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NIHVIVO-3877 and NIHVIVO-3872 using RDFService for aspects of import and export

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This commit is contained in:
brianjlowe 2012-07-06 15:05:29 +00:00
parent 0f9d1a79d1
commit eace91759a
5 changed files with 129 additions and 54 deletions
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122
webapp/src/edu/cornell/mannlib/vitro/webapp/controller/jena/JenaExportController.java
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@ -3,7 +3,10 @@
package edu.cornell.mannlib.vitro.webapp.controller.jena;
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
import java.io.PipedInputStream;
import java.io.PipedOutputStream;
import java.util.HashMap;
import java.util.Map;
@ -11,6 +14,7 @@ import javax.servlet.RequestDispatcher;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
import org.apache.commons.io.IOUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
@ -28,6 +32,11 @@ import edu.cornell.mannlib.vitro.webapp.controller.Controllers;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.dao.jena.JenaModelUtils;
import edu.cornell.mannlib.vitro.webapp.dao.jena.ModelContext;
import edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceModelMaker;
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException;
import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.RDFServiceUtils;
import edu.cornell.mannlib.vitro.webapp.servlet.setup.JenaDataSourceSetupBase;
import edu.cornell.mannlib.vitro.webapp.utils.jena.JenaOutputUtils;
public class JenaExportController extends BaseEditController {
@ -116,12 +125,10 @@ public class JenaExportController extends BaseEditController {
getServletContext()).getABoxModel();
}
else if("full".equals(assertedOrInferredParam)){
model = ModelContext.getUnionOntModelSelector(
getServletContext()).getABoxModel();
outputSparqlConstruct(ABOX_FULL_CONSTRUCT, formatParam, response);
}
else if("asserted".equals(assertedOrInferredParam)){
model = ModelContext.getBaseOntModelSelector(
getServletContext()).getABoxModel();
outputSparqlConstruct(ABOX_ASSERTED_CONSTRUCT, formatParam, response);
}
}
else if("tbox".equals(subgraphParam)){
@ -161,47 +168,17 @@ public class JenaExportController extends BaseEditController {
getServletContext()).getTBoxModel());
}
else if("full".equals(assertedOrInferredParam)){
ontModel = xutil.extractTBox(dataset, ontologyURI, FULL_GRAPH);
ontModel.addSubModel(ModelContext.getUnionOntModelSelector(
getServletContext()).getABoxModel());
ontModel.addSubModel(ModelContext.getUnionOntModelSelector(
getServletContext()).getTBoxModel());
ontModel.addSubModel(ModelContext.getUnionOntModelSelector(
getServletContext()).getApplicationMetadataModel());
outputSparqlConstruct(FULL_FULL_CONSTRUCT, formatParam, response);
}
else{
ontModel = xutil.extractTBox(
dataset, ontologyURI, ASSERTIONS_GRAPH);
ontModel.addSubModel(ModelContext.getBaseOntModelSelector(
getServletContext()).getABoxModel());
ontModel.addSubModel(ModelContext.getBaseOntModelSelector(
getServletContext()).getTBoxModel());
ontModel.addSubModel(ModelContext.getBaseOntModelSelector(
getServletContext()).getApplicationMetadataModel());
outputSparqlConstruct(FULL_ASSERTED_CONSTRUCT, formatParam, response);
}
}
JenaOutputUtils.setNameSpacePrefixes(model,vreq.getWebappDaoFactory());
if ( formatParam == null ) {
formatParam = "RDF/XML-ABBREV"; // default
}
String mime = formatToMimetype.get( formatParam );
if ( mime == null ) {
throw new RuntimeException( "Unsupported RDF format " + formatParam);
}
response.setContentType( mime );
if(mime.equals("application/rdf+xml"))
response.setHeader("content-disposition", "attachment; filename=" + "export.rdf");
else if(mime.equals("text/n3"))
response.setHeader("content-disposition", "attachment; filename=" + "export.n3");
else if(mime.equals("text/plain"))
response.setHeader("content-disposition", "attachment; filename=" + "export.txt");
