List of usage examples for org.apache.commons.collections ListUtils removeAll
public static List removeAll(Collection collection, Collection remove)
remove from collection. From source file:com.agiletec.plugins.jpldap.apsadmin.user.UserFinderAction.java
@Override public List<String> getSearchResult() { List<String> mainSearchResult = super.getSearchResult(); try {/* w w w . java2 s . c o m*/ Integer userType = this.getUserType(); if (null == userType || userType == 0) { return mainSearchResult; } else { Boolean entandoUser = (userType == 1); List<String> ldapUsernames = this.getLdapUsernames(); List<String> newList = null; if (entandoUser) { newList = (List<String>) ListUtils.removeAll(mainSearchResult, ldapUsernames); } else { newList = (List<String>) ListUtils.intersection(mainSearchResult, ldapUsernames); } return newList; } } catch (Throwable t) { ApsSystemUtils.logThrowable(t, this, "getSearchResult"); throw new RuntimeException("Error while searching users", t); } }
From source file:com.wizecommerce.hecuba.HecubaCassandraManagerTestBase.java
public void testConstructor() { String clusterName = "My Awesome Cluster"; String locationURL = "africa:northamerica:southamerica:asia:europe"; String thriftPorts = "3726"; String keyspace = "WizeCommerce"; String cf = "Platform and Infra"; String secondaryIndexColumns = "Column_1:Column_2:Column_3"; CassandraParamsBean bean = new CassandraParamsBean(); bean.setClustername(clusterName);//from w w w . jav a 2 s . co m bean.setLocationURLs(locationURL); bean.setThriftPorts(thriftPorts); bean.setKeyspace(keyspace); bean.setColumnFamily(cf); bean.setSiColumns(secondaryIndexColumns); assertEquals(clusterName, bean.getClustername()); assertEquals(locationURL, bean.getLocationURLs()); assertEquals(thriftPorts, bean.getThriftPorts()); assertEquals(keyspace, bean.getKeyspace()); assertEquals(cf, bean.getColumnFamily()); assertEquals(secondaryIndexColumns, bean.getSiColumns()); HecubaClientManager<Long> cassandraManager = getHecubaClientManager(bean); assertEquals(clusterName, cassandraManager.getClusterName()); assertEquals(locationURL, cassandraManager.getLocationURL()); assertEquals(thriftPorts, cassandraManager.getPort()); assertEquals(keyspace, cassandraManager.getKeyspace()); assertEquals(cf, cassandraManager.getColumnFamilyName()); assertTrue(ListUtils.removeAll(Arrays.asList(secondaryIndexColumns.split(":")), cassandraManager.getColumnsToIndexOnColumnNameAndValue()).size() == 0); }
From source file:edu.isistan.carcha.CarchaPipelineTest.java
/** * Test calculate metrics.// w w w . j av a 2 s. c om * * @param output the result file from executing the annotator * @param golden the golden file annotated by experts * @throws UIMAException the UIMA exception * @throws IOException Signals that an I/O exception has occurred. */ private void testCalculateMetrics(String output, String golden) throws UIMAException, IOException { List<String> goldenDesignDecisions = Utils.extractCoveredTextAnnotations(golden, DesignDecision.class); List<String> goldenSentences = Utils.extractCoveredTextAnnotations(golden, Sentence.class); List<String> discoveredDesignDecisions = Utils.extractCoveredTextAnnotations(output, DesignDecision.class); List<String> discoveredSentences = Utils.extractCoveredTextAnnotations(output, Sentence.class); //Golden design decision that were not discovered double fn = ListUtils.removeAll(goldenDesignDecisions, discoveredDesignDecisions).size(); //Sentences that were discovered but are not design decisions double fp = ListUtils.removeAll(discoveredDesignDecisions, goldenDesignDecisions).size(); //Discovered Design Decisions. double tp = ListUtils.intersection(discoveredDesignDecisions, goldenDesignDecisions).size(); //non