Adding changes and code for terminology annotation support and integration of UMLS vocabulary
This commit is contained in:
hjkhjk54
parent
a3f174f813
commit
dc46b3e195
9 changed files with 1005 additions and 1 deletions
29
productMods/edit/forms/css/addTerminology.css
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29
productMods/edit/forms/css/addTerminology.css
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/* $This file is distributed under the terms of the license in /doc/license.txt$ */
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.terminology .column {
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float:left;
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padding-right:3px;
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}
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.terminology .row {
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clear:both;
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float:left;
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border-bottom: 1px solid #5F6464;
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}
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.termLabel {
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width:220px;
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font-weight:bold;
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}
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.termType {
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width: 40px;
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}
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.termDefinition{
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width:400px;
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}
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form#addTerminologyForm {
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display:none;
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}
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239
productMods/edit/forms/js/addTerminology.js
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239
productMods/edit/forms/js/addTerminology.js
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/* $This file is distributed under the terms of the license in /doc/license.txt$ */
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var addTerminologyForm = {
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/* *** Initial page setup *** */
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onLoad: function() {
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if (this.disableFormInUnsupportedBrowsers()) {
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return;
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}
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this.mixIn();
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this.initObjects();
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this.initPage();
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},
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disableFormInUnsupportedBrowsers: function() {
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var disableWrapper = $('#ie67DisableWrapper');
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// Check for unsupported browsers only if the element exists on the page
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if (disableWrapper.length) {
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if (vitro.browserUtils.isIELessThan8()) {
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disableWrapper.show();
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$('.noIE67').hide();
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return true;
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}
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}
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return false;
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},
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mixIn: function() {
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// Mix in the custom form utility methods
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$.extend(this, vitro.customFormUtils);
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// Get the custom form data from the page
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$.extend(this, customFormData);
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//test
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alert(addTerminologyForm.UMLSCUIURL);
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alert(addTerminologyForm.dataServiceUri);
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},
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// On page load, create references for easy access to form elements.
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initObjects: function() {
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this.form = $('#addTerminologyForm');
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this.showFormButtonWrapper = $('#showAddForm');
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this.submit = this.form.find(':submit');
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this.cancel = this.form.find('.cancel');
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//Add term
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this.addTermButton = $('#showAddFormButton');
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//section where results should be displayed
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this.selectedTerm = $('#selectedTerm');
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//input for search term form
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this.searchTerm = $('#searchTerm');
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this.searchSubmit = $('#searchButton');
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//Hidden inputs for eventual submission
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this.referencedTerm = $('#referencedTerm');
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this.entryTerm = $('#entryTerm');
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this.termLabel = $('#termLabel');
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this.termType = $('#termType');
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this.removeTermLinks = $('a.remove');
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},
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initPage: function() {
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this.initTermData();
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this.bindEventListeners();
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},
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bindEventListeners: function() {
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this.searchSubmit.click(function() {
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addTerminologyForm.submitSearchTerm();
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return false;
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});
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this.form.submit(function() {
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return addTerminologyForm.prepareSubmit();
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});
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this.addTermButton.click(function() {
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addTerminologyForm.initForm();
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});
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this.removeTermLinks.click(function() {
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addTerminologyForm.removeExistingTerm(this);
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return false;
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});
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},
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initForm: function() {
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// Hide the button that shows the form
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this.showFormButtonWrapper.hide();
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this.clearSearchResults();
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this.cancel.unbind('click');
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this.cancel.bind('click', function() {
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//show only list of existing terms and hide adding term form
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addTerminologyForm.showTermListOnlyView();
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return false;
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});
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// Show the form
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this.form.show();
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},
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// On page load, associate data with each existing term element. Then we don't
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// have to keep retrieving data from or modifying the DOM as we manipulate the
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// authorships.
