Update sprint-i18n with master branch (#166)

* Make data property richtext editor option selectable from UI * [VIVO-1755] - Better error handling when reasoner disabled (#137) * Better error handling when reasoner disabled * Change reasoner error log message to debug * Extend reasoner status error handling * Improve reasoner error log message and extend to JenaAdminActions * Bump up log level for admin action to 'warn' and edit admin panel error message * Change Model writer lang from "N3-PP" to "N3" (#149) Resolves: https://jira.lyrasis.org/browse/VIVO-1761 Co-authored-by: Andrew Woods <awoods@duraspace.org> * [VIVO-1851] - Add 'remove' option to named graph management page (#162) * Add 'remove' option to named graph management page Resolves: https://jira.lyrasis.org/browse/VIVO-1851 * [VIVO-1872] - Add download option to SPARQL Query page (#164) * Add download option to SPARQL Query page * Set SPARQL query results content type even if downloading * Address pull request comments Co-authored-by: gneissone <mbgross@wustl.edu> Co-authored-by: Ralph O'Flinn <roflinn@users.noreply.github.com> Co-authored-by: Andrew Woods <awoods@duraspace.org>
vivo-project · Jun 19, 2020 · 52f2d53 · 52f2d53
1 parent 9c0050c
commit 52f2d53
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Showing 16 changed files with 214 additions and 62 deletions.
diff --git a/...rc/main/java/edu/cornell/mannlib/vitro/webapp/controller/admin/SparqlQueryController.java b/...rc/main/java/edu/cornell/mannlib/vitro/webapp/controller/admin/SparqlQueryController.java
@@ -40,6 +40,8 @@
 import edu.cornell.mannlib.vitro.webapp.utils.http.AcceptHeaderParsingException;
 import edu.cornell.mannlib.vitro.webapp.utils.http.NotAcceptableException;
 import edu.cornell.mannlib.vitro.webapp.utils.sparql.SparqlQueryUtils;
+import edu.cornell.mannlib.vitro.webapp.controller.api.sparqlquery.RdfResultMediaType;
+import edu.cornell.mannlib.vitro.webapp.controller.api.sparqlquery.ResultSetMediaType;
 
 /**
  * Present the SPARQL Query form, and execute the queries.
@@ -110,11 +112,20 @@ private void respondToQuery(HttpServletRequest req, HttpServletResponse resp)
 				.getRDFService();
 
 		String queryString = req.getParameter("query");
+		boolean download = Boolean.parseBoolean(req.getParameter("download"));
+		Query query = SparqlQueryUtils.create(queryString);
 		try {
-			String format = interpretRequestedFormats(req, queryString);
+			String format = interpretRequestedFormats(req, query);
 			SparqlQueryApiExecutor core = SparqlQueryApiExecutor.instance(
 					rdfService, queryString, format);
 			resp.setContentType(core.getMediaType());
+
+			if (download) {	
+				String extension = getFilenameExtension(req, query, format);
+				resp.setHeader("Content-Transfer-Encoding", "binary");
+				resp.setHeader("Content-disposition", "attachment; filename=query-results." + extension);
+			}
+
 			core.executeAndFormat(resp.getOutputStream());
 		} catch (InvalidQueryTypeException e) {
 			do400BadRequest("Query type is not SELECT, ASK, CONSTRUCT, "
@@ -132,8 +143,7 @@ private void respondToQuery(HttpServletRequest req, HttpServletResponse resp)
 	}
 
 	private String interpretRequestedFormats(HttpServletRequest req,
-			String queryString) throws NotAcceptableException {
-		Query query = SparqlQueryUtils.create(queryString);
+			Query query) throws NotAcceptableException {
 		String parameterName = (query.isSelectType() || query.isAskType()) ? "resultFormat"
 				: "rdfResultFormat";
 		String parameterValue = req.getParameter(parameterName);
@@ -145,6 +155,20 @@ private String interpretRequestedFormats(HttpServletRequest req,
 		}
 	}
 
