Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Added code for deleting individuals (#213)
* Added code for deleting individuals * Allow admins delete individuals * Fixed delete individual url params * Improved query safety * refact: fixed constants' names, fixed mistakes, removed useless code * refact: refactored sparql queries * fix: fixed error logging mistakes * fix: use CONSTRUCT instead of DESCRIBE as less potentionally problematic, lookup for mostSpecificTypes * feat: add delete link in vitro individual profile if individual is editable * fix: renamed individualURI to individualUri and added safety check * fix: use ABox model to construct triples to delete
- Loading branch information
Showing
11 changed files
with
327 additions
and
9 deletions.
There are no files selected for viewing
211 changes: 211 additions & 0 deletions
211
...va/edu/cornell/mannlib/vitro/webapp/controller/freemarker/DeleteIndividualController.java
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,211 @@ | ||
| package edu.cornell.mannlib.vitro.webapp.controller.freemarker; | ||
|
|
||
| import java.io.ByteArrayInputStream; | ||
| import java.io.ByteArrayOutputStream; | ||
| import java.io.InputStream; | ||
| import java.io.StringWriter; | ||
| import java.util.HashMap; | ||
| import java.util.LinkedList; | ||
| import java.util.List; | ||
| import java.util.stream.Collectors; | ||
|
|
||
| import javax.servlet.annotation.WebServlet; | ||
| import javax.servlet.http.HttpServletResponse; | ||
|
|
||
| import org.apache.commons.logging.Log; | ||
| import org.apache.commons.logging.LogFactory; | ||
| import org.apache.jena.query.Query; | ||
| import org.apache.jena.query.QueryExecution; | ||
| import org.apache.jena.query.QueryExecutionFactory; | ||
| import org.apache.jena.query.QueryFactory; | ||
| import org.apache.jena.query.QuerySolution; | ||
| import org.apache.jena.query.QuerySolutionMap; | ||
| import org.apache.jena.query.ResultSet; | ||
| import org.apache.jena.rdf.model.Model; | ||
| import org.apache.jena.rdf.model.ModelFactory; | ||
| import org.apache.jena.rdf.model.ResourceFactory; | ||
| import org.apache.jena.shared.Lock; | ||
|
|
||
| import edu.cornell.mannlib.vitro.webapp.auth.permissions.SimplePermission; | ||
| import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.AuthorizationRequest; | ||
| import edu.cornell.mannlib.vitro.webapp.beans.Individual; | ||
| import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest; | ||
| import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.RedirectResponseValues; | ||
| import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.ResponseValues; | ||
| import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.TemplateResponseValues; | ||
| import static edu.cornell.mannlib.vitro.webapp.dao.DisplayVocabulary.HAS_DELETE_QUERY; | ||
|
|
||
| import edu.cornell.mannlib.vitro.webapp.dao.jena.event.BulkUpdateEvent; | ||
| import edu.cornell.mannlib.vitro.webapp.modelaccess.ModelAccess; | ||
| import edu.cornell.mannlib.vitro.webapp.modelaccess.ModelNames; | ||
| import edu.cornell.mannlib.vitro.webapp.rdfservice.ChangeSet; | ||
| import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService; | ||
| import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.RDFServiceUtils; | ||
|
|
||
| @WebServlet(name = "DeleteIndividualController", urlPatterns = "/deleteIndividualController") | ||
| public class DeleteIndividualController extends FreemarkerHttpServlet { | ||
