diff --git a/.gitignore b/.gitignore index ae5cbdb8..e656b107 100644 --- a/.gitignore +++ b/.gitignore @@ -6,3 +6,4 @@ /deploy.properties /build.properties /runtime.properties +/ontology/public/catalog-v0001.xml \ No newline at end of file diff --git a/ontology/public/catalog-v001.xml b/ontology/public/catalog-v001.xml deleted file mode 100644 index 1b92b5e2..00000000 --- a/ontology/public/catalog-v001.xml +++ /dev/null @@ -1,5 +0,0 @@ - - - - - diff --git a/productMods/WEB-INF/filegraph/tbox/ConceptSemanticType.owl b/productMods/WEB-INF/filegraph/tbox/ConceptSemanticType.owl new file mode 100644 index 00000000..04ab3d10 --- /dev/null +++ b/productMods/WEB-INF/filegraph/tbox/ConceptSemanticType.owl @@ -0,0 +1,47 @@ + + + 0.7 + + + + Semantic Type for given concept, for example UMLS's type returned for concepts + Semantic Type for given concept, for example UMLS's type returned for concepts. + + Concept Semantic Type + + + + + + + + diff --git a/src/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/AddAssociatedConceptGenerator.java b/src/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/AddAssociatedConceptGenerator.java index a06fe85a..23d2053c 100644 --- a/src/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/AddAssociatedConceptGenerator.java +++ b/src/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/AddAssociatedConceptGenerator.java @@ -16,6 +16,7 @@ import javax.servlet.http.HttpSession; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; +import com.hp.hpl.jena.ontology.OntModel; import com.hp.hpl.jena.rdf.model.Literal; import com.hp.hpl.jena.rdf.model.Model; import com.hp.hpl.jena.vocabulary.RDF; @@ -27,6 +28,7 @@ import edu.cornell.mannlib.vitro.webapp.beans.ObjectProperty; import edu.cornell.mannlib.vitro.webapp.beans.ObjectPropertyStatement; import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest; import edu.cornell.mannlib.vitro.webapp.controller.freemarker.UrlBuilder; +import edu.cornell.mannlib.vitro.webapp.dao.ModelAccess; import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory; import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.EditConfigurationUtils; import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.EditConfigurationVTwo; @@ -85,7 +87,7 @@ public class AddAssociatedConceptGenerator extends VivoBaseGenerator implements setTemplate(editConfiguration, vreq); // No validators required here // Add preprocessors - addPreprocessors(editConfiguration, vreq.getWebappDaoFactory()); + addPreprocessors(editConfiguration, ModelAccess.on(vreq).getJenaOntModel()); // Adding additional data, specifically edit mode addFormSpecificData(editConfiguration, vreq); // One override for basic functionality, changing url pattern @@ -174,8 +176,10 @@ public class AddAssociatedConceptGenerator extends VivoBaseGenerator implements private List generateN3Optional() { return list("?conceptNode <" + RDFS.label.getURI() + "> ?conceptLabel .\n" + "?conceptNode <" + RDFS.isDefinedBy.getURI() + "> ?conceptSource .", - "?conceptNode <" + VIVOCore + "conceptSemanticType> ?conceptSemanticTypeURI ." + - "?conceptSemanticTypeURI <" + RDFS.label.getURI() + "> ?conceptSemanticTypeLabel ." + "?conceptNode <" + VIVOCore + "hasConceptSemanticType> ?conceptSemanticTypeURI ." + + "?conceptSemanticTypeURI <" + VIVOCore + "isConceptSemanticTypeOf> ?conceptNode ." + + "?conceptSemanticTypeURI <" + RDFS.label.getURI() + "> ?conceptSemanticTypeLabel ." + + "?conceptSemanticTypeURI <" + RDF.type.getURI() + "> <" + VIVOCore + "ConceptSemanticType> ." ); } @@ -190,7 +194,7 @@ public class AddAssociatedConceptGenerator extends VivoBaseGenerator implements //There are no new resources here, the concept node uri doesn't //get created but already exists, and vocab uri should already exist as well //Adding concept semantic type uri just to test - note this isn't really on the form at all - //newResources.put("conceptSemanticTypeURI", null); + newResources.put("conceptSemanticTypeURI", null); return newResources; } @@ -239,11 +243,11 @@ public class AddAssociatedConceptGenerator extends VivoBaseGenerator implements //The URI of the node that defines the concept urisOnForm.add("conceptNode"); urisOnForm.add("conceptSource"); - // urisOnForm.add("conceptSemanticTypeURI"); + urisOnForm.add("conceptSemanticTypeURI"); editConfiguration.setUrisOnform(urisOnForm); //Also need to add the label of the concept literalsOnForm.add("conceptLabel"); - // literalsOnForm.add("conceptSemanticTypeLabel"); + literalsOnForm.add("conceptSemanticTypeLabel"); editConfiguration.setLiteralsOnForm(literalsOnForm); } @@ -272,8 +276,8 @@ public class AddAssociatedConceptGenerator extends VivoBaseGenerator implements setConceptNodeField(editConfiguration, vreq); setConceptLabelField(editConfiguration, vreq); setVocabURIField(editConfiguration, vreq); - //setConceptSemanticTypeURIField(editConfiguration,vreq); - //setConceptSemanticTypeLabelField(editConfiguration,vreq); + setConceptSemanticTypeURIField(editConfiguration,vreq); + setConceptSemanticTypeLabelField(editConfiguration,vreq); } //this field will be hidden and include the concept node URI @@ -321,12 +325,14 @@ public class AddAssociatedConceptGenerator extends VivoBaseGenerator implements //Add preprocessor - private void addPreprocessors(EditConfigurationVTwo editConfiguration, WebappDaoFactory wadf) { + private void addPreprocessors(EditConfigurationVTwo editConfiguration, OntModel ontModel) { //An Edit submission preprocessor for enabling addition of multiple terms for a single search //TODO: Check if this is the appropriate way of getting model + //Passing model to check for any URIs that are present + editConfiguration.addEditSubmissionPreprocessor( - new AddAssociatedConceptsPreprocessor(editConfiguration, wadf)); + new AddAssociatedConceptsPreprocessor(editConfiguration, ontModel)); } @@ -412,13 +418,13 @@ public class AddAssociatedConceptGenerator extends VivoBaseGenerator implements String conceptSemanticTypeURI = null; String conceptSemanticTypeLabel = null; //Can a concept have multiple semantic types? Currently we are only returning the first one - /* - List semanticTypeStatements = conceptIndividual.getObjectPropertyStatements(VIVOCore + "conceptSemanticType"); + + List semanticTypeStatements = conceptIndividual.getObjectPropertyStatements(VIVOCore + "hasConceptSemanticType"); if(semanticTypeStatements.size() > 0) { conceptSemanticTypeURI = semanticTypeStatements.get(0).getObjectURI(); Individual conceptSemanticTypeIndividual = EditConfigurationUtils.getIndividual(vreq, conceptSemanticTypeURI); conceptSemanticTypeLabel = conceptSemanticTypeIndividual.getName(); - }*/ + } //get label //Assuming this is from an external vocabulary source @@ -443,8 +449,8 @@ public class AddAssociatedConceptGenerator extends VivoBaseGenerator implements this.vocabURI = inputVocabURI; this.vocabLabel = inputVocabLabel; this.type = inputType; - //this.conceptSemanticTypeURI = inputConceptSemanticTypeURI; - //this.conceptSemanticTypeLabel = inputConceptSemanticTypeLabel; + this.conceptSemanticTypeURI = inputConceptSemanticTypeURI; + this.conceptSemanticTypeLabel = inputConceptSemanticTypeLabel; } //Getters diff --git a/src/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/preprocessors/AddAssociatedConceptsPreprocessor.java b/src/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/preprocessors/AddAssociatedConceptsPreprocessor.java index 22359108..549c56ed 100644 --- a/src/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/preprocessors/AddAssociatedConceptsPreprocessor.java +++ b/src/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/preprocessors/AddAssociatedConceptsPreprocessor.java @@ -4,18 +4,27 @@ package edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.preprocess import java.util.ArrayList; import java.util.HashMap; +import java.util.HashSet; import java.util.List; import java.util.Map; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; +import com.hp.hpl.jena.ontology.OntModel; +import com.hp.hpl.jena.query.Query; +import com.hp.hpl.jena.query.QueryExecution; +import com.hp.hpl.jena.query.QueryExecutionFactory; +import com.hp.hpl.jena.query.QueryFactory; +import com.hp.hpl.jena.query.QuerySolution; +import com.hp.hpl.jena.query.ResultSet; import com.hp.hpl.jena.rdf.model.Literal; +import com.hp.hpl.jena.rdf.model.Resource; +import com.hp.hpl.jena.vocabulary.RDF; import com.hp.hpl.jena.vocabulary.RDFS; import com.hp.hpl.jena.vocabulary.XSD; -import edu.cornell.mannlib.vitro.webapp.beans.Individual; -import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory; + import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.BaseEditSubmissionPreprocessorVTwo; import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.EditConfigurationUtils; import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.EditConfigurationVTwo; @@ -27,13 +36,18 @@ public class AddAssociatedConceptsPreprocessor extends protected static final Log log = LogFactory .getLog(AddAssociatedConceptsPreprocessor.class.getName()); - protected WebappDaoFactory wadf = null; - + //TODO: Check if better way to do this? + protected OntModel ontModel = null; // Field names/variables names for n3 - these will have numbers added as // suffix if more than one term private static String conceptNodeBase = "conceptNode"; private static String sourceBase = "conceptSource"; private static String labelBase = "conceptLabel"; + private static String conceptSemanticTypeLabelBase = "conceptSemanticTypeLabel"; + private static String conceptSemanticTypeURIBase = "conceptSemanticTypeURI"; + //keyed off label variable, specifies which uri variable should be used, useful if same label repeated twice + private HashMap labelVarToUriVarHash = null; + //Also storing submission values private static String conceptNodeValues = null; private static String conceptLabelValues = null; @@ -46,9 +60,10 @@ public class AddAssociatedConceptsPreprocessor extends // Will be editing the edit configuration as well as edit submission here - public AddAssociatedConceptsPreprocessor(EditConfigurationVTwo editConfig, WebappDaoFactory wadf) { + public AddAssociatedConceptsPreprocessor(EditConfigurationVTwo editConfig, OntModel ontModel) { super(editConfig); - this.wadf = wadf; + this.ontModel = ontModel; + this.labelVarToUriVarHash = new HashMap(); } public void preprocess(MultiValueEditSubmission inputSubmission) { @@ -57,12 +72,14 @@ public class AddAssociatedConceptsPreprocessor extends // as vocab uri (which is based on thge // For query parameters, check whether CUI copySubmissionValues(); - //This will put the URI value in scope for the first semantic type label - //and generate the rest if need be - //processConceptSemanticValues(); + + if (conceptNodeValues != null) { String[] conceptNodes = convertDelimitedStringToArray(conceptNodeValues); int numberConcepts = conceptNodes.length; + //This will put the URI value in scope for the first semantic type label + //and generate the rest if need be + processConceptSemanticValues(); if (numberConcepts > 1) { processConceptNodes(numberConcepts); } @@ -80,6 +97,7 @@ public class AddAssociatedConceptsPreprocessor extends conceptLabelValues = getConceptLabelValues(); conceptNodeValues = getConceptNodeValues(); conceptSourceValues = getConceptSourceValues(); + log.debug("concept label values are " + conceptLabelValues); } @@ -94,14 +112,11 @@ public class AddAssociatedConceptsPreprocessor extends } - - - - - //This is for