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if (event.type == 'keyup') jQuery.ppa.o = 0;
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function autocomplete(event) { /* if pressing enter, fire a click on the selected line */ if (event.keyCode == 13) { if (jQuery.ppa.i > 0) { jQuery.ppa.fklist.find('tr').eq(jQuery.ppa.i).click(); } hideAc(); return false; } /* ignoring 38:up and 40:down */ else if ( event.keyCode == 38 || event.keyCode == 40 ) { return false; } /* ignoring 9:tab, 37:left, 39:right, 16:shift, ctrl: 17, alt:18, 20:lockmaj */ else if ( event.keyCode == 9 || event.keyCode == 37 || event.keyCode == 39 || event.keyCode == 16 || event.keyCode == 17 || event.keyCode == 18 || event.keyCode == 20) { return true; } /* esc */ else if (event.keyCode == 27) { hideAc(); } /* request the list of possible values asynchronously */ else { openlist(this); } return true;}
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function autocompleteCallback() { var name = this.attr('name'); var select = this.parent().parent().find('select[name ^= field]'); if (select) { return select.val(); } else return 'noparam';
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function autocompleteCallback(node, params) { var name = node.attr('name'); var select = node.parent().parent().find('select[name ^= field]'); if (select.length == 1) { params.field = select.val(); }
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function autocompleteCallback() { var name = this.attr('name'); var select = this.parent().parent().find('select[name ^= field]'); if (select) { return select.val(); } else return 'noparam';}
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this.relayEvents(k, ['done']);
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this.relayEvents(k, ['done', 'fail']);
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autoTag : function(id) { var callParams = []; callParams.push(id); callParams.push({ callback : function(data) { var k = new Gemma.WaitHandler(); this.relayEvents(k, ['done']); k.handleWait(data, false); k.on('done', function(payload) { this.fireEvent('tagsUpdated', payload); }); }.createDelegate(this) }); AnnotationController.autoTag.apply(this, callParams); },
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alert("Hi, this isn't set up yet!");
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AnnotationController.autoTag.apply(this, callParams);
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autoTag : function(id) { /* * TODO: call AnnotationController.annotate(id). Need a progress bar of some sort. */ alert("Hi, this isn't set up yet!"); },
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if (settings.fixed_height == 0) { var $ht = $(this).height(); $(this).parent().animate({height: $ht}); }
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before:function(current, next) { var currId = (currId=$(current).attr('id')).substring(currId.lastIndexOf('_')+1) var nextId = (nextId=$(next).attr('id')).substring(nextId.lastIndexOf('_')+1) $('#views_slideshow_thumbnailhover_div_breakout_teaser_' + settings.id + '_' + currId).removeClass('activeSlide'); $('#views_slideshow_thumbnailhover_div_breakout_teaser_' + settings.id + '_' + nextId).addClass('activeSlide'); },
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firstInitDone = true;
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this.firstInitDone = true;
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Gemma.BioMaterialEditor = function(config) { return { firstInitDone : false, originalConfig : config, expressionExperiment : { id : config.eeId, classDelegatingFor : "ExpressionExperiment" }, /** * We make two ajax calls; the first gets the biomaterials, the second gets the experimentalfactors. These are * run in succession so both values can be given to the BioMaterialGrid constructor. */ firstCallback : function(data) { // second ajax call. ExperimentalDesignController.getExperimentalFactors(this.expressionExperiment, function(factorData) { config = { factors : factorData, bioMaterials : data }; Ext.apply(config, this.originalConfig); this.grid = new Gemma.BioMaterialGrid(config); this.grid.init = this.init.createDelegate(this); }.createDelegate(this)); }, /** * Gets called on startup but also when a refresh is needed. */ init : function() { if (this.grid) { try { this.grid.destroy(); } catch (e) { } } firstInitDone = true; ExperimentalDesignController.getBioMaterials(this.expressionExperiment, this.firstCallback .createDelegate(this)); } };};
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return {
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this.originalConfig = config; this.expressionExperiment = { id : config.eeId, classDelegatingFor : "ExpressionExperiment" };
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Gemma.BioMaterialEditor = function(config) { return { firstInitDone : false, originalConfig : config, expressionExperiment : { id : config.eeId, classDelegatingFor : "ExpressionExperiment" }, /** * We make two ajax calls; the first gets the biomaterials, the second gets the experimentalfactors. These are * run in succession so both values can be given to the BioMaterialGrid constructor. */ firstCallback : function(data) { // second ajax call. ExperimentalDesignController.getExperimentalFactors(this.expressionExperiment, function(factorData) { config = { factors : factorData, bioMaterials : data }; Ext.apply(config, this.originalConfig); this.grid = new Gemma.BioMaterialGrid(config); this.grid.init = this.init.createDelegate(this); this.loadMask.hide(); }.createDelegate(this)); }, /** * Gets called on startup but also when a refresh is needed. */ init : function() { this.loadMask = new Ext.LoadMask(Ext.getBody(), { msg : "Please wait..." }); this.loadMask.show(); if (this.grid) { try { this.grid.destroy(); } catch (e) { } } this.firstInitDone = true; ExperimentalDesignController.getBioMaterials(this.expressionExperiment, this.firstCallback .createDelegate(this)); } };};
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firstInitDone : false, originalConfig : config, expressionExperiment : { id : config.eeId, classDelegatingFor : "ExpressionExperiment" }, firstCallback : function(data) { ExperimentalDesignController.getExperimentalFactors(this.expressionExperiment, function(factorData) { config = { factors : factorData, bioMaterials : data }; Ext.apply(config, this.originalConfig); this.grid = new Gemma.BioMaterialGrid(config); this.grid.init = this.init.createDelegate(this); this.loadMask.hide(); }.createDelegate(this)); }, init : function() { this.loadMask = new Ext.LoadMask(Ext.getBody(), { msg : "Please wait..." }); this.loadMask.show(); if (this.grid) { try { this.grid.destroy(); } catch (e) { } } this.firstInitDone = true; ExperimentalDesignController.getBioMaterials(this.expressionExperiment, this.firstCallback .createDelegate(this)); } }; };
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Gemma.BioMaterialEditor.superclass.constructor.call(this, config); }
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Gemma.BioMaterialEditor = function(config) { return { firstInitDone : false, originalConfig : config, expressionExperiment : { id : config.eeId, classDelegatingFor : "ExpressionExperiment" }, /** * We make two ajax calls; the first gets the biomaterials, the second gets the experimentalfactors. These are * run in succession so both values can be given to the BioMaterialGrid constructor. */ firstCallback : function(data) { // second ajax call. ExperimentalDesignController.getExperimentalFactors(this.expressionExperiment, function(factorData) { config = { factors : factorData, bioMaterials : data }; Ext.apply(config, this.originalConfig); this.grid = new Gemma.BioMaterialGrid(config); this.grid.init = this.init.createDelegate(this); this.loadMask.hide(); }.createDelegate(this)); }, /** * Gets called on startup but also when a refresh is needed. */ init : function() { this.loadMask = new Ext.LoadMask(Ext.getBody(), { msg : "Please wait..." }); this.loadMask.show(); if (this.grid) { try { this.grid.destroy(); } catch (e) { } } this.firstInitDone = true; ExperimentalDesignController.getBioMaterials(this.expressionExperiment, this.firstCallback .createDelegate(this)); } };};
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var link = "http: + "&hgt.customText=" + Gemma.GEMMA_BASE_URL + "blatTrack.html?id=" + d.id;
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var link = UCSC_TRACKS + "?org=" + organism + "&pix=850&db=" + database + "&hgt.customText=" + Gemma.BASEURL + "blatTrack.html?id=" + d.id;
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blatResRender : function(d, metadata, record, row, column, store) { if (!d.targetChromosome) { return ""; } var res = "chr" + d.targetChromosome.name + " (" + d.strand + ") " + d.targetStart + "-" + d.targetEnd; var organism = d.targetChromosome.taxon; var database = this.getDb(organism); if (database) { var link = "http://genome.ucsc.edu/cgi-bin/hgTracks?org=" + organism + "&pix=850&db=" + database + "&hgt.customText=" + Gemma.GEMMA_BASE_URL + "blatTrack.html?id=" + d.id; res = res + " <a title='Genome browser view (opens in new window)' target='_blank' href='" + link + "'><img src='" + Gemma.UCSC_ICON + "' /></a>"; } return res; },
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if (!d.targetChromosome) {
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if (!d.targetChromosomeName) {
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blatResRender : function(d, metadata, record, row, column, store) { if (!d.targetChromosome) { return ""; } var res = "chr" + d.targetChromosome.name + " (" + d.strand + ") " + d.targetStart + "-" + d.targetEnd; var organism = d.targetChromosome.taxon; var database = this.getDb(organism); if (database) { var link = UCSC_TRACKS + "?org=" + organism + "&pix=850&db=" + database + "&hgt.customText=" + Gemma.BASEURL + "blatTrack.html?id=" + d.id; res = res + " <a title='Genome browser view (opens in new window)' target='_blank' href='" + link + "'><img src='" + Gemma.UCSC_ICON + "' /></a>"; } return res; },
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var res = "chr" + d.targetChromosome.name + " (" + d.strand + ") " + d.targetStart + "-" + d.targetEnd;
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var res = "chr" + d.targetChromosomeName + " (" + d.strand + ") " + d.targetStart + "-" + d.targetEnd;
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blatResRender : function(d, metadata, record, row, column, store) { if (!d.targetChromosome) { return ""; } var res = "chr" + d.targetChromosome.name + " (" + d.strand + ") " + d.targetStart + "-" + d.targetEnd; var organism = d.targetChromosome.taxon; var database = this.getDb(organism); if (database) { var link = UCSC_TRACKS + "?org=" + organism + "&pix=850&db=" + database + "&hgt.customText=" + Gemma.BASEURL + "blatTrack.html?id=" + d.id; res = res + " <a title='Genome browser view (opens in new window)' target='_blank' href='" + link + "'><img src='" + Gemma.UCSC_ICON + "' /></a>"; } return res; },
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var organism = d.targetChromosome.taxon;
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var organism = d.taxon;
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blatResRender : function(d, metadata, record, row, column, store) { if (!d.targetChromosome) { return ""; } var res = "chr" + d.targetChromosome.name + " (" + d.strand + ") " + d.targetStart + "-" + d.targetEnd; var organism = d.targetChromosome.taxon; var database = this.getDb(organism); if (database) { var link = UCSC_TRACKS + "?org=" + organism + "&pix=850&db=" + database + "&hgt.customText=" + Gemma.BASEURL + "blatTrack.html?id=" + d.id; res = res + " <a title='Genome browser view (opens in new window)' target='_blank' href='" + link + "'><img src='" + Gemma.UCSC_ICON + "' /></a>"; } return res; },
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var link = UCSC_TRACKS + "?org=" + organism + "&pix=850&db=" + database + "&hgt.customText=" + Gemma.BASEURL + "blatTrack.html?id=" + d.id;
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var link = UCSC_TRACKS + "?org=" + organism.commonName + "&pix=850&db=" + database + "&hgt.customText=" + Gemma.BASEURL + "/blatTrack.html?id=" + d.id;
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blatResRender : function(d, metadata, record, row, column, store) { if (!d.targetChromosome) { return ""; } var res = "chr" + d.targetChromosome.name + " (" + d.strand + ") " + d.targetStart + "-" + d.targetEnd; var organism = d.targetChromosome.taxon; var database = this.getDb(organism); if (database) { var link = UCSC_TRACKS + "?org=" + organism + "&pix=850&db=" + database + "&hgt.customText=" + Gemma.BASEURL + "blatTrack.html?id=" + d.id; res = res + " <a title='Genome browser view (opens in new window)' target='_blank' href='" + link + "'><img src='" + Gemma.UCSC_ICON + "' /></a>"; } return res; },
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var link = "http: + "&hgt.customText=" + Gemma.GEMMA_BASE_URL + "blatTrack.html?id=" + d.id; res = res + " <a title='Genome browser view (opens in new window)' target='_blank' href='" + link + "'><img src='" + Gemma.UCSC_ICON + "' /></a>";
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var link = "http: "&hgt.customText=" + Gemma.GEMMA_BASE_URL + "blatTrack.html?id=" + d.id; res = res + " <a title='Genome browser view (opens in new window)' target='_blank' href='" + link + "'><img src='" + Gemma.UCSC_ICON + "' /></a>";
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blatResRender : function(d, metadata, record, row, column, store) { if (!d.targetChromosome) { return ""; } var res = "chr" + d.targetChromosome.name + " (" + d.strand + ") " + d.targetStart + "-" + d.targetEnd; var organism = d.targetChromosome.taxon; var database = this.getDb(organism); if (database) { var link = "http://genome.ucsc.edu/cgi-bin/hgTracks?org=" + organism + "&pix=850&db=" + database + "&hgt.customText=" + Gemma.GEMMA_BASE_URL + "blatTrack.html?id=" + d.id; res = res + " <a title='Genome browser view (opens in new window)' target='_blank' href='" + link + "'><img src='" + Gemma.UCSC_ICON + "' /></a>"; } return res; },
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if (onSuccessFn) onSuccessFn(r.getResult().Item);
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if (onSuccessFn) onSuccessFn(r.Item);
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blockingDequeueItemFromList: function(id, timeOut, onSuccessFn, onErrorFn) { this.gateway.getFromService('BlockingDequeueItemFromList', { Id: id || null, TimeOut: timeOut || null }, function(r) { if (onSuccessFn) onSuccessFn(r.getResult().Item); }, onErrorFn || RedisClient.errorFn); },
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if (onSuccessFn) onSuccessFn(r.getResult().Item);
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if (onSuccessFn) onSuccessFn(r.Item);
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blockingPopItemFromList: function(id, timeOut, onSuccessFn, onErrorFn) { this.gateway.getFromService('BlockingPopItemFromList', { Id: id || null, TimeOut: timeOut || null }, function(r) { if (onSuccessFn) onSuccessFn(r.getResult().Item); }, onErrorFn || RedisClient.errorFn); },
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if (onSuccessFn) onSuccessFn(r.getResult().Item);
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if (onSuccessFn) onSuccessFn(r.Item);
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blockingRemoveStartFromList: function(id, timeOut, onSuccessFn, onErrorFn) { this.gateway.getFromService('BlockingRemoveStartFromList', { Id: id || null, TimeOut: timeOut || null }, function(r) { if (onSuccessFn) onSuccessFn(r.getResult().Item); }, onErrorFn || RedisClient.errorFn); },
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this.button.blur();
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if (this.button) { this.button.blur(); }
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blur: function() { this.button.blur(); }
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}
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},
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blur: function() { this.button.blur(); }
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if (book.asin && book.asin.length == 10) return text + ' <a target="_blank" title="explore this book @ amazon" href="'+amz_url.replace("asin", book.asin)+'">'+'»'+'</a>';
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if (book.asin && book.asin.length == 10) return text + ' <a target="_blank" title="explore this book @ amazon" href="'+amz_url.replace("asin", book.asin)+'">'+'»»'+'</a>';
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function book_link(book){ text = book.title; if(book.author != "unknown") text = text + " by " + book.author; if (book.asin && book.asin.length == 10) return text + ' <a target="_blank" title="explore this book @ amazon" href="'+amz_url.replace("asin", book.asin)+'">'+'»'+'</a>'; return text; }
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if (not_to_be_shown(this)) return; $("#borrowed_table").append("<tr id=" + this.key + "><td>" + this.owner + "</td><td>" + book_link(this) +
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$("#borrowed_table").append("<tr id=" + this.key + "\" class=\""+ toggleOddEven() + "\"><td>" + this.owner + "</td><td>" + book_link(this) +
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borrowedBookrow: function(){ if (not_to_be_shown(this)) return; $("#borrowed_table").append("<tr id=" + this.key + "><td>" + this.owner + "</td><td>" + book_link(this) + "</td><td></td><td class='action'>" + return_link(this, "return", "return book to owner") + "</td></tr>");}
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html : '<div id="downloads"> ' + e.processedExpressionVectorCount + ' <a title="click to download the tab delimited data" href="#" onClick="fetchData(true,' + e.id + ', \'text\', null, null)">Filtered</a> '
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html : '<div id="downloads"> ' + this.renderProcessedExpressionVectorCount(e) + ' ' + '<i>Downloads:</i> <a title="click to download the tab delimited data" href="#" onClick="fetchData(true,' + e.id + ', \'text\', null, null)">Filtered</a> '
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build : function(e) { var manager = new Gemma.EEManager({ editable : this.editable, id : "eemanager" }); this.manager = manager; // // /* // * Create a store with one record. // */ // var store = new Ext.data.Store({ // proxy : new Ext.data.MemoryProxy([e]), // reader : new Ext.data.ListRangeReader({}, // this.manager.record) // }); // // this.rec = store.getAt(0); adminLinks = '<a href="#" onClick="Ext.getCmp(\'eemanager\').updateEEReport(' + e.id + ')"><img src="/Gemma/images/icons/arrow_refresh_small.png" ext:qtip="Refresh statistics" title="refresh"/></a>' + ' <a href="/Gemma/expressionExperiment/editExpressionExperiment.html?id=' + e.id + '" ><img src="/Gemma/images/icons/wrench.png" ext:qtip="Go to editor page for this experiment" title="edit"/></a> '; if (this.isAdmin) { adminLinks = adminLinks + '<a href="#" onClick="return Ext.getCmp(\'eemanager\').deleteExperiment(' + e.id + ')"><img src="/Gemma/images/icons/cross.png" ext:qtip="Delete the experiment from the system" title="delete" /></a> '; } var pubmedRegion = {}; if (e.pubmedId) { // display the citation, with link out and delete // button. pubmedRegion = this.getPubMedHtml(e); } else { // offer to create a citation link. pubmedRegion = this.getPubMedForm(e); } /* * Show the experimental design */ DesignMatrix.init({ id : e.id }); var vizPanel = new Gemma.EEDetailsVisualizationWidget({ renderTo : 'visualization', taxon : e.taxon }); /* * This is needed to make the annotator initialize properly. */ new Gemma.MGEDCombo({}); var taggerurl = '<a href="#" onClick="return Ext.getCmp(\'eemanager\').tagger(' + e.id + ',' + e.taxonId +')"><img src="/Gemma/images/icons/pencil.png" alt="view tags" title="view tags"/></a>'; tagView = new Gemma.AnnotationDataView({ readParams : [{ id : e.id, classDelegatingFor : "ExpressionExperimentImpl" }] }); manager.on('tagsUpdated', function() { tagView.store.reload(); }); manager.on('done', function() { window.location.reload(); }); manager.on('reportUpdated', function(data) { ob = data[0]; // console.log(ob); var k = Ext.get('coexpressionLinkCount-region'); Ext.DomHelper.overwrite(k, { html : ob.coexpressionLinkCount }); k.highlight(); k = Ext.get('processedExpressionVectorCount-region'); Ext.DomHelper.overwrite(k, { html : ob.processedExpressionVectorCount }); k.highlight(); }); manager.on('pubmedUpdated', function(e) { var html = this.getPubMedHtml(e); Ext.getCmp('pubmed-region-wrap').remove(Ext.getCmp('pubmed-region')); Ext.DomHelper.append('pubmed-region-wrap', html); }.createDelegate(this)); manager.on('pubmedRemove', function(success) { if (success) { var r = Ext.getCmp('pubmed-region-wrap'); r.remove(Ext.getCmp('pubmed-region')); var form = this.getPubMedForm(this.eeId); r.add(form); r.doLayout(); } }.createDelegate(this)); manager.on('updated', function(data) { Ext.getCmp('update-button-region').getEl().hide(); /* * Really we won't need to do this -- as the state on the database is supposed to match this one. */ var k = Ext.getCmp('shortname'); k.setValue(data.shortName); k = Ext.getCmp('name'); k.setValue(data.name); k = Ext.getCmp('description'); k.setValue(data.description); }.createDelegate(this)); // manager.on('reportUpdated', function() { // store.reload(); // }); // // manager.on('differential', function() { // store.reload(); // }); // manager.on('processedVector', function() { // store.reload(); // }); // manager.on('link', function() { // store.reload(); // }); // manager.on('missingValue', function() { // store.reload(); // }); var descriptionArea = new Ext.form.TextArea({ id : 'description', allowBlank : true, grow : true, growMax : 300, readOnly : !this.editable, disabledClass : 'disabled-plain', growMin : 40, emptyText : 'No description provided', enableKeyEvents : true, listeners : { 'keyup' : { fn : function(e) { if (Ext.getCmp('description').isDirty() && Ext.getCmp('description').isValid()) { // show save button Ext.getCmp('update-button-region').show(); } else { Ext.getCmp('update-button-region').hide(); } } } }, width : 500, // height : 100, value : e.description }); var nameArea = new Ext.form.TextArea({ id : 'name', fieldLabel : 'Name', allowBlank : false, grow : true, growMax : 300, readOnly : !this.editable, disabledClass : 'disabled-plain', growMin : 40, emptyText : 'No description provided', enableKeyEvents : true, listeners : { 'keyup' : { fn : function(e) { if (Ext.getCmp('name').isDirty() && Ext.getCmp('name').isValid()) { // show save button Ext.getCmp('update-button-region').show(); } else { Ext.getCmp('update-button-region').hide(); } } } }, width : 500, value : e.name }); var basics = new Ext.Panel({ autoHeight : true, layout : 'table', layoutConfig : { columns : 2 }, renderTo : 'basics', collapsible : false, bodyBorder : false, frame : false, baseCls : 'x-plain-panel', bodyStyle : 'padding:10px', defaults : { bodyStyle : 'vertical-align:top;font-size:12px;color:black', baseCls : 'x-plain-panel', fieldClass : 'x-bare-field' }, items : [{ html : 'Short name:' }, { xtype : 'panel', layout : 'table', baseCls : 'x-plain-panel', layoutConfig : { columns : 2 }, items : [{ xtype : 'textfield', id : 'shortname', enableKeyEvents : true, allowBlank : false, disabledClass : 'disabled-plain', fieldClass : 'x-bare-field', readOnly : !this.editable, listeners : { 'keyup' : { fn : function(e) { if (Ext.getCmp('shortname').isDirty() && Ext.getCmp('shortname').isValid()) { // show // save // button Ext.getCmp('update-button-region').show(); } else { Ext.getCmp('update-button-region').hide(); } }, scope : this } }, width : 250, value : e.shortName }, { baseCls : 'x-plain-panel', id : 'update-button-region', html : '<a href="#" onClick="Ext.getCmp(\'ee-details-panel\').save(' + e.id + ',[\'shortname\',\'name\',\'description\'])" ><img src="/Gemma/images/icons/database_save.png" title="Click to save changes" alt="Click to save changes"/></a>', hidden : true }] }, { html : 'Name:' }, nameArea, { html : "Taxon:" }, { html : e.taxon }, { html : 'Description:' }, descriptionArea, { html : 'Created:' }, { html : Ext.util.Format.date(e.dateCreated) }, { html : 'Source:' }, { html : this.renderSourceDatabaseEntry(e) }, { html : 'Samples:' }, { html : this.renderSamples(e), width : 60 }, { html : 'Profiles:' }, { id : 'processedExpressionVectorCount-region', html : '<div id="downloads"> ' + e.processedExpressionVectorCount + ' <a title="click to download the tab delimited data" href="#" onClick="fetchData(true,' + e.id + ', \'text\', null, null)">Filtered</a> ' + '<a href="#" title="click to download the tab delimited data" onClick="fetchData(false,' + e.id + ', \'text\', null, null)">Unfiltered</a> ' + '<a class="helpLink" href="?" onclick="showHelpTip(event, \'Tab-delimited data file for this experiment. The filtered version corresponds to what is used in most Gemma analyses, removing some probes. Unfiltered includes all probes\'); return false"> <img src="/Gemma/images/help.png" /> </a>' + '</div>', width : 200 }, { html : 'Array designs:' }, { id : 'arrayDesign-region', html : this.renderArrayDesigns(e.arrayDesigns), width : 480 }, { html : 'Coexpr. Links:' }, { id : 'coexpressionLinkCount-region', html : this.renderCoExpressionLinkCount(e), width : 80 }, { html : 'Diff. expr. Probes' }, { id : 'DiffExpressedProbes-region', html : this.renderDiffExpressionDetails(e), width : 200 }, { html : 'Publication:' }, { xtype : 'panel', id : 'pubmed-region-wrap', layout : 'fit', bodyBorder : false, baseCls : 'x-plain-panel', disabled : false, items : [pubmedRegion] }, { html : 'Tags ' + taggerurl }, tagView, { html : 'Status' }, { html : this.renderStatus(e) }, { html : this.editable ? 'Admin' : '' }, { id : 'admin-links', html : this.editable ? adminLinks : '' } /* * authors */ ] }); if (this.editable) { Ext.DomHelper.append('admin-links', { tag : 'ul', cls : 'plainlist', children : [{ tag : 'li', html : 'Missing values: ' + this.missingValueAnalysisRenderer(e) }, { tag : 'li', html : 'Proc. vec: ' + this.processedVectorCreateRenderer(e) }, { tag : 'li', html : 'Diff ex: ' + this.differentialAnalysisRenderer(e) }, { tag : 'li', html : 'Link an.: ' + this.linkAnalysisRenderer(e) }] }); } if (Ext.get('history')) { var history = new Gemma.AuditTrailGrid({ renderTo : 'history', bodyBorder : false, collapsible : true, auditable : { id : e.id, classDelegatingFor : "ubic.gemma.model.expression.experiment.ExpressionExperimentImpl" } }); } this.fireEvent("ready"); }
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width : 200
|
width : 400
|
build : function(e) { var manager = new Gemma.EEManager({ editable : this.editable, id : "eemanager" }); this.manager = manager; // // /* // * Create a store with one record. // */ // var store = new Ext.data.Store({ // proxy : new Ext.data.MemoryProxy([e]), // reader : new Ext.data.ListRangeReader({}, // this.manager.record) // }); // // this.rec = store.getAt(0); adminLinks = '<a href="#" onClick="Ext.getCmp(\'eemanager\').updateEEReport(' + e.id + ')"><img src="/Gemma/images/icons/arrow_refresh_small.png" ext:qtip="Refresh statistics" title="refresh"/></a>' + ' <a href="/Gemma/expressionExperiment/editExpressionExperiment.html?id=' + e.id + '" ><img src="/Gemma/images/icons/wrench.png" ext:qtip="Go to editor page for this experiment" title="edit"/></a> '; if (this.isAdmin) { adminLinks = adminLinks + '<a href="#" onClick="return Ext.getCmp(\'eemanager\').deleteExperiment(' + e.id + ')"><img src="/Gemma/images/icons/cross.png" ext:qtip="Delete the experiment from the system" title="delete" /></a> '; } var pubmedRegion = {}; if (e.pubmedId) { // display the citation, with link out and delete // button. pubmedRegion = this.getPubMedHtml(e); } else { // offer to create a citation link. pubmedRegion = this.getPubMedForm(e); } /* * Show the experimental design */ DesignMatrix.init({ id : e.id }); var vizPanel = new Gemma.EEDetailsVisualizationWidget({ renderTo : 'visualization', taxon : e.taxon }); /* * This is needed to make the annotator initialize properly. */ new Gemma.MGEDCombo({}); var taggerurl = '<a href="#" onClick="return Ext.getCmp(\'eemanager\').tagger(' + e.id + ',' + e.taxonId +')"><img src="/Gemma/images/icons/pencil.png" alt="view tags" title="view tags"/></a>'; tagView = new Gemma.AnnotationDataView({ readParams : [{ id : e.id, classDelegatingFor : "ExpressionExperimentImpl" }] }); manager.on('tagsUpdated', function() { tagView.store.reload(); }); manager.on('done', function() { window.location.reload(); }); manager.on('reportUpdated', function(data) { ob = data[0]; // console.log(ob); var k = Ext.get('coexpressionLinkCount-region'); Ext.DomHelper.overwrite(k, { html : ob.coexpressionLinkCount }); k.highlight(); k = Ext.get('processedExpressionVectorCount-region'); Ext.DomHelper.overwrite(k, { html : ob.processedExpressionVectorCount }); k.highlight(); }); manager.on('pubmedUpdated', function(e) { var html = this.getPubMedHtml(e); Ext.getCmp('pubmed-region-wrap').remove(Ext.getCmp('pubmed-region')); Ext.DomHelper.append('pubmed-region-wrap', html); }.createDelegate(this)); manager.on('pubmedRemove', function(success) { if (success) { var r = Ext.getCmp('pubmed-region-wrap'); r.remove(Ext.getCmp('pubmed-region')); var form = this.getPubMedForm(this.eeId); r.add(form); r.doLayout(); } }.createDelegate(this)); manager.on('updated', function(data) { Ext.getCmp('update-button-region').getEl().hide(); /* * Really we won't need to do this -- as the state on the database is supposed to match this one. */ var k = Ext.getCmp('shortname'); k.setValue(data.shortName); k = Ext.getCmp('name'); k.setValue(data.name); k = Ext.getCmp('description'); k.setValue(data.description); }.createDelegate(this)); // manager.on('reportUpdated', function() { // store.reload(); // }); // // manager.on('differential', function() { // store.reload(); // }); // manager.on('processedVector', function() { // store.reload(); // }); // manager.on('link', function() { // store.reload(); // }); // manager.on('missingValue', function() { // store.reload(); // }); var descriptionArea = new Ext.form.TextArea({ id : 'description', allowBlank : true, grow : true, growMax : 300, readOnly : !this.editable, disabledClass : 'disabled-plain', growMin : 40, emptyText : 'No description provided', enableKeyEvents : true, listeners : { 'keyup' : { fn : function(e) { if (Ext.getCmp('description').isDirty() && Ext.getCmp('description').isValid()) { // show save button Ext.getCmp('update-button-region').show(); } else { Ext.getCmp('update-button-region').hide(); } } } }, width : 500, // height : 100, value : e.description }); var nameArea = new Ext.form.TextArea({ id : 'name', fieldLabel : 'Name', allowBlank : false, grow : true, growMax : 300, readOnly : !this.editable, disabledClass : 'disabled-plain', growMin : 40, emptyText : 'No description provided', enableKeyEvents : true, listeners : { 'keyup' : { fn : function(e) { if (Ext.getCmp('name').isDirty() && Ext.getCmp('name').isValid()) { // show save button Ext.getCmp('update-button-region').show(); } else { Ext.getCmp('update-button-region').hide(); } } } }, width : 500, value : e.name }); var basics = new Ext.Panel({ autoHeight : true, layout : 'table', layoutConfig : { columns : 2 }, renderTo : 'basics', collapsible : false, bodyBorder : false, frame : false, baseCls : 'x-plain-panel', bodyStyle : 'padding:10px', defaults : { bodyStyle : 'vertical-align:top;font-size:12px;color:black', baseCls : 'x-plain-panel', fieldClass : 'x-bare-field' }, items : [{ html : 'Short name:' }, { xtype : 'panel', layout : 'table', baseCls : 'x-plain-panel', layoutConfig : { columns : 2 }, items : [{ xtype : 'textfield', id : 'shortname', enableKeyEvents : true, allowBlank : false, disabledClass : 'disabled-plain', fieldClass : 'x-bare-field', readOnly : !this.editable, listeners : { 'keyup' : { fn : function(e) { if (Ext.getCmp('shortname').isDirty() && Ext.getCmp('shortname').isValid()) { // show // save // button Ext.getCmp('update-button-region').show(); } else { Ext.getCmp('update-button-region').hide(); } }, scope : this } }, width : 250, value : e.shortName }, { baseCls : 'x-plain-panel', id : 'update-button-region', html : '<a href="#" onClick="Ext.getCmp(\'ee-details-panel\').save(' + e.id + ',[\'shortname\',\'name\',\'description\'])" ><img src="/Gemma/images/icons/database_save.png" title="Click to save changes" alt="Click to save changes"/></a>', hidden : true }] }, { html : 'Name:' }, nameArea, { html : "Taxon:" }, { html : e.taxon }, { html : 'Description:' }, descriptionArea, { html : 'Created:' }, { html : Ext.util.Format.date(e.dateCreated) }, { html : 'Source:' }, { html : this.renderSourceDatabaseEntry(e) }, { html : 'Samples:' }, { html : this.renderSamples(e), width : 60 }, { html : 'Profiles:' }, { id : 'processedExpressionVectorCount-region', html : '<div id="downloads"> ' + e.processedExpressionVectorCount + ' <a title="click to download the tab delimited data" href="#" onClick="fetchData(true,' + e.id + ', \'text\', null, null)">Filtered</a> ' + '<a href="#" title="click to download the tab delimited data" onClick="fetchData(false,' + e.id + ', \'text\', null, null)">Unfiltered</a> ' + '<a class="helpLink" href="?" onclick="showHelpTip(event, \'Tab-delimited data file for this experiment. The filtered version corresponds to what is used in most Gemma analyses, removing some probes. Unfiltered includes all probes\'); return false"> <img src="/Gemma/images/help.png" /> </a>' + '</div>', width : 200 }, { html : 'Array designs:' }, { id : 'arrayDesign-region', html : this.renderArrayDesigns(e.arrayDesigns), width : 480 }, { html : 'Coexpr. Links:' }, { id : 'coexpressionLinkCount-region', html : this.renderCoExpressionLinkCount(e), width : 80 }, { html : 'Diff. expr. Probes' }, { id : 'DiffExpressedProbes-region', html : this.renderDiffExpressionDetails(e), width : 200 }, { html : 'Publication:' }, { xtype : 'panel', id : 'pubmed-region-wrap', layout : 'fit', bodyBorder : false, baseCls : 'x-plain-panel', disabled : false, items : [pubmedRegion] }, { html : 'Tags ' + taggerurl }, tagView, { html : 'Status' }, { html : this.renderStatus(e) }, { html : this.editable ? 'Admin' : '' }, { id : 'admin-links', html : this.editable ? adminLinks : '' } /* * authors */ ] }); if (this.editable) { Ext.DomHelper.append('admin-links', { tag : 'ul', cls : 'plainlist', children : [{ tag : 'li', html : 'Missing values: ' + this.missingValueAnalysisRenderer(e) }, { tag : 'li', html : 'Proc. vec: ' + this.processedVectorCreateRenderer(e) }, { tag : 'li', html : 'Diff ex: ' + this.differentialAnalysisRenderer(e) }, { tag : 'li', html : 'Link an.: ' + this.linkAnalysisRenderer(e) }] }); } if (Ext.get('history')) { var history = new Gemma.AuditTrailGrid({ renderTo : 'history', bodyBorder : false, collapsible : true, auditable : { id : e.id, classDelegatingFor : "ubic.gemma.model.expression.experiment.ExpressionExperimentImpl" } }); } this.fireEvent("ready"); }
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taxon : e.taxon
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taxon : e.parentTaxon