design decision that were not marked as design decision double tn = ListUtils.intersection(discoveredSentences, goldenSentences).size(); Double presicion = tp / (tp + fp); double recall = tp / (tp + fn); double fMeasure = 5 * ((presicion * recall) / ((4 * presicion) + recall)); double accuracy = (tp + tn) / (fn + fp + tp + tn); NumberFormat df = new DecimalFormat("#0.00"); logger.info("Golden DDs: " + goldenDesignDecisions.size()); logger.info("Golden Sentences: " + goldenSentences.size()); logger.info("Discovered DDs: " + discoveredDesignDecisions.size()); logger.info("Discovered Sentences: " + discoveredSentences.size()); logger.info("------------------"); logger.info("False Negative: " + fn); logger.info("False Positive: " + fp); logger.info("True Negative: " + tn); logger.info("True Positive: " + tp); logger.info("------------------"); logger.info("Presition: " + df.format(presicion * 100) + "%"); logger.info("Recall: " + df.format(recall * 100) + "%"); logger.info("Acurracy: " + df.format(accuracy * 100) + "%"); logger.info("F-Measure: " + df.format(fMeasure * 100) + "%"); }
From source file:edu.isistan.carcha.lsa.LSARunnerTest.java
/** * Test calculate metrics.//from ww w . j ava 2s . co m * * @param result * the result * @param golden * the golden */ public void calculateMetrics(TraceabilityDocument result, TraceabilityDocument golden) { double fn = ListUtils.removeAll(golden.getLinks(), result.getLinks()).size(); double fp = ListUtils.removeAll(result.getLinks(), golden.getLinks()).size(); double tn = Utils.calculateTrueNegatives(golden, result); double tp = ListUtils.intersection(result.getLinks(), golden.getLinks()).size(); double presicion = tp / (tp + fp + 0.0000000001); double recall = tp / (tp + fn); double fMeasure = 5 * ((presicion * recall) / ((4 * presicion) + recall + 0.0000000001)); double accuracy = (tp + tn) / (fn + fp + tp + tn); NumberFormat df = new DecimalFormat("#0.00"); logger.info("Golden TRAs:" + golden.getLinks().size()); logger.info("Discovered TRAs:" + result.getLinks().size()); logger.info("------------------"); logger.info("False Negative:\t" + fn); logger.info("False Positive:\t" + fp); logger.info("True Negative:\t" + tn); logger.info("True Positive:\t" + tp); logger.info("------------------"); logger.info("Presition:\t" + df.format(presicion * 100) + "%"); logger.info("Recall:\t" + df.format(recall * 100) + "%"); logger.info("Acurracy:\t" + df.format(accuracy * 100) + "%"); logger.info("F-Measure:\t" + df.format(fMeasure * 100) + "%"); logger.info(""); logger.info(""); }
From source file:com.qrmedia.commons.graph.traverser.AbstractNodeIteratingGraphTraverser.java
/** * See {@link GraphTraverser#addNode(Collection)}. * <p>// w w w . ja va2 s. co m * The order in which these nodes will be visited is <u>not</u> guaranteed - they will, * of course, be visited after any node(s) registered in previous <code>addNode</code> calls, * and before any queued in subsequent calls. * * @param nodes the node to be queued for visiting * @see #addNode(Object) */ @SuppressWarnings("unchecked") public void addNode(Collection<? extends T> nodes) { /* * Strip out all the nodes that have already been visited, *without* modifying the * original. Can't call CollectionUtils.removeAll as the 3.2.1 version contains a bug! */ Collection<T> unseenNodes = (Collection<T>) ListUtils.removeAll(nodes, visitedOrQueuedNodes); if (!unseenNodes.isEmpty()) { visitedOrQueuedNodes.addAll(unseenNodes); enqueueNodes(unseenNodes); } }
From source file:com.doculibre.constellio.solr.handler.component.ConstellioAuthorizationComponent.java