|
|
||
| private static final String INDIVIDUAL_URI = "individualUri"; | ||
| private static final long serialVersionUID = 1L; | ||
| private static final Log log = LogFactory.getLog(DeleteIndividualController.class); | ||
| private static final boolean BEGIN = true; | ||
| private static final boolean END = !BEGIN; | ||
|
|
||
| private static String queryForDeleteQuery = "" | ||
| + "SELECT ?deleteQueryText WHERE { " | ||
| + "?associatedUri <" + HAS_DELETE_QUERY + "> ?deleteQueryText ." | ||
| + "}"; | ||
|
|
||
| private static final String DEFAULT_DELETE_QUERY_TEXT = "" | ||
| + "CONSTRUCT { ?individualUri ?p1 ?o1 . ?s2 ?p2 ?individualUri . } " | ||
| + "WHERE {" | ||
| + " { ?individualUri ?p1 ?o1 . } UNION { ?s2 ?p2 ?individualUri. } " | ||
| + "}"; | ||
|
|
||
| @Override | ||
| protected AuthorizationRequest requiredActions(VitroRequest vreq) { | ||
| return SimplePermission.DO_FRONT_END_EDITING.ACTION; | ||
| } | ||
|
|
||
| protected ResponseValues processRequest(VitroRequest vreq) { | ||
| String errorMessage = handleErrors(vreq); | ||
| if (!errorMessage.isEmpty()) { | ||
| return prepareErrorMessage(errorMessage); | ||
| } | ||
| String individualUri = vreq.getParameter(INDIVIDUAL_URI); | ||
| List<String> types = getObjectMostSpecificTypes(individualUri, vreq); | ||
| Model displayModel = vreq.getDisplayModel(); | ||
|
|
||
| String deleteQueryText = getDeleteQueryForTypes(types, displayModel); | ||
| Model toRemove = getIndividualsToDelete(individualUri, deleteQueryText, vreq); | ||
| if (toRemove.size() > 0) { | ||
| deleteIndividuals(toRemove, vreq); | ||
| } | ||
| String redirectUrl = getRedirectUrl(vreq); | ||
|
|
||
| return new RedirectResponseValues(redirectUrl, HttpServletResponse.SC_SEE_OTHER); | ||
| } | ||
|
|
||
| private String getRedirectUrl(VitroRequest vreq) { | ||
| String redirectUrl = vreq.getParameter("redirectUrl"); | ||
| if (redirectUrl != null) { | ||
| return redirectUrl; | ||
| } | ||
| return "/"; | ||
| } | ||
|
|
||
| private TemplateResponseValues prepareErrorMessage(String errorMessage) { | ||
| HashMap<String, Object> map = new HashMap<String, Object>(); | ||
| map.put("errorMessage", errorMessage); | ||
| return new TemplateResponseValues("error-message.ftl", map); | ||
| } | ||
|
|
||
| private String handleErrors(VitroRequest vreq) { | ||
| String uri = vreq.getParameter(INDIVIDUAL_URI); | ||
| if (uri == null) { | ||
| return "Individual uri is null. No object to delete."; | ||
| } | ||
| if (uri.contains("<") || uri.contains(">")) { | ||
| return "Individual IRI shouldn't contain '<' or '>"; | ||
| } | ||
| return ""; | ||
| } | ||
|
|
||
| private static String getDeleteQueryForTypes(List<String> types, Model displayModel) { | ||
| String deleteQueryText = DEFAULT_DELETE_QUERY_TEXT; | ||
| String foundType = ""; | ||
| for ( String type: types) { | ||
| Query queryForTypeSpecificDeleteQuery = QueryFactory.create(queryForDeleteQuery); | ||
| QuerySolutionMap initialBindings = new QuerySolutionMap(); | ||
| initialBindings.add("associatedURI", ResourceFactory.createResource(type)); | ||
| displayModel.enterCriticalSection(Lock.READ); | ||
| try { | ||
| QueryExecution qexec = QueryExecutionFactory.create(queryForTypeSpecificDeleteQuery, displayModel, | ||
| initialBindings); | ||
| try { | ||
| ResultSet results = qexec.execSelect(); | ||
| if (results.hasNext()) { | ||
| QuerySolution solution = results.nextSolution(); | ||
| deleteQueryText = solution.get("deleteQueryText").toString(); | ||