+	private String getFilenameExtension(HttpServletRequest req, 
+			Query query, String format) {
+		String extension;
+		if (query.isSelectType() || query.isAskType()) {
+			ResultSetMediaType mediaType = ResultSetMediaType.fromContentType(format);
+			extension = mediaType.getExtension();
+		}
+		else {
+			RdfResultMediaType mediaType = RdfResultMediaType.fromContentType(format);
+			extension = mediaType.getExtension();
+		}
+		return extension;
+	}
+
 	private void do400BadRequest(String message, HttpServletResponse resp)
 			throws IOException {
 		resp.setStatus(400);

diff --git a/.../java/edu/cornell/mannlib/vitro/webapp/controller/api/sparqlquery/RdfResultMediaType.java b/.../java/edu/cornell/mannlib/vitro/webapp/controller/api/sparqlquery/RdfResultMediaType.java
@@ -12,17 +12,17 @@
  * and DESCRIBE).
  */
 public enum RdfResultMediaType {
-	TEXT("text/plain", true, "NTRIPLE", "N-TRIPLE"),
+	TEXT("text/plain", true, "NTRIPLE", "N-TRIPLE", "nt"),
 
-	RDF_XML("application/rdf+xml", true, "RDFXML", "RDF/XML"),
+	RDF_XML("application/rdf+xml", true, "RDFXML", "RDF/XML", "rdf"),
 
-	N3("text/n3", true, "N3", "N3"),
+	N3("text/n3", true, "N3", "N3", "n3"),
 
-	TTL("text/turtle", false, "N3", "TTL"),
+	TTL("text/turtle", false, "N3", "TTL", "ttl"),
 
-	JSON("application/json", false, "N3", "JSON"),
+	JSON("application/json", false, "N3", "JSON", "json"),
 
-	JSON_LD("application/ld+json", false, "N3", "JSON");
+	JSON_LD("application/ld+json", false, "N3", "JSON", "jsonld");
 
 	// ----------------------------------------------------------------------
 	// Keep a map of content types, for easy conversion back and forth
@@ -79,12 +79,18 @@ public static RdfResultMediaType fromContentType(String contentType)
 	 */
 	private final String jenaResponseFormat;
 
+	/**
+	 * What extension should be used if file is downloaded?
+	 */
+	private final String extension;
+
 	private RdfResultMediaType(String contentType, boolean nativeFormat,
-			String serializationFormat, String jenaResponseFormat) {
+			String serializationFormat, String jenaResponseFormat, String extension) {
 		this.contentType = contentType;
 		this.nativeFormat = nativeFormat;
 		this.serializationFormat = serializationFormat;
 		this.jenaResponseFormat = jenaResponseFormat;
+		this.extension = extension;
 	}
 
 	public String getContentType() {
@@ -103,4 +109,8 @@ public String getJenaResponseFormat() {
 		return jenaResponseFormat;
 	}
 
+	public String getExtension() {
+		return extension;
+	}
+
 }
diff --git a/.../java/edu/cornell/mannlib/vitro/webapp/controller/api/sparqlquery/ResultSetMediaType.java b/.../java/edu/cornell/mannlib/vitro/webapp/controller/api/sparqlquery/ResultSetMediaType.java
@@ -12,15 +12,15 @@
  * SELECT and ASK).
  */
 public enum ResultSetMediaType {
-	TEXT("text/plain", true, "TEXT", null),
+	TEXT("text/plain", true, "TEXT", null, "txt"),
 
-	CSV("text/csv", true, "CSV", null),
+	CSV("text/csv", true, "CSV", null, "csv"),
 
-	TSV("text/tab-separated-values", false, "CSV", "tsv"),
+	TSV("text/tab-separated-values", false, "CSV", "tsv", "tsv"),
 
-	XML("application/sparql-results+xml", true, "XML", null),
+	XML("application/sparql-results+xml", true, "XML", null, "xml"),
 
-	JSON("application/sparql-results+json", true, "JSON", null);
+	JSON("application/sparql-results+json", true, "JSON", null, "json");
 
 	// ----------------------------------------------------------------------
 	// Keep a map of content types, for easy conversion back and forth
@@ -78,12 +78,18 @@ public static ResultSetMediaType fromContentType(String contentType)
 	 */
 	private final String jenaResponseFormat;
 
+	/**
+	 * What extension should be used if file is downloaded?
+	 */
+	private final String extension;
+
 	private ResultSetMediaType(String contentType, boolean nativeFormat,
-			String rdfServiceFormat, String jenaResponseFormat) {
+			String rdfServiceFormat, String jenaResponseFormat, String extension) {
 		this.contentType = contentType;
 		this.nativeFormat = nativeFormat;
 		this.rdfServiceFormat = rdfServiceFormat;
 		this.jenaResponseFormat = jenaResponseFormat;
+		this.extension = extension;
 	}
 
 	public String getContentType() {
@@ -102,4 +108,8 @@ public String getJenaResponseFormat() {
 		return jenaResponseFormat;
 	}
 
