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NIHVIVO-3130 NIHVIVO-3089 ingest tools fixes and improvements

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This commit is contained in:
brianjlowe 2011-11-04 21:01:34 +00:00
parent 4d8206b018
commit f5e1661f9a
22 changed files with 331 additions and 309 deletions
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42
webapp/src/edu/cornell/mannlib/vitro/webapp/controller/jena/JenaCsv2RdfController.java
View file

@ -5,6 +5,7 @@ package edu.cornell.mannlib.vitro.webapp.controller.jena;
import java.io.IOException; import java.io.IOException;
import java.io.InputStream; import java.io.InputStream;
import java.net.URL; import java.net.URL;
import java.util.ArrayList;
import java.util.LinkedList; import java.util.LinkedList;
import java.util.List; import java.util.List;
import java.util.Map; import java.util.Map;
@ -34,7 +35,6 @@ import edu.cornell.mannlib.vitro.webapp.utils.jena.JenaIngestUtils;
public class JenaCsv2RdfController extends BaseEditController{ public class JenaCsv2RdfController extends BaseEditController{
private static final String CSV2RDF_JSP = "/jenaIngest/csv2rdf.jsp"; private static final String CSV2RDF_JSP = "/jenaIngest/csv2rdf.jsp";
private static final String INGEST_MENU_JSP = "/jenaIngest/ingestMenu.jsp";
private static final String CSV2RDF_SELECT_URI_JSP = "/jenaIngest/csv2rdfSelectUri.jsp"; private static final String CSV2RDF_SELECT_URI_JSP = "/jenaIngest/csv2rdfSelectUri.jsp";
private static int maxFileSizeInBytes = 1024 * 1024 * 2000; //2000mb private static int maxFileSizeInBytes = 1024 * 1024 * 2000; //2000mb
@ -62,17 +62,20 @@ public class JenaCsv2RdfController extends BaseEditController{
if ("csv2rdf".equals(actionStr)) { if ("csv2rdf".equals(actionStr)) {
String csvUrl = request.getParameter("csvUrl"); String csvUrl = request.getParameter("csvUrl");
if (!csvUrl.isEmpty() || !filePath.isEmpty()) { if (!csvUrl.isEmpty() || !filePath.isEmpty()) {
String[] sourceModel = new String[1]; String destinationModelNameStr = request.getParameter(
sourceModel[0] = doExecuteCsv2Rdf(request,fileStream,filePath); "destinationModelName");
Model model = ModelFactory.createDefaultModel(); Model csv2rdfResult = doExecuteCsv2Rdf(
request, fileStream, filePath);
ModelMaker maker = getVitroJenaModelMaker(request); ModelMaker maker = getVitroJenaModelMaker(request);
Boolean csv2rdf = true; Boolean csv2rdf = true;
JenaIngestUtils utils = new JenaIngestUtils(); JenaIngestUtils utils = new JenaIngestUtils();
Map<String,LinkedList<String>> propertyMap = utils.generatePropertyMap(sourceModel, model, maker); List<Model> resultList = new ArrayList<Model>();
resultList.add(csv2rdfResult);
Map<String,LinkedList<String>> propertyMap =
utils.generatePropertyMap(resultList, maker);
request.setAttribute("propertyMap",propertyMap); request.setAttribute("propertyMap",propertyMap);
getServletContext().setAttribute("sourceModel", sourceModel); request.setAttribute("csv2rdf", csv2rdf);
getServletContext().setAttribute("csv2rdf",csv2rdf); request.setAttribute("destinationModelName", destinationModelNameStr);
request.setAttribute("destinationModelName", sourceModel[0]);
request.setAttribute("title","URI Select"); request.setAttribute("title","URI Select");
request.setAttribute("bodyJsp", CSV2RDF_SELECT_URI_JSP); request.setAttribute("bodyJsp", CSV2RDF_SELECT_URI_JSP);
} else { } else {
@ -88,9 +91,7 @@ public class JenaCsv2RdfController extends BaseEditController{
try { try {
rd.forward(request, response); rd.forward(request, response);
} catch (Exception e) { } catch (Exception e) {
System.out.println(this.getClass().getName()+" could not forward to view."); throw new RuntimeException(e);
System.out.println(e.getMessage());
System.out.println(e.getStackTrace());
} }
} }
@ -106,7 +107,7 @@ public class JenaCsv2RdfController extends BaseEditController{
return; return;
} }
public String doExecuteCsv2Rdf(VitroRequest vreq,FileItem fileStream, String filePath) { public Model doExecuteCsv2Rdf(VitroRequest vreq, FileItem fileStream, String filePath) {
char[] quoteChars = {'"'}; char[] quoteChars = {'"'};
String namespace = ""; String namespace = "";
String tboxNamespace = vreq.getParameter("tboxNamespace"); String tboxNamespace = vreq.getParameter("tboxNamespace");
@ -139,25 +140,26 @@ public class JenaCsv2RdfController extends BaseEditController{
is = fileStream.getInputStream(); is = fileStream.getInputStream();
} catch (IOException e) { } catch (IOException e) {
System.out.println("IOException opening URL "+csvUrl); throw new RuntimeException("Unable to access URL " + csvUrl);
return null;
} }
Model[] models = null; Model[] models = null;
try { try {
models = c2r.convertToRdf(is,vreq,destination); models = c2r.convertToRdf(
is, vreq.getWebappDaoFactory(), destination);
} catch (IOException e) { } catch (IOException e) {
System.out.println("IOException converting "+csvUrl+" to RDF"); throw new RuntimeException(
"Unable to convert " + csvUrl + " to RDF");
} }
if (destination != null) { // TODO: rework this
destination.add(models[0]); vreq.getSession().setAttribute("csv2rdfResult", models[0]);
}
if (tboxDestination != null) { if (tboxDestination != null) {
tboxDestination.add(models[1]); tboxDestination.add(models[1]);
} }
return destinationModelNameStr;
return models[0];
} }
private Model getModel(String name, HttpServletRequest request) { private Model getModel(String name, HttpServletRequest request) {

235
webapp/src/edu/cornell/mannlib/vitro/webapp/controller/jena/JenaIngestController.java
View file

