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
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@ -145,4 +145,8 @@
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<display:listViewConfigFile rdf:datatype="http://www.w3.org/2001/XMLSchema#string">listViewConfig-webpage.xml</display:listViewConfigFile>
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<display:listViewConfigFile rdf:datatype="http://www.w3.org/2001/XMLSchema#string">listViewConfig-webpage.xml</display:listViewConfigFile>
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</rdf:Description>
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</rdf:Description>
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<rdf:Description rdf:about="http://vivoweb.org/ontology/core#terminologyAnnotation">
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<display:listViewConfigFile rdf:datatype="http://www.w3.org/2001/XMLSchema#string">listViewConfig-terminologyAnnotation.xml</display:listViewConfigFile>
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</rdf:Description>
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</rdf:RDF>
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</rdf:RDF>
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@ -1048,6 +1048,24 @@
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<url-pattern>/dataservice</url-pattern>
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<url-pattern>/dataservice</url-pattern>
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</servlet-mapping>
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</servlet-mapping>
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<servlet>
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<servlet-name>UMLSTerminology</servlet-name>
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<servlet-class>edu.cornell.mannlib.vitro.webapp.servlet.UMLSTerminologyAnnotation</servlet-class>
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</servlet>
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<servlet-mapping>
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<servlet-name>UMLSTerminology</servlet-name>
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<url-pattern>/UMLSTermsRetrieval</url-pattern>
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</servlet-mapping>
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<servlet>
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<servlet-name>ProcessTerminologyAnnotation</servlet-name>
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<servlet-class>edu.cornell.mannlib.vitro.webapp.servlet.ProcessTerminologyController</servlet-class>
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</servlet>
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<servlet-mapping>
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<servlet-name>ProcessTerminologyAnnotation</servlet-name>
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<url-pattern>/edit/processTerminologyAnnotation</url-pattern>
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</servlet-mapping>
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<!-- Google Refine servlets begins -->
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<!-- Google Refine servlets begins -->
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<servlet>
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<servlet>
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43
productMods/config/listViewConfig-terminologyAnnotation.xml
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43
productMods/config/listViewConfig-terminologyAnnotation.xml
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<?xml version="1.0" encoding="ISO-8859-1"?>
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<!-- $This file is distributed under the terms of the license in /doc/license.txt$ -->
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<!-- See guidelines in vitro/doc/list_view_configuration_guidelines.txt -->
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<list-view-config>
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<query-select>
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PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
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PREFIX core: <http://vivoweb.org/ontology/core#>
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PREFIX afn: <http://jena.hpl.hp.com/ARQ/function#>
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SELECT ?terminologyContextNode ?referencedTerm ?entryTerm ?termLabel WHERE {
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?subject ?property ?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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} ORDER BY ?termLabel
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</query-select>
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<query-construct>
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PREFIX core: <http://vivoweb.org/ontology/core#>
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PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
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CONSTRUCT {
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?subject ?property ?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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} WHERE {
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?subject ?property ?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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}
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</query-construct>
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<template>propStatement-terminologyAnnotation.ftl</template>
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</list-view-config>
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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
Normal file
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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" %>
|
||||||
|
<%@ page import="org.json.JSONObject" %>
|
||||||
|
<%@ page import="org.apache.commons.logging.Log" %>
|
||||||
|
<%@ page import="org.apache.commons.logging.LogFactory" %>
|
||||||
|
|
||||||
|
<%@ taglib prefix="c" uri="http://java.sun.com/jstl/core"%>
|
||||||
|
<%@ taglib prefix="v" uri="http://vitro.mannlib.cornell.edu/vitro/tags" %>
|
||||||
|
|
||||||
|
<%!
