From bb6a256be39dcba8db3311706832d9d9fcbf7470 Mon Sep 17 00:00:00 2001 From: Brian Caruso Date: Thu, 3 Oct 2013 16:14:54 -0400 Subject: [PATCH 1/6] Improving error messages from ContextNodeFields and PagedSearchController --- .../vitro/webapp/search/controller/PagedSearchController.java | 2 +- .../search/solr/documentBuilding/ContextNodeFields.java | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/webapp/src/edu/cornell/mannlib/vitro/webapp/search/controller/PagedSearchController.java b/webapp/src/edu/cornell/mannlib/vitro/webapp/search/controller/PagedSearchController.java index 3e27899e3..8ed988e25 100644 --- a/webapp/src/edu/cornell/mannlib/vitro/webapp/search/controller/PagedSearchController.java +++ b/webapp/src/edu/cornell/mannlib/vitro/webapp/search/controller/PagedSearchController.java @@ -228,7 +228,7 @@ public class PagedSearchController extends FreemarkerHttpServlet { Map body = new HashMap(); String classGroupParam = vreq.getParameter(PARAM_CLASSGROUP); - log.debug("Query text is \""+ classGroupParam + "\""); + log.debug("ClassGroupParam is \""+ classGroupParam + "\""); boolean classGroupFilterRequested = false; if (!StringUtils.isEmpty(classGroupParam)) { VClassGroup grp = grpDao.getGroupByURI(classGroupParam); diff --git a/webapp/src/edu/cornell/mannlib/vitro/webapp/search/solr/documentBuilding/ContextNodeFields.java b/webapp/src/edu/cornell/mannlib/vitro/webapp/search/solr/documentBuilding/ContextNodeFields.java index b9d71beb6..1ae12b010 100644 --- a/webapp/src/edu/cornell/mannlib/vitro/webapp/search/solr/documentBuilding/ContextNodeFields.java +++ b/webapp/src/edu/cornell/mannlib/vitro/webapp/search/solr/documentBuilding/ContextNodeFields.java @@ -99,8 +99,8 @@ public class ContextNodeFields implements DocumentModifier{ } }catch(Throwable t){ - if( ! shutdown ) - log.error(t,t); + if( ! shutdown ) + log.error("problem while running query '" + subInUriQuery + "'",t); } if(log.isDebugEnabled()){ From a4d007e05c0e344c894d80a08096288ad6f59476 Mon Sep 17 00:00:00 2001 From: j2blake Date: Fri, 4 Oct 2013 10:56:06 -0400 Subject: [PATCH 2/6] VIVO-281 Fix a bug in the display filter. --- .../webapp/auth/permissions/DisplayByRolePermission.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/webapp/src/edu/cornell/mannlib/vitro/webapp/auth/permissions/DisplayByRolePermission.java b/webapp/src/edu/cornell/mannlib/vitro/webapp/auth/permissions/DisplayByRolePermission.java index 19b9e141f..74917860b 100644 --- a/webapp/src/edu/cornell/mannlib/vitro/webapp/auth/permissions/DisplayByRolePermission.java +++ b/webapp/src/edu/cornell/mannlib/vitro/webapp/auth/permissions/DisplayByRolePermission.java @@ -113,10 +113,10 @@ public class DisplayByRolePermission extends Permission { private boolean isAuthorized(DisplayObjectPropertyStatement action) { ObjectPropertyStatement stmt = action.getObjectPropertyStatement(); String subjectUri = stmt.getSubjectURI(); - Property predicate = stmt.getProperty(); + String predicateUri = stmt.getPropertyURI(); String objectUri = stmt.getObjectURI(); return canDisplayResource(subjectUri) - && canDisplayPredicate(predicate) + && canDisplayPredicate(new Property(predicateUri)) && canDisplayResource(objectUri); } From aad1f023cc21017e8caaa6c46f124d8f5d3a4c69 Mon Sep 17 00:00:00 2001 From: brianjlowe Date: Fri, 4 Oct 2013 14:27:32 -0400 Subject: [PATCH 3/6] disabling knowledge base migration in plain vitro --- webapp/web/WEB-INF/resources/startup_listeners.