else if(mime.equals("application/x-turtle"))
response.setHeader("content-disposition", "attachment; filename=" + "export.ttl");
setHeaders(response, formatParam);
try {
OutputStream outStream = response.getOutputStream();
if ( formatParam.startsWith("RDF/XML") ) {
@ -237,6 +214,50 @@ public class JenaExportController extends BaseEditController {
}
private void setHeaders(HttpServletResponse response, String formatParam) {
if ( formatParam == null ) {
formatParam = "RDF/XML-ABBREV"; // default
}
String mime = formatToMimetype.get( formatParam );
if ( mime == null ) {
throw new RuntimeException( "Unsupported RDF format " + formatParam);
}
response.setContentType( mime );
if(mime.equals("application/rdf+xml"))
response.setHeader("content-disposition", "attachment; filename=" + "export.rdf");
else if(mime.equals("text/n3"))
response.setHeader("content-disposition", "attachment; filename=" + "export.n3");
else if(mime.equals("text/plain"))
response.setHeader("content-disposition", "attachment; filename=" + "export.txt");
else if(mime.equals("application/x-turtle"))
response.setHeader("content-disposition", "attachment; filename=" + "export.ttl");
}
private void outputSparqlConstruct(String queryStr, String formatParam,
HttpServletResponse response) {
RDFService rdfService = RDFServiceUtils.getRDFServiceFactory(getServletContext()).getRDFService();
try {
setHeaders(response, formatParam);
OutputStream out = response.getOutputStream();
if ( formatParam.startsWith("RDF/XML") ) {
out.write("<?xml version=\"1.0\" encoding=\"UTF-8\"?>".getBytes());
}
InputStream in = rdfService.sparqlConstructQuery(
queryStr, RDFServiceUtils.getSerializationFormatFromJenaString(
formatParam));
IOUtils.copy(in, out);
out.flush();
out.close();
} catch (RDFServiceException e) {
throw new RuntimeException(e);
} catch (IOException ioe) {
throw new RuntimeException(ioe);
} finally {
rdfService.close();
}
}
private void prepareExportSelectionPage( VitroRequest vreq, HttpServletResponse response ) {
vreq.setAttribute( "bodyJsp", Controllers.EXPORT_SELECTION_JSP );
RequestDispatcher dispatcher = vreq.getRequestDispatcher( Controllers.BASIC_JSP );
@ -278,16 +299,35 @@ public class JenaExportController extends BaseEditController {
formatToExtension.put("RDF/XML",".rdf");
formatToExtension.put("RDF/XML-ABBREV",".rdf");
formatToExtension.put("N3",".n3");
formatToExtension.put("N-TRIPLES",".nt");
formatToExtension.put("N-TRIPLE",".nt");
formatToExtension.put("TURTLE",".ttl");
formatToMimetype = new HashMap<String,String>();
formatToMimetype.put("RDF/XML","application/rdf+xml");
formatToMimetype.put("RDF/XML-ABBREV","application/rdf+xml");
formatToMimetype.put("N3","text/n3");
formatToMimetype.put("N-TRIPLES", "text/plain");
formatToMimetype.put("N-TRIPLE", "text/plain");
formatToMimetype.put("TURTLE", "application/x-turtle");
}
private static final String ABOX_FULL_CONSTRUCT = "CONSTRUCT { ?s ?p ?o } " +
"WHERE { GRAPH ?g { ?s ?p ?o } FILTER (!regex(str(?g), \"tbox\")) " +
"FILTER (?g != <" + JenaDataSourceSetupBase.JENA_APPLICATION_METADATA_MODEL + ">) " +
"FILTER (?g != <" + RDFServiceModelMaker.METADATA_MODEL_URI + ">) }";
private static final String ABOX_ASSERTED_CONSTRUCT = "CONSTRUCT { ?s ?p ?o } " +
"WHERE { GRAPH ?g { ?s ?p ?o } FILTER (!regex(str(?g), \"tbox\")) " +
"FILTER (?g != <" + JenaDataSourceSetupBase.JENA_INF_MODEL + ">) " +
"FILTER (?g != <" + JenaDataSourceSetupBase.JENA_APPLICATION_METADATA_MODEL + ">) " +
"FILTER (?g != <" + RDFServiceModelMaker.METADATA_MODEL_URI + ">) }";
private static final String FULL_FULL_CONSTRUCT = "CONSTRUCT { ?s ?p ?o } " +
"WHERE { ?s ?p ?o }";
private static final String FULL_ASSERTED_CONSTRUCT = "CONSTRUCT { ?s ?p ?o } " +
"WHERE { GRAPH ?g { ?s ?p ?o } " +
"FILTER (?g != <" + JenaDataSourceSetupBase.JENA_INF_MODEL + ">) " +
"FILTER (?g != <" + JenaDataSourceSetupBase.JENA_TBOX_INF_MODEL + ">) }";
}