|
||||||
|
public static Log log = LogFactory.getLog("edu.cornell.mannlib.vitro.webapp.jsp.edit.forms.terminologyAnnotation.jsp");
|
||||||
|
%>
|
||||||
|
<%
|
||||||
|
VitroRequest vreq = new VitroRequest(request);
|
||||||
|
WebappDaoFactory wdf = vreq.getWebappDaoFactory();
|
||||||
|
vreq.setAttribute("defaultNamespace", ""); //empty string triggers default new URI behavior
|
||||||
|
|
||||||
|
vreq.setAttribute("stringDatatypeUriJson", MiscWebUtils.escape(XSD.xstring.toString()));
|
||||||
|
|
||||||
|
%>
|
||||||
|
|
||||||
|
<c:set var="vivoCore" value="http://vivoweb.org/ontology/core#" />
|
||||||
|
<c:set var="rdfs" value="<%= VitroVocabulary.RDFS %>" />
|
||||||
|
<c:set var="label" value="${rdfs}label" />
|
||||||
|
<c:set var="foaf" value="http://xmlns.com/foaf/0.1/" />
|
||||||
|
<c:set var="personClassUri" value="${foaf}Person" />
|
||||||
|
|
||||||
|
<%-- Unlike other custom forms, this form does not allow edits of existing authors, so there are no
|
||||||
|
SPARQL queries for existing values. --%>
|
||||||
|
|
||||||
|
|
||||||
|
<v:jsonset var="n3ForTerminology">
|
||||||
|
@prefix core: <${vivoCore}> .
|
||||||
|
?subject ?predicate ?terminologyContextNode .
|
||||||
|
?terminologyContextNode core:referencedTerm ?referencedTerm .
|
||||||
|
?terminologyContextNode core:entryTerm ?entryTerm .
|
||||||
|
?terminologyContextNode core:termLabel ?termLabel .
|
||||||
|
</v:jsonset>
|
||||||
|
|
||||||
|
<c:set var="returnPathAfterSubmit" value="/edit/editRequestDispatch.jsp?subjectUri=${subjectUri}&predicateUri=${predicateUri}" />
|
||||||
|
<c:set var="submitSearchUrl" value="/UMLSTermsRetrieval"/>
|
||||||
|
<c:url var="UMLSCUIURL" value="http://link.informatics.stonybrook.edu/umls/CUI/" />
|
||||||
|
<c:set var="editjson" scope="request">
|
||||||
|
{
|
||||||
|
"formUrl" : "${formUrl}",
|
||||||
|
"editKey" : "${editKey}",
|
||||||
|
"urlPatternToReturnTo" : "${returnPathAfterSubmit}",
|
||||||
|
|
||||||
|
"subject" : ["subject", "${subjectUriJson}" ],
|
||||||
|
"predicate" : ["predicate", "${predicateUriJson}" ],
|
||||||
|
"object" : ["terminologyContextNode", "${objectUriJson}", "URI" ],
|
||||||
|
|
||||||
|
"n3required" : [ "${n3ForTerminology}" ],
|
||||||
|
|
||||||
|
"n3optional" : [ ],
|
||||||
|
|
||||||
|
"newResources" : { "terminologyContextNode" : "${defaultNamespace}" },
|
||||||
|
|
||||||
|
"urisInScope" : { },
|
||||||
|
"literalsInScope": { },
|
||||||
|
"urisOnForm" : [ "referencedTerm" ],
|
||||||
|
"literalsOnForm" : [ "entryTerm", "termLabel" ],
|
||||||
|
"filesOnForm" : [ ],
|
||||||
|
"sparqlForLiterals" : { },
|
||||||
|
"sparqlForUris" : { },
|
||||||
|
"sparqlForExistingLiterals" : { },
|
||||||
|
"sparqlForExistingUris" : { },
|
||||||
|
"fields" : {
|
||||||
|
"referencedTerm" : {
|
||||||
|
"newResource" : "false",
|
||||||
|
"validators" : [ "nonempty" ],
|
||||||
|
"optionsType" : "UNDEFINED", //UNSURE WHAT TO KEEP HERE
|
||||||
|
"literalOptions" : [ ],
|
||||||
|
"predicateUri" : "",
|
||||||
|
"objectClassUri" : "",
|
||||||
|
"rangeDatatypeUri" : "",
|
||||||
|
"rangeLang" : "",
|
||||||
|
"assertions" : [ "${n3ForTerminology}" ]
|
||||||
|
},
|
||||||
|
"entryTerm" : {
|
||||||
|
"newResource" : "false",
|
||||||
|
"validators" : [ "nonempty" ],
|
||||||
|
"optionsType" : "UNDEFINED",
|
||||||
|
"literalOptions" : [ ],
|
||||||
|
"predicateUri" : "",
|
||||||
|
"objectClassUri" : "",
|
||||||
|
"rangeDatatypeUri" : "",
|
||||||
|
"rangeLang" : "",
|
||||||
|
"assertions" : [ "${n3ForTerminology}" ]
|
||||||
|
},
|
||||||
|
"termLabel" : {
|
||||||
|