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/webapp/web/WEB-INF/resources/startup_listeners.txt b/webapp/web/WEB-INF/resources/startup_listeners.txt index 657915abc..9129ea5ca 100644 --- a/webapp/web/WEB-INF/resources/startup_listeners.txt +++ b/webapp/web/WEB-INF/resources/startup_listeners.txt @@ -36,7 +36,7 @@ edu.cornell.mannlib.vitro.webapp.servlet.setup.FileGraphSetup edu.cornell.mannlib.vitro.webapp.servlet.setup.SimpleReasonerSetup -edu.cornell.mannlib.vitro.webapp.servlet.setup.UpdateKnowledgeBase +#edu.cornell.mannlib.vitro.webapp.servlet.setup.UpdateKnowledgeBase # Must run after JenaDataSourceSetup edu.cornell.mannlib.vitro.webapp.servlet.setup.ThemeInfoSetup From 3a5fa4c5515d91850ff0595de860331bdb2a4a0d Mon Sep 17 00:00:00 2001 From: brianjlowe Date: Fri, 4 Oct 2013 14:27:52 -0400 Subject: [PATCH 4/6] various minor improvements --- .../webapp/rdfservice/impl/jena/RDFServiceJena.java | 3 ++- .../mannlib/vitro/webapp/reasoner/ABoxRecomputer.java | 3 ++- .../utils/ApplicationConfigurationOntologyUtils.java | 10 ++++++++-- 3 files changed, 12 insertions(+), 4 deletions(-) diff --git a/webapp/src/edu/cornell/mannlib/vitro/webapp/rdfservice/impl/jena/RDFServiceJena.java b/webapp/src/edu/cornell/mannlib/vitro/webapp/rdfservice/impl/jena/RDFServiceJena.java index b851fab9b..f2eae2554 100644 --- a/webapp/src/edu/cornell/mannlib/vitro/webapp/rdfservice/impl/jena/RDFServiceJena.java +++ b/webapp/src/edu/cornell/mannlib/vitro/webapp/rdfservice/impl/jena/RDFServiceJena.java @@ -226,7 +226,8 @@ public abstract class RDFServiceJena extends RDFServiceImpl implements RDFServic } } if (subjQueue.isEmpty()) { - throw new RuntimeException("No named subject in statement patterns"); + log.warn("No named subject in statement patterns"); + return stmts; } while(remaining.size() > 0) { if(subjQueue.isEmpty()) { diff --git a/webapp/src/edu/cornell/mannlib/vitro/webapp/reasoner/ABoxRecomputer.java b/webapp/src/edu/cornell/mannlib/vitro/webapp/reasoner/ABoxRecomputer.java index 78244216b..0aa537aaa 100644 --- a/webapp/src/edu/cornell/mannlib/vitro/webapp/reasoner/ABoxRecomputer.java +++ b/webapp/src/edu/cornell/mannlib/vitro/webapp/reasoner/ABoxRecomputer.java @@ -295,7 +295,8 @@ public class ABoxRecomputer { */ protected Collection getAllIndividualURIs() { - String queryString = "select ?s where {?s a ?type}"; + String queryString = "SELECT DISTINCT ?s WHERE { GRAPH ?g { ?s a ?type } " + + " FILTER (!bound(?g) || !regex(str(?g),\"tbox\")) } ORDER BY ?s"; return getIndividualURIs(queryString); } diff --git a/webapp/src/edu/cornell/mannlib/vitro/webapp/utils/ApplicationConfigurationOntologyUtils.java b/webapp/src/edu/cornell/mannlib/vitro/webapp/utils/ApplicationConfigurationOntologyUtils.java index ee25e2c07..24341a0f4 100644 --- a/webapp/src/edu/cornell/mannlib/vitro/webapp/utils/ApplicationConfigurationOntologyUtils.java +++ b/webapp/src/edu/cornell/mannlib/vitro/webapp/utils/ApplicationConfigurationOntologyUtils.java @@ -82,8 +82,14 @@ public class ApplicationConfigurationOntologyUtils { String domainURI = (domainRes != null) ? domainRes.getURI() : null; String rangeURI = qsoln.getResource("range").getURI(); if (appropriateDomain(domainRes, subject, tboxModel)) { - additionalProps.add(opDao.getObjectPropertyByURIs( - opURI, domainURI, rangeURI)); + ObjectProperty