List of usage examples for java.util Map.Entry get
V get(Object key);
From source file:io.hops.hopsworks.api.jobs.JobService.java
/** * Get application run info for the specified job * <p>/* w w w .j a va 2 s. c o m*/ * @param appId * @param sc * @param req * @return url */ @GET @Path("/{appId}/appinfo") @Produces(MediaType.APPLICATION_JSON) @AllowedProjectRoles({ AllowedProjectRoles.DATA_OWNER, AllowedProjectRoles.DATA_SCIENTIST }) public Response getAppInfo(@PathParam("appId") String appId, @Context SecurityContext sc, @Context HttpServletRequest req) { Response response = checkAccessRight(appId); if (response != null) { return response; } else { Execution execution = exeFacade.findByAppId(appId); try { long startTime = System.currentTimeMillis() - 60000; long endTime = System.currentTimeMillis(); boolean running = true; if (execution != null) { startTime = execution.getSubmissionTime().getTime(); endTime = startTime + execution.getExecutionDuration(); running = false; if (!execution.getState().isFinalState()) { running = true; } } InfluxDB influxDB = InfluxDBFactory.connect(settings.getInfluxDBAddress(), settings.getInfluxDBUser(), settings.getInfluxDBPW()); // Transform application_1493112123688_0001 to 1493112123688_0001 // application_ = 12 chars String timestamp_attempt = appId.substring(12); Query query = new Query("show tag values from nodemanager with key=\"source\" " + "where source =~ /^.*" + timestamp_attempt + ".*$/", "graphite"); QueryResult queryResult = influxDB.query(query, TimeUnit.MILLISECONDS); int nbExecutors = 0; HashMap<Integer, List<String>> executorInfo = new HashMap<>(); int index = 0; if (queryResult != null && queryResult.getResults() != null) { for (QueryResult.Result res : queryResult.getResults()) { if (res.getSeries() != null) { for (QueryResult.Series series : res.getSeries()) { List<List<Object>> values = series.getValues(); if (values != null) { nbExecutors += values.size(); for (List<Object> l : values) { executorInfo.put(index, Stream.of(Objects.toString(l.get(1))).collect(Collectors.toList())); index++; } } } } } } /* * At this point executor info contains the keys and a list with a single value, the YARN container id */ String vCoreTemp = null; HashMap<String, String> hostnameVCoreCache = new HashMap<>(); for (Map.Entry<Integer, List<String>> entry : executorInfo.entrySet()) { query = new Query( "select MilliVcoreUsageAvgMilliVcores, hostname from nodemanager where source = \'" + entry.getValue().get(0) + "\' limit 1", "graphite"); queryResult = influxDB.query(query, TimeUnit.MILLISECONDS); if (queryResult != null && queryResult.getResults() != null && queryResult.getResults().get(0) != null && queryResult.getResults().get(0).getSeries() != null) { List<List<Object>> values = queryResult.getResults().get(0).getSeries().get(0).getValues(); String hostname = Objects.toString(values.get(0).get(2)).split("=")[1]; entry.getValue().add(hostname); if (!hostnameVCoreCache.containsKey(hostname)) { // Not in cache, get the vcores of the host machine query = new Query("select AllocatedVCores+AvailableVCores from nodemanager " + "where hostname =~ /.*" + hostname + ".*/ limit 1", "graphite"); queryResult = influxDB.query(query, TimeUnit.MILLISECONDS); if (queryResult != null && queryResult.getResults() != null && queryResult.getResults().get(0) != null && queryResult.getResults().get(0).getSeries() != null) { values = queryResult.getResults().get(0).getSeries().get(0).getValues(); vCoreTemp = Objects.toString(values.get(0).get(1)); entry.getValue().add(vCoreTemp); hostnameVCoreCache.put(hostname, vCoreTemp); // cache it } } else { // It's a hit, skip the database query entry.getValue().add(hostnameVCoreCache.get(hostname)); } } } influxDB.close(); AppInfoDTO appInfo = new AppInfoDTO(appId, startTime, running, endTime, nbExecutors, executorInfo); return noCacheResponse.getNoCacheResponseBuilder(Response.Status.OK).entity(appInfo).build(); } catch (Exception e) { LOGGER.log(Level.SEVERE, "exception while geting job ui " + e.getLocalizedMessage(), e); } return noCacheResponse.getNoCacheResponseBuilder(Response.Status.NOT_FOUND).build(); } }