"newResource" : "false",
|
||||||
|
"validators" : [ "nonempty" ],
|
||||||
|
"optionsType" : "UNDEFINED",
|
||||||
|
"literalOptions" : [ ],
|
||||||
|
"predicateUri" : "",
|
||||||
|
"objectClassUri" : "",
|
||||||
|
"rangeDatatypeUri" : "",
|
||||||
|
"rangeLang" : "",
|
||||||
|
"assertions" : [ "${n3ForTerminology}" ]
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
</c:set>
|
||||||
|
|
||||||
|
<%
|
||||||
|
log.debug(request.getAttribute("editjson"));
|
||||||
|
|
||||||
|
EditConfiguration editConfig = EditConfiguration.getConfigFromSession(session,request);
|
||||||
|
if (editConfig == null) {
|
||||||
|
editConfig = new EditConfiguration((String) request.getAttribute("editjson"));
|
||||||
|
EditConfiguration.putConfigInSession(editConfig,session);
|
||||||
|
}
|
||||||
|
|
||||||
|
//Specific validators can be included here
|
||||||
|
|
||||||
|
Model model = (Model) application.getAttribute("jenaOntModel");
|
||||||
|
String objectUri = (String) request.getAttribute("objectUri");
|
||||||
|
|
||||||
|
//for some reason we are comming from the add new and that is working
|
||||||
|
//but we also come from the edit, and that is not working.
|
||||||
|
editConfig.setObject(""); //this will force the edit config to always be an add, never an update
|
||||||
|
|
||||||
|
editConfig.prepareForNonUpdate(model); // we're only adding new, not editing existing
|
||||||
|
|
||||||
|
String subjectUri = vreq.getParameter("subjectUri");
|
||||||
|
String predicateUri = vreq.getParameter("predicateUri");
|
||||||
|
|
||||||
|
String vivoCore = "http://vivoweb.org/ontology/core#";
|
||||||
|
|
||||||
|
//Individual infoResource = vreq.getWebappDaoFactory().getIndividualDao().getIndividualByURI(subjectUri);
|
||||||
|
Individual subject = ((Individual) request.getAttribute("subject"));
|
||||||
|
vreq.setAttribute("subjectName", subject.getName());
|
||||||
|
//Get existing terminology annotations
|
||||||
|
List<Individual> terminologyAnnotationNodes = subject.getRelatedIndividuals(predicateUri);
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
List<String> customJs = new ArrayList<String>(Arrays.asList(JavaScript.JQUERY_UI.path(),
|
||||||
|
JavaScript.CUSTOM_FORM_UTILS.path(),
|
||||||
|
"/js/browserUtils.js",
|
||||||
|
"/edit/forms/js/addTerminology.js"
|
||||||
|
));
|
||||||
|
request.setAttribute("customJs", customJs);
|
||||||
|
|
||||||
|
//no custom css we know of yet
|
||||||
|
|
||||||
|
List<String> customCss = new ArrayList<String>(Arrays.asList(Css.JQUERY_UI.path(),
|
||||||
|
Css.CUSTOM_FORM.path(),
|
||||||
|
"/edit/forms/css/addTerminology.css"
|
||||||
|
));
|
||||||
|
request.setAttribute("customCss", customCss);
|
||||||
|
|
||||||
|
|
||||||
|
%>
|
||||||
|
|
||||||
|
<c:set var="title" value="<em>${subjectName}</em>"/>
|
||||||
|
|
||||||
|
<jsp:include page="${preForm}" />
|
||||||
|
|
||||||
|
<%-- DO NOT CHANGE IDS, CLASSES, OR HTML STRUCTURE ON THIS PAGE WITHOUT UNDERSTANDING THE IMPACT ON THE JAVASCRIPT! --%>
|
||||||
|
<h2>${title}</h2>
|
||||||
|
|
||||||
|
<%@ include file="unsupportedBrowserMessage.jsp" %>
|
||||||
|
|
||||||
|
<div class="noIE67">
|
||||||
|
<h3>Manage Terminology Annotations</h3>
|
||||||
|
|
||||||
|
<ul id="existingTerms" >
|
||||||
|
<%
|
||||||
|
|
||||||
|
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}"/>
|
||||||
|
|
||||||
|
|
@ -0,0 +1,18 @@
|
||||||
|
<#-- $This file is distributed under the terms of the license in /doc/license.txt$ -->
|
||||||
|
|
||||||
|
<#-- Custom object property statement view for http://vivoweb.org/ontology/core#authorInAuthorship.