@ -11,6 +11,7 @@ import java.lang.reflect.Method;
import java.sql.SQLException; import java.sql.SQLException;
import java.text.Collator; import java.text.Collator;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections; import java.util.Collections;
import java.util.Comparator; import java.util.Comparator;
import java.util.HashMap; import java.util.HashMap;
@ -68,7 +69,6 @@ import edu.cornell.mannlib.vitro.webapp.beans.Ontology;
import edu.cornell.mannlib.vitro.webapp.controller.Controllers; import edu.cornell.mannlib.vitro.webapp.controller.Controllers;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest; import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.dao.OntologyDao; import edu.cornell.mannlib.vitro.webapp.dao.OntologyDao;
import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
import edu.cornell.mannlib.vitro.webapp.dao.jena.JenaBaseDao; import edu.cornell.mannlib.vitro.webapp.dao.jena.JenaBaseDao;
import edu.cornell.mannlib.vitro.webapp.dao.jena.ModelContext; import edu.cornell.mannlib.vitro.webapp.dao.jena.ModelContext;
import edu.cornell.mannlib.vitro.webapp.dao.jena.VitroJenaModelMaker; import edu.cornell.mannlib.vitro.webapp.dao.jena.VitroJenaModelMaker;
@ -145,8 +145,6 @@ public class JenaIngestController extends BaseEditController {
return; // don't attempt to display a JSP return; // don't attempt to display a JSP
} else if("clearModel".equals(actionStr)) { } else if("clearModel".equals(actionStr)) {
processClearModelRequest(vreq, maker, modelType); processClearModelRequest(vreq, maker, modelType);
} else if("setWriteLayer".equals(actionStr)) {
processSetWriteLayerRequest(vreq, maker, modelType);
} else if("attachModel".equals(actionStr)) { } else if("attachModel".equals(actionStr)) {
processAttachModelRequest(vreq, maker, modelType); processAttachModelRequest(vreq, maker, modelType);
} else if("detachModel".equals(actionStr)) { } else if("detachModel".equals(actionStr)) {
@ -337,13 +335,13 @@ public class JenaIngestController extends BaseEditController {
} catch (com.hp.hpl.jena.shared.CannotEncodeCharacterException cece) { } catch (com.hp.hpl.jena.shared.CannotEncodeCharacterException cece) {
// there's got to be a better way to do this // there's got to be a better way to do this
byte[] badCharBytes = String.valueOf(cece.getBadChar()).getBytes(); byte[] badCharBytes = String.valueOf(cece.getBadChar()).getBytes();
System.out.println("Cannot encode character with byte values: (decimal) "); String errorMsg = "Cannot encode character with byte values: (decimal) ";
for (int i=0; i<badCharBytes.length; i++) { for (int i=0; i<badCharBytes.length; i++) {
System.out.println(badCharBytes[i]); errorMsg += badCharBytes[i];
} }
throw new RuntimeException(errorMsg, cece);
} catch (Exception e) { } catch (Exception e) {
// Well if we can't write out to the response I guess there ain't much we can do. log.error(e, e);
e.printStackTrace();
} finally { } finally {
model.leaveCriticalSection(); model.leaveCriticalSection();
} }
@ -357,30 +355,6 @@ public class JenaIngestController extends BaseEditController {
vreq.setAttribute("bodyJsp",INGEST_MENU_JSP); vreq.setAttribute("bodyJsp",INGEST_MENU_JSP);
} }
private void processSetWriteLayerRequest(VitroRequest vreq, ModelMaker maker, String modelType) {
// String modelName = vreq.getParameter("modelName");
// if (modelName != null) {
// OntModel mainModel = (OntModel) getServletContext().getAttribute("jenaOntModel");
// WebappDaoFactoryJena existingDaoFactory = null;
// try {
// existingDaoFactory = (WebappDaoFactoryJena) getServletContext().getAttribute("webappDaoFactory");
// } catch (Exception e) {}
// Model writeModel = maker.getModel(modelName);
// Model dynamicUnion = ModelFactory.createUnion(writeModel,mainModel);
// OntModel ontModelForDaos = ModelFactory.createOntologyModel(ONT_MODEL_SPEC, dynamicUnion);
// WebappDaoFactory wadf = new WebappDaoFactoryJena(new SimpleOntModelSelector(ontModelForDaos), (existingDaoFactory != null) ? existingDaoFactory.getDefaultNamespace() : null, null, null);
// request.getSession().setAttribute("webappDaoFactory", wadf);
// request.getSession().setAttribute("jenaOntModel",ontModelForDaos);
// System.out.println("Setting jenaOntModel session attribute");
// Model baseModel = (OntModel) getServletContext().getAttribute("baseOntModel");
// OntModel ontModelForAssertions = ModelFactory.createOntologyModel(OntModelSpec.OWL_DL_MEM,ModelFactory.createUnion(writeModel,baseModel));
// request.getSession().setAttribute("assertionsWebappDaoFactory", new WebappDaoFactoryJena(new SimpleOntModelSelector(ontModelForAssertions)));
// request.getSession().setAttribute("baseOntModel", ontModelForAssertions);
// }
// request.setAttribute("title","Ingest Menu");
// request.setAttribute("bodyJsp",INGEST_MENU_JSP);
}
private void processAttachModelRequest(VitroRequest vreq, ModelMaker maker, String modelType) { private void processAttachModelRequest(VitroRequest vreq, ModelMaker maker, String modelType) {
String modelName = vreq.getParameter("modelName"); String modelName = vreq.getParameter("modelName");
if (modelName != null) { if (modelName != null) {
@ -403,12 +377,21 @@ public class JenaIngestController extends BaseEditController {
private void processRenameBNodesRequest(VitroRequest vreq, ModelMaker maker, String modelType) { private void processRenameBNodesRequest(VitroRequest vreq, ModelMaker maker, String modelType) {
String[] sourceModel = vreq.getParameterValues("sourceModelName"); String[] sourceModel = vreq.getParameterValues("sourceModelName");
Model model = ModelFactory.createDefaultModel();
JenaIngestUtils utils = new JenaIngestUtils(); JenaIngestUtils utils = new JenaIngestUtils();
if(sourceModel!=null && sourceModel.length!=0){ if(sourceModel != null && sourceModel.length != 0) {
Map<String,LinkedList<String>> propertyMap = utils.generatePropertyMap(sourceModel, model, maker); List<Model> sourceModelList = new ArrayList<Model>();
getServletContext().setAttribute("sourceModel",sourceModel); for (int i = 0; i < sourceModel.length ; i++) {
Model m = maker.getModel(sourceModel[i]);
if (m != null) {
sourceModelList.add(m);
}
}
Map<String,LinkedList<String>> propertyMap =
utils.generatePropertyMap(sourceModelList, maker);
List<String> sourceModelNameList = Arrays.asList(sourceModel);
vreq.setAttribute("sourceModel",sourceModelNameList);
vreq.setAttribute("propertyMap", propertyMap); vreq.setAttribute("propertyMap", propertyMap);
vreq.setAttribute("enablePropertyPatternURIs", !propertyMap.isEmpty());
vreq.setAttribute("title","URI Select"); vreq.setAttribute("title","URI Select");
vreq.setAttribute("bodyJsp",RENAME_BNODES_URI_SELECT_JSP); vreq.setAttribute("bodyJsp",RENAME_BNODES_URI_SELECT_JSP);
} else { } else {
@ -421,12 +404,21 @@ public class JenaIngestController extends BaseEditController {
String namespaceEtcStr = vreq.getParameter("namespaceEtcStr"); String namespaceEtcStr = vreq.getParameter("namespaceEtcStr");
String pattern = vreq.getParameter("pattern"); String pattern = vreq.getParameter("pattern");
String concatenate = vreq.getParameter("concatenate"); String concatenate = vreq.getParameter("concatenate");
String[] sourceModel = (String[])getServletContext().getAttribute("sourceModel"); String[] sourceModel = (String[]) vreq.getParameterValues("sourceModelName");
if(namespaceEtcStr!=null && !namespaceEtcStr.isEmpty()){ if(namespaceEtcStr != null) {
if(concatenate.equals("integer")){ if (namespaceEtcStr.isEmpty()) {
doRenameBNodes(vreq,namespaceEtcStr, false, null, sourceModel); if ("true".equals(vreq.getParameter("csv2rdf"))) {
processCsv2rdfRequest(vreq, maker, modelType);
return;
} else {
vreq.setAttribute("errorMsg", "Please enter a value.");
processRenameBNodesRequest(vreq, maker, modelType);