@SuppressWarnings("unchecked") @Override//from w ww . j av a 2 s . co m public void prepare(ResponseBuilder rb) throws IOException { SolrQueryRequest req = rb.req; SolrIndexSearcher searcher = req.getSearcher(); //IndexReader reader = req.getSearcher().getReader(); SolrParams params = req.getParams(); // A runtime param can skip if (!params.getBool(ENABLE, true)) { return; } Query query = rb.getQuery(); String qstr = rb.getQueryString(); if (query == null || qstr == null) { return; } ConstellioUser user; String userIdStr = params.get(ConstellioSolrQueryParams.USER_ID); if (userIdStr != null) { UserServices userServices = ConstellioSpringUtils.getUserServices(); try { user = userServices.get(new Long(userIdStr)); } catch (NumberFormatException e) { user = null; } } else { user = null; } String collectionName = params.get(ConstellioSolrQueryParams.COLLECTION_NAME); RecordCollectionServices collectionServices = ConstellioSpringUtils.getRecordCollectionServices(); FederationServices federationServices = ConstellioSpringUtils.getFederationServices(); RecordCollection collection = collectionServices.get(collectionName); List<TermQuery> restrictedCollectionQueries = new ArrayList<TermQuery>(); if (collection.isFederationOwner()) { List<RecordCollection> includedCollections = federationServices.listIncludedCollections(collection); for (RecordCollection includedCollection : includedCollections) { if (includedCollection.hasSearchPermission() && (user == null || !user.hasSearchPermission(includedCollection))) { restrictedCollectionQueries.add(new TermQuery( new Term(IndexField.COLLECTION_ID_FIELD, "" + includedCollection.getId()))); } } } // User must be logged in to see private records if (user != null) { String luceneQueryStr = params.get(ConstellioSolrQueryParams.LUCENE_QUERY); if (StringUtils.isBlank(luceneQueryStr)) { return; } IndexSchema schema = req.getSchema(); SolrQueryParser queryParser = new SolrQueryParser(rb.getQparser(), IndexField.DEFAULT_SEARCH_FIELD); Query luceneQuery; try { luceneQuery = queryParser.parse(luceneQueryStr); } catch (SyntaxError e) { log.error("Error parsing lucene query " + luceneQueryStr, e); return; } // Create a new query which will only include private records BooleanQuery privateRecordQuery = new BooleanQuery(true); privateRecordQuery.add(luceneQuery, BooleanClause.Occur.MUST); for (TermQuery restrictionCollectionQuery : restrictedCollectionQueries) { privateRecordQuery.add(restrictionCollectionQuery, BooleanClause.Occur.MUST_NOT); } TermQuery privateRecordTQ = new TermQuery(new Term(IndexField.PUBLIC_RECORD_FIELD, "F")); privateRecordQuery.add(privateRecordTQ, BooleanClause.Occur.MUST); DocSet privateRecordIdDocSet = searcher.getDocSet(privateRecordQuery); if (privateRecordIdDocSet.size() > 0) { RecordServices recordServices = ConstellioSpringUtils.getRecordServices(); ACLServices aclServices = ConstellioSpringUtils.getACLServices(); ConnectorManagerServices connectorManagerServices = ConstellioSpringUtils .getConnectorManagerServices(); List<Record> privateRecords = new ArrayList<Record>(); DocIterator docIt = privateRecordIdDocSet.iterator(); while (docIt.hasNext()) { int docId = docIt.nextDoc(); Document luceneDoc = searcher.doc(docId); Long recordId = new Long(luceneDoc.get(IndexField.RECORD_ID_FIELD)); Record record = recordServices.get(recordId, collection); privateRecords.add(record); } // First pass : Remove ACL authorized records List<Record> unevaluatedPrivateRecords = aclServices.removeAuthorizedRecords(privateRecords, user); if (!unevaluatedPrivateRecords.isEmpty()) { Set<UserCredentials> userCredentials = user.getUserCredentials(); // Second pass : Ask the connector manager ConnectorManager connectorManager = connectorManagerServices.getDefaultConnectorManager(); List<Record> authorizedRecords = connectorManagerServices .authorizeByConnector(unevaluatedPrivateRecords, userCredentials, connectorManager); List<Record> unauthorizedRecords = ListUtils.removeAll(unevaluatedPrivateRecords, authorizedRecords); if (!unauthorizedRecords.isEmpty()) { // Create a new query which will exclude unauthorized records BooleanQuery authorizedRecordQuery = new BooleanQuery(true); authorizedRecordQuery.add(query, BooleanClause.Occur.MUST); for (Record unauthorizedRecord : unauthorizedRecords) { TermQuery unauthorizedRecordTQ = new TermQuery( new Term(IndexField.RECORD_ID_FIELD, "" + unauthorizedRecord.getId())); authorizedRecordQuery.add(unauthorizedRecordTQ, BooleanClause.Occur.MUST_NOT); } rb.setQuery(authorizedRecordQuery); } } } } else { BooleanQuery publicRecordQuery = new BooleanQuery(true); publicRecordQuery.add(query, BooleanClause.Occur.MUST); TermQuery publicRecordTQ = new TermQuery(new Term(IndexField.PUBLIC_RECORD_FIELD, "T")); publicRecordQuery.add(publicRecordTQ, BooleanClause.Occur.MUST); for (TermQuery restrictionCollectionQuery : restrictedCollectionQueries) { publicRecordQuery.add(restrictionCollectionQuery, BooleanClause.Occur.MUST_NOT); } rb.setQuery(publicRecordQuery); } }
From source file:org.ensembl.healthcheck.testcase.generic.Karyotype.java
protected boolean checkKaryotype(DatabaseRegistryEntry dbre) { Connection con = dbre.getConnection(); boolean result = true; String[] seqRegionNames = DBUtils.getColumnValues(con, "SELECT s.name FROM seq_region s, coord_system cs WHERE s.coord_system_id=cs.coord_system_id AND cs.name='chromosome' AND cs.attrib='default_version' AND s.name NOT LIKE 'LRG%' AND s.name != 'MT'"); String[] patches = DBUtils.getColumnValues(con, "SELECT sr.name FROM seq_region sr, assembly_exception ae WHERE sr.seq_region_id=ae.seq_region_id AND ae.exc_type IN ('PATCH_NOVEL', 'PATCH_FIX', 'HAP')"); List<String> patchList = Arrays.asList(patches); List<String> nonPatchSeqRegions = ListUtils.removeAll(Arrays.asList(seqRegionNames), patchList); int count = 0; try {/*from ww w . j a v a 2 s.c om*/ PreparedStatement stmt = con.prepareStatement( "SELECT sr.name, MAX(kar.seq_region_end), sr.length FROM seq_region sr, karyotype kar WHERE sr.seq_region_id=kar.seq_region_id AND sr.name = ? GROUP BY kar.seq_region_id"); for (String seqRegion : seqRegionNames) { stmt.setString(1, seqRegion); ResultSet rs = stmt.executeQuery(); boolean hasKaryotype = false; while (rs.next() && count < 50) { hasKaryotype = true; if (patchList.contains(seqRegion)) { continue; } String chrName = rs.getString(1); int karLen = rs.getInt(2); int chrLen = rs.getInt(3); String prob = ""; int bp = 0; if (karLen > chrLen) { bp = karLen - chrLen; prob = "longer"; } else { bp = chrLen - karLen; prob = "shorter"; } if (bp > 0) { result = false; count++; ReportManager.problem(this, con, "Chromosome " + chrName + " is " + bp + "bp " + prob + " in the karyotype table than " + "in the seq_region table"); } } if (!hasKaryotype) { result = false; ReportManager.problem(this, con, "Chromosome " + seqRegion + " has no karyotype data"); } } } catch (SQLException e) { e.printStackTrace(); } if (count == 0) { ReportManager.correct(this, con, "Chromosome lengths are the same" + " in karyotype and seq_region tables"); } return result; }
From source file:org.jtalks.jcommune.service.transactional.TransactionalLastReadPostService.java
