com.rits.cloning.Cloner Java Examples

private Thread fullConfigSaveThread(final int counter) throws InterruptedException {
    return createThread(new Runnable() {
        @Override
        public void run() {
            try {
                CruiseConfig cruiseConfig = cachedGoConfig.loadForEditing();
                CruiseConfig cruiseConfig1 = new Cloner().deepClone(cruiseConfig);
                cruiseConfig1.addEnvironment(UUID.randomUUID().toString());

                goConfigDao.updateFullConfig(new FullConfigUpdateCommand(cruiseConfig1, cruiseConfig.getMd5()));
            } catch (Exception e) {
                e.printStackTrace();
            }
        }
    }, "full-config-save-thread" + counter);

}
 

@Test
void shouldDetectCyclicDependencies() {
    String pipelineName = "p1";
    BasicCruiseConfig cruiseConfig = GoConfigMother.configWithPipelines(pipelineName, "p2", "p3");
    PipelineConfig p2 = cruiseConfig.getPipelineConfigByName(new CaseInsensitiveString("p2"));
    p2.addMaterialConfig(new DependencyMaterialConfig(new CaseInsensitiveString(pipelineName), new CaseInsensitiveString("stage")));
    PipelineConfig p3 = cruiseConfig.getPipelineConfigByName(new CaseInsensitiveString("p3"));
    p3.addMaterialConfig(new DependencyMaterialConfig(new CaseInsensitiveString("p2"), new CaseInsensitiveString("stage")));

    PipelineConfig p1 = cruiseConfig.getPipelineConfigByName(new CaseInsensitiveString(pipelineName));
    p1 = new Cloner().deepClone(p1); // Do not remove cloning else it changes the underlying cache object defeating the purpose of the test.
    p1.addMaterialConfig(new DependencyMaterialConfig(new CaseInsensitiveString("p3"), new CaseInsensitiveString("stage")));
    p1.validateTree(PipelineConfigSaveValidationContext.forChain(true, cruiseConfig.getGroups().first().getGroup(), cruiseConfig, p1));
    assertThat(p1.materialConfigs().errors().isEmpty()).isFalse();
    assertThat(p1.materialConfigs().errors().on("base")).isEqualTo("Circular dependency: p1 <- p2 <- p3 <- p1");
}
 

private void validateFetchTasksForOtherPipelines(PipelineConfigSaveValidationContext validationContext, PipelineConfig downstreamPipeline) {
    for (StageConfig stageConfig : downstreamPipeline.getStages()) {
        for (JobConfig jobConfig : stageConfig.getJobs()) {
            for (Task task : jobConfig.getTasks()) {
                if (task instanceof FetchTask) {
                    FetchTask fetchTask = (FetchTask) task;
                    if (fetchTask.getPipelineNamePathFromAncestor() != null && !StringUtils.isBlank(CaseInsensitiveString.str(fetchTask.getPipelineNamePathFromAncestor().getPath())) && fetchTask.getPipelineNamePathFromAncestor().pathIncludingAncestor().contains(pipelineConfig.name())) {
                        fetchTask = new Cloner().deepClone(fetchTask);
                        fetchTask.validateTask(validationContext.withParent(downstreamPipeline).withParent(stageConfig).withParent(jobConfig));
                        List<String> allErrors = fetchTask.errors().getAll();
                        for (String error : allErrors) {
                            pipelineConfig.errors().add("base", error);
                        }
                    }
                }
            }
        }
    }
}
 

private void validateDependencyMaterialsForDownstreams(PipelineConfigSaveValidationContext validationContext, CaseInsensitiveString selected, PipelineConfig downstreamPipeline) {
    Node dependenciesOfSelectedPipeline = validationContext.getDependencyMaterialsFor(selected);
    for (Node.DependencyNode dependencyNode : dependenciesOfSelectedPipeline.getDependencies()) {
        if (dependencyNode.getPipelineName().equals(pipelineConfig.name())) {
            for (MaterialConfig materialConfig : downstreamPipeline.materialConfigs()) {
                if (materialConfig instanceof DependencyMaterialConfig) {
                    DependencyMaterialConfig dependencyMaterialConfig = new Cloner().deepClone((DependencyMaterialConfig) materialConfig);
                    dependencyMaterialConfig.validate(validationContext.withParent(downstreamPipeline));
                    List<String> allErrors = dependencyMaterialConfig.errors().getAll();
                    for (String error : allErrors) {
                        pipelineConfig.errors().add("base", error);
                    }
                }
            }
        }
    }
}
 