return;
}
} }
else{ if (concatenate.equals("integer")) {
doRenameBNodes(vreq,namespaceEtcStr, false, null, sourceModel);
} else {
pattern = pattern.trim(); pattern = pattern.trim();
doRenameBNodes(vreq,namespaceEtcStr, true, pattern, sourceModel); doRenameBNodes(vreq,namespaceEtcStr, true, pattern, sourceModel);
} }
@ -695,7 +687,7 @@ public class JenaIngestController extends BaseEditController {
* calling method that does the merge operation. * calling method that does the merge operation.
*/ */
String result = utils.doMerge(uri1,uri2,baseOntModel,ontModel,infOntModel,usePrimaryLabelOnly); String result = utils.doMerge(uri1,uri2,baseOntModel,ontModel,infOntModel,usePrimaryLabelOnly);
getServletContext().setAttribute("leftoverModel", utils.getLeftOverModel()); vreq.getSession().setAttribute("leftoverModel", utils.getLeftOverModel());
vreq.setAttribute("result",result); vreq.setAttribute("result",result);
vreq.setAttribute("title","Merge Resources"); vreq.setAttribute("title","Merge Resources");
vreq.setAttribute("bodyJsp",MERGE_RESULT); vreq.setAttribute("bodyJsp",MERGE_RESULT);
@ -710,15 +702,32 @@ public class JenaIngestController extends BaseEditController {
HttpServletResponse response, HttpServletResponse response,
ModelMaker maker, ModelMaker maker,
String modelType) { String modelType) {
String uri1 = vreq.getParameter("uri1"); String oldNamespace = vreq.getParameter("oldNamespace");
String uri2 = vreq.getParameter("uri2"); String newNamespace = vreq.getParameter("newNamespace");
if(uri1!=null){ String errorMsg = "";
String result = doRename(uri1,uri2,response); if (oldNamespace != null) {
vreq.setAttribute("result",result); if (oldNamespace.isEmpty() && !newNamespace.isEmpty()) {
vreq.setAttribute("title","Rename Resources"); errorMsg = "Please enter the old namespace to be changed.";
vreq.setAttribute("bodyJsp",RENAME_RESULT); } else if (!oldNamespace.isEmpty() && newNamespace.isEmpty()) {
} errorMsg = "Please enter the new namespace.";
else{ } else if (oldNamespace.isEmpty() && newNamespace.isEmpty()) {
errorMsg = "Please enter the namespaces.";
} else if (oldNamespace.equals(newNamespace)) {
errorMsg = "Please enter two different namespaces.";
}
if (!errorMsg.isEmpty()) {
vreq.setAttribute("errorMsg", errorMsg);
vreq.setAttribute("oldNamespace", oldNamespace);
vreq.setAttribute("newNamespace", newNamespace);
vreq.setAttribute("title","Rename Resource");
vreq.setAttribute("bodyJsp",RENAME_RESOURCE);
} else {
String result = doRename(oldNamespace, newNamespace, response);
vreq.setAttribute("result",result);
vreq.setAttribute("title","Rename Resources");
vreq.setAttribute("bodyJsp",RENAME_RESULT);
}
} else{
vreq.setAttribute("title","Rename Resource"); vreq.setAttribute("title","Rename Resource");
vreq.setAttribute("bodyJsp",RENAME_RESOURCE); vreq.setAttribute("bodyJsp",RENAME_RESOURCE);
} }
@ -728,8 +737,8 @@ public class JenaIngestController extends BaseEditController {
HttpServletResponse response, HttpServletResponse response,
ModelMaker maker, ModelMaker maker,
String modelType) { String modelType) {
//Model lmodel = (Model)request.getSession().getAttribute("leftoverModel");
Model lmodel = (Model)getServletContext().getAttribute("leftoverModel"); Model lmodel = (Model) vreq.getSession().getAttribute("leftoverModel");
response.setContentType("RDF/XML-ABBREV"); response.setContentType("RDF/XML-ABBREV");
try { try {
OutputStream outStream = response.getOutputStream(); OutputStream outStream = response.getOutputStream();
@ -745,7 +754,7 @@ public class JenaIngestController extends BaseEditController {
private ModelMaker getVitroJenaModelMaker(HttpServletRequest request) { private ModelMaker getVitroJenaModelMaker(HttpServletRequest request) {
ModelMaker myVjmm = (ModelMaker) request.getSession().getAttribute("vitroJenaModelMaker"); ModelMaker myVjmm = (ModelMaker) request.getSession().getAttribute("vitroJenaModelMaker");
myVjmm = (myVjmm == null) ? (ModelMaker) getServletContext().getAttribute("vitroJenaModelMaker") : myVjmm; myVjmm = (myVjmm == null) ? (ModelMaker) getServletContext().getAttribute("vitroJenaSDBModelMaker") : myVjmm;
return new VitroJenaSpecialModelMaker(myVjmm, request); return new VitroJenaSpecialModelMaker(myVjmm, request);
} }
@ -783,7 +792,7 @@ public class JenaIngestController extends BaseEditController {
private void doRemoveModel(String modelName, ModelMaker modelMaker) { private void doRemoveModel(String modelName, ModelMaker modelMaker) {
//Try to detach first since it cause problems to remove an attached model. //Try to detach first since it cause problems to remove an attached model.
doDetachModel(modelName, modelMaker); doDetachModel(modelName, modelMaker);
System.out.println("Removing "+modelName+" from webapp"); log.debug("Removing " + modelName + " from webapp");
modelMaker.removeModel(modelName); modelMaker.removeModel(modelName);
} }
@ -861,13 +870,28 @@ public class JenaIngestController extends BaseEditController {
private void doRenameBNodes(VitroRequest vreq, String namespaceEtc, boolean patternBoolean, String pattern, String[] sourceModel) { private void doRenameBNodes(VitroRequest vreq, String namespaceEtc, boolean patternBoolean, String pattern, String[] sourceModel) {
OntModel source = ModelFactory.createOntologyModel(OntModelSpec.OWL_DL_MEM); OntModel source = ModelFactory.createOntologyModel(OntModelSpec.OWL_DL_MEM);
String property = vreq.getParameter("property"); String property = vreq.getParameter("property");
Boolean csv2rdf = (Boolean)getServletContext().getAttribute("csv2rdf");
for (int i=0; i<sourceModel.length; i++) { Boolean csv2rdf = false;
Model m = getModel(sourceModel[i],vreq); try {
source.addSubModel(m); csv2rdf = (Boolean) Boolean.parseBoolean(vreq.getParameter("csv2rdf"));
} catch (Exception e) {
log.error(e, e);
} }
System.out.println(vreq.getParameter("destinationModelName"));
Model destination = getModel(vreq.getParameter("destinationModelName"),vreq); if (csv2rdf) {
source.addSubModel(
(Model) vreq.getSession().getAttribute("csv2rdfResult"));
} else {
for (int i=0; i<sourceModel.length; i++) {
Model m = getModel(sourceModel[i],vreq);
source.addSubModel(m);
}
}
Model destination = (csv2rdf)
? ModelFactory.createDefaultModel()
: getModel(vreq.getParameter("destinationModelName"),vreq);
JenaIngestUtils utils = new JenaIngestUtils(); JenaIngestUtils utils = new JenaIngestUtils();
destination.enterCriticalSection(Lock.WRITE); destination.enterCriticalSection(Lock.WRITE);
try { try {
@ -877,52 +901,10 @@ public class JenaIngestController extends BaseEditController {
else{ else{
destination.add(utils.renameBNodesByPattern(source, namespaceEtc, vreq.getJenaOntModel(), pattern, property)); destination.add(utils.renameBNodesByPattern(source, namespaceEtc, vreq.getJenaOntModel(), pattern, property));
} }
if(csv2rdf!=null){ if (csv2rdf) {
if(csv2rdf && property!=null){ Model ultimateDestination = getModel(vreq.getParameter("destinationModelName"),vreq);
ClosableIterator closeIt = destination.listSubjects(); ultimateDestination.add(destination);
Property prop = ResourceFactory.createProperty(property);
try {
for (Iterator it = closeIt; it.hasNext();) {
Resource res = (Resource) it.next();
if (res.isAnon()) {
ClosableIterator closfIt = destination.listStatements(res,prop,(RDFNode)null);
Statement stmt = null;
try {
if (closfIt.hasNext()) {
stmt = (Statement) closfIt.next();
}
} finally {
closfIt.close();
}
if (stmt != null) {
Resource outRes = stmt.getSubject();
destination.removeAll(outRes,(Property)null,(RDFNode)null);
}
}
}
} finally {
closeIt.close();
}
csv2rdf = false;
getServletContext().setAttribute("csv2rdf", csv2rdf);
}
else if(csv2rdf && property == null){
ClosableIterator closeIt = destination.listSubjects();
