Example usage for org.eclipse.jgit.api Git getRepository

Introduction

In this page you can find the example usage for org.eclipse.jgit.api Git getRepository.

Prototype

public Repository getRepository() 

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Document

Get repository

Usage

From source file:org.commonwl.view.workflow.WorkflowService.java

License:Apache License

/**
 * Get a list of workflows from a directory
 * @param gitInfo The Git directory information
 * @return The list of workflow overviews
 *//*from  w w w.  java 2s  .com*/
public List<WorkflowOverview> getWorkflowsFromDirectory(GitDetails gitInfo)
        throws IOException, GitAPIException {
    List<WorkflowOverview> workflowsInDir = new ArrayList<>();
    try {
        boolean safeToAccess = gitSemaphore.acquire(gitInfo.getRepoUrl());
        Git repo = null;
        while (repo == null) {
            try {
                repo = gitService.getRepository(gitInfo, safeToAccess);
            } catch (RefNotFoundException ex) {
                // Attempt slashes in branch fix
                GitDetails correctedForSlash = gitService.transferPathToBranch(gitInfo);
                if (correctedForSlash != null) {
                    gitInfo = correctedForSlash;
                } else {
                    throw ex;
                }
            }
        }

        Path localPath = repo.getRepository().getWorkTree().toPath();
        Path pathToDirectory = localPath.resolve(gitInfo.getPath()).normalize().toAbsolutePath();
        Path root = Paths.get("/").toAbsolutePath();
        if (pathToDirectory.equals(root)) {
            pathToDirectory = localPath;
        } else if (!pathToDirectory.startsWith(localPath.normalize().toAbsolutePath())) {
            // Prevent path traversal attacks
            throw new WorkflowNotFoundException();
        }

        File directory = new File(pathToDirectory.toString());
        if (directory.exists() && directory.isDirectory()) {
            for (final File file : directory.listFiles()) {
                int eIndex = file.getName().lastIndexOf('.') + 1;
                if (eIndex > 0) {
                    String extension = file.getName().substring(eIndex);
                    if (extension.equals("cwl")) {
                        WorkflowOverview overview = cwlService.getWorkflowOverview(file);
                        if (overview != null) {
                            workflowsInDir.add(overview);
                        }
                    }
                }
            }
        }
    } finally {
        gitSemaphore.release(gitInfo.getRepoUrl());
    }
    return workflowsInDir;
}

---

From source file:org.commonwl.view.workflow.WorkflowService.java

License:Apache License

/**
 * Builds a new queued workflow from Git
 * @param gitInfo Git information for the workflow
 * @return A queued workflow model//from  w  w  w.ja  v a 2 s .  c  o m
 * @throws GitAPIException Git errors
 * @throws WorkflowNotFoundException Workflow was not found within the repository
 * @throws IOException Other file handling exceptions
 */
public QueuedWorkflow createQueuedWorkflow(GitDetails gitInfo)
        throws GitAPIException, WorkflowNotFoundException, IOException {
    QueuedWorkflow queuedWorkflow;

    try {
        boolean safeToAccess = gitSemaphore.acquire(gitInfo.getRepoUrl());
        Git repo = null;
        while (repo == null) {
            try {
                repo = gitService.getRepository(gitInfo, safeToAccess);
            } catch (RefNotFoundException ex) {
                // Attempt slashes in branch fix
                GitDetails correctedForSlash = gitService.transferPathToBranch(gitInfo);
                if (correctedForSlash != null) {
                    gitInfo = correctedForSlash;
                } else {
                    throw ex;
                }
            }
        }
        Path localPath = repo.getRepository().getWorkTree().toPath();
        String latestCommit = gitService.getCurrentCommitID(repo);

        Path workflowFile = localPath.resolve(gitInfo.getPath()).normalize().toAbsolutePath();
        // Prevent path traversal attacks
        if (!workflowFile.startsWith(localPath.normalize().toAbsolutePath())) {
            throw new WorkflowNotFoundException();
        }

        // Check workflow is readable
        if (!Files.isReadable(workflowFile)) {
            throw new WorkflowNotFoundException();
        }

        // Handling of packed workflows
        String packedWorkflowId = gitInfo.getPackedId();
        if (packedWorkflowId == null) {
            if (cwlService.isPacked(workflowFile.toFile())) {
                List<WorkflowOverview> overviews = cwlService
                        .getWorkflowOverviewsFromPacked(workflowFile.toFile());
                if (overviews.size() == 0) {
                    throw new IOException("No workflow was found within the packed CWL file");
                } else {
                    // Dummy queued workflow object to return the list
                    QueuedWorkflow overviewList = new QueuedWorkflow();
                    overviewList.setWorkflowList(overviews);
                    return overviewList;
                }
            }
        } else {
            // Packed ID specified but was not found
            if (!cwlService.isPacked(workflowFile.toFile())) {
                throw new WorkflowNotFoundException();
            }
        }