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build : function(e) { var manager = new Gemma.EEManager({ editable : this.editable, id : "eemanager" }); this.manager = manager; // // /* // * Create a store with one record. // */ // var store = new Ext.data.Store({ // proxy : new Ext.data.MemoryProxy([e]), // reader : new Ext.data.ListRangeReader({}, // this.manager.record) // }); // // this.rec = store.getAt(0); adminLinks = '<a href="#" onClick="Ext.getCmp(\'eemanager\').updateEEReport(' + e.id + ')"><img src="/Gemma/images/icons/arrow_refresh_small.png" ext:qtip="Refresh statistics" title="refresh"/></a>' + ' <a href="/Gemma/expressionExperiment/editExpressionExperiment.html?id=' + e.id + '" ><img src="/Gemma/images/icons/wrench.png" ext:qtip="Go to editor page for this experiment" title="edit"/></a> '; if (this.isAdmin) { adminLinks = adminLinks + '<a href="#" onClick="return Ext.getCmp(\'eemanager\').deleteExperiment(' + e.id + ')"><img src="/Gemma/images/icons/cross.png" ext:qtip="Delete the experiment from the system" title="delete" /></a> '; } var pubmedRegion = {}; if (e.pubmedId) { // display the citation, with link out and delete // button. pubmedRegion = this.getPubMedHtml(e); } else { // offer to create a citation link. pubmedRegion = this.getPubMedForm(e); } /* * Show the experimental design */ DesignMatrix.init({ id : e.id }); var vizPanel = new Gemma.EEDetailsVisualizationWidget({ renderTo : 'visualization', taxon : e.taxon }); /* * This is needed to make the annotator initialize properly. */ new Gemma.MGEDCombo({}); var taggerurl = '<a href="#" onClick="return Ext.getCmp(\'eemanager\').tagger(' + e.id + ',' + e.taxonId +')"><img src="/Gemma/images/icons/pencil.png" alt="view tags" title="view tags"/></a>'; tagView = new Gemma.AnnotationDataView({ readParams : [{ id : e.id, classDelegatingFor : "ExpressionExperimentImpl" }] }); manager.on('tagsUpdated', function() { tagView.store.reload(); }); manager.on('done', function() { window.location.reload(); }); manager.on('reportUpdated', function(data) { ob = data[0]; // console.log(ob); var k = Ext.get('coexpressionLinkCount-region'); Ext.DomHelper.overwrite(k, { html : ob.coexpressionLinkCount }); k.highlight(); k = Ext.get('processedExpressionVectorCount-region'); Ext.DomHelper.overwrite(k, { html : ob.processedExpressionVectorCount }); k.highlight(); }); manager.on('pubmedUpdated', function(e) { var html = this.getPubMedHtml(e); Ext.getCmp('pubmed-region-wrap').remove(Ext.getCmp('pubmed-region')); Ext.DomHelper.append('pubmed-region-wrap', html); }.createDelegate(this)); manager.on('pubmedRemove', function(success) { if (success) { var r = Ext.getCmp('pubmed-region-wrap'); r.remove(Ext.getCmp('pubmed-region')); var form = this.getPubMedForm(this.eeId); r.add(form); r.doLayout(); } }.createDelegate(this)); manager.on('updated', function(data) { Ext.getCmp('update-button-region').getEl().hide(); /* * Really we won't need to do this -- as the state on the database is supposed to match this one. */ var k = Ext.getCmp('shortname'); k.setValue(data.shortName); k = Ext.getCmp('name'); k.setValue(data.name); k = Ext.getCmp('description'); k.setValue(data.description); }.createDelegate(this)); // manager.on('reportUpdated', function() { // store.reload(); // }); // // manager.on('differential', function() { // store.reload(); // }); // manager.on('processedVector', function() { // store.reload(); // }); // manager.on('link', function() { // store.reload(); // }); // manager.on('missingValue', function() { // store.reload(); // }); var descriptionArea = new Ext.form.TextArea({ id : 'description', allowBlank : true, grow : true, growMax : 300, readOnly : !this.editable, disabledClass : 'disabled-plain', growMin : 40, emptyText : 'No description provided', enableKeyEvents : true, listeners : { 'keyup' : { fn : function(e) { if (Ext.getCmp('description').isDirty() && Ext.getCmp('description').isValid()) { // show save button Ext.getCmp('update-button-region').show(); } else { Ext.getCmp('update-button-region').hide(); } } } }, width : 500, // height : 100, value : e.description }); var nameArea = new Ext.form.TextArea({ id : 'name', fieldLabel : 'Name', allowBlank : false, grow : true, growMax : 300, readOnly : !this.editable, disabledClass : 'disabled-plain', growMin : 40, emptyText : 'No description provided', enableKeyEvents : true, listeners : { 'keyup' : { fn : function(e) { if (Ext.getCmp('name').isDirty() && Ext.getCmp('name').isValid()) { // show save button Ext.getCmp('update-button-region').show(); } else { Ext.getCmp('update-button-region').hide(); } } } }, width : 500, value : e.name }); var basics = new Ext.Panel({ autoHeight : true, layout : 'table', layoutConfig : { columns : 2 }, renderTo : 'basics', collapsible : false, bodyBorder : false, frame : false, baseCls : 'x-plain-panel', bodyStyle : 'padding:10px', defaults : { bodyStyle : 'vertical-align:top;font-size:12px;color:black', baseCls : 'x-plain-panel', fieldClass : 'x-bare-field' }, items : [{ html : 'Short name:' }, { xtype : 'panel', layout : 'table', baseCls : 'x-plain-panel', layoutConfig : { columns : 2 }, items : [{ xtype : 'textfield', id : 'shortname', enableKeyEvents : true, allowBlank : false, disabledClass : 'disabled-plain', fieldClass : 'x-bare-field', readOnly : !this.editable, listeners : { 'keyup' : { fn : function(e) { if (Ext.getCmp('shortname').isDirty() && Ext.getCmp('shortname').isValid()) { // show // save // button Ext.getCmp('update-button-region').show(); } else { Ext.getCmp('update-button-region').hide(); } }, scope : this } }, width : 250, value : e.shortName }, { baseCls : 'x-plain-panel', id : 'update-button-region', html : '<a href="#" onClick="Ext.getCmp(\'ee-details-panel\').save(' + e.id + ',[\'shortname\',\'name\',\'description\'])" ><img src="/Gemma/images/icons/database_save.png" title="Click to save changes" alt="Click to save changes"/></a>', hidden : true }] }, { html : 'Name:' }, nameArea, { html : "Taxon:" }, { html : e.taxon }, { html : 'Description:' }, descriptionArea, { html : 'Created:' }, { html : Ext.util.Format.date(e.dateCreated) }, { html : 'Source:' }, { html : this.renderSourceDatabaseEntry(e) }, { html : 'Samples:' }, { html : this.renderSamples(e), width : 60 }, { html : 'Profiles:' }, { id : 'processedExpressionVectorCount-region', html : '<div id="downloads"> ' + this.renderProcessedExpressionVectorCount(e) + ' ' + '<i>Downloads:</i> <a title="click to download the tab delimited data" href="#" onClick="fetchData(true,' + e.id + ', \'text\', null, null)">Filtered</a> ' + '<a href="#" title="click to download the tab delimited data" onClick="fetchData(false,' + e.id + ', \'text\', null, null)">Unfiltered</a> ' + '<a class="helpLink" href="?" onclick="showHelpTip(event, \'Tab-delimited data file for this experiment. The filtered version corresponds to what is used in most Gemma analyses, removing some probes. Unfiltered includes all probes\'); return false"> <img src="/Gemma/images/help.png" /> </a>' + '</div>', width : 400 }, { html : 'Array designs:' }, { id : 'arrayDesign-region', html : this.renderArrayDesigns(e.arrayDesigns), width : 480 }, { html : 'Coexpr. Links:' }, { id : 'coexpressionLinkCount-region', html : this.renderCoExpressionLinkCount(e), width : 80 }, { html : 'Diff. expr. Probes' }, { id : 'DiffExpressedProbes-region', html : this.renderDiffExpressionDetails(e), width : 200 }, { html : 'Publication:' }, { xtype : 'panel', id : 'pubmed-region-wrap', layout : 'fit', bodyBorder : false, baseCls : 'x-plain-panel', disabled : false, items : [pubmedRegion] }, { html : 'Tags ' + taggerurl }, tagView, { html : 'Status' }, { html : this.renderStatus(e) }, { html : this.editable ? 'Admin' : '' }, { id : 'admin-links', html : this.editable ? adminLinks : '' } /* * authors */ ] }); if (this.editable) { Ext.DomHelper.append('admin-links', { tag : 'ul', cls : 'plainlist', children : [{ tag : 'li', html : 'Missing values: ' + this.missingValueAnalysisRenderer(e) }, { tag : 'li', html : 'Proc. vec: ' + this.processedVectorCreateRenderer(e) }, { tag : 'li', html : 'Diff ex: ' + this.differentialAnalysisRenderer(e) }, { tag : 'li', html : 'Link an.: ' + this.linkAnalysisRenderer(e) }] }); } if (Ext.get('history')) { var history = new Gemma.AuditTrailGrid({ renderTo : 'history', bodyBorder : false, collapsible : true, auditable : { id : e.id, classDelegatingFor : "ubic.gemma.model.expression.experiment.ExpressionExperimentImpl" } }); } this.fireEvent("ready"); }
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manager.on('differential', function() { window.location.reload(true); });
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build : function(e) { var manager = new Gemma.EEManager({ editable : this.editable, id : "eemanager" }); this.manager = manager; // // /* // * Create a store with one record. // */ // var store = new Ext.data.Store({ // proxy : new Ext.data.MemoryProxy([e]), // reader : new Ext.data.ListRangeReader({}, // this.manager.record) // }); // // this.rec = store.getAt(0); adminLinks = '<span style="cursor:pointer" onClick="Ext.getCmp(\'eemanager\').updateEEReport(' + e.id + ',\'admin-links\'' + ')"><img src="/Gemma/images/icons/arrow_refresh_small.png" ext:qtip="Refresh statistics" title="refresh"/></span>' + ' <a href="/Gemma/expressionExperiment/editExpressionExperiment.html?id=' + e.id + '" ><img src="/Gemma/images/icons/wrench.png" ext:qtip="Go to editor page for this experiment" title="edit"/></span> '; if (this.isAdmin) { adminLinks = adminLinks + '<span style="cursor:pointer" onClick="return Ext.getCmp(\'eemanager\').deleteExperiment(' + e.id + ')"><img src="/Gemma/images/icons/cross.png" ext:qtip="Delete the experiment from the system" title="delete" /></span> '; } var pubmedRegion = {}; if (e.pubmedId) { // display the citation, with link out and delete // button. pubmedRegion = this.getPubMedHtml(e); } else { // offer to create a citation link. pubmedRegion = this.getPubMedForm(e); } /* * Show the experimental design */ DesignMatrix.init({ id : e.id }); var vizPanel = new Gemma.EEDetailsVisualizationWidget({ renderTo : 'visualization', taxon : e.parentTaxon }); /* * This is needed to make the annotator initialize properly. */ new Gemma.MGEDCombo({}); var taggerurl = '<span style="cursor:pointer" onClick="return Ext.getCmp(\'eemanager\').tagger(' + e.id + ',' + e.taxonId + ',' + this.editable + ')"><img src="/Gemma/images/icons/pencil.png" alt="view tags" title="view tags"/></span>'; tagView = new Gemma.AnnotationDataView({ readParams : [{ id : e.id, classDelegatingFor : "ExpressionExperimentImpl" }] }); manager.on('tagsUpdated', function() { tagView.store.reload(); }); manager.on('done', function() { /* * After a process that requires refreshing the page. */ window.location.reload(); }); manager.on('reportUpdated', function(data) { ob = data[0]; var k = Ext.get('coexpressionLinkCount-region'); Ext.DomHelper.overwrite(k, { html : ob.coexpressionLinkCount }); k.highlight(); k = Ext.get('processedExpressionVectorCount-region'); Ext.DomHelper.overwrite(k, { html : ob.processedExpressionVectorCount }); k.highlight(); }); // manager.on('pubmedUpdated', function(e) { // var html = this.getPubMedHtml(e); // Ext.getCmp('pubmed-region-wrap').remove(Ext.getCmp('pubmed-region')); // Ext.DomHelper.append('pubmed-region-wrap', html); // }.createDelegate(this)); // // manager.on('pubmedRemove', function(success) { // if (success) { // var r = Ext.getCmp('pubmed-region-wrap'); // r.remove(Ext.getCmp('pubmed-region')); // var form = this.getPubMedForm(this.eeId); // r.add(form); // r.doLayout(); // } // }.createDelegate(this)); // manager.on('reportUpdated', function() { // // window.location.reload(true); // }); // manager.on('differential', function() { // window.location.reload(true); // }); // manager.on('processedVector', function() { // window.location.reload(true); // }); // manager.on('link', function() { // window.location.reload(true); // }); // // manager.on('missingValue', function() { // window.location.reload(true); // }); var descriptionArea = new Ext.form.TextArea({ id : 'description', allowBlank : true, grow : true, growMax : 300, readOnly : !this.editable, disabledClass : 'disabled-plain', growMin : 40, emptyText : 'No description provided', enableKeyEvents : true, listeners : { 'keyup' : { fn : function(e) { if (Ext.getCmp('description').isDirty() && Ext.getCmp('description').isValid()) { // show save button Ext.getCmp('update-button-region').show(true); } else { Ext.getCmp('update-button-region').hide(true); } } } }, width : 500, // height : 100, value : e.description }); var nameArea = new Ext.form.TextArea({ id : 'name', fieldLabel : 'Name', allowBlank : false, grow : true, growMax : 300, readOnly : !this.editable, disabledClass : 'disabled-plain', growMin : 40, emptyText : 'No description provided', enableKeyEvents : true, listeners : { 'keyup' : { fn : function(e) { if (Ext.getCmp('name').isDirty() && Ext.getCmp('name').isValid()) { // show save button Ext.getCmp('update-button-region').show(true); } else { Ext.getCmp('update-button-region').hide(true); } } } }, width : 500, value : e.name }); var basics = new Ext.Panel({ autoHeight : true, layout : 'table', layoutConfig : { columns : 2 }, renderTo : 'basics', collapsible : false, bodyBorder : false, frame : false, baseCls : 'x-plain-panel', bodyStyle : 'padding:10px', defaults : { bodyStyle : 'vertical-align:top;font-size:12px;color:black', baseCls : 'x-plain-panel', fieldClass : 'x-bare-field' }, items : [{ html : 'Short name:' }, { xtype : 'panel', layout : 'table', baseCls : 'x-plain-panel', layoutConfig : { columns : 2 }, items : [{ xtype : 'textfield', id : 'shortname', enableKeyEvents : true, allowBlank : false, disabledClass : 'disabled-plain', fieldClass : 'x-bare-field', readOnly : !this.editable, listeners : { 'keyup' : { fn : function(e) { if (Ext.getCmp('shortname').isDirty() && Ext.getCmp('shortname').isValid()) { // show // save // button Ext.getCmp('update-button-region').show(true); } else { Ext.getCmp('update-button-region').hide(true); } }, scope : this } }, width : 250, value : e.shortName }, { baseCls : 'x-plain-panel', id : 'update-button-region', html : '<span style="cursor:pointer" onClick="Ext.getCmp(\'ee-details-panel\').save(' + e.id + ',[\'shortname\',\'name\',\'description\'])" ><img src="/Gemma/images/icons/database_save.png" ext:qtip="Click to save changes" alt="Click to save changes"/></span>', hidden : true }] }, { html : 'Name:' }, nameArea, { html : "Taxon:" }, { html : e.taxon }, { html : 'Description:' }, descriptionArea, { html : 'Created:' }, { html : Ext.util.Format.date(e.dateCreated) }, { html : 'Source:' }, { html : this.renderSourceDatabaseEntry(e) }, { html : 'Samples:' }, { html : this.renderSamples(e), width : 60 }, { html : 'Profiles:' }, { id : 'processedExpressionVectorCount-region', html : '<div id="downloads"> ' + this.renderProcessedExpressionVectorCount(e) + ' ' + '<i>Downloads:</i> <span class="link" ext:qtip="Download the tab delimited data" onClick="fetchData(true,' + e.id + ', \'text\', null, null)">Filtered</span> ' + '<span class="link" ext:qtip="Download the tab delimited data" onClick="fetchData(false,' + e.id + ', \'text\', null, null)">Unfiltered</span> ' + '<a class="helpLink" href="?" onclick="showHelpTip(event, \'Tab-delimited data file for this experiment. The filtered version corresponds to what is used in most Gemma analyses, removing some probes. Unfiltered includes all probes\'); return false"> <img src="/Gemma/images/help.png" /> </a>' + '</div>', width : 400 }, { html : 'Array designs:' }, { id : 'arrayDesign-region', html : this.renderArrayDesigns(e.arrayDesigns), width : 480 }, { html : 'Coexpr. Links:' }, { id : 'coexpressionLinkCount-region', html : this.renderCoExpressionLinkCount(e), width : 80 }, { html : 'Diff. expr. Probes' }, { id : 'DiffExpressedProbes-region', html : this.renderDiffExpressionDetails(e), width : 200 }, { html : 'Publication:' }, { xtype : 'panel', id : 'pubmed-region-wrap', layout : 'fit', bodyBorder : false, baseCls : 'x-plain-panel', disabled : false, items : [pubmedRegion] }, { html : 'Tags ' + taggerurl }, tagView, { html : 'Status' }, { html : this.renderStatus(e) }, { html : this.editable ? 'Admin' : '' }, { id : 'admin-links', html : this.editable ? adminLinks : '' } /* * authors */ ] }); if (this.editable) { Ext.DomHelper.append('admin-links', { tag : 'ul', cls : 'plainlist', children : [{ tag : 'li', html : 'Missing values: ' + this.missingValueAnalysisRenderer(e) }, { tag : 'li', html : 'Proc. vec: ' + this.processedVectorCreateRenderer(e) }, { tag : 'li', html : 'Diff ex: ' + this.differentialAnalysisRenderer(e) }, { tag : 'li', html : 'Link an.: ' + this.linkAnalysisRenderer(e) }] }); } if (Ext.get('history')) { var history = new Gemma.AuditTrailGrid({ renderTo : 'history', bodyBorder : false, collapsible : true, auditable : { id : e.id, classDelegatingFor : "ubic.gemma.model.expression.experiment.ExpressionExperimentImpl" } }); } this.fireEvent("ready"); }
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+ ')"><img src="/Gemma/images/icons/pencil.png" alt="view tags" title="view tags"/></a>';
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+ ',' + e.taxonId +')"><img src="/Gemma/images/icons/pencil.png" alt="view tags" title="view tags"/></a>';
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build : function(e) { var manager = new Gemma.EEManager({ editable : this.editable, id : "eemanager" }); this.manager = manager; // // /* // * Create a store with one record. // */ // var store = new Ext.data.Store({ // proxy : new Ext.data.MemoryProxy([e]), // reader : new Ext.data.ListRangeReader({}, // this.manager.record) // }); // // this.rec = store.getAt(0); adminLinks = '<a href="#" onClick="Ext.getCmp(\'eemanager\').updateEEReport(' + e.id + ')"><img src="/Gemma/images/icons/arrow_refresh_small.png" ext:qtip="Refresh statistics" title="refresh"/></a>' + ' <a href="/Gemma/expressionExperiment/editExpressionExperiment.html?id=' + e.id + '" ><img src="/Gemma/images/icons/wrench.png" ext:qtip="Go to editor page for this experiment" title="edit"/></a> '; if (this.isAdmin) { adminLinks = adminLinks + '<a href="#" onClick="return Ext.getCmp(\'eemanager\').deleteExperiment(' + e.id + ')"><img src="/Gemma/images/icons/cross.png" ext:qtip="Delete the experiment from the system" title="delete" /></a> '; } var pubmedRegion = {}; if (e.pubmedId) { // display the citation, with link out and delete // button. pubmedRegion = this.getPubMedHtml(e); } else { // offer to create a citation link. pubmedRegion = this.getPubMedForm(e); } /* * Show the experimental design */ DesignMatrix.init({ id : e.id }); var vizPanel = new Gemma.EEDetailsVisualizationWidget({ renderTo : 'visualization', taxon : e.taxon }); /* * This is needed to make the annotator initialize properly. */ new Gemma.MGEDCombo({}); var taggerurl = '<a href="#" onClick="return Ext.getCmp(\'eemanager\').tagger(' + e.id + ')"><img src="/Gemma/images/icons/pencil.png" alt="view tags" title="view tags"/></a>'; tagView = new Gemma.AnnotationDataView({ readParams : [{ id : e.id, classDelegatingFor : "ExpressionExperimentImpl" }] }); manager.on('tagsUpdated', function() { tagView.store.reload(); }); manager.on('done', function() { window.location.reload(); }); manager.on('reportUpdated', function(data) { ob = data[0]; // console.log(ob); var k = Ext.get('coexpressionLinkCount-region'); Ext.DomHelper.overwrite(k, { html : ob.coexpressionLinkCount }); k.highlight(); k = Ext.get('processedExpressionVectorCount-region'); Ext.DomHelper.overwrite(k, { html : ob.processedExpressionVectorCount }); k.highlight(); }); manager.on('pubmedUpdated', function(e) { var html = this.getPubMedHtml(e); Ext.getCmp('pubmed-region-wrap').remove(Ext.getCmp('pubmed-region')); Ext.DomHelper.append('pubmed-region-wrap', html); }.createDelegate(this)); manager.on('pubmedRemove', function(success) { if (success) { var r = Ext.getCmp('pubmed-region-wrap'); r.remove(Ext.getCmp('pubmed-region')); var form = this.getPubMedForm(this.eeId); r.add(form); r.doLayout(); } }.createDelegate(this)); manager.on('updated', function(data) { Ext.getCmp('update-button-region').getEl().hide(); /* * Really we won't need to do this -- as the state on the database is supposed to match this one. */ var k = Ext.getCmp('shortname'); k.setValue(data.shortName); k = Ext.getCmp('name'); k.setValue(data.name); k = Ext.getCmp('description'); k.setValue(data.description); }.createDelegate(this)); // manager.on('reportUpdated', function() { // store.reload(); // }); // // manager.on('differential', function() { // store.reload(); // }); // manager.on('processedVector', function() { // store.reload(); // }); // manager.on('link', function() { // store.reload(); // }); // manager.on('missingValue', function() { // store.reload(); // }); var descriptionArea = new Ext.form.TextArea({ id : 'description', allowBlank : true, grow : true, growMax : 300, readOnly : !this.editable, disabledClass : 'disabled-plain', growMin : 40, emptyText : 'No description provided', enableKeyEvents : true, listeners : { 'keyup' : { fn : function(e) { if (Ext.getCmp('description').isDirty() && Ext.getCmp('description').isValid()) { // show save button Ext.getCmp('update-button-region').show(); } else { Ext.getCmp('update-button-region').hide(); } } } }, width : 500, // height : 100, value : e.description }); var nameArea = new Ext.form.TextArea({ id : 'name', fieldLabel : 'Name', allowBlank : false, grow : true, growMax : 300, readOnly : !this.editable, disabledClass : 'disabled-plain', growMin : 40, emptyText : 'No description provided', enableKeyEvents : true, listeners : { 'keyup' : { fn : function(e) { if (Ext.getCmp('name').isDirty() && Ext.getCmp('name').isValid()) { // show save button Ext.getCmp('update-button-region').show(); } else { Ext.getCmp('update-button-region').hide(); } } } }, width : 500, value : e.name }); var basics = new Ext.Panel({ autoHeight : true, layout : 'table', layoutConfig : { columns : 2 }, renderTo : 'basics', collapsible : true, bodyBorder : false, frame : false, baseCls : 'x-plain-panel', bodyStyle : 'padding:10px', defaults : { bodyStyle : 'vertical-align:top;font-size:12px;color:black', baseCls : 'x-plain-panel', fieldClass : 'x-bare-field' }, items : [{ html : 'Short name:' }, { xtype : 'panel', layout : 'table', baseCls : 'x-plain-panel', layoutConfig : { columns : 2 }, items : [{ xtype : 'textfield', id : 'shortname', enableKeyEvents : true, allowBlank : false, disabledClass : 'disabled-plain', fieldClass : 'x-bare-field', readOnly : !this.editable, listeners : { 'keyup' : { fn : function(e) { if (Ext.getCmp('shortname').isDirty() && Ext.getCmp('shortname').isValid()) { // show // save // button Ext.getCmp('update-button-region').show(); } else { Ext.getCmp('update-button-region').hide(); } }, scope : this } }, width : 250, value : e.shortName }, { baseCls : 'x-plain-panel', id : 'update-button-region', html : '<a href="#" onClick="Ext.getCmp(\'ee-details-panel\').save(' + e.id + ',[\'shortname\',\'name\',\'description\'])" ><img src="/Gemma/images/icons/database_save.png" title="Click to save changes" alt="Click to save changes"/></a>', hidden : true }] }, { html : 'Name:' }, nameArea, { html : "Taxon:" }, { html : e.taxon }, { html : 'Description:' }, descriptionArea, { html : 'Created:' }, { html : Ext.util.Format.date(e.dateCreated) }, { html : 'Source:' }, { html : this.renderSourceDatabaseEntry(e) }, { html : 'Samples:' }, { html : this.renderSamples(e), width : 60 }, { html : 'Profiles:' }, { id : 'processedExpressionVectorCount-region', html : e.processedExpressionVectorCount, width : 60 }, { html : 'Array designs:' }, { id : 'arrayDesign-region', html : this.renderArrayDesigns(e.arrayDesigns), width : 480 }, { html : 'Coexpr. Links:' }, { id : 'coexpressionLinkCount-region', html : this.renderCoExpressionLinkCount(e), width : 80 }, { html : 'Diff. expr. Probes' }, { id : 'DiffExpressedProbes-region', html : this.renderDiffExpressionDetails(e), width : 200 }, { html : 'Publication:' }, { xtype : 'panel', id : 'pubmed-region-wrap', layout : 'fit', bodyBorder : false, baseCls : 'x-plain-panel', disabled : false, items : [pubmedRegion] }, { html : 'Tags ' + taggerurl }, tagView, { html : 'Status' }, { html : this.renderStatus(e) }, { html : this.editable ? 'Admin' : '' }, { id : 'admin-links', html : this.editable ? adminLinks : '' } /* * authors */ ] }); if (this.editable) { Ext.DomHelper.append('admin-links', { tag : 'ul', cls : 'plainlist', children : [{ tag : 'li', html : 'Missing values: ' + this.missingValueAnalysisRenderer(e) }, { tag : 'li', html : 'Proc. vec: ' + this.processedVectorCreateRenderer(e) }, { tag : 'li', html : 'Diff ex: ' + this.differentialAnalysisRenderer(e) }, { tag : 'li', html : 'Link an.: ' + this.linkAnalysisRenderer(e) }] }); } if (Ext.get('history')) { var history = new Gemma.AuditTrailGrid({ renderTo : 'history', bodyBorder : false, collapsible : true, auditable : { id : e.id, classDelegatingFor : "ubic.gemma.model.expression.experiment.ExpressionExperimentImpl" } }); } this.fireEvent("ready"); }
|
name : factors[i],
|
name : cleanName(fn),
|
build : function(rows) { var factors = rows[0].factors; var record = []; var columns = []; columns.push({ header : "Assays", dataIndex : "count", sortable : "true", tooltip : "How many assays are in this group" }); for (var i = 0; i < factors.length; ++i) { record.push({ name : factors[i], type : "string" }); columns.push({ header : factors[i], dataIndex : factors[i], sortable : "true", tooltip : factors[i] }); } record.push({ name : "count", type : "int" }); var DesignMatrixRow = Ext.data.Record.create(record); var cm = new Ext.grid.ColumnModel(columns); var data = []; for (var k = 0; k < rows.length; ++k) { data[k] = []; for (var j = 0; j < factors.length; ++j) { data[k][j] = rows[k].factorValueMap[factors[j]]; } data[k][factors.length] = rows[k].count; } this.ds = new Ext.data.Store({ proxy : new Ext.data.MemoryProxy(data), reader : new Ext.data.ArrayReader({}, DesignMatrixRow), remoteSort : false }); this.ds.load(); this.grid = new Ext.grid.GridPanel({ ds : this.ds, cm : cm, collapsible : true, title : "Experimental Design overview", renderTo : "eeDesignMatrix", height : 125, width : 600, viewConfig : { forceFit : true } }); },
|
header : factors[i], dataIndex : factors[i],
|
header : fn, dataIndex : cleanName(fn),
|
build : function(rows) { var factors = rows[0].factors; var record = []; var columns = []; columns.push({ header : "Assays", dataIndex : "count", sortable : "true", tooltip : "How many assays are in this group" }); for (var i = 0; i < factors.length; ++i) { record.push({ name : factors[i], type : "string" }); columns.push({ header : factors[i], dataIndex : factors[i], sortable : "true", tooltip : factors[i] }); } record.push({ name : "count", type : "int" }); var DesignMatrixRow = Ext.data.Record.create(record); var cm = new Ext.grid.ColumnModel(columns); var data = []; for (var k = 0; k < rows.length; ++k) { data[k] = []; for (var j = 0; j < factors.length; ++j) { data[k][j] = rows[k].factorValueMap[factors[j]]; } data[k][factors.length] = rows[k].count; } this.ds = new Ext.data.Store({ proxy : new Ext.data.MemoryProxy(data), reader : new Ext.data.ArrayReader({}, DesignMatrixRow), remoteSort : false }); this.ds.load(); this.grid = new Ext.grid.GridPanel({ ds : this.ds, cm : cm, collapsible : true, title : "Experimental Design overview", renderTo : "eeDesignMatrix", height : 125, width : 600, viewConfig : { forceFit : true } }); },
|
tooltip : factors[i]
|
tooltip : fn
|
build : function(rows) { var factors = rows[0].factors; var record = []; var columns = []; columns.push({ header : "Assays", dataIndex : "count", sortable : "true", tooltip : "How many assays are in this group" }); for (var i = 0; i < factors.length; ++i) { record.push({ name : factors[i], type : "string" }); columns.push({ header : factors[i], dataIndex : factors[i], sortable : "true", tooltip : factors[i] }); } record.push({ name : "count", type : "int" }); var DesignMatrixRow = Ext.data.Record.create(record); var cm = new Ext.grid.ColumnModel(columns); var data = []; for (var k = 0; k < rows.length; ++k) { data[k] = []; for (var j = 0; j < factors.length; ++j) { data[k][j] = rows[k].factorValueMap[factors[j]]; } data[k][factors.length] = rows[k].count; } this.ds = new Ext.data.Store({ proxy : new Ext.data.MemoryProxy(data), reader : new Ext.data.ArrayReader({}, DesignMatrixRow), remoteSort : false }); this.ds.load(); this.grid = new Ext.grid.GridPanel({ ds : this.ds, cm : cm, collapsible : true, title : "Experimental Design overview", renderTo : "eeDesignMatrix", height : 125, width : 600, viewConfig : { forceFit : true } }); },
|
e.taxonId + ',' + this.editable +
|
e.taxonId + ',' + this.editable + ',' + (e.validatedAnnotations !== null) +
|
build : function(e) { var manager = new Gemma.EEManager({ editable : this.editable, id : "eemanager" }); this.manager = manager; // // /* // * Create a store with one record. // */ // var store = new Ext.data.Store({ // proxy : new Ext.data.MemoryProxy([e]), // reader : new Ext.data.ListRangeReader({}, // this.manager.record) // }); // // this.rec = store.getAt(0); adminLinks = '<span style="cursor:pointer" onClick="Ext.getCmp(\'eemanager\').updateEEReport(' + e.id + ',\'admin-links\'' + ')"><img src="/Gemma/images/icons/arrow_refresh_small.png" ext:qtip="Refresh statistics" title="refresh"/></span>' + ' <a href="/Gemma/expressionExperiment/editExpressionExperiment.html?id=' + e.id + '" ><img src="/Gemma/images/icons/wrench.png" ext:qtip="Go to editor page for this experiment" title="edit"/></span> '; if (this.isAdmin) { adminLinks = adminLinks + '<span style="cursor:pointer" onClick="return Ext.getCmp(\'eemanager\').deleteExperiment(' + e.id + ')"><img src="/Gemma/images/icons/cross.png" ext:qtip="Delete the experiment from the system" title="delete" /></span> '; } var pubmedRegion = {}; if (e.pubmedId) { // display the citation, with link out and delete // button. pubmedRegion = this.getPubMedHtml(e); } else { // offer to create a citation link. pubmedRegion = this.getPubMedForm(e); } /* * Show the experimental design */ DesignMatrix.init({ id : e.id }); var vizPanel = new Gemma.EEDetailsVisualizationWidget({ renderTo : 'visualization', taxon : { commonName : e.parentTaxon, id : e.parentTaxonId } }); /* * This is needed to make the annotator initialize properly. */ new Gemma.MGEDCombo({}); var taggerurl = '<span style="cursor:pointer" onClick="return Ext.getCmp(\'eemanager\').tagger(' + e.id + ',' + e.taxonId + ',' + this.editable + ')"><img src="/Gemma/images/icons/pencil.png" alt="view tags" title="view tags"/></span>'; tagView = new Gemma.AnnotationDataView({ readParams : [{ id : e.id, classDelegatingFor : "ExpressionExperimentImpl" }] }); manager.on('tagsUpdated', function() { tagView.store.reload(); }); manager.on('done', function() { /* * After a process that requires refreshing the page. */ window.location.reload(); }); manager.on('reportUpdated', function(data) { ob = data[0]; var k = Ext.get('coexpressionLinkCount-region'); Ext.DomHelper.overwrite(k, { html : ob.coexpressionLinkCount }); k.highlight(); k = Ext.get('processedExpressionVectorCount-region'); Ext.DomHelper.overwrite(k, { html : ob.processedExpressionVectorCount }); k.highlight(); }); // manager.on('pubmedUpdated', function(e) { // var html = this.getPubMedHtml(e); // Ext.getCmp('pubmed-region-wrap').remove(Ext.getCmp('pubmed-region')); // Ext.DomHelper.append('pubmed-region-wrap', html); // }.createDelegate(this)); // // manager.on('pubmedRemove', function(success) { // if (success) { // var r = Ext.getCmp('pubmed-region-wrap'); // r.remove(Ext.getCmp('pubmed-region')); // var form = this.getPubMedForm(this.eeId); // r.add(form); // r.doLayout(); // } // }.createDelegate(this)); // manager.on('reportUpdated', function() { // // window.location.reload(true); // }); manager.on('differential', function() { window.location.reload(true); }); // manager.on('processedVector', function() { // window.location.reload(true); // }); // manager.on('link', function() { // window.location.reload(true); // }); // // manager.on('missingValue', function() { // window.location.reload(true); // }); var descriptionArea = new Ext.form.TextArea({ id : 'description', allowBlank : true, grow : true, growMax : 300, readOnly : !this.editable, disabledClass : 'disabled-plain', growMin : 40, emptyText : 'No description provided', enableKeyEvents : true, listeners : { 'keyup' : { fn : function(e) { if (Ext.getCmp('description').isDirty() && Ext.getCmp('description').isValid()) { // show save button Ext.getCmp('update-button-region').show(true); } else { Ext.getCmp('update-button-region').hide(true); } } } }, width : 500, // height : 100, value : e.description }); var nameArea = new Ext.form.TextArea({ id : 'name', fieldLabel : 'Name', allowBlank : false, grow : true, growMax : 300, readOnly : !this.editable, disabledClass : 'disabled-plain', growMin : 40, emptyText : 'No description provided', enableKeyEvents : true, listeners : { 'keyup' : { fn : function(e) { if (Ext.getCmp('name').isDirty() && Ext.getCmp('name').isValid()) { // show save button Ext.getCmp('update-button-region').show(true); } else { Ext.getCmp('update-button-region').hide(true); } } } }, width : 500, value : e.name }); var basics = new Ext.Panel({ autoHeight : true, layout : 'table', layoutConfig : { columns : 2 }, renderTo : 'basics', collapsible : false, bodyBorder : false, frame : false, baseCls : 'x-plain-panel', bodyStyle : 'padding:10px', defaults : { bodyStyle : 'vertical-align:top;font-size:12px;color:black', baseCls : 'x-plain-panel', fieldClass : 'x-bare-field' }, items : [{ html : 'Short name:' }, { xtype : 'panel', layout : 'table', baseCls : 'x-plain-panel', layoutConfig : { columns : 2 }, items : [{ xtype : 'textfield', id : 'shortname', enableKeyEvents : true, allowBlank : false, disabledClass : 'disabled-plain', fieldClass : 'x-bare-field', readOnly : !this.editable, listeners : { 'keyup' : { fn : function(e) { if (Ext.getCmp('shortname').isDirty() && Ext.getCmp('shortname').isValid()) { // show // save // button Ext.getCmp('update-button-region').show(true); } else { Ext.getCmp('update-button-region').hide(true); } }, scope : this } }, width : 250, value : e.shortName }, { baseCls : 'x-plain-panel', id : 'update-button-region', html : '<span style="cursor:pointer" onClick="Ext.getCmp(\'ee-details-panel\').save(' + e.id + ',[\'shortname\',\'name\',\'description\'])" ><img src="/Gemma/images/icons/database_save.png" ext:qtip="Click to save changes" alt="Click to save changes"/></span>', hidden : true }] }, { html : 'Name:' }, nameArea, { html : "Taxon:" }, { html : e.taxon }, { html : 'Description:' }, descriptionArea, { html : 'Created:' }, { html : Ext.util.Format.date(e.dateCreated) }, { html : 'Source:' }, { html : this.renderSourceDatabaseEntry(e) }, { html : 'Samples:' }, { html : this.renderSamples(e), width : 60 }, { html : 'Profiles:' }, { id : 'processedExpressionVectorCount-region', html : '<div id="downloads"> ' + this.renderProcessedExpressionVectorCount(e) + ' ' + '<i>Downloads:</i> <span class="link" ext:qtip="Download the tab delimited data" onClick="fetchData(true,' + e.id + ', \'text\', null, null)">Filtered</span> ' + '<span class="link" ext:qtip="Download the tab delimited data" onClick="fetchData(false,' + e.id + ', \'text\', null, null)">Unfiltered</span> ' + '<a class="helpLink" href="?" onclick="showHelpTip(event, \'Tab-delimited data file for this experiment. The filtered version corresponds to what is used in most Gemma analyses, removing some probes. Unfiltered includes all probes\'); return false"> <img src="/Gemma/images/help.png" /> </a>' + '</div>', width : 400 }, { html : 'Array designs:' }, { id : 'arrayDesign-region', html : this.renderArrayDesigns(e.arrayDesigns), width : 480 }, { html : 'Coexpr. Links:' }, { id : 'coexpressionLinkCount-region', html : this.renderCoExpressionLinkCount(e), width : 80 }, { html : 'Diff. expr. Probes' }, { id : 'DiffExpressedProbes-region', html : this.renderDiffExpressionDetails(e), width : 200 }, { html : 'Publication:' }, { xtype : 'panel', id : 'pubmed-region-wrap', layout : 'fit', bodyBorder : false, baseCls : 'x-plain-panel', disabled : false, items : [pubmedRegion] }, { html : 'Tags ' + taggerurl }, tagView, { html : 'Status' }, { html : this.renderStatus(e) }, { html : this.editable ? 'Admin' : '' }, { id : 'admin-links', html : this.editable ? adminLinks : '' } /* * authors */ ] }); if (this.editable) { Ext.DomHelper.append('admin-links', { tag : 'ul', cls : 'plainlist', children : [{ tag : 'li', html : 'Missing values: ' + this.missingValueAnalysisRenderer(e) }, { tag : 'li', html : 'Proc. vec: ' + this.processedVectorCreateRenderer(e) }, { tag : 'li', html : 'Diff ex: ' + this.differentialAnalysisRenderer(e) }, { tag : 'li', html : 'Link an.: ' + this.linkAnalysisRenderer(e) }] }); } if (Ext.get('history')) { var history = new Gemma.AuditTrailGrid({ renderTo : 'history', bodyBorder : false, collapsible : true, auditable : { id : e.id, classDelegatingFor : "ubic.gemma.model.expression.experiment.ExpressionExperimentImpl" } }); } this.fireEvent("ready"); }