try {
for (Iterator it = closeIt; it.hasNext();) {
Resource res = (Resource) it.next();
if (res.isAnon()) {
destination.removeAll(res,(Property)null,(RDFNode)null);
}
}
} finally {
closeIt.close();
}
csv2rdf = false;
getServletContext().setAttribute("csv2rdf", csv2rdf);
}
} }
} finally { } finally {
destination.leaveCriticalSection(); destination.leaveCriticalSection();
} }
@ -965,21 +947,20 @@ public class JenaIngestController extends BaseEditController {
String savedQueryURIStr = vreq.getParameter("savedQuery"); String savedQueryURIStr = vreq.getParameter("savedQuery");
String queryStr; String queryStr;
if (savedQueryURIStr.length()==0) { if (savedQueryURIStr.length()==0) {
System.out.println("Using entered query"); log.debug("Using entered query");
queryStr = sparqlQueryStr; queryStr = sparqlQueryStr;
} else { } else {
Property queryStrProp = ResourceFactory.createProperty(SPARQL_QUERYSTR_PROP); Property queryStrProp = ResourceFactory.createProperty(SPARQL_QUERYSTR_PROP);
jenaOntModel.enterCriticalSection(Lock.READ); jenaOntModel.enterCriticalSection(Lock.READ);
try { try {
Individual ind = jenaOntModel.getIndividual(savedQueryURIStr); Individual ind = jenaOntModel.getIndividual(savedQueryURIStr);
System.out.println("Using query "+savedQueryURIStr); log.debug("Using query "+savedQueryURIStr);
queryStr = ( (Literal) ind.getPropertyValue(queryStrProp)).getLexicalForm(); queryStr = ( (Literal) ind.getPropertyValue(queryStrProp)).getLexicalForm();
queryStr = StringEscapeUtils.unescapeHtml(queryStr); // !!! We need to turn off automatic HTML-escaping for data property editing. queryStr = StringEscapeUtils.unescapeHtml(queryStr); // !!! We need to turn off automatic HTML-escaping for data property editing.
} finally { } finally {
jenaOntModel.leaveCriticalSection(); jenaOntModel.leaveCriticalSection();
} }
} }
//System.out.println(queryStr);
Model tempModel = ModelFactory.createDefaultModel(); Model tempModel = ModelFactory.createDefaultModel();
Query query = QueryFactory.create(queryStr, Syntax.syntaxARQ); Query query = QueryFactory.create(queryStr, Syntax.syntaxARQ);
QueryExecution qexec = QueryExecutionFactory.create(query,source); QueryExecution qexec = QueryExecutionFactory.create(query,source);
@ -1020,7 +1001,7 @@ public class JenaIngestController extends BaseEditController {
} }
dbTypeObj = DatabaseType.fetch(dbType); dbTypeObj = DatabaseType.fetch(dbType);
String driver = loadDriver(dbTypeObj); String driver = loadDriver(dbTypeObj);
System.out.println("Connecting to DB at "+jdbcUrl); log.debug("Connecting to DB at "+jdbcUrl);
StoreDesc storeDesc = new StoreDesc(LayoutType.LayoutTripleNodesHash,dbTypeObj) ; StoreDesc storeDesc = new StoreDesc(LayoutType.LayoutTripleNodesHash,dbTypeObj) ;
ServletContext ctx = vreq.getSession().getServletContext(); ServletContext ctx = vreq.getSession().getServletContext();
BasicDataSource bds = JenaDataSourceSetup.makeBasicDataSource( BasicDataSource bds = JenaDataSourceSetup.makeBasicDataSource(
@ -1124,7 +1105,7 @@ public class JenaIngestController extends BaseEditController {
try { try {
newLex = (String) meth.invoke(processor,args); newLex = (String) meth.invoke(processor,args);
} catch (InvocationTargetException e) { } catch (InvocationTargetException e) {
e.getTargetException().printStackTrace(); throw new RuntimeException(e);
} }
if (!newLex.equals(lex)) { if (!newLex.equals(lex)) {
retractionsModel.add(stmt); retractionsModel.add(stmt);
@ -1156,7 +1137,7 @@ public class JenaIngestController extends BaseEditController {
destination.leaveCriticalSection(); destination.leaveCriticalSection();
} }
} catch (Exception e) { } catch (Exception e) {
e.printStackTrace(); throw new RuntimeException(e);
} }
} }
@ -1181,8 +1162,8 @@ public class JenaIngestController extends BaseEditController {
cleanChars[cleanPos] = chars[i]; cleanChars[cleanPos] = chars[i];
cleanPos++; cleanPos++;
} else { } else {
System.out.println("Bad char in "+lex); log.error("Bad char in " + lex);
System.out.println("Numeric value "+java.lang.Character.getNumericValue(chars[i])); log.error("Numeric value " + java.lang.Character.getNumericValue(chars[i]));
badChar = true; badChar = true;
} }
} }
@ -1206,7 +1187,7 @@ public class JenaIngestController extends BaseEditController {
} }
model.remove(retractionsModel); model.remove(retractionsModel);
model.add(additionsModel); model.add(additionsModel);
System.out.println("Cleaned "+additionsModel.size()+" literals"); log.debug("Cleaned " + additionsModel.size() + " literals");
} finally { } finally {
model.leaveCriticalSection(); model.leaveCriticalSection();
} }
@ -1222,7 +1203,6 @@ public class JenaIngestController extends BaseEditController {
} }
private String doRename(String oldNamespace,String newNamespace,HttpServletResponse response){ private String doRename(String oldNamespace,String newNamespace,HttpServletResponse response){
String userURI = null;
String uri = null; String uri = null;
String result = null; String result = null;
Integer counter = 0; Integer counter = 0;
@ -1233,8 +1213,6 @@ public class JenaIngestController extends BaseEditController {
getServletContext().getAttribute("jenaOntModel"); getServletContext().getAttribute("jenaOntModel");
OntModel infOntModel = (OntModel) OntModel infOntModel = (OntModel)
getServletContext().getAttribute(JenaBaseDao.INFERENCE_ONT_MODEL_ATTRIBUTE_NAME); getServletContext().getAttribute(JenaBaseDao.INFERENCE_ONT_MODEL_ATTRIBUTE_NAME);
WebappDaoFactory wdf =
(WebappDaoFactory)getServletContext().getAttribute("webappDaoFactory");
List<String> urisToChange = new LinkedList<String>(); List<String> urisToChange = new LinkedList<String>();
ontModel.enterCriticalSection(Lock.READ); ontModel.enterCriticalSection(Lock.READ);
try { try {
@ -1272,37 +1250,22 @@ public class JenaIngestController extends BaseEditController {
Matcher matcher = p.matcher(candidateString); Matcher matcher = p.matcher(candidateString);
newURIStr = matcher.replaceFirst(newNamespace); newURIStr = matcher.replaceFirst(newNamespace);
long time3 = System.currentTimeMillis(); long time3 = System.currentTimeMillis();
log.info("time to get new uri: " + log.debug("time to get new uri: " +
Long.toString(time3 - time2)); Long.toString(time3 - time2));
log.info("Renaming "+ oldURIStr + " to " + newURIStr); log.debug("Renaming "+ oldURIStr + " to " + newURIStr);
ResourceUtils.renameResource(res,newURIStr); ResourceUtils.renameResource(res,newURIStr);
ResourceUtils.renameResource(infRes,newURIStr); ResourceUtils.renameResource(infRes,newURIStr);
long time4 = System.currentTimeMillis(); long time4 = System.currentTimeMillis();
log.info(" time to rename : " + Long.toString( time4 - time3)); log.debug(" time to rename : " + Long.toString( time4 - time3));
log.info(" time for one resource: " + log.debug(" time for one resource: " +
Long.toString( time4 -time1)); Long.toString( time4 -time1));
} finally { } finally {
infOntModel.leaveCriticalSection(); infOntModel.leaveCriticalSection();
ontModel.leaveCriticalSection(); ontModel.leaveCriticalSection();
baseOntModel.leaveCriticalSection(); baseOntModel.leaveCriticalSection();
} }
try {
Thread.currentThread().sleep(200);
} catch (InterruptedException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
counter++; counter++;
} }
/*baseOntModel.enterCriticalSection(Lock.WRITE);
ontModel.enterCriticalSection(Lock.WRITE);
try{
baseOntModel.getBaseModel().notifyEvent(new EditEvent(null,true));
baseOntModel.getBaseModel().notifyEvent(new EditEvent(null,false));
} finally {
ontModel.leaveCriticalSection();
baseOntModel.leaveCriticalSection();
}*/
result = counter.toString() + " resources renamed"; result = counter.toString() + " resources renamed";
return result; return result;
} }