|
||||||
|
|
||||||
|
This template must be self-contained and not rely on other variables set for the individual page, because it
|
||||||
|
is also used to generate the property statement during a deletion.
|
||||||
|
-->
|
||||||
|
|
||||||
|
<#import "lib-sequence.ftl" as s>
|
||||||
|
<#import "lib-datetime.ftl" as dt>
|
||||||
|
|
||||||
|
<@showTerm statement />
|
||||||
|
|
||||||
|
<#-- Use a macro to keep variable assignments local; otherwise the values carry over to the
|
||||||
|
next statement -->
|
||||||
|
<#macro showTerm statement>
|
||||||
|
<a href="${statement.referencedTerm}">${statement.termLabel}</a>
|
||||||
|
</#macro>
|
||||||
|
|
@ -0,0 +1,291 @@
|
||||||
|
/* $This file is distributed under the terms of the license in /doc/license.txt$ */
|
||||||
|
|
||||||
|
package edu.cornell.mannlib.vitro.webapp.servlet;
|
||||||
|
|
||||||
|
import java.io.BufferedReader;
|
||||||
|
import java.io.IOException;
|
||||||
|
import java.io.InputStreamReader;
|
||||||
|
import java.net.URL;
|
||||||
|
import java.net.URLEncoder;
|
||||||
|
import java.util.HashMap;
|
||||||
|
import java.util.Map;
|
||||||
|
import java.util.List;
|
||||||
|
import java.util.ArrayList;
|
||||||
|
import javax.servlet.ServletOutputStream;
|
||||||
|
import javax.servlet.ServletException;
|
||||||
|
import javax.servlet.http.HttpServletRequest;
|
||||||
|
import javax.servlet.http.HttpServletResponse;
|
||||||
|
import edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.EditConfiguration;
|
||||||
|
import org.apache.commons.logging.Log;
|
||||||
|
import org.apache.commons.logging.LogFactory;
|
||||||
|
import edu.cornell.mannlib.vitro.webapp.controller.VitroHttpServlet;
|
||||||
|
import edu.cornell.mannlib.vitro.webapp.beans.Individual;
|
||||||
|
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
|
||||||
|
import freemarker.ext.beans.BeansWrapper;
|
||||||
|
import freemarker.template.DefaultObjectWrapper;
|
||||||
|
import edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.Field;
|
||||||
|
import javax.servlet.RequestDispatcher;
|
||||||
|
public class ProcessTerminologyController extends VitroHttpServlet {
|
||||||
|
|
||||||
|
private static final long serialVersionUID = 1L;
|
||||||
|
private static final Log log = LogFactory.getLog(ProcessTerminologyController.class);
|
||||||
|
private static final String submissionUrl = "/edit/processRdfForm2.jsp";
|
||||||
|
|
||||||
|
@Override
|
||||||
|
protected void doPost(HttpServletRequest req, HttpServletResponse resp) throws ServletException, IOException {
|
||||||
|
super.doPost(req, resp);
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
protected void doGet(HttpServletRequest req, HttpServletResponse resp) throws ServletException, IOException {
|
||||||
|
super.doGet(req, resp);
|
||||||
|
VitroRequest vreq = new VitroRequest(req);
|
||||||
|
|
||||||
|
try{
|
||||||
|
|
||||||
|
|
||||||
|
EditConfiguration editConfig = EditConfiguration.getConfigFromSession(req.getSession(), req);
|
||||||
|
//For query parameters, check whether CUI
|
||||||
|
String[] termsArray = new String[1];
|
||||||
|
String referencedTerms = vreq.getParameter("referencedTerm");
|
||||||
|
if(referencedTerms.indexOf(",") != -1) {
|
||||||
|
termsArray = referencedTerms.split(",");
|
||||||
|
}
|
||||||
|
|
||||||
|
int numberTerms = termsArray.length;
|
||||||
|
//if multiple values then need to process this differently by adding additional
|
||||||
|