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initTermData: function() {
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$('.existingTerm').each(function(index) {
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$(this).data(existingTermsData[index]);
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$(this).data('position', index+1);
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});
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},
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clearSearchResults:function() {
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$('#selectedTerm').empty();
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},
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showTermListOnlyView: function() {
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this.hideForm();
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this.showFormButtonWrapper.show();
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},
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submitSearchTerm: function() {
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//Get value of search term
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var searchValue = this.searchTerm.val();
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this.entryTerm.val(searchValue);
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var dataServiceUrl = addTerminologyForm.dataServiceUrl + "?searchTerm=" + encodeURIComponent(searchValue);
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$.getJSON(dataServiceUrl, function(results) {
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if ( results.All.length == 0 ) {
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} else {
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//update existing content type with correct class group name and hide class group select again
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var bestMatchResults = results["Best Match"];
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var numberMatches = bestMatchResults.length;
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var i;
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//For each result, display
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var htmlAdd = "";
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if(numberMatches > 0) {
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htmlAdd = "<ul class='dd' id='terms' name='terms'>";
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htmlAdd+= addTerminologyForm.addResultsHeader();
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for(i = 0; i < numberMatches; i++) {
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var termResult = bestMatchResults[i];
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var CUI = termResult.CUI;
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var label = termResult.label;
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var definition = termResult.definition;
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var type = termResult.type;
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var cuiURI = addTerminologyForm.UMLSCUIURL + CUI;
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htmlAdd+= addTerminologyForm.generateIndividualTermDisplay(cuiURI, label, definition, type);
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}
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htmlAdd+= "</ul>";
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} else {
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htmlAdd+= "<p>No search results found.</p>";
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}
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$('#selectedTerm').html(htmlAdd);
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}
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});
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},
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addResultsHeader:function() {
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var htmlAdd = "<li class='terminology'><div class='row'><span class='column termLabel'>Label (Type) </span><span class='column termDefinition'>Definition</span></div></li>";
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return htmlAdd;
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},
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hideSearchResults:function() {
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this.selectedTerm.hide();
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},
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prepareSubmit:function() {
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var checkedElements = $("#CUI:checked");
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var i;
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var len = checkedElements.length;
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var checkedTerm, checkedTermElement, termLabel, termType;
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var referencedTerms = [];
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var termLabels = [];
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var termTypes = [];
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checkedElements.each(function() {
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checkedTermElement = $(this);
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checkedTerm = checkedTermElement.val();
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termType = checkedTermElement.attr("termType");
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termLabel = checkedTermElement.attr("label");
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referencedTerms.push(checkedTerm);
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termLabels.push(termLabel);
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termTypes.push(termType);
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});
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this.referencedTerm.val(referencedTerms);
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this.termLabel.val(termLabels);
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this.termType.val(termTypes);
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return true;
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},
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generateIndividualTermDisplay: function(cuiURI, label, definition, type) {
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var htmlAdd = "<li class='terminology'>" +
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"<div class='row'>" +
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"<span class='column termLabel'>" +
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"<input type='checkbox' id='CUI' name='CUI' value='" + cuiURI + "' label='" + label + "' termType='" + type + "'/>" +
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label + "( " + type + ")</span>" +
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"<span class='column termDefinition'>" + definition + "</span>" +
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"</div>" +
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"</li>";
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return htmlAdd;
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}, removeExistingTerm: function(link) {
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var removeLast = false,
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message = 'Are you sure you want to remove this term?';
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if (!confirm(message)) {
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return false;
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}
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if ($(link)[0] === $('.remove:last')[0]) {