/** * {@inheritDoc}// ww w . j ava 2s .c om */ @Override public List<Topic> fillLastReadPostForTopics(List<Topic> topics) { JCUser currentUser = userService.getCurrentUser(); if (!currentUser.isAnonymous()) { List<Topic> notModifiedTopics = extractNotModifiedTopicsSinceForumMarkedAsRead(currentUser, topics); for (Topic notModifiedTopic : notModifiedTopics) { Post lastPost = notModifiedTopic.getLastPost(); notModifiedTopic.setLastReadPostDate(lastPost.getCreationDate()); } // @SuppressWarnings("unchecked") List<Topic> modifiedTopics = ListUtils.removeAll(topics, notModifiedTopics); fillLastReadPostsForModifiedTopics(modifiedTopics, currentUser); } return topics; }
From source file:org.kuali.rice.krad.datadictionary.DataDictionary.java
/** * Populates and processes the dictionary bean factory based on the configured files * * @param beans - The bean factory for the dictionary bean * @param moduleDictionaryFiles - List of bean xml files * @param index - Index of the data dictionary beans * @param validationFiles - The List of bean xml files loaded into the bean file *///from w w w . j a va2 s . c o m public void loadDictionaryBeans(DefaultListableBeanFactory beans, Map<String, List<String>> moduleDictionaryFiles, DataDictionaryIndex index, ArrayList<String> validationFiles) { // expand configuration locations into files timer.start("XML File Loading"); LOG.info("Starting DD XML File Load"); List<String> allBeanNames = new ArrayList<String>(); for (String namespaceCode : moduleLoadOrder) { LOG.info("Processing Module: " + namespaceCode); List<String> moduleDictionaryLocations = moduleDictionaryFiles.get(namespaceCode); if (LOG.isDebugEnabled()) { LOG.debug("DD Locations in Module: " + moduleDictionaryLocations); } if (moduleDictionaryLocations == null) { continue; } XmlBeanDefinitionReader xmlReader = new XmlBeanDefinitionReader(beans); String configFileLocationsArray[] = new String[moduleDictionaryLocations.size()]; configFileLocationsArray = moduleDictionaryLocations.toArray(configFileLocationsArray); for (int i = 0; i < configFileLocationsArray.length; i++) { validationFiles.add(configFileLocationsArray[i]); } try { xmlReader.loadBeanDefinitions(configFileLocationsArray); // get updated bean names from factory and compare to our previous list to get those that // were added by the last namespace List<String> addedBeanNames = Arrays.asList(beans.getBeanDefinitionNames()); addedBeanNames = ListUtils.removeAll(addedBeanNames, allBeanNames); index.addBeanNamesToNamespace(namespaceCode, addedBeanNames); allBeanNames.addAll(addedBeanNames); } catch (Exception e) { throw new DataDictionaryException("Error loading bean definitions: " + e.getLocalizedMessage(), e); } } LOG.info("Completed DD XML File Load"); timer.stop(); }
From source file:org.kuali.rice.krad.devtools.datadictionary.ReloadingDataDictionary.java
/** * Call back when a dictionary file is changed. Calls the spring bean reader * to reload the file (which will override beans as necessary and destroy * singletons) and runs the indexer// ww w. j a v a 2 s. c o m * * @see no.geosoft.cc.io.FileListener#fileChanged(java.io.File) */ public void fileChanged(File file) { LOG.info("reloading dictionary configuration for " + file.getName()); try { List<String> beforeReloadBeanNames = Arrays.asList(ddBeans.getBeanDefinitionNames()); Resource resource = new FileSystemResource(file); xmlReader.loadBeanDefinitions(resource); List<String> afterReloadBeanNames = Arrays.asList(ddBeans.getBeanDefinitionNames()); List<String> addedBeanNames = ListUtils.removeAll(afterReloadBeanNames, beforeReloadBeanNames); String namespace = KRADConstants.DEFAULT_NAMESPACE; if (fileToNamespaceMapping.containsKey(file.getAbsolutePath())) { namespace = fileToNamespaceMapping.get(file.getAbsolutePath()); } ddIndex.addBeanNamesToNamespace(namespace, addedBeanNames); performDictionaryPostProcessing(true); } catch (Exception e) { LOG.info("Exception in dictionary hot deploy: " + e.getMessage(), e); } }