From source file:com.espertech.esper.core.InternalEventRouterImpl.java
private NullableObject<InternalEventRouterPreprocessor> initialize(EventType eventType) { EventTypeSPI eventTypeSPI = (EventTypeSPI) eventType; List<InternalEventRouterEntry> desc = new ArrayList<InternalEventRouterEntry>(); // determine which ones to process for this types, and what priority and drop Set<String> eventPropertiesWritten = new HashSet<String>(); for (Map.Entry<UpdateDesc, IRDescEntry> entry : descriptors.entrySet()) { boolean applicable = entry.getValue().getEventType() == eventType; if (!applicable) { if (eventType.getDeepSuperTypes() != null) { for (Iterator<EventType> it = eventType.getDeepSuperTypes(); it.hasNext();) { if (it.next() == entry.getValue().getEventType()) { applicable = true; break; }/* www. j a va2s. co m*/ } } } if (!applicable) { continue; } int priority = 0; boolean isDrop = false; Annotation[] annotations = entry.getValue().getAnnotations(); for (int i = 0; i < annotations.length; i++) { if (annotations[i] instanceof Priority) { priority = ((Priority) annotations[i]).value(); } if (annotations[i] instanceof Drop) { isDrop = true; } } List<String> properties = new ArrayList<String>(); ExprNode[] expressions = new ExprNode[entry.getKey().getAssignments().size()]; for (int i = 0; i < entry.getKey().getAssignments().size(); i++) { OnTriggerSetAssignment assignment = entry.getKey().getAssignments().get(i); expressions[i] = assignment.getExpression(); properties.add(assignment.getVariableName()); eventPropertiesWritten.add(assignment.getVariableName()); } EventBeanWriter writer = eventTypeSPI.getWriter(properties.toArray(new String[properties.size()])); desc.add(new InternalEventRouterEntry(priority, isDrop, entry.getKey().getOptionalWhereClause(), expressions, writer, entry.getValue().getWideners(), entry.getValue().getOutputView())); } EventBeanCopyMethod copyMethod = eventTypeSPI .getCopyMethod(eventPropertiesWritten.toArray(new String[eventPropertiesWritten.size()])); if (copyMethod == null) { return new NullableObject<InternalEventRouterPreprocessor>(null); } return new NullableObject<InternalEventRouterPreprocessor>( new InternalEventRouterPreprocessor(copyMethod, desc)); }
From source file:com.espertech.esper.core.service.InternalEventRouterImpl.java
private NullableObject<InternalEventRouterPreprocessor> initialize(EventType eventType) { EventTypeSPI eventTypeSPI = (EventTypeSPI) eventType; List<InternalEventRouterEntry> desc = new ArrayList<InternalEventRouterEntry>(); // determine which ones to process for this types, and what priority and drop Set<String> eventPropertiesWritten = new HashSet<String>(); for (Map.Entry<UpdateDesc, IRDescEntry> entry : descriptors.entrySet()) { boolean applicable = entry.getValue().getEventType() == eventType; if (!applicable) { if (eventType.getDeepSuperTypes() != null) { for (Iterator<EventType> it = eventType.getDeepSuperTypes(); it.hasNext();) { if (it.next() == entry.getValue().getEventType()) { applicable = true; break; }/*from w w w . ja va 2s. co m*/ } } } if (!applicable) { continue; } int priority = 0; boolean isDrop = false; Annotation[] annotations = entry.getValue().getAnnotations(); for (int i = 0; i < annotations.length; i++) { if (annotations[i] instanceof Priority) { priority = ((Priority) annotations[i]).value(); } if (annotations[i] instanceof Drop) { isDrop = true; } } List<String> properties = new ArrayList<String>(); ExprNode[] expressions = new ExprNode[entry.getKey().getAssignments().size()]; for (int i = 0; i < entry.getKey().getAssignments().size(); i++) { OnTriggerSetAssignment