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removeLast = true;
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}
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$.ajax({
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url: $(link).attr('href'),
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type: 'POST',
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data: {
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deletion: $(link).parents('.existingTerm').data('termNodeUri')
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},
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dataType: 'json',
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context: link, // context for callback
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complete: function(request, status) {
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var existingTerm,
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termNodeUri;
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if (status === 'success') {
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existingTerm = $(this).parents('.existingTerm');
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existingTerm.fadeOut(400, function() {
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var numTerms;
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// For undo link: add to a deletedAuthorships array
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// Remove from the DOM
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$(this).remove();
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// Actions that depend on the author having been removed from the DOM:
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numTerms = $('.existingTerm').length; // retrieve the length after removing authorship from the DOM
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});
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} else {
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alert('Error processing request: author not removed');
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}
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}
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});
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}
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};
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$(document).ready(function() {
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addTerminologyForm.onLoad();
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});
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286
productMods/edit/forms/terminologyAnnotation.jsp
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286
productMods/edit/forms/terminologyAnnotation.jsp
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<%-- $This file is distributed under the terms of the license in /doc/license.txt$ --%>
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<%-- Custom form for adding terminology annotation
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--%>
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<%@ page import="java.util.List" %>
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<%@ page import="java.util.ArrayList" %>
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<%@ page import="java.util.Arrays" %>
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<%@ page import="java.util.Collections" %>
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<%@ page import="com.hp.hpl.jena.rdf.model.Model" %>
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<%@ page import="com.hp.hpl.jena.vocabulary.XSD" %>
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<%@ page import="edu.cornell.mannlib.vitro.webapp.beans.Individual" %>
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<%@ page import="edu.cornell.mannlib.vitro.webapp.beans.DataPropertyComparator" %>
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<%@ page import="edu.cornell.mannlib.vitro.webapp.beans.DataPropertyStatement" %>
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<%@ page import="edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary" %>
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<%@ page import="edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.EditConfiguration" %>
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<%@ page import="edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory" %>
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<%@ page import="edu.cornell.mannlib.vitro.webapp.controller.VitroRequest" %>
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<%@ page import="edu.cornell.mannlib.vitro.webapp.web.MiscWebUtils" %>
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<%@ page import="edu.cornell.mannlib.vitro.webapp.controller.freemarker.UrlBuilder.JavaScript" %>
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<%@ page import="edu.cornell.mannlib.vitro.webapp.controller.freemarker.UrlBuilder.Css" %>
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<%@ page import="org.apache.commons.lang.StringUtils" %>
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<%@ page import="org.json.JSONObject" %>
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<%@ page import="org.apache.commons.logging.Log" %>
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<%@ page import="org.apache.commons.logging.LogFactory" %>
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<%@ taglib prefix="c" uri="http://java.sun.com/jstl/core"%>
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<%@ taglib prefix="v" uri="http://vitro.mannlib.cornell.edu/vitro/tags" %>
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<%!
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public static Log log = LogFactory.getLog("edu.cornell.mannlib.vitro.webapp.jsp.edit.forms.terminologyAnnotation.jsp");
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%>
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<%
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VitroRequest vreq = new VitroRequest(request);
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WebappDaoFactory wdf = vreq.getWebappDaoFactory();
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vreq.setAttribute("defaultNamespace", ""); //empty string triggers default new URI behavior
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vreq.setAttribute("stringDatatypeUriJson", MiscWebUtils.escape(XSD.xstring.toString()));
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%>
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<c:set var="vivoCore" value="http://vivoweb.org/ontology/core#" />
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<c:set var="rdfs" value="<%= VitroVocabulary.RDFS %>" />
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<c:set var="label" value="${rdfs}label" />
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<c:set var="foaf" value="http://xmlns.com/foaf/0.1/" />
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<c:set var="personClassUri" value="${foaf}Person" />
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<%-- Unlike other custom forms, this form does not allow edits of existing authors, so there are no
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SPARQL queries for existing values. --%>
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<v:jsonset var="n3ForTerminology">
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@prefix core: <${vivoCore}> .
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?subject ?predicate ?terminologyContextNode .
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?terminologyContextNode core:referencedTerm ?referencedTerm .
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?terminologyContextNode core:entryTerm ?entryTerm .
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?terminologyContextNode core:termLabel ?termLabel .
