovering over a saved query where only subset 2 was used, the query summary tooltip window would not appear. --- grails-app/controllers/SubsetController.groovy | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/grails-app/controllers/SubsetController.groovy b/grails-app/controllers/SubsetController.groovy index 5e0badaed..3becc2d3f 100644 --- a/grails-app/controllers/SubsetController.groovy +++ b/grails-app/controllers/SubsetController.groovy @@ -100,9 +100,11 @@ class SubsetController { Subset subset = Subset.get(subsetId) - def queryID1 = queriesResourceService.getQueryDefinitionForResult( - queriesResourceService.getQueryResultFromId(subset.queryID1)) - displayQuery1 = generateDisplayOutput(queryID1) + if (subset.queryID1 != -1) { + def queryID1 = queriesResourceService.getQueryDefinitionForResult( + queriesResourceService.getQueryResultFromId(subset.queryID1)) + displayQuery1 = generateDisplayOutput(queryID1) + } if (subset.queryID2 != -1) { def queryID2 = queriesResourceService.getQueryDefinitionForResult( From 8659ebecd471edd7276399ec0c8ab66f115cae5c Mon Sep 17 00:00:00 2001 From: Peter Rice Date: Thu, 9 Mar 2017 13:47:16 +0000 Subject: [PATCH 030/136] restore gene list functionality --- .../GeneSignatureController.groovy | 42 +-- .../services/GeneSignatureService.groovy | 8 +- .../org/transmart/SearchKeywordService.groovy | 15 +- .../geneSignature/_list_summary_record.gsp | 46 +++ ...ure_gene1.txt => gene_signature_gene1.txt} | 0 ...ure_gene2.txt => gene_signature_gene2.txt} | 0 ...ure_gene3.txt => gene_signature_gene3.txt} | 0 ...eset1.txt => gene_signature_probeset1.txt} | 0 ...eset2.txt => gene_signature_probeset2.txt} | 0 ...eset3.txt => gene_signature_probeset3.txt} | 0 grails-app/views/geneSignature/list.gsp | 12 +- .../views/geneSignature/wizard_list.gsp | 294 ++++++++++++++++++ 12 files changed, 383 insertions(+), 34 deletions(-) create mode 100644 grails-app/views/geneSignature/_list_summary_record.gsp rename grails-app/views/geneSignature/{gene_signiture_gene1.txt => gene_signature_gene1.txt} (100%) rename grails-app/views/geneSignature/{gene_signiture_gene2.txt => gene_signature_gene2.txt} (100%) rename grails-app/views/geneSignature/{gene_signiture_gene3.txt => gene_signature_gene3.txt} (100%) rename grails-app/views/geneSignature/{gene_signiture_probeset1.txt => gene_signature_probeset1.txt} (100%) rename grails-app/views/geneSignature/{gene_signiture_probeset2.txt => gene_signature_probeset2.txt} (100%) rename grails-app/views/geneSignature/{gene_signiture_probeset3.txt => gene_signature_probeset3.txt} (100%) create mode 100644 grails-app/views/geneSignature/wizard_list.gsp diff --git a/grails-app/controllers/GeneSignatureController.groovy b/grails-app/controllers/GeneSignatureController.groovy index bbc1421ac..ab7857ca4 100644 --- a/grails-app/controllers/GeneSignatureController.groovy +++ b/grails-app/controllers/GeneSignatureController.groovy @@ -80,7 +80,7 @@ class GeneSignatureController { session.setAttribute(WIZ_DETAILS_ATTRIBUTE, null) // logged in user - def user = springSecurityService.getPrincipal() + def user = AuthUser.findByUsername(springSecurityService.getPrincipal().username) def bAdmin = user.isAdmin() log.info "Admin? " + bAdmin @@ -122,9 +122,9 @@ class GeneSignatureController { */ def createWizard = { // initialize session model data - def user = springSecurityService.getPrincipal() + def user = AuthUser.findByUsername(springSecurityService.getPrincipal().username) - // initialzize new gs inst + // initialize new gene signature instance def geneSigInst = new GeneSignature(); geneSigInst.properties.createdByAuthUser = user; geneSigInst.properties.publicFlag = false; @@ -144,7 +144,7 @@ class GeneSignatureController { // initialize session