additional concept nodes (i.e. if user selects more than one concept) private void processConceptNodes(int numberConcepts) { //There are no "new" resources b/c the concept nodes are URIs from external vocabularies + //New resources for concept semantic type uris + addNewResources(numberConcepts); // Add N3Required addN3Required(numberConcepts); //Add N3 Optional as well @@ -115,6 +130,31 @@ public class AddAssociatedConceptsPreprocessor extends } + //This is specifically for concept semantic type URIs which may need to be generated + private void addNewResources(int numberConcepts) { + // TODO Auto-generated method stub + addConceptSemanticTypeURIResources(numberConcepts); + } + + private void addConceptSemanticTypeURIResources(int numberConcepts) { + String[] conceptSemanticTypeURIs= convertDelimitedStringToArray(conceptSemanticTypeURIValues); + //the number of existing values may not match up, or at least existing populated ones + if(conceptSemanticTypeURIs != null && conceptSemanticTypeURIs.length == numberConcepts) { + int i; + for(i = 0; i < numberConcepts; i++) { + int suffix = i + 1; + String newResourceName = conceptSemanticTypeURIBase + suffix; + editConfiguration.addNewResource(newResourceName, null); + + } + } else if(conceptSemanticTypeURIs != null && conceptSemanticTypeURIs.length != numberConcepts){ + log.error("Number of concept semantic type uris does not match the number of concepts"); + } else{ + log.error("Concept semantic type uris returned as null"); + } + + } + //This is where the actual values will be submitted as if they were separate input fields //Each field name will correspond to the names of the fileds/uris on form/literals on form //generated here @@ -126,8 +166,8 @@ public class AddAssociatedConceptsPreprocessor extends addConceptSourceInputs(numberConcepts); addConceptLabelInputs(numberConcepts); //for concept semantic type labels and uris where they exist - //addConceptSemanticTypeLabelInputs(numberConcepts); - //addConceptSemanticTypeURIInputs(numberConcepts); + addConceptSemanticTypeLabelInputs(numberConcepts); + addConceptSemanticTypeURIInputs(numberConcepts); } @@ -199,11 +239,51 @@ public class AddAssociatedConceptsPreprocessor extends } private void addConceptSemanticTypeLabelInputs(int numberConcepts) { - + String[] labels = convertDelimitedStringToArray(conceptSemanticTypeLabelValues); + if(labels != null && labels.length == numberConcepts) { + int i; + for(i = 0; i < numberConcepts; i++) { + int suffix = i + 1; + String labelInputName = conceptSemanticTypeLabelBase + suffix; + String[] labelValues = new String[1]; + labelValues[0] = labels[i]; + //TODO: Check if there are no funky typed information also stored + //At this point the field should already have been added to edit configuration + FieldVTwo labelField = editConfiguration.getField(labelInputName); + //TODO: Also check to see whether the label is actually populate or will n3 editing take care of that? + if(labelField != null) { + submission.addLiteralToForm(editConfiguration, labelField, labelInputName, labelValues); + } else { + log.error("Corresponding field for " + labelInputName + " was not added to edit configuration"); + } + + } + } else if(labels != null && labels.length != numberConcepts){ + log.error("Number of concept semantic type labels did not match the number of concepts to be added"); + } else{ + log.error("Concept labels returned were null"); + } } private void addConceptSemanticTypeURIInputs(int numberConcepts) { - + String[] conceptSemanticTypeURIs= convertDelimitedStringToArray(conceptSemanticTypeURIValues); + //the number of existing values may not match up, or at least existing populated ones + if(conceptSemanticTypeURIs != null && conceptSemanticTypeURIs.length == numberConcepts) { + int i; + for(i = 0; i < numberConcepts; i++) { + int