@Test
public void shouldAddErrorsToRawCruiseConfigWhenTemplateHasErrors() {
    CruiseConfig cruiseConfig = GoConfigMother.configWithPipelines("pipeline-1");
    cruiseConfig.getTemplates().add(
            new PipelineTemplateConfig(new CaseInsensitiveString("invalid template name"), new StageConfig(new CaseInsensitiveString("stage-1"), new JobConfigs(new JobConfig("job-1"))
            )));
    PipelineConfig pipelineWithTemplate = new PipelineConfig(new CaseInsensitiveString("pipeline-with-template"), MaterialConfigsMother.defaultMaterialConfigs());
    pipelineWithTemplate.setTemplateName(new CaseInsensitiveString("invalid template name"));
    cruiseConfig.getGroups().get(0).add(pipelineWithTemplate);

    CruiseConfig rawCruiseConfig = new Cloner().deepClone(cruiseConfig);
    MagicalGoConfigXmlLoader.validate(cruiseConfig);
    cruiseConfig.copyErrorsTo(rawCruiseConfig);

    ConfigErrors templateErrors = rawCruiseConfig.getTemplateByName(new CaseInsensitiveString("invalid template name")).errors();
    assertThat(templateErrors.getAll().size(), is(1));
    assertThat(templateErrors.getAll().get(0),
            is("Invalid template name 'invalid template name'. This must be alphanumeric and can contain underscores, hyphens and periods (however, it cannot start with a period). The maximum allowed length is 255 characters."));
}
 

@Test
public void shouldHandlePipelinesWithTemplates() {
    CruiseConfig cruiseConfig = GoConfigMother.configWithPipelines("pipeline-1");
    cruiseConfig.getTemplates().add(
            new PipelineTemplateConfig(new CaseInsensitiveString("template-1"), new StageConfig(new CaseInsensitiveString("invalid stage name"), new JobConfigs(new JobConfig("job-1"))
            )));
    PipelineConfig pipelineWithTemplate = new PipelineConfig(new CaseInsensitiveString("pipeline-with-template"), MaterialConfigsMother.defaultMaterialConfigs());
    pipelineWithTemplate.setTemplateName(new CaseInsensitiveString("template-1"));
    cruiseConfig.getGroups().get(0).add(pipelineWithTemplate);

    CruiseConfig rawCruiseConfig = new Cloner().deepClone(cruiseConfig);
    MagicalGoConfigXmlLoader.validate(cruiseConfig);
    cruiseConfig.copyErrorsTo(rawCruiseConfig);
    assertThat(rawCruiseConfig.pipelineConfigByName(new CaseInsensitiveString("pipeline-with-template")).errors().isEmpty(), is(true));
    assertThat(cruiseConfig.pipelineConfigByName(new CaseInsensitiveString("pipeline-with-template")).getStage(new CaseInsensitiveString("invalid stage name")).errors().isEmpty(), is(false));

    assertThat(rawCruiseConfig.getTemplateByName(new CaseInsensitiveString("template-1")).errors().isEmpty(), is(true));
}
 

@Test
public void shouldErrorOutOnUpdateConfigWithValidPartials_WithMainConfigBreakingPartials() throws GitAPIException, IOException {
    setupExternalConfigRepoWithDependencyMaterialOnPipelineInMainXml("upstream", "downstream");
    String gitShaBeforeSave = configRepository.getCurrentRevCommit().getName();
    CruiseConfig originalConfig = cachedGoConfig.loadForEditing();
    CruiseConfig editedConfig = new Cloner().deepClone(originalConfig);

    editedConfig.getGroups().remove(editedConfig.findGroup("default"));

    try {
        cachedGoConfig.writeFullConfigWithLock(new FullConfigUpdateCommand(editedConfig, goConfigService.configFileMd5()));
        fail("Expected the test to fail");
    } catch (Exception e) {
        String gitShaAfterSave = configRepository.getCurrentRevCommit().getName();
        String configXmlFromConfigFolder = FileUtils.readFileToString(new File(goConfigDao.fileLocation()), UTF_8);
        assertThat(cachedGoConfig.loadForEditing()).isEqualTo(originalConfig);
        assertThat(gitShaAfterSave).isEqualTo(gitShaBeforeSave);
        assertThat(cachedGoConfig.loadForEditing().getMd5()).isEqualTo(configRepository.getCurrentRevision().getMd5());
        assertThat(cachedGoConfig.currentConfig().getMd5()).isEqualTo(configRepository.getCurrentRevision().getMd5());
        assertThat(configXmlFromConfigFolder).isEqualTo(configRepository.getCurrentRevision().getContent());
        RepoConfigOrigin origin = (RepoConfigOrigin) cachedGoPartials.lastValidPartials().get(0).getOrigin();
        assertThat(origin.getRevision()).isEqualTo("r1");
    }
}
 