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</v:jsonset>
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<c:set var="returnPathAfterSubmit" value="/edit/editRequestDispatch.jsp?subjectUri=${subjectUri}&predicateUri=${predicateUri}" />
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<c:set var="submitSearchUrl" value="/UMLSTermsRetrieval"/>
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<c:url var="UMLSCUIURL" value="http://link.informatics.stonybrook.edu/umls/CUI/" />
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<c:set var="editjson" scope="request">
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{
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"formUrl" : "${formUrl}",
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"editKey" : "${editKey}",
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"urlPatternToReturnTo" : "${returnPathAfterSubmit}",
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"subject" : ["subject", "${subjectUriJson}" ],
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"predicate" : ["predicate", "${predicateUriJson}" ],
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"object" : ["terminologyContextNode", "${objectUriJson}", "URI" ],
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"n3required" : [ "${n3ForTerminology}" ],
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"n3optional" : [ ],
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"newResources" : { "terminologyContextNode" : "${defaultNamespace}" },
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"urisInScope" : { },
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"literalsInScope": { },
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"urisOnForm" : [ "referencedTerm" ],
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"literalsOnForm" : [ "entryTerm", "termLabel" ],
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"filesOnForm" : [ ],
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"sparqlForLiterals" : { },
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"sparqlForUris" : { },
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"sparqlForExistingLiterals" : { },
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"sparqlForExistingUris" : { },
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"fields" : {
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"referencedTerm" : {
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"newResource" : "false",
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"validators" : [ "nonempty" ],
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"optionsType" : "UNDEFINED", //UNSURE WHAT TO KEEP HERE
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"literalOptions" : [ ],
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"predicateUri" : "",
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"objectClassUri" : "",
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"rangeDatatypeUri" : "",
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"rangeLang" : "",
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"assertions" : [ "${n3ForTerminology}" ]
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},
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"entryTerm" : {
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"newResource" : "false",
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"validators" : [ "nonempty" ],
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"optionsType" : "UNDEFINED",
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"literalOptions" : [ ],
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"predicateUri" : "",
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"objectClassUri" : "",
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"rangeDatatypeUri" : "",
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"rangeLang" : "",
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"assertions" : [ "${n3ForTerminology}" ]
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},
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"termLabel" : {
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"newResource" : "false",
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"validators" : [ "nonempty" ],
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"optionsType" : "UNDEFINED",
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"literalOptions" : [ ],
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"predicateUri" : "",
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"objectClassUri" : "",
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"rangeDatatypeUri" : "",
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"rangeLang" : "",
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"assertions" : [ "${n3ForTerminology}" ]
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}
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}
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}
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</c:set>
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<%
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log.debug(request.getAttribute("editjson"));
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EditConfiguration editConfig = EditConfiguration.getConfigFromSession(session,request);
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if (editConfig == null) {
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editConfig = new EditConfiguration((String) request.getAttribute("editjson"));
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EditConfiguration.putConfigInSession(editConfig,session);
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}
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//Specific validators can be included here
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Model model = (Model) application.getAttribute("jenaOntModel");
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String objectUri = (String) request.getAttribute("objectUri");
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//for some reason we are comming from the add new and that is working
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//but we also come from the edit, and that is not working.
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editConfig.setObject(""); //this will force the edit config to always be an add, never an update
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editConfig.prepareForNonUpdate(model); // we're only adding new, not editing existing
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String subjectUri = vreq.getParameter("subjectUri");
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String predicateUri = vreq.getParameter("predicateUri");
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String vivoCore = "http://vivoweb.org/ontology/core#";
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//Individual infoResource = vreq.getWebappDaoFactory().getIndividualDao().getIndividualByURI(subjectUri);
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Individual subject = ((Individual) request.getAttribute("subject"));
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vreq.setAttribute("subjectName", subject.getName());
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//Get existing terminology annotations
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List<Individual> terminologyAnnotationNodes = subject.getRelatedIndividuals(predicateUri);
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List<String> customJs = new ArrayList<String>(Arrays.asList(JavaScript.JQUERY_UI.path(),
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JavaScript.CUSTOM_FORM_UTILS.path(),
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"/js/browserUtils.js",
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"/edit/forms/js/addTerminology.js"
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));
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request.setAttribute("customJs", customJs);
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//no custom css we know of yet
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List<String> customCss = new ArrayList<String>(Arrays.asList(Css.JQUERY_UI.path(),
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Css.CUSTOM_FORM.path(),
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"/edit/forms/css/addTerminology.css"
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));
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request.setAttribute("customCss", customCss);
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%>
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<c:set var="title" value="<em>${subjectName}</em>"/>
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<jsp:include page="${preForm}" />
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<%-- DO NOT CHANGE IDS, CLASSES, OR HTML STRUCTURE ON THIS PAGE WITHOUT UNDERSTANDING THE IMPACT ON THE JAVASCRIPT! --%>
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<h2>${title}</h2>
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<%@ include file="unsupportedBrowserMessage.jsp" %>
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<div class="noIE67">
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<h3>Manage Terminology Annotations</h3>
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<ul id="existingTerms" >
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<%
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|
||||
int existingTermsCount = terminologyAnnotationNodes.size();
|
||||
|
||||
%>
|
||||
<script type="text/javascript">
|
||||
var existingTermsData = [];
|
||||
</script>
|
||||
|
||||
<%
|
||||
String termLabelUri = vivoCore + "termLabel";
|
||||
for ( Individual termNode : terminologyAnnotationNodes ) {
|
||||
request.setAttribute("termNodeUri", termNode.getURI());
|
||||
//Get label and type only as mirroring authorship where labels but no links for individuals incoldued
|
||||
DataPropertyStatement termLabelStatement = termNode.getDataPropertyStatement(termLabelUri);
|
||||
String termLabel = termLabelStatement.getData();
|
||||
request.setAttribute("termLabel", termLabel);
|
||||
//Possible to get referenced term using object property statement?