+	public String getExtension() {
+		return extension;
+	}
+
 }
diff --git a/...rc/main/java/edu/cornell/mannlib/vitro/webapp/controller/edit/DatapropEditController.java b/...rc/main/java/edu/cornell/mannlib/vitro/webapp/controller/edit/DatapropEditController.java
@@ -42,7 +42,7 @@ public void doPost (HttpServletRequest request, HttpServletResponse response) {
 
     	VitroRequest vreq = new VitroRequest(request);
 
-        final int NUM_COLS=18;
+        final int NUM_COLS=19;
 
         String datapropURI = request.getParameter("uri");
 
@@ -73,8 +73,9 @@ public void doPost (HttpServletRequest request, HttpServletResponse response) {
         results.add("display tier");          // column 14
         results.add("display limit");         // column 15
         results.add("custom entry form");     // column 16
-        results.add("URI");                   // column 17
-        results.add("publish level");         // column 18
+        results.add("editing");               // column 17
+        results.add("URI");                   // column 18
+        results.add("publish level");         // column 19
 
         results.add(dp.getPickListName()); // column 1
         results.add(dp.getPublicName() == null ? "(no public label)" : dp.getPublicName()); // column 2
@@ -142,9 +143,10 @@ public void doPost (HttpServletRequest request, HttpServletResponse response) {
         results.add(String.valueOf(dp.getDisplayTier()));  // column 14
         results.add(String.valueOf(dp.getDisplayLimit()));  // column 15
         results.add(dp.getCustomEntryForm() == null ? "(unspecified)" : dp.getCustomEntryForm());  // column 16
-        results.add(dp.getURI() == null ? "" : dp.getURI()); // column 17
+        results.add(dp.getEditing() == null ? "" : dp.getEditing()); // column 17
+        results.add(dp.getURI() == null ? "" : dp.getURI()); // column 18
 		results.add(dp.getHiddenFromPublishBelowRoleLevel() == null ? "(unspecified)"
-				: dp.getHiddenFromPublishBelowRoleLevel().getDisplayLabel()); // column 18
+				: dp.getHiddenFromPublishBelowRoleLevel().getDisplayLabel()); // column 19
         request.setAttribute("results",results);
         request.setAttribute("columncount",NUM_COLS);
         request.setAttribute("suppressquery","true");

diff --git a/...c/main/java/edu/cornell/mannlib/vitro/webapp/controller/edit/DatapropRetryController.java b/...c/main/java/edu/cornell/mannlib/vitro/webapp/controller/edit/DatapropRetryController.java
@@ -168,13 +168,26 @@ public void doPost (HttpServletRequest request, HttpServletResponse response) {
         optionMap.put("ProhibitedFromUpdateBelowRoleLevelUsingRoleUri",RoleLevelOptionsSetup.getUpdateOptionsList(objectForEditing));
         optionMap.put("HiddenFromPublishBelowRoleLevelUsingRoleUri",RoleLevelOptionsSetup.getPublishOptionsList(objectForEditing));
 
+        // Set the value of the editing parameter (as defined in VitroVocabulary.java). 
+        // Use value to control form types as in defaultDataPropertyForm.ftl
+        String editingVal = objectForEditing.getEditing();
+        List<Option> editingOptList = new ArrayList<Option>();
+        editingOptList.add(0,new Option("","plaintext"));
+        editingOptList.add(1,new Option("HTML","rich text"));
+        for (Option val : editingOptList) {
+            if(editingVal != null && editingVal.equals(val.getValue())) {
+                val.setSelected(true);
+            }
+        }
+        optionMap.put("Editing", editingOptList);
+
         foo.setOptionLists(optionMap);
 
         request.setAttribute("functional",objectForEditing.getFunctional());
 
         //checkboxes are pretty annoying : we don't know if someone *unchecked* a box, so we have to default to false on updates.
         if (objectForEditing.getURI() != null) {
-        	objectForEditing.setFunctional(false);
+              objectForEditing.setFunctional(false);
         }
 
         foo.setErrorMap(epo.getErrMsgMap());

diff --git a/.../java/edu/cornell/mannlib/vitro/webapp/controller/freemarker/BaseSiteAdminController.java b/.../java/edu/cornell/mannlib/vitro/webapp/controller/freemarker/BaseSiteAdminController.java
@@ -199,12 +199,17 @@ protected Map<String, Object> getOntologyEditorData(VitroRequest vreq) {
 