        Workflow basicModel = cwlService.parseWorkflowNative(workflowFile, packedWorkflowId);

        // Set origin details
        basicModel.setRetrievedOn(new Date());
        basicModel.setRetrievedFrom(gitInfo);
        basicModel.setLastCommit(latestCommit);

        // Save the queued workflow to database
        queuedWorkflow = new QueuedWorkflow();
        queuedWorkflow.setTempRepresentation(basicModel);
        queuedWorkflowRepository.save(queuedWorkflow);

        // ASYNC OPERATIONS
        // Parse with cwltool and update model
        try {
            cwlToolRunner.createWorkflowFromQueued(queuedWorkflow);
        } catch (Exception e) {
            logger.error("Could not update workflow with cwltool", e);
        }

    } finally {
        gitSemaphore.release(gitInfo.getRepoUrl());
    }

    // Return this model to be displayed
    return queuedWorkflow;
}

---

From source file:org.commonwl.view.workflow.WorkflowServiceTest.java

License:Apache License

/**
 * Getting a list of workflow overviews from a directory
 *///from   w  w  w  .  java  2 s.c om
@Test
public void getWorkflowsFromDirectory() throws Exception {

    // Mock CWL service which returns simple overview once simulating 1 workflow found
    CWLService mockCWLService = Mockito.mock(CWLService.class);
    when(mockCWLService.getWorkflowOverview(anyObject()))
            .thenReturn(new WorkflowOverview("workflow.cwl", "label", "doc"))
            .thenReturn(new WorkflowOverview("workflow2.cwl", "label2", "doc2")).thenReturn(null);

    Repository mockRepo = Mockito.mock(Repository.class);
    when(mockRepo.getWorkTree()).thenReturn(new File("src/test/resources/cwl/hello"));

    Git mockGitRepo = Mockito.mock(Git.class);
    when(mockGitRepo.getRepository()).thenReturn(mockRepo);

    GitService mockGitService = Mockito.mock(GitService.class);
    when(mockGitService.getRepository(anyObject(), anyBoolean())).thenReturn(mockGitRepo);

    // Create service under test
    WorkflowService testWorkflowService = new WorkflowService(mockGitService, mockCWLService,
            Mockito.mock(WorkflowRepository.class), Mockito.mock(QueuedWorkflowRepository.class),
            Mockito.mock(ROBundleFactory.class), Mockito.mock(GraphVizService.class),
            Mockito.mock(CWLToolRunner.class), Mockito.mock(GitSemaphore.class), 1);

    // Get a list of workflows from the directory
    List<WorkflowOverview> list = testWorkflowService
            .getWorkflowsFromDirectory(new GitDetails(null, null, "/"));

    // 1 workflow should be found
    assertTrue(list.size() == 2);
    assertEquals("workflow.cwl", list.get(0).getFileName());
    assertEquals("label", list.get(0).getLabel());
    assertEquals("doc", list.get(0).getDoc());

    assertEquals("workflow2.cwl", list.get(1).getFileName());
    assertEquals("label2", list.get(1).getLabel());
    assertEquals("doc2", list.get(1).getDoc());

}

---

From source file:org.commonwl.view.workflow.WorkflowServiceTest.java

License:Apache License

/**
 * Getting a workflow when cache has expired
 * And a new workflow needs to be created
 *///from   ww  w.  j  a v  a 2s  . co  m
@Test
public void getWorkflowCacheHasExpired() throws Exception {

    GitDetails githubInfo = new GitDetails("https://github.com/common-workflow-language/workflows.git",
            "master", "dna.cwl");

    Workflow oldWorkflow = new Workflow("old", "This is the expired workflow", new HashMap<>(), new HashMap<>(),
            new HashMap<>());
    oldWorkflow.setId("theworkflowid");
    oldWorkflow.setRetrievedOn(new Date());
    oldWorkflow.setRetrievedFrom(githubInfo);
    oldWorkflow.setLastCommit("d46ce365f1a10c4c4d6b0caed51c6f64b84c2f63");
    oldWorkflow.setRoBundlePath(roBundleFolder.newFile("robundle.zip").getAbsolutePath());

    Workflow updatedWorkflow = new Workflow("new", "This is the updated workflow", new HashMap<>(),
            new HashMap<>(), new HashMap<>());
    updatedWorkflow.setId("newworkflowid");

    WorkflowRepository mockWorkflowRepo = Mockito.mock(WorkflowRepository.class);
    when(mockWorkflowRepo.findByRetrievedFrom(anyObject())).thenReturn(oldWorkflow);

    CWLService mockCWLService = Mockito.mock(CWLService.class);
    when(mockCWLService.parseWorkflowNative(anyObject(), anyObject())).thenReturn(updatedWorkflow);