//fields, assertions, etc. as well as changing the URL slightly
|
||||||
|
String url = "/edit/processRdfForm2.jsp?" + vreq.getQueryString();
|
||||||
|
if(numberTerms > 1) {
|
||||||
|
//Add new resources, i.e. the additional terminology context nodes
|
||||||
|
addNewResources(editConfig, vreq, numberTerms);
|
||||||
|
//Add N3Required
|
||||||
|
addN3Required(editConfig,vreq, numberTerms);
|
||||||
|
//Add URIs on Form and Add Literals On Form
|
||||||
|
addLiteralsAndUrisOnForm(editConfig, vreq, numberTerms);
|
||||||
|
//Add fields
|
||||||
|
addFields(editConfig, vreq, numberTerms);
|
||||||
|
//Generate new url which will map input fields to value
|
||||||
|
url = generateUrl(editConfig, vreq);
|
||||||
|
}
|
||||||
|
|
||||||
|
RequestDispatcher dispatcher = req.getRequestDispatcher(url);
|
||||||
|
dispatcher.forward(req, resp);
|
||||||
|
|
||||||
|
|
||||||
|
} catch(Exception ex) {
|
||||||
|
log.error("error occurred in servlet", ex);
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
private String generateUrl(EditConfiguration editConfig, VitroRequest vreq) {
|
||||||
|
|
||||||
|
//Get original url and query string
|
||||||
|
String newUrl = "/edit/processRdfForm2.jsp?" + vreq.getQueryString();
|
||||||
|
//Iterate through the terms and include appropriate values
|
||||||
|
Map <String,String[]> queryParameters = null;
|
||||||
|
queryParameters = vreq.getParameterMap();
|
||||||
|
//Use same query parameters to forward
|
||||||
|
String termParam = vreq.getParameter("referencedTerm");
|
||||||
|
String labelParam = vreq.getParameter("termLabel");
|
||||||
|
String typeParam = vreq.getParameter("termType");
|
||||||
|
if(!labelParam.contains(",")){
|
||||||
|
log.error("Multiple labels are not being sent back, this is an error");
|
||||||
|
}
|
||||||
|
if(!typeParam.contains(",")) {
|
||||||
|
log.error("Multiple types are not being sent back, this is an error");
|
||||||
|
}
|
||||||
|
|
||||||
|
String[] termsArray = termParam.split(",");
|
||||||
|
String[] termLabels = labelParam.split(",");
|
||||||
|
String[] termTypes = typeParam.split(",");
|
||||||
|
String entryTerm = vreq.getParameter("entryTerm");
|
||||||
|
int numberParameters = termsArray.length;
|
||||||
|
int index;
|
||||||
|
String referencedBase = "referencedTerm";
|
||||||
|
String labelBase = "termLabel";
|
||||||
|
String termBase = "termType";
|
||||||
|
//Should already include entry term so no need to include here
|
||||||
|
//newUrl += "&entryTerm=" + URLEncoder.encode(entryTerm);
|
||||||
|
//Add entry
|
||||||
|
for(index = 1; index <= numberParameters; index++) {
|
||||||
|
String referencedInputName = referencedBase + index;
|
||||||
|
String termLabelInputName = labelBase + index;
|
||||||
|
String termTypeInputName =termBase + index;
|
||||||
|
//array is set to start at 0, not 1
|
||||||
|
String referencedTerm = termsArray[index - 1];
|
||||||
|
String termLabel = termLabels[index - 1];
|
||||||
|
String termType = termTypes[index - 1];
|
||||||
|
newUrl += "&" + referencedInputName + "=" + URLEncoder.encode(referencedTerm);
|
||||||
|
newUrl += "&" + termLabelInputName + "=" + URLEncoder.encode(termLabel);
|
||||||
|
newUrl += "&" + termTypeInputName + "=" + URLEncoder.encode(termType);
|
||||||
|
}
|
||||||
|
return newUrl;
|
||||||
|
}
|
||||||
|
|
||||||
|
private void addNewResources(EditConfiguration editConfig, VitroRequest vreq, int numberTerms) {
|
||||||
|