model data def user = AuthUser.findByUsername(springSecurityService.getPrincipal().username) - // initialize new gs inst + // initialize new gene signature instance def geneSigInst = new GeneSignature(); geneSigInst.properties.createdByAuthUser = user; geneSigInst.properties.publicFlag = false; @@ -163,14 +163,15 @@ class GeneSignatureController { */ def editWizard = { // initialize session model data - def user = springSecurityService.getPrincipal() + def user = AuthUser.findByUsername(springSecurityService.getPrincipal().username) // load gs instance def geneSigInst = GeneSignature.get(params.id) def clone = geneSigInst.clone() - clone.modifiedByAuthUser = AuthUser.findByUsername(user.username) + clone.modifiedByAuthUser = user if (clone.experimentTypeCellLine?.id == null) clone.experimentTypeCellLine = null // this is hack, don't know how to get around this! + log.debug "experimentTypeCellLine: " + clone.experimentTypeCellLine + "; null? " + (clone.experimentTypeCellLine == null) // set onto session def newWizard = new WizardModelDetails(loggedInUser: user, geneSigInst: clone, wizardType: WizardModelDetails.WIZ_TYPE_EDIT, editId: geneSigInst.id); @@ -184,12 +185,12 @@ class GeneSignatureController { */ def cloneWizard = { // initialize session model data - def user = springSecurityService.getPrincipal() + def user = AuthUser.findByUsername(springSecurityService.getPrincipal().username) // load gs inst to clone def geneSigInst = GeneSignature.get(params.id) def clone = geneSigInst.clone() - clone.createdByAuthUser = AuthUser.findByUsername(user.username) + clone.createdByAuthUser = user clone.modifiedByAuthUser = null; clone.name = clone.name + " (clone)" clone.description = clone.description + " (clone)" @@ -214,9 +215,9 @@ class GeneSignatureController { * set the indicated gs public for access by everyone */ def makePublic = { - def user = springSecurityService.getPrincipal() + def user = AuthUser.findByUsername(springSecurityService.getPrincipal().username) def gsInst = GeneSignature.get(params.id) - gsInst.modifiedByAuthUser = AuthUser.findByUsername(user.username) + gsInst.modifiedByAuthUser = user geneSignatureService.makePublic(gsInst, true) flash.message = "GeneSignature '${gsInst.name}' was made public to everyone" @@ -227,9 +228,9 @@ class GeneSignatureController { * set the indicated gs private */ def makePrivate = { - def user = springSecurityService.getPrincipal() + def user = AuthUser.findByUsername(springSecurityService.getPrincipal().username) def gsInst = GeneSignature.get(params.id) - gsInst.modifiedByAuthUser = AuthUser.findByUsername(user.username) + gsInst.modifiedByAuthUser = user geneSignatureService.makePublic(gsInst, false) flash.message = "GeneSignature '${gsInst.name}' was made private" @@ -240,9 +241,9 @@ class GeneSignatureController { * mark the indicated gs as deleted by setting deletedFlag as true */ def delete = { - def user = springSecurityService.getPrincipal() + def user = AuthUser.findByUsername(springSecurityService.getPrincipal().username) def gsInst = GeneSignature.get(params.id) - gsInst.modifiedByAuthUser = AuthUser.findByUsername(user.username) + gsInst.modifiedByAuthUser = user geneSignatureService.delete(gsInst) flash.message = "GeneSignature '${gsInst.name}' was marked as deleted" @@ -463,6 +464,7 @@ class GeneSignatureController { def wizard = session.getAttribute(WIZ_DETAILS_ATTRIBUTE) def gs = wizard.geneSigInst gs.properties.list = true + if (!params.boolean('isEdit')) { assert null == gs.properties.id } @@ -479,8 +481,9 @@ class GeneSignatureController { gs.speciesConceptCode = ConceptCode.findByCodeTypeNameAndBioConceptCode("OTHER", "OTHER") // technology platforms - gs.techPlatform = BioAssayPlatform.findByName("Multiple or