assignment = entry.getKey().getAssignments().get(i); Pair<String, ExprNode> assignmentPair = ExprNodeUtility .checkGetAssignmentToProp(assignment.getExpression()); expressions[i] = assignmentPair.getSecond(); properties.add(assignmentPair.getFirst()); eventPropertiesWritten.add(assignmentPair.getFirst()); } EventBeanWriter writer = eventTypeSPI.getWriter(properties.toArray(new String[properties.size()])); desc.add(new InternalEventRouterEntry(priority, isDrop, entry.getKey().getOptionalWhereClause(), expressions, writer, entry.getValue().getWideners(), entry.getValue().getOutputView(), entry.getValue().getAgentInstanceLock(), entry.getValue().hasSubselect)); } EventBeanCopyMethod copyMethod = eventTypeSPI .getCopyMethod(eventPropertiesWritten.toArray(new String[eventPropertiesWritten.size()])); if (copyMethod == null) { return new NullableObject<InternalEventRouterPreprocessor>(null); } return new NullableObject<InternalEventRouterPreprocessor>( new InternalEventRouterPreprocessor(copyMethod, desc)); }
From source file:org.apache.solr.cloud.FullSolrCloudTest.java
protected void updateMappingsFromZk(List<JettySolrRunner> jettys, List<SolrServer> clients) throws Exception, IOException, KeeperException, URISyntaxException { zkStateReader.updateCloudState(true); shardToClient.clear();/* ww w .ja v a 2 s . c o m*/ shardToJetty.clear(); jettyToInfo.clear(); CloudState cloudState = zkStateReader.getCloudState(); Map<String, Slice> slices = cloudState.getSlices(DEFAULT_COLLECTION); if (slices == null) { throw new RuntimeException( "No slices found for collection " + DEFAULT_COLLECTION + " in " + cloudState.getCollections()); } for (SolrServer client : clients) { // find info for this client in zk nextClient: // we find ou state by simply matching ports... for (Map.Entry<String, Slice> slice : slices.entrySet()) { Map<String, ZkNodeProps> theShards = slice.getValue().getShards(); for (Map.Entry<String, ZkNodeProps> shard : theShards.entrySet()) { int port = new URI(((HttpSolrServer) client).getBaseURL()).getPort(); if (shard.getKey().contains(":" + port + "_")) { CloudSolrServerClient csc = new CloudSolrServerClient(); csc.client = client; csc.shardName = shard.getValue().get(ZkStateReader.NODE_NAME_PROP); boolean isLeader = shard.getValue().containsKey(ZkStateReader.LEADER_PROP); clientToInfo.put(csc, shard.getValue()); List<SolrServer> list = shardToClient.get(slice.getKey()); if (list == null) { list = new ArrayList<SolrServer>(); shardToClient.put(slice.getKey(), list); } list.add(client); if (isLeader) { shardToLeaderClient.put(slice.getKey(), client); } break nextClient; } } } } for (Map.Entry<String, Slice> slice : slices.entrySet()) { // check that things look right assertEquals(slice.getValue().getShards().size(), shardToClient.get(slice.getKey()).size()); } for (JettySolrRunner jetty : jettys) { int port = jetty.getLocalPort(); if (port == -1) { continue; // If we cannot get the port, this jetty is down } nextJetty: for (Map.Entry<String, Slice> slice : slices.entrySet()) { Map<String, ZkNodeProps> theShards = slice.getValue().getShards(); for (Map.Entry<String, ZkNodeProps> shard : theShards.entrySet()) { if (shard.getKey().contains(":" + port + "_")) { jettyToInfo.put(jetty, shard.getValue()); List<CloudJettyRunner> list = shardToJetty.get(slice.getKey()); if (list == null) { list = new ArrayList<CloudJettyRunner>(); shardToJetty.put(slice.getKey(), list); } boolean isLeader = shard.getValue().containsKey(ZkStateReader.LEADER_PROP); CloudJettyRunner cjr = new CloudJettyRunner(); cjr.jetty = jetty; cjr.nodeName = shard.getValue().get(ZkStateReader.NODE_NAME_PROP); cjr.coreNodeName = shard.getKey(); list.add(cjr); if (isLeader) { shardToLeaderJetty.put(slice.getKey(), cjr); } break nextJetty; } } } } // # of jetties may not match replicas in shard here, because we don't map // jetties that are not running - every shard should have at least one // running jetty though for (Map.Entry<String, Slice> slice : slices.entrySet()) { // check that things look right List<CloudJettyRunner> jetties = shardToJetty.get(slice.getKey()); assertNotNull("Test setup problem: We found no jetties for shard: " + slice.getKey() + " just:" + shardToJetty.keySet(), jetties); assertTrue(jetties.size() > 0); } }