|
var taggerurl = '<a href="#" onClick="return Ext.getCmp(\'eemanager\').tagger(' + e.id + ',' + e.taxonId
|
var taggerurl = '<a href="#" onClick="return Ext.getCmp(\'eemanager\').tagger(' + e.id + ',' + e.taxonId+ ',' + this.editable
|
build : function(e) { var manager = new Gemma.EEManager({ editable : this.editable, id : "eemanager" }); this.manager = manager; // // /* // * Create a store with one record. // */ // var store = new Ext.data.Store({ // proxy : new Ext.data.MemoryProxy([e]), // reader : new Ext.data.ListRangeReader({}, // this.manager.record) // }); // // this.rec = store.getAt(0); adminLinks = '<a href="#" onClick="Ext.getCmp(\'eemanager\').updateEEReport(' + e.id + ')"><img src="/Gemma/images/icons/arrow_refresh_small.png" ext:qtip="Refresh statistics" title="refresh"/></a>' + ' <a href="/Gemma/expressionExperiment/editExpressionExperiment.html?id=' + e.id + '" ><img src="/Gemma/images/icons/wrench.png" ext:qtip="Go to editor page for this experiment" title="edit"/></a> '; if (this.isAdmin) { adminLinks = adminLinks + '<a href="#" onClick="return Ext.getCmp(\'eemanager\').deleteExperiment(' + e.id + ')"><img src="/Gemma/images/icons/cross.png" ext:qtip="Delete the experiment from the system" title="delete" /></a> '; } var pubmedRegion = {}; if (e.pubmedId) { // display the citation, with link out and delete // button. pubmedRegion = this.getPubMedHtml(e); } else { // offer to create a citation link. pubmedRegion = this.getPubMedForm(e); } /* * Show the experimental design */ DesignMatrix.init({ id : e.id }); var vizPanel = new Gemma.EEDetailsVisualizationWidget({ renderTo : 'visualization', taxon : e.parentTaxon }); /* * This is needed to make the annotator initialize properly. */ new Gemma.MGEDCombo({}); var taggerurl = '<a href="#" onClick="return Ext.getCmp(\'eemanager\').tagger(' + e.id + ',' + e.taxonId + ')"><img src="/Gemma/images/icons/pencil.png" alt="view tags" title="view tags"/></a>'; tagView = new Gemma.AnnotationDataView({ readParams : [{ id : e.id, classDelegatingFor : "ExpressionExperimentImpl" }] }); manager.on('tagsUpdated', function() { tagView.store.reload(); }); manager.on('done', function() { window.location.reload(); }); manager.on('reportUpdated', function(data) { ob = data[0]; // console.log(ob); var k = Ext.get('coexpressionLinkCount-region'); Ext.DomHelper.overwrite(k, { html : ob.coexpressionLinkCount }); k.highlight(); k = Ext.get('processedExpressionVectorCount-region'); Ext.DomHelper.overwrite(k, { html : ob.processedExpressionVectorCount }); k.highlight(); }); manager.on('pubmedUpdated', function(e) { var html = this.getPubMedHtml(e); Ext.getCmp('pubmed-region-wrap').remove(Ext.getCmp('pubmed-region')); Ext.DomHelper.append('pubmed-region-wrap', html); }.createDelegate(this)); manager.on('pubmedRemove', function(success) { if (success) { var r = Ext.getCmp('pubmed-region-wrap'); r.remove(Ext.getCmp('pubmed-region')); var form = this.getPubMedForm(this.eeId); r.add(form); r.doLayout(); } }.createDelegate(this)); manager.on('updated', function(data) { Ext.getCmp('update-button-region').getEl().hide(); /* * Really we won't need to do this -- as the state on the database is supposed to match this one. */ var k = Ext.getCmp('shortname'); k.setValue(data.shortName); k = Ext.getCmp('name'); k.setValue(data.name); k = Ext.getCmp('description'); k.setValue(data.description); }.createDelegate(this)); // manager.on('reportUpdated', function() { // store.reload(); // }); // // manager.on('differential', function() { // store.reload(); // }); // manager.on('processedVector', function() { // store.reload(); // }); // manager.on('link', function() { // store.reload(); // }); // manager.on('missingValue', function() { // store.reload(); // }); var descriptionArea = new Ext.form.TextArea({ id : 'description', allowBlank : true, grow : true, growMax : 300, readOnly : !this.editable, disabledClass : 'disabled-plain', growMin : 40, emptyText : 'No description provided', enableKeyEvents : true, listeners : { 'keyup' : { fn : function(e) { if (Ext.getCmp('description').isDirty() && Ext.getCmp('description').isValid()) { // show save button Ext.getCmp('update-button-region').show(); } else { Ext.getCmp('update-button-region').hide(); } } } }, width : 500, // height : 100, value : e.description }); var nameArea = new Ext.form.TextArea({ id : 'name', fieldLabel : 'Name', allowBlank : false, grow : true, growMax : 300, readOnly : !this.editable, disabledClass : 'disabled-plain', growMin : 40, emptyText : 'No description provided', enableKeyEvents : true, listeners : { 'keyup' : { fn : function(e) { if (Ext.getCmp('name').isDirty() && Ext.getCmp('name').isValid()) { // show save button Ext.getCmp('update-button-region').show(); } else { Ext.getCmp('update-button-region').hide(); } } } }, width : 500, value : e.name }); var basics = new Ext.Panel({ autoHeight : true, layout : 'table', layoutConfig : { columns : 2 }, renderTo : 'basics', collapsible : false, bodyBorder : false, frame : false, baseCls : 'x-plain-panel', bodyStyle : 'padding:10px', defaults : { bodyStyle : 'vertical-align:top;font-size:12px;color:black', baseCls : 'x-plain-panel', fieldClass : 'x-bare-field' }, items : [{ html : 'Short name:' }, { xtype : 'panel', layout : 'table', baseCls : 'x-plain-panel', layoutConfig : { columns : 2 }, items : [{ xtype : 'textfield', id : 'shortname', enableKeyEvents : true, allowBlank : false, disabledClass : 'disabled-plain', fieldClass : 'x-bare-field', readOnly : !this.editable, listeners : { 'keyup' : { fn : function(e) { if (Ext.getCmp('shortname').isDirty() && Ext.getCmp('shortname').isValid()) { // show // save // button Ext.getCmp('update-button-region').show(); } else { Ext.getCmp('update-button-region').hide(); } }, scope : this } }, width : 250, value : e.shortName }, { baseCls : 'x-plain-panel', id : 'update-button-region', html : '<a href="#" onClick="Ext.getCmp(\'ee-details-panel\').save(' + e.id + ',[\'shortname\',\'name\',\'description\'])" ><img src="/Gemma/images/icons/database_save.png" title="Click to save changes" alt="Click to save changes"/></a>', hidden : true }] }, { html : 'Name:' }, nameArea, { html : "Taxon:" }, { html : e.taxon }, { html : 'Description:' }, descriptionArea, { html : 'Created:' }, { html : Ext.util.Format.date(e.dateCreated) }, { html : 'Source:' }, { html : this.renderSourceDatabaseEntry(e) }, { html : 'Samples:' }, { html : this.renderSamples(e), width : 60 }, { html : 'Profiles:' }, { id : 'processedExpressionVectorCount-region', html : '<div id="downloads"> ' + this.renderProcessedExpressionVectorCount(e) + ' ' + '<i>Downloads:</i> <a title="click to download the tab delimited data" href="#" onClick="fetchData(true,' + e.id + ', \'text\', null, null)">Filtered</a> ' + '<a href="#" title="click to download the tab delimited data" onClick="fetchData(false,' + e.id + ', \'text\', null, null)">Unfiltered</a> ' + '<a class="helpLink" href="?" onclick="showHelpTip(event, \'Tab-delimited data file for this experiment. The filtered version corresponds to what is used in most Gemma analyses, removing some probes. Unfiltered includes all probes\'); return false"> <img src="/Gemma/images/help.png" /> </a>' + '</div>', width : 400 }, { html : 'Array designs:' }, { id : 'arrayDesign-region', html : this.renderArrayDesigns(e.arrayDesigns), width : 480 }, { html : 'Coexpr. Links:' }, { id : 'coexpressionLinkCount-region', html : this.renderCoExpressionLinkCount(e), width : 80 }, { html : 'Diff. expr. Probes' }, { id : 'DiffExpressedProbes-region', html : this.renderDiffExpressionDetails(e), width : 200 }, { html : 'Publication:' }, { xtype : 'panel', id : 'pubmed-region-wrap', layout : 'fit', bodyBorder : false, baseCls : 'x-plain-panel', disabled : false, items : [pubmedRegion] }, { html : 'Tags ' + taggerurl }, tagView, { html : 'Status' }, { html : this.renderStatus(e) }, { html : this.editable ? 'Admin' : '' }, { id : 'admin-links', html : this.editable ? adminLinks : '' } /* * authors */ ] }); if (this.editable) { Ext.DomHelper.append('admin-links', { tag : 'ul', cls : 'plainlist', children : [{ tag : 'li', html : 'Missing values: ' + this.missingValueAnalysisRenderer(e) }, { tag : 'li', html : 'Proc. vec: ' + this.processedVectorCreateRenderer(e) }, { tag : 'li', html : 'Diff ex: ' + this.differentialAnalysisRenderer(e) }, { tag : 'li', html : 'Link an.: ' + this.linkAnalysisRenderer(e) }] }); } if (Ext.get('history')) { var history = new Gemma.AuditTrailGrid({ renderTo : 'history', bodyBorder : false, collapsible : true, auditable : { id : e.id, classDelegatingFor : "ubic.gemma.model.expression.experiment.ExpressionExperimentImpl" } }); } this.fireEvent("ready"); }
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collapsible : true,
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collapsible : false,
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build : function(e) { var manager = new Gemma.EEManager({ editable : this.editable, id : "eemanager" }); this.manager = manager; // // /* // * Create a store with one record. // */ // var store = new Ext.data.Store({ // proxy : new Ext.data.MemoryProxy([e]), // reader : new Ext.data.ListRangeReader({}, // this.manager.record) // }); // // this.rec = store.getAt(0); adminLinks = '<a href="#" onClick="Ext.getCmp(\'eemanager\').updateEEReport(' + e.id + ')"><img src="/Gemma/images/icons/arrow_refresh_small.png" ext:qtip="Refresh statistics" title="refresh"/></a>' + ' <a href="/Gemma/expressionExperiment/editExpressionExperiment.html?id=' + e.id + '" ><img src="/Gemma/images/icons/wrench.png" ext:qtip="Go to editor page for this experiment" title="edit"/></a> '; if (this.isAdmin) { adminLinks = adminLinks + '<a href="#" onClick="return Ext.getCmp(\'eemanager\').deleteExperiment(' + e.id + ')"><img src="/Gemma/images/icons/cross.png" ext:qtip="Delete the experiment from the system" title="delete" /></a> '; } var pubmedRegion = {}; if (e.pubmedId) { // display the citation, with link out and delete // button. pubmedRegion = this.getPubMedHtml(e); } else { // offer to create a citation link. pubmedRegion = this.getPubMedForm(e); } /* * Show the experimental design */ DesignMatrix.init({ id : e.id }); var vizPanel = new Gemma.EEDetailsVisualizationWidget({ renderTo : 'visualization', taxon : e.taxon }); /* * This is needed to make the annotator initialize properly. */ new Gemma.MGEDCombo({}); var taggerurl = '<a href="#" onClick="return Ext.getCmp(\'eemanager\').tagger(' + e.id + ',' + e.taxonId +')"><img src="/Gemma/images/icons/pencil.png" alt="view tags" title="view tags"/></a>'; tagView = new Gemma.AnnotationDataView({ readParams : [{ id : e.id, classDelegatingFor : "ExpressionExperimentImpl" }] }); manager.on('tagsUpdated', function() { tagView.store.reload(); }); manager.on('done', function() { window.location.reload(); }); manager.on('reportUpdated', function(data) { ob = data[0]; // console.log(ob); var k = Ext.get('coexpressionLinkCount-region'); Ext.DomHelper.overwrite(k, { html : ob.coexpressionLinkCount }); k.highlight(); k = Ext.get('processedExpressionVectorCount-region'); Ext.DomHelper.overwrite(k, { html : ob.processedExpressionVectorCount }); k.highlight(); }); manager.on('pubmedUpdated', function(e) { var html = this.getPubMedHtml(e); Ext.getCmp('pubmed-region-wrap').remove(Ext.getCmp('pubmed-region')); Ext.DomHelper.append('pubmed-region-wrap', html); }.createDelegate(this)); manager.on('pubmedRemove', function(success) { if (success) { var r = Ext.getCmp('pubmed-region-wrap'); r.remove(Ext.getCmp('pubmed-region')); var form = this.getPubMedForm(this.eeId); r.add(form); r.doLayout(); } }.createDelegate(this)); manager.on('updated', function(data) { Ext.getCmp('update-button-region').getEl().hide(); /* * Really we won't need to do this -- as the state on the database is supposed to match this one. */ var k = Ext.getCmp('shortname'); k.setValue(data.shortName); k = Ext.getCmp('name'); k.setValue(data.name); k = Ext.getCmp('description'); k.setValue(data.description); }.createDelegate(this)); // manager.on('reportUpdated', function() { // store.reload(); // }); // // manager.on('differential', function() { // store.reload(); // }); // manager.on('processedVector', function() { // store.reload(); // }); // manager.on('link', function() { // store.reload(); // }); // manager.on('missingValue', function() { // store.reload(); // }); var descriptionArea = new Ext.form.TextArea({ id : 'description', allowBlank : true, grow : true, growMax : 300, readOnly : !this.editable, disabledClass : 'disabled-plain', growMin : 40, emptyText : 'No description provided', enableKeyEvents : true, listeners : { 'keyup' : { fn : function(e) { if (Ext.getCmp('description').isDirty() && Ext.getCmp('description').isValid()) { // show save button Ext.getCmp('update-button-region').show(); } else { Ext.getCmp('update-button-region').hide(); } } } }, width : 500, // height : 100, value : e.description }); var nameArea = new Ext.form.TextArea({ id : 'name', fieldLabel : 'Name', allowBlank : false, grow : true, growMax : 300, readOnly : !this.editable, disabledClass : 'disabled-plain', growMin : 40, emptyText : 'No description provided', enableKeyEvents : true, listeners : { 'keyup' : { fn : function(e) { if (Ext.getCmp('name').isDirty() && Ext.getCmp('name').isValid()) { // show save button Ext.getCmp('update-button-region').show(); } else { Ext.getCmp('update-button-region').hide(); } } } }, width : 500, value : e.name }); var basics = new Ext.Panel({ autoHeight : true, layout : 'table', layoutConfig : { columns : 2 }, renderTo : 'basics', collapsible : true, bodyBorder : false, frame : false, baseCls : 'x-plain-panel', bodyStyle : 'padding:10px', defaults : { bodyStyle : 'vertical-align:top;font-size:12px;color:black', baseCls : 'x-plain-panel', fieldClass : 'x-bare-field' }, items : [{ html : 'Short name:' }, { xtype : 'panel', layout : 'table', baseCls : 'x-plain-panel', layoutConfig : { columns : 2 }, items : [{ xtype : 'textfield', id : 'shortname', enableKeyEvents : true, allowBlank : false, disabledClass : 'disabled-plain', fieldClass : 'x-bare-field', readOnly : !this.editable, listeners : { 'keyup' : { fn : function(e) { if (Ext.getCmp('shortname').isDirty() && Ext.getCmp('shortname').isValid()) { // show // save // button Ext.getCmp('update-button-region').show(); } else { Ext.getCmp('update-button-region').hide(); } }, scope : this } }, width : 250, value : e.shortName }, { baseCls : 'x-plain-panel', id : 'update-button-region', html : '<a href="#" onClick="Ext.getCmp(\'ee-details-panel\').save(' + e.id + ',[\'shortname\',\'name\',\'description\'])" ><img src="/Gemma/images/icons/database_save.png" title="Click to save changes" alt="Click to save changes"/></a>', hidden : true }] }, { html : 'Name:' }, nameArea, { html : "Taxon:" }, { html : e.taxon }, { html : 'Description:' }, descriptionArea, { html : 'Created:' }, { html : Ext.util.Format.date(e.dateCreated) }, { html : 'Source:' }, { html : this.renderSourceDatabaseEntry(e) }, { html : 'Samples:' }, { html : this.renderSamples(e), width : 60 }, { html : 'Profiles:' }, { id : 'processedExpressionVectorCount-region', html : e.processedExpressionVectorCount, width : 60 }, { html : 'Array designs:' }, { id : 'arrayDesign-region', html : this.renderArrayDesigns(e.arrayDesigns), width : 480 }, { html : 'Coexpr. Links:' }, { id : 'coexpressionLinkCount-region', html : this.renderCoExpressionLinkCount(e), width : 80 }, { html : 'Diff. expr. Probes' }, { id : 'DiffExpressedProbes-region', html : this.renderDiffExpressionDetails(e), width : 200 }, { html : 'Publication:' }, { xtype : 'panel', id : 'pubmed-region-wrap', layout : 'fit', bodyBorder : false, baseCls : 'x-plain-panel', disabled : false, items : [pubmedRegion] }, { html : 'Tags ' + taggerurl }, tagView, { html : 'Status' }, { html : this.renderStatus(e) }, { html : this.editable ? 'Admin' : '' }, { id : 'admin-links', html : this.editable ? adminLinks : '' } /* * authors */ ] }); if (this.editable) { Ext.DomHelper.append('admin-links', { tag : 'ul', cls : 'plainlist', children : [{ tag : 'li', html : 'Missing values: ' + this.missingValueAnalysisRenderer(e) }, { tag : 'li', html : 'Proc. vec: ' + this.processedVectorCreateRenderer(e) }, { tag : 'li', html : 'Diff ex: ' + this.differentialAnalysisRenderer(e) }, { tag : 'li', html : 'Link an.: ' + this.linkAnalysisRenderer(e) }] }); } if (Ext.get('history')) { var history = new Gemma.AuditTrailGrid({ renderTo : 'history', bodyBorder : false, collapsible : true, auditable : { id : e.id, classDelegatingFor : "ubic.gemma.model.expression.experiment.ExpressionExperimentImpl" } }); } this.fireEvent("ready"); }
|
html : e.processedExpressionVectorCount, width : 60
|
html : '<div id="downloads"> ' + e.processedExpressionVectorCount + ' <a title="click to download the tab delimited data" href="#" onClick="fetchData(true,' + e.id + ', \'text\', null, null)">Filtered</a> ' + '<a href="#" title="click to download the tab delimited data" onClick="fetchData(false,' + e.id + ', \'text\', null, null)">Unfiltered</a> ' + '<a class="helpLink" href="?" onclick="showHelpTip(event, \'Tab-delimited data file for this experiment. The filtered version corresponds to what is used in most Gemma analyses, removing some probes. Unfiltered includes all probes\'); return false"> <img src="/Gemma/images/help.png" /> </a>' + '</div>', width : 200
|
build : function(e) { var manager = new Gemma.EEManager({ editable : this.editable, id : "eemanager" }); this.manager = manager; // // /* // * Create a store with one record. // */ // var store = new Ext.data.Store({ // proxy : new Ext.data.MemoryProxy([e]), // reader : new Ext.data.ListRangeReader({}, // this.manager.record) // }); // // this.rec = store.getAt(0); adminLinks = '<a href="#" onClick="Ext.getCmp(\'eemanager\').updateEEReport(' + e.id + ')"><img src="/Gemma/images/icons/arrow_refresh_small.png" ext:qtip="Refresh statistics" title="refresh"/></a>' + ' <a href="/Gemma/expressionExperiment/editExpressionExperiment.html?id=' + e.id + '" ><img src="/Gemma/images/icons/wrench.png" ext:qtip="Go to editor page for this experiment" title="edit"/></a> '; if (this.isAdmin) { adminLinks = adminLinks + '<a href="#" onClick="return Ext.getCmp(\'eemanager\').deleteExperiment(' + e.id + ')"><img src="/Gemma/images/icons/cross.png" ext:qtip="Delete the experiment from the system" title="delete" /></a> '; } var pubmedRegion = {}; if (e.pubmedId) { // display the citation, with link out and delete // button. pubmedRegion = this.getPubMedHtml(e); } else { // offer to create a citation link. pubmedRegion = this.getPubMedForm(e); } /* * Show the experimental design */ DesignMatrix.init({ id : e.id }); var vizPanel = new Gemma.EEDetailsVisualizationWidget({ renderTo : 'visualization', taxon : e.taxon }); /* * This is needed to make the annotator initialize properly. */ new Gemma.MGEDCombo({}); var taggerurl = '<a href="#" onClick="return Ext.getCmp(\'eemanager\').tagger(' + e.id + ',' + e.taxonId +')"><img src="/Gemma/images/icons/pencil.png" alt="view tags" title="view tags"/></a>'; tagView = new Gemma.AnnotationDataView({ readParams : [{ id : e.id, classDelegatingFor : "ExpressionExperimentImpl" }] }); manager.on('tagsUpdated', function() { tagView.store.reload(); }); manager.on('done', function() { window.location.reload(); }); manager.on('reportUpdated', function(data) { ob = data[0]; // console.log(ob); var k = Ext.get('coexpressionLinkCount-region'); Ext.DomHelper.overwrite(k, { html : ob.coexpressionLinkCount }); k.highlight(); k = Ext.get('processedExpressionVectorCount-region'); Ext.DomHelper.overwrite(k, { html : ob.processedExpressionVectorCount }); k.highlight(); }); manager.on('pubmedUpdated', function(e) { var html = this.getPubMedHtml(e); Ext.getCmp('pubmed-region-wrap').remove(Ext.getCmp('pubmed-region')); Ext.DomHelper.append('pubmed-region-wrap', html); }.createDelegate(this)); manager.on('pubmedRemove', function(success) { if (success) { var r = Ext.getCmp('pubmed-region-wrap'); r.remove(Ext.getCmp('pubmed-region')); var form = this.getPubMedForm(this.eeId); r.add(form); r.doLayout(); } }.createDelegate(this)); manager.on('updated', function(data) { Ext.getCmp('update-button-region').getEl().hide(); /* * Really we won't need to do this -- as the state on the database is supposed to match this one. */ var k = Ext.getCmp('shortname'); k.setValue(data.shortName); k = Ext.getCmp('name'); k.setValue(data.name); k = Ext.getCmp('description'); k.setValue(data.description); }.createDelegate(this)); // manager.on('reportUpdated', function() { // store.reload(); // }); // // manager.on('differential', function() { // store.reload(); // }); // manager.on('processedVector', function() { // store.reload(); // }); // manager.on('link', function() { // store.reload(); // }); // manager.on('missingValue', function() { // store.reload(); // }); var descriptionArea = new Ext.form.TextArea({ id : 'description', allowBlank : true, grow : true, growMax : 300, readOnly : !this.editable, disabledClass : 'disabled-plain', growMin : 40, emptyText : 'No description provided', enableKeyEvents : true, listeners : { 'keyup' : { fn : function(e) { if (Ext.getCmp('description').isDirty() && Ext.getCmp('description').isValid()) { // show save button Ext.getCmp('update-button-region').show(); } else { Ext.getCmp('update-button-region').hide(); } } } }, width : 500, // height : 100, value : e.description }); var nameArea = new Ext.form.TextArea({ id : 'name', fieldLabel : 'Name', allowBlank : false, grow : true, growMax : 300, readOnly : !this.editable, disabledClass : 'disabled-plain', growMin : 40, emptyText : 'No description provided', enableKeyEvents : true, listeners : { 'keyup' : { fn : function(e) { if (Ext.getCmp('name').isDirty() && Ext.getCmp('name').isValid()) { // show save button Ext.getCmp('update-button-region').show(); } else { Ext.getCmp('update-button-region').hide(); } } } }, width : 500, value : e.name }); var basics = new Ext.Panel({ autoHeight : true, layout : 'table', layoutConfig : { columns : 2 }, renderTo : 'basics', collapsible : false, bodyBorder : false, frame : false, baseCls : 'x-plain-panel', bodyStyle : 'padding:10px', defaults : { bodyStyle : 'vertical-align:top;font-size:12px;color:black', baseCls : 'x-plain-panel', fieldClass : 'x-bare-field' }, items : [{ html : 'Short name:' }, { xtype : 'panel', layout : 'table', baseCls : 'x-plain-panel', layoutConfig : { columns : 2 }, items : [{ xtype : 'textfield', id : 'shortname', enableKeyEvents : true, allowBlank : false, disabledClass : 'disabled-plain', fieldClass : 'x-bare-field', readOnly : !this.editable, listeners : { 'keyup' : { fn : function(e) { if (Ext.getCmp('shortname').isDirty() && Ext.getCmp('shortname').isValid()) { // show // save // button Ext.getCmp('update-button-region').show(); } else { Ext.getCmp('update-button-region').hide(); } }, scope : this } }, width : 250, value : e.shortName }, { baseCls : 'x-plain-panel', id : 'update-button-region', html : '<a href="#" onClick="Ext.getCmp(\'ee-details-panel\').save(' + e.id + ',[\'shortname\',\'name\',\'description\'])" ><img src="/Gemma/images/icons/database_save.png" title="Click to save changes" alt="Click to save changes"/></a>', hidden : true }] }, { html : 'Name:' }, nameArea, { html : "Taxon:" }, { html : e.taxon }, { html : 'Description:' }, descriptionArea, { html : 'Created:' }, { html : Ext.util.Format.date(e.dateCreated) }, { html : 'Source:' }, { html : this.renderSourceDatabaseEntry(e) }, { html : 'Samples:' }, { html : this.renderSamples(e), width : 60 }, { html : 'Profiles:' }, { id : 'processedExpressionVectorCount-region', html : e.processedExpressionVectorCount, width : 60 }, { html : 'Array designs:' }, { id : 'arrayDesign-region', html : this.renderArrayDesigns(e.arrayDesigns), width : 480 }, { html : 'Coexpr. Links:' }, { id : 'coexpressionLinkCount-region', html : this.renderCoExpressionLinkCount(e), width : 80 }, { html : 'Diff. expr. Probes' }, { id : 'DiffExpressedProbes-region', html : this.renderDiffExpressionDetails(e), width : 200 }, { html : 'Publication:' }, { xtype : 'panel', id : 'pubmed-region-wrap', layout : 'fit', bodyBorder : false, baseCls : 'x-plain-panel', disabled : false, items : [pubmedRegion] }, { html : 'Tags ' + taggerurl }, tagView, { html : 'Status' }, { html : this.renderStatus(e) }, { html : this.editable ? 'Admin' : '' }, { id : 'admin-links', html : this.editable ? adminLinks : '' } /* * authors */ ] }); if (this.editable) { Ext.DomHelper.append('admin-links', { tag : 'ul', cls : 'plainlist', children : [{ tag : 'li', html : 'Missing values: ' + this.missingValueAnalysisRenderer(e) }, { tag : 'li', html : 'Proc. vec: ' + this.processedVectorCreateRenderer(e) }, { tag : 'li', html : 'Diff ex: ' + this.differentialAnalysisRenderer(e) }, { tag : 'li', html : 'Link an.: ' + this.linkAnalysisRenderer(e) }] }); } if (Ext.get('history')) { var history = new Gemma.AuditTrailGrid({ renderTo : 'history', bodyBorder : false, collapsible : true, auditable : { id : e.id, classDelegatingFor : "ubic.gemma.model.expression.experiment.ExpressionExperimentImpl" } }); } this.fireEvent("ready"); }
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adminLinks = '<a href="#" onClick="Ext.getCmp(\'eemanager\').updateEEReport(' +
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adminLinks = '<span style="cursor:pointer" onClick="Ext.getCmp(\'eemanager\').updateEEReport(' +
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build : function(e) { var manager = new Gemma.EEManager({ editable : this.editable, id : "eemanager" }); this.manager = manager; // // /* // * Create a store with one record. // */ // var store = new Ext.data.Store({ // proxy : new Ext.data.MemoryProxy([e]), // reader : new Ext.data.ListRangeReader({}, // this.manager.record) // }); // // this.rec = store.getAt(0); adminLinks = '<a href="#" onClick="Ext.getCmp(\'eemanager\').updateEEReport(' + e.id + ')"><img src="/Gemma/images/icons/arrow_refresh_small.png" ext:qtip="Refresh statistics" title="refresh"/></a>' + ' <a href="/Gemma/expressionExperiment/editExpressionExperiment.html?id=' + e.id + '" ><img src="/Gemma/images/icons/wrench.png" ext:qtip="Go to editor page for this experiment" title="edit"/></a> '; if (this.isAdmin) { adminLinks = adminLinks + '<a href="#" onClick="return Ext.getCmp(\'eemanager\').deleteExperiment(' + e.id + ')"><img src="/Gemma/images/icons/cross.png" ext:qtip="Delete the experiment from the system" title="delete" /></a> '; } var pubmedRegion = {}; if (e.pubmedId) { // display the citation, with link out and delete // button. pubmedRegion = this.getPubMedHtml(e); } else { // offer to create a citation link. pubmedRegion = this.getPubMedForm(e); } /* * Show the experimental design */ DesignMatrix.init({ id : e.id }); var vizPanel = new Gemma.EEDetailsVisualizationWidget({ renderTo : 'visualization', taxon : e.parentTaxon }); /* * This is needed to make the annotator initialize properly. */ new Gemma.MGEDCombo({}); var taggerurl = '<a href="#" onClick="return Ext.getCmp(\'eemanager\').tagger(' + e.id + ',' + e.taxonId + ',' + this.editable + ')"><img src="/Gemma/images/icons/pencil.png" alt="view tags" title="view tags"/></a>'; tagView = new Gemma.AnnotationDataView({ readParams : [{ id : e.id, classDelegatingFor : "ExpressionExperimentImpl" }] }); manager.on('tagsUpdated', function() { tagView.store.reload(); }); manager.on('done', function() { window.location.reload(); }); manager.on('reportUpdated', function(data) { ob = data[0]; // console.log(ob); var k = Ext.get('coexpressionLinkCount-region'); Ext.DomHelper.overwrite(k, { html : ob.coexpressionLinkCount }); k.highlight(); k = Ext.get('processedExpressionVectorCount-region'); Ext.DomHelper.overwrite(k, { html : ob.processedExpressionVectorCount }); k.highlight(); }); manager.on('pubmedUpdated', function(e) { var html = this.getPubMedHtml(e); Ext.getCmp('pubmed-region-wrap').remove(Ext.getCmp('pubmed-region')); Ext.DomHelper.append('pubmed-region-wrap', html); }.createDelegate(this)); manager.on('pubmedRemove', function(success) { if (success) { var r = Ext.getCmp('pubmed-region-wrap'); r.remove(Ext.getCmp('pubmed-region')); var form = this.getPubMedForm(this.eeId); r.add(form); r.doLayout(); } }.createDelegate(this)); manager.on('updated', function(data) { Ext.getCmp('update-button-region').getEl().hide(); /* * Really we won't need to do this -- as the state on the database is supposed to match this one. */ var k = Ext.getCmp('shortname'); k.setValue(data.shortName); k = Ext.getCmp('name'); k.setValue(data.name); k = Ext.getCmp('description'); k.setValue(data.description); }.createDelegate(this)); // manager.on('reportUpdated', function() { // store.reload(); // }); // // manager.on('differential', function() { // store.reload(); // }); // manager.on('processedVector', function() { // store.reload(); // }); // manager.on('link', function() { // store.reload(); // }); // manager.on('missingValue', function() { // store.reload(); // }); var descriptionArea = new Ext.form.TextArea({ id : 'description', allowBlank : true, grow : true, growMax : 300, readOnly : !this.editable, disabledClass : 'disabled-plain', growMin : 40, emptyText : 'No description provided', enableKeyEvents : true, listeners : { 'keyup' : { fn : function(e) { if (Ext.getCmp('description').isDirty() && Ext.getCmp('description').isValid()) { // show save button Ext.getCmp('update-button-region').show(); } else { Ext.getCmp('update-button-region').hide(); } } } }, width : 500, // height : 100, value : e.description }); var nameArea = new Ext.form.TextArea({ id : 'name', fieldLabel : 'Name', allowBlank : false, grow : true, growMax : 300, readOnly : !this.editable, disabledClass : 'disabled-plain', growMin : 40, emptyText : 'No description provided', enableKeyEvents : true, listeners : { 'keyup' : { fn : function(e) { if (Ext.getCmp('name').isDirty() && Ext.getCmp('name').isValid()) { // show save button Ext.getCmp('update-button-region').show(); } else { Ext.getCmp('update-button-region').hide(); } } } }, width : 500, value : e.name }); var basics = new Ext.Panel({ autoHeight : true, layout : 'table', layoutConfig : { columns : 2 }, renderTo : 'basics', collapsible : false, bodyBorder : false, frame : false, baseCls : 'x-plain-panel', bodyStyle : 'padding:10px', defaults : { bodyStyle : 'vertical-align:top;font-size:12px;color:black', baseCls : 'x-plain-panel', fieldClass : 'x-bare-field' }, items : [{ html : 'Short name:' }, { xtype : 'panel', layout : 'table', baseCls : 'x-plain-panel', layoutConfig : { columns : 2 }, items : [{ xtype : 'textfield', id : 'shortname', enableKeyEvents : true, allowBlank : false, disabledClass : 'disabled-plain', fieldClass : 'x-bare-field', readOnly : !this.editable, listeners : { 'keyup' : { fn : function(e) { if (Ext.getCmp('shortname').isDirty() && Ext.getCmp('shortname').isValid()) { // show // save // button Ext.getCmp('update-button-region').show(); } else { Ext.getCmp('update-button-region').hide(); } }, scope : this } }, width : 250, value : e.shortName }, { baseCls : 'x-plain-panel', id : 'update-button-region', html : '<a href="#" onClick="Ext.getCmp(\'ee-details-panel\').save(' + e.id + ',[\'shortname\',\'name\',\'description\'])" ><img src="/Gemma/images/icons/database_save.png" title="Click to save changes" alt="Click to save changes"/></a>', hidden : true }] }, { html : 'Name:' }, nameArea, { html : "Taxon:" }, { html : e.taxon }, { html : 'Description:' }, descriptionArea, { html : 'Created:' }, { html : Ext.util.Format.date(e.dateCreated) }, { html : 'Source:' }, { html : this.renderSourceDatabaseEntry(e) }, { html : 'Samples:' }, { html : this.renderSamples(e), width : 60 }, { html : 'Profiles:' }, { id : 'processedExpressionVectorCount-region', html : '<div id="downloads"> ' + this.renderProcessedExpressionVectorCount(e) + ' ' + '<i>Downloads:</i> <a title="click to download the tab delimited data" href="#" onClick="fetchData(true,' + e.id + ', \'text\', null, null)">Filtered</a> ' + '<a href="#" title="click to download the tab delimited data" onClick="fetchData(false,' + e.id + ', \'text\', null, null)">Unfiltered</a> ' + '<a class="helpLink" href="?" onclick="showHelpTip(event, \'Tab-delimited data file for this experiment. The filtered version corresponds to what is used in most Gemma analyses, removing some probes. Unfiltered includes all probes\'); return false"> <img src="/Gemma/images/help.png" /> </a>' + '</div>', width : 400 }, { html : 'Array designs:' }, { id : 'arrayDesign-region', html : this.renderArrayDesigns(e.arrayDesigns), width : 480 }, { html : 'Coexpr. Links:' }, { id : 'coexpressionLinkCount-region', html : this.renderCoExpressionLinkCount(e), width : 80 }, { html : 'Diff. expr. Probes' }, { id : 'DiffExpressedProbes-region', html : this.renderDiffExpressionDetails(e), width : 200 }, { html : 'Publication:' }, { xtype : 'panel', id : 'pubmed-region-wrap', layout : 'fit', bodyBorder : false, baseCls : 'x-plain-panel', disabled : false, items : [pubmedRegion] }, { html : 'Tags ' + taggerurl }, tagView, { html : 'Status' }, { html : this.renderStatus(e) }, { html : this.editable ? 'Admin' : '' }, { id : 'admin-links', html : this.editable ? adminLinks : '' } /* * authors */ ] }); if (this.editable) { Ext.DomHelper.append('admin-links', { tag : 'ul', cls : 'plainlist', children : [{ tag : 'li', html : 'Missing values: ' + this.missingValueAnalysisRenderer(e) }, { tag : 'li', html : 'Proc. vec: ' + this.processedVectorCreateRenderer(e) }, { tag : 'li', html : 'Diff ex: ' + this.differentialAnalysisRenderer(e) }, { tag : 'li', html : 'Link an.: ' + this.linkAnalysisRenderer(e) }] }); } if (Ext.get('history')) { var history = new Gemma.AuditTrailGrid({ renderTo : 'history', bodyBorder : false, collapsible : true, auditable : { id : e.id, classDelegatingFor : "ubic.gemma.model.expression.experiment.ExpressionExperimentImpl" } }); } this.fireEvent("ready"); }