14
webapp/src/edu/cornell/mannlib/vitro/webapp/utils/Csv2Rdf.java
View file

@ -60,7 +60,7 @@ public class Csv2Rdf {
return convertToRdf(fis, null, null); return convertToRdf(fis, null, null);
} }
public Model[] convertToRdf(InputStream fis,VitroRequest vreq, Model destination) throws IOException { public Model[] convertToRdf(InputStream fis, WebappDaoFactory wadf, Model destination) throws IOException {
OntModel ontModel = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM); OntModel ontModel = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
OntModel tboxOntModel = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM); OntModel tboxOntModel = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
ontModel.addSubModel(tboxOntModel); ontModel.addSubModel(tboxOntModel);
@ -70,8 +70,8 @@ public class Csv2Rdf {
cReader.setSeperator(separatorChar); cReader.setSeperator(separatorChar);
cReader.setQuoteCharacters(quoteChars); cReader.setQuoteCharacters(quoteChars);
URIGenerator uriGen = (vreq != null && destination != null) URIGenerator uriGen = (wadf != null && destination != null)
? new RandomURIGenerator(vreq, destination) ? new RandomURIGenerator(wadf, destination)
: new SequentialURIGenerator(); : new SequentialURIGenerator();
List<String[]> fileRows = cReader.parse(fis); List<String[]> fileRows = cReader.parse(fis);
@ -115,12 +115,12 @@ public class Csv2Rdf {
private class RandomURIGenerator implements URIGenerator { private class RandomURIGenerator implements URIGenerator {
private VitroRequest vreq; private WebappDaoFactory wadf;
private Model destination; private Model destination;
private Random random = new Random(System.currentTimeMillis()); private Random random = new Random(System.currentTimeMillis());
public RandomURIGenerator(VitroRequest vreq, Model destination) { public RandomURIGenerator(WebappDaoFactory webappDaoFactory, Model destination) {
this.vreq = vreq; this.wadf = webappDaoFactory;
this.destination = destination; this.destination = destination;
} }
@ -132,7 +132,7 @@ public class Csv2Rdf {
if(namespace!=null && !namespace.isEmpty()){ if(namespace!=null && !namespace.isEmpty()){
while( uriIsGood == false && attempts < 30 ){ while( uriIsGood == false && attempts < 30 ){
uri = namespace+individualNameBase+random.nextInt( Math.min(Integer.MAX_VALUE,(int)Math.pow(2,attempts + 13)) ); uri = namespace+individualNameBase+random.nextInt( Math.min(Integer.MAX_VALUE,(int)Math.pow(2,attempts + 13)) );
String errMsg = vreq.getWebappDaoFactory().checkURI(uri); String errMsg = wadf.checkURI(uri);
Resource res = ResourceFactory.createResource(uri); Resource res = ResourceFactory.createResource(uri);
inDestination = destination.contains(res, null); inDestination = destination.contains(res, null);
if( errMsg != null && !inDestination) if( errMsg != null && !inDestination)

110
webapp/src/edu/cornell/mannlib/vitro/webapp/utils/jena/JenaIngestUtils.java
View file

@ -173,7 +173,11 @@ public class JenaIngestUtils {
if (stmt != null) { if (stmt != null) {
Resource outRes = stmt.getSubject(); Resource outRes = stmt.getSubject();
if(stmt.getObject().isLiteral()){ if(stmt.getObject().isLiteral()){
ResourceUtils.renameResource(outRes,namespaceEtc+pattern+"_"+stmt.getObject().toString()); String value = ((Literal) stmt.getObject()).getLexicalForm();
String suffix = (pattern.contains("$$$"))
? pattern.replace("$$$", value)
: pattern + value;
ResourceUtils.renameResource(outRes, namespaceEtc + suffix);
} }
doneSet.add(res.getId().toString()); doneSet.add(res.getId().toString());
} }
@ -191,70 +195,58 @@ public class JenaIngestUtils {
} }
public Map generatePropertyMap(String[] sourceModel, Model model, ModelMaker maker){ public Map<String, LinkedList<String>> generatePropertyMap(List<Model> sourceModels, ModelMaker maker){
Map<String,LinkedList<String>> propertyMap = Collections.synchronizedMap(new HashMap<String, LinkedList<String>>()); Map<String,LinkedList<String>> propertyMap = Collections.synchronizedMap(new HashMap<String, LinkedList<String>>());
Set<String> doneList = new HashSet<String>(); Set<String> doneList = new HashSet<String>();
if(sourceModel!=null && sourceModel.length!=0){ for(Model model : sourceModels) {
for(String modelName : sourceModel){ ClosableIterator cItr = model.listSubjects();
if(modelName != null){ while(cItr.hasNext()){
model = maker.getModel(modelName); Resource res = (Resource) cItr.next();
ClosableIterator cItr = model.listSubjects(); if(res.isAnon() && !doneList.contains(res.getId())){
while(cItr.hasNext()){ doneList.add(res.getId().toString());
Resource res = (Resource) cItr.next(); StmtIterator stmtItr = model.listStatements(res, (Property)null, (RDFNode)null);
if(res.isAnon() && !doneList.contains(res.getId())){ while(stmtItr.hasNext()){
Statement stmt = stmtItr.next();
doneList.add(res.getId().toString()); if(!stmt.getObject().isResource()){
StmtIterator stmtItr = model.listStatements(res, (Property)null, (RDFNode)null); if(propertyMap.containsKey(stmt.getPredicate().getURI())){
while(stmtItr.hasNext()){ LinkedList linkList = propertyMap.get(stmt.getPredicate().getURI());
Statement stmt = stmtItr.next(); linkList.add(stmt.getObject().toString());
if(!stmt.getObject().isResource()){
if(propertyMap.containsKey(stmt.getPredicate().getURI())){
LinkedList linkList = propertyMap.get(stmt.getPredicate().getURI());
linkList.add(stmt.getObject().toString());
}
else{
propertyMap.put(stmt.getPredicate().getURI(), new LinkedList());
LinkedList linkList = propertyMap.get(stmt.getPredicate().getURI());
linkList.add(stmt.getObject().toString());
}
}
} }
} else{
propertyMap.put(stmt.getPredicate().getURI(), new LinkedList());
LinkedList linkList = propertyMap.get(stmt.getPredicate().getURI());
linkList.add(stmt.getObject().toString());
}
}
} }
cItr = model.listObjects();
while(cItr.hasNext()){
RDFNode rdfn = (RDFNode) cItr.next();
if(rdfn.isResource()){
Resource res = (Resource)rdfn;
if(res.isAnon() && !doneList.contains(res.getId())){
doneList.add(res.getId().toString());
StmtIterator stmtItr = model.listStatements(res, (Property)null, (RDFNode)null);
while(stmtItr.hasNext()){
Statement stmt = stmtItr.next();
if(!stmt.getObject().isResource()){
if(propertyMap.containsKey(stmt.getPredicate().getURI())){
LinkedList linkList = propertyMap.get(stmt.getPredicate().getURI());
linkList.add(stmt.getObject().toString());
}
else{
propertyMap.put(stmt.getPredicate().getURI(), new LinkedList());
LinkedList linkList = propertyMap.get(stmt.getPredicate().getURI());
linkList.add(stmt.getObject().toString());
}
}
}
}
}
}
cItr.close();
} }
} }
cItr = model.listObjects();
while(cItr.hasNext()){
RDFNode rdfn = (RDFNode) cItr.next();
if(rdfn.isResource()){
Resource res = (Resource)rdfn;
if(res.isAnon() && !doneList.contains(res.getId())){
doneList.add(res.getId().toString());
StmtIterator stmtItr = model.listStatements(res, (Property)null, (RDFNode)null);
while(stmtItr.hasNext()){
Statement stmt = stmtItr.next();
if(!stmt.getObject().isResource()){
if(propertyMap.containsKey(stmt.getPredicate().getURI())){
LinkedList linkList = propertyMap.get(stmt.getPredicate().getURI());
linkList.add(stmt.getObject().toString());
}
else{
propertyMap.put(stmt.getPredicate().getURI(), new LinkedList());
LinkedList linkList = propertyMap.get(stmt.getPredicate().getURI());
linkList.add(stmt.getObject().toString());
}
}
}
}
}
}
cItr.close();
} }
return propertyMap; return propertyMap;
} }

67
webapp/src/edu/cornell/mannlib/vitro/webapp/utils/jena/SesameSyncUtils.java
View file