@Test
public void shouldCancelBuildsForAllJobsWhenPipelineIsDeleted() throws Exception {
    buildAssignmentService.initialize();
    fixture = new PipelineWithTwoStages(materialRepository, transactionTemplate, temporaryFolder).usingTwoJobs();
    fixture.usingConfigHelper(configHelper).usingDbHelper(dbHelper).onSetUp();
    fixture.createPipelineWithFirstStageScheduled();

    buildAssignmentService.onTimer();

    PipelineConfig pipelineConfig = new Cloner().deepClone(configHelper.getCachedGoConfig().currentConfig().getPipelineConfigByName(new CaseInsensitiveString(fixture.pipelineName)));

    pipelineConfigService.deletePipelineConfig(loserUser, pipelineConfig, new HttpLocalizedOperationResult());

    Pipeline pipeline = pipelineDao.mostRecentPipeline(fixture.pipelineName);
    JobInstance job1 = pipeline.getFirstStage().getJobInstances().getByName(fixture.JOB_FOR_DEV_STAGE);
    JobInstance job2 = pipeline.getFirstStage().getJobInstances().getByName(fixture.DEV_STAGE_SECOND_JOB);

    assertThat(job1.getState(), is(JobState.Completed));
    assertThat(job1.getResult(), is(JobResult.Cancelled));
    assertThat(job2.getState(), is(JobState.Completed));
    assertThat(job2.getResult(), is(JobResult.Cancelled));

    buildAssignmentService.onTimer();
    List<JobPlan> latestJobPlans = buildAssignmentService.jobPlans();
    assertThat(latestJobPlans.size(), is(0));
}
 

@Test
public void shouldCancelBuildsForDeletedStagesWhenPipelineConfigChanges() throws Exception {
    buildAssignmentService.initialize();

    fixture.createPipelineWithFirstStageScheduled();
    buildAssignmentService.onTimer();

    PipelineConfig originalPipelineConfig = configHelper.getCachedGoConfig().currentConfig().getPipelineConfigByName(new CaseInsensitiveString(fixture.pipelineName));
    PipelineConfig pipelineConfig = new Cloner().deepClone(originalPipelineConfig);
    String md5 = entityHashingService.hashForEntity(originalPipelineConfig, fixture.groupName);
    StageConfig devStage = pipelineConfig.findBy(new CaseInsensitiveString(fixture.devStage));
    pipelineConfig.remove(devStage);
    HttpLocalizedOperationResult result = new HttpLocalizedOperationResult();
    pipelineConfigService.updatePipelineConfig(loserUser, pipelineConfig, fixture.groupName, md5, result);

    Pipeline pipeline = pipelineDao.mostRecentPipeline(fixture.pipelineName);
    JobInstance job = pipeline.getFirstStage().getJobInstances().first();
    assertThat(job.getState(), is(JobState.Completed));
    assertThat(job.getResult(), is(JobResult.Cancelled));

    buildAssignmentService.onTimer();
    List<JobPlan> latestJobPlans = buildAssignmentService.jobPlans();
    assertThat(latestJobPlans.size(), is(0));
}
 

@Test
public void shouldReturnTheLatestConfigAsResultWhenThereIsAnMd5Conflict() {
    configHelper.addPipeline("pipeline", "stage");
    String md5 = goConfigService.getConfigForEditing().getMd5();
    goConfigService.updateConfigFromUI(new AddStageToPipelineCommand("secondStage"), md5, Username.ANONYMOUS, new HttpLocalizedOperationResult());