| foundType = type; | ||
| } | ||
| } finally { | ||
| qexec.close(); | ||
| } | ||
| } finally { | ||
| displayModel.leaveCriticalSection(); | ||
| } | ||
| if (!foundType.isEmpty()) { | ||
| break; | ||
| } | ||
| } | ||
|
|
||
| if (!foundType.isEmpty()) { | ||
| log.debug("For " + foundType + " found delete query \n" + deleteQueryText); | ||
| if (!deleteQueryText.contains(INDIVIDUAL_URI)){ | ||
| log.error("Safety check failed. Delete query text should contain " + INDIVIDUAL_URI + ", " | ||
| + "but it didn't. To prevent bad consequences query was rejected."); | ||
| log.error("Delete query which caused the error: \n" + deleteQueryText); | ||
| deleteQueryText = DEFAULT_DELETE_QUERY_TEXT; | ||
| } | ||
| } else { | ||
| log.debug("For most specific types: " + types.stream().collect(Collectors.joining(",")) + " no delete query was found. Using default query \n" + deleteQueryText); | ||
| } | ||
| return deleteQueryText; | ||
| } | ||
|
|
||
| private List<String> getObjectMostSpecificTypes(String individualUri, VitroRequest vreq) { | ||
| List<String> types = new LinkedList<String>(); | ||
| Individual individual = vreq.getWebappDaoFactory().getIndividualDao().getIndividualByURI(individualUri); | ||
| if (individual != null) { | ||
| types = individual.getMostSpecificTypeURIs(); | ||
| } | ||
| if (types.isEmpty()) { | ||
| log.error("Failed to get most specific type for individual Uri " + individualUri); | ||
| } | ||
| return types; | ||
| } | ||
|
|
||
| private Model getIndividualsToDelete(String targetIndividual, String deleteQuery, VitroRequest vreq) { | ||
| try { | ||
| Query queryForTypeSpecificDeleteQuery = QueryFactory.create(deleteQuery); | ||
| QuerySolutionMap bindings = new QuerySolutionMap(); | ||
| bindings.add(INDIVIDUAL_URI, ResourceFactory.createResource(targetIndividual)); | ||
| Model ontModel = ModelAccess.on(vreq).getOntModelSelector().getABoxModel(); | ||
| QueryExecution qexec = QueryExecutionFactory.create(queryForTypeSpecificDeleteQuery, ontModel, bindings); | ||
| Model results = qexec.execConstruct(); | ||
| return results; | ||
|
|
||
| } catch (Exception e) { | ||
| log.error("Query raised an error \n" + deleteQuery); | ||
| log.error(e, e); | ||
| } | ||
| return ModelFactory.createDefaultModel(); | ||
| } | ||
|
|
||
| private void deleteIndividuals(Model model, VitroRequest vreq) { | ||
| RDFService rdfService = vreq.getRDFService(); | ||
| ChangeSet cs = makeChangeSet(rdfService); | ||
| try { | ||
| ByteArrayOutputStream out = new ByteArrayOutputStream(); | ||
| model.write(out, "N3"); | ||
| InputStream in = new ByteArrayInputStream(out.toByteArray()); | ||
| cs.addRemoval(in, RDFServiceUtils.getSerializationFormatFromJenaString("N3"), ModelNames.ABOX_ASSERTIONS); | ||
| rdfService.changeSetUpdate(cs); | ||
| } catch (Exception e) { | ||
| StringWriter sw = new StringWriter(); | ||
| model.write(sw, "N3"); | ||
| log.error("Got " + e.getClass().getSimpleName() + " while removing\n" + sw.toString()); | ||
| log.error(e,e); | ||
| throw new RuntimeException(e); | ||
| } | ||
| } | ||
|
|
||
| private ChangeSet makeChangeSet(RDFService rdfService) { | ||
| ChangeSet cs = rdfService.manufactureChangeSet(); | ||
| cs.addPreChangeEvent(new BulkUpdateEvent(null, BEGIN)); | ||
| cs.addPostChangeEvent(new BulkUpdateEvent(null, END)); | ||
| return cs; | ||
| } | ||
|
|
||
| } |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Oops, something went wrong.