Map<String, String> newResources = new HashMap<String, String>();
|
||||||
|
//Based on number of terms, add new
|
||||||
|
int n;
|
||||||
|
String defaultNamespace = "";
|
||||||
|
|
||||||
|
String base = "terminologyContextNode";
|
||||||
|
for(n = 1; n <= numberTerms; n++) {
|
||||||
|
String newNode = base + n;
|
||||||
|
newResources.put(newNode, defaultNamespace);
|
||||||
|
}
|
||||||
|
//TODO: Check if below is required as this is a reference
|
||||||
|
editConfig.setNewResources(newResources);
|
||||||
|
}
|
||||||
|
|
||||||
|
/*
|
||||||
|
* "referencedTerm" : {
|
||||||
|
"newResource" : "false",
|
||||||
|
"validators" : [ "nonempty" ],
|
||||||
|
"optionsType" : "UNDEFINED", //UNSURE WHAT TO KEEP HERE
|
||||||
|
"literalOptions" : [ ],
|
||||||
|
"predicateUri" : "",
|
||||||
|
"objectClassUri" : "",
|
||||||
|
"rangeDatatypeUri" : "",
|
||||||
|
"rangeLang" : "",
|
||||||
|
"assertions" : [ "${n3ForTerminology}" ]
|
||||||
|
},
|
||||||
|
"entryTerm" : {
|
||||||
|
"newResource" : "false",
|
||||||
|
"validators" : [ "nonempty" ],
|
||||||
|
"optionsType" : "UNDEFINED",
|
||||||
|
"literalOptions" : [ ],
|
||||||
|
"predicateUri" : "",
|
||||||
|
"objectClassUri" : "",
|
||||||
|
"rangeDatatypeUri" : "",
|
||||||
|
"rangeLang" : "",
|
||||||
|
"assertions" : [ "${n3ForTerminology}" ]
|
||||||
|
},
|
||||||
|
"termLabel" : {
|
||||||
|
"newResource" : "false",
|
||||||
|
"validators" : [ "nonempty" ],
|
||||||
|
"optionsType" : "UNDEFINED",
|
||||||
|
"literalOptions" : [ ],
|
||||||
|
"predicateUri" : "",
|
||||||
|
"objectClassUri" : "",
|
||||||
|
"rangeDatatypeUri" : "",
|
||||||
|
"rangeLang" : "",
|
||||||
|
"assertions" : [ "${n3ForTerminology}" ]
|
||||||
|
}
|
||||||
|
*/
|
||||||
|
|
||||||
|
private void addFields(EditConfiguration editConfig, VitroRequest vreq, int numberTerms) {
|
||||||
|
Map<String, Field> fieldMap = new HashMap<String, Field>();
|
||||||
|
int index;
|
||||||
|
String referencedBase = "referencedTerm";
|
||||||
|
String entryBase = "entryTerm";
|
||||||
|
String labelBase = "termLabel";
|
||||||
|
|
||||||
|
//Entry only needs to be added once
|
||||||
|
fieldMap.put(entryBase, generateField(editConfig));
|
||||||
|
|
||||||
|
//First one already included so add new ones here
|
||||||
|
for(index = 1; index <= numberTerms; index++) {
|
||||||
|
int suffix = index;
|
||||||
|
String referencedTerm = referencedBase + suffix;
|
||||||
|
String label = labelBase + suffix;
|
||||||
|
//need to add termType
|
||||||
|
//Generate Field for each
|
||||||
|
fieldMap.put(referencedTerm, generateField(editConfig));
|
||||||
|
fieldMap.put(label, generateField(editConfig));
|
||||||
|
//termType would also go in here
|
||||||
|
}
|
||||||
|
editConfig.setFields(fieldMap);
|
||||||
|
}
|
||||||
|
|
||||||
|
/*
|
||||||
|
"newResource" : "false",
|
||||||
|
"validators" : [ "nonempty" ],
|
||||||
|
"optionsType" : "UNDEFINED",
|
||||||
|
"literalOptions" : [ ],
|
||||||
|
"predicateUri" : "",
|
||||||
|
"objectClassUri" : "",
|
||||||
|
"rangeDatatypeUri" : "",
|
||||||
|
"rangeLang" : "",
|
||||||
|
"assertions" : [ "${n3ForTerminology}" ]*/
|
||||||
|
private Field generateField(EditConfiguration editConfig) {
|
||||||
|
List<String> n3Required = editConfig.getN3Required();
|
||||||
|
Field field = new Field();
|
||||||
|
field.setNewResource(false);
|
||||||
|
List<String> validators = new ArrayList<String>();
|
||||||
|
validators.add("nonempty");
|
||||||
|
field.setValidators(validators);
|