Unknown") - + gs.techPlatform = BioAssayPlatform.findByName("Other") + if(!gs.techPlatform) {gs.techPlatform = BioAssayPlatform.findByName("None")} + // p value cutoffs gs.pValueCutoffConceptCode = ConceptCode.findByCodeTypeNameAndBioConceptCode(P_VAL_CUTOFF_CATEGORY, "UNDEFINED") @@ -532,7 +535,6 @@ class GeneSignatureController { List markers = [] if(key.startsWith("biomarker_") && val != null && val != "") { markers.add(val.trim()) - } def gsItems = geneSignatureService.loadGeneSigItemsFromList(markers) def geneSigUniqueIds = gs.geneSigItems*.bioDataUniqueId @@ -577,7 +579,7 @@ class GeneSignatureController { * update gene signature and the associated items (new file only) */ def update = { - def user = springSecurityService.getPrincipal() + def user = AuthUser.findByUsername(springSecurityService.getPrincipal().username) // retrieve clone def wizard = session.getAttribute(WIZ_DETAILS_ATTRIBUTE) @@ -590,7 +592,7 @@ class GeneSignatureController { def gsReal = GeneSignature.get(wizard.editId) def origFile = gsReal.uploadFile clone.copyPropertiesTo(gsReal) - gsReal.modifiedByAuthUser = AuthUser.findByUsername(user.username) + gsReal.modifiedByAuthUser = user gsReal.uploadFile = origFile // refresh items if new file uploaded @@ -988,7 +990,7 @@ class GeneSignatureController { case 2: // sources wizard.sources = ConceptCode.findAllByCodeTypeName(SOURCE_CATEGORY, [sort: "bioConceptCode"]) - wizard.sources.add(genericOtherConceptCode) + wizard.sources.add(genericOtherConceptCode) // Pfizer code depends on this having ID=1 //WizardModelDetails.addOtherItem(wizard.sources, "other") // owners diff --git a/grails-app/services/GeneSignatureService.groovy b/grails-app/services/GeneSignatureService.groovy index ccd756f75..c78913d9a 100644 --- a/grails-app/services/GeneSignatureService.groovy +++ b/grails-app/services/GeneSignatureService.groovy @@ -561,7 +561,7 @@ public class GeneSignatureService { } /** - * create new GeneSignature and all dependendant objects from wizard + * create new GeneSignature and all dependant objects from wizard */ def saveWizard(GeneSignature gs, MultipartFile file) { @@ -591,7 +591,9 @@ public class GeneSignatureService { def nsave = savedInst; if (savedInst.uniqueId == null || savedInst.uniqueId == "") { // need to refresh this object - savedInst.updateUniqueId(); + if(gs.properties.uploadFile == 'Manual Item Entry') {savedInst.updateUniqueIdList()} + else{savedInst.updateUniqueId()} + //nsave = savedInst.save(flush:true) } @@ -599,8 +601,8 @@ public class GeneSignatureService { //if(nsave) updateGenSigItems(nsave) // link objects to search - searchKeywordService.updateGeneSignatureLink(nsave, GeneSignature.DOMAIN_KEY_GL, true) searchKeywordService.updateGeneSignatureLink(nsave, GeneSignature.DOMAIN_KEY, true) + searchKeywordService.updateGeneSignatureLink(nsave, GeneSignature.DOMAIN_KEY_GL, true) return nsave; } diff --git a/grails-app/services/org/transmart/SearchKeywordService.groovy b/grails-app/services/org/transmart/SearchKeywordService.groovy index 5d3070db3..fa6dd4dd2 100644 --- a/grails-app/services/org/transmart/SearchKeywordService.groovy +++ b/grails-app/services/org/transmart/SearchKeywordService.groovy @@ -440,33 +440,36 @@ public class SearchKeywordService { def updateGeneSignatureLink(GeneSignature gs, String domainKey, boolean bFlush) { // find keyword record SearchKeyword keyword = SearchKeyword.findByBioDataIdAndDataCategory(gs.id, domainKey) - println("INFO: retrieved " + keyword) + log.info("updateGeneSignatureLink: domainKey ${domainKey} concept ${gs.foldChgMetricConceptCode.bioConceptCode} retrieved ${keyword}") // delete search keywords if (gs.deletedFlag || (domainKey == GeneSignature.DOMAIN_KEY_GL && gs.foldChgMetricConceptCode.bioConceptCode != 'NOT_USED') || (domainKey == GeneSignature.DOMAIN_KEY && gs.foldChgMetricConceptCode.bioConceptCode == 'NOT_USED')) { + log.info("updateGeneSignatureLink delete keyword") if (keyword != null) keyword.delete(flush: bFlush) } else { // add if does not exist if (keyword == null) { + log.info("updateGeneSignatureLink create keyword") keyword = createSearchKeywordFromGeneSig(gs, domainKey) } else { // update keyword + log.info("updateGeneSignatureLink update keyword ${gs.name} ") keyword.keyword = gs.name keyword.ownerAuthUserId = gs.publicFlag ? null : gs.createdByAuthUser.id keyword.terms.each { - println("INFO: " + it) + log.info("INFO: " + it) it.keywordTerm = gs.name.toUpperCase() it.ownerAuthUserId = gs.publicFlag ? null : gs.createdByAuthUser.id - //println("INFO: setting owner to: "+it.ownerAuthUserId) + //log.info("INFO: setting owner to: "+it.ownerAuthUserId) } } keyword.validate() if (keyword.hasErrors()) { - println("WARN: SearchKeyword validation error!") - keyword.errors.each { println it } + log.info("WARN: SearchKeyword validation error!") + keyword.errors.each {log.info("keyword error: ${it}")} } - println("INFO: trying to save SearchKeyword") + log.info("INFO: trying to save SearchKeyword") keyword.save(flush: bFlush) } } diff --git a/grails-app/views/geneSignature/_list_summary_record.gsp b/grails-app/views/geneSignature/_list_summary_record.gsp new file mode 100644 index 000000000..6d7956bb5 --- /dev/null +++ b/grails-app/views/geneSignature/_list_summary_record.gsp @@ -0,0 +1,46 @@ + + + + + + + + + detail ${gs.name?.replaceAll("'","\\\\'").encodeAsHTML()} + ${gs.createdByAuthUser.userRealName?.encodeAsHTML()} + + ${gs.publicFlag ? 'Yes' : 'No'} + + ${ctLkup?.getAt(1)} + + + 0 + + + + diff --git a/grails-app/views/geneSignature/gene_signiture_gene1.txt b/grails-app/views/geneSignature/gene_signature_gene1.txt similarity index 100% rename from grails-app/views/geneSignature/gene_signiture_gene1.txt rename to grails-app/views/geneSignature/gene_signature_gene1.txt diff --git a/grails-app/views/geneSignature/gene_signiture_gene2.txt b/grails-app/views/geneSignature/gene_signature_gene2.txt similarity index 100% rename from grails-app/views/geneSignature/gene_signiture_gene2.txt rename to grails-app/views/geneSignature/gene_signature_gene2.txt diff --git a/grails-app/views/geneSignature/gene_signiture_gene3.txt b/grails-app/views/geneSignature/gene_signature_gene3.txt similarity index 100% rename from grails-app/views/geneSignature/gene_signiture_gene3.txt rename to grails-app/views/geneSignature/gene_signature_gene3.txt diff --git a/grails-app/views/geneSignature/gene_signiture_probeset1.txt b/grails-app/views/geneSignature/gene_signature_probeset1.txt similarity index 100% rename from grails-app/views/geneSignature/gene_signiture_probeset1.txt rename to grails-app/views/geneSignature/gene_signature_probeset1.txt diff --git a/grails-app/views/geneSignature/gene_signiture_probeset2.txt b/grails-app/views/geneSignature/gene_signature_probeset2.txt similarity index 100% rename from grails-app/views/geneSignature/gene_signiture_probeset2.txt rename to grails-app/views/geneSignature/gene_signature_probeset2.txt diff --git a/grails-app/views/geneSignature/gene_signiture_probeset3.txt b/grails-app/views/geneSignature/gene_signature_probeset3.txt similarity index 100% rename from grails-app/views/geneSignature/gene_signiture_probeset3.txt rename to grails-app/views/geneSignature/gene_signature_probeset3.txt diff --git a/grails-app/views/geneSignature/list.gsp b/grails-app/views/geneSignature/list.gsp index 5b341b67b..52d3b336b 100644 --- a/grails-app/views/geneSignature/list.gsp +++ b/grails-app/views/geneSignature/list.gsp @@ -88,7 +88,7 @@
    ${flash.message}

    -

