Revision 5632
Added by ben leinfelder about 14 years ago
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<%@ page language="java"%> |
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<%@page import="java.util.List"%> |
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<%@page import="java.util.ArrayList"%> |
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<%@page import="org.ecoinformatics.sms.SMS"%> |
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<%@page import="org.ecoinformatics.sms.ontology.OntologyClass"%> |
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<% |
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/** |
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* |
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*/ |
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%> |
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<% |
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//harvest parameters |
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String[] entityParam = request.getParameterValues("entity");
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String[] characteristicParam = request.getParameterValues("characteristic");
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String[] standardParam = request.getParameterValues("standard");
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String[] protocolParam = request.getParameterValues("protocol");
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String[] measurementParam = request.getParameterValues("measurement");
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List<OntologyClass> activeEntities = new ArrayList<OntologyClass>(); |
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List<OntologyClass> activeCharacteristics = new ArrayList<OntologyClass>(); |
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List<OntologyClass> activeStandards = new ArrayList<OntologyClass>(); |
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List<OntologyClass> activeProtocols = new ArrayList<OntologyClass>(); |
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List<OntologyClass> activeMeasurements = new ArrayList<OntologyClass>(); |
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// Entity |
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if (entityParam != null) {
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for (String entityString: entityParam) {
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OntologyClass e = new OntologyClass(entityString); |
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activeEntities.add(e); |
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} |
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} |
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// Characteristic |
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if (characteristicParam != null) {
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for (String classString: characteristicParam) {
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OntologyClass c = new OntologyClass(classString); |
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activeCharacteristics.add(c); |
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} |
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} |
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// Standard |
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if (standardParam != null) {
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for (String classString: standardParam) {
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OntologyClass c = new OntologyClass(classString); |
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activeStandards.add(c); |
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} |
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} |
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// Protocol |
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if (protocolParam != null) {
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for (String classString: protocolParam) {
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OntologyClass c = new OntologyClass(classString); |
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activeProtocols.add(c); |
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} |
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} |
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// Measurement |
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// TODO: implement measurement expansion |
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// construct the selection fields for existing annotations |
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// Entity |
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StringBuffer entityOptions = new StringBuffer(); |
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List<OntologyClass> entities = SMS.getInstance().getAnnotationManager().getActiveEntities(); |
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List<OntologyClass> entities = SMS.getInstance().getAnnotationManager().getActiveEntities(activeCharacteristics, activeStandards);
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for (OntologyClass oc: entities) {
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entityOptions.append("<option ");
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entityOptions.append("title='");
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} |
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// Characteristic |
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StringBuffer characteristicOptions = new StringBuffer(); |
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List<OntologyClass> characteristics = SMS.getInstance().getAnnotationManager().getActiveCharacteristics(); |
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List<OntologyClass> characteristics = SMS.getInstance().getAnnotationManager().getActiveCharacteristics(activeEntities, activeStandards);
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for (OntologyClass oc: characteristics) {
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characteristicOptions.append("<option ");
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characteristicOptions.append("title='");
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} |
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// Standard |
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StringBuffer standardOptions = new StringBuffer(); |
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List<OntologyClass> standards = SMS.getInstance().getAnnotationManager().getActiveStandards(); |
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List<OntologyClass> standards = SMS.getInstance().getAnnotationManager().getActiveStandards(activeEntities, activeCharacteristics);
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for (OntologyClass oc: standards) {
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standardOptions.append("<option ");
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standardOptions.append("title='");
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standardOptions.append(oc.getName()); |
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standardOptions.append("</option>");
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} |
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// Protocol |
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// Protocol TODO: filtering
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StringBuffer protocolOptions = new StringBuffer(); |
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List<OntologyClass> protocols = SMS.getInstance().getAnnotationManager().getActiveProtocols(); |
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for (OntologyClass oc: protocols) {
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protocolOptions.append(oc.getName()); |
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protocolOptions.append("</option>");
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} |
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// Measurement |
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// Measurement TODO: filtering
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StringBuffer measurementOptions = new StringBuffer(); |
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List<OntologyClass> measurements = SMS.getInstance().getAnnotationManager().getActiveMeasurements(); |
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for (OntologyClass oc: measurements) {
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<table class="group group_border"> |
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<tr> |
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<th colspan="5">
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<th colspan="3">
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<p> |
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Locate <b>data packages</b> that have been semantically annotated within the observation model by |
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selecting concepts from |
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</p> |
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</th> |
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</tr> |
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<!-- measurement --> |
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<tr> |
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<td colspan="3"> |
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<table class="subGroup subGroup_border onehundred_percent"> |
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<tr> |
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<th colspan="2"> |
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Measurement |
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</th> |
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</tr> |
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<tr> |
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<td>a template that defines Entity, Characteristic, Standard, and/or Protocol</td> |
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</tr> |
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<tr> |
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<td> |
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<select name="dynamicValue" id="dynamicValue" multiple="multiple" size="5" style="width: 100%"> |