|
')"><img src="/Gemma/images/icons/arrow_refresh_small.png" ext:qtip="Refresh statistics" title="refresh"/></a>' +
|
',\'admin-links\'' + ')"><img src="/Gemma/images/icons/arrow_refresh_small.png" ext:qtip="Refresh statistics" title="refresh"/></span>' +
|
build : function(e) { var manager = new Gemma.EEManager({ editable : this.editable, id : "eemanager" }); this.manager = manager; // // /* // * Create a store with one record. // */ // var store = new Ext.data.Store({ // proxy : new Ext.data.MemoryProxy([e]), // reader : new Ext.data.ListRangeReader({}, // this.manager.record) // }); // // this.rec = store.getAt(0); adminLinks = '<a href="#" onClick="Ext.getCmp(\'eemanager\').updateEEReport(' + e.id + ')"><img src="/Gemma/images/icons/arrow_refresh_small.png" ext:qtip="Refresh statistics" title="refresh"/></a>' + ' <a href="/Gemma/expressionExperiment/editExpressionExperiment.html?id=' + e.id + '" ><img src="/Gemma/images/icons/wrench.png" ext:qtip="Go to editor page for this experiment" title="edit"/></a> '; if (this.isAdmin) { adminLinks = adminLinks + '<a href="#" onClick="return Ext.getCmp(\'eemanager\').deleteExperiment(' + e.id + ')"><img src="/Gemma/images/icons/cross.png" ext:qtip="Delete the experiment from the system" title="delete" /></a> '; } var pubmedRegion = {}; if (e.pubmedId) { // display the citation, with link out and delete // button. pubmedRegion = this.getPubMedHtml(e); } else { // offer to create a citation link. pubmedRegion = this.getPubMedForm(e); } /* * Show the experimental design */ DesignMatrix.init({ id : e.id }); var vizPanel = new Gemma.EEDetailsVisualizationWidget({ renderTo : 'visualization', taxon : e.parentTaxon }); /* * This is needed to make the annotator initialize properly. */ new Gemma.MGEDCombo({}); var taggerurl = '<a href="#" onClick="return Ext.getCmp(\'eemanager\').tagger(' + e.id + ',' + e.taxonId + ',' + this.editable + ')"><img src="/Gemma/images/icons/pencil.png" alt="view tags" title="view tags"/></a>'; tagView = new Gemma.AnnotationDataView({ readParams : [{ id : e.id, classDelegatingFor : "ExpressionExperimentImpl" }] }); manager.on('tagsUpdated', function() { tagView.store.reload(); }); manager.on('done', function() { window.location.reload(); }); manager.on('reportUpdated', function(data) { ob = data[0]; // console.log(ob); var k = Ext.get('coexpressionLinkCount-region'); Ext.DomHelper.overwrite(k, { html : ob.coexpressionLinkCount }); k.highlight(); k = Ext.get('processedExpressionVectorCount-region'); Ext.DomHelper.overwrite(k, { html : ob.processedExpressionVectorCount }); k.highlight(); }); manager.on('pubmedUpdated', function(e) { var html = this.getPubMedHtml(e); Ext.getCmp('pubmed-region-wrap').remove(Ext.getCmp('pubmed-region')); Ext.DomHelper.append('pubmed-region-wrap', html); }.createDelegate(this)); manager.on('pubmedRemove', function(success) { if (success) { var r = Ext.getCmp('pubmed-region-wrap'); r.remove(Ext.getCmp('pubmed-region')); var form = this.getPubMedForm(this.eeId); r.add(form); r.doLayout(); } }.createDelegate(this)); manager.on('updated', function(data) { Ext.getCmp('update-button-region').getEl().hide(); /* * Really we won't need to do this -- as the state on the database is supposed to match this one. */ var k = Ext.getCmp('shortname'); k.setValue(data.shortName); k = Ext.getCmp('name'); k.setValue(data.name); k = Ext.getCmp('description'); k.setValue(data.description); }.createDelegate(this)); // manager.on('reportUpdated', function() { // store.reload(); // }); // // manager.on('differential', function() { // store.reload(); // }); // manager.on('processedVector', function() { // store.reload(); // }); // manager.on('link', function() { // store.reload(); // }); // manager.on('missingValue', function() { // store.reload(); // }); var descriptionArea = new Ext.form.TextArea({ id : 'description', allowBlank : true, grow : true, growMax : 300, readOnly : !this.editable, disabledClass : 'disabled-plain', growMin : 40, emptyText : 'No description provided', enableKeyEvents : true, listeners : { 'keyup' : { fn : function(e) { if (Ext.getCmp('description').isDirty() && Ext.getCmp('description').isValid()) { // show save button Ext.getCmp('update-button-region').show(); } else { Ext.getCmp('update-button-region').hide(); } } } }, width : 500, // height : 100, value : e.description }); var nameArea = new Ext.form.TextArea({ id : 'name', fieldLabel : 'Name', allowBlank : false, grow : true, growMax : 300, readOnly : !this.editable, disabledClass : 'disabled-plain', growMin : 40, emptyText : 'No description provided', enableKeyEvents : true, listeners : { 'keyup' : { fn : function(e) { if (Ext.getCmp('name').isDirty() && Ext.getCmp('name').isValid()) { // show save button Ext.getCmp('update-button-region').show(); } else { Ext.getCmp('update-button-region').hide(); } } } }, width : 500, value : e.name }); var basics = new Ext.Panel({ autoHeight : true, layout : 'table', layoutConfig : { columns : 2 }, renderTo : 'basics', collapsible : false, bodyBorder : false, frame : false, baseCls : 'x-plain-panel', bodyStyle : 'padding:10px', defaults : { bodyStyle : 'vertical-align:top;font-size:12px;color:black', baseCls : 'x-plain-panel', fieldClass : 'x-bare-field' }, items : [{ html : 'Short name:' }, { xtype : 'panel', layout : 'table', baseCls : 'x-plain-panel', layoutConfig : { columns : 2 }, items : [{ xtype : 'textfield', id : 'shortname', enableKeyEvents : true, allowBlank : false, disabledClass : 'disabled-plain', fieldClass : 'x-bare-field', readOnly : !this.editable, listeners : { 'keyup' : { fn : function(e) { if (Ext.getCmp('shortname').isDirty() && Ext.getCmp('shortname').isValid()) { // show // save // button Ext.getCmp('update-button-region').show(); } else { Ext.getCmp('update-button-region').hide(); } }, scope : this } }, width : 250, value : e.shortName }, { baseCls : 'x-plain-panel', id : 'update-button-region', html : '<a href="#" onClick="Ext.getCmp(\'ee-details-panel\').save(' + e.id + ',[\'shortname\',\'name\',\'description\'])" ><img src="/Gemma/images/icons/database_save.png" title="Click to save changes" alt="Click to save changes"/></a>', hidden : true }] }, { html : 'Name:' }, nameArea, { html : "Taxon:" }, { html : e.taxon }, { html : 'Description:' }, descriptionArea, { html : 'Created:' }, { html : Ext.util.Format.date(e.dateCreated) }, { html : 'Source:' }, { html : this.renderSourceDatabaseEntry(e) }, { html : 'Samples:' }, { html : this.renderSamples(e), width : 60 }, { html : 'Profiles:' }, { id : 'processedExpressionVectorCount-region', html : '<div id="downloads"> ' + this.renderProcessedExpressionVectorCount(e) + ' ' + '<i>Downloads:</i> <a title="click to download the tab delimited data" href="#" onClick="fetchData(true,' + e.id + ', \'text\', null, null)">Filtered</a> ' + '<a href="#" title="click to download the tab delimited data" onClick="fetchData(false,' + e.id + ', \'text\', null, null)">Unfiltered</a> ' + '<a class="helpLink" href="?" onclick="showHelpTip(event, \'Tab-delimited data file for this experiment. The filtered version corresponds to what is used in most Gemma analyses, removing some probes. Unfiltered includes all probes\'); return false"> <img src="/Gemma/images/help.png" /> </a>' + '</div>', width : 400 }, { html : 'Array designs:' }, { id : 'arrayDesign-region', html : this.renderArrayDesigns(e.arrayDesigns), width : 480 }, { html : 'Coexpr. Links:' }, { id : 'coexpressionLinkCount-region', html : this.renderCoExpressionLinkCount(e), width : 80 }, { html : 'Diff. expr. Probes' }, { id : 'DiffExpressedProbes-region', html : this.renderDiffExpressionDetails(e), width : 200 }, { html : 'Publication:' }, { xtype : 'panel', id : 'pubmed-region-wrap', layout : 'fit', bodyBorder : false, baseCls : 'x-plain-panel', disabled : false, items : [pubmedRegion] }, { html : 'Tags ' + taggerurl }, tagView, { html : 'Status' }, { html : this.renderStatus(e) }, { html : this.editable ? 'Admin' : '' }, { id : 'admin-links', html : this.editable ? adminLinks : '' } /* * authors */ ] }); if (this.editable) { Ext.DomHelper.append('admin-links', { tag : 'ul', cls : 'plainlist', children : [{ tag : 'li', html : 'Missing values: ' + this.missingValueAnalysisRenderer(e) }, { tag : 'li', html : 'Proc. vec: ' + this.processedVectorCreateRenderer(e) }, { tag : 'li', html : 'Diff ex: ' + this.differentialAnalysisRenderer(e) }, { tag : 'li', html : 'Link an.: ' + this.linkAnalysisRenderer(e) }] }); } if (Ext.get('history')) { var history = new Gemma.AuditTrailGrid({ renderTo : 'history', bodyBorder : false, collapsible : true, auditable : { id : e.id, classDelegatingFor : "ubic.gemma.model.expression.experiment.ExpressionExperimentImpl" } }); } this.fireEvent("ready"); }
|
'" ><img src="/Gemma/images/icons/wrench.png" ext:qtip="Go to editor page for this experiment" title="edit"/></a> ';
|
'" ><img src="/Gemma/images/icons/wrench.png" ext:qtip="Go to editor page for this experiment" title="edit"/></span> ';
|
build : function(e) { var manager = new Gemma.EEManager({ editable : this.editable, id : "eemanager" }); this.manager = manager; // // /* // * Create a store with one record. // */ // var store = new Ext.data.Store({ // proxy : new Ext.data.MemoryProxy([e]), // reader : new Ext.data.ListRangeReader({}, // this.manager.record) // }); // // this.rec = store.getAt(0); adminLinks = '<a href="#" onClick="Ext.getCmp(\'eemanager\').updateEEReport(' + e.id + ')"><img src="/Gemma/images/icons/arrow_refresh_small.png" ext:qtip="Refresh statistics" title="refresh"/></a>' + ' <a href="/Gemma/expressionExperiment/editExpressionExperiment.html?id=' + e.id + '" ><img src="/Gemma/images/icons/wrench.png" ext:qtip="Go to editor page for this experiment" title="edit"/></a> '; if (this.isAdmin) { adminLinks = adminLinks + '<a href="#" onClick="return Ext.getCmp(\'eemanager\').deleteExperiment(' + e.id + ')"><img src="/Gemma/images/icons/cross.png" ext:qtip="Delete the experiment from the system" title="delete" /></a> '; } var pubmedRegion = {}; if (e.pubmedId) { // display the citation, with link out and delete // button. pubmedRegion = this.getPubMedHtml(e); } else { // offer to create a citation link. pubmedRegion = this.getPubMedForm(e); } /* * Show the experimental design */ DesignMatrix.init({ id : e.id }); var vizPanel = new Gemma.EEDetailsVisualizationWidget({ renderTo : 'visualization', taxon : e.parentTaxon }); /* * This is needed to make the annotator initialize properly. */ new Gemma.MGEDCombo({}); var taggerurl = '<a href="#" onClick="return Ext.getCmp(\'eemanager\').tagger(' + e.id + ',' + e.taxonId + ',' + this.editable + ')"><img src="/Gemma/images/icons/pencil.png" alt="view tags" title="view tags"/></a>'; tagView = new Gemma.AnnotationDataView({ readParams : [{ id : e.id, classDelegatingFor : "ExpressionExperimentImpl" }] }); manager.on('tagsUpdated', function() { tagView.store.reload(); }); manager.on('done', function() { window.location.reload(); }); manager.on('reportUpdated', function(data) { ob = data[0]; // console.log(ob); var k = Ext.get('coexpressionLinkCount-region'); Ext.DomHelper.overwrite(k, { html : ob.coexpressionLinkCount }); k.highlight(); k = Ext.get('processedExpressionVectorCount-region'); Ext.DomHelper.overwrite(k, { html : ob.processedExpressionVectorCount }); k.highlight(); }); manager.on('pubmedUpdated', function(e) { var html = this.getPubMedHtml(e); Ext.getCmp('pubmed-region-wrap').remove(Ext.getCmp('pubmed-region')); Ext.DomHelper.append('pubmed-region-wrap', html); }.createDelegate(this)); manager.on('pubmedRemove', function(success) { if (success) { var r = Ext.getCmp('pubmed-region-wrap'); r.remove(Ext.getCmp('pubmed-region')); var form = this.getPubMedForm(this.eeId); r.add(form); r.doLayout(); } }.createDelegate(this)); manager.on('updated', function(data) { Ext.getCmp('update-button-region').getEl().hide(); /* * Really we won't need to do this -- as the state on the database is supposed to match this one. */ var k = Ext.getCmp('shortname'); k.setValue(data.shortName); k = Ext.getCmp('name'); k.setValue(data.name); k = Ext.getCmp('description'); k.setValue(data.description); }.createDelegate(this)); // manager.on('reportUpdated', function() { // store.reload(); // }); // // manager.on('differential', function() { // store.reload(); // }); // manager.on('processedVector', function() { // store.reload(); // }); // manager.on('link', function() { // store.reload(); // }); // manager.on('missingValue', function() { // store.reload(); // }); var descriptionArea = new Ext.form.TextArea({ id : 'description', allowBlank : true, grow : true, growMax : 300, readOnly : !this.editable, disabledClass : 'disabled-plain', growMin : 40, emptyText : 'No description provided', enableKeyEvents : true, listeners : { 'keyup' : { fn : function(e) { if (Ext.getCmp('description').isDirty() && Ext.getCmp('description').isValid()) { // show save button Ext.getCmp('update-button-region').show(); } else { Ext.getCmp('update-button-region').hide(); } } } }, width : 500, // height : 100, value : e.description }); var nameArea = new Ext.form.TextArea({ id : 'name', fieldLabel : 'Name', allowBlank : false, grow : true, growMax : 300, readOnly : !this.editable, disabledClass : 'disabled-plain', growMin : 40, emptyText : 'No description provided', enableKeyEvents : true, listeners : { 'keyup' : { fn : function(e) { if (Ext.getCmp('name').isDirty() && Ext.getCmp('name').isValid()) { // show save button Ext.getCmp('update-button-region').show(); } else { Ext.getCmp('update-button-region').hide(); } } } }, width : 500, value : e.name }); var basics = new Ext.Panel({ autoHeight : true, layout : 'table', layoutConfig : { columns : 2 }, renderTo : 'basics', collapsible : false, bodyBorder : false, frame : false, baseCls : 'x-plain-panel', bodyStyle : 'padding:10px', defaults : { bodyStyle : 'vertical-align:top;font-size:12px;color:black', baseCls : 'x-plain-panel', fieldClass : 'x-bare-field' }, items : [{ html : 'Short name:' }, { xtype : 'panel', layout : 'table', baseCls : 'x-plain-panel', layoutConfig : { columns : 2 }, items : [{ xtype : 'textfield', id : 'shortname', enableKeyEvents : true, allowBlank : false, disabledClass : 'disabled-plain', fieldClass : 'x-bare-field', readOnly : !this.editable, listeners : { 'keyup' : { fn : function(e) { if (Ext.getCmp('shortname').isDirty() && Ext.getCmp('shortname').isValid()) { // show // save // button Ext.getCmp('update-button-region').show(); } else { Ext.getCmp('update-button-region').hide(); } }, scope : this } }, width : 250, value : e.shortName }, { baseCls : 'x-plain-panel', id : 'update-button-region', html : '<a href="#" onClick="Ext.getCmp(\'ee-details-panel\').save(' + e.id + ',[\'shortname\',\'name\',\'description\'])" ><img src="/Gemma/images/icons/database_save.png" title="Click to save changes" alt="Click to save changes"/></a>', hidden : true }] }, { html : 'Name:' }, nameArea, { html : "Taxon:" }, { html : e.taxon }, { html : 'Description:' }, descriptionArea, { html : 'Created:' }, { html : Ext.util.Format.date(e.dateCreated) }, { html : 'Source:' }, { html : this.renderSourceDatabaseEntry(e) }, { html : 'Samples:' }, { html : this.renderSamples(e), width : 60 }, { html : 'Profiles:' }, { id : 'processedExpressionVectorCount-region', html : '<div id="downloads"> ' + this.renderProcessedExpressionVectorCount(e) + ' ' + '<i>Downloads:</i> <a title="click to download the tab delimited data" href="#" onClick="fetchData(true,' + e.id + ', \'text\', null, null)">Filtered</a> ' + '<a href="#" title="click to download the tab delimited data" onClick="fetchData(false,' + e.id + ', \'text\', null, null)">Unfiltered</a> ' + '<a class="helpLink" href="?" onclick="showHelpTip(event, \'Tab-delimited data file for this experiment. The filtered version corresponds to what is used in most Gemma analyses, removing some probes. Unfiltered includes all probes\'); return false"> <img src="/Gemma/images/help.png" /> </a>' + '</div>', width : 400 }, { html : 'Array designs:' }, { id : 'arrayDesign-region', html : this.renderArrayDesigns(e.arrayDesigns), width : 480 }, { html : 'Coexpr. Links:' }, { id : 'coexpressionLinkCount-region', html : this.renderCoExpressionLinkCount(e), width : 80 }, { html : 'Diff. expr. Probes' }, { id : 'DiffExpressedProbes-region', html : this.renderDiffExpressionDetails(e), width : 200 }, { html : 'Publication:' }, { xtype : 'panel', id : 'pubmed-region-wrap', layout : 'fit', bodyBorder : false, baseCls : 'x-plain-panel', disabled : false, items : [pubmedRegion] }, { html : 'Tags ' + taggerurl }, tagView, { html : 'Status' }, { html : this.renderStatus(e) }, { html : this.editable ? 'Admin' : '' }, { id : 'admin-links', html : this.editable ? adminLinks : '' } /* * authors */ ] }); if (this.editable) { Ext.DomHelper.append('admin-links', { tag : 'ul', cls : 'plainlist', children : [{ tag : 'li', html : 'Missing values: ' + this.missingValueAnalysisRenderer(e) }, { tag : 'li', html : 'Proc. vec: ' + this.processedVectorCreateRenderer(e) }, { tag : 'li', html : 'Diff ex: ' + this.differentialAnalysisRenderer(e) }, { tag : 'li', html : 'Link an.: ' + this.linkAnalysisRenderer(e) }] }); } if (Ext.get('history')) { var history = new Gemma.AuditTrailGrid({ renderTo : 'history', bodyBorder : false, collapsible : true, auditable : { id : e.id, classDelegatingFor : "ubic.gemma.model.expression.experiment.ExpressionExperimentImpl" } }); } this.fireEvent("ready"); }
|
'<a href="#" onClick="return Ext.getCmp(\'eemanager\').deleteExperiment(' +
|
'<span style="cursor:pointer" onClick="return Ext.getCmp(\'eemanager\').deleteExperiment(' +
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build : function(e) { var manager = new Gemma.EEManager({ editable : this.editable, id : "eemanager" }); this.manager = manager; // // /* // * Create a store with one record. // */ // var store = new Ext.data.Store({ // proxy : new Ext.data.MemoryProxy([e]), // reader : new Ext.data.ListRangeReader({}, // this.manager.record) // }); // // this.rec = store.getAt(0); adminLinks = '<a href="#" onClick="Ext.getCmp(\'eemanager\').updateEEReport(' + e.id + ')"><img src="/Gemma/images/icons/arrow_refresh_small.png" ext:qtip="Refresh statistics" title="refresh"/></a>' + ' <a href="/Gemma/expressionExperiment/editExpressionExperiment.html?id=' + e.id + '" ><img src="/Gemma/images/icons/wrench.png" ext:qtip="Go to editor page for this experiment" title="edit"/></a> '; if (this.isAdmin) { adminLinks = adminLinks + '<a href="#" onClick="return Ext.getCmp(\'eemanager\').deleteExperiment(' + e.id + ')"><img src="/Gemma/images/icons/cross.png" ext:qtip="Delete the experiment from the system" title="delete" /></a> '; } var pubmedRegion = {}; if (e.pubmedId) { // display the citation, with link out and delete // button. pubmedRegion = this.getPubMedHtml(e); } else { // offer to create a citation link. pubmedRegion = this.getPubMedForm(e); } /* * Show the experimental design */ DesignMatrix.init({ id : e.id }); var vizPanel = new Gemma.EEDetailsVisualizationWidget({ renderTo : 'visualization', taxon : e.parentTaxon }); /* * This is needed to make the annotator initialize properly. */ new Gemma.MGEDCombo({}); var taggerurl = '<a href="#" onClick="return Ext.getCmp(\'eemanager\').tagger(' + e.id + ',' + e.taxonId + ',' + this.editable + ')"><img src="/Gemma/images/icons/pencil.png" alt="view tags" title="view tags"/></a>'; tagView = new Gemma.AnnotationDataView({ readParams : [{ id : e.id, classDelegatingFor : "ExpressionExperimentImpl" }] }); manager.on('tagsUpdated', function() { tagView.store.reload(); }); manager.on('done', function() { window.location.reload(); }); manager.on('reportUpdated', function(data) { ob = data[0]; // console.log(ob); var k = Ext.get('coexpressionLinkCount-region'); Ext.DomHelper.overwrite(k, { html : ob.coexpressionLinkCount }); k.highlight(); k = Ext.get('processedExpressionVectorCount-region'); Ext.DomHelper.overwrite(k, { html : ob.processedExpressionVectorCount }); k.highlight(); }); manager.on('pubmedUpdated', function(e) { var html = this.getPubMedHtml(e); Ext.getCmp('pubmed-region-wrap').remove(Ext.getCmp('pubmed-region')); Ext.DomHelper.append('pubmed-region-wrap', html); }.createDelegate(this)); manager.on('pubmedRemove', function(success) { if (success) { var r = Ext.getCmp('pubmed-region-wrap'); r.remove(Ext.getCmp('pubmed-region')); var form = this.getPubMedForm(this.eeId); r.add(form); r.doLayout(); } }.createDelegate(this)); manager.on('updated', function(data) { Ext.getCmp('update-button-region').getEl().hide(); /* * Really we won't need to do this -- as the state on the database is supposed to match this one. */ var k = Ext.getCmp('shortname'); k.setValue(data.shortName); k = Ext.getCmp('name'); k.setValue(data.name); k = Ext.getCmp('description'); k.setValue(data.description); }.createDelegate(this)); // manager.on('reportUpdated', function() { // store.reload(); // }); // // manager.on('differential', function() { // store.reload(); // }); // manager.on('processedVector', function() { // store.reload(); // }); // manager.on('link', function() { // store.reload(); // }); // manager.on('missingValue', function() { // store.reload(); // }); var descriptionArea = new Ext.form.TextArea({ id : 'description', allowBlank : true, grow : true, growMax : 300, readOnly : !this.editable, disabledClass : 'disabled-plain', growMin : 40, emptyText : 'No description provided', enableKeyEvents : true, listeners : { 'keyup' : { fn : function(e) { if (Ext.getCmp('description').isDirty() && Ext.getCmp('description').isValid()) { // show save button Ext.getCmp('update-button-region').show(); } else { Ext.getCmp('update-button-region').hide(); } } } }, width : 500, // height : 100, value : e.description }); var nameArea = new Ext.form.TextArea({ id : 'name', fieldLabel : 'Name', allowBlank : false, grow : true, growMax : 300, readOnly : !this.editable, disabledClass : 'disabled-plain', growMin : 40, emptyText : 'No description provided', enableKeyEvents : true, listeners : { 'keyup' : { fn : function(e) { if (Ext.getCmp('name').isDirty() && Ext.getCmp('name').isValid()) { // show save button Ext.getCmp('update-button-region').show(); } else { Ext.getCmp('update-button-region').hide(); } } } }, width : 500, value : e.name }); var basics = new Ext.Panel({ autoHeight : true, layout : 'table', layoutConfig : { columns : 2 }, renderTo : 'basics', collapsible : false, bodyBorder : false, frame : false, baseCls : 'x-plain-panel', bodyStyle : 'padding:10px', defaults : { bodyStyle : 'vertical-align:top;font-size:12px;color:black', baseCls : 'x-plain-panel', fieldClass : 'x-bare-field' }, items : [{ html : 'Short name:' }, { xtype : 'panel', layout : 'table', baseCls : 'x-plain-panel', layoutConfig : { columns : 2 }, items : [{ xtype : 'textfield', id : 'shortname', enableKeyEvents : true, allowBlank : false, disabledClass : 'disabled-plain', fieldClass : 'x-bare-field', readOnly : !this.editable, listeners : { 'keyup' : { fn : function(e) { if (Ext.getCmp('shortname').isDirty() && Ext.getCmp('shortname').isValid()) { // show // save // button Ext.getCmp('update-button-region').show(); } else { Ext.getCmp('update-button-region').hide(); } }, scope : this } }, width : 250, value : e.shortName }, { baseCls : 'x-plain-panel', id : 'update-button-region', html : '<a href="#" onClick="Ext.getCmp(\'ee-details-panel\').save(' + e.id + ',[\'shortname\',\'name\',\'description\'])" ><img src="/Gemma/images/icons/database_save.png" title="Click to save changes" alt="Click to save changes"/></a>', hidden : true }] }, { html : 'Name:' }, nameArea, { html : "Taxon:" }, { html : e.taxon }, { html : 'Description:' }, descriptionArea, { html : 'Created:' }, { html : Ext.util.Format.date(e.dateCreated) }, { html : 'Source:' }, { html : this.renderSourceDatabaseEntry(e) }, { html : 'Samples:' }, { html : this.renderSamples(e), width : 60 }, { html : 'Profiles:' }, { id : 'processedExpressionVectorCount-region', html : '<div id="downloads"> ' + this.renderProcessedExpressionVectorCount(e) + ' ' + '<i>Downloads:</i> <a title="click to download the tab delimited data" href="#" onClick="fetchData(true,' + e.id + ', \'text\', null, null)">Filtered</a> ' + '<a href="#" title="click to download the tab delimited data" onClick="fetchData(false,' + e.id + ', \'text\', null, null)">Unfiltered</a> ' + '<a class="helpLink" href="?" onclick="showHelpTip(event, \'Tab-delimited data file for this experiment. The filtered version corresponds to what is used in most Gemma analyses, removing some probes. Unfiltered includes all probes\'); return false"> <img src="/Gemma/images/help.png" /> </a>' + '</div>', width : 400 }, { html : 'Array designs:' }, { id : 'arrayDesign-region', html : this.renderArrayDesigns(e.arrayDesigns), width : 480 }, { html : 'Coexpr. Links:' }, { id : 'coexpressionLinkCount-region', html : this.renderCoExpressionLinkCount(e), width : 80 }, { html : 'Diff. expr. Probes' }, { id : 'DiffExpressedProbes-region', html : this.renderDiffExpressionDetails(e), width : 200 }, { html : 'Publication:' }, { xtype : 'panel', id : 'pubmed-region-wrap', layout : 'fit', bodyBorder : false, baseCls : 'x-plain-panel', disabled : false, items : [pubmedRegion] }, { html : 'Tags ' + taggerurl }, tagView, { html : 'Status' }, { html : this.renderStatus(e) }, { html : this.editable ? 'Admin' : '' }, { id : 'admin-links', html : this.editable ? adminLinks : '' } /* * authors */ ] }); if (this.editable) { Ext.DomHelper.append('admin-links', { tag : 'ul', cls : 'plainlist', children : [{ tag : 'li', html : 'Missing values: ' + this.missingValueAnalysisRenderer(e) }, { tag : 'li', html : 'Proc. vec: ' + this.processedVectorCreateRenderer(e) }, { tag : 'li', html : 'Diff ex: ' + this.differentialAnalysisRenderer(e) }, { tag : 'li', html : 'Link an.: ' + this.linkAnalysisRenderer(e) }] }); } if (Ext.get('history')) { var history = new Gemma.AuditTrailGrid({ renderTo : 'history', bodyBorder : false, collapsible : true, auditable : { id : e.id, classDelegatingFor : "ubic.gemma.model.expression.experiment.ExpressionExperimentImpl" } }); } this.fireEvent("ready"); }
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')"><img src="/Gemma/images/icons/cross.png" ext:qtip="Delete the experiment from the system" title="delete" /></a> ';
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')"><img src="/Gemma/images/icons/cross.png" ext:qtip="Delete the experiment from the system" title="delete" /></span> ';
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build : function(e) { var manager = new Gemma.EEManager({ editable : this.editable, id : "eemanager" }); this.manager = manager; // // /* // * Create a store with one record. // */ // var store = new Ext.data.Store({ // proxy : new Ext.data.MemoryProxy([e]), // reader : new Ext.data.ListRangeReader({}, // this.manager.record) // }); // // this.rec = store.getAt(0); adminLinks = '<a href="#" onClick="Ext.getCmp(\'eemanager\').updateEEReport(' + e.id + ')"><img src="/Gemma/images/icons/arrow_refresh_small.png" ext:qtip="Refresh statistics" title="refresh"/></a>' + ' <a href="/Gemma/expressionExperiment/editExpressionExperiment.html?id=' + e.id + '" ><img src="/Gemma/images/icons/wrench.png" ext:qtip="Go to editor page for this experiment" title="edit"/></a> '; if (this.isAdmin) { adminLinks = adminLinks + '<a href="#" onClick="return Ext.getCmp(\'eemanager\').deleteExperiment(' + e.id + ')"><img src="/Gemma/images/icons/cross.png" ext:qtip="Delete the experiment from the system" title="delete" /></a> '; } var pubmedRegion = {}; if (e.pubmedId) { // display the citation, with link out and delete // button. pubmedRegion = this.getPubMedHtml(e); } else { // offer to create a citation link. pubmedRegion = this.getPubMedForm(e); } /* * Show the experimental design */ DesignMatrix.init({ id : e.id }); var vizPanel = new Gemma.EEDetailsVisualizationWidget({ renderTo : 'visualization', taxon : e.parentTaxon }); /* * This is needed to make the annotator initialize properly. */ new Gemma.MGEDCombo({}); var taggerurl = '<a href="#" onClick="return Ext.getCmp(\'eemanager\').tagger(' + e.id + ',' + e.taxonId + ',' + this.editable + ')"><img src="/Gemma/images/icons/pencil.png" alt="view tags" title="view tags"/></a>'; tagView = new Gemma.AnnotationDataView({ readParams : [{ id : e.id, classDelegatingFor : "ExpressionExperimentImpl" }] }); manager.on('tagsUpdated', function() { tagView.store.reload(); }); manager.on('done', function() { window.location.reload(); }); manager.on('reportUpdated', function(data) { ob = data[0]; // console.log(ob); var k = Ext.get('coexpressionLinkCount-region'); Ext.DomHelper.overwrite(k, { html : ob.coexpressionLinkCount }); k.highlight(); k = Ext.get('processedExpressionVectorCount-region'); Ext.DomHelper.overwrite(k, { html : ob.processedExpressionVectorCount }); k.highlight(); }); manager.on('pubmedUpdated', function(e) { var html = this.getPubMedHtml(e); Ext.getCmp('pubmed-region-wrap').remove(Ext.getCmp('pubmed-region')); Ext.DomHelper.append('pubmed-region-wrap', html); }.createDelegate(this)); manager.on('pubmedRemove', function(success) { if (success) { var r = Ext.getCmp('pubmed-region-wrap'); r.remove(Ext.getCmp('pubmed-region')); var form = this.getPubMedForm(this.eeId); r.add(form); r.doLayout(); } }.createDelegate(this)); manager.on('updated', function(data) { Ext.getCmp('update-button-region').getEl().hide(); /* * Really we won't need to do this -- as the state on the database is supposed to match this one. */ var k = Ext.getCmp('shortname'); k.setValue(data.shortName); k = Ext.getCmp('name'); k.setValue(data.name); k = Ext.getCmp('description'); k.setValue(data.description); }.createDelegate(this)); // manager.on('reportUpdated', function() { // store.reload(); // }); // // manager.on('differential', function() { // store.reload(); // }); // manager.on('processedVector', function() { // store.reload(); // }); // manager.on('link', function() { // store.reload(); // }); // manager.on('missingValue', function() { // store.reload(); // }); var descriptionArea = new Ext.form.TextArea({ id : 'description', allowBlank : true, grow : true, growMax : 300, readOnly : !this.editable, disabledClass : 'disabled-plain', growMin : 40, emptyText : 'No description provided', enableKeyEvents : true, listeners : { 'keyup' : { fn : function(e) { if (Ext.getCmp('description').isDirty() && Ext.getCmp('description').isValid()) { // show save button Ext.getCmp('update-button-region').show(); } else { Ext.getCmp('update-button-region').hide(); } } } }, width : 500, // height : 100, value : e.description }); var nameArea = new Ext.form.TextArea({ id : 'name', fieldLabel : 'Name', allowBlank : false, grow : true, growMax : 300, readOnly : !this.editable, disabledClass : 'disabled-plain', growMin : 40, emptyText : 'No description provided', enableKeyEvents : true, listeners : { 'keyup' : { fn : function(e) { if (Ext.getCmp('name').isDirty() && Ext.getCmp('name').isValid()) { // show save button Ext.getCmp('update-button-region').show(); } else { Ext.getCmp('update-button-region').hide(); } } } }, width : 500, value : e.name }); var basics = new Ext.Panel({ autoHeight : true, layout : 'table', layoutConfig : { columns : 2 }, renderTo : 'basics', collapsible : false, bodyBorder : false, frame : false, baseCls : 'x-plain-panel', bodyStyle : 'padding:10px', defaults : { bodyStyle : 'vertical-align:top;font-size:12px;color:black', baseCls : 'x-plain-panel', fieldClass : 'x-bare-field' }, items : [{ html : 'Short name:' }, { xtype : 'panel', layout : 'table', baseCls : 'x-plain-panel', layoutConfig : { columns : 2 }, items : [{ xtype : 'textfield', id : 'shortname', enableKeyEvents : true, allowBlank : false, disabledClass : 'disabled-plain', fieldClass : 'x-bare-field', readOnly : !this.editable, listeners : { 'keyup' : { fn : function(e) { if (Ext.getCmp('shortname').isDirty() && Ext.getCmp('shortname').isValid()) { // show // save // button Ext.getCmp('update-button-region').show(); } else { Ext.getCmp('update-button-region').hide(); } }, scope : this } }, width : 250, value : e.shortName }, { baseCls : 'x-plain-panel', id : 'update-button-region', html : '<a href="#" onClick="Ext.getCmp(\'ee-details-panel\').save(' + e.id + ',[\'shortname\',\'name\',\'description\'])" ><img src="/Gemma/images/icons/database_save.png" title="Click to save changes" alt="Click to save changes"/></a>', hidden : true }] }, { html : 'Name:' }, nameArea, { html : "Taxon:" }, { html : e.taxon }, { html : 'Description:' }, descriptionArea, { html : 'Created:' }, { html : Ext.util.Format.date(e.dateCreated) }, { html : 'Source:' }, { html : this.renderSourceDatabaseEntry(e) }, { html : 'Samples:' }, { html : this.renderSamples(e), width : 60 }, { html : 'Profiles:' }, { id : 'processedExpressionVectorCount-region', html : '<div id="downloads"> ' + this.renderProcessedExpressionVectorCount(e) + ' ' + '<i>Downloads:</i> <a title="click to download the tab delimited data" href="#" onClick="fetchData(true,' + e.id + ', \'text\', null, null)">Filtered</a> ' + '<a href="#" title="click to download the tab delimited data" onClick="fetchData(false,' + e.id + ', \'text\', null, null)">Unfiltered</a> ' + '<a class="helpLink" href="?" onclick="showHelpTip(event, \'Tab-delimited data file for this experiment. The filtered version corresponds to what is used in most Gemma analyses, removing some probes. Unfiltered includes all probes\'); return false"> <img src="/Gemma/images/help.png" /> </a>' + '</div>', width : 400 }, { html : 'Array designs:' }, { id : 'arrayDesign-region', html : this.renderArrayDesigns(e.arrayDesigns), width : 480 }, { html : 'Coexpr. Links:' }, { id : 'coexpressionLinkCount-region', html : this.renderCoExpressionLinkCount(e), width : 80 }, { html : 'Diff. expr. Probes' }, { id : 'DiffExpressedProbes-region', html : this.renderDiffExpressionDetails(e), width : 200 }, { html : 'Publication:' }, { xtype : 'panel', id : 'pubmed-region-wrap', layout : 'fit', bodyBorder : false, baseCls : 'x-plain-panel', disabled : false, items : [pubmedRegion] }, { html : 'Tags ' + taggerurl }, tagView, { html : 'Status' }, { html : this.renderStatus(e) }, { html : this.editable ? 'Admin' : '' }, { id : 'admin-links', html : this.editable ? adminLinks : '' } /* * authors */ ] }); if (this.editable) { Ext.DomHelper.append('admin-links', { tag : 'ul', cls : 'plainlist', children : [{ tag : 'li', html : 'Missing values: ' + this.missingValueAnalysisRenderer(e) }, { tag : 'li', html : 'Proc. vec: ' + this.processedVectorCreateRenderer(e) }, { tag : 'li', html : 'Diff ex: ' + this.differentialAnalysisRenderer(e) }, { tag : 'li', html : 'Link an.: ' + this.linkAnalysisRenderer(e) }] }); } if (Ext.get('history')) { var history = new Gemma.AuditTrailGrid({ renderTo : 'history', bodyBorder : false, collapsible : true, auditable : { id : e.id, classDelegatingFor : "ubic.gemma.model.expression.experiment.ExpressionExperimentImpl" } }); } this.fireEvent("ready"); }