    HttpLocalizedOperationResult result = new HttpLocalizedOperationResult();
    ConfigUpdateResponse response = goConfigService.updateConfigFromUI(new AddStageToPipelineCommand("thirdStage"), md5, Username.ANONYMOUS, result);

    assertFailedResult(result, "Save failed. Configuration file has been modified by someone else.");
    CruiseConfig expectedConfig = goConfigService.getConfigForEditing();
    CruiseConfig modifiedConfig = new Cloner().deepClone(expectedConfig);
    ReflectionUtil.setField(modifiedConfig, "md5", expectedConfig.getMd5());
    PipelineConfig expected = modifiedConfig.pipelineConfigByName(new CaseInsensitiveString("pipeline"));
    expected.addStageWithoutValidityAssertion(StageConfigMother.custom("thirdStage", "job"));

    PipelineConfig actual = (PipelineConfig) response.getNode();

    assertThat(response.configAfterUpdate(), is(expectedConfig));
    assertThat(response.getCruiseConfig(), is(modifiedConfig));
    assertThat(actual, is(expected));
    assertFailedResult(result, "Save failed. Configuration file has been modified by someone else.");
}
 

@Test
void shouldInvalidateAuthenticationTokenIfTheSecurityConfigHasChanged() throws IOException, ServletException {
    request = HttpRequestBuilder.GET("/")
            .withRequestedSessionIdFromSession()
            .build();

    final AuthenticationToken<UsernamePassword> authenticationToken = setupAuthentication();
    SessionUtils.setAuthenticationTokenAfterRecreatingSession(authenticationToken, request);
    final HttpSession originalSession = request.getSession(false);

    assertThat(SessionUtils.getAuthenticationToken(request).isAuthenticated(clock, systemEnvironment)).isTrue();
    filter.doFilter(request, response, filterChain);

    clock.addSeconds(1);
    GoConfigMother.addUserAsSuperAdmin(cruiseConfig, "bob");
    filter.onConfigChange(new Cloner().deepClone(cruiseConfig));

    response.reset();
    filter.doFilter(request, response, filterChain);

    assertThat(SessionUtils.getAuthenticationToken(request).isAuthenticated(clock, systemEnvironment)).isFalse();
    assertThat(request.getSession(false)).isSameAs(originalSession);
    verify(cacheService, times(1)).invalidateCache();
}
 

@BeforeEach
void setUp() {
    initMocks(this);
    //request = new MockHttpServletRequest();
    response = new MockHttpServletResponse();
    clock = new TestingClock();
    systemEnvironment = new SystemEnvironment();
    filterChain = mock(FilterChain.class);

    cruiseConfig = new BasicCruiseConfig();
    GoConfigMother.enableSecurityWithPasswordFilePlugin(cruiseConfig);

    filter = new InvalidateAuthenticationOnSecurityConfigChangeFilter(goConfigService, clock, cacheService, pluginRoleService);
    filter.initialize();
    filter.onPluginRoleChange();
    filter.onConfigChange(new Cloner().deepClone(cruiseConfig));
    reset(cacheService);
}
 

@Test
public void shouldGetAllViewableGroups() throws Exception {
    CruiseConfig cruiseConfig = new Cloner().deepClone(this.cruiseConfig);
    ReflectionUtil.setField(cruiseConfig, "allPipelineConfigs", null);
    cruiseConfig.addPipeline("group1", PipelineConfigMother.pipelineConfig(UUID.randomUUID().toString()));
    cruiseConfig.addPipeline("group2", PipelineConfigMother.pipelineConfig(UUID.randomUUID().toString()));

    when(goConfigService.cruiseConfig()).thenReturn(cruiseConfig);
    when(goConfigService.getAllPipelineConfigs()).thenReturn(cruiseConfig.getAllPipelineConfigs());

    Username username = new Username("user1");

    when(securityService.hasViewPermissionForGroup(CaseInsensitiveString.str(username.getUsername()), "group1")).thenReturn(true);
    when(securityService.hasViewPermissionForGroup(CaseInsensitiveString.str(username.getUsername()), "group2")).thenReturn(false);

    List<PipelineConfigs> pipelineConfigs = pipelineConfigService.viewableGroupsFor(username);

    assertThat(pipelineConfigs.size(), is(1));
    assertThat(pipelineConfigs.get(0).getGroup(), is("group1"));
}
 