37
webapp/src/edu/cornell/mannlib/vitro/webapp/controller/jena/RDFUploadController.java
View file

@ -5,6 +5,7 @@ package edu.cornell.mannlib.vitro.webapp.controller.jena;
import java.io.File;
import java.io.IOException;
import java.io.InputStream;
import java.net.URL;
import java.util.List;
import java.util.Map;
@ -41,6 +42,7 @@ import edu.cornell.mannlib.vitro.webapp.filestorage.uploadrequest.FileUploadServ
import edu.cornell.mannlib.vitro.webapp.rdfservice.ChangeSet;
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException;
import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.RDFServiceUtils;
import edu.cornell.mannlib.vitro.webapp.servlet.setup.JenaDataSourceSetupBase;
public class RDFUploadController extends JenaIngestController {
@ -239,7 +241,13 @@ public class RDFUploadController extends JenaIngestController {
ModelMaker maker = getVitroJenaModelMaker(request);
if (docLoc!=null && modelName != null) {
doLoadRDFData(modelName, docLoc, filePath, languageStr, maker);
RDFService rdfService = RDFServiceUtils.getRDFServiceFactory(
getServletContext()).getRDFService();
try {
doLoadRDFData(modelName, docLoc, filePath, languageStr, rdfService);
} finally {
rdfService.close();
}
String modelType = getModelType(request, maker);
showModelList(request, maker, modelType);
} else {
@ -319,12 +327,12 @@ public class RDFUploadController extends JenaIngestController {
String docLoc,
String filePath,
String language,
ModelMaker modelMaker) {
Model m = modelMaker.getModel(modelName);
m.enterCriticalSection(Lock.WRITE);
RDFService rdfService) {
try {
if ( (docLoc != null) && (docLoc.length()>0) ) {
m.read(docLoc, language);
URL docLocURL = new URL(docLoc);
InputStream in = docLocURL.openStream();
readIntoModel(in, language, rdfService, modelName);
} else if ( (filePath != null) && (filePath.length()>0) ) {
File file = new File(filePath);
File[] files;
@ -338,7 +346,8 @@ public class RDFUploadController extends JenaIngestController {
File currentFile = files[i];
log.debug("Reading file " + currentFile.getName());
try {
m.read(fileStream.getInputStream(), null, language);
readIntoModel(fileStream.getInputStream(), language,
rdfService, modelName);
fileStream.delete();
} catch (IOException ioe) {
String errMsg = "Error loading RDF from " +
@ -348,8 +357,20 @@ public class RDFUploadController extends JenaIngestController {
}
}
}
} finally {
m.leaveCriticalSection();
} catch (IOException e) {
throw new RuntimeException(e);
}
}
private void readIntoModel(InputStream in, String language,
RDFService rdfService, String modelName) {
ChangeSet cs = rdfService.manufactureChangeSet();
cs.addAddition(in, RDFServiceUtils.getSerializationFormatFromJenaString(
language), modelName);
try {
rdfService.changeSetUpdate(cs);
} catch (RDFServiceException e) {
throw new RuntimeException(e);
}
}

18
webapp/src/edu/cornell/mannlib/vitro/webapp/rdfservice/impl/RDFServiceUtils.java
View file

@ -30,8 +30,6 @@ public class RDFServiceUtils {
private static final String RDFSERVICEFACTORY_ATTR =
RDFServiceUtils.class.getName() + ".RDFServiceFactory";
private static final String RDFSERVICEFACTORY_FILTERING_ATTR =
RDFServiceUtils.class.getName() + ".RDFServiceFactory.Filtering";
public static RDFServiceFactory getRDFServiceFactory(ServletContext context) {
@ -80,11 +78,27 @@ public class RDFServiceUtils {
return "RDF/XML";
case N3:
return "N3";
case NTRIPLE:
return "N-TRIPLE";
default:
throw new RuntimeException("unexpected format in getSerializationFormatString");
}
}
public static ModelSerializationFormat getSerializationFormatFromJenaString(String jenaString) {
if ("N3".equals(jenaString) || "TTL".equals(jenaString)
|| "TURTLE".equals(jenaString)) {
return ModelSerializationFormat.N3;
} else if ("N-TRIPLE".equals(jenaString)) {
return ModelSerializationFormat.NTRIPLE;
} else if ("RDF/XML".equals(jenaString)
|| "RDF/XML-ABBREV".equals(jenaString)) {
return ModelSerializationFormat.RDFXML;
} else {
throw new RuntimeException("unrecognized format " + jenaString);
}
}
public static RDFService getRDFService(VitroRequest vreq) {
return getRDFServiceFactory(
vreq.getSession().getServletContext()).getRDFService();