||||||
|
field.setOptionsType("UNDEFINED");
|
||||||
|
field.setLiteralOptions(new ArrayList<List<String>>());
|
||||||
|
field.setPredicateUri("");
|
||||||
|
field.setObjectClassUri("");
|
||||||
|
field.setRangeDatatypeUri("");
|
||||||
|
field.setRangeLang("");
|
||||||
|
field.setAssertions(n3Required);
|
||||||
|
return field;
|
||||||
|
}
|
||||||
|
|
||||||
|
//Original uris and literals included:
|
||||||
|
/*
|
||||||
|
* "urisOnForm" : [ "referencedTerm" ],
|
||||||
|
"literalsOnForm" : [ "entryTerm", "termLabel" ],
|
||||||
|
*/
|
||||||
|
private void addLiteralsAndUrisOnForm(EditConfiguration editConfig,
|
||||||
|
VitroRequest vreq, int numberTerms) {
|
||||||
|
List<String> urisOnForm = new ArrayList<String>();
|
||||||
|
List<String> literalsOnForm = new ArrayList<String>();
|
||||||
|
|
||||||
|
int index;
|
||||||
|
String referencedBase = "referencedTerm";
|
||||||
|
String entryBase = "entryTerm";
|
||||||
|
String labelBase = "termLabel";
|
||||||
|
//entry term needs to be added only once
|
||||||
|
literalsOnForm.add(entryBase);
|
||||||
|
|
||||||
|
//First one already included so add new ones here
|
||||||
|
for(index = 1; index <= numberTerms; index++) {
|
||||||
|
int suffix = index;
|
||||||
|
String referencedTerm = referencedBase + suffix;
|
||||||
|
String label = labelBase + suffix;
|
||||||
|
urisOnForm.add(referencedTerm);
|
||||||
|
literalsOnForm.add(label);
|
||||||
|
}
|
||||||
|
editConfig.setUrisOnform(urisOnForm);
|
||||||
|
editConfig.setLiteralsOnForm(literalsOnForm);
|
||||||
|
}
|
||||||
|
|
||||||
|
//original n3 required is of this format
|
||||||
|
/*@prefix core: <${vivoCore}> .
|
||||||
|
?subject ?predicate ?terminologyContextNode .
|
||||||
|
?terminologyContextNode core:referencedTerm ?referencedTerm .
|
||||||
|
?terminologyContextNode core:entryTerm ?entryTerm .
|
||||||
|
?terminologyContextNode core:termLabel ?termLabel .
|
||||||
|
*/
|
||||||
|
private void addN3Required(EditConfiguration editConfig, VitroRequest vreq, int numberTerms) {
|
||||||
|
//List<String> n3Required = editConfig.getN3Required();
|
||||||
|
List<String> n3Required = new ArrayList<String>();
|
||||||
|
int index;
|
||||||
|
String nodeBase = "?terminologyContextNode";
|
||||||
|
String referencedBase = "?referencedTerm";
|
||||||
|
//there's only one entry term in this case
|
||||||
|
String entryBase = "?entryTerm";
|
||||||
|
String labelBase = "?termLabel";
|
||||||
|
String prefixStr = "@prefix core: <http://vivoweb.org/ontology/core#> .";
|
||||||
|
//First one already included so add new ones here
|
||||||
|
for(index = 1; index <= numberTerms; index++) {
|
||||||
|
int suffix = index;
|
||||||
|
String node = nodeBase + suffix;
|
||||||
|
String referencedTerm = referencedBase + suffix;
|
||||||
|
String label = labelBase + suffix;
|
||||||
|
String n3String = prefixStr;
|
||||||
|
n3String += "?subject ?predicate " + node + " . " +
|
||||||
|
node + " core:entryTerm " + entryBase + " . " +
|
||||||
|
node + " core:termLabel " + label + " . " +
|
||||||
|
node + " core:referencedTerm " + referencedTerm + " . ";
|
||||||
|
n3Required.add(n3String);
|
||||||
|
}
|
||||||
|
editConfig.setN3Required(n3Required);
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
@ -0,0 +1,76 @@
|
||||||
|
/* $This file is distributed under the terms of the license in /doc/license.txt$ */
|
||||||
|
|
||||||
|
package edu.cornell.mannlib.vitro.webapp.servlet;
|
||||||
|
|
||||||