    Repository mockRepo = Mockito.mock(Repository.class);
    when(mockRepo.getWorkTree()).thenReturn(new File("src/test/resources/cwl/make_to_cwl"));

    Git mockGitRepo = Mockito.mock(Git.class);
    when(mockGitRepo.getRepository()).thenReturn(mockRepo);

    GitService mockGitService = Mockito.mock(GitService.class);
    when(mockGitService.getRepository(anyObject(), anyBoolean())).thenReturn(mockGitRepo);
    when(mockGitService.getCurrentCommitID(anyObject())).thenReturn("newCommitId");

    // Create service under test with negative cache time (always create new workflow)
    WorkflowService testWorkflowService = new WorkflowService(mockGitService, mockCWLService, mockWorkflowRepo,
            Mockito.mock(QueuedWorkflowRepository.class), Mockito.mock(ROBundleFactory.class),
            Mockito.mock(GraphVizService.class), Mockito.mock(CWLToolRunner.class),
            Mockito.mock(GitSemaphore.class), -1);

    // Will use check cache algorithm, find expired,
    // check git and find commit IDs do not match,
    // and thus create a new workflow + matching RO bundle
    Workflow workflow = testWorkflowService.getWorkflow(githubInfo);

    // Check the old workflow was deleted
    // TODO: check new workflow was queued
    assertEquals(workflow, null);

}

---

From source file:org.craftercms.commons.git.impl.GitRepositoryFactoryImpl.java

License:Open Source License

@Override
public GitRepository open(File dir) throws GitException {
    try {/*from w w w .  j  av  a 2s.c  o  m*/
        Git git = Git.open(dir);

        logger.debug("Git repository opened at {}", git.getRepository().getDirectory());

        return new GitRepositoryImpl(git);
    } catch (IOException e) {
        throw new GitException("Error opening Git repository at " + dir, e);
    }
}

---

From source file:org.craftercms.commons.git.impl.GitRepositoryFactoryImpl.java

License:Open Source License

@Override
public GitRepository init(File dir, boolean bare) throws GitException {
    try {//from   w ww. j  av a  2 s .  com
        Git git = Git.init().setDirectory(dir).setBare(bare).call();

        logger.info("New Git repository created at {}", git.getRepository().getDirectory());

        return new GitRepositoryImpl(git);
    } catch (GitAPIException e) {
        throw new GitException("Error creating new Git repository in " + dir, e);
    }
}

---

From source file:org.craftercms.commons.git.impl.GitRepositoryFactoryImplTest.java

License:Open Source License

@Test
public void testOpen() throws Exception {
    Git git = Git.init().setDirectory(tmpDir.getRoot()).call();

    GitRepository repo = repositoryFactory.open(tmpDir.getRoot());

    assertNotNull(repo);//from  w  ww  .j a va2s  .c  om
    assertEquals(git.getRepository().getDirectory().getCanonicalPath(), repo.getDirectory().getCanonicalPath());
}

---

From source file:org.craftercms.commons.git.impl.GitRepositoryImplTest.java

License:Open Source License

@Test
public void testPush() throws Exception {
    File masterRepoDir = tmpDir.newFolder("master.git");
    File cloneRepoDir = tmpDir.newFolder("clone");

    Git masterGit = Git.init().setDirectory(masterRepoDir).setBare(true).call();
    Git cloneGit = Git.cloneRepository().setURI(masterRepoDir.getCanonicalPath()).setDirectory(cloneRepoDir)
            .call();//from  ww w .  ja  va 2s . co  m
    GitRepositoryImpl cloneRepo = new GitRepositoryImpl(cloneGit);

    File testFile = new File(cloneRepoDir, "test");
    testFile.createNewFile();

    cloneGit.add().addFilepattern("test").call();
    cloneGit.commit().setMessage("Test message").call();

    cloneRepo.push();

    List<RevCommit> commits = IterableUtils.toList(masterGit.log().all().call());

    assertNotNull(commits);
    assertEquals(1, commits.size());
    assertEquals("Test message", commits.get(0).getFullMessage());

    List<String> committedFiles = getCommittedFiles(masterGit.getRepository(), commits.get(0));

    assertNotNull(committedFiles);
    assertEquals(1, committedFiles.size());
    assertEquals("test", committedFiles.get(0));
}

---

From source file:org.craftercms.commons.git.impl.GitRepositoryImplTest.java

License:Open Source License

@Test
public void testPull() throws Exception {
    File masterRepoDir = tmpDir.newFolder("master");
    File cloneRepoDir = tmpDir.newFolder("clone");

    Git masterGit = Git.init().setDirectory(masterRepoDir).call();
    Git cloneGit = Git.cloneRepository().setURI(masterRepoDir.getCanonicalPath()).setDirectory(cloneRepoDir)
            .call();/*ww w  . j  av a  2 