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var taggerurl = '<a href="#" onClick="return Ext.getCmp(\'eemanager\').tagger(' + e.id + ',' + e.taxonId + ',' + this.editable + ')"><img src="/Gemma/images/icons/pencil.png" alt="view tags" title="view tags"/></a>';
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var taggerurl = '<span style="cursor:pointer" onClick="return Ext.getCmp(\'eemanager\').tagger(' + e.id + ',' + e.taxonId + ',' + this.editable + ')"><img src="/Gemma/images/icons/pencil.png" alt="view tags" title="view tags"/></span>';
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build : function(e) { var manager = new Gemma.EEManager({ editable : this.editable, id : "eemanager" }); this.manager = manager; // // /* // * Create a store with one record. // */ // var store = new Ext.data.Store({ // proxy : new Ext.data.MemoryProxy([e]), // reader : new Ext.data.ListRangeReader({}, // this.manager.record) // }); // // this.rec = store.getAt(0); adminLinks = '<a href="#" onClick="Ext.getCmp(\'eemanager\').updateEEReport(' + e.id + ')"><img src="/Gemma/images/icons/arrow_refresh_small.png" ext:qtip="Refresh statistics" title="refresh"/></a>' + ' <a href="/Gemma/expressionExperiment/editExpressionExperiment.html?id=' + e.id + '" ><img src="/Gemma/images/icons/wrench.png" ext:qtip="Go to editor page for this experiment" title="edit"/></a> '; if (this.isAdmin) { adminLinks = adminLinks + '<a href="#" onClick="return Ext.getCmp(\'eemanager\').deleteExperiment(' + e.id + ')"><img src="/Gemma/images/icons/cross.png" ext:qtip="Delete the experiment from the system" title="delete" /></a> '; } var pubmedRegion = {}; if (e.pubmedId) { // display the citation, with link out and delete // button. pubmedRegion = this.getPubMedHtml(e); } else { // offer to create a citation link. pubmedRegion = this.getPubMedForm(e); } /* * Show the experimental design */ DesignMatrix.init({ id : e.id }); var vizPanel = new Gemma.EEDetailsVisualizationWidget({ renderTo : 'visualization', taxon : e.parentTaxon }); /* * This is needed to make the annotator initialize properly. */ new Gemma.MGEDCombo({}); var taggerurl = '<a href="#" onClick="return Ext.getCmp(\'eemanager\').tagger(' + e.id + ',' + e.taxonId + ',' + this.editable + ')"><img src="/Gemma/images/icons/pencil.png" alt="view tags" title="view tags"/></a>'; tagView = new Gemma.AnnotationDataView({ readParams : [{ id : e.id, classDelegatingFor : "ExpressionExperimentImpl" }] }); manager.on('tagsUpdated', function() { tagView.store.reload(); }); manager.on('done', function() { window.location.reload(); }); manager.on('reportUpdated', function(data) { ob = data[0]; // console.log(ob); var k = Ext.get('coexpressionLinkCount-region'); Ext.DomHelper.overwrite(k, { html : ob.coexpressionLinkCount }); k.highlight(); k = Ext.get('processedExpressionVectorCount-region'); Ext.DomHelper.overwrite(k, { html : ob.processedExpressionVectorCount }); k.highlight(); }); manager.on('pubmedUpdated', function(e) { var html = this.getPubMedHtml(e); Ext.getCmp('pubmed-region-wrap').remove(Ext.getCmp('pubmed-region')); Ext.DomHelper.append('pubmed-region-wrap', html); }.createDelegate(this)); manager.on('pubmedRemove', function(success) { if (success) { var r = Ext.getCmp('pubmed-region-wrap'); r.remove(Ext.getCmp('pubmed-region')); var form = this.getPubMedForm(this.eeId); r.add(form); r.doLayout(); } }.createDelegate(this)); manager.on('updated', function(data) { Ext.getCmp('update-button-region').getEl().hide(); /* * Really we won't need to do this -- as the state on the database is supposed to match this one. */ var k = Ext.getCmp('shortname'); k.setValue(data.shortName); k = Ext.getCmp('name'); k.setValue(data.name); k = Ext.getCmp('description'); k.setValue(data.description); }.createDelegate(this)); // manager.on('reportUpdated', function() { // store.reload(); // }); // // manager.on('differential', function() { // store.reload(); // }); // manager.on('processedVector', function() { // store.reload(); // }); // manager.on('link', function() { // store.reload(); // }); // manager.on('missingValue', function() { // store.reload(); // }); var descriptionArea = new Ext.form.TextArea({ id : 'description', allowBlank : true, grow : true, growMax : 300, readOnly : !this.editable, disabledClass : 'disabled-plain', growMin : 40, emptyText : 'No description provided', enableKeyEvents : true, listeners : { 'keyup' : { fn : function(e) { if (Ext.getCmp('description').isDirty() && Ext.getCmp('description').isValid()) { // show save button Ext.getCmp('update-button-region').show(); } else { Ext.getCmp('update-button-region').hide(); } } } }, width : 500, // height : 100, value : e.description }); var nameArea = new Ext.form.TextArea({ id : 'name', fieldLabel : 'Name', allowBlank : false, grow : true, growMax : 300, readOnly : !this.editable, disabledClass : 'disabled-plain', growMin : 40, emptyText : 'No description provided', enableKeyEvents : true, listeners : { 'keyup' : { fn : function(e) { if (Ext.getCmp('name').isDirty() && Ext.getCmp('name').isValid()) { // show save button Ext.getCmp('update-button-region').show(); } else { Ext.getCmp('update-button-region').hide(); } } } }, width : 500, value : e.name }); var basics = new Ext.Panel({ autoHeight : true, layout : 'table', layoutConfig : { columns : 2 }, renderTo : 'basics', collapsible : false, bodyBorder : false, frame : false, baseCls : 'x-plain-panel', bodyStyle : 'padding:10px', defaults : { bodyStyle : 'vertical-align:top;font-size:12px;color:black', baseCls : 'x-plain-panel', fieldClass : 'x-bare-field' }, items : [{ html : 'Short name:' }, { xtype : 'panel', layout : 'table', baseCls : 'x-plain-panel', layoutConfig : { columns : 2 }, items : [{ xtype : 'textfield', id : 'shortname', enableKeyEvents : true, allowBlank : false, disabledClass : 'disabled-plain', fieldClass : 'x-bare-field', readOnly : !this.editable, listeners : { 'keyup' : { fn : function(e) { if (Ext.getCmp('shortname').isDirty() && Ext.getCmp('shortname').isValid()) { // show // save // button Ext.getCmp('update-button-region').show(); } else { Ext.getCmp('update-button-region').hide(); } }, scope : this } }, width : 250, value : e.shortName }, { baseCls : 'x-plain-panel', id : 'update-button-region', html : '<a href="#" onClick="Ext.getCmp(\'ee-details-panel\').save(' + e.id + ',[\'shortname\',\'name\',\'description\'])" ><img src="/Gemma/images/icons/database_save.png" title="Click to save changes" alt="Click to save changes"/></a>', hidden : true }] }, { html : 'Name:' }, nameArea, { html : "Taxon:" }, { html : e.taxon }, { html : 'Description:' }, descriptionArea, { html : 'Created:' }, { html : Ext.util.Format.date(e.dateCreated) }, { html : 'Source:' }, { html : this.renderSourceDatabaseEntry(e) }, { html : 'Samples:' }, { html : this.renderSamples(e), width : 60 }, { html : 'Profiles:' }, { id : 'processedExpressionVectorCount-region', html : '<div id="downloads"> ' + this.renderProcessedExpressionVectorCount(e) + ' ' + '<i>Downloads:</i> <a title="click to download the tab delimited data" href="#" onClick="fetchData(true,' + e.id + ', \'text\', null, null)">Filtered</a> ' + '<a href="#" title="click to download the tab delimited data" onClick="fetchData(false,' + e.id + ', \'text\', null, null)">Unfiltered</a> ' + '<a class="helpLink" href="?" onclick="showHelpTip(event, \'Tab-delimited data file for this experiment. The filtered version corresponds to what is used in most Gemma analyses, removing some probes. Unfiltered includes all probes\'); return false"> <img src="/Gemma/images/help.png" /> </a>' + '</div>', width : 400 }, { html : 'Array designs:' }, { id : 'arrayDesign-region', html : this.renderArrayDesigns(e.arrayDesigns), width : 480 }, { html : 'Coexpr. Links:' }, { id : 'coexpressionLinkCount-region', html : this.renderCoExpressionLinkCount(e), width : 80 }, { html : 'Diff. expr. Probes' }, { id : 'DiffExpressedProbes-region', html : this.renderDiffExpressionDetails(e), width : 200 }, { html : 'Publication:' }, { xtype : 'panel', id : 'pubmed-region-wrap', layout : 'fit', bodyBorder : false, baseCls : 'x-plain-panel', disabled : false, items : [pubmedRegion] }, { html : 'Tags ' + taggerurl }, tagView, { html : 'Status' }, { html : this.renderStatus(e) }, { html : this.editable ? 'Admin' : '' }, { id : 'admin-links', html : this.editable ? adminLinks : '' } /* * authors */ ] }); if (this.editable) { Ext.DomHelper.append('admin-links', { tag : 'ul', cls : 'plainlist', children : [{ tag : 'li', html : 'Missing values: ' + this.missingValueAnalysisRenderer(e) }, { tag : 'li', html : 'Proc. vec: ' + this.processedVectorCreateRenderer(e) }, { tag : 'li', html : 'Diff ex: ' + this.differentialAnalysisRenderer(e) }, { tag : 'li', html : 'Link an.: ' + this.linkAnalysisRenderer(e) }] }); } if (Ext.get('history')) { var history = new Gemma.AuditTrailGrid({ renderTo : 'history', bodyBorder : false, collapsible : true, auditable : { id : e.id, classDelegatingFor : "ubic.gemma.model.expression.experiment.ExpressionExperimentImpl" } }); } this.fireEvent("ready"); }
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manager.on('pubmedUpdated', function(e) { var html = this.getPubMedHtml(e); Ext.getCmp('pubmed-region-wrap').remove(Ext.getCmp('pubmed-region')); Ext.DomHelper.append('pubmed-region-wrap', html); }.createDelegate(this)); manager.on('pubmedRemove', function(success) { if (success) { var r = Ext.getCmp('pubmed-region-wrap'); r.remove(Ext.getCmp('pubmed-region')); var form = this.getPubMedForm(this.eeId); r.add(form); r.doLayout(); } }.createDelegate(this)); manager.on('updated', function(data) { Ext.getCmp('update-button-region').getEl().hide(); var k = Ext.getCmp('shortname'); k.setValue(data.shortName); k = Ext.getCmp('name'); k.setValue(data.name); k = Ext.getCmp('description'); k.setValue(data.description); }.createDelegate(this));
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build : function(e) { var manager = new Gemma.EEManager({ editable : this.editable, id : "eemanager" }); this.manager = manager; // // /* // * Create a store with one record. // */ // var store = new Ext.data.Store({ // proxy : new Ext.data.MemoryProxy([e]), // reader : new Ext.data.ListRangeReader({}, // this.manager.record) // }); // // this.rec = store.getAt(0); adminLinks = '<a href="#" onClick="Ext.getCmp(\'eemanager\').updateEEReport(' + e.id + ')"><img src="/Gemma/images/icons/arrow_refresh_small.png" ext:qtip="Refresh statistics" title="refresh"/></a>' + ' <a href="/Gemma/expressionExperiment/editExpressionExperiment.html?id=' + e.id + '" ><img src="/Gemma/images/icons/wrench.png" ext:qtip="Go to editor page for this experiment" title="edit"/></a> '; if (this.isAdmin) { adminLinks = adminLinks + '<a href="#" onClick="return Ext.getCmp(\'eemanager\').deleteExperiment(' + e.id + ')"><img src="/Gemma/images/icons/cross.png" ext:qtip="Delete the experiment from the system" title="delete" /></a> '; } var pubmedRegion = {}; if (e.pubmedId) { // display the citation, with link out and delete // button. pubmedRegion = this.getPubMedHtml(e); } else { // offer to create a citation link. pubmedRegion = this.getPubMedForm(e); } /* * Show the experimental design */ DesignMatrix.init({ id : e.id }); var vizPanel = new Gemma.EEDetailsVisualizationWidget({ renderTo : 'visualization', taxon : e.parentTaxon }); /* * This is needed to make the annotator initialize properly. */ new Gemma.MGEDCombo({}); var taggerurl = '<a href="#" onClick="return Ext.getCmp(\'eemanager\').tagger(' + e.id + ',' + e.taxonId + ',' + this.editable + ')"><img src="/Gemma/images/icons/pencil.png" alt="view tags" title="view tags"/></a>'; tagView = new Gemma.AnnotationDataView({ readParams : [{ id : e.id, classDelegatingFor : "ExpressionExperimentImpl" }] }); manager.on('tagsUpdated', function() { tagView.store.reload(); }); manager.on('done', function() { window.location.reload(); }); manager.on('reportUpdated', function(data) { ob = data[0]; // console.log(ob); var k = Ext.get('coexpressionLinkCount-region'); Ext.DomHelper.overwrite(k, { html : ob.coexpressionLinkCount }); k.highlight(); k = Ext.get('processedExpressionVectorCount-region'); Ext.DomHelper.overwrite(k, { html : ob.processedExpressionVectorCount }); k.highlight(); }); manager.on('pubmedUpdated', function(e) { var html = this.getPubMedHtml(e); Ext.getCmp('pubmed-region-wrap').remove(Ext.getCmp('pubmed-region')); Ext.DomHelper.append('pubmed-region-wrap', html); }.createDelegate(this)); manager.on('pubmedRemove', function(success) { if (success) { var r = Ext.getCmp('pubmed-region-wrap'); r.remove(Ext.getCmp('pubmed-region')); var form = this.getPubMedForm(this.eeId); r.add(form); r.doLayout(); } }.createDelegate(this)); manager.on('updated', function(data) { Ext.getCmp('update-button-region').getEl().hide(); /* * Really we won't need to do this -- as the state on the database is supposed to match this one. */ var k = Ext.getCmp('shortname'); k.setValue(data.shortName); k = Ext.getCmp('name'); k.setValue(data.name); k = Ext.getCmp('description'); k.setValue(data.description); }.createDelegate(this)); // manager.on('reportUpdated', function() { // store.reload(); // }); // // manager.on('differential', function() { // store.reload(); // }); // manager.on('processedVector', function() { // store.reload(); // }); // manager.on('link', function() { // store.reload(); // }); // manager.on('missingValue', function() { // store.reload(); // }); var descriptionArea = new Ext.form.TextArea({ id : 'description', allowBlank : true, grow : true, growMax : 300, readOnly : !this.editable, disabledClass : 'disabled-plain', growMin : 40, emptyText : 'No description provided', enableKeyEvents : true, listeners : { 'keyup' : { fn : function(e) { if (Ext.getCmp('description').isDirty() && Ext.getCmp('description').isValid()) { // show save button Ext.getCmp('update-button-region').show(); } else { Ext.getCmp('update-button-region').hide(); } } } }, width : 500, // height : 100, value : e.description }); var nameArea = new Ext.form.TextArea({ id : 'name', fieldLabel : 'Name', allowBlank : false, grow : true, growMax : 300, readOnly : !this.editable, disabledClass : 'disabled-plain', growMin : 40, emptyText : 'No description provided', enableKeyEvents : true, listeners : { 'keyup' : { fn : function(e) { if (Ext.getCmp('name').isDirty() && Ext.getCmp('name').isValid()) { // show save button Ext.getCmp('update-button-region').show(); } else { Ext.getCmp('update-button-region').hide(); } } } }, width : 500, value : e.name }); var basics = new Ext.Panel({ autoHeight : true, layout : 'table', layoutConfig : { columns : 2 }, renderTo : 'basics', collapsible : false, bodyBorder : false, frame : false, baseCls : 'x-plain-panel', bodyStyle : 'padding:10px', defaults : { bodyStyle : 'vertical-align:top;font-size:12px;color:black', baseCls : 'x-plain-panel', fieldClass : 'x-bare-field' }, items : [{ html : 'Short name:' }, { xtype : 'panel', layout : 'table', baseCls : 'x-plain-panel', layoutConfig : { columns : 2 }, items : [{ xtype : 'textfield', id : 'shortname', enableKeyEvents : true, allowBlank : false, disabledClass : 'disabled-plain', fieldClass : 'x-bare-field', readOnly : !this.editable, listeners : { 'keyup' : { fn : function(e) { if (Ext.getCmp('shortname').isDirty() && Ext.getCmp('shortname').isValid()) { // show // save // button Ext.getCmp('update-button-region').show(); } else { Ext.getCmp('update-button-region').hide(); } }, scope : this } }, width : 250, value : e.shortName }, { baseCls : 'x-plain-panel', id : 'update-button-region', html : '<a href="#" onClick="Ext.getCmp(\'ee-details-panel\').save(' + e.id + ',[\'shortname\',\'name\',\'description\'])" ><img src="/Gemma/images/icons/database_save.png" title="Click to save changes" alt="Click to save changes"/></a>', hidden : true }] }, { html : 'Name:' }, nameArea, { html : "Taxon:" }, { html : e.taxon }, { html : 'Description:' }, descriptionArea, { html : 'Created:' }, { html : Ext.util.Format.date(e.dateCreated) }, { html : 'Source:' }, { html : this.renderSourceDatabaseEntry(e) }, { html : 'Samples:' }, { html : this.renderSamples(e), width : 60 }, { html : 'Profiles:' }, { id : 'processedExpressionVectorCount-region', html : '<div id="downloads"> ' + this.renderProcessedExpressionVectorCount(e) + ' ' + '<i>Downloads:</i> <a title="click to download the tab delimited data" href="#" onClick="fetchData(true,' + e.id + ', \'text\', null, null)">Filtered</a> ' + '<a href="#" title="click to download the tab delimited data" onClick="fetchData(false,' + e.id + ', \'text\', null, null)">Unfiltered</a> ' + '<a class="helpLink" href="?" onclick="showHelpTip(event, \'Tab-delimited data file for this experiment. The filtered version corresponds to what is used in most Gemma analyses, removing some probes. Unfiltered includes all probes\'); return false"> <img src="/Gemma/images/help.png" /> </a>' + '</div>', width : 400 }, { html : 'Array designs:' }, { id : 'arrayDesign-region', html : this.renderArrayDesigns(e.arrayDesigns), width : 480 }, { html : 'Coexpr. Links:' }, { id : 'coexpressionLinkCount-region', html : this.renderCoExpressionLinkCount(e), width : 80 }, { html : 'Diff. expr. Probes' }, { id : 'DiffExpressedProbes-region', html : this.renderDiffExpressionDetails(e), width : 200 }, { html : 'Publication:' }, { xtype : 'panel', id : 'pubmed-region-wrap', layout : 'fit', bodyBorder : false, baseCls : 'x-plain-panel', disabled : false, items : [pubmedRegion] }, { html : 'Tags ' + taggerurl }, tagView, { html : 'Status' }, { html : this.renderStatus(e) }, { html : this.editable ? 'Admin' : '' }, { id : 'admin-links', html : this.editable ? adminLinks : '' } /* * authors */ ] }); if (this.editable) { Ext.DomHelper.append('admin-links', { tag : 'ul', cls : 'plainlist', children : [{ tag : 'li', html : 'Missing values: ' + this.missingValueAnalysisRenderer(e) }, { tag : 'li', html : 'Proc. vec: ' + this.processedVectorCreateRenderer(e) }, { tag : 'li', html : 'Diff ex: ' + this.differentialAnalysisRenderer(e) }, { tag : 'li', html : 'Link an.: ' + this.linkAnalysisRenderer(e) }] }); } if (Ext.get('history')) { var history = new Gemma.AuditTrailGrid({ renderTo : 'history', bodyBorder : false, collapsible : true, auditable : { id : e.id, classDelegatingFor : "ubic.gemma.model.expression.experiment.ExpressionExperimentImpl" } }); } this.fireEvent("ready"); }
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Ext.getCmp('update-button-region').show();
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Ext.getCmp('update-button-region').show(true);
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build : function(e) { var manager = new Gemma.EEManager({ editable : this.editable, id : "eemanager" }); this.manager = manager; // // /* // * Create a store with one record. // */ // var store = new Ext.data.Store({ // proxy : new Ext.data.MemoryProxy([e]), // reader : new Ext.data.ListRangeReader({}, // this.manager.record) // }); // // this.rec = store.getAt(0); adminLinks = '<a href="#" onClick="Ext.getCmp(\'eemanager\').updateEEReport(' + e.id + ')"><img src="/Gemma/images/icons/arrow_refresh_small.png" ext:qtip="Refresh statistics" title="refresh"/></a>' + ' <a href="/Gemma/expressionExperiment/editExpressionExperiment.html?id=' + e.id + '" ><img src="/Gemma/images/icons/wrench.png" ext:qtip="Go to editor page for this experiment" title="edit"/></a> '; if (this.isAdmin) { adminLinks = adminLinks + '<a href="#" onClick="return Ext.getCmp(\'eemanager\').deleteExperiment(' + e.id + ')"><img src="/Gemma/images/icons/cross.png" ext:qtip="Delete the experiment from the system" title="delete" /></a> '; } var pubmedRegion = {}; if (e.pubmedId) { // display the citation, with link out and delete // button. pubmedRegion = this.getPubMedHtml(e); } else { // offer to create a citation link. pubmedRegion = this.getPubMedForm(e); } /* * Show the experimental design */ DesignMatrix.init({ id : e.id }); var vizPanel = new Gemma.EEDetailsVisualizationWidget({ renderTo : 'visualization', taxon : e.parentTaxon }); /* * This is needed to make the annotator initialize properly. */ new Gemma.MGEDCombo({}); var taggerurl = '<a href="#" onClick="return Ext.getCmp(\'eemanager\').tagger(' + e.id + ',' + e.taxonId + ',' + this.editable + ')"><img src="/Gemma/images/icons/pencil.png" alt="view tags" title="view tags"/></a>'; tagView = new Gemma.AnnotationDataView({ readParams : [{ id : e.id, classDelegatingFor : "ExpressionExperimentImpl" }] }); manager.on('tagsUpdated', function() { tagView.store.reload(); }); manager.on('done', function() { window.location.reload(); }); manager.on('reportUpdated', function(data) { ob = data[0]; // console.log(ob); var k = Ext.get('coexpressionLinkCount-region'); Ext.DomHelper.overwrite(k, { html : ob.coexpressionLinkCount }); k.highlight(); k = Ext.get('processedExpressionVectorCount-region'); Ext.DomHelper.overwrite(k, { html : ob.processedExpressionVectorCount }); k.highlight(); }); manager.on('pubmedUpdated', function(e) { var html = this.getPubMedHtml(e); Ext.getCmp('pubmed-region-wrap').remove(Ext.getCmp('pubmed-region')); Ext.DomHelper.append('pubmed-region-wrap', html); }.createDelegate(this)); manager.on('pubmedRemove', function(success) { if (success) { var r = Ext.getCmp('pubmed-region-wrap'); r.remove(Ext.getCmp('pubmed-region')); var form = this.getPubMedForm(this.eeId); r.add(form); r.doLayout(); } }.createDelegate(this)); manager.on('updated', function(data) { Ext.getCmp('update-button-region').getEl().hide(); /* * Really we won't need to do this -- as the state on the database is supposed to match this one. */ var k = Ext.getCmp('shortname'); k.setValue(data.shortName); k = Ext.getCmp('name'); k.setValue(data.name); k = Ext.getCmp('description'); k.setValue(data.description); }.createDelegate(this)); // manager.on('reportUpdated', function() { // store.reload(); // }); // // manager.on('differential', function() { // store.reload(); // }); // manager.on('processedVector', function() { // store.reload(); // }); // manager.on('link', function() { // store.reload(); // }); // manager.on('missingValue', function() { // store.reload(); // }); var descriptionArea = new Ext.form.TextArea({ id : 'description', allowBlank : true, grow : true, growMax : 300, readOnly : !this.editable, disabledClass : 'disabled-plain', growMin : 40, emptyText : 'No description provided', enableKeyEvents : true, listeners : { 'keyup' : { fn : function(e) { if (Ext.getCmp('description').isDirty() && Ext.getCmp('description').isValid()) { // show save button Ext.getCmp('update-button-region').show(); } else { Ext.getCmp('update-button-region').hide(); } } } }, width : 500, // height : 100, value : e.description }); var nameArea = new Ext.form.TextArea({ id : 'name', fieldLabel : 'Name', allowBlank : false, grow : true, growMax : 300, readOnly : !this.editable, disabledClass : 'disabled-plain', growMin : 40, emptyText : 'No description provided', enableKeyEvents : true, listeners : { 'keyup' : { fn : function(e) { if (Ext.getCmp('name').isDirty() && Ext.getCmp('name').isValid()) { // show save button Ext.getCmp('update-button-region').show(); } else { Ext.getCmp('update-button-region').hide(); } } } }, width : 500, value : e.name }); var basics = new Ext.Panel({ autoHeight : true, layout : 'table', layoutConfig : { columns : 2 }, renderTo : 'basics', collapsible : false, bodyBorder : false, frame : false, baseCls : 'x-plain-panel', bodyStyle : 'padding:10px', defaults : { bodyStyle : 'vertical-align:top;font-size:12px;color:black', baseCls : 'x-plain-panel', fieldClass : 'x-bare-field' }, items : [{ html : 'Short name:' }, { xtype : 'panel', layout : 'table', baseCls : 'x-plain-panel', layoutConfig : { columns : 2 }, items : [{ xtype : 'textfield', id : 'shortname', enableKeyEvents : true, allowBlank : false, disabledClass : 'disabled-plain', fieldClass : 'x-bare-field', readOnly : !this.editable, listeners : { 'keyup' : { fn : function(e) { if (Ext.getCmp('shortname').isDirty() && Ext.getCmp('shortname').isValid()) { // show // save // button Ext.getCmp('update-button-region').show(); } else { Ext.getCmp('update-button-region').hide(); } }, scope : this } }, width : 250, value : e.shortName }, { baseCls : 'x-plain-panel', id : 'update-button-region', html : '<a href="#" onClick="Ext.getCmp(\'ee-details-panel\').save(' + e.id + ',[\'shortname\',\'name\',\'description\'])" ><img src="/Gemma/images/icons/database_save.png" title="Click to save changes" alt="Click to save changes"/></a>', hidden : true }] }, { html : 'Name:' }, nameArea, { html : "Taxon:" }, { html : e.taxon }, { html : 'Description:' }, descriptionArea, { html : 'Created:' }, { html : Ext.util.Format.date(e.dateCreated) }, { html : 'Source:' }, { html : this.renderSourceDatabaseEntry(e) }, { html : 'Samples:' }, { html : this.renderSamples(e), width : 60 }, { html : 'Profiles:' }, { id : 'processedExpressionVectorCount-region', html : '<div id="downloads"> ' + this.renderProcessedExpressionVectorCount(e) + ' ' + '<i>Downloads:</i> <a title="click to download the tab delimited data" href="#" onClick="fetchData(true,' + e.id + ', \'text\', null, null)">Filtered</a> ' + '<a href="#" title="click to download the tab delimited data" onClick="fetchData(false,' + e.id + ', \'text\', null, null)">Unfiltered</a> ' + '<a class="helpLink" href="?" onclick="showHelpTip(event, \'Tab-delimited data file for this experiment. The filtered version corresponds to what is used in most Gemma analyses, removing some probes. Unfiltered includes all probes\'); return false"> <img src="/Gemma/images/help.png" /> </a>' + '</div>', width : 400 }, { html : 'Array designs:' }, { id : 'arrayDesign-region', html : this.renderArrayDesigns(e.arrayDesigns), width : 480 }, { html : 'Coexpr. Links:' }, { id : 'coexpressionLinkCount-region', html : this.renderCoExpressionLinkCount(e), width : 80 }, { html : 'Diff. expr. Probes' }, { id : 'DiffExpressedProbes-region', html : this.renderDiffExpressionDetails(e), width : 200 }, { html : 'Publication:' }, { xtype : 'panel', id : 'pubmed-region-wrap', layout : 'fit', bodyBorder : false, baseCls : 'x-plain-panel', disabled : false, items : [pubmedRegion] }, { html : 'Tags ' + taggerurl }, tagView, { html : 'Status' }, { html : this.renderStatus(e) }, { html : this.editable ? 'Admin' : '' }, { id : 'admin-links', html : this.editable ? adminLinks : '' } /* * authors */ ] }); if (this.editable) { Ext.DomHelper.append('admin-links', { tag : 'ul', cls : 'plainlist', children : [{ tag : 'li', html : 'Missing values: ' + this.missingValueAnalysisRenderer(e) }, { tag : 'li', html : 'Proc. vec: ' + this.processedVectorCreateRenderer(e) }, { tag : 'li', html : 'Diff ex: ' + this.differentialAnalysisRenderer(e) }, { tag : 'li', html : 'Link an.: ' + this.linkAnalysisRenderer(e) }] }); } if (Ext.get('history')) { var history = new Gemma.AuditTrailGrid({ renderTo : 'history', bodyBorder : false, collapsible : true, auditable : { id : e.id, classDelegatingFor : "ubic.gemma.model.expression.experiment.ExpressionExperimentImpl" } }); } this.fireEvent("ready"); }
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Ext.getCmp('update-button-region').hide();
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Ext.getCmp('update-button-region').hide(true);
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build : function(e) { var manager = new Gemma.EEManager({ editable : this.editable, id : "eemanager" }); this.manager = manager; // // /* // * Create a store with one record. // */ // var store = new Ext.data.Store({ // proxy : new Ext.data.MemoryProxy([e]), // reader : new Ext.data.ListRangeReader({}, // this.manager.record) // }); // // this.rec = store.getAt(0); adminLinks = '<a href="#" onClick="Ext.getCmp(\'eemanager\').updateEEReport(' + e.id + ')"><img src="/Gemma/images/icons/arrow_refresh_small.png" ext:qtip="Refresh statistics" title="refresh"/></a>' + ' <a href="/Gemma/expressionExperiment/editExpressionExperiment.html?id=' + e.id + '" ><img src="/Gemma/images/icons/wrench.png" ext:qtip="Go to editor page for this experiment" title="edit"/></a> '; if (this.isAdmin) { adminLinks = adminLinks + '<a href="#" onClick="return Ext.getCmp(\'eemanager\').deleteExperiment(' + e.id + ')"><img src="/Gemma/images/icons/cross.png" ext:qtip="Delete the experiment from the system" title="delete" /></a> '; } var pubmedRegion = {}; if (e.pubmedId) { // display the citation, with link out and delete // button. pubmedRegion = this.getPubMedHtml(e); } else { // offer to create a citation link. pubmedRegion = this.getPubMedForm(e); } /* * Show the experimental design */ DesignMatrix.init({ id : e.id }); var vizPanel = new Gemma.EEDetailsVisualizationWidget({ renderTo : 'visualization', taxon : e.parentTaxon }); /* * This is needed to make the annotator initialize properly. */ new Gemma.MGEDCombo({}); var taggerurl = '<a href="#" onClick="return Ext.getCmp(\'eemanager\').tagger(' + e.id + ',' + e.taxonId + ',' + this.editable + ')"><img src="/Gemma/images/icons/pencil.png" alt="view tags" title="view tags"/></a>'; tagView = new Gemma.AnnotationDataView({ readParams : [{ id : e.id, classDelegatingFor : "ExpressionExperimentImpl" }] }); manager.on('tagsUpdated', function() { tagView.store.reload(); }); manager.on('done', function() { window.location.reload(); }); manager.on('reportUpdated', function(data) { ob = data[0]; // console.log(ob); var k = Ext.get('coexpressionLinkCount-region'); Ext.DomHelper.overwrite(k, { html : ob.coexpressionLinkCount }); k.highlight(); k = Ext.get('processedExpressionVectorCount-region'); Ext.DomHelper.overwrite(k, { html : ob.processedExpressionVectorCount }); k.highlight(); }); manager.on('pubmedUpdated', function(e) { var html = this.getPubMedHtml(e); Ext.getCmp('pubmed-region-wrap').remove(Ext.getCmp('pubmed-region')); Ext.DomHelper.append('pubmed-region-wrap', html); }.createDelegate(this)); manager.on('pubmedRemove', function(success) { if (success) { var r = Ext.getCmp('pubmed-region-wrap'); r.remove(Ext.getCmp('pubmed-region')); var form = this.getPubMedForm(this.eeId); r.add(form); r.doLayout(); } }.createDelegate(this)); manager.on('updated', function(data) { Ext.getCmp('update-button-region').getEl().hide(); /* * Really we won't need to do this -- as the state on the database is supposed to match this one. */ var k = Ext.getCmp('shortname'); k.setValue(data.shortName); k = Ext.getCmp('name'); k.setValue(data.name); k = Ext.getCmp('description'); k.setValue(data.description); }.createDelegate(this)); // manager.on('reportUpdated', function() { // store.reload(); // }); // // manager.on('differential', function() { // store.reload(); // }); // manager.on('processedVector', function() { // store.reload(); // }); // manager.on('link', function() { // store.reload(); // }); // manager.on('missingValue', function() { // store.reload(); // }); var descriptionArea = new Ext.form.TextArea({ id : 'description', allowBlank : true, grow : true, growMax : 300, readOnly : !this.editable, disabledClass : 'disabled-plain', growMin : 40, emptyText : 'No description provided', enableKeyEvents : true, listeners : { 'keyup' : { fn : function(e) { if (Ext.getCmp('description').isDirty() && Ext.getCmp('description').isValid()) { // show save button Ext.getCmp('update-button-region').show(); } else { Ext.getCmp('update-button-region').hide(); } } } }, width : 500, // height : 100, value : e.description }); var nameArea = new Ext.form.TextArea({ id : 'name', fieldLabel : 'Name', allowBlank : false, grow : true, growMax : 300, readOnly : !this.editable, disabledClass : 'disabled-plain', growMin : 40, emptyText : 'No description provided', enableKeyEvents : true, listeners : { 'keyup' : { fn : function(e) { if (Ext.getCmp('name').isDirty() && Ext.getCmp('name').isValid()) { // show save button Ext.getCmp('update-button-region').show(); } else { Ext.getCmp('update-button-region').hide(); } } } }, width : 500, value : e.name }); var basics = new Ext.Panel({ autoHeight : true, layout : 'table', layoutConfig : { columns : 2 }, renderTo : 'basics', collapsible : false, bodyBorder : false, frame : false, baseCls : 'x-plain-panel', bodyStyle : 'padding:10px', defaults : { bodyStyle : 'vertical-align:top;font-size:12px;color:black', baseCls : 'x-plain-panel', fieldClass : 'x-bare-field' }, items : [{ html : 'Short name:' }, { xtype : 'panel', layout : 'table', baseCls : 'x-plain-panel', layoutConfig : { columns : 2 }, items : [{ xtype : 'textfield', id : 'shortname', enableKeyEvents : true, allowBlank : false, disabledClass : 'disabled-plain', fieldClass : 'x-bare-field', readOnly : !this.editable, listeners : { 'keyup' : { fn : function(e) { if (Ext.getCmp('shortname').isDirty() && Ext.getCmp('shortname').isValid()) { // show // save // button Ext.getCmp('update-button-region').show(); } else { Ext.getCmp('update-button-region').hide(); } }, scope : this } }, width : 250, value : e.shortName }, { baseCls : 'x-plain-panel', id : 'update-button-region', html : '<a href="#" onClick="Ext.getCmp(\'ee-details-panel\').save(' + e.id + ',[\'shortname\',\'name\',\'description\'])" ><img src="/Gemma/images/icons/database_save.png" title="Click to save changes" alt="Click to save changes"/></a>', hidden : true }] }, { html : 'Name:' }, nameArea, { html : "Taxon:" }, { html : e.taxon }, { html : 'Description:' }, descriptionArea, { html : 'Created:' }, { html : Ext.util.Format.date(e.dateCreated) }, { html : 'Source:' }, { html : this.renderSourceDatabaseEntry(e) }, { html : 'Samples:' }, { html : this.renderSamples(e), width : 60 }, { html : 'Profiles:' }, { id : 'processedExpressionVectorCount-region', html : '<div id="downloads"> ' + this.renderProcessedExpressionVectorCount(e) + ' ' + '<i>Downloads:</i> <a title="click to download the tab delimited data" href="#" onClick="fetchData(true,' + e.id + ', \'text\', null, null)">Filtered</a> ' + '<a href="#" title="click to download the tab delimited data" onClick="fetchData(false,' + e.id + ', \'text\', null, null)">Unfiltered</a> ' + '<a class="helpLink" href="?" onclick="showHelpTip(event, \'Tab-delimited data file for this experiment. The filtered version corresponds to what is used in most Gemma analyses, removing some probes. Unfiltered includes all probes\'); return false"> <img src="/Gemma/images/help.png" /> </a>' + '</div>', width : 400 }, { html : 'Array designs:' }, { id : 'arrayDesign-region', html : this.renderArrayDesigns(e.arrayDesigns), width : 480 }, { html : 'Coexpr. Links:' }, { id : 'coexpressionLinkCount-region', html : this.renderCoExpressionLinkCount(e), width : 80 }, { html : 'Diff. expr. Probes' }, { id : 'DiffExpressedProbes-region', html : this.renderDiffExpressionDetails(e), width : 200 }, { html : 'Publication:' }, { xtype : 'panel', id : 'pubmed-region-wrap', layout : 'fit', bodyBorder : false, baseCls : 'x-plain-panel', disabled : false, items : [pubmedRegion] }, { html : 'Tags ' + taggerurl }, tagView, { html : 'Status' }, { html : this.renderStatus(e) }, { html : this.editable ? 'Admin' : '' }, { id : 'admin-links', html : this.editable ? adminLinks : '' } /* * authors */ ] }); if (this.editable) { Ext.DomHelper.append('admin-links', { tag : 'ul', cls : 'plainlist', children : [{ tag : 'li', html : 'Missing values: ' + this.missingValueAnalysisRenderer(e) }, { tag : 'li', html : 'Proc. vec: ' + this.processedVectorCreateRenderer(e) }, { tag : 'li', html : 'Diff ex: ' + this.differentialAnalysisRenderer(e) }, { tag : 'li', html : 'Link an.: ' + this.linkAnalysisRenderer(e) }] }); } if (Ext.get('history')) { var history = new Gemma.AuditTrailGrid({ renderTo : 'history', bodyBorder : false, collapsible : true, auditable : { id : e.id, classDelegatingFor : "ubic.gemma.model.expression.experiment.ExpressionExperimentImpl" } }); } this.fireEvent("ready"); }