             String error = null;
             String explanation = null;
-            TBoxReasonerStatus status = ApplicationUtils.instance().getTBoxReasonerModule().getStatus();
-            if (!status.isConsistent()) {
-                error = "INCONSISTENT ONTOLOGY: reasoning halted.";
-                explanation = status.getExplanation();
-            } else if ( status.isInErrorState() ) {
-                error = "An error occurred during reasoning. Reasoning has been halted. See error log for details.";
+            try {
+                TBoxReasonerStatus status = ApplicationUtils.instance().getTBoxReasonerModule().getStatus();
+                if (!status.isConsistent()) {
+                    error = "INCONSISTENT ONTOLOGY: reasoning halted.";
+                    explanation = status.getExplanation();
+                } else if ( status.isInErrorState() ) {
+                    error = "An error occurred during reasoning. Reasoning has been halted. See error log for details.";
+                }
+            } catch (IllegalStateException e) {
+                error = "The inferencing engine is disabled. Data entered manually may exhibit unexpected behavior prior to inferencing.";
+                log.debug("Status of reasoner could not be determined. It is likely disabled.", e);
             }
 
             if (error != null) {

diff --git a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/jena/JenaAdminActions.java b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/jena/JenaAdminActions.java
@@ -192,29 +192,33 @@ private String testWriteXML() {
 	}
 
     private void printRestrictions() {
-    	TBoxReasonerModule reasoner = ApplicationUtils.instance().getTBoxReasonerModule();
-    	for (Restriction rest : reasoner.listRestrictions() ) {
-    		if (rest.isAllValuesFromRestriction()) {
-    			log.trace("All values from: ");
-    			AllValuesFromRestriction avfr = rest.asAllValuesFromRestriction();
-    			Resource res = avfr.getAllValuesFrom();
-    			if (res.canAs(OntClass.class)) {
-    				OntClass resClass = res.as(OntClass.class);
-    				for (Resource inst : resClass.listInstances().toList() ) {
-    					log.trace("    -"+inst.getURI());
-    				}
-    			}
-    		} else if (rest.isSomeValuesFromRestriction()) {
-    			log.trace("Some values from: ");
-    		} else if (rest.isHasValueRestriction()) {
-    			log.trace("Has value: ");
-    		}
-    		log.trace("On property "+rest.getOnProperty().getURI());
-    		for (Resource inst : rest.listInstances().toList() ) {
-    			log.trace("     "+inst.getURI());
-    		}
-
-    	}
+		try {
+			TBoxReasonerModule reasoner = ApplicationUtils.instance().getTBoxReasonerModule();
+			for (Restriction rest : reasoner.listRestrictions() ) {
+				if (rest.isAllValuesFromRestriction()) {
+					log.trace("All values from: ");
+					AllValuesFromRestriction avfr = rest.asAllValuesFromRestriction();
+					Resource res = avfr.getAllValuesFrom();
+					if (res.canAs(OntClass.class)) {
+						OntClass resClass = res.as(OntClass.class);
+						for (Resource inst : resClass.listInstances().toList() ) {
+							log.trace("    -"+inst.getURI());
+						}
+					}
+				} else if (rest.isSomeValuesFromRestriction()) {
+					log.trace("Some values from: ");
+				} else if (rest.isHasValueRestriction()) {
+					log.trace("Has value: ");
+				}
+				log.trace("On property "+rest.getOnProperty().getURI());
+				for (Resource inst : rest.listInstances().toList() ) {
+					log.trace("     "+inst.getURI());
+				}
+			}
+		}
+		catch (IllegalStateException e) {
+			log.warn("Status of reasoner could not be determined. It is likely disabled", e);
+		}
     }
 
     private void removeLongLiterals() {

diff --git a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/jena/RDFUploadController.java b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/jena/RDFUploadController.java
@@ -270,6 +270,7 @@ public void loadRDF(VitroRequest request, HttpServletResponse response)
         String modelName = request.getParameter("modelName");
         String docLoc = request.getParameter("docLoc");
         String languageStr = request.getParameter("language");
+        boolean remove = "remove".equals(request.getParameter("mode"));
         ModelMaker maker = getModelMaker(request);
 