@ -6,6 +6,8 @@ import java.io.IOException;
import java.io.OutputStream; import java.io.OutputStream;
import java.io.PipedInputStream; import java.io.PipedInputStream;
import java.io.PipedOutputStream; import java.io.PipedOutputStream;
import java.util.ArrayList;
import java.util.List;
import org.apache.commons.logging.Log; import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory; import org.apache.commons.logging.LogFactory;
@ -18,7 +20,16 @@ import org.openrdf.repository.http.HTTPRepository;
import org.openrdf.rio.RDFFormat; import org.openrdf.rio.RDFFormat;
import org.openrdf.rio.RDFParseException; import org.openrdf.rio.RDFParseException;
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.Model; import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory;
import com.hp.hpl.jena.rdf.model.RDFNode;
import com.hp.hpl.jena.vocabulary.OWL;
public class SesameSyncUtils { public class SesameSyncUtils {
@ -42,11 +53,16 @@ public class SesameSyncUtils {
} else { } else {
myConn.clear(); myConn.clear();
} }
PipedInputStream in = new PipedInputStream(); PipedInputStream in = new PipedInputStream();
PipedOutputStream out = new PipedOutputStream(in); PipedOutputStream out = new PipedOutputStream(in);
try { try {
new Thread(new JenaOutputter(jenaModel, out), "SesameSyncUtilities.JenaOutputter").start();
new Thread(new JenaOutputter(jenaModel, out, myConn), "SesameSyncUtilities.JenaOutputter").start();
if (contextRes != null) { if (contextRes != null) {
myConn.add(in,"http://example.org/base/", RDFFormat.NTRIPLES, contextRes); myConn.add(in,"http://example.org/base/", RDFFormat.NTRIPLES, contextRes);
} else { } else {
@ -69,19 +85,62 @@ public class SesameSyncUtils {
} }
private List<String> getIndividualURIs(Model model) {
List<String> individualURIs = new ArrayList<String>();
String queryStr = "SELECT DISTINCT ?s WHERE { \n" +
" ?s a <" + OWL.Thing.getURI() + "> \n" +
"}";
Query query = QueryFactory.create(queryStr);
QueryExecution qe = QueryExecutionFactory.create(query, model);
try {
ResultSet rs = qe.execSelect();
while (rs.hasNext()) {
QuerySolution qsoln = rs.nextSolution();
String individualURI = qsoln.getResource("s").getURI();
if (individualURI != null) {
individualURIs.add(individualURI);
}
}
} finally {
qe.close();
}
return individualURIs;
}
private class JenaOutputter implements Runnable { private class JenaOutputter implements Runnable {
private Model model; private Model model;
private OutputStream out; private OutputStream out;
private RepositoryConnection rconn;
public JenaOutputter(Model model, OutputStream out) { public JenaOutputter(Model model, OutputStream out, RepositoryConnection rconn) {
this.model = model; this.model = model;
this.out = out; this.out = out;
this.rconn = rconn;
} }
public void run() { public void run() {
Model t = ModelFactory.createDefaultModel();
try { try {
model.write(out, "N-TRIPLE"); List<String> individualURIs = getIndividualURIs(model);
log.info(individualURIs.size() + " individuals to send to Sesame");
int i = 0;
for (String individualURI : individualURIs) {
t.removeAll();
t.add(model.listStatements(
model.getResource(
individualURI), null, (RDFNode) null));
t.write(out, "N-TRIPLE");
i++;
if (i % 100 == 0) {
try {
rconn.commit();
} catch (Throwable e) {
log.error(e, e);
}
log.info(i + " individuals sent to Sesame");
}
}
} finally { } finally {
try { try {
out.flush(); out.flush();

27
webapp/web/jenaIngest/csv2rdf.jsp
View file

@ -17,7 +17,7 @@
ModelMaker maker = (ModelMaker) request.getSession().getAttribute("vitroJenaModelMaker"); ModelMaker maker = (ModelMaker) request.getSession().getAttribute("vitroJenaModelMaker");
if (maker == null) { if (maker == null) {
maker = (ModelMaker) getServletContext().getAttribute("vitroJenaModelMaker"); maker = (ModelMaker) getServletContext().getAttribute("vitroJenaSDBModelMaker");
} }
%> %>
@ -36,15 +36,27 @@
<p>Or upload a file from your computer:</p> <p>Or upload a file from your computer:</p>
<p><input type="file" name="filePath" /></p> <p><input type="file" name="filePath" /></p>
<p/>
<p>This tool will automatically generate a mini ontology to represent the
data in the CSV file. A property will be produced for each column in the
spreadsheet, based on the text in the header for that column.</p><p>In what
namespace should these properties be created?</p>
<input type="text" name="tboxNamespace"/> <input type="text" name="tboxNamespace"/>
<p>Namespace in which to generate class and properties</p> <p>Namespace in which to generate properties</p>
<!-- <!--
<input type="checkbox" name="discardTbox"/> do not add TBox or RBox to result model <input type="checkbox" name="discardTbox"/> do not add TBox or RBox to result model
--> -->
<p>
<p>Each row in the spreadsheet will produce an resource. Each of these
resources will be a member of a class in the namespace selected above.</p>
<p>What should the local name of this class be? This is normally a word or two
in "camel case" starting with an uppercase letter. (For example, if the
spreadsheet represents a list of faculty members, you might enter
"FacultyMember" on the next line.)</p>
<input type="text" name="typeName"/> <input type="text" name="typeName"/>
<p>Class Name for Resources</p> <p>Class Local Name for Resources</p>
<select name="destinationModelName"> <select name="destinationModelName">
<option value="vitro:baseOntModel">webapp assertions</option> <option value="vitro:baseOntModel">webapp assertions</option>
@ -56,7 +68,7 @@
} }
%> <option value="">(none)</option> %> <option value="">(none)</option>
</select> </select>
<p>Destination Model</p> <p>Model in which to save the converted spreadsheet data</p>
<select name="tboxDestinationModelName"> <select name="tboxDestinationModelName">
<option value="vitro:baseOntModel">webapp assertions</option> <option value="vitro:baseOntModel">webapp assertions</option>
@ -68,6 +80,11 @@
} }
%> <option value="">(none)</option> %> <option value="">(none)</option>
</select> </select>
<p>Destination Model for TBox</p> <p>Model in which to save the automatically-generated ontology</p>
<p/>
<p>The data in the CSV file will initially be represented using blank
nodes (RDF resources without URIs). You will choose how to assign
URIs to these resources in the next step.</p>
<input class="submit" type="submit" value="Next Step"/> <input class="submit" type="submit" value="Next Step"/>

28
webapp/web/jenaIngest/csv2rdfSelectUri.jsp
View file

@ -1,5 +1,8 @@
<%-- $This file is distributed under the terms of the license in /doc/license.txt$ --%> <%-- $This file is distributed under the terms of the license in /doc/license.txt$ --%>
<%@ taglib uri="http://java.sun.com/jstl/core" prefix="c"%>
<%@ taglib prefix="vitro" uri="/WEB-INF/tlds/VitroUtils.tld" %>
<%@ page import="com.hp.hpl.jena.ontology.Individual" %> <%@ page import="com.hp.hpl.jena.ontology.Individual" %>
<%@ page import="com.hp.hpl.jena.ontology.OntModel" %> <%@ page import="com.hp.hpl.jena.ontology.OntModel" %>
<%@ page import="com.hp.hpl.jena.rdf.model.ModelMaker" %> <%@ page import="com.hp.hpl.jena.rdf.model.ModelMaker" %>
@ -13,8 +16,7 @@
<%@ page import="java.util.Set" %> <%@ page import="java.util.Set" %>
<%@ page import="java.util.Map.Entry" %> <%@ page import="java.util.Map.Entry" %>
<%@taglib prefix="vitro" uri="/WEB-INF/tlds/VitroUtils.tld" %> <%@ page import="edu.cornell.mannlib.vitro.webapp.auth.requestedAction.usepages.UseAdvancedDataToolsPages" %>
<%@page import="edu.cornell.mannlib.vitro.webapp.auth.requestedAction.usepages.UseAdvancedDataToolsPages" %>
<% request.setAttribute("requestedActions", new UseAdvancedDataToolsPages()); %> <% request.setAttribute("requestedActions", new UseAdvancedDataToolsPages()); %>
<vitro:confirmAuthorization /> <vitro:confirmAuthorization />
@ -22,7 +24,7 @@
ModelMaker maker = (ModelMaker) request.getSession().getAttribute("vitroJenaModelMaker"); ModelMaker maker = (ModelMaker) request.getSession().getAttribute("vitroJenaModelMaker");
if (maker == null) { if (maker == null) {
maker = (ModelMaker) getServletContext().getAttribute("vitroJenaModelMaker"); maker = (ModelMaker) getServletContext().getAttribute("vitroJenaSDBModelMaker");
} }
%> %>
@ -46,16 +48,18 @@ function disableProperties(){
<h3>Select URI prefix</h3> <h3>Select URI prefix</h3>
<p>URIs will be constructed from the following string:</p> <p>URIs will be constructed using the following base string:</p>
<input id="namespace" type="text" style="width:65%;" name="namespaceEtcStr"/> <input id="namespace" type="text" style="width:65%;" name="namespaceEtcStr"/>
<p/> <p/>
<p>You can concatenate above string with random integer OR your own pattern based on <b>values</b> of one of the properties (Properties will be enabled in the dropdown) </p> <p>Each resource will be assigned a URI by taking the above string and
adding either a random integer, or a string based on the value of one of the
the properties of the resource</p>
<input type="radio" value="integer" name="concatenate" checked="checked" onclick="disableProperties()"><b>No</b>, concatenate with random integer</input> <input type="radio" value="integer" name="concatenate" checked="checked" onclick="disableProperties()">Use random integer</input>
<br></br> <br></br>
<input type="radio" value="pattern" name="concatenate" onclick="selectProperties()"><b>Yes</b>, concatenate with my pattern</input> <input type="radio" value="pattern" name="concatenate" onclick="selectProperties()">Use pattern based on values of </input>
<% Map<String,LinkedList<String>> propertyMap = (Map) request.getAttribute("propertyMap"); <% Map<String,LinkedList<String>> propertyMap = (Map) request.getAttribute("propertyMap");
@ -75,12 +79,16 @@ function disableProperties(){
%> %>
</select> </select>
<br></br> <br></br>
<p>Enter your pattern that will prefix property value with an underscore eg. depID_$$$ where depID is your pattern and $$$ is the property value.</p> <p>Enter a pattern using $$$ as the placeholder for the value of the property selected above.</p>
<p>For example, entering dept_$$$ might generate URIs with endings such as dept_Art or dept_Classics.</p>
<input id="pattern" disabled="disabled" type="text" style="width:35%;" name="pattern"/> <input id="pattern" disabled="disabled" type="text" style="width:35%;" name="pattern"/>
<%String modelName = (String) request.getAttribute("destinationModelName"); %> <input type="hidden" name="destinationModelName" value="${destinationModelName}"/>
<input type="hidden" name="csv2rdf" value="${csv2rdf}"/>
<input type="hidden" name="destinationModelName" value="<%=modelName%>"/> <c:forEach var="sourceModelValue" items="${sourceModel}">
<input type="hidden" name="sourceModelName" value="${sourceModelValue}"/>
</c:forEach>
<input class="submit" type="submit" value="Convert CSV"/> <input class="submit" type="submit" value="Convert CSV"/>