|
html : '<a href="#" onClick="Ext.getCmp(\'ee-details-panel\').save(' +
|
html : '<span style="cursor:pointer" onClick="Ext.getCmp(\'ee-details-panel\').save(' +
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build : function(e) { var manager = new Gemma.EEManager({ editable : this.editable, id : "eemanager" }); this.manager = manager; // // /* // * Create a store with one record. // */ // var store = new Ext.data.Store({ // proxy : new Ext.data.MemoryProxy([e]), // reader : new Ext.data.ListRangeReader({}, // this.manager.record) // }); // // this.rec = store.getAt(0); adminLinks = '<a href="#" onClick="Ext.getCmp(\'eemanager\').updateEEReport(' + e.id + ')"><img src="/Gemma/images/icons/arrow_refresh_small.png" ext:qtip="Refresh statistics" title="refresh"/></a>' + ' <a href="/Gemma/expressionExperiment/editExpressionExperiment.html?id=' + e.id + '" ><img src="/Gemma/images/icons/wrench.png" ext:qtip="Go to editor page for this experiment" title="edit"/></a> '; if (this.isAdmin) { adminLinks = adminLinks + '<a href="#" onClick="return Ext.getCmp(\'eemanager\').deleteExperiment(' + e.id + ')"><img src="/Gemma/images/icons/cross.png" ext:qtip="Delete the experiment from the system" title="delete" /></a> '; } var pubmedRegion = {}; if (e.pubmedId) { // display the citation, with link out and delete // button. pubmedRegion = this.getPubMedHtml(e); } else { // offer to create a citation link. pubmedRegion = this.getPubMedForm(e); } /* * Show the experimental design */ DesignMatrix.init({ id : e.id }); var vizPanel = new Gemma.EEDetailsVisualizationWidget({ renderTo : 'visualization', taxon : e.parentTaxon }); /* * This is needed to make the annotator initialize properly. */ new Gemma.MGEDCombo({}); var taggerurl = '<a href="#" onClick="return Ext.getCmp(\'eemanager\').tagger(' + e.id + ',' + e.taxonId + ',' + this.editable + ')"><img src="/Gemma/images/icons/pencil.png" alt="view tags" title="view tags"/></a>'; tagView = new Gemma.AnnotationDataView({ readParams : [{ id : e.id, classDelegatingFor : "ExpressionExperimentImpl" }] }); manager.on('tagsUpdated', function() { tagView.store.reload(); }); manager.on('done', function() { window.location.reload(); }); manager.on('reportUpdated', function(data) { ob = data[0]; // console.log(ob); var k = Ext.get('coexpressionLinkCount-region'); Ext.DomHelper.overwrite(k, { html : ob.coexpressionLinkCount }); k.highlight(); k = Ext.get('processedExpressionVectorCount-region'); Ext.DomHelper.overwrite(k, { html : ob.processedExpressionVectorCount }); k.highlight(); }); manager.on('pubmedUpdated', function(e) { var html = this.getPubMedHtml(e); Ext.getCmp('pubmed-region-wrap').remove(Ext.getCmp('pubmed-region')); Ext.DomHelper.append('pubmed-region-wrap', html); }.createDelegate(this)); manager.on('pubmedRemove', function(success) { if (success) { var r = Ext.getCmp('pubmed-region-wrap'); r.remove(Ext.getCmp('pubmed-region')); var form = this.getPubMedForm(this.eeId); r.add(form); r.doLayout(); } }.createDelegate(this)); manager.on('updated', function(data) { Ext.getCmp('update-button-region').getEl().hide(); /* * Really we won't need to do this -- as the state on the database is supposed to match this one. */ var k = Ext.getCmp('shortname'); k.setValue(data.shortName); k = Ext.getCmp('name'); k.setValue(data.name); k = Ext.getCmp('description'); k.setValue(data.description); }.createDelegate(this)); // manager.on('reportUpdated', function() { // store.reload(); // }); // // manager.on('differential', function() { // store.reload(); // }); // manager.on('processedVector', function() { // store.reload(); // }); // manager.on('link', function() { // store.reload(); // }); // manager.on('missingValue', function() { // store.reload(); // }); var descriptionArea = new Ext.form.TextArea({ id : 'description', allowBlank : true, grow : true, growMax : 300, readOnly : !this.editable, disabledClass : 'disabled-plain', growMin : 40, emptyText : 'No description provided', enableKeyEvents : true, listeners : { 'keyup' : { fn : function(e) { if (Ext.getCmp('description').isDirty() && Ext.getCmp('description').isValid()) { // show save button Ext.getCmp('update-button-region').show(); } else { Ext.getCmp('update-button-region').hide(); } } } }, width : 500, // height : 100, value : e.description }); var nameArea = new Ext.form.TextArea({ id : 'name', fieldLabel : 'Name', allowBlank : false, grow : true, growMax : 300, readOnly : !this.editable, disabledClass : 'disabled-plain', growMin : 40, emptyText : 'No description provided', enableKeyEvents : true, listeners : { 'keyup' : { fn : function(e) { if (Ext.getCmp('name').isDirty() && Ext.getCmp('name').isValid()) { // show save button Ext.getCmp('update-button-region').show(); } else { Ext.getCmp('update-button-region').hide(); } } } }, width : 500, value : e.name }); var basics = new Ext.Panel({ autoHeight : true, layout : 'table', layoutConfig : { columns : 2 }, renderTo : 'basics', collapsible : false, bodyBorder : false, frame : false, baseCls : 'x-plain-panel', bodyStyle : 'padding:10px', defaults : { bodyStyle : 'vertical-align:top;font-size:12px;color:black', baseCls : 'x-plain-panel', fieldClass : 'x-bare-field' }, items : [{ html : 'Short name:' }, { xtype : 'panel', layout : 'table', baseCls : 'x-plain-panel', layoutConfig : { columns : 2 }, items : [{ xtype : 'textfield', id : 'shortname', enableKeyEvents : true, allowBlank : false, disabledClass : 'disabled-plain', fieldClass : 'x-bare-field', readOnly : !this.editable, listeners : { 'keyup' : { fn : function(e) { if (Ext.getCmp('shortname').isDirty() && Ext.getCmp('shortname').isValid()) { // show // save // button Ext.getCmp('update-button-region').show(); } else { Ext.getCmp('update-button-region').hide(); } }, scope : this } }, width : 250, value : e.shortName }, { baseCls : 'x-plain-panel', id : 'update-button-region', html : '<a href="#" onClick="Ext.getCmp(\'ee-details-panel\').save(' + e.id + ',[\'shortname\',\'name\',\'description\'])" ><img src="/Gemma/images/icons/database_save.png" title="Click to save changes" alt="Click to save changes"/></a>', hidden : true }] }, { html : 'Name:' }, nameArea, { html : "Taxon:" }, { html : e.taxon }, { html : 'Description:' }, descriptionArea, { html : 'Created:' }, { html : Ext.util.Format.date(e.dateCreated) }, { html : 'Source:' }, { html : this.renderSourceDatabaseEntry(e) }, { html : 'Samples:' }, { html : this.renderSamples(e), width : 60 }, { html : 'Profiles:' }, { id : 'processedExpressionVectorCount-region', html : '<div id="downloads"> ' + this.renderProcessedExpressionVectorCount(e) + ' ' + '<i>Downloads:</i> <a title="click to download the tab delimited data" href="#" onClick="fetchData(true,' + e.id + ', \'text\', null, null)">Filtered</a> ' + '<a href="#" title="click to download the tab delimited data" onClick="fetchData(false,' + e.id + ', \'text\', null, null)">Unfiltered</a> ' + '<a class="helpLink" href="?" onclick="showHelpTip(event, \'Tab-delimited data file for this experiment. The filtered version corresponds to what is used in most Gemma analyses, removing some probes. Unfiltered includes all probes\'); return false"> <img src="/Gemma/images/help.png" /> </a>' + '</div>', width : 400 }, { html : 'Array designs:' }, { id : 'arrayDesign-region', html : this.renderArrayDesigns(e.arrayDesigns), width : 480 }, { html : 'Coexpr. Links:' }, { id : 'coexpressionLinkCount-region', html : this.renderCoExpressionLinkCount(e), width : 80 }, { html : 'Diff. expr. Probes' }, { id : 'DiffExpressedProbes-region', html : this.renderDiffExpressionDetails(e), width : 200 }, { html : 'Publication:' }, { xtype : 'panel', id : 'pubmed-region-wrap', layout : 'fit', bodyBorder : false, baseCls : 'x-plain-panel', disabled : false, items : [pubmedRegion] }, { html : 'Tags ' + taggerurl }, tagView, { html : 'Status' }, { html : this.renderStatus(e) }, { html : this.editable ? 'Admin' : '' }, { id : 'admin-links', html : this.editable ? adminLinks : '' } /* * authors */ ] }); if (this.editable) { Ext.DomHelper.append('admin-links', { tag : 'ul', cls : 'plainlist', children : [{ tag : 'li', html : 'Missing values: ' + this.missingValueAnalysisRenderer(e) }, { tag : 'li', html : 'Proc. vec: ' + this.processedVectorCreateRenderer(e) }, { tag : 'li', html : 'Diff ex: ' + this.differentialAnalysisRenderer(e) }, { tag : 'li', html : 'Link an.: ' + this.linkAnalysisRenderer(e) }] }); } if (Ext.get('history')) { var history = new Gemma.AuditTrailGrid({ renderTo : 'history', bodyBorder : false, collapsible : true, auditable : { id : e.id, classDelegatingFor : "ubic.gemma.model.expression.experiment.ExpressionExperimentImpl" } }); } this.fireEvent("ready"); }
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',[\'shortname\',\'name\',\'description\'])" ><img src="/Gemma/images/icons/database_save.png" title="Click to save changes" alt="Click to save changes"/></a>',
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',[\'shortname\',\'name\',\'description\'])" ><img src="/Gemma/images/icons/database_save.png" ext:qtip="Click to save changes" alt="Click to save changes"/></span>',
|
build : function(e) { var manager = new Gemma.EEManager({ editable : this.editable, id : "eemanager" }); this.manager = manager; // // /* // * Create a store with one record. // */ // var store = new Ext.data.Store({ // proxy : new Ext.data.MemoryProxy([e]), // reader : new Ext.data.ListRangeReader({}, // this.manager.record) // }); // // this.rec = store.getAt(0); adminLinks = '<a href="#" onClick="Ext.getCmp(\'eemanager\').updateEEReport(' + e.id + ')"><img src="/Gemma/images/icons/arrow_refresh_small.png" ext:qtip="Refresh statistics" title="refresh"/></a>' + ' <a href="/Gemma/expressionExperiment/editExpressionExperiment.html?id=' + e.id + '" ><img src="/Gemma/images/icons/wrench.png" ext:qtip="Go to editor page for this experiment" title="edit"/></a> '; if (this.isAdmin) { adminLinks = adminLinks + '<a href="#" onClick="return Ext.getCmp(\'eemanager\').deleteExperiment(' + e.id + ')"><img src="/Gemma/images/icons/cross.png" ext:qtip="Delete the experiment from the system" title="delete" /></a> '; } var pubmedRegion = {}; if (e.pubmedId) { // display the citation, with link out and delete // button. pubmedRegion = this.getPubMedHtml(e); } else { // offer to create a citation link. pubmedRegion = this.getPubMedForm(e); } /* * Show the experimental design */ DesignMatrix.init({ id : e.id }); var vizPanel = new Gemma.EEDetailsVisualizationWidget({ renderTo : 'visualization', taxon : e.parentTaxon }); /* * This is needed to make the annotator initialize properly. */ new Gemma.MGEDCombo({}); var taggerurl = '<a href="#" onClick="return Ext.getCmp(\'eemanager\').tagger(' + e.id + ',' + e.taxonId + ',' + this.editable + ')"><img src="/Gemma/images/icons/pencil.png" alt="view tags" title="view tags"/></a>'; tagView = new Gemma.AnnotationDataView({ readParams : [{ id : e.id, classDelegatingFor : "ExpressionExperimentImpl" }] }); manager.on('tagsUpdated', function() { tagView.store.reload(); }); manager.on('done', function() { window.location.reload(); }); manager.on('reportUpdated', function(data) { ob = data[0]; // console.log(ob); var k = Ext.get('coexpressionLinkCount-region'); Ext.DomHelper.overwrite(k, { html : ob.coexpressionLinkCount }); k.highlight(); k = Ext.get('processedExpressionVectorCount-region'); Ext.DomHelper.overwrite(k, { html : ob.processedExpressionVectorCount }); k.highlight(); }); manager.on('pubmedUpdated', function(e) { var html = this.getPubMedHtml(e); Ext.getCmp('pubmed-region-wrap').remove(Ext.getCmp('pubmed-region')); Ext.DomHelper.append('pubmed-region-wrap', html); }.createDelegate(this)); manager.on('pubmedRemove', function(success) { if (success) { var r = Ext.getCmp('pubmed-region-wrap'); r.remove(Ext.getCmp('pubmed-region')); var form = this.getPubMedForm(this.eeId); r.add(form); r.doLayout(); } }.createDelegate(this)); manager.on('updated', function(data) { Ext.getCmp('update-button-region').getEl().hide(); /* * Really we won't need to do this -- as the state on the database is supposed to match this one. */ var k = Ext.getCmp('shortname'); k.setValue(data.shortName); k = Ext.getCmp('name'); k.setValue(data.name); k = Ext.getCmp('description'); k.setValue(data.description); }.createDelegate(this)); // manager.on('reportUpdated', function() { // store.reload(); // }); // // manager.on('differential', function() { // store.reload(); // }); // manager.on('processedVector', function() { // store.reload(); // }); // manager.on('link', function() { // store.reload(); // }); // manager.on('missingValue', function() { // store.reload(); // }); var descriptionArea = new Ext.form.TextArea({ id : 'description', allowBlank : true, grow : true, growMax : 300, readOnly : !this.editable, disabledClass : 'disabled-plain', growMin : 40, emptyText : 'No description provided', enableKeyEvents : true, listeners : { 'keyup' : { fn : function(e) { if (Ext.getCmp('description').isDirty() && Ext.getCmp('description').isValid()) { // show save button Ext.getCmp('update-button-region').show(); } else { Ext.getCmp('update-button-region').hide(); } } } }, width : 500, // height : 100, value : e.description }); var nameArea = new Ext.form.TextArea({ id : 'name', fieldLabel : 'Name', allowBlank : false, grow : true, growMax : 300, readOnly : !this.editable, disabledClass : 'disabled-plain', growMin : 40, emptyText : 'No description provided', enableKeyEvents : true, listeners : { 'keyup' : { fn : function(e) { if (Ext.getCmp('name').isDirty() && Ext.getCmp('name').isValid()) { // show save button Ext.getCmp('update-button-region').show(); } else { Ext.getCmp('update-button-region').hide(); } } } }, width : 500, value : e.name }); var basics = new Ext.Panel({ autoHeight : true, layout : 'table', layoutConfig : { columns : 2 }, renderTo : 'basics', collapsible : false, bodyBorder : false, frame : false, baseCls : 'x-plain-panel', bodyStyle : 'padding:10px', defaults : { bodyStyle : 'vertical-align:top;font-size:12px;color:black', baseCls : 'x-plain-panel', fieldClass : 'x-bare-field' }, items : [{ html : 'Short name:' }, { xtype : 'panel', layout : 'table', baseCls : 'x-plain-panel', layoutConfig : { columns : 2 }, items : [{ xtype : 'textfield', id : 'shortname', enableKeyEvents : true, allowBlank : false, disabledClass : 'disabled-plain', fieldClass : 'x-bare-field', readOnly : !this.editable, listeners : { 'keyup' : { fn : function(e) { if (Ext.getCmp('shortname').isDirty() && Ext.getCmp('shortname').isValid()) { // show // save // button Ext.getCmp('update-button-region').show(); } else { Ext.getCmp('update-button-region').hide(); } }, scope : this } }, width : 250, value : e.shortName }, { baseCls : 'x-plain-panel', id : 'update-button-region', html : '<a href="#" onClick="Ext.getCmp(\'ee-details-panel\').save(' + e.id + ',[\'shortname\',\'name\',\'description\'])" ><img src="/Gemma/images/icons/database_save.png" title="Click to save changes" alt="Click to save changes"/></a>', hidden : true }] }, { html : 'Name:' }, nameArea, { html : "Taxon:" }, { html : e.taxon }, { html : 'Description:' }, descriptionArea, { html : 'Created:' }, { html : Ext.util.Format.date(e.dateCreated) }, { html : 'Source:' }, { html : this.renderSourceDatabaseEntry(e) }, { html : 'Samples:' }, { html : this.renderSamples(e), width : 60 }, { html : 'Profiles:' }, { id : 'processedExpressionVectorCount-region', html : '<div id="downloads"> ' + this.renderProcessedExpressionVectorCount(e) + ' ' + '<i>Downloads:</i> <a title="click to download the tab delimited data" href="#" onClick="fetchData(true,' + e.id + ', \'text\', null, null)">Filtered</a> ' + '<a href="#" title="click to download the tab delimited data" onClick="fetchData(false,' + e.id + ', \'text\', null, null)">Unfiltered</a> ' + '<a class="helpLink" href="?" onclick="showHelpTip(event, \'Tab-delimited data file for this experiment. The filtered version corresponds to what is used in most Gemma analyses, removing some probes. Unfiltered includes all probes\'); return false"> <img src="/Gemma/images/help.png" /> </a>' + '</div>', width : 400 }, { html : 'Array designs:' }, { id : 'arrayDesign-region', html : this.renderArrayDesigns(e.arrayDesigns), width : 480 }, { html : 'Coexpr. Links:' }, { id : 'coexpressionLinkCount-region', html : this.renderCoExpressionLinkCount(e), width : 80 }, { html : 'Diff. expr. Probes' }, { id : 'DiffExpressedProbes-region', html : this.renderDiffExpressionDetails(e), width : 200 }, { html : 'Publication:' }, { xtype : 'panel', id : 'pubmed-region-wrap', layout : 'fit', bodyBorder : false, baseCls : 'x-plain-panel', disabled : false, items : [pubmedRegion] }, { html : 'Tags ' + taggerurl }, tagView, { html : 'Status' }, { html : this.renderStatus(e) }, { html : this.editable ? 'Admin' : '' }, { id : 'admin-links', html : this.editable ? adminLinks : '' } /* * authors */ ] }); if (this.editable) { Ext.DomHelper.append('admin-links', { tag : 'ul', cls : 'plainlist', children : [{ tag : 'li', html : 'Missing values: ' + this.missingValueAnalysisRenderer(e) }, { tag : 'li', html : 'Proc. vec: ' + this.processedVectorCreateRenderer(e) }, { tag : 'li', html : 'Diff ex: ' + this.differentialAnalysisRenderer(e) }, { tag : 'li', html : 'Link an.: ' + this.linkAnalysisRenderer(e) }] }); } if (Ext.get('history')) { var history = new Gemma.AuditTrailGrid({ renderTo : 'history', bodyBorder : false, collapsible : true, auditable : { id : e.id, classDelegatingFor : "ubic.gemma.model.expression.experiment.ExpressionExperimentImpl" } }); } this.fireEvent("ready"); }
|
'<i>Downloads:</i> <a title="click to download the tab delimited data" href="#" onClick="fetchData(true,' +
|
'<i>Downloads:</i> <span class="link" ext:qtip="Download the tab delimited data" onClick="fetchData(true,' +
|
build : function(e) { var manager = new Gemma.EEManager({ editable : this.editable, id : "eemanager" }); this.manager = manager; // // /* // * Create a store with one record. // */ // var store = new Ext.data.Store({ // proxy : new Ext.data.MemoryProxy([e]), // reader : new Ext.data.ListRangeReader({}, // this.manager.record) // }); // // this.rec = store.getAt(0); adminLinks = '<a href="#" onClick="Ext.getCmp(\'eemanager\').updateEEReport(' + e.id + ')"><img src="/Gemma/images/icons/arrow_refresh_small.png" ext:qtip="Refresh statistics" title="refresh"/></a>' + ' <a href="/Gemma/expressionExperiment/editExpressionExperiment.html?id=' + e.id + '" ><img src="/Gemma/images/icons/wrench.png" ext:qtip="Go to editor page for this experiment" title="edit"/></a> '; if (this.isAdmin) { adminLinks = adminLinks + '<a href="#" onClick="return Ext.getCmp(\'eemanager\').deleteExperiment(' + e.id + ')"><img src="/Gemma/images/icons/cross.png" ext:qtip="Delete the experiment from the system" title="delete" /></a> '; } var pubmedRegion = {}; if (e.pubmedId) { // display the citation, with link out and delete // button. pubmedRegion = this.getPubMedHtml(e); } else { // offer to create a citation link. pubmedRegion = this.getPubMedForm(e); } /* * Show the experimental design */ DesignMatrix.init({ id : e.id }); var vizPanel = new Gemma.EEDetailsVisualizationWidget({ renderTo : 'visualization', taxon : e.parentTaxon }); /* * This is needed to make the annotator initialize properly. */ new Gemma.MGEDCombo({}); var taggerurl = '<a href="#" onClick="return Ext.getCmp(\'eemanager\').tagger(' + e.id + ',' + e.taxonId + ',' + this.editable + ')"><img src="/Gemma/images/icons/pencil.png" alt="view tags" title="view tags"/></a>'; tagView = new Gemma.AnnotationDataView({ readParams : [{ id : e.id, classDelegatingFor : "ExpressionExperimentImpl" }] }); manager.on('tagsUpdated', function() { tagView.store.reload(); }); manager.on('done', function() { window.location.reload(); }); manager.on('reportUpdated', function(data) { ob = data[0]; // console.log(ob); var k = Ext.get('coexpressionLinkCount-region'); Ext.DomHelper.overwrite(k, { html : ob.coexpressionLinkCount }); k.highlight(); k = Ext.get('processedExpressionVectorCount-region'); Ext.DomHelper.overwrite(k, { html : ob.processedExpressionVectorCount }); k.highlight(); }); manager.on('pubmedUpdated', function(e) { var html = this.getPubMedHtml(e); Ext.getCmp('pubmed-region-wrap').remove(Ext.getCmp('pubmed-region')); Ext.DomHelper.append('pubmed-region-wrap', html); }.createDelegate(this)); manager.on('pubmedRemove', function(success) { if (success) { var r = Ext.getCmp('pubmed-region-wrap'); r.remove(Ext.getCmp('pubmed-region')); var form = this.getPubMedForm(this.eeId); r.add(form); r.doLayout(); } }.createDelegate(this)); manager.on('updated', function(data) { Ext.getCmp('update-button-region').getEl().hide(); /* * Really we won't need to do this -- as the state on the database is supposed to match this one. */ var k = Ext.getCmp('shortname'); k.setValue(data.shortName); k = Ext.getCmp('name'); k.setValue(data.name); k = Ext.getCmp('description'); k.setValue(data.description); }.createDelegate(this)); // manager.on('reportUpdated', function() { // store.reload(); // }); // // manager.on('differential', function() { // store.reload(); // }); // manager.on('processedVector', function() { // store.reload(); // }); // manager.on('link', function() { // store.reload(); // }); // manager.on('missingValue', function() { // store.reload(); // }); var descriptionArea = new Ext.form.TextArea({ id : 'description', allowBlank : true, grow : true, growMax : 300, readOnly : !this.editable, disabledClass : 'disabled-plain', growMin : 40, emptyText : 'No description provided', enableKeyEvents : true, listeners : { 'keyup' : { fn : function(e) { if (Ext.getCmp('description').isDirty() && Ext.getCmp('description').isValid()) { // show save button Ext.getCmp('update-button-region').show(); } else { Ext.getCmp('update-button-region').hide(); } } } }, width : 500, // height : 100, value : e.description }); var nameArea = new Ext.form.TextArea({ id : 'name', fieldLabel : 'Name', allowBlank : false, grow : true, growMax : 300, readOnly : !this.editable, disabledClass : 'disabled-plain', growMin : 40, emptyText : 'No description provided', enableKeyEvents : true, listeners : { 'keyup' : { fn : function(e) { if (Ext.getCmp('name').isDirty() && Ext.getCmp('name').isValid()) { // show save button Ext.getCmp('update-button-region').show(); } else { Ext.getCmp('update-button-region').hide(); } } } }, width : 500, value : e.name }); var basics = new Ext.Panel({ autoHeight : true, layout : 'table', layoutConfig : { columns : 2 }, renderTo : 'basics', collapsible : false, bodyBorder : false, frame : false, baseCls : 'x-plain-panel', bodyStyle : 'padding:10px', defaults : { bodyStyle : 'vertical-align:top;font-size:12px;color:black', baseCls : 'x-plain-panel', fieldClass : 'x-bare-field' }, items : [{ html : 'Short name:' }, { xtype : 'panel', layout : 'table', baseCls : 'x-plain-panel', layoutConfig : { columns : 2 }, items : [{ xtype : 'textfield', id : 'shortname', enableKeyEvents : true, allowBlank : false, disabledClass : 'disabled-plain', fieldClass : 'x-bare-field', readOnly : !this.editable, listeners : { 'keyup' : { fn : function(e) { if (Ext.getCmp('shortname').isDirty() && Ext.getCmp('shortname').isValid()) { // show // save // button Ext.getCmp('update-button-region').show(); } else { Ext.getCmp('update-button-region').hide(); } }, scope : this } }, width : 250, value : e.shortName }, { baseCls : 'x-plain-panel', id : 'update-button-region', html : '<a href="#" onClick="Ext.getCmp(\'ee-details-panel\').save(' + e.id + ',[\'shortname\',\'name\',\'description\'])" ><img src="/Gemma/images/icons/database_save.png" title="Click to save changes" alt="Click to save changes"/></a>', hidden : true }] }, { html : 'Name:' }, nameArea, { html : "Taxon:" }, { html : e.taxon }, { html : 'Description:' }, descriptionArea, { html : 'Created:' }, { html : Ext.util.Format.date(e.dateCreated) }, { html : 'Source:' }, { html : this.renderSourceDatabaseEntry(e) }, { html : 'Samples:' }, { html : this.renderSamples(e), width : 60 }, { html : 'Profiles:' }, { id : 'processedExpressionVectorCount-region', html : '<div id="downloads"> ' + this.renderProcessedExpressionVectorCount(e) + ' ' + '<i>Downloads:</i> <a title="click to download the tab delimited data" href="#" onClick="fetchData(true,' + e.id + ', \'text\', null, null)">Filtered</a> ' + '<a href="#" title="click to download the tab delimited data" onClick="fetchData(false,' + e.id + ', \'text\', null, null)">Unfiltered</a> ' + '<a class="helpLink" href="?" onclick="showHelpTip(event, \'Tab-delimited data file for this experiment. The filtered version corresponds to what is used in most Gemma analyses, removing some probes. Unfiltered includes all probes\'); return false"> <img src="/Gemma/images/help.png" /> </a>' + '</div>', width : 400 }, { html : 'Array designs:' }, { id : 'arrayDesign-region', html : this.renderArrayDesigns(e.arrayDesigns), width : 480 }, { html : 'Coexpr. Links:' }, { id : 'coexpressionLinkCount-region', html : this.renderCoExpressionLinkCount(e), width : 80 }, { html : 'Diff. expr. Probes' }, { id : 'DiffExpressedProbes-region', html : this.renderDiffExpressionDetails(e), width : 200 }, { html : 'Publication:' }, { xtype : 'panel', id : 'pubmed-region-wrap', layout : 'fit', bodyBorder : false, baseCls : 'x-plain-panel', disabled : false, items : [pubmedRegion] }, { html : 'Tags ' + taggerurl }, tagView, { html : 'Status' }, { html : this.renderStatus(e) }, { html : this.editable ? 'Admin' : '' }, { id : 'admin-links', html : this.editable ? adminLinks : '' } /* * authors */ ] }); if (this.editable) { Ext.DomHelper.append('admin-links', { tag : 'ul', cls : 'plainlist', children : [{ tag : 'li', html : 'Missing values: ' + this.missingValueAnalysisRenderer(e) }, { tag : 'li', html : 'Proc. vec: ' + this.processedVectorCreateRenderer(e) }, { tag : 'li', html : 'Diff ex: ' + this.differentialAnalysisRenderer(e) }, { tag : 'li', html : 'Link an.: ' + this.linkAnalysisRenderer(e) }] }); } if (Ext.get('history')) { var history = new Gemma.AuditTrailGrid({ renderTo : 'history', bodyBorder : false, collapsible : true, auditable : { id : e.id, classDelegatingFor : "ubic.gemma.model.expression.experiment.ExpressionExperimentImpl" } }); } this.fireEvent("ready"); }
|
', \'text\', null, null)">Filtered</a> ' + '<a href="#" title="click to download the tab delimited data" onClick="fetchData(false,' +
|
', \'text\', null, null)">Filtered</span> ' + '<span class="link" ext:qtip="Download the tab delimited data" onClick="fetchData(false,' +
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build : function(e) { var manager = new Gemma.EEManager({ editable : this.editable, id : "eemanager" }); this.manager = manager; // // /* // * Create a store with one record. // */ // var store = new Ext.data.Store({ // proxy : new Ext.data.MemoryProxy([e]), // reader : new Ext.data.ListRangeReader({}, // this.manager.record) // }); // // this.rec = store.getAt(0); adminLinks = '<a href="#" onClick="Ext.getCmp(\'eemanager\').updateEEReport(' + e.id + ')"><img src="/Gemma/images/icons/arrow_refresh_small.png" ext:qtip="Refresh statistics" title="refresh"/></a>' + ' <a href="/Gemma/expressionExperiment/editExpressionExperiment.html?id=' + e.id + '" ><img src="/Gemma/images/icons/wrench.png" ext:qtip="Go to editor page for this experiment" title="edit"/></a> '; if (this.isAdmin) { adminLinks = adminLinks + '<a href="#" onClick="return Ext.getCmp(\'eemanager\').deleteExperiment(' + e.id + ')"><img src="/Gemma/images/icons/cross.png" ext:qtip="Delete the experiment from the system" title="delete" /></a> '; } var pubmedRegion = {}; if (e.pubmedId) { // display the citation, with link out and delete // button. pubmedRegion = this.getPubMedHtml(e); } else { // offer to create a citation link. pubmedRegion = this.getPubMedForm(e); } /* * Show the experimental design */ DesignMatrix.init({ id : e.id }); var vizPanel = new Gemma.EEDetailsVisualizationWidget({ renderTo : 'visualization', taxon : e.parentTaxon }); /* * This is needed to make the annotator initialize properly. */ new Gemma.MGEDCombo({}); var taggerurl = '<a href="#" onClick="return Ext.getCmp(\'eemanager\').tagger(' + e.id + ',' + e.taxonId + ',' + this.editable + ')"><img src="/Gemma/images/icons/pencil.png" alt="view tags" title="view tags"/></a>'; tagView = new Gemma.AnnotationDataView({ readParams : [{ id : e.id, classDelegatingFor : "ExpressionExperimentImpl" }] }); manager.on('tagsUpdated', function() { tagView.store.reload(); }); manager.on('done', function() { window.location.reload(); }); manager.on('reportUpdated', function(data) { ob = data[0]; // console.log(ob); var k = Ext.get('coexpressionLinkCount-region'); Ext.DomHelper.overwrite(k, { html : ob.coexpressionLinkCount }); k.highlight(); k = Ext.get('processedExpressionVectorCount-region'); Ext.DomHelper.overwrite(k, { html : ob.processedExpressionVectorCount }); k.highlight(); }); manager.on('pubmedUpdated', function(e) { var html = this.getPubMedHtml(e); Ext.getCmp('pubmed-region-wrap').remove(Ext.getCmp('pubmed-region')); Ext.DomHelper.append('pubmed-region-wrap', html); }.createDelegate(this)); manager.on('pubmedRemove', function(success) { if (success) { var r = Ext.getCmp('pubmed-region-wrap'); r.remove(Ext.getCmp('pubmed-region')); var form = this.getPubMedForm(this.eeId); r.add(form); r.doLayout(); } }.createDelegate(this)); manager.on('updated', function(data) { Ext.getCmp('update-button-region').getEl().hide(); /* * Really we won't need to do this -- as the state on the database is supposed to match this one. */ var k = Ext.getCmp('shortname'); k.setValue(data.shortName); k = Ext.getCmp('name'); k.setValue(data.name); k = Ext.getCmp('description'); k.setValue(data.description); }.createDelegate(this)); // manager.on('reportUpdated', function() { // store.reload(); // }); // // manager.on('differential', function() { // store.reload(); // }); // manager.on('processedVector', function() { // store.reload(); // }); // manager.on('link', function() { // store.reload(); // }); // manager.on('missingValue', function() { // store.reload(); // }); var descriptionArea = new Ext.form.TextArea({ id : 'description', allowBlank : true, grow : true, growMax : 300, readOnly : !this.editable, disabledClass : 'disabled-plain', growMin : 40, emptyText : 'No description provided', enableKeyEvents : true, listeners : { 'keyup' : { fn : function(e) { if (Ext.getCmp('description').isDirty() && Ext.getCmp('description').isValid()) { // show save button Ext.getCmp('update-button-region').show(); } else { Ext.getCmp('update-button-region').hide(); } } } }, width : 500, // height : 100, value : e.description }); var nameArea = new Ext.form.TextArea({ id : 'name', fieldLabel : 'Name', allowBlank : false, grow : true, growMax : 300, readOnly : !this.editable, disabledClass : 'disabled-plain', growMin : 40, emptyText : 'No description provided', enableKeyEvents : true, listeners : { 'keyup' : { fn : function(e) { if (Ext.getCmp('name').isDirty() && Ext.getCmp('name').isValid()) { // show save button Ext.getCmp('update-button-region').show(); } else { Ext.getCmp('update-button-region').hide(); } } } }, width : 500, value : e.name }); var basics = new Ext.Panel({ autoHeight : true, layout : 'table', layoutConfig : { columns : 2 }, renderTo : 'basics', collapsible : false, bodyBorder : false, frame : false, baseCls : 'x-plain-panel', bodyStyle : 'padding:10px', defaults : { bodyStyle : 'vertical-align:top;font-size:12px;color:black', baseCls : 'x-plain-panel', fieldClass : 'x-bare-field' }, items : [{ html : 'Short name:' }, { xtype : 'panel', layout : 'table', baseCls : 'x-plain-panel', layoutConfig : { columns : 2 }, items : [{ xtype : 'textfield', id : 'shortname', enableKeyEvents : true, allowBlank : false, disabledClass : 'disabled-plain', fieldClass : 'x-bare-field', readOnly : !this.editable, listeners : { 'keyup' : { fn : function(e) { if (Ext.getCmp('shortname').isDirty() && Ext.getCmp('shortname').isValid()) { // show // save // button Ext.getCmp('update-button-region').show(); } else { Ext.getCmp('update-button-region').hide(); } }, scope : this } }, width : 250, value : e.shortName }, { baseCls : 'x-plain-panel', id : 'update-button-region', html : '<a href="#" onClick="Ext.getCmp(\'ee-details-panel\').save(' + e.id + ',[\'shortname\',\'name\',\'description\'])" ><img src="/Gemma/images/icons/database_save.png" title="Click to save changes" alt="Click to save changes"/></a>', hidden : true }] }, { html : 'Name:' }, nameArea, { html : "Taxon:" }, { html : e.taxon }, { html : 'Description:' }, descriptionArea, { html : 'Created:' }, { html : Ext.util.Format.date(e.dateCreated) }, { html : 'Source:' }, { html : this.renderSourceDatabaseEntry(e) }, { html : 'Samples:' }, { html : this.renderSamples(e), width : 60 }, { html : 'Profiles:' }, { id : 'processedExpressionVectorCount-region', html : '<div id="downloads"> ' + this.renderProcessedExpressionVectorCount(e) + ' ' + '<i>Downloads:</i> <a title="click to download the tab delimited data" href="#" onClick="fetchData(true,' + e.id + ', \'text\', null, null)">Filtered</a> ' + '<a href="#" title="click to download the tab delimited data" onClick="fetchData(false,' + e.id + ', \'text\', null, null)">Unfiltered</a> ' + '<a class="helpLink" href="?" onclick="showHelpTip(event, \'Tab-delimited data file for this experiment. The filtered version corresponds to what is used in most Gemma analyses, removing some probes. Unfiltered includes all probes\'); return false"> <img src="/Gemma/images/help.png" /> </a>' + '</div>', width : 400 }, { html : 'Array designs:' }, { id : 'arrayDesign-region', html : this.renderArrayDesigns(e.arrayDesigns), width : 480 }, { html : 'Coexpr. Links:' }, { id : 'coexpressionLinkCount-region', html : this.renderCoExpressionLinkCount(e), width : 80 }, { html : 'Diff. expr. Probes' }, { id : 'DiffExpressedProbes-region', html : this.renderDiffExpressionDetails(e), width : 200 }, { html : 'Publication:' }, { xtype : 'panel', id : 'pubmed-region-wrap', layout : 'fit', bodyBorder : false, baseCls : 'x-plain-panel', disabled : false, items : [pubmedRegion] }, { html : 'Tags ' + taggerurl }, tagView, { html : 'Status' }, { html : this.renderStatus(e) }, { html : this.editable ? 'Admin' : '' }, { id : 'admin-links', html : this.editable ? adminLinks : '' } /* * authors */ ] }); if (this.editable) { Ext.DomHelper.append('admin-links', { tag : 'ul', cls : 'plainlist', children : [{ tag : 'li', html : 'Missing values: ' + this.missingValueAnalysisRenderer(e) }, { tag : 'li', html : 'Proc. vec: ' + this.processedVectorCreateRenderer(e) }, { tag : 'li', html : 'Diff ex: ' + this.differentialAnalysisRenderer(e) }, { tag : 'li', html : 'Link an.: ' + this.linkAnalysisRenderer(e) }] }); } if (Ext.get('history')) { var history = new Gemma.AuditTrailGrid({ renderTo : 'history', bodyBorder : false, collapsible : true, auditable : { id : e.id, classDelegatingFor : "ubic.gemma.model.expression.experiment.ExpressionExperimentImpl" } }); } this.fireEvent("ready"); }