@Test
public void shouldGetAllViewableMergePipelineConfigs() throws Exception {
    CruiseConfig mergedCruiseConfig = new Cloner().deepClone(cruiseConfig);
    ReflectionUtil.setField(mergedCruiseConfig, "allPipelineConfigs", null);
    mergedCruiseConfig.addPipeline("group1", PipelineConfigMother.pipelineConfig(UUID.randomUUID().toString()));
    mergedCruiseConfig.addPipeline("group2", PipelineConfigMother.pipelineConfig(UUID.randomUUID().toString()));
    mergedCruiseConfig.addPipeline("group3", PipelineConfigMother.pipelineConfig(UUID.randomUUID().toString()));

    when(goConfigService.getMergedConfigForEditing()).thenReturn(mergedCruiseConfig);
    when(goConfigService.getAllPipelineConfigs()).thenReturn(mergedCruiseConfig.getAllPipelineConfigs());

    Username username = new Username("user1");

    when(securityService.hasViewPermissionForGroup(CaseInsensitiveString.str(username.getUsername()), "group1")).thenReturn(true);
    when(securityService.hasViewPermissionForGroup(CaseInsensitiveString.str(username.getUsername()), "group2")).thenReturn(true);
    when(securityService.hasViewPermissionForGroup(CaseInsensitiveString.str(username.getUsername()), "group3")).thenReturn(false);

    List<PipelineConfigs> pipelineConfigs = pipelineConfigService.viewableGroupsForUserIncludingConfigRepos(username);

    assertThat(pipelineConfigs.size(), is(2));
    assertThat(pipelineConfigs.get(0).getGroup(), is("group2"));
    assertThat(pipelineConfigs.get(1).getGroup(), is("group1"));
}
 

@Test
void shouldReturnAllTheLocalEnvironments() {
    String uat = "uat";

    BasicEnvironmentConfig local = new BasicEnvironmentConfig(new CaseInsensitiveString("uat"));
    local.addEnvironmentVariable("user", "admin");
    BasicEnvironmentConfig remote = new BasicEnvironmentConfig(new CaseInsensitiveString("uat"));
    remote.addEnvironmentVariable("foo", "bar");
    MergeEnvironmentConfig merged = new MergeEnvironmentConfig(local, remote);

    EnvironmentsConfig environments = new EnvironmentsConfig();
    environments.add(merged);

    when(agentService.getAgentInstances()).thenReturn(new AgentInstances(null));

    environmentConfigService.syncEnvironments(environments);

    BasicCruiseConfig cruiseConfig = new BasicCruiseConfig();
    BasicEnvironmentConfig env = (BasicEnvironmentConfig) environmentConfigService.getEnvironmentConfig(uat).getLocal();
    cruiseConfig.addEnvironment(env);
    List<BasicEnvironmentConfig> expectedToEdit = singletonList(new Cloner().deepClone(env));

    when(mockGoConfigService.getConfigForEditing()).thenReturn(cruiseConfig);

    assertThat(environmentConfigService.getAllLocalEnvironments(), is(expectedToEdit));
}
 

@BeforeEach
void setUp() {
    goCache = new StubGoCache(new TestTransactionSynchronizationManager());
    sqlMapClientTemplate = mock(SqlMapClientTemplate.class);
    stageSqlMapDao = new StageSqlMapDao(mock(JobInstanceSqlMapDao.class), new Cache(true, false, false), mock(TransactionTemplate.class), mock(SqlSessionFactory.class), goCache,
            mock(TransactionSynchronizationManager.class), mock(SystemEnvironment.class), null);
    stageSqlMapDao.setSqlMapClientTemplate(sqlMapClientTemplate);
    cloner = mock(Cloner.class);
    ReflectionUtil.setField(stageSqlMapDao, "cloner", cloner);
    doAnswer(new Answer() {
        @Override
        public Object answer(InvocationOnMock invocationOnMock) {
            return invocationOnMock.getArguments()[0];
        }
    }).when(cloner).deepClone(anyObject());
}
 

public void run() throws OutOfMemoryError {
	int numberOfColumns = this.numberOfColumns;
	
	DifferenceSets[] differenceSetsModulo = this.differenceSets.allModulo(this.numberOfColumns);
	for (int rhsIndex = 0; rhsIndex < numberOfColumns; rhsIndex++) {
		DifferenceSets orig = differenceSetsModulo[rhsIndex];
		Cloner cloner = new Cloner();
		DifferenceSets uncovered = cloner.deepClone(orig);
		if (orig.isEmpty()) {
			ColumnCollection lhs = new ColumnCollection(this.numberOfColumns);
			
			for (int lhsIndex : lhs.setCopy(rhsIndex).complement().getSetBits()) {
				this.minimalDependencies.addRHSColumn(lhs.setCopy(lhsIndex), rhsIndex);
			}
		} 
		else if (!orig.containsEmptySet()) {
			PartialOrder currentOrder = new PartialOrder(orig);
			Path path = new Path(numberOfColumns);
			findCovers(rhsIndex, orig, uncovered, path, currentOrder);
		}
	}
}
 