suffix = i + 1; + String conceptInputName = conceptSemanticTypeURIBase + suffix; + String[] uriValues = new String[1]; + uriValues[0] = conceptSemanticTypeURIs[i]; + //Add value for uri to form + //TODO: Check if value is empty in which case don't add to submission + submission.addUriToForm(editConfiguration, conceptInputName, uriValues); + } + } else if(conceptSemanticTypeURIs != null && conceptSemanticTypeURIs.length != numberConcepts){ + log.error("Number of concept nodes did not match the number of concepts to be added"); + } else{ + log.error("Concept nodes returned were null"); + } } //Fields @@ -218,10 +298,16 @@ public class AddAssociatedConceptsPreprocessor extends String conceptNode = conceptNodeBase + suffix; String label = labelBase + suffix; String source = sourceBase + suffix; + String conceptSemanticTypeLabel = conceptSemanticTypeLabelBase + suffix; + String conceptSemanticTypeURI = conceptSemanticTypeURIBase + suffix; addConceptNodeField(conceptNode); addLabelField(label); addSourceField(source); + //Also add fields for concept semantic type label + addConceptSemanticTypeLabelField(conceptSemanticTypeLabel); + //and concept semantic type URI + addConceptSemanticTypeURIField(conceptSemanticTypeURI); } } @@ -246,6 +332,21 @@ public class AddAssociatedConceptsPreprocessor extends setName(source)); } + + //Will need to check whether or not semantic type label even exists though? + private void addConceptSemanticTypeLabelField(String label) { + editConfiguration.addField(new FieldVTwo(). + setName(label). + setRangeDatatypeUri(XSD.xstring.toString()) + ); + + } + + private void addConceptSemanticTypeURIField(String conceptSemanticTypeURI) { + editConfiguration.addField(new FieldVTwo(). + setName(conceptSemanticTypeURI)); + } + //original literals on form: label, uris on form: conceptNode and conceptSource //This will overwrite the original values in the edit configuration @@ -261,9 +362,13 @@ public class AddAssociatedConceptsPreprocessor extends String conceptNode = conceptNodeBase + suffix; String label = labelBase + suffix; String source = sourceBase + suffix; + String conceptSemanticTypeLabel = conceptSemanticTypeLabelBase + suffix; + String conceptSemanticTypeURI = conceptSemanticTypeURIBase + suffix; urisOnForm.add(conceptNode); urisOnForm.add(source); + urisOnForm.add(conceptSemanticTypeURI); literalsOnForm.add(label); + literalsOnForm.add(conceptSemanticTypeLabel); } editConfiguration.setUrisOnform(urisOnForm); editConfiguration.setLiteralsOnForm(literalsOnForm); @@ -279,8 +384,7 @@ public class AddAssociatedConceptsPreprocessor extends List n3Required = new ArrayList(); int index; String nodeBase = "?" + conceptNodeBase; - String labelVar = "?" + labelBase; - String sourceVar = "?" + sourceBase; + String prefixStr = "@prefix core: ."; // First one already included so add new ones here for (index = 1; index <= numberConcepts; index++) { @@ -293,23 +397,30 @@ public class AddAssociatedConceptsPreprocessor extends editConfiguration.setN3Required(n3Required); } //Add n3 optional - + //TODO: Rewrite optional N3 private void addN3Optional(int numberConcepts) { List n3Optional = new ArrayList(); int index; String nodeBase = "?" + conceptNodeBase; - String labelVar = "?" + labelBase; - String sourceVar = "?" + sourceBase; + + String conceptSemanticTypeLabelVar = "?" + conceptSemanticTypeLabelBase; + String conceptSemanticTypeURIVar = "?" + conceptSemanticTypeURIBase; String prefixStr = "@prefix core: ."; // First one already included so add new ones here for (index = 1; index <= numberConcepts; index++) { int suffix = index; String node = nodeBase + suffix; - String label = labelVar + suffix; - String source = sourceVar + suffix; + + String conceptSemanticTypeLabel = conceptSemanticTypeLabelVar + suffix; + String conceptSemanticTypeURI = conceptSemanticTypeURIVar + suffix; String n3String = prefixStr; - n3String += node + " <" + RDFS.label.getURI() + "> " + label + " .