From source file:org.opencb.opencga.storage.variant.sqlite.VariantSqliteDBAdaptor.java
@Override public List<VariantInfo> getRecords(Map<String, String> options) { Connection con;//from w ww.j a va 2 s . co m Statement stmt; List<VariantInfo> list = new ArrayList<>(100); String dbName = options.get("db_name"); showDb(dbName); try { Class.forName("org.sqlite.JDBC"); con = DriverManager.getConnection("jdbc:sqlite:" + dbName); List<String> whereClauses = new ArrayList<>(10); Map<String, List<String>> sampleGenotypes; Map<String, String> controlsMAFs = new LinkedHashMap<>(); sampleGenotypes = processSamplesGT(options); if (options.containsKey("region_list") && !options.get("region_list").equals("")) { StringBuilder regionClauses = new StringBuilder("("); String[] regions = options.get("region_list").split(","); Pattern patternReg = Pattern.compile("(\\w+):(\\d+)-(\\d+)"); Matcher matcherReg, matcherChr; for (int i = 0; i < regions.length; i++) { String region = regions[i]; matcherReg = patternReg.matcher(region); if (matcherReg.find()) { String chr = matcherReg.group(1); int start = Integer.valueOf(matcherReg.group(2)); int end = Integer.valueOf(matcherReg.group(3)); regionClauses.append("( variant_stats.chromosome='").append(chr).append("' AND "); regionClauses.append("variant_stats.position>=").append(start).append(" AND "); regionClauses.append("variant_stats.position<=").append(end).append(" )"); if (i < (regions.length - 1)) { regionClauses.append(" OR "); } } else { Pattern patternChr = Pattern.compile("(\\w+)"); matcherChr = patternChr.matcher(region); if (matcherChr.find()) { String chr = matcherChr.group(); regionClauses.append("( variant_stats.chromosome='").append(chr).append("')"); if (i < (regions.length - 1)) { regionClauses.append(" OR "); } } else { System.err.println("ERROR: Region (" + region + ")"); } } } regionClauses.append(" ) "); whereClauses.add(regionClauses.toString()); } if (options.containsKey("chr_pos") && !options.get("chr_pos").equals("")) { whereClauses.add("variant_stats.chromosome='" + options.get("chr_pos") + "'"); if (options.containsKey("start_pos") && !options.get("start_pos").equals("")) { whereClauses.add("variant_stats.position>=" + options.get("start_pos")); } if (options.containsKey("end_pos") && !options.get("end_pos").equals("")) { whereClauses.add("variant_stats.position<=" + options.get("end_pos")); } } if (options.containsKey("mend_error") && !options.get("mend_error").equals("")) { String val = options.get("mend_error"); String opt = options.get("option_mend_error"); whereClauses.add("variant_stats.mendel_err " + opt + " " + val); } if (options.containsKey("is_indel") && options.get("is_indel").equalsIgnoreCase("on")) { whereClauses.add("variant_stats.is_indel=1"); } if (options.containsKey("maf") && !options.get("maf").equals("")) { String val = options.get("maf"); String opt = options.get("option_maf"); whereClauses.add("variant_stats.maf " + opt + " " + val); } if (options.containsKey("mgf") && !options.get("mgf").equals("")) { String val = options.get("mgf"); String opt = options.get("option_mgf"); whereClauses.add("variant_stats.mgf " + opt + " " + val); } if (options.containsKey("miss_allele") && !options.get("miss_allele").equals("")) { String val = options.get("miss_allele"); String opt = options.get("option_miss_allele"); whereClauses.add("variant_stats.miss_allele " + opt + " " + val); } if (options.containsKey("miss_gt") && !options.get("miss_gt").equals("")) { String val = options.get("miss_gt"); String opt = options.get("option_miss_gt"); whereClauses.add("variant_stats.miss_gt " + opt + " " + val); } if (options.containsKey("cases_percent_dominant") && !options.get("cases_percent_dominant").equals("")) { String val = options.get("cases_percent_dominant"); String opt = options.get("option_cases_dom"); whereClauses.add("variant_stats.cases_percent_dominant " + opt + " " + val); } if (options.containsKey("controls_percent_dominant") && !options.get("controls_percent_dominant").equals("")) { String val = options.get("controls_percent_dominant"); String opt = options.get("option_controls_dom"); whereClauses.add("variant_stats.controls_percent_dominant " + opt + " " + val); } if (options.containsKey("cases_percent_recessive") && !options.get("cases_percent_recessive").equals("")) { String val = options.get("cases_percent_recessive"); String opt = options.get("option_cases_rec"); whereClauses.add("variant_stats.cases_percent_recessive " + opt + " " + val); } if (options.containsKey("controls_percent_recessive") && !options.get("controls_percent_recessive").equals("")) { String val = options.get("controls_percent_recessive"); String opt = options.get("option_controls_rec"); whereClauses.add("variant_stats.controls_percent_recessive " + opt + " " + val); } if (options.containsKey("biotype") && !options.get("biotype").equals("")) { String[] biotypes = options.get("biotype").split(","); StringBuilder biotypesClauses = new StringBuilder(" ( "); for (int i = 0; i < biotypes.length; i++) { biotypesClauses.append("variant_effect.feature_biotype LIKE '%").append(biotypes[i]) .append("%'"); if (i < (biotypes.length - 1)) { biotypesClauses.append(" OR "); } } biotypesClauses.append(" ) "); whereClauses.add(biotypesClauses.toString()); } if (options.containsKey("exc_1000g_controls") && options.get("exc_1000g_controls").equalsIgnoreCase("on")) { whereClauses.add("(key NOT LIKE '1000G%' OR key is null)"); } else if (options.containsKey("maf_1000g_controls") && !options.get("maf_1000g_controls").equals("")) { controlsMAFs.put("1000G", options.get("maf_1000g_controls")); } if (options.containsKey("exc_bier_controls") && options.get("exc_bier_controls").equalsIgnoreCase("on")) { whereClauses.add("(key NOT LIKE 'BIER%' OR key is null)"); } else if (options.containsKey("maf_bier_controls") && !options.get("maf_bier_controls").equals("")) { controlsMAFs.put("BIER", options.get("maf_bier_controls")); } if (options.containsKey("exc_evs_controls") && options.get("exc_evs_controls").equalsIgnoreCase("on")) { whereClauses.add("(key NOT LIKE 'EVS%' OR key is null)"); } else if (options.containsKey("maf_evs_controls") && !options.get("maf_evs_controls").equals("")) { controlsMAFs.put("BIER", options.get("maf_evs_controls")); } if (options.containsKey("conseq_type[]") && !options.get("conseq_type[]").equals("")) { whereClauses.add(processConseqType(options.get("conseq_type[]"))); } if (options.containsKey("genes") && !options.get("genes").equals("")) { whereClauses.add(processGeneList(options.get("genes"))); // processGeneList(options.get("genes")); } if (sampleGenotypes.size() > 0) { StringBuilder sg = new StringBuilder(); int csg = 0; sg.append("("); for (Map.Entry<String, List<String>> entry : sampleGenotypes.entrySet()) { sg.append("("); sg.append("sample_name='").append(entry.getKey()).append("' AND ("); for (int i = 0; i < entry.getValue().size(); i++) { String[] aux = entry.getValue().get(i).split("/"); sg.append("("); sg.append("allele_1=").append(aux[0]).append(" AND allele_2=").append(aux[1]); sg.append(")"); if (i + 1 < entry.getValue().size()) { sg.append(" OR "); } } sg.append(")"); sg.append(" OR sample_name<>'").append(entry.getKey()).append("'"); sg.append(")"); if (csg + 1 < sampleGenotypes.entrySet().size()) { sg.append(" AND "); } csg++; } sg.append(")"); System.out.println(sg); whereClauses.add(sg.toString()); } String sql = "SELECT count(*) as count FROM sample ;"; stmt = con.createStatement(); ResultSet rs = stmt.executeQuery(sql); int numSamples = 0; while (rs.next()) { numSamples = rs.getInt("count"); } stmt.close(); System.out.println("controlsMAFs = " + controlsMAFs); System.out.println("sampleGenotypes = " + sampleGenotypes); String innerJoinVariantSQL = " left join variant_info on variant.id_variant=variant_info.id_variant "; // String innerJoinEffectSQL = " inner join variant_effect on variant_effect.chromosome=variant.chromosome AND variant_effect.position=variant.position AND variant_effect.reference_allele=variant.ref AND variant_effect.alternative_allele = variant.alt "; sql = "SELECT distinct variant.genes,variant.consequence_types, variant.id_variant, variant_info.key, variant_info.value, sample_info.sample_name, sample_info.allele_1, sample_info.allele_2, variant_stats.chromosome ," + "variant_stats.position , variant_stats.allele_ref , variant_stats.allele_alt , variant_stats.id , variant_stats.maf , variant_stats.mgf, " + "variant_stats.allele_maf , variant_stats.genotype_maf , variant_stats.miss_allele , variant_stats.miss_gt , variant_stats.mendel_err ," + "variant_stats.is_indel , variant_stats.cases_percent_dominant , variant_stats.controls_percent_dominant , variant_stats.cases_percent_recessive , variant_stats.controls_percent_recessive, " + "variant.polyphen_score, variant.polyphen_effect, variant.sift_score, variant.sift_effect " + " FROM variant_stats " + "inner join variant on variant_stats.chromosome=variant.chromosome AND variant_stats.position=variant.position AND variant_stats.allele_ref=variant.ref AND variant_stats.allele_alt=variant.alt " + "inner join sample_info on variant.id_variant=sample_info.id_variant " + innerJoinVariantSQL; if (whereClauses.size() > 0) { StringBuilder where = new StringBuilder(" where "); for (int i = 0; i < whereClauses.size(); i++) { where.append(whereClauses.get(i)); if (i < whereClauses.size() - 1) { where.append(" AND "); } } sql += where.toString() + " ORDER BY variant_stats.chromosome , variant_stats.position , variant_stats.allele_ref , variant_stats.allele_alt ;"; } System.out.println(sql); System.out.println("Start SQL"); long start = System.currentTimeMillis(); stmt = con.createStatement(); rs = stmt.executeQuery(sql); VariantStats vs; VariantInfo vi = null; String chr = ""; int pos = 0; String ref = "", alt = ""; System.out.println("End SQL: " + ((System.currentTimeMillis() - start) / 1000.0) + " s."); System.out.println("Processing"); while (rs.next()) { if (!rs.getString("chromosome").equals(chr) || rs.getInt("position") != pos || !rs.getString("allele_ref").equals(ref) || !rs.getString("allele_alt").equals(alt)) { chr = rs.getString("chromosome"); pos = rs.getInt("position"); ref = rs.getString("allele_ref"); alt = rs.getString("allele_alt"); if (vi != null && filterGenotypes(vi, numSamples) && filterControls(vi, controlsMAFs)) { list.add(vi); } vi = new VariantInfo(chr, pos, ref, alt); vs = new VariantStats(chr, pos, ref, alt, rs.getDouble("maf"), rs.getDouble("mgf"), rs.getString("allele_maf"), rs.getString("genotype_maf"), rs.getInt("miss_allele"), rs.getInt("miss_gt"), rs.getInt("mendel_err"), rs.getInt("is_indel") == 1, rs.getDouble("cases_percent_dominant"), rs.getDouble("controls_percent_dominant"), rs.getDouble("cases_percent_recessive"), rs.getDouble("controls_percent_recessive")); vs.setId(rs.getString("id")); // vi.addGenotypes(rs.getString("genotypes")); vi.addStats(vs); vi.addGenes(rs.getString("genes")); vi.addConsequenceTypes(rs.getString("consequence_types")); vi.setPolyphen_score(rs.getDouble("polyphen_score")); vi.setSift_score(rs.getDouble("sift_score")); vi.setPolyphen_effect(rs.getInt("polyphen_effect")); vi.setSift_effect(rs.getInt("sift_effect")); } if (rs.getString("key") != null && rs.getString("value") != null) { vi.addControl(rs.getString("key"), rs.getString("value")); } String sample = rs.getString("sample_name"); String gt = rs.getInt("allele_1") + "/" + rs.getInt("allele_2"); vi.addSammpleGenotype(sample, gt); // vi.addGeneAndConsequenceType(rs.getString("gene_name"), rs.getString("consequence_type_obo")); } if (vi != null && filterGenotypes(vi, numSamples) && filterControls(vi, controlsMAFs)) { list.add(vi); } stmt.close(); System.out.println("Total: (" + list.size() + ")"); System.out.println("End processing: " + ((System.currentTimeMillis() - start) / 1000.0) + " s."); con.close(); } catch (ClassNotFoundException | SQLException e) { System.err.println("STATS: " + e.getClass().getName() + ": " + e.getMessage()); } return list; }
From source file:edu.emory.cci.aiw.umls.UMLSDatabaseConnection.java
@Override public Map<String, MapToIdResult<AtomUID>> mapToAUI(String phrase, List<SAB> sab) throws UMLSQueryException { Map<String, MapToIdResult<AtomUID>> result = new HashMap<String, MapToIdResult<AtomUID>>(); try {// w w w .j a v a 2s. com setupConn(); Map<String, List<String>> matches = matches(phrase, mapToId(phrase, IdType.AUI_IDTYPE, sab)); if (matches.containsKey(phrase)) { for (Map.Entry<String, List<String>> entry : matches.entrySet()) { result.put(entry.getKey(), MapToIdResult.<AtomUID>fromUidAndStr(AtomUID.fromString(entry.getValue().get(0)), UMLSQueryStringValue.fromString(entry.getValue().get(1)))); } return result; } else { String[] words = phrase.split("\\s"); for (String[] p : allLengthPermutations(words)) { if (p.length == 1 && p[0].length() < 4) { continue; } String permutedString = StringUtils.join(p, ' '); matches = (matches(permutedString, mapToId(permutedString, IdType.AUI_IDTYPE, sab))); for (Map.Entry<String, List<String>> entry : matches.entrySet()) { result.put(entry.getKey(), MapToIdResult.<AtomUID>fromUidAndStr(AtomUID.fromString(entry.getValue().get(0)), UMLSQueryStringValue.fromString(entry.getValue().get(1)))); } } return result; } } catch (SQLException sqle) { throw new UMLSQueryException(sqle); } catch (MalformedUMLSUniqueIdentifierException muuie) { throw new UMLSQueryException(muuie); } finally { tearDownConn(); } }
From source file:edu.emory.cci.aiw.umls.UMLSDatabaseConnection.java
@Override public Map<String, MapToIdResult<StringUID>> mapToSUI(String phrase, List<SAB> sab) throws UMLSQueryException { Map<String, MapToIdResult<StringUID>> result = new HashMap<String, MapToIdResult<StringUID>>(); try {/*from w w w . j a v a 2 s .co m*/ setupConn(); Map<String, List<String>> matches = matches(phrase, mapToId(phrase, IdType.CUI_IDTYPE, sab)); if (matches.containsKey(phrase)) { for (Map.Entry<String, List<String>> entry : matches.entrySet()) { result.put(entry.getKey(), MapToIdResult.<StringUID>fromUidAndStr(StringUID.fromString(entry.getValue().get(0)), UMLSQueryStringValue.fromString(entry.getValue().get(1)))); } return result; } else { String[] words = phrase.split("\\s"); for (String[] p : allLengthPermutations(words)) { if (p.length == 1 && p[0].length() < 4) { continue; } String permutedString = StringUtils.join(p, ' '); matches = (matches(permutedString, mapToId(permutedString, IdType.CUI_IDTYPE, sab))); for (Map.Entry<String, List<String>> entry : matches.entrySet()) { result.put(entry.getKey(), MapToIdResult.<StringUID>fromUidAndStr( StringUID.fromString(entry.getValue().get(0)), UMLSQueryStringValue.fromString(entry.getValue().get(1)))); } } return result; } } catch (SQLException sqle) { throw new UMLSQueryException(sqle); } catch (MalformedUMLSUniqueIdentifierException muuie) { throw new UMLSQueryException(muuie); } finally { tearDownConn(); } }
From source file:edu.emory.cci.aiw.umls.UMLSDatabaseConnection.java