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', \'text\', null, null)">Unfiltered</a> ' +
|
', \'text\', null, null)">Unfiltered</span> ' +
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build : function(e) { var manager = new Gemma.EEManager({ editable : this.editable, id : "eemanager" }); this.manager = manager; // // /* // * Create a store with one record. // */ // var store = new Ext.data.Store({ // proxy : new Ext.data.MemoryProxy([e]), // reader : new Ext.data.ListRangeReader({}, // this.manager.record) // }); // // this.rec = store.getAt(0); adminLinks = '<a href="#" onClick="Ext.getCmp(\'eemanager\').updateEEReport(' + e.id + ')"><img src="/Gemma/images/icons/arrow_refresh_small.png" ext:qtip="Refresh statistics" title="refresh"/></a>' + ' <a href="/Gemma/expressionExperiment/editExpressionExperiment.html?id=' + e.id + '" ><img src="/Gemma/images/icons/wrench.png" ext:qtip="Go to editor page for this experiment" title="edit"/></a> '; if (this.isAdmin) { adminLinks = adminLinks + '<a href="#" onClick="return Ext.getCmp(\'eemanager\').deleteExperiment(' + e.id + ')"><img src="/Gemma/images/icons/cross.png" ext:qtip="Delete the experiment from the system" title="delete" /></a> '; } var pubmedRegion = {}; if (e.pubmedId) { // display the citation, with link out and delete // button. pubmedRegion = this.getPubMedHtml(e); } else { // offer to create a citation link. pubmedRegion = this.getPubMedForm(e); } /* * Show the experimental design */ DesignMatrix.init({ id : e.id }); var vizPanel = new Gemma.EEDetailsVisualizationWidget({ renderTo : 'visualization', taxon : e.parentTaxon }); /* * This is needed to make the annotator initialize properly. */ new Gemma.MGEDCombo({}); var taggerurl = '<a href="#" onClick="return Ext.getCmp(\'eemanager\').tagger(' + e.id + ',' + e.taxonId + ',' + this.editable + ')"><img src="/Gemma/images/icons/pencil.png" alt="view tags" title="view tags"/></a>'; tagView = new Gemma.AnnotationDataView({ readParams : [{ id : e.id, classDelegatingFor : "ExpressionExperimentImpl" }] }); manager.on('tagsUpdated', function() { tagView.store.reload(); }); manager.on('done', function() { window.location.reload(); }); manager.on('reportUpdated', function(data) { ob = data[0]; // console.log(ob); var k = Ext.get('coexpressionLinkCount-region'); Ext.DomHelper.overwrite(k, { html : ob.coexpressionLinkCount }); k.highlight(); k = Ext.get('processedExpressionVectorCount-region'); Ext.DomHelper.overwrite(k, { html : ob.processedExpressionVectorCount }); k.highlight(); }); manager.on('pubmedUpdated', function(e) { var html = this.getPubMedHtml(e); Ext.getCmp('pubmed-region-wrap').remove(Ext.getCmp('pubmed-region')); Ext.DomHelper.append('pubmed-region-wrap', html); }.createDelegate(this)); manager.on('pubmedRemove', function(success) { if (success) { var r = Ext.getCmp('pubmed-region-wrap'); r.remove(Ext.getCmp('pubmed-region')); var form = this.getPubMedForm(this.eeId); r.add(form); r.doLayout(); } }.createDelegate(this)); manager.on('updated', function(data) { Ext.getCmp('update-button-region').getEl().hide(); /* * Really we won't need to do this -- as the state on the database is supposed to match this one. */ var k = Ext.getCmp('shortname'); k.setValue(data.shortName); k = Ext.getCmp('name'); k.setValue(data.name); k = Ext.getCmp('description'); k.setValue(data.description); }.createDelegate(this)); // manager.on('reportUpdated', function() { // store.reload(); // }); // // manager.on('differential', function() { // store.reload(); // }); // manager.on('processedVector', function() { // store.reload(); // }); // manager.on('link', function() { // store.reload(); // }); // manager.on('missingValue', function() { // store.reload(); // }); var descriptionArea = new Ext.form.TextArea({ id : 'description', allowBlank : true, grow : true, growMax : 300, readOnly : !this.editable, disabledClass : 'disabled-plain', growMin : 40, emptyText : 'No description provided', enableKeyEvents : true, listeners : { 'keyup' : { fn : function(e) { if (Ext.getCmp('description').isDirty() && Ext.getCmp('description').isValid()) { // show save button Ext.getCmp('update-button-region').show(); } else { Ext.getCmp('update-button-region').hide(); } } } }, width : 500, // height : 100, value : e.description }); var nameArea = new Ext.form.TextArea({ id : 'name', fieldLabel : 'Name', allowBlank : false, grow : true, growMax : 300, readOnly : !this.editable, disabledClass : 'disabled-plain', growMin : 40, emptyText : 'No description provided', enableKeyEvents : true, listeners : { 'keyup' : { fn : function(e) { if (Ext.getCmp('name').isDirty() && Ext.getCmp('name').isValid()) { // show save button Ext.getCmp('update-button-region').show(); } else { Ext.getCmp('update-button-region').hide(); } } } }, width : 500, value : e.name }); var basics = new Ext.Panel({ autoHeight : true, layout : 'table', layoutConfig : { columns : 2 }, renderTo : 'basics', collapsible : false, bodyBorder : false, frame : false, baseCls : 'x-plain-panel', bodyStyle : 'padding:10px', defaults : { bodyStyle : 'vertical-align:top;font-size:12px;color:black', baseCls : 'x-plain-panel', fieldClass : 'x-bare-field' }, items : [{ html : 'Short name:' }, { xtype : 'panel', layout : 'table', baseCls : 'x-plain-panel', layoutConfig : { columns : 2 }, items : [{ xtype : 'textfield', id : 'shortname', enableKeyEvents : true, allowBlank : false, disabledClass : 'disabled-plain', fieldClass : 'x-bare-field', readOnly : !this.editable, listeners : { 'keyup' : { fn : function(e) { if (Ext.getCmp('shortname').isDirty() && Ext.getCmp('shortname').isValid()) { // show // save // button Ext.getCmp('update-button-region').show(); } else { Ext.getCmp('update-button-region').hide(); } }, scope : this } }, width : 250, value : e.shortName }, { baseCls : 'x-plain-panel', id : 'update-button-region', html : '<a href="#" onClick="Ext.getCmp(\'ee-details-panel\').save(' + e.id + ',[\'shortname\',\'name\',\'description\'])" ><img src="/Gemma/images/icons/database_save.png" title="Click to save changes" alt="Click to save changes"/></a>', hidden : true }] }, { html : 'Name:' }, nameArea, { html : "Taxon:" }, { html : e.taxon }, { html : 'Description:' }, descriptionArea, { html : 'Created:' }, { html : Ext.util.Format.date(e.dateCreated) }, { html : 'Source:' }, { html : this.renderSourceDatabaseEntry(e) }, { html : 'Samples:' }, { html : this.renderSamples(e), width : 60 }, { html : 'Profiles:' }, { id : 'processedExpressionVectorCount-region', html : '<div id="downloads"> ' + this.renderProcessedExpressionVectorCount(e) + ' ' + '<i>Downloads:</i> <a title="click to download the tab delimited data" href="#" onClick="fetchData(true,' + e.id + ', \'text\', null, null)">Filtered</a> ' + '<a href="#" title="click to download the tab delimited data" onClick="fetchData(false,' + e.id + ', \'text\', null, null)">Unfiltered</a> ' + '<a class="helpLink" href="?" onclick="showHelpTip(event, \'Tab-delimited data file for this experiment. The filtered version corresponds to what is used in most Gemma analyses, removing some probes. Unfiltered includes all probes\'); return false"> <img src="/Gemma/images/help.png" /> </a>' + '</div>', width : 400 }, { html : 'Array designs:' }, { id : 'arrayDesign-region', html : this.renderArrayDesigns(e.arrayDesigns), width : 480 }, { html : 'Coexpr. Links:' }, { id : 'coexpressionLinkCount-region', html : this.renderCoExpressionLinkCount(e), width : 80 }, { html : 'Diff. expr. Probes' }, { id : 'DiffExpressedProbes-region', html : this.renderDiffExpressionDetails(e), width : 200 }, { html : 'Publication:' }, { xtype : 'panel', id : 'pubmed-region-wrap', layout : 'fit', bodyBorder : false, baseCls : 'x-plain-panel', disabled : false, items : [pubmedRegion] }, { html : 'Tags ' + taggerurl }, tagView, { html : 'Status' }, { html : this.renderStatus(e) }, { html : this.editable ? 'Admin' : '' }, { id : 'admin-links', html : this.editable ? adminLinks : '' } /* * authors */ ] }); if (this.editable) { Ext.DomHelper.append('admin-links', { tag : 'ul', cls : 'plainlist', children : [{ tag : 'li', html : 'Missing values: ' + this.missingValueAnalysisRenderer(e) }, { tag : 'li', html : 'Proc. vec: ' + this.processedVectorCreateRenderer(e) }, { tag : 'li', html : 'Diff ex: ' + this.differentialAnalysisRenderer(e) }, { tag : 'li', html : 'Link an.: ' + this.linkAnalysisRenderer(e) }] }); } if (Ext.get('history')) { var history = new Gemma.AuditTrailGrid({ renderTo : 'history', bodyBorder : false, collapsible : true, auditable : { id : e.id, classDelegatingFor : "ubic.gemma.model.expression.experiment.ExpressionExperimentImpl" } }); } this.fireEvent("ready"); }
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width : 200
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width : 700
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build : function(e) { var manager = new Gemma.EEManager({ editable : this.editable, id : "eemanager" }); this.manager = manager; // // /* // * Create a store with one record. // */ // var store = new Ext.data.Store({ // proxy : new Ext.data.MemoryProxy([e]), // reader : new Ext.data.ListRangeReader({}, // this.manager.record) // }); // // this.rec = store.getAt(0); adminLinks = '<span style="cursor:pointer" onClick="Ext.getCmp(\'eemanager\').updateEEReport(' + e.id + ',\'admin-links\'' + ')"><img src="/Gemma/images/icons/arrow_refresh_small.png" ext:qtip="Refresh statistics" title="refresh"/></span>' + ' <a href="/Gemma/expressionExperiment/editExpressionExperiment.html?id=' + e.id + '" ><img src="/Gemma/images/icons/wrench.png" ext:qtip="Go to editor page for this experiment" title="edit"/></span> '; if (this.isAdmin) { adminLinks = adminLinks + '<span style="cursor:pointer" onClick="return Ext.getCmp(\'eemanager\').deleteExperiment(' + e.id + ')"><img src="/Gemma/images/icons/cross.png" ext:qtip="Delete the experiment from the system" title="delete" /></span> '; } var pubmedRegion = {}; if (e.pubmedId) { // display the citation, with link out and delete // button. pubmedRegion = this.getPubMedHtml(e); } else { // offer to create a citation link. pubmedRegion = this.getPubMedForm(e); } /* * Show the experimental design */ DesignMatrix.init({ id : e.id }); var vizPanel = new Gemma.EEDetailsVisualizationWidget({ renderTo : 'visualization', taxon : { commonName : e.parentTaxon, id : e.parentTaxonId } }); /* * This is needed to make the annotator initialize properly. */ new Gemma.MGEDCombo({}); var taggerurl = '<span style="cursor:pointer" onClick="return Ext.getCmp(\'eemanager\').tagger(' + e.id + ',' + e.taxonId + ',' + this.editable + ',' + (e.validatedAnnotations !== null) + ')"><img src="/Gemma/images/icons/pencil.png" alt="view tags" title="view tags"/></span>'; tagView = new Gemma.AnnotationDataView({ readParams : [{ id : e.id, classDelegatingFor : "ExpressionExperimentImpl" }] }); manager.on('tagsUpdated', function() { tagView.store.reload(); }); manager.on('done', function() { /* * After a process that requires refreshing the page. */ window.location.reload(); }); manager.on('reportUpdated', function(data) { ob = data[0]; var k = Ext.get('coexpressionLinkCount-region'); Ext.DomHelper.overwrite(k, { html : ob.coexpressionLinkCount }); k.highlight(); k = Ext.get('processedExpressionVectorCount-region'); Ext.DomHelper.overwrite(k, { html : ob.processedExpressionVectorCount }); k.highlight(); }); // manager.on('pubmedUpdated', function(e) { // var html = this.getPubMedHtml(e); // Ext.getCmp('pubmed-region-wrap').remove(Ext.getCmp('pubmed-region')); // Ext.DomHelper.append('pubmed-region-wrap', html); // }.createDelegate(this)); // // manager.on('pubmedRemove', function(success) { // if (success) { // var r = Ext.getCmp('pubmed-region-wrap'); // r.remove(Ext.getCmp('pubmed-region')); // var form = this.getPubMedForm(this.eeId); // r.add(form); // r.doLayout(); // } // }.createDelegate(this)); // manager.on('reportUpdated', function() { // // window.location.reload(true); // }); manager.on('differential', function() { window.location.reload(true); }); // manager.on('processedVector', function() { // window.location.reload(true); // }); // manager.on('link', function() { // window.location.reload(true); // }); // // manager.on('missingValue', function() { // window.location.reload(true); // }); var descriptionArea = new Ext.form.TextArea({ id : 'description', allowBlank : true, grow : true, growMax : 300, readOnly : !this.editable, disabledClass : 'disabled-plain', growMin : 40, emptyText : 'No description provided', enableKeyEvents : true, listeners : { 'keyup' : { fn : function(e) { if (Ext.getCmp('description').isDirty() && Ext.getCmp('description').isValid()) { // show save button Ext.getCmp('update-button-region').show(true); } else { Ext.getCmp('update-button-region').hide(true); } } } }, width : 500, // height : 100, value : e.description }); var nameArea = new Ext.form.TextArea({ id : 'name', fieldLabel : 'Name', allowBlank : false, grow : true, growMax : 300, readOnly : !this.editable, disabledClass : 'disabled-plain', growMin : 40, emptyText : 'No description provided', enableKeyEvents : true, listeners : { 'keyup' : { fn : function(e) { if (Ext.getCmp('name').isDirty() && Ext.getCmp('name').isValid()) { // show save button Ext.getCmp('update-button-region').show(true); } else { Ext.getCmp('update-button-region').hide(true); } } } }, width : 500, value : e.name }); var basics = new Ext.Panel({ autoHeight : true, layout : 'table', layoutConfig : { columns : 2 }, renderTo : 'basics', collapsible : false, bodyBorder : false, frame : false, baseCls : 'x-plain-panel', bodyStyle : 'padding:10px', defaults : { bodyStyle : 'vertical-align:top;font-size:12px;color:black', baseCls : 'x-plain-panel', fieldClass : 'x-bare-field' }, items : [{ html : 'Short name:' }, { xtype : 'panel', layout : 'table', baseCls : 'x-plain-panel', layoutConfig : { columns : 2 }, items : [{ xtype : 'textfield', id : 'shortname', enableKeyEvents : true, allowBlank : false, disabledClass : 'disabled-plain', fieldClass : 'x-bare-field', readOnly : !this.editable, listeners : { 'keyup' : { fn : function(e) { if (Ext.getCmp('shortname').isDirty() && Ext.getCmp('shortname').isValid()) { // show // save // button Ext.getCmp('update-button-region').show(true); } else { Ext.getCmp('update-button-region').hide(true); } }, scope : this } }, width : 250, value : e.shortName }, { baseCls : 'x-plain-panel', id : 'update-button-region', html : '<span style="cursor:pointer" onClick="Ext.getCmp(\'ee-details-panel\').save(' + e.id + ',[\'shortname\',\'name\',\'description\'])" ><img src="/Gemma/images/icons/database_save.png" ext:qtip="Click to save changes" alt="Click to save changes"/></span>', hidden : true }] }, { html : 'Name:' }, nameArea, { html : "Taxon:" }, { html : e.taxon }, { html : 'Description:' }, descriptionArea, { html : 'Created:' }, { html : Ext.util.Format.date(e.dateCreated) }, { html : 'Source:' }, { html : this.renderSourceDatabaseEntry(e) }, { html : 'Samples:' }, { html : this.renderSamples(e), width : 60 }, { html : 'Profiles:' }, { id : 'processedExpressionVectorCount-region', html : '<div id="downloads"> ' + this.renderProcessedExpressionVectorCount(e) + ' ' + '<i>Downloads:</i> <span class="link" ext:qtip="Download the tab delimited data" onClick="fetchData(true,' + e.id + ', \'text\', null, null)">Filtered</span> ' + '<span class="link" ext:qtip="Download the tab delimited data" onClick="fetchData(false,' + e.id + ', \'text\', null, null)">Unfiltered</span> ' + '<a class="helpLink" href="?" onclick="showHelpTip(event, \'Tab-delimited data file for this experiment. The filtered version corresponds to what is used in most Gemma analyses, removing some probes. Unfiltered includes all probes\'); return false"> <img src="/Gemma/images/help.png" /> </a>' + '</div>', width : 400 }, { html : 'Array designs:' }, { id : 'arrayDesign-region', html : this.renderArrayDesigns(e.arrayDesigns), width : 480 }, { html : 'Coexpr. Links:' }, { id : 'coexpressionLinkCount-region', html : this.renderCoExpressionLinkCount(e), width : 80 }, { html : 'Diff. expr. Probes' }, { id : 'DiffExpressedProbes-region', html : this.renderDiffExpressionDetails(e), width : 200 }, { html : 'Publication:' }, { xtype : 'panel', id : 'pubmed-region-wrap', layout : 'fit', bodyBorder : false, baseCls : 'x-plain-panel', disabled : false, items : [pubmedRegion] }, { html : 'Tags ' + taggerurl }, tagView, { html : 'Status' }, { html : this.renderStatus(e) }, { html : this.editable ? 'Admin' : '' }, { id : 'admin-links', html : this.editable ? adminLinks : '' } /* * authors */ ] }); if (this.editable) { Ext.DomHelper.append('admin-links', { tag : 'ul', cls : 'plainlist', children : [{ tag : 'li', html : 'Missing values: ' + this.missingValueAnalysisRenderer(e) }, { tag : 'li', html : 'Proc. vec: ' + this.processedVectorCreateRenderer(e) }, { tag : 'li', html : 'Diff ex: ' + this.differentialAnalysisRenderer(e) }, { tag : 'li', html : 'Link an.: ' + this.linkAnalysisRenderer(e) }] }); } if (Ext.get('history')) { var history = new Gemma.AuditTrailGrid({ renderTo : 'history', bodyBorder : false, collapsible : true, auditable : { id : e.id, classDelegatingFor : "ubic.gemma.model.expression.experiment.ExpressionExperimentImpl" } }); } this.fireEvent("ready"); }
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var DesignMatrixRow = Ext.data.Record.create(record);
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var designMatrixRow = Ext.data.Record.create(record);
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build : function(rows) { var factors = rows[0].factors; var record = []; var columns = []; columns.push({ header : "Assays", dataIndex : "count", sortable : "true", tooltip : "How many assays are in this group" }); for (var i = 0; i < factors.length; ++i) { var fn = factors[i] ; record.push({ name : cleanName(fn), type : "string" }); columns.push({ header : fn, dataIndex : cleanName(fn), sortable : "true", tooltip : fn }); } record.push({ name : "count", type : "int" }); var DesignMatrixRow = Ext.data.Record.create(record); var cm = new Ext.grid.ColumnModel(columns); var data = []; for (var k = 0; k < rows.length; ++k) { data[k] = []; for (var j = 0; j < factors.length; ++j) { data[k][j] = rows[k].factorValueMap[factors[j]]; } data[k][factors.length] = rows[k].count; } this.ds = new Ext.data.Store({ proxy : new Ext.data.MemoryProxy(data), reader : new Ext.data.ArrayReader({}, DesignMatrixRow), remoteSort : false }); this.ds.load(); this.grid = new Ext.grid.GridPanel({ ds : this.ds, cm : cm, collapsible : true, title : "Experimental Design overview", renderTo : "eeDesignMatrix", height : 125, width : 600, viewConfig : { forceFit : true } }); },
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reader : new Ext.data.ArrayReader({}, DesignMatrixRow),
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reader : new Ext.data.ArrayReader({}, designMatrixRow),
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build : function(rows) { var factors = rows[0].factors; var record = []; var columns = []; columns.push({ header : "Assays", dataIndex : "count", sortable : "true", tooltip : "How many assays are in this group" }); for (var i = 0; i < factors.length; ++i) { var fn = factors[i] ; record.push({ name : cleanName(fn), type : "string" }); columns.push({ header : fn, dataIndex : cleanName(fn), sortable : "true", tooltip : fn }); } record.push({ name : "count", type : "int" }); var DesignMatrixRow = Ext.data.Record.create(record); var cm = new Ext.grid.ColumnModel(columns); var data = []; for (var k = 0; k < rows.length; ++k) { data[k] = []; for (var j = 0; j < factors.length; ++j) { data[k][j] = rows[k].factorValueMap[factors[j]]; } data[k][factors.length] = rows[k].count; } this.ds = new Ext.data.Store({ proxy : new Ext.data.MemoryProxy(data), reader : new Ext.data.ArrayReader({}, DesignMatrixRow), remoteSort : false }); this.ds.load(); this.grid = new Ext.grid.GridPanel({ ds : this.ds, cm : cm, collapsible : true, title : "Experimental Design overview", renderTo : "eeDesignMatrix", height : 125, width : 600, viewConfig : { forceFit : true } }); },
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th.insert(new Element('span').update(h.title));
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th.insert(new Element('span').update(h.title || ''));
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buildHeaders : function(headers) { this.head.update(); this.columns = []; var tr = new Element('tr'); this.head.insert(tr); headers.each(function(h,i) { var th = new Element('th'); if (h.width) { th.setStyle({width:h.width+'%'}); } if (h.sortable) { th.observe('click',function() {this.sort(i)}.bind(this)); th.addClassName('sortable'); } th.insert(new Element('span').update(h.title)); tr.insert(th); this.columns.push(h); }.bind(this)); },
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th.insert(new Element('span').update(h.title || ''));
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th.insert(new Element('span').update(h.title));
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buildHeaders : function(headers) { this.head.update(); this.columns = []; var tr = new Element('tr'); this.head.insert(tr); headers.each(function(h,i) { var th = new Element('th'); if (h.width) { th.setStyle({width:h.width+'%'}); } if (h.sortable) { th.observe('click',function() {this.sort(i)}.bind(this)); th.addClassName('sortable'); } th.insert(new Element('span').update(h.title || '')); tr.insert(th); this.columns.push(h); }.bind(this)); },
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axis.c2p = function (p) { return axis.max - p / axis.scale; };
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axis.c2p = function (c) { return it(m - c / s); };
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axis.c2p = function (p) { return axis.max - p / axis.scale; };
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var s = row.getMarginBoxSize();
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var s = row.getContentBoxSize();
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calculateHeights : function () { //grab all rows in the grid body document.id(this.grid.gridTableBody).getChildren().each(function(row){ row = document.id(row); var data = row.retrieve('jxRowData'); var s = row.getMarginBoxSize(); this.heights[data.row] = s.height; },this); document.id(this.grid.rowTableHead).getChildren().each(function(row){ row = document.id(row); var data = row.retrieve('jxRowData'); if (data) { var s = row.getMarginBoxSize(); this.heights[data.row] = Math.max(this.heights[data.row],s.height); } },this); },
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if (Browser.Engine.webkit) { this.heights[data.row] -= 1; }
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calculateHeights : function () { //grab all rows in the grid body document.id(this.grid.gridTableBody).getChildren().each(function(row){ row = document.id(row); var data = row.retrieve('jxRowData'); var s = row.getMarginBoxSize(); this.heights[data.row] = s.height; },this); document.id(this.grid.rowTableHead).getChildren().each(function(row){ row = document.id(row); var data = row.retrieve('jxRowData'); if (data) { var s = row.getMarginBoxSize(); this.heights[data.row] = Math.max(this.heights[data.row],s.height); } },this); },
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var oldPos = model.getPosition(); maxWidth = 0;
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calculateWidth : function (rowHeader) { //if this gets called then we assume that we want to calculate the width rowHeader = $defined(rowHeader) ? rowHeader : false; var maxWidth; //calculate the width var model = this.grid.getModel(); var oldPos = model.getPosition(); maxWidth = 0; model.first(); while (model.valid()) { //check size by placing text into a TD and measuring it. this.options.renderer.render(); var text = $(this.options.renderer); var klass = 'jxGridCell'; if (this.grid.row.useHeaders() && this.options.name === this.grid.row .getRowHeaderColumn()) { klass = 'jxGridRowHead'; } var s = this.measure(text, klass, rowHeader, model.getPosition()); if (s.width > maxWidth) { maxWidth = s.width; } if (model.hasNext()) { model.next(); } else { break; } } //check the column header as well (unless this is the row header) if (!(this.grid.row.useHeaders() && this.options.name === this.grid.row .getRowHeaderColumn())) { klass = 'jxGridColHead'; if (this.isEditable()) { klass += ' jxColEditable'; } if (this.isResizable()) { klass += ' jxColResizable'; } if (this.isSortable()) { klass += ' jxColSortable'; } s = this.measure(this.domObj.clone(), klass); if (s.width > maxWidth) { maxWidth = s.width; } } this.width = maxWidth; model.moveTo(oldPos); return this.width; },
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while (model.valid()) { this.options.renderer.render(); var text = $(this.options.renderer); var klass = 'jxGridCell'; if (this.grid.row.useHeaders() && this.options.name === this.grid.row .getRowHeaderColumn()) { klass = 'jxGridRowHead';
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if (this.options.renderMode == 'fixed' && model.valid) { var t = new Element('span', { 'class': 'jxGridCellContent', html: 'a', styles: { width: this.options.width
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calculateWidth : function (rowHeader) { //if this gets called then we assume that we want to calculate the width rowHeader = $defined(rowHeader) ? rowHeader : false; var maxWidth; //calculate the width var model = this.grid.getModel(); var oldPos = model.getPosition(); maxWidth = 0; model.first(); while (model.valid()) { //check size by placing text into a TD and measuring it. this.options.renderer.render(); var text = $(this.options.renderer); var klass = 'jxGridCell'; if (this.grid.row.useHeaders() && this.options.name === this.grid.row .getRowHeaderColumn()) { klass = 'jxGridRowHead'; } var s = this.measure(text, klass, rowHeader, model.getPosition()); if (s.width > maxWidth) { maxWidth = s.width; } if (model.hasNext()) { model.next(); } else { break; } } //check the column header as well (unless this is the row header) if (!(this.grid.row.useHeaders() && this.options.name === this.grid.row .getRowHeaderColumn())) { klass = 'jxGridColHead'; if (this.isEditable()) { klass += ' jxColEditable'; } if (this.isResizable()) { klass += ' jxColResizable'; } if (this.isSortable()) { klass += ' jxColSortable'; } s = this.measure(this.domObj.clone(), klass); if (s.width > maxWidth) { maxWidth = s.width; } } this.width = maxWidth; model.moveTo(oldPos); return this.width; },
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var s = this.measure(text, klass, rowHeader, model.getPosition()); if (s.width > maxWidth) { maxWidth = s.width;
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}); var s = this.measure(t,'jxGridCell'); maxWidth = s.content.width; maxCellWidth = s.cell.width; } else { var oldPos = model.getPosition(); maxWidth = maxCellWidth = 0; while (model.valid()) { this.options.renderer.render(); var text = $(this.options.renderer); var klass = 'jxGridCell'; if (this.grid.row.useHeaders() && this.options.name === this.grid.row .getRowHeaderColumn()) { klass = 'jxGridRowHead'; } var s = this.measure(text, klass, rowHeader, model.getPosition()); if (s.content.width > maxWidth) { maxWidth = s.content.width; } if (s.cell.width > maxCellWidth) { maxCellWidth = s.cell.width } if (model.hasNext()) { model.next(); } else { break; }
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calculateWidth : function (rowHeader) { //if this gets called then we assume that we want to calculate the width rowHeader = $defined(rowHeader) ? rowHeader : false; var maxWidth; //calculate the width var model = this.grid.getModel(); var oldPos = model.getPosition(); maxWidth = 0; model.first(); while (model.valid()) { //check size by placing text into a TD and measuring it. this.options.renderer.render(); var text = $(this.options.renderer); var klass = 'jxGridCell'; if (this.grid.row.useHeaders() && this.options.name === this.grid.row .getRowHeaderColumn()) { klass = 'jxGridRowHead'; } var s = this.measure(text, klass, rowHeader, model.getPosition()); if (s.width > maxWidth) { maxWidth = s.width; } if (model.hasNext()) { model.next(); } else { break; } } //check the column header as well (unless this is the row header) if (!(this.grid.row.useHeaders() && this.options.name === this.grid.row .getRowHeaderColumn())) { klass = 'jxGridColHead'; if (this.isEditable()) { klass += ' jxColEditable'; } if (this.isResizable()) { klass += ' jxColResizable'; } if (this.isSortable()) { klass += ' jxColSortable'; } s = this.measure(this.domObj.clone(), klass); if (s.width > maxWidth) { maxWidth = s.width; } } this.width = maxWidth; model.moveTo(oldPos); return this.width; },
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if (model.hasNext()) { model.next(); } else { break;
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if (!(this.grid.row.useHeaders() && this.options.name === this.grid.row.getRowHeaderColumn())) { klass = 'jxGridColHead'; if (this.isEditable()) { klass += ' jxColEditable'; } if (this.isResizable()) { klass += ' jxColResizable'; } if (this.isSortable()) { klass += ' jxColSortable'; } s = this.measure(this.domObj.clone(), klass); if (s.content.width > maxWidth) { maxWidth = s.content.width; } if (s.cell.width > maxCellWidth) { maxCellWidth = s.cell.width }
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calculateWidth : function (rowHeader) { //if this gets called then we assume that we want to calculate the width rowHeader = $defined(rowHeader) ? rowHeader : false; var maxWidth; //calculate the width var model = this.grid.getModel(); var oldPos = model.getPosition(); maxWidth = 0; model.first(); while (model.valid()) { //check size by placing text into a TD and measuring it. this.options.renderer.render(); var text = $(this.options.renderer); var klass = 'jxGridCell'; if (this.grid.row.useHeaders() && this.options.name === this.grid.row .getRowHeaderColumn()) { klass = 'jxGridRowHead'; } var s = this.measure(text, klass, rowHeader, model.getPosition()); if (s.width > maxWidth) { maxWidth = s.width; } if (model.hasNext()) { model.next(); } else { break; } } //check the column header as well (unless this is the row header) if (!(this.grid.row.useHeaders() && this.options.name === this.grid.row .getRowHeaderColumn())) { klass = 'jxGridColHead'; if (this.isEditable()) { klass += ' jxColEditable'; } if (this.isResizable()) { klass += ' jxColResizable'; } if (this.isSortable()) { klass += ' jxColSortable'; } s = this.measure(this.domObj.clone(), klass); if (s.width > maxWidth) { maxWidth = s.width; } } this.width = maxWidth; model.moveTo(oldPos); return this.width; },
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if (!(this.grid.row.useHeaders() && this.options.name === this.grid.row .getRowHeaderColumn())) { klass = 'jxGridColHead'; if (this.isEditable()) { klass += ' jxColEditable'; } if (this.isResizable()) { klass += ' jxColResizable'; } if (this.isSortable()) { klass += ' jxColSortable'; } s = this.measure(this.domObj.clone(), klass); if (s.width > maxWidth) { maxWidth = s.width; } }
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calculateWidth : function (rowHeader) { //if this gets called then we assume that we want to calculate the width rowHeader = $defined(rowHeader) ? rowHeader : false; var maxWidth; //calculate the width var model = this.grid.getModel(); var oldPos = model.getPosition(); maxWidth = 0; model.first(); while (model.valid()) { //check size by placing text into a TD and measuring it. this.options.renderer.render(); var text = $(this.options.renderer); var klass = 'jxGridCell'; if (this.grid.row.useHeaders() && this.options.name === this.grid.row .getRowHeaderColumn()) { klass = 'jxGridRowHead'; } var s = this.measure(text, klass, rowHeader, model.getPosition()); if (s.width > maxWidth) { maxWidth = s.width; } if (model.hasNext()) { model.next(); } else { break; } } //check the column header as well (unless this is the row header) if (!(this.grid.row.useHeaders() && this.options.name === this.grid.row .getRowHeaderColumn())) { klass = 'jxGridColHead'; if (this.isEditable()) { klass += ' jxColEditable'; } if (this.isResizable()) { klass += ' jxColResizable'; } if (this.isSortable()) { klass += ' jxColSortable'; } s = this.measure(this.domObj.clone(), klass); if (s.width > maxWidth) { maxWidth = s.width; } } this.width = maxWidth; model.moveTo(oldPos); return this.width; },
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this.cellWidth = maxCellWidth;
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calculateWidth : function (rowHeader) { //if this gets called then we assume that we want to calculate the width rowHeader = $defined(rowHeader) ? rowHeader : false; var maxWidth; //calculate the width var model = this.grid.getModel(); var oldPos = model.getPosition(); maxWidth = 0; model.first(); while (model.valid()) { //check size by placing text into a TD and measuring it. this.options.renderer.render(); var text = $(this.options.renderer); var klass = 'jxGridCell'; if (this.grid.row.useHeaders() && this.options.name === this.grid.row .getRowHeaderColumn()) { klass = 'jxGridRowHead'; } var s = this.measure(text, klass, rowHeader, model.getPosition()); if (s.width > maxWidth) { maxWidth = s.width; } if (model.hasNext()) { model.next(); } else { break; } } //check the column header as well (unless this is the row header) if (!(this.grid.row.useHeaders() && this.options.name === this.grid.row .getRowHeaderColumn())) { klass = 'jxGridColHead'; if (this.isEditable()) { klass += ' jxColEditable'; } if (this.isResizable()) { klass += ' jxColResizable'; } if (this.isSortable()) { klass += ' jxColSortable'; } s = this.measure(this.domObj.clone(), klass); if (s.width > maxWidth) { maxWidth = s.width; } } this.width = maxWidth; model.moveTo(oldPos); return this.width; },
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totalWidth += Jx.getNumber(col.getWidth()); if (rowHeader) { rowHeaderWidth = col.getWidth();
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if (!col.isHidden() && !(col.name == this.grid.row.options.headerColumn)) { totalWidth += Jx.getNumber(col.getWidth()); if (rowHeader) { rowHeaderWidth = col.getWidth(); }
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calculateWidths: function () { //to calculate widths we loop through each column var expand = null; var totalWidth = 0; var rowHeaderWidth = 0; this.columns.each(function(col,idx){ //are we checking the rowheader? var rowHeader = false; if (col.name == this.grid.row.options.headerColumn) { rowHeader = true; } //if it's fixed, set the width to the passed in width if (col.options.renderMode == 'fixed') { col.calculateWidth(); //col.setWidth(col.options.width); } else if (col.options.renderMode == 'fit') { col.calculateWidth(rowHeader); } else if (col.options.renderMode == 'expand' && !$defined(expand)) { expand = col; } else { //treat it as fixed if has width, otherwise as fit if ($defined(col.options.width)) { col.setWidth(col.options.width); } else { col.calculateWidth(rowHeader); } } totalWidth += Jx.getNumber(col.getWidth()); if (rowHeader) { rowHeaderWidth = col.getWidth(); } },this); // width of the container var containerWidth = this.grid.gridObj.getParent().getContentBoxSize(); var gridSize = this.grid.gridObj.getMarginBoxSize(); if (containerWidth.width > totalWidth) { //now figure the expand column if ($defined(expand)) { // var leftOverSpace = gridSize.width - totalWidth + rowHeaderWidth; var leftOverSpace = gridSize.width - totalWidth; if (leftOverSpace >= expand.options.width) { expand.options.width = leftOverSpace; expand.calculateWidth(); expand.setWidth(leftOverSpace); totalWidth += leftOverSpace; } else { expand.setWidth(expand.options.width); } } } //else { this.grid.gridTable.setContentBoxSize({'width': totalWidth - rowHeaderWidth}); this.grid.colTable.setContentBoxSize({'width': totalWidth - rowHeaderWidth}); // } },