    Gene Signature List    +

    Gene Signature Lists    Help

    @@ -147,12 +147,12 @@
    - @@ -162,6 +162,7 @@ + @@ -180,6 +181,7 @@ + diff --git a/grails-app/views/geneSignature/wizard_list.gsp b/grails-app/views/geneSignature/wizard_list.gsp new file mode 100644 index 000000000..d416f36b2 --- /dev/null +++ b/grails-app/views/geneSignature/wizard_list.gsp @@ -0,0 +1,294 @@ + + + + + + + + Gene List Edit + + + Gene List Create + + + $j = jQuery.noConflict(); + + + + jQuery(document).ready(function() { + var pasteContent; + + jQuery('#biomarkerList').on('change', '.biomarkerEntry', function(event) { + var name = jQuery(this).attr('name'); + var index = parseInt(name.substring(10)); + checkGene(index); + }); + + jQuery('#biomarkerList').on('keypress', '.biomarkerEntry', function(event) { + if (event.which == 13) { + event.preventDefault(); + + var name = jQuery(this).attr('name'); + var startingIndex = parseInt(name.substring(10)); + createNewInputIfRequired(startingIndex); + $j('#biomarker_' + (startingIndex+1)).focus(); + } + }); + + jQuery('#biomarkerList').on('paste', '.biomarkerEntry', function(event) { + pasteContent = null; + var startingInput = jQuery(this); + startingInput.val(''); + if (window.clipboardData) { + pasteContent = window.clipboardData.getData('Text'); + } + //Paste is ABOUT TO happen, so set timeout + setTimeout(function() { + if (pasteContent == null) { + pasteContent = startingInput.val(); + } + var pasteList = pasteContent.split(","); + if (pasteList.length < 2) { + pasteList = pasteContent.split("\n"); + } + var name = startingInput.attr('name'); + var startingIndex = parseInt(name.substring(10)); + for (var i = 0; i < pasteList.length; i++) { + var currentIndex = startingIndex + i; + $j('#biomarker_' + currentIndex).val(pasteList[i].trim()); + checkGene(currentIndex); + } + jQuery('#pasteSource').val(''); + }, 1); + }); + + jQuery('#biomarkerList').on('click', '.biomarkerDelete', function(event) { + var name = jQuery(this).attr('name'); + var index = parseInt(name.substring(10)); + jQuery('#biomarker_' + index).val(''); + jQuery('#geneCheckIcon' + index).removeClass('loading').removeClass('success').removeClass('failure').text(''); + }); + + <%-- Add checks for all fields if this is an edit --%> + + + + checkGene(${n}); + + + + }); + + function checkBiomarkerValues() { + var foundEntry = false; + var biomarkerFields = jQuery(".biomarkerEntry"); + + for (var n = 0; n < biomarkerFields.size(); n++) { + var textContent = jQuery(biomarkerFields[n]).val(); + if (textContent != null && textContent.trim() != "") { + foundEntry = true; + break; + } + } + return foundEntry; + } + + function validate() { + + var errorMsg = ""; + // list name required + if(document.geneSignatureFrm.name.value=="") { + errorMsg = "You must specify a list name"; + } + + if(document.geneSignatureFrm.uploadFile.value=="" && !checkBiomarkerValues()) + errorMsg = errorMsg + "\n- Please select a file, or manually enter a gene list"; + + if(document.geneSignatureFrm.uploadFile.value!="" && checkBiomarkerValues()) + errorMsg = errorMsg + "\n- You have both specified a file and manually entered a list"; + // if no errors, continue submission + if(errorMsg=="") return true; + + alert("Please correct the following errors:\n" + errorMsg); + return false; + } + + function createNewInputIfRequired(index) { + var removeImage = "${resource(dir:'images',file:'remove.png')}" + var newIndex = index+1; + var checkInputField = jQuery('#biomarker_' + newIndex); + if (checkInputField.length == 0) { + var newtr = jQuery('').attr('id', 'new_item_' + newIndex); + var newtdTextArea = jQuery('
    Name Author Date CreatedPublic # Genes  
    Name Author Date CreatedPublic # Genes  
    ').append(jQuery('