@Override public Map<String, MapToIdResult<ConceptUID>> mapToCUI(String phrase, List<SAB> sab) throws UMLSQueryException { Map<String, MapToIdResult<ConceptUID>> result = new HashMap<String, MapToIdResult<ConceptUID>>(); try {/* w ww . j a v a 2 s . co m*/ setupConn(); Map<String, List<String>> matches = matches(phrase, mapToId(phrase, IdType.CUI_IDTYPE, sab)); if (matches.containsKey(phrase)) { for (Map.Entry<String, List<String>> entry : matches.entrySet()) { result.put(entry.getKey(), MapToIdResult.<ConceptUID>fromUidAndStr(ConceptUID.fromString(entry.getValue().get(0)), UMLSQueryStringValue.fromString(entry.getValue().get(1)))); } return result; } else { String[] words = phrase.split("\\s"); for (String[] p : allLengthPermutations(words)) { if (p.length == 1 && p[0].length() < 4) { continue; } String permutedString = StringUtils.join(p, ' '); matches = (matches(permutedString, mapToId(permutedString, IdType.CUI_IDTYPE, sab))); for (Map.Entry<String, List<String>> entry : matches.entrySet()) { result.put(entry.getKey(), MapToIdResult.<ConceptUID>fromUidAndStr( ConceptUID.fromString(entry.getValue().get(0)), UMLSQueryStringValue.fromString(entry.getValue().get(1)))); } } return result; } } catch (SQLException sqle) { throw new UMLSQueryException(sqle); } catch (MalformedUMLSUniqueIdentifierException muuie) { throw new UMLSQueryException(muuie); } finally { tearDownConn(); } }
From source file:edu.emory.cci.aiw.umls.UMLSDatabaseConnection.java
@Override public Map<String, MapToIdResult<LexicalUID>> mapToLUI(String phrase, List<SAB> sab) throws UMLSQueryException { Map<String, MapToIdResult<LexicalUID>> result = new HashMap<String, MapToIdResult<LexicalUID>>(); try {/* w ww .j a v a 2s . c o m*/ setupConn(); Map<String, List<String>> matches = matches(phrase, mapToId(phrase, IdType.LUI_IDTYPE, sab)); if (matches.containsKey(phrase)) { for (Map.Entry<String, List<String>> entry : matches.entrySet()) { result.put(entry.getKey(), MapToIdResult.<LexicalUID>fromUidAndStr(LexicalUID.fromString(entry.getValue().get(0)), UMLSQueryStringValue.fromString(entry.getValue().get(1)))); } return result; } else { String[] words = phrase.split("\\s"); for (String[] p : allLengthPermutations(words)) { if (p.length == 1 && p[0].length() < 4) { continue; } String permutedString = StringUtils.join(p, ' '); matches = (matches(permutedString, mapToId(permutedString, IdType.LUI_IDTYPE, sab))); for (Map.Entry<String, List<String>> entry : matches.entrySet()) { result.put(entry.getKey(), MapToIdResult.<LexicalUID>fromUidAndStr( LexicalUID.fromString(entry.getValue().get(0)), UMLSQueryStringValue.fromString(entry.getValue().get(1)))); } } return result; } } catch (SQLException sqle) { throw new UMLSQueryException(sqle); } catch (MalformedUMLSUniqueIdentifierException muuie) { throw new UMLSQueryException(muuie); } finally { tearDownConn(); } }
From source file:org.apache.falcon.resource.AbstractEntityManager.java
private boolean isEntityFiltered(Entity entity, EntityList.EntityFilterByFields filter, Map.Entry<String, List<String>> pair) { switch (filter) { case TYPE:/*from w w w .j a v a 2s. c o m*/ return !containsIgnoreCase(pair.getValue(), entity.getEntityType().toString()); case NAME: return !containsIgnoreCase(pair.getValue(), entity.getName()); case STATUS: return !containsIgnoreCase(pair.getValue(), getStatusString(entity)); case PIPELINES: if (!entity.getEntityType().equals(EntityType.PROCESS)) { throw FalconWebException.newException( "Invalid filterBy key for non process entities " + pair.getKey(), Response.Status.BAD_REQUEST); } return !EntityUtil.getPipelines(entity).contains(pair.getValue().get(0)); case CLUSTER: return !EntityUtil.getClustersDefined(entity).contains(pair.getValue().get(0)); case TAGS: return isFilteredByTags(getFilterByTags(pair.getValue()), EntityUtil.getTags(entity)); default: return false; } }