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<%=measurementOptions %> |
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</select> |
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<input type="hidden" name="dynamicClass" id="dynamicClass" value="http://ecoinformatics.org/oboe/oboe.1.0/oboe-core.owl#Measurement"/> |
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</td> |
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</tr> |
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<tr> |
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<td colspan="1"> |
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<input type="text" name="dynamicValue" id="dynamicValue" class="bp_form_complete-all-uri" size="60" /> |
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<input type="hidden" name="dynamicClass" id="dynamicClass" value="http://ecoinformatics.org/oboe/oboe.1.0/oboe-core.owl#Measurement"/> |
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</td> |
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</tr> |
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</table> |
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</td> |
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</tr> |
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<tr> |
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<td> |
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<table class="subGroup subGroup_border"> |
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<tr> |
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</th> |
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</tr> |
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<tr> |
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<td>where measurements of</td>
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<td>with measurements of</td>
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</tr> |
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<tr> |
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<td> |
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</tr> |
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</table> |
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</td> |
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<!-- removing Standard |
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<td> |
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<table class="subGroup subGroup_border"> |
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<tr> |
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</tr> |
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</table> |
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</td> |
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--> |
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<td> |
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<table class="subGroup subGroup_border"> |
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<tr> |
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</th> |
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</tr> |
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<tr> |
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<td>following procedures outlined by</td>
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<td>using procedures outlined by</td>
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</tr> |
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<tr> |
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<td> |
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</tr> |
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</table> |
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</td> |
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<td> |
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<table class="subGroup subGroup_border"> |
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<tr> |
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<th colspan="2"> |
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Measurement |
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</th> |
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</tr> |
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<tr> |
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<td>typically defined as</td> |
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</tr> |
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<tr> |
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<td> |
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<select name="dynamicValue" id="dynamicValue" multiple="multiple" size="5" style="width: 216px"> |
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<%=measurementOptions %> |
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</select> |
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<input type="hidden" name="dynamicClass" id="dynamicClass" value="http://ecoinformatics.org/oboe/oboe.1.0/oboe-core.owl#Measurement"/> |
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</td> |
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</tr> |
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<tr> |
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<td colspan="1"> |
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<input type="text" name="dynamicValue" id="dynamicValue" class="bp_form_complete-all-uri" size="30" /> |
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<input type="hidden" name="dynamicClass" id="dynamicClass" value="http://ecoinformatics.org/oboe/oboe.1.0/oboe-core.owl#Measurement"/> |
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</td> |
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</tr> |
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</table> |
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</td> |
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</tr> |
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<tr> |
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<td colspan="5">Match All? <input type="checkbox" name="matchAll" checked="checked"/></td>
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<td colspan="3">Match All? <input type="checkbox" name="matchAll" checked="checked"/></td>
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</tr> |
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<tr> |
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<td colspan="5">From same Observation? <input type="checkbox" name="strict"/></td>
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<td colspan="3">From same Observation? <input type="checkbox" name="strict"/></td>
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</tr> |
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<tr> |
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<td colspan="5"><input type="submit" value="Search"/></td>
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<td colspan="3"><input type="submit" value="Search"/></td>
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</tr> |
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</table> |
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<!-- |
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--> |
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</form> |
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<!-- |
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<h2>Ontology search</h2> |
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<div id="bp_quick_jump"></div> |
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<script type="text/javascript"> |
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var BP_ontology_id = "all"; |
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</script> |
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<script src="<%=STYLE_SKINS_URL%>/semtools/bioportal/quick_jump.js" type="text/javascript" charset="utf-8"> |
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</script> |
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<h2>Tree browser</h2> |
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<object classid="clsid:D27CDB6E-AE6D-11cf-96B8-444553540000" |
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id="OntologyTree" width="300" height="100%" |
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codebase="http://fpdownload.macromedia.com/get/flashplayer/current/swflash.cab"> |
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<param name="movie" value="http://keg.cs.uvic.ca/ncbo/ontologytree/OntologyTree.swf" /> |
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<param name="quality" value="high" /> |
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<param name="bgcolor" value="#ffffff" /> |
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<param name="allowScriptAccess" value="always" /> |
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<param name="flashVars" value="ontology=1523&alerterrors=false&canchangeontology=false&virtual=true" /> |
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<embed src="http://keg.cs.uvic.ca/ncbo/ontologytree/OntologyTree.swf" quality="high" bgcolor="#ffffff" |
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width="300" height="100%" name="OntologyTree" align="middle" |
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play="true" |
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loop="false" |
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allowScriptAccess="always" |
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type="application/x-shockwave-flash" |
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flashVars="ontology=1523&alerterrors=false&canchangeontology=false&virtual=true" |
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pluginspage="http://www.adobe.com/go/getflashplayer"> |
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</embed> |
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</object> |
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--> |
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<!-- Included default search/login --> |
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<% if ( PropertyService.getProperty("spatial.runSpatialOption").equals("true") ) { %>
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<script language="javascript"> |
Also available in: Unified diff
starting to filter by active domains. still request-based, but would like to make asynchronous calls when populating the fields.