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var containerWidth = this.grid.gridObj.getParent().getContentBoxSize(); var gridSize = this.grid.gridObj.getMarginBoxSize(); if (containerWidth.width > totalWidth) {
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var gridSize = this.grid.gridObj.getContentBoxSize(); if (gridSize.width > totalWidth) {
|
calculateWidths: function () { //to calculate widths we loop through each column var expand = null; var totalWidth = 0; var rowHeaderWidth = 0; this.columns.each(function(col,idx){ //are we checking the rowheader? var rowHeader = false; if (col.name == this.grid.row.options.headerColumn) { rowHeader = true; } //if it's fixed, set the width to the passed in width if (col.options.renderMode == 'fixed') { col.calculateWidth(); //col.setWidth(col.options.width); } else if (col.options.renderMode == 'fit') { col.calculateWidth(rowHeader); } else if (col.options.renderMode == 'expand' && !$defined(expand)) { expand = col; } else { //treat it as fixed if has width, otherwise as fit if ($defined(col.options.width)) { col.setWidth(col.options.width); } else { col.calculateWidth(rowHeader); } } totalWidth += Jx.getNumber(col.getWidth()); if (rowHeader) { rowHeaderWidth = col.getWidth(); } },this); // width of the container var containerWidth = this.grid.gridObj.getParent().getContentBoxSize(); var gridSize = this.grid.gridObj.getMarginBoxSize(); if (containerWidth.width > totalWidth) { //now figure the expand column if ($defined(expand)) { // var leftOverSpace = gridSize.width - totalWidth + rowHeaderWidth; var leftOverSpace = gridSize.width - totalWidth; if (leftOverSpace >= expand.options.width) { expand.options.width = leftOverSpace; expand.calculateWidth(); expand.setWidth(leftOverSpace); totalWidth += leftOverSpace; } else { expand.setWidth(expand.options.width); } } } //else { this.grid.gridTable.setContentBoxSize({'width': totalWidth - rowHeaderWidth}); this.grid.colTable.setContentBoxSize({'width': totalWidth - rowHeaderWidth}); // } },
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var expand = null; var totalWidth = 0; this.columns.each(function(col,idx){ var rowHeader = false; if (col.name == this.grid.row.options.headerColumn) { rowHeader = true; } if (col.options.renderMode == 'fixed') { col.setWidth(col.options.width); } else if (col.options.renderMode == 'fit') { col.calculateWidth(rowHeader); } else if (col.options.renderMode == 'expand' && !$defined(expand)) { expand = col; } else { if ($defined(col.options.width)) { col.setWidth(col.options.width); } else { col.calculateWidth(rowHeader); } } totalWidth += col.getWidth(); },this); if ($defined(expand)) { var size = this.grid.gridObj.getMarginBoxSize(); var leftOverSpace = size.width - totalWidth; if (leftOverSpace >= expand.options.width) { expand.setWidth(leftOverSpace); } else { expand.setWidth(expand.options.width); } }
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var expand = null; var totalWidth = 0; var rowHeaderWidth = 0; this.columns.each(function(col,idx){ var rowHeader = false; if (col.name == this.grid.row.options.headerColumn) { rowHeader = true; } if (col.options.renderMode == 'fixed') { col.calculateWidth(); } else if (col.options.renderMode == 'fit') { col.calculateWidth(rowHeader); } else if (col.options.renderMode == 'expand' && !$defined(expand)) { expand = col; } else { if ($defined(col.options.width)) { col.setWidth(col.options.width); } else { col.calculateWidth(rowHeader); } } totalWidth += col.getWidth(); if (rowHeader) { rowHeaderWidth = col.getWidth(); } },this); var containerWidth = this.grid.gridObj.getParent().getContentBoxSize(); var gridSize = this.grid.gridObj.getMarginBoxSize(); if (containerWidth > totalWidth) { if ($defined(expand)) { var leftOverSpace = gridSize.width - totalWidth; if (leftOverSpace >= expand.options.width) { expand.setWidth(leftOverSpace); } else { expand.setWidth(expand.options.width); } } } else { this.grid.gridTable.setContentBoxSize({'width': totalWidth - rowHeaderWidth}); this.grid.colTable.setContentBoxSize({'width': totalWidth - rowHeaderWidth}); }
|
calculateWidths: function () { //to calculate widths we loop through each column var expand = null; var totalWidth = 0; this.columns.each(function(col,idx){ //are we checking the rowheader? var rowHeader = false; if (col.name == this.grid.row.options.headerColumn) { rowHeader = true; } //if it's fixed, set the width to the passed in width if (col.options.renderMode == 'fixed') { col.setWidth(col.options.width); } else if (col.options.renderMode == 'fit') { col.calculateWidth(rowHeader); } else if (col.options.renderMode == 'expand' && !$defined(expand)) { expand = col; } else { //treat it as fixed if has width, otherwise as fit if ($defined(col.options.width)) { col.setWidth(col.options.width); } else { col.calculateWidth(rowHeader); } } totalWidth += col.getWidth(); },this); //now figure the expand column if ($defined(expand)) { var size = this.grid.gridObj.getMarginBoxSize(); var leftOverSpace = size.width - totalWidth; if (leftOverSpace >= expand.options.width) { expand.setWidth(leftOverSpace); } else { expand.setWidth(expand.options.width); } } },
|
totalWidth += Jx.getNumber(col.getWidth());
|
totalWidth += Jx.getNumber(col.getCellWidth());
|
calculateWidths: function () { //to calculate widths we loop through each column var expand = null; var totalWidth = 0; var rowHeaderWidth = 0; this.columns.each(function(col,idx){ //are we checking the rowheader? var rowHeader = false; if (col.name == this.grid.row.options.headerColumn) { rowHeader = true; } //if it's fixed, set the width to the passed in width if (col.options.renderMode == 'fixed') { col.calculateWidth(); //col.setWidth(col.options.width); } else if (col.options.renderMode == 'fit') { col.calculateWidth(rowHeader); } else if (col.options.renderMode == 'expand' && !$defined(expand)) { expand = col; } else { //treat it as fixed if has width, otherwise as fit if ($defined(col.options.width)) { col.setWidth(col.options.width); } else { col.calculateWidth(rowHeader); } } if (!col.isHidden() && !(col.name == this.grid.row.options.headerColumn)) { totalWidth += Jx.getNumber(col.getWidth()); if (rowHeader) { rowHeaderWidth = col.getWidth(); } } },this); // width of the container //var containerWidth = this.grid.gridObj.getContentBoxSize(); var gridSize = this.grid.gridObj.getContentBoxSize(); if (gridSize.width > totalWidth) { //now figure the expand column if ($defined(expand)) { // var leftOverSpace = gridSize.width - totalWidth + rowHeaderWidth; var leftOverSpace = gridSize.width - totalWidth; if (leftOverSpace >= expand.options.width) { expand.options.width = leftOverSpace; expand.calculateWidth(); expand.setWidth(leftOverSpace); totalWidth += leftOverSpace; } else { expand.setWidth(expand.options.width); } } } //else { this.grid.gridTable.setContentBoxSize({'width': totalWidth - rowHeaderWidth}); this.grid.colTable.setContentBoxSize({'width': totalWidth - rowHeaderWidth}); // } },
|
var leftOverSpace = gridSize.width - totalWidth;
|
var leftOverSpace = gridSize.width - totalWidth - 2;
|
calculateWidths: function () { //to calculate widths we loop through each column var expand = null; var totalWidth = 0; var rowHeaderWidth = 0; this.columns.each(function(col,idx){ //are we checking the rowheader? var rowHeader = false; if (col.name == this.grid.row.options.headerColumn) { rowHeader = true; } //if it's fixed, set the width to the passed in width if (col.options.renderMode == 'fixed') { col.calculateWidth(); //col.setWidth(col.options.width); } else if (col.options.renderMode == 'fit') { col.calculateWidth(rowHeader); } else if (col.options.renderMode == 'expand' && !$defined(expand)) { expand = col; } else { //treat it as fixed if has width, otherwise as fit if ($defined(col.options.width)) { col.setWidth(col.options.width); } else { col.calculateWidth(rowHeader); } } if (!col.isHidden() && !(col.name == this.grid.row.options.headerColumn)) { totalWidth += Jx.getNumber(col.getWidth()); if (rowHeader) { rowHeaderWidth = col.getWidth(); } } },this); // width of the container //var containerWidth = this.grid.gridObj.getContentBoxSize(); var gridSize = this.grid.gridObj.getContentBoxSize(); if (gridSize.width > totalWidth) { //now figure the expand column if ($defined(expand)) { // var leftOverSpace = gridSize.width - totalWidth + rowHeaderWidth; var leftOverSpace = gridSize.width - totalWidth; if (leftOverSpace >= expand.options.width) { expand.options.width = leftOverSpace; expand.calculateWidth(); expand.setWidth(leftOverSpace); totalWidth += leftOverSpace; } else { expand.setWidth(expand.options.width); } } } //else { this.grid.gridTable.setContentBoxSize({'width': totalWidth - rowHeaderWidth}); this.grid.colTable.setContentBoxSize({'width': totalWidth - rowHeaderWidth}); // } },
|
expand.setWidth(leftOverSpace);
|
expand.setWidth(leftOverSpace, true);
|
calculateWidths: function () { //to calculate widths we loop through each column var expand = null; var totalWidth = 0; var rowHeaderWidth = 0; this.columns.each(function(col,idx){ //are we checking the rowheader? var rowHeader = false; if (col.name == this.grid.row.options.headerColumn) { rowHeader = true; } //if it's fixed, set the width to the passed in width if (col.options.renderMode == 'fixed') { col.calculateWidth(); //col.setWidth(col.options.width); } else if (col.options.renderMode == 'fit') { col.calculateWidth(rowHeader); } else if (col.options.renderMode == 'expand' && !$defined(expand)) { expand = col; } else { //treat it as fixed if has width, otherwise as fit if ($defined(col.options.width)) { col.setWidth(col.options.width); } else { col.calculateWidth(rowHeader); } } if (!col.isHidden() && !(col.name == this.grid.row.options.headerColumn)) { totalWidth += Jx.getNumber(col.getWidth()); if (rowHeader) { rowHeaderWidth = col.getWidth(); } } },this); // width of the container //var containerWidth = this.grid.gridObj.getContentBoxSize(); var gridSize = this.grid.gridObj.getContentBoxSize(); if (gridSize.width > totalWidth) { //now figure the expand column if ($defined(expand)) { // var leftOverSpace = gridSize.width - totalWidth + rowHeaderWidth; var leftOverSpace = gridSize.width - totalWidth; if (leftOverSpace >= expand.options.width) { expand.options.width = leftOverSpace; expand.calculateWidth(); expand.setWidth(leftOverSpace); totalWidth += leftOverSpace; } else { expand.setWidth(expand.options.width); } } } //else { this.grid.gridTable.setContentBoxSize({'width': totalWidth - rowHeaderWidth}); this.grid.colTable.setContentBoxSize({'width': totalWidth - rowHeaderWidth}); // } },
|
var leftOverSpace = gridSize.width - totalWidth - 2;
|
var leftOverSpace = gridSize.width - totalWidth if (Browser.Engine.gecko) { leftOverSpace -= this.getColumnCount(true); } else { leftOverSpace -= 2; }
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calculateWidths: function () { //to calculate widths we loop through each column var expand = null; var totalWidth = 0; var rowHeaderWidth = 0; this.columns.each(function(col,idx){ //are we checking the rowheader? var rowHeader = false; if (col.name == this.grid.row.options.headerColumn) { rowHeader = true; } //if it's fixed, set the width to the passed in width if (col.options.renderMode == 'fixed') { col.calculateWidth(); //col.setWidth(col.options.width); } else if (col.options.renderMode == 'fit') { col.calculateWidth(rowHeader); } else if (col.options.renderMode == 'expand' && !$defined(expand)) { expand = col; } else { //treat it as fixed if has width, otherwise as fit if ($defined(col.options.width)) { col.setWidth(col.options.width); } else { col.calculateWidth(rowHeader); } } if (!col.isHidden() && !(col.name == this.grid.row.options.headerColumn)) { totalWidth += Jx.getNumber(col.getCellWidth()); if (rowHeader) { rowHeaderWidth = col.getWidth(); } } },this); // width of the container //var containerWidth = this.grid.gridObj.getContentBoxSize(); var gridSize = this.grid.gridObj.getContentBoxSize(); if (gridSize.width > totalWidth) { //now figure the expand column if ($defined(expand)) { // var leftOverSpace = gridSize.width - totalWidth + rowHeaderWidth; // -2 is for the right hand border on the cell and the table var leftOverSpace = gridSize.width - totalWidth - 2; if (leftOverSpace >= expand.options.width) { //in order for this to be set properly the cellWidth must be the //leftover space. we need to figure out the delta value and //subtract it from the leftover width expand.options.width = leftOverSpace; expand.calculateWidth(); expand.setWidth(leftOverSpace, true); totalWidth += leftOverSpace; } else { expand.setWidth(expand.options.width); } } } //else { this.grid.gridTable.setContentBoxSize({'width': totalWidth - rowHeaderWidth}); this.grid.colTable.setContentBoxSize({'width': totalWidth - rowHeaderWidth}); // } },
|
this.grid.gridTable.setContentBoxSize({'width': totalWidth - rowHeaderWidth}); this.grid.colTable.setContentBoxSize({'width': totalWidth - rowHeaderWidth});
|
this.grid.gridTable.setContentBoxSize({'width': totalWidth}); this.grid.colTable.setContentBoxSize({'width': totalWidth});
|
calculateWidths: function () { //to calculate widths we loop through each column var expand = null; var totalWidth = 0; var rowHeaderWidth = 0; this.columns.each(function(col,idx){ //are we checking the rowheader? var rowHeader = false; if (col.name == this.grid.row.options.headerColumn) { rowHeader = true; } //if it's fixed, set the width to the passed in width if (col.options.renderMode == 'fixed') { col.calculateWidth(); //col.setWidth(col.options.width); } else if (col.options.renderMode == 'fit') { col.calculateWidth(rowHeader); } else if (col.options.renderMode == 'expand' && !$defined(expand)) { expand = col; } else { //treat it as fixed if has width, otherwise as fit if ($defined(col.options.width)) { col.setWidth(col.options.width); } else { col.calculateWidth(rowHeader); } } if (!col.isHidden() && !(col.name == this.grid.row.options.headerColumn)) { totalWidth += Jx.getNumber(col.getCellWidth()); if (rowHeader) { rowHeaderWidth = col.getWidth(); } } },this); // width of the container //var containerWidth = this.grid.gridObj.getContentBoxSize(); var gridSize = this.grid.gridObj.getContentBoxSize(); if (gridSize.width > totalWidth) { //now figure the expand column if ($defined(expand)) { // var leftOverSpace = gridSize.width - totalWidth + rowHeaderWidth; // -2 is for the right hand border on the cell and the table var leftOverSpace = gridSize.width - totalWidth - 2; if (leftOverSpace >= expand.options.width) { //in order for this to be set properly the cellWidth must be the //leftover space. we need to figure out the delta value and //subtract it from the leftover width expand.options.width = leftOverSpace; expand.calculateWidth(); expand.setWidth(leftOverSpace, true); totalWidth += leftOverSpace; } else { expand.setWidth(expand.options.width); } } } //else { this.grid.gridTable.setContentBoxSize({'width': totalWidth - rowHeaderWidth}); this.grid.colTable.setContentBoxSize({'width': totalWidth - rowHeaderWidth}); // } },
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post_new_book(obj.value, obj.info, obj.id); }
|
showLoadingGif(); post_new_book(obj.value, obj.info, obj.id); hideLoadingGif(); }
|
callback: function(obj){ post_new_book(obj.value, obj.info, obj.id); }
|
var k = new Gemma.WaitHandler(); k.handleWait(data, true); deasw.relayEvents(k, ['done']); Ext.getBody().unmask(); k.on('done', function(payload) { this.fireEvent('differential', payload) }); }.createDelegate(this),
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var k = new Gemma.WaitHandler({ throbberEl : throbberEl }); this.relayEvents(k, ['done', 'fail']); k.handleWait(data, false); k.on('done', function(payload) { this.fireEvent('reportUpdated', payload); }); }.createDelegate(this),
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callback : function(data) { var k = new Gemma.WaitHandler(); k.handleWait(data, true); deasw.relayEvents(k, ['done']); Ext.getBody().unmask(); k.on('done', function(payload) { this.fireEvent('differential', payload) }); }.createDelegate(this),
|
Ext.getCmp('biomaterial-grid-panel').init();
|
callback : function() { Ext.getCmp('experimental-design-upload-form-window').close(); Ext.Msg.alert("Success", "Design imported."); Ext.getCmp('experimental-factor-grid').getStore().reload(); // Ext.getCmp('factor-value-grid').getStore().reload(); // should have started out empty anyway. Ext.getCmp('biomaterial-grid-panel').init(); }
|
|
if (!groupId)
|
if (!groupId){
|
callback : function() { // for selecting the desired row, if given groupid given if (!groupId) return; var groupPanel = Ext.getCmp('gene-group-panel'); var row = groupPanel.getStore().findExact("id", groupId); groupPanel.getSelectionModel().selectRow(row, false); }
|
}
|
callback : function() { // for selecting the desired row, if given groupid given if (!groupId) return; var groupPanel = Ext.getCmp('gene-group-panel'); var row = groupPanel.getStore().findExact("id", groupId); groupPanel.getSelectionModel().selectRow(row, false); }
|
|
geneData.push([genes[i].id, genes[i].taxon.scientificName,
|
geneData.push([genes[i].id, genes[i].taxonScientificName,
|
callback : function(genes) { var geneData = []; var warned = false; for (var i = 0; i < genes.length; ++i) { if (i >= Gemma.MAX_GENES_PER_QUERY) { if (!warned) { Ext.Msg.alert("Too many genes", "You can only search up to " + Gemma.MAX_GENES_PER_QUERY + " genes, some of your selections will be ignored."); warned = true; } break; } if (this.getStore().find("id", genes[i].id) < 0) { geneData.push([genes[i].id, genes[i].taxon.scientificName, genes[i].officialSymbol, genes[i].officialName]); } } this.getStore().loadData(geneData, true); loadMask.hide(); }.createDelegate(this),
|
callback : function() { sp.destroy(); Gemma.SecurityManager.updateSecurityLink( elid, securityInfo.publiclyReadable, shared); },
|
callback : function(securityInfo) { showSecurityForm(securityInfo); },
|
callback : function() { sp.destroy(); Gemma.SecurityManager.updateSecurityLink( elid, securityInfo.publiclyReadable, shared); },
|
width: fWidth + 'px', height: (fHeight - 30) + 'px',
|
width: shimWidth + 'px', height: shimHeight + 'px',
|
callback: function() { urls = []; var index = 0; urls.push([options.href, options.title]); // calculate top and left offset for the lightbox var pageScroll = Ext.fly(document).getScroll(); var lightboxTop = pageScroll.top + (Ext.lib.Dom.getViewportHeight() / 10); var lightboxLeft = pageScroll.left; els.lightbox.setStyle({ top: lightboxTop + 'px', left: lightboxLeft + 'px' }).show(); els.shim.setStyle({ width: fWidth + 'px', height: (fHeight - 30) + 'px', alpha: '(opacity=100)' }); this.setUrl(index, fWidth, fHeight); els.header.update('<h3>' + options.title + '</h3>'); this.fireEvent('open', urls[index]); },
|
this.setUrl(index, fWidth, fHeight);
|
this.setUrl(index, shimWidth, shimHeight);
|
callback: function() { urls = []; var index = 0; urls.push([options.href, options.title]); // calculate top and left offset for the lightbox var pageScroll = Ext.fly(document).getScroll(); var lightboxTop = pageScroll.top + (Ext.lib.Dom.getViewportHeight() / 10); var lightboxLeft = pageScroll.left; els.lightbox.setStyle({ top: lightboxTop + 'px', left: lightboxLeft + 'px' }).show(); els.shim.setStyle({ width: fWidth + 'px', height: (fHeight - 30) + 'px', alpha: '(opacity=100)' }); this.setUrl(index, fWidth, fHeight); els.header.update('<h3>' + options.title + '</h3>'); this.fireEvent('open', urls[index]); },
|
this.relayEvents(k, ['done']);
|
this.relayEvents(k, ['done', 'fail']);
|
callback : function(data) { var k = new Gemma.WaitHandler({ throbberEl : throbberEl }); this.relayEvents(k, ['done']); k.handleWait(data, false); k.on('done', function(payload) { this.fireEvent('reportUpdated', payload); }); }.createDelegate(this)
|
callback : function(data) { if (!groupId) { return; } }
|
var callback = function(data) { if (data) { this.ownerCt.getStore().remove(rec); this.ownerCt.getStore().clearSelected(); this.resetBut.disable(); this.deleteBut.disable(); this.commitBut.disable(); this.ownerCt.loadMask.hide(); } }.createDelegate(this);
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callback : function(data) { // for selecting the desired row, if given groupid given if (!groupId) { return; } // FIXME: this doesn't work because for data that takes awhile to load. // Callback returns prematurley, data isn't done loading, if the following code // selects an empty record which loads instantly, by then the previous load finishes and the // wrong info is shown in the gene panel but the correct group is seleted.... // var groupPanel = Ext.getCmp('gene-group-panel'); // var row = groupPanel.getStore().findExact("id", groupId); // groupPanel.getSelectionModel().selectRow(row, false); }
|
var k = new Gemma.WaitHandler();
|
var k = new Gemma.WaitHandler({ throbberEl : throbberEl });
|
callback : function(data) { var k = new Gemma.WaitHandler(); this.relayEvents(k, ['done']); k.handleWait(data, false); k.on('done', function(payload) { this.fireEvent('reportUpdated', payload); }); }.createDelegate(this)
|
width: (fWidth - 20) + 'px', height: (fHeight - 50) + 'px',
|
width: fWidth + 'px', height: (fHeight - 30) + 'px',
|
callback: function() { urls = []; var index = 0; urls.push([options.href, options.title]); // calculate top and left offset for the lightbox var pageScroll = Ext.fly(document).getScroll(); var lightboxTop = pageScroll.top + (Ext.lib.Dom.getViewportHeight() / 10); var lightboxLeft = pageScroll.left; els.lightbox.setStyle({ top: lightboxTop + 'px', left: lightboxLeft + 'px' }).show(); els.shim.setStyle({ width: (fWidth - 20) + 'px', height: (fHeight - 50) + 'px', alpha: '(opacity=100)' }); this.setUrl(index, fWidth, fHeight); els.header.update('<h3>' + options.title + '</h3>'); this.fireEvent('open', urls[index]); },
|
callback : function(){ console.log(groupId); if (!groupId){
|
callback : function() { if (!groupId)
|
callback : function(){ //for selecting the desired row console.log(groupId); if (!groupId){ return; } var groupPanel = Ext.getCmp('gene-group-panel'); var row = groupPanel.getStore().findExact(id,groupId); groupPanel.getSelectionModel().selectRow(row, false); }
|
}
|
callback : function(){ //for selecting the desired row console.log(groupId); if (!groupId){ return; } var groupPanel = Ext.getCmp('gene-group-panel'); var row = groupPanel.getStore().findExact(id,groupId); groupPanel.getSelectionModel().selectRow(row, false); }
|
|
var row = groupPanel.getStore().findExact(id,groupId);
|
var row = groupPanel.getStore().findExact("id", groupId);
|
callback : function(){ //for selecting the desired row console.log(groupId); if (!groupId){ return; } var groupPanel = Ext.getCmp('gene-group-panel'); var row = groupPanel.getStore().findExact(id,groupId); groupPanel.getSelectionModel().selectRow(row, false); }
|
k.handleWait(data, 'pubmedUpdated', false);
|
k.on('done', function(e) { window.location.reload(); }, this) k.handleWait(data, false);
|
callback : function(data) { var k = new Gemma.WaitHandler(); k.handleWait(data, 'pubmedUpdated', false); }.createDelegate(this)
|
callback : function() {
|
callback : function(data) {
|
callback : function() { // for selecting the desired row, if given groupid given if (!groupId){ return; } var groupPanel = Ext.getCmp('gene-group-panel'); var row = groupPanel.getStore().findExact("id", groupId); groupPanel.getSelectionModel().selectRow(row, false); }
|
var groupPanel = Ext.getCmp('gene-group-panel'); var row = groupPanel.getStore().findExact("id", groupId); groupPanel.getSelectionModel().selectRow(row, false);
|
callback : function() { // for selecting the desired row, if given groupid given if (!groupId){ return; } var groupPanel = Ext.getCmp('gene-group-panel'); var row = groupPanel.getStore().findExact("id", groupId); groupPanel.getSelectionModel().selectRow(row, false); }
|
|
object.attr("src", scriptUrl + "media/images/vote-accepted.png");
|
object.attr("src", mediaUrl("media/images/vote-accepted.png"));
|
var callback_accept = function(object, voteType, data){ if(data.allowed == "0" && data.success == "0"){ showMessage(object, acceptAnonymousMessage); } else if(data.allowed == "-1"){ showMessage(object, acceptOwnAnswerMessage); } else if(data.status == "1"){ object.attr("src", scriptUrl + "media/images/vote-accepted.png"); $("#"+answerContainerIdPrefix+postId).removeClass("accepted-answer"); $("#"+commentLinkIdPrefix+postId).removeClass("comment-link-accepted"); } else if(data.success == "1"){ var acceptedButtons = 'div.'+ voteContainerId +' img[id^='+ imgIdPrefixAccept +']'; $(acceptedButtons).attr("src", scriptUrl + "media/images/vote-accepted.png"); var answers = ("div[id^="+answerContainerIdPrefix +"]"); $(answers).removeClass("accepted-answer"); var commentLinks = ("div[id^="+answerContainerIdPrefix +"] div[id^="+ commentLinkIdPrefix +"]"); $(commentLinks).removeClass("comment-link-accepted"); object.attr("src", scriptUrl + "media/images/vote-accepted-on.png"); $("#"+answerContainerIdPrefix+postId).addClass("accepted-answer"); $("#"+commentLinkIdPrefix+postId).addClass("comment-link-accepted"); } else{ showMessage(object, data.message); } };
|
$(acceptedButtons).attr("src", scriptUrl + "media/images/vote-accepted.png");
|
$(acceptedButtons).attr("src", mediaUrl("media/images/vote-accepted.png"));
|
var callback_accept = function(object, voteType, data){ if(data.allowed == "0" && data.success == "0"){ showMessage(object, acceptAnonymousMessage); } else if(data.allowed == "-1"){ showMessage(object, acceptOwnAnswerMessage); } else if(data.status == "1"){ object.attr("src", scriptUrl + "media/images/vote-accepted.png"); $("#"+answerContainerIdPrefix+postId).removeClass("accepted-answer"); $("#"+commentLinkIdPrefix+postId).removeClass("comment-link-accepted"); } else if(data.success == "1"){ var acceptedButtons = 'div.'+ voteContainerId +' img[id^='+ imgIdPrefixAccept +']'; $(acceptedButtons).attr("src", scriptUrl + "media/images/vote-accepted.png"); var answers = ("div[id^="+answerContainerIdPrefix +"]"); $(answers).removeClass("accepted-answer"); var commentLinks = ("div[id^="+answerContainerIdPrefix +"] div[id^="+ commentLinkIdPrefix +"]"); $(commentLinks).removeClass("comment-link-accepted"); object.attr("src", scriptUrl + "media/images/vote-accepted-on.png"); $("#"+answerContainerIdPrefix+postId).addClass("accepted-answer"); $("#"+commentLinkIdPrefix+postId).addClass("comment-link-accepted"); } else{ showMessage(object, data.message); } };
|
object.attr("src", scriptUrl + "media/images/vote-accepted-on.png");
|
object.attr("src", mediaUrl("media/images/vote-accepted-on.png"));
|
var callback_accept = function(object, voteType, data){ if(data.allowed == "0" && data.success == "0"){ showMessage(object, acceptAnonymousMessage); } else if(data.allowed == "-1"){ showMessage(object, acceptOwnAnswerMessage); } else if(data.status == "1"){ object.attr("src", scriptUrl + "media/images/vote-accepted.png"); $("#"+answerContainerIdPrefix+postId).removeClass("accepted-answer"); $("#"+commentLinkIdPrefix+postId).removeClass("comment-link-accepted"); } else if(data.success == "1"){ var acceptedButtons = 'div.'+ voteContainerId +' img[id^='+ imgIdPrefixAccept +']'; $(acceptedButtons).attr("src", scriptUrl + "media/images/vote-accepted.png"); var answers = ("div[id^="+answerContainerIdPrefix +"]"); $(answers).removeClass("accepted-answer"); var commentLinks = ("div[id^="+answerContainerIdPrefix +"] div[id^="+ commentLinkIdPrefix +"]"); $(commentLinks).removeClass("comment-link-accepted"); object.attr("src", scriptUrl + "media/images/vote-accepted-on.png"); $("#"+answerContainerIdPrefix+postId).addClass("accepted-answer"); $("#"+commentLinkIdPrefix+postId).addClass("comment-link-accepted"); } else{ showMessage(object, data.message); } };
|
if(data.count == 0)
|
if(data.count === 0){
|
var callback_favorite = function(object, voteType, data){ if(data.allowed == "0" && data.success == "0"){ showMessage(object, favoriteAnonymousMessage.replace("{{QuestionID}}", questionId)); } else if(data.status == "1"){ object.attr("src", scriptUrl + "content/images/vote-favorite-off.png"); var fav = getFavoriteNumber(); fav.removeClass("my-favorite-number"); if(data.count == 0) data.count = ''; fav.text(data.count); } else if(data.success == "1"){ object.attr("src", scriptUrl + "content/images/vote-favorite-on.png"); var fav = getFavoriteNumber(); fav.text(data.count); fav.addClass("my-favorite-number"); } else{ showMessage(object, data.message); } };
|
}
|
var callback_favorite = function(object, voteType, data){ if(data.allowed == "0" && data.success == "0"){ showMessage(object, favoriteAnonymousMessage.replace("{{QuestionID}}", questionId)); } else if(data.status == "1"){ object.attr("src", scriptUrl + "content/images/vote-favorite-off.png"); var fav = getFavoriteNumber(); fav.removeClass("my-favorite-number"); if(data.count == 0) data.count = ''; fav.text(data.count); } else if(data.success == "1"){ object.attr("src", scriptUrl + "content/images/vote-favorite-on.png"); var fav = getFavoriteNumber(); fav.text(data.count); fav.addClass("my-favorite-number"); } else{ showMessage(object, data.message); } };
|
|
object.attr("src", scriptUrl + "media/images/vote-favorite-off.png");
|
object.attr("src", mediaUrl("media/images/vote-favorite-off.png"));
|
var callback_favorite = function(object, voteType, data){ if(data.allowed == "0" && data.success == "0"){ showMessage(object, favoriteAnonymousMessage.replace("{{QuestionID}}", questionId)); } else if(data.status == "1"){ object.attr("src", scriptUrl + "media/images/vote-favorite-off.png"); var fav = getFavoriteNumber(); fav.removeClass("my-favorite-number"); if(data.count === 0){ data.count = ''; } fav.text(data.count); } else if(data.success == "1"){ object.attr("src", scriptUrl + "media/images/vote-favorite-on.png"); var fav = getFavoriteNumber(); fav.text(data.count); fav.addClass("my-favorite-number"); } else{ showMessage(object, data.message); } };
|
object.attr("src", scriptUrl + "media/images/vote-favorite-on.png");
|
object.attr("src", mediaUrl("media/images/vote-favorite-on.png"));
|
var callback_favorite = function(object, voteType, data){ if(data.allowed == "0" && data.success == "0"){ showMessage(object, favoriteAnonymousMessage.replace("{{QuestionID}}", questionId)); } else if(data.status == "1"){ object.attr("src", scriptUrl + "media/images/vote-favorite-off.png"); var fav = getFavoriteNumber(); fav.removeClass("my-favorite-number"); if(data.count === 0){ data.count = ''; } fav.text(data.count); } else if(data.success == "1"){ object.attr("src", scriptUrl + "media/images/vote-favorite-on.png"); var fav = getFavoriteNumber(); fav.text(data.count); fav.addClass("my-favorite-number"); } else{ showMessage(object, data.message); } };
|
if (data.message.length > 0){
|
if (data.message && data.message.length > 0){
|
var callback_vote = function(object, voteType, data){ if (data.success == '0'){ showMessage(object, data.message); return; } else { if (data.status == '1'){ setVoteImage(voteType, true, object); } else { setVoteImage(voteType, false, object); } setVoteNumber(object, data.count); if (data.message.length > 0){ showMessage(object, data.message); } return; } //may need to take a look at this again if (data.status == "1"){ setVoteImage(voteType, true, object); setVoteNumber(object, data.count); } else if (data.success == "1"){ setVoteImage(voteType, false, object); setVoteNumber(object, data.count); if (data.message.length > 0){ showMessage(object, data.message); } } };
|
return function() { before_func.apply(null, arguments); new_func.apply(null, arguments);
|
return function() { before_func.apply(null, arguments); new_func.apply(null, arguments); };
|
var callboth = function(before_func, new_func) { return function() { before_func.apply(null, arguments); new_func.apply(null, arguments); }; };
|
};
|
var callboth = function(before_func, new_func) { return function() { before_func.apply(null, arguments); new_func.apply(null, arguments); }; };
|
|
for (var property in options) this.options[property] = options[property];
|
for (var prop in options) this.options[prop] = options[prop];
|
callService : function(method, parameters, options) { if (options) { for (var property in options) this.options[property] = options[property]; } try { this.transport = new XMLHttpRequest();} catch(e) { try { this.transport = new ActiveXObject('Msxml2.XMLHTTP'); } catch(e) { try { this.transport = new ActiveXObject('Microsoft.XMLHTTP'); } catch (e){ dispatchError(0, "Cannot create request object"); } } } this.transport.onreadystatechange = this.onStateChange.pwgBind(this); var url = this.urlRoot+"ws.php?format=json"; var body = "method="+method; if (parameters) { for (var property in parameters) { if ( typeof parameters[property] == 'object' && parameters[property]) { for (var i=0; i<parameters[property].length; i++) body += "&"+property+"[]="+encodeURIComponent(parameters[property][i]); } else body += "&"+property+"="+encodeURIComponent(parameters[property]); } } if (this.options.method == "POST" ) { this.transport.open(this.options.method, url, this.options.async); this.transport.setRequestHeader("Content-Type", "application/x-www-form-urlencoded"); this.transport.send(body); } else { url += "&"+body; this.transport.open(this.options.method, url, this.options.async); this.transport.send(null); } },
|
try { this.transport = new XMLHttpRequest();}
|
try { this.xhr = new XMLHttpRequest();}
|
callService : function(method, parameters, options) { if (options) { for (var property in options) this.options[property] = options[property]; } try { this.transport = new XMLHttpRequest();} catch(e) { try { this.transport = new ActiveXObject('Msxml2.XMLHTTP'); } catch(e) { try { this.transport = new ActiveXObject('Microsoft.XMLHTTP'); } catch (e){ dispatchError(0, "Cannot create request object"); } } } this.transport.onreadystatechange = this.onStateChange.pwgBind(this); var url = this.urlRoot+"ws.php?format=json"; var body = "method="+method; if (parameters) { for (var property in parameters) { if ( typeof parameters[property] == 'object' && parameters[property]) { for (var i=0; i<parameters[property].length; i++) body += "&"+property+"[]="+encodeURIComponent(parameters[property][i]); } else body += "&"+property+"="+encodeURIComponent(parameters[property]); } } if (this.options.method == "POST" ) { this.transport.open(this.options.method, url, this.options.async); this.transport.setRequestHeader("Content-Type", "application/x-www-form-urlencoded"); this.transport.send(body); } else { url += "&"+body; this.transport.open(this.options.method, url, this.options.async); this.transport.send(null); } },
|
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