@Test
void shouldGetEditablePartOfEnvironmentConfig() {
    String uat = "uat";

    BasicEnvironmentConfig local = new BasicEnvironmentConfig(new CaseInsensitiveString("uat"));
    local.addEnvironmentVariable("user", "admin");
    BasicEnvironmentConfig remote = new BasicEnvironmentConfig(new CaseInsensitiveString("uat"));
    remote.addEnvironmentVariable("foo", "bar");
    MergeEnvironmentConfig merged = new MergeEnvironmentConfig(local, remote);

    EnvironmentsConfig environments = new EnvironmentsConfig();
    environments.add(merged);

    environmentConfigService.syncEnvironments(environments);

    BasicCruiseConfig cruiseConfig = new BasicCruiseConfig();
    BasicEnvironmentConfig env = (BasicEnvironmentConfig) environmentConfigService.getEnvironmentConfig(uat).getLocal();
    cruiseConfig.addEnvironment(env);
    BasicEnvironmentConfig expectedToEdit = new Cloner().deepClone(env);

    when(mockGoConfigService.getConfigForEditing()).thenReturn(cruiseConfig);

    assertThat(environmentConfigService.getEnvironmentForEdit(uat), is(expectedToEdit));
}
 

@Test
public void shouldUpdateConfigWithNoValidPartialsAndInvalidKnownPartials() throws GitAPIException, IOException {
    String gitShaBeforeSave = configRepository.getCurrentRevCommit().getName();
    PartialConfig invalidPartial = PartialConfigMother.invalidPartial("invalid", new RepoConfigOrigin(configRepo, "revision1"));
    goPartialConfig.onSuccessPartialConfig(configRepo, invalidPartial);

    assertThat(cachedGoPartials.lastValidPartials().isEmpty()).isTrue();
    assertThat(cachedGoPartials.lastKnownPartials().contains(invalidPartial)).isTrue();

    CruiseConfig config = new Cloner().deepClone(cachedGoConfig.loadForEditing());

    config.addEnvironment(UUID.randomUUID().toString());

    ConfigSaveState state = cachedGoConfig.writeFullConfigWithLock(new FullConfigUpdateCommand(config, goConfigService.configFileMd5()));

    String gitShaAfterSave = configRepository.getCurrentRevCommit().getName();
    String configXmlFromConfigFolder = FileUtils.readFileToString(new File(goConfigDao.fileLocation()), UTF_8);

    assertThat(state).isEqualTo(ConfigSaveState.UPDATED);
    assertThat(cachedGoConfig.loadForEditing()).isEqualTo(config);
    assertThat(gitShaAfterSave).isNotEqualTo(gitShaBeforeSave);
    assertThat(cachedGoConfig.loadForEditing().getMd5()).isEqualTo(configRepository.getCurrentRevision().getMd5());
    assertThat(cachedGoConfig.currentConfig().getMd5()).isEqualTo(configRepository.getCurrentRevision().getMd5());
    assertThat(configXmlFromConfigFolder).isEqualTo(configRepository.getCurrentRevision().getContent());
    assertThat(cachedGoPartials.lastValidPartials().isEmpty()).isTrue();
    assertThat(cachedGoPartials.lastKnownPartials().contains(invalidPartial)).isTrue();
}
 

@SuppressWarnings("unchecked")
public static <K, V> HashMap<K, V> deepCopy(Map<K, V> map) {

    if (map == null) {
        return (HashMap) Collections.emptyMap();
    }

    Cloner cloner = new Cloner();
    HashMap<K, V> copy = (HashMap<K, V>) cloner.deepClone(map);

    return copy;
}
 

public static PipelineConfig renamePipeline(PipelineConfig oldConfig, String newPipelineName) {
    PipelineConfig newConfig = new Cloner().deepClone(oldConfig);
    HashMap attributes = new HashMap();
    attributes.put(PipelineConfig.NAME, newPipelineName);
    newConfig.setConfigAttributes(attributes);
    return newConfig;
}
 