faux = opDao.getObjectPropertyByURIs( + opURI, domainURI, rangeURI); + if (faux != null) { + additionalProps.add(faux); + } else { + log.error("Could not retrieve " + opURI + " qualified by " + + " domain " + domainURI + " and range " + rangeURI); + } } } } finally { From d546a5ace3e777253e6d6239fb87ac4bae323d6f Mon Sep 17 00:00:00 2001 From: brianjlowe Date: Fri, 4 Oct 2013 15:02:46 -0400 Subject: [PATCH 5/6] VIVO-323 fixes SQLException adding class groups and property groups --- .../webapp/controller/edit/ClassgroupRetryController.java | 4 +++- .../webapp/controller/edit/PropertyGroupRetryController.java | 4 +++- 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/webapp/src/edu/cornell/mannlib/vitro/webapp/controller/edit/ClassgroupRetryController.java b/webapp/src/edu/cornell/mannlib/vitro/webapp/controller/edit/ClassgroupRetryController.java index 236c2c38f..41089aaa8 100644 --- a/webapp/src/edu/cornell/mannlib/vitro/webapp/controller/edit/ClassgroupRetryController.java +++ b/webapp/src/edu/cornell/mannlib/vitro/webapp/controller/edit/ClassgroupRetryController.java @@ -25,6 +25,7 @@ import edu.cornell.mannlib.vitro.webapp.auth.permissions.SimplePermission; import edu.cornell.mannlib.vitro.webapp.beans.VClassGroup; import edu.cornell.mannlib.vitro.webapp.controller.Controllers; import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest; +import edu.cornell.mannlib.vitro.webapp.dao.ModelAccess; import edu.cornell.mannlib.vitro.webapp.dao.VClassGroupDao; @@ -51,7 +52,8 @@ public class ClassgroupRetryController extends BaseEditController { action = epo.getAction(); } - VClassGroupDao cgDao = request.getUnfilteredWebappDaoFactory().getVClassGroupDao(); + VClassGroupDao cgDao = ModelAccess.on( + getServletContext()).getWebappDaoFactory().getVClassGroupDao(); epo.setDataAccessObject(cgDao); diff --git a/webapp/src/edu/cornell/mannlib/vitro/webapp/controller/edit/PropertyGroupRetryController.java b/webapp/src/edu/cornell/mannlib/vitro/webapp/controller/edit/PropertyGroupRetryController.java index 0eeb5dc28..e3b4b0b2c 100644 --- a/webapp/src/edu/cornell/mannlib/vitro/webapp/controller/edit/PropertyGroupRetryController.java +++ b/webapp/src/edu/cornell/mannlib/vitro/webapp/controller/edit/PropertyGroupRetryController.java @@ -25,6 +25,7 @@ import edu.cornell.mannlib.vitro.webapp.auth.permissions.SimplePermission; import edu.cornell.mannlib.vitro.webapp.beans.PropertyGroup; import edu.cornell.mannlib.vitro.webapp.controller.Controllers; import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest; +import edu.cornell.mannlib.vitro.webapp.dao.ModelAccess; import edu.cornell.mannlib.vitro.webapp.dao.PropertyGroupDao; public class PropertyGroupRetryController extends BaseEditController { @@ -50,7 +51,8 @@ public class PropertyGroupRetryController extends BaseEditController { action = epo.getAction(); } - PropertyGroupDao pgDao = request.getUnfilteredWebappDaoFactory().getPropertyGroupDao(); + PropertyGroupDao pgDao = ModelAccess.on( + getServletContext()).getWebappDaoFactory().getPropertyGroupDao(); epo.setDataAccessObject(pgDao); From d6094eeb5010cedc74502c70951c43475961e6ec Mon Sep 17 00:00:00 2001 From: j2blake Date: Fri, 4 Oct 2013 15:37:17 -0400 Subject: [PATCH 6/6] VIVO-295 Added a metadata section to LOD results. Includes date and rights, among other things. While we're at