|
||||
|
||||
%>
|
||||
<li class="existingTerm">
|
||||
<%-- span.author will be used in the next phase, when we display a message that the author has been
|
||||
removed. That text will replace the a.authorName, which will be removed. --%>
|
||||
<span class="term">
|
||||
<%-- This span is here to assign a width to. We can't assign directly to the a.authorName,
|
||||
for the case when it's followed by an em tag - we want the width to apply to the whole thing. --%>
|
||||
<span class="termWrapper">
|
||||
<span class="termLabel">
|
||||
${termLabel}</span>
|
||||
</span>
|
||||
<c:url var="deleteTermHref" value="/edit/primitiveDelete" />
|
||||
<a href="${deleteTermHref}" class="remove">Remove</a>
|
||||
</span>
|
||||
</li>
|
||||
|
||||
<script type="text/javascript">
|
||||
existingTermsData.push({
|
||||
"termNodeUri": "${termNodeUri}",
|
||||
"termLabel": "${termLabel}"
|
||||
});
|
||||
</script>
|
||||
<%
|
||||
}
|
||||
%>
|
||||
|
||||
</ul>
|
||||
|
||||
<% if (existingTermsCount == 0) { %>
|
||||
<p>There are currently no terms specified.</p>
|
||||
<% } %>
|
||||
|
||||
<div id="showAddForm">
|
||||
<v:input type="submit" value="Add Term" id="showAddFormButton" name="showAddFormButton" cancel="true" cancelLabel="Return" cancelUrl="/individual" />
|
||||
</div>
|
||||
|
||||
<form id="addTerminologyForm" class="customForm" action="<c:url value="/edit/processTerminologyAnnotation"/>" >
|
||||
|
||||
<h3>Search UMLS Terms</h3>
|
||||
|
||||
<p class="inline"><v:input type="text" id="searchTerm" label="Search UMLS" cssClass="acSelector" size="35" />
|
||||
<input type="button" id="searchButton" name="searchButton" value="Search"/>
|
||||
</p>
|
||||
<input type="hidden" id="entryTerm" name="entryTerm" value="" /> <!-- Field value populated by JavaScript -->
|
||||
<input type="hidden" id="referencedTerm" name="referencedTerm" value=""/> <!-- Field value populated by JavaScript -->
|
||||
<input type="hidden" id="termLabel" name="termLabel" value="" /> <!-- Field value populated by JavaScript -->
|
||||
<input type="hidden" id="termType" name="termType" value="" /> <!-- Field value populated by JavaScript -->
|
||||
|
||||
|
||||
|
||||
<div id="selectedTerm" name="selectedTerm" class="acSelection">
|
||||
<%-- RY maybe make this a label and input field. See what looks best. --%>
|
||||
<p class="inline">
|
||||
|
||||
</p>
|
||||
<!-- Field value populated by JavaScript -->
|
||||
|
||||
</div>
|
||||
|
||||
|
||||
<p class="submit"><v:input type="submit" id="submit" name="submit" value="Add Term" cancel="true" /></p>
|
||||
|
||||
</form>
|
||||
</div>
|
||||
|
||||
|
||||
<script type="text/javascript">
|
||||
var customFormData = {
|
||||
dataServiceUrl: '${submitSearchUrl}',
|
||||
UMLSCUIURL: '${UMLSCUIURL}'
|
||||
};
|
||||
</script>
|
||||
|
||||
<jsp:include page="${postForm}"/>
|
||||
|
||||
Loading…
Add table
Add a link
Reference in a new issue