|
import java.io.BufferedReader;
|
||||||
|
import java.io.IOException;
|
||||||
|
import java.io.InputStreamReader;
|
||||||
|
import java.net.URL;
|
||||||
|
import java.net.URLEncoder;
|
||||||
|
import java.util.HashMap;
|
||||||
|
import java.util.Map;
|
||||||
|
import javax.servlet.ServletOutputStream;
|
||||||
|
import javax.servlet.ServletException;
|
||||||
|
import javax.servlet.http.HttpServletRequest;
|
||||||
|
import javax.servlet.http.HttpServletResponse;
|
||||||
|
|
||||||
|
import org.apache.commons.logging.Log;
|
||||||
|
import org.apache.commons.logging.LogFactory;
|
||||||
|
import edu.cornell.mannlib.vitro.webapp.controller.VitroHttpServlet;
|
||||||
|
import edu.cornell.mannlib.vitro.webapp.beans.Individual;
|
||||||
|
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
|
||||||
|
import edu.cornell.mannlib.vitro.webapp.controller.freemarker.FreemarkerHttpServlet;
|
||||||
|
import edu.cornell.mannlib.vitro.webapp.controller.freemarker.IndividualController;
|
||||||
|
import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.ExceptionResponseValues;
|
||||||
|
import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.ResponseValues;
|
||||||
|
import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.TemplateResponseValues;
|
||||||
|
import edu.cornell.mannlib.vitro.webapp.web.templatemodels.individual.IndividualTemplateModel;
|
||||||
|
import freemarker.ext.beans.BeansWrapper;
|
||||||
|
import freemarker.template.DefaultObjectWrapper;
|
||||||
|
|
||||||
|
public class UMLSTerminologyAnnotation extends VitroHttpServlet {
|
||||||
|
|
||||||
|
private static final long serialVersionUID = 1L;
|
||||||
|
private static final Log log = LogFactory.getLog(UMLSTerminologyAnnotation.class);
|
||||||
|
private static final String submissionUrl = "http://link.informatics.stonybrook.edu/MeaningLookup/MlServiceServlet?";
|
||||||
|
|
||||||
|
@Override
|
||||||
|
protected void doPost(HttpServletRequest req, HttpServletResponse resp) throws ServletException, IOException {
|
||||||
|
super.doPost(req, resp);
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
protected void doGet(HttpServletRequest req, HttpServletResponse resp) throws ServletException, IOException {
|
||||||
|
super.doGet(req, resp);
|
||||||
|
VitroRequest vreq = new VitroRequest(req);
|
||||||
|
|
||||||
|
try{
|
||||||
|
//Get parameter
|
||||||
|
String entryText = vreq.getParameter("searchTerm");
|
||||||
|
System.out.println("Entry text is " + entryText);
|
||||||
|
//TODO: Find a non-deprecated mechanism to do so
|
||||||
|
String dataUrl = submissionUrl + "textToProcess=" + URLEncoder.encode(entryText) + "&format=json";
|
||||||
|
try{
|
||||||
|
ServletOutputStream sos = resp.getOutputStream();
|
||||||
|
|
||||||
|
resp.setCharacterEncoding("UTF-8");
|
||||||
|
resp.setContentType("application/json;charset=UTF-8");
|
||||||
|
URL rss = new URL(dataUrl);
|
||||||
|
|
||||||
|
BufferedReader in = new BufferedReader(new InputStreamReader(rss.openStream()));
|
||||||
|
String inputLine;
|
||||||
|
while((inputLine = in.readLine()) != null) {
|
||||||
|
sos.println(inputLine);
|
||||||
|
}
|
||||||
|
in.close();
|
||||||
|
|
||||||
|
} catch(Exception ex) {
|
||||||
|
log.error("error occurred in servlet", ex);
|
||||||
|
}
|
||||||
|
|
||||||
|
}catch(Exception ex){
|
||||||
|
log.warn(ex,ex);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
Loading…
Add table
Add a link
Reference in a new issue