private GrobidPDFProcessor() throws IOException, Exception {
        prop = new Properties();
        prop.load(new FileReader("config.properties"));
        grobidHome = prop.getProperty("pGrobidHome");
        grobidProperties = prop.getProperty("pGrobidProperties");
        GrobidHomeFinder grobidHomeFinder = new GrobidHomeFinder(Arrays.asList(grobidHome));
        GrobidProperties.getInstance(grobidHomeFinder);
//        System.out.println(">>>>>>>> GROBID_HOME="+GrobidProperties.get_GROBID_HOME_PATH());
        engine = GrobidFactory.getInstance().createEngine();
        parsers = new EngineParsers();
        gson = new Gson();
        cloner = new Cloner();
    }
 

private CollectionSet<ColumnCollection> generateNextLevel(CollectionSet<ColumnCollection> currentLevel) {
	CollectionSet<ColumnCollection> nextLevel = new CollectionSet<>();
	
	Cloner cloner = new Cloner();
	AprioriGeneration<ColumnCollection> prefixBlockGenerator = new AprioriGeneration<>(cloner.deepClone(currentLevel));
	for (CollectionSet<ColumnCollection> k : prefixBlockGenerator.prefixBlocks()) {
		for (ColumnCollection y : k) {
			for (ColumnCollection z : k.tailSet(y)) {
				ColumnCollection x = y.orCopy(z);
				boolean xInNextLevel = true;
				for (int a : x.getSetBits()) {
					x.clear(a);
					if (!currentLevel.contains(x)) {
						xInNextLevel = false;
						break;
					}
					x.set(a);
				}
				if (xInNextLevel) {
					nextLevel.add(x);
					strippedPartitions.put(x, strippedProduct(strippedPartitions.get(y), strippedPartitions.get(z)));
				}
			}
		}
	}

	return nextLevel;
}
 

@Override
public CruiseConfig cloneForValidation() {
    Cloner cloner = new Cloner();
    BasicCruiseConfig configForValidation = cloner.deepClone(BasicCruiseConfig.this);
    // This needs to be done clear the cached fields else the cloned object will all get them.
    configForValidation.resetAllPipelineConfigsCache();
    return configForValidation;
}
 

@Test
public void shouldCollectPipelineNameConflictErrorsInTheChildren_InMergedConfig_WhenCloned() {
    //we need this case because cloning has proven to be problematic with complex object graph in merged config
    BasicCruiseConfig mainCruiseConfig = GoConfigMother.configWithPipelines("pipeline-1");
    PartialConfig partialConfig = PartialConfigMother.withPipelineInGroup("pipeline-1", "g2");
    partialConfig.setOrigin(new RepoConfigOrigin());
    CruiseConfig config = new BasicCruiseConfig(mainCruiseConfig, partialConfig);
    Cloner CLONER = new Cloner();
    CruiseConfig cloned = CLONER.deepClone(config);

    List<ConfigErrors> allErrors = cloned.validateAfterPreprocess();
    assertThat(allErrors.size(), is(2));
    assertThat(allErrors.get(0).on("name"), is("You have defined multiple pipelines named 'pipeline-1'. Pipeline names must be unique. Source(s): [http://some.git at 1234fed, cruise-config.xml]"));
    assertThat(allErrors.get(1).on("name"), is("You have defined multiple pipelines named 'pipeline-1'. Pipeline names must be unique. Source(s): [http://some.git at 1234fed, cruise-config.xml]"));
}
 

@Test
public void shouldCopyErrorsForFieldsOnPipelineConfig(){
    PipelineConfig pipelineConfig = PipelineConfigMother.pipelineConfig("pipeline", MaterialConfigsMother.defaultMaterialConfigs(), new JobConfigs(JobConfigMother.createJobConfigWithJobNameAndEmptyResources()));
    pipelineConfig.setVariables(new EnvironmentVariablesConfig(asList(new EnvironmentVariableConfig("name", "value"))));

    PipelineConfig pipelineWithErrors = new Cloner().deepClone(pipelineConfig);
    pipelineWithErrors.getVariables().get(0).addError("name", "error on environment variable");
    pipelineWithErrors.first().addError("name", "error on stage");
    pipelineWithErrors.first().getJobs().first().addError("name", "error on job");
    BasicCruiseConfig.copyErrors(pipelineWithErrors, pipelineConfig);
    assertThat(pipelineConfig.getVariables().get(0).errors().on("name"), is("error on environment variable"));
    assertThat(pipelineConfig.first().errors().on("name"), is("error on stage"));
    assertThat(pipelineConfig.first().getJobs().first().errors().on("name"), is("error on job"));
}
 