\n" + - node + " <" + RDFS.isDefinedBy.getURI() + "> " + source + " ."; + + + n3String += node + " core:hasConceptSemanticType " + conceptSemanticTypeURI + " ." + + conceptSemanticTypeURI + " core:isConceptSemanticTypeOf " + node + ". " + + conceptSemanticTypeURI + " <" + RDFS.label.getURI() + "> " + conceptSemanticTypeLabel + " .\n" + + conceptSemanticTypeURI + " <" + RDF.type.getURI() + "> core:ConceptSemanticType .\n" ; + n3Optional.add(n3String); } //Already have n3 required so need to add to that @@ -357,33 +468,71 @@ public class AddAssociatedConceptsPreprocessor extends //This will either generate or retrieve URIs for the concept semantic type labels if they exist //We will then update the submission to include this private String getConceptSemanticTypeURIValues() { - List conceptSemanticTypeURIs = new ArrayList(); String[] conceptSemanticTypeLabels = convertDelimitedStringToArray(conceptSemanticTypeLabelValues); + //keep track of unique labels + HashSet allSemanticTypeLabels = new HashSet(); int numberLabels = conceptSemanticTypeLabels.length; - + String pseudoInputString = ""; for(int i = 0; i < numberLabels; i++) { String label = conceptSemanticTypeLabels[i]; + //if label not already in the hash, then create key + if(!allSemanticTypeLabels.contains(label)) { + + } //Make or retrieve URI for this label String uri = getURIForSemanticTypeLabel(label); - conceptSemanticTypeURIs.add(uri); + if(i != 0) { + pseudoInputString += ","; + } + pseudoInputString += uri; + } - //Set uris as string - //Essentially this will allow the URI to be put in scope - return conceptSemanticTypeURIs.toString(); + String[] urisToAdd = new String[1]; + urisToAdd[0] = pseudoInputString; + log.debug("uris to add" + pseudoInputString); + submission.addUriToForm(this.editConfiguration, "conceptSemanticTypeURI", urisToAdd); + return pseudoInputString; } private String getURIForSemanticTypeLabel(String label) { - //Check if system has an individual with this URI - // - List individualsWithLabel = this.wadf.getIndividualDao().getIndividualsByDataProperty(RDFS.label.getURI(), label); - //We are only interested in semantic type objects and this may return multiple elements (perhaps too many? - //getting the model requires servlet and context and we don't want to pass that here do we//Return all semantic type objects with this label - //this.modelSelector. - return null; + String existingURI = this.getExistingSemanticTypeURI(label); + if(existingURI != null) { + return existingURI; + } + //if we leave this as null, we should be able to generate a new resource + //empty string because there may be more than one value returned for labels + else return ""; } + private String getExistingSemanticTypeURI(String label) { + String queryStr = "SELECT ?semanticType WHERE { ?semanticType <" + RDF.type.getURI() + "> . " + + "?semanticType <" + RDFS.label.getURI() + "> \"" + label + "\"^^ . }"; + QueryExecution qe = null; + try{ + Query query = QueryFactory.create(queryStr); + qe = QueryExecutionFactory.create(query, this.ontModel); + ResultSet results = null; + results = qe.execSelect(); + + while( results.hasNext()){ + QuerySolution qs = results.nextSolution(); + if(qs.get("semanticType") != null) { + Resource semanticTypeURI = qs.getResource("semanticType"); + log.debug("Semantic Type URI returned " + semanticTypeURI.getURI()); + return semanticTypeURI.getURI(); + } + } + }catch(Exception ex){ + throw new Error("Error in executing query string: \n" + queryStr + '\n' + ex.getMessage()); + }finally{ + if( qe != null) + qe.close(); + } + return null; + } + private Object getFirstElement(List inputList) { if(inputList == null || inputList.size() == 0) return null;