it, support LOD requests with /n123/n123.jsonld --- .../individual/IndividualRdfAssembler.java | 78 +++++++++++++++++++ .../individual/IndividualRequestAnalyzer.java | 9 ++- 2 files changed, 85 insertions(+), 2 deletions(-) diff --git a/webapp/src/edu/cornell/mannlib/vitro/webapp/controller/individual/IndividualRdfAssembler.java b/webapp/src/edu/cornell/mannlib/vitro/webapp/controller/individual/IndividualRdfAssembler.java index 50d4d40c2..90e79cde7 100644 --- a/webapp/src/edu/cornell/mannlib/vitro/webapp/controller/individual/IndividualRdfAssembler.java +++ b/webapp/src/edu/cornell/mannlib/vitro/webapp/controller/individual/IndividualRdfAssembler.java @@ -2,6 +2,7 @@ package edu.cornell.mannlib.vitro.webapp.controller.individual; +import java.util.Date; import java.util.HashSet; import java.util.Set; @@ -11,10 +12,13 @@ import org.apache.commons.lang.StringUtils; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; +import com.hp.hpl.jena.datatypes.xsd.XSDDatatype; import com.hp.hpl.jena.ontology.OntModel; import com.hp.hpl.jena.ontology.OntModelSpec; +import com.hp.hpl.jena.rdf.model.Literal; import com.hp.hpl.jena.rdf.model.Model; import com.hp.hpl.jena.rdf.model.ModelFactory; +import com.hp.hpl.jena.rdf.model.NodeIterator; import com.hp.hpl.jena.rdf.model.RDFNode; import com.hp.hpl.jena.rdf.model.Resource; import com.hp.hpl.jena.rdf.model.Statement; @@ -33,6 +37,7 @@ import edu.cornell.mannlib.vitro.webapp.beans.ObjectPropertyStatementImpl; import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest; import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.RdfResponseValues; import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.ResponseValues; +import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary; import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory; import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService; import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException; @@ -71,6 +76,17 @@ public class IndividualRdfAssembler { private static final String RICH_EXPORT_ROOT = "/WEB-INF/rich-export/"; private static final String INCLUDE_ALL = "all"; + private static final String NS_DC = "http://purl.org/dc/elements/1.1/"; + private static final String URI_RIGHTS = NS_DC + "rights"; + private static final String URI_DATE = NS_DC + "date"; + private static final String URI_PUBLISHER = NS_DC + "publisher"; + + private static final String NS_FOAF = "http://xmlns.com/foaf/0.1/"; + private static final String URI_DOCUMENT = NS_FOAF + "Document"; + + private static final String URI_LABEL = VitroVocabulary.RDFS + "label"; + private static final String URI_TYPE = VitroVocabulary.RDF_TYPE; + private final VitroRequest vreq; private final ServletContext ctx; private final String individualUri; @@ -118,6 +134,7 @@ public class IndividualRdfAssembler { o.add(getStatementsAboutEntity()); o.add(getLabelsAndTypesOfRelatedObjects()); filterByPolicy(o); + addDocumentMetadata(o); return o; } @@ -268,4 +285,65 @@ public class IndividualRdfAssembler { return richExportModel; } + /** + * Add info about the RDF itself. + * + * It will look something like this: + * + * 
+	 * 
+	 *     rdfs:label "RDF description of Baker, Able - http://vivo.cornell.edu/individual/n6628" ;
+	 *     rdf:type foaf:Document ;
+	 *     dc:publisher  ;
+	 *     dc:date "2007-07-13"^^xsd:date ;
+	 *     dc:rights  .