@Test
void shouldBeAbleToCreateACopyOfItself() {
    Resource existingResource = new Resource("some-name");
    existingResource.setId(2);
    existingResource.setBuildId(10);

    assertThat(existingResource).isEqualTo(new Resource(existingResource));
    assertThat(existingResource).isEqualTo(new Cloner().deepClone(existingResource));
}
 

@Test
public void shouldWalkCruiseConfigObjectsParallelly() {
    CruiseConfig cruiseConfig = GoConfigMother.configWithPipelines("bad pipeline name");
    CruiseConfig rawCruiseConfig = new Cloner().deepClone(cruiseConfig);
    MagicalGoConfigXmlLoader.validate(cruiseConfig);
    cruiseConfig.copyErrorsTo(rawCruiseConfig);
    assertThat(rawCruiseConfig.pipelineConfigByName(new CaseInsensitiveString("bad pipeline name")).errors(),
            is(cruiseConfig.pipelineConfigByName(new CaseInsensitiveString("bad pipeline name")).errors()));
}
 

private void updateConfigOnFileSystem(UpdateConfig updateConfig) throws Exception {
    String cruiseConfigFile = systemEnvironment.getCruiseConfigFile();
    CruiseConfig updatedConfig = new Cloner().deepClone(goConfigService.getConfigForEditing());
    updateConfig.update(updatedConfig);
    File configFile = new File(cruiseConfigFile);
    FileOutputStream outputStream = new FileOutputStream(configFile);
    new MagicalGoConfigXmlWriter(configCache, configElementImplementationRegistry).write(updatedConfig, outputStream, true);
}
 

@Test
public void shouldMarkAPreviousInvalidPartialAsValid_IfMainXMLSatisfiesTheDependency() throws GitAPIException, IOException {
    String gitShaBeforeSave = configRepository.getCurrentRevCommit().getName();
    PipelineConfig upstream = PipelineConfigMother.createPipelineConfig("upstream", "S", "J");
    PartialConfig partialConfig = PartialConfigMother.pipelineWithDependencyMaterial("downstream", upstream, new RepoConfigOrigin(configRepo, "r2"));
    goPartialConfig.onSuccessPartialConfig(configRepo, partialConfig);

    assertThat(cachedGoPartials.lastKnownPartials().contains(partialConfig)).isTrue();
    assertThat(cachedGoPartials.lastValidPartials().isEmpty()).isTrue();

    CruiseConfig originalConfig = cachedGoConfig.loadForEditing();
    CruiseConfig editedConfig = new Cloner().deepClone(originalConfig);

    editedConfig.addPipeline("default", upstream);
    ConfigSaveState state = cachedGoConfig.writeFullConfigWithLock(new FullConfigUpdateCommand(editedConfig, goConfigService.configFileMd5()));

    String gitShaAfterSave = configRepository.getCurrentRevCommit().getName();
    String configXmlFromConfigFolder = FileUtils.readFileToString(new File(goConfigDao.fileLocation()), UTF_8);

    assertThat(state).isEqualTo(ConfigSaveState.UPDATED);
    assertThat(cachedGoConfig.loadForEditing()).isEqualTo(editedConfig);
    assertThat(gitShaAfterSave).isNotEqualTo(gitShaBeforeSave);
    assertThat(cachedGoConfig.loadForEditing().getMd5()).isEqualTo(configRepository.getCurrentRevision().getMd5());
    assertThat(cachedGoConfig.currentConfig().getMd5()).isEqualTo(configRepository.getCurrentRevision().getMd5());
    assertThat(configXmlFromConfigFolder).isEqualTo(configRepository.getCurrentRevision().getContent());
    RepoConfigOrigin origin = (RepoConfigOrigin) cachedGoPartials.lastValidPartials().get(0).getOrigin();
    assertThat(origin.getRevision()).isEqualTo("r2");
    assertThat(cachedGoPartials.lastKnownPartials().contains(partialConfig)).isTrue();
    assertThat(cachedGoPartials.lastValidPartials().contains(partialConfig)).isTrue();
}