2
webapp/web/jenaIngest/executeWorkflow.jsp
View file

@ -17,7 +17,7 @@
ModelMaker maker = (ModelMaker) request.getSession().getAttribute("vitroJenaModelMaker"); ModelMaker maker = (ModelMaker) request.getSession().getAttribute("vitroJenaModelMaker");
if (maker == null) { if (maker == null) {
maker = (ModelMaker) getServletContext().getAttribute("vitroJenaModelMaker"); maker = (ModelMaker) getServletContext().getAttribute("vitroJenaSDBModelMaker");
} }
%> %>

2
webapp/web/jenaIngest/generateTBox.jsp
View file

@ -17,7 +17,7 @@
ModelMaker maker = (ModelMaker) request.getSession().getAttribute("vitroJenaModelMaker"); ModelMaker maker = (ModelMaker) request.getSession().getAttribute("vitroJenaModelMaker");
if (maker == null) { if (maker == null) {
maker = (ModelMaker) getServletContext().getAttribute("vitroJenaModelMaker"); maker = (ModelMaker) getServletContext().getAttribute("vitroJenaSDBModelMaker");
} }
%> %>

4
webapp/web/jenaIngest/mergeResources.jsp
View file

@ -16,7 +16,7 @@
ModelMaker maker = (ModelMaker) request.getSession().getAttribute("vitroJenaModelMaker"); ModelMaker maker = (ModelMaker) request.getSession().getAttribute("vitroJenaModelMaker");
if (maker == null) { if (maker == null) {
maker = (ModelMaker) getServletContext().getAttribute("vitroJenaModelMaker"); maker = (ModelMaker) getServletContext().getAttribute("vitroJenaSDBModelMaker");
} }
%> %>
@ -46,4 +46,4 @@
<input type="checkbox" name="usePrimaryLabelOnly" value="Use Primary Label Only">Retain rdfs:labels only from Primary Resource</input> <input type="checkbox" name="usePrimaryLabelOnly" value="Use Primary Label Only">Retain rdfs:labels only from Primary Resource</input>
<p><input class="submit"type="submit" name="submit" value="Merge resources" /></p> <p><input class="submit"type="submit" name="submit" value="Merge resources" /></p>
</form> </form>

4
webapp/web/jenaIngest/permanentURI.jsp
View file

@ -16,7 +16,7 @@
ModelMaker maker = (ModelMaker) request.getSession().getAttribute("vitroJenaModelMaker"); ModelMaker maker = (ModelMaker) request.getSession().getAttribute("vitroJenaModelMaker");
if (maker == null) { if (maker == null) {
maker = (ModelMaker) getServletContext().getAttribute("vitroJenaModelMaker"); maker = (ModelMaker) getServletContext().getAttribute("vitroJenaSDBModelMaker");
} }
%> %>
@ -63,4 +63,4 @@ Or <%String defaultNamespace = (String)request.getAttribute("defaultNamespace");
</p> </p>
<p><input class="submit" type="submit" name="submit" value="Generate URIs" /></p> <p><input class="submit" type="submit" name="submit" value="Generate URIs" /></p>
</form> </form>

2
webapp/web/jenaIngest/processStrings.jsp
View file

@ -17,7 +17,7 @@
ModelMaker maker = (ModelMaker) request.getSession().getAttribute("vitroJenaModelMaker"); ModelMaker maker = (ModelMaker) request.getSession().getAttribute("vitroJenaModelMaker");
if (maker == null) { if (maker == null) {
maker = (ModelMaker) getServletContext().getAttribute("vitroJenaModelMaker"); maker = (ModelMaker) getServletContext().getAttribute("vitroJenaSDBModelMaker");
} }
%> %>

2
webapp/web/jenaIngest/renameBNodes.jsp
View file

@ -17,7 +17,7 @@
ModelMaker maker = (ModelMaker) request.getSession().getAttribute("vitroJenaModelMaker"); ModelMaker maker = (ModelMaker) request.getSession().getAttribute("vitroJenaModelMaker");
if (maker == null) { if (maker == null) {
maker = (ModelMaker) getServletContext().getAttribute("vitroJenaModelMaker"); maker = (ModelMaker) getServletContext().getAttribute("vitroJenaSDBModelMaker");
} }
%> %>

38
webapp/web/jenaIngest/renameBNodesURISelect.jsp
View file

@ -12,6 +12,7 @@
<%@ page import="java.util.HashMap" %> <%@ page import="java.util.HashMap" %>
<%@ page import="java.util.Set" %> <%@ page import="java.util.Set" %>
<%@ page import="java.util.Map.Entry" %> <%@ page import="java.util.Map.Entry" %>
<%@ taglib uri="http://java.sun.com/jstl/core" prefix="c"%>
<%@taglib prefix="vitro" uri="/WEB-INF/tlds/VitroUtils.tld" %> <%@taglib prefix="vitro" uri="/WEB-INF/tlds/VitroUtils.tld" %>
<%@page import="edu.cornell.mannlib.vitro.webapp.auth.requestedAction.usepages.UseAdvancedDataToolsPages" %> <%@page import="edu.cornell.mannlib.vitro.webapp.auth.requestedAction.usepages.UseAdvancedDataToolsPages" %>
@ -22,12 +23,11 @@
ModelMaker maker = (ModelMaker) request.getSession().getAttribute("vitroJenaModelMaker"); ModelMaker maker = (ModelMaker) request.getSession().getAttribute("vitroJenaModelMaker");
if (maker == null) { if (maker == null) {
maker = (ModelMaker) getServletContext().getAttribute("vitroJenaModelMaker"); maker = (ModelMaker) getServletContext().getAttribute("vitroJenaSDBModelMaker");
} }
%> %>
<script type="text/javascript" src="js/jquery.js"></script> <script type="text/javascript" src="js/jquery.js"></script>
<script type="text/javascript" src="js/jenaIngest/renameNode.js"></script>
<script type="text/javascript"> <script type="text/javascript">
function selectProperties(){ function selectProperties(){
document.getElementById("properties").disabled = false; document.getElementById("properties").disabled = false;
@ -46,16 +46,24 @@ function disableProperties(){
<h3>Select URI prefix</h3> <h3>Select URI prefix</h3>
<p>URIs will be constructed from the following string:</p> <c:if test="${!empty errorMsg}">
<p class="notice">${errorMsg}</p>
</c:if>
<p>URIs will be constructed using the following base string:</p>
<input id="namespace" type="text" style="width:65%;" name="namespaceEtcStr"/> <input id="namespace" type="text" style="width:65%;" name="namespaceEtcStr"/>
<p/> <p/>
<c:choose>
<c:when test="${enablePropertyPatternURIs}">
<p>Each resource will be assigned a URI by taking the above string and
adding either a random integer, or a string based on the value of one of the
the properties of the resource</p>
<p>You can concatenate above string with random integer OR your own pattern based on <b>values</b> of one of the properties (Properties will be enabled in the dropdown) </p> <input type="radio" value="integer" name="concatenate" checked="checked" onclick="disableProperties()">Use random integer</input>
<input type="radio" value="integer" name="concatenate" checked="checked" onclick="disableProperties()"><b>No</b>, concatenate with random integer</input>
<br></br> <br></br>
<input type="radio" value="pattern" name="concatenate" onclick="selectProperties()"><b>Yes</b>, concatenate with my pattern</input> <input type="radio" value="pattern" name="concatenate" onclick="selectProperties()">Use pattern based on values of </input>
<% Map<String,LinkedList<String>> propertyMap = (Map) request.getAttribute("propertyMap"); <% Map<String,LinkedList<String>> propertyMap = (Map) request.getAttribute("propertyMap");
@ -75,9 +83,21 @@ function disableProperties(){
%> %>
</select> </select>
<br></br> <br></br>
<p>Enter your pattern that will prefix property value with an underscore eg. depID_$$$ where depID is your pattern and $$$ is the property value.</p> <p>Enter a pattern using $$$ as the placeholder for the value of the property selected above.</p>
<p>For example, entering dept_$$$ might generate URIs with endings such as dept_Art or dept_Classics.</p>
<input id="pattern" disabled="disabled" type="text" style="width:35%;" name="pattern"/> <input id="pattern" disabled="disabled" type="text" style="width:35%;" name="pattern"/>
</c:when>
<c:otherwise>
<p>Each resource will be assigned a URI by taking the above string and
adding a random integer.</p>
<input type="hidden" value="integer" name="concatenate"/>
</c:otherwise>
</c:choose>
<c:forEach var="sourceModelValue" items="${sourceModel}">
<input type="hidden" name="sourceModelName" value="${sourceModelValue}"/>
</c:forEach>
<h3>Select Destination Model</h3> <h3>Select Destination Model</h3>