         String bodyJsp;
@@ -279,7 +280,7 @@ public void loadRDF(VitroRequest request, HttpServletResponse response)
         } else {
             RDFService rdfService = getRDFService(request, maker, modelName);
             try {
-                doLoadRDFData(modelName, docLoc, filePath, languageStr, rdfService);
+                doLoadRDFData(modelName, docLoc, filePath, languageStr, rdfService, remove);
             } finally {
                 rdfService.close();
             }
@@ -378,12 +379,19 @@ private void doLoadRDFData(String modelName,
                                String docLoc,
                                String filePath,
                                String language,
-                               RDFService rdfService) {
+                               RDFService rdfService,
+                               boolean remove) {
         try {
             if ( (docLoc != null) && (docLoc.length()>0) ) {
                 URL docLocURL = new URL(docLoc);
                 InputStream in = docLocURL.openStream();
-                readIntoModel(in, language, rdfService, modelName);
+                if(!remove) {
+                    readIntoModel(in, language, rdfService,
+                            modelName);
+                } else {
+                    removeFromModel(in, language, rdfService,
+                            modelName);
+                }
             } else if ( (filePath != null) && (filePath.length()>0) ) {
                 File file = new File(filePath);
                 File[] files;
@@ -396,8 +404,13 @@ private void doLoadRDFData(String modelName,
                 for (File currentFile : files) {
                     log.debug("Reading file " + currentFile.getName());
                     try {
-                        readIntoModel(fileStream.getInputStream(), language,
-                                rdfService, modelName);
+                        if(!remove) {
+                            readIntoModel(fileStream.getInputStream(), language, rdfService,
+                                    modelName);
+                        } else {
+                            removeFromModel(fileStream.getInputStream(), language, rdfService,
+                                    modelName);
+                        }
                         fileStream.delete();
                     } catch (IOException ioe) {
                         String errMsg = "Error loading RDF from " +

diff --git a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/dao/jena/DataPropertyDaoJena.java b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/dao/jena/DataPropertyDaoJena.java
@@ -360,8 +360,13 @@ private List<DataProperty> filterAndConvertToDataProperties(
     }
 
     protected boolean reasoningAvailable() {
-    	TBoxReasonerStatus status = ApplicationUtils.instance().getTBoxReasonerModule().getStatus();
-    	return status.isConsistent() && !status.isInErrorState();
+        try {
+            TBoxReasonerStatus status = ApplicationUtils.instance().getTBoxReasonerModule().getStatus();
+            return status.isConsistent() && !status.isInErrorState();
+        } catch (IllegalStateException e) {
+            log.debug("Status of reasoner could not be determined. It is likely disabled.", e);
+            return false;
+        }
     }
 
     private String getRequiredDatatypeURI(Individual individual, DataProperty dataprop, List<String> vclassURIs) {
@@ -514,6 +519,7 @@ public String insertDataProperty(DataProperty dtp, OntModel ontModel) throws Ins
             addPropertyStringValue(jDataprop, EXAMPLE, dtp.getExample(), ontModel);
             addPropertyStringValue(jDataprop, DESCRIPTION_ANNOT, dtp.getDescription(), ontModel);
             addPropertyStringValue(jDataprop, PUBLIC_DESCRIPTION_ANNOT, dtp.getPublicDescription(), ontModel);
+            addPropertyStringValue(jDataprop, EDITING, dtp.getEditing(), ontModel);
             addPropertyNonNegativeIntValue(jDataprop, DISPLAY_RANK_ANNOT, dtp.getDisplayTier(), ontModel);
             addPropertyNonNegativeIntValue(jDataprop, DISPLAY_LIMIT, dtp.getDisplayLimit(), ontModel);
             //addPropertyStringValue(jDataprop, HIDDEN_ANNOT, dtp.getHidden(), ontModel);
@@ -584,6 +590,7 @@ public void updateDataProperty(DataProperty dtp, OntModel ontModel) {
             updatePropertyStringValue(jDataprop, EXAMPLE, dtp.getExample(), ontModel);
             updatePropertyStringValue(jDataprop, DESCRIPTION_ANNOT, dtp.getDescription(), ontModel);
             updatePropertyStringValue(jDataprop, PUBLIC_DESCRIPTION_ANNOT, dtp.getPublicDescription(), ontModel);
+            updatePropertyStringValue(jDataprop, EDITING, dtp.getEditing(), ontModel);
             updatePropertyNonNegativeIntValue(jDataprop, DISPLAY_RANK_ANNOT, dtp.getDisplayTier(), ontModel);
             updatePropertyNonNegativeIntValue(jDataprop, DISPLAY_LIMIT, dtp.getDisplayLimit(), ontModel);