+	 *
+ */ + private void addDocumentMetadata(OntModel o) { + String baseUrl = figureBaseUrl(); + String documentUri = createDocumentUri(); + String label = createDocumentLabel(o); + Literal dateLiteral = createDateLiteral(o); + + Resource md = o.getResource(documentUri); + + o.add(md, o.getProperty(URI_LABEL), label); + o.add(md, o.getProperty(URI_TYPE), o.getResource(URI_DOCUMENT)); + o.add(md, o.getProperty(URI_PUBLISHER), o.getResource(baseUrl)); + o.add(md, o.getProperty(URI_DATE), dateLiteral); + o.add(md, o.getProperty(URI_RIGHTS), + o.getResource(baseUrl + "/termsOfUse")); + } + + private String figureBaseUrl() { + int cutHere = individualUri.indexOf("/individual"); + return (cutHere > 0) ? individualUri.substring(0, cutHere) + : individualUri; + } + + private String createDocumentUri() { + return vreq.getRequestURL().toString(); + } + + private String createDocumentLabel(OntModel o) { + String label = null; + NodeIterator nodes = o.listObjectsOfProperty( + o.getResource(individualUri), o.getProperty(URI_LABEL)); + while (nodes.hasNext()) { + RDFNode n = nodes.nextNode(); + if (n.isLiteral()) { + label = n.asLiteral().getString(); + } + } + if (label == null) { + return "RDF description of " + individualUri; + } else { + return "RDF description of " + label + " - " + individualUri; + } + } + + private Literal createDateLiteral(OntModel o) { + return o.createTypedLiteral(new Date(), XSDDatatype.XSDdate); + } + } diff --git a/webapp/src/edu/cornell/mannlib/vitro/webapp/controller/individual/IndividualRequestAnalyzer.java b/webapp/src/edu/cornell/mannlib/vitro/webapp/controller/individual/IndividualRequestAnalyzer.java index c0e8561d9..24c69d358 100644 --- a/webapp/src/edu/cornell/mannlib/vitro/webapp/controller/individual/IndividualRequestAnalyzer.java +++ b/webapp/src/edu/cornell/mannlib/vitro/webapp/controller/individual/IndividualRequestAnalyzer.java @@ -28,7 +28,7 @@ public class IndividualRequestAnalyzer { .getLog(IndividualRequestAnalyzer.class); - private static Pattern RDF_REQUEST = Pattern.compile("^/individual/([^/]+)/\\1\\.(rdf|n3|ttl)$"); + private static Pattern RDF_REQUEST = Pattern.compile("^/individual/([^/]+)/\\1\\.(rdf|n3|ttl|jsonld)$"); private static Pattern HTML_REQUEST = Pattern.compile("^/display/([^/]+)$"); private static Pattern LINKED_DATA_URL = Pattern.compile("^/individual/([^/]+)$"); @@ -145,7 +145,7 @@ public class IndividualRequestAnalyzer { IndividualController.ACCEPTED_CONTENT_TYPES); if (RDFXML_MIMETYPE.equals(ctStr) || N3_MIMETYPE.equals(ctStr) - || TTL_MIMETYPE.equals(ctStr)) { + || TTL_MIMETYPE.equals(ctStr) || JSON_MIMETYPE.equals(ctStr)) { return new ContentType(ctStr); } } catch (Throwable th) { @@ -167,6 +167,7 @@ public class IndividualRequestAnalyzer { * /individual/localname/localname.rdf * /individual/localname/localname.n3 * /individual/localname/localname.ttl + * /individual/localname/localname.jsonld * * * @return null on failure. @@ -257,6 +258,7 @@ public class IndividualRequestAnalyzer { * http://vivo.cornell.edu/individual/n23/n23.rdf * http://vivo.cornell.edu/individual/n23/n23.n3 * http://vivo.cornell.edu/individual/n23/n23.ttl + * http://vivo.cornell.edu/individual/n23/n23.jsonld */ Matcher rdfMatch = RDF_REQUEST.matcher(url); if (rdfMatch.matches() && rdfMatch.groupCount() == 2) { @@ -270,6 +272,9 @@ public class IndividualRequestAnalyzer { if ("ttl".equals(rdfType)) { return ContentType.TURTLE; } + if ("jsonld".equals(rdfType)) { + return ContentType.JSON; + } } return null;