9
webapp/web/jenaIngest/renameResource.jsp
View file

@ -13,7 +13,6 @@
<vitro:confirmAuthorization /> <vitro:confirmAuthorization />
<script type="text/javascript" src="js/jquery.js"></script> <script type="text/javascript" src="js/jquery.js"></script>
<script type="text/javascript" src="js/jenaIngest/ingestUtils.js"></script>
<h2><a class="ingestMenu" href="ingest">Ingest Menu</a> > Change Namespace of Resources</h2> <h2><a class="ingestMenu" href="ingest">Ingest Menu</a> > Change Namespace of Resources</h2>
@ -25,9 +24,13 @@ they will be updated to this format.</p>
<p>This tool operates on the main web application model only, not on any <p>This tool operates on the main web application model only, not on any
of the additional Jena models.</p> of the additional Jena models.</p>
<c:if test="${!empty errorMsg}">
<p class="notice">${errorMsg}</p>
</c:if>
<form id="takeuri" action="ingest" method="get"> <form id="takeuri" action="ingest" method="get">
<input type="hidden" name="action" value="renameResource"/> <input type="hidden" name="action" value="renameResource"/>
<p>Old namespace: <input id="uri1" type="text" size="52" name="uri1"/></p> <p>Old namespace: <input id="uri1" type="text" size="52" name="oldNamespace" value="${oldNamespace}" /></p>
<p>New namespace: <input id="uri2" type="text" size="52" name="uri2"/></p> <p>New namespace: <input id="uri2" type="text" size="52" name="newNamespace" value="${newNamespace}" /></p>
<p><input id="submit" type="submit" name="submit" value="Change namespace" /></p> <p><input id="submit" type="submit" name="submit" value="Change namespace" /></p>
</form> </form>

2
webapp/web/jenaIngest/smushSingleModel.jsp
View file

@ -17,7 +17,7 @@
ModelMaker maker = (ModelMaker) request.getSession().getAttribute("vitroJenaModelMaker"); ModelMaker maker = (ModelMaker) request.getSession().getAttribute("vitroJenaModelMaker");
if (maker == null) { if (maker == null) {
maker = (ModelMaker) getServletContext().getAttribute("vitroJenaModelMaker"); maker = (ModelMaker) getServletContext().getAttribute("vitroJenaSDBModelMaker");
} }
%> %>

4
webapp/web/jenaIngest/sparqlConstruct.jsp
View file

@ -19,7 +19,7 @@
ModelMaker maker = (ModelMaker) request.getSession().getAttribute("vitroJenaModelMaker"); ModelMaker maker = (ModelMaker) request.getSession().getAttribute("vitroJenaModelMaker");
if (maker == null) { if (maker == null) {
maker = (ModelMaker) getServletContext().getAttribute("vitroJenaModelMaker"); maker = (ModelMaker) getServletContext().getAttribute("vitroJenaSDBModelMaker");
} }
%> %>
@ -188,4 +188,4 @@ PREFIX <%=prefixText%>: <<%=urlText%>><%}}%>
<p><input type="checkbox" name="reasoning" value="pellet" /> <p><input type="checkbox" name="reasoning" value="pellet" />
include Pellet OWL-DL reasoning</p> include Pellet OWL-DL reasoning</p>
</c:otherwise> </c:otherwise>
</c:choose> <input id="submit" type="submit" value="Execute CONSTRUCT" /> </c:choose> <input id="submit" type="submit" value="Execute CONSTRUCT" />

2
webapp/web/jenaIngest/splitPropertyValues.jsp
View file

@ -17,7 +17,7 @@
ModelMaker maker = (ModelMaker) request.getSession().getAttribute("vitroJenaModelMaker"); ModelMaker maker = (ModelMaker) request.getSession().getAttribute("vitroJenaModelMaker");
if (maker == null) { if (maker == null) {
maker = (ModelMaker) getServletContext().getAttribute("vitroJenaModelMaker"); maker = (ModelMaker) getServletContext().getAttribute("vitroJenaSDBModelMaker");
} }
%> %>

2
webapp/web/jenaIngest/subtractModels.jsp
View file

@ -17,7 +17,7 @@
ModelMaker maker = (ModelMaker) request.getSession().getAttribute("vitroJenaModelMaker"); ModelMaker maker = (ModelMaker) request.getSession().getAttribute("vitroJenaModelMaker");
if (maker == null) { if (maker == null) {
maker = (ModelMaker) getServletContext().getAttribute("vitroJenaModelMaker"); maker = (ModelMaker) getServletContext().getAttribute("vitroJenaSDBModelMaker");
} }
%> %>

2
webapp/web/jenaIngest/xmlFileUpload.jsp
View file

@ -14,7 +14,7 @@
ModelMaker maker = (ModelMaker) request.getSession().getAttribute("vitroJenaModelMaker"); ModelMaker maker = (ModelMaker) request.getSession().getAttribute("vitroJenaModelMaker");
if (maker == null) { if (maker == null) {
maker = (ModelMaker) getServletContext().getAttribute("vitroJenaModelMaker"); maker = (ModelMaker) getServletContext().getAttribute("vitroJenaSDBModelMaker");
} }
%> %>

28
webapp/web/js/jenaIngest/ingestUtils.js
View file

@ -1,28 +0,0 @@
/* $This file is distributed under the terms of the license in /doc/license.txt$ */
$(document).ready(function(){
$('#takeuri').submit(function() {
if ($('#uri1').val() == '') {
alert('Please enter a value for Individual URI 1.');
return false;
}
if ($('#uri2').val() == '') {
alert('Please enter a value for Individual URI 2.');
return false;
}
if (!$('#uri1').val().match(/\/$/)) {
$('#uri1').val($('#uri1').val() + "/");
}
if (!$('#uri2').val().match(/\/$/)) {
$('#uri2').val($('#uri2').val() + "/");
}
if ($('#uri1').val() == $('#uri2').val()){
alert('Primary and duplicate URI cannot be same.');
return false;
}
});
});

14
webapp/web/js/jenaIngest/renameNode.js
View file

@ -1,14 +0,0 @@
/* $This file is distributed under the terms of the license in /doc/license.txt$ */
$(document).ready(function(){
$('#takeuri').submit(function() {
if ($('#namespace').val() == '') {
alert('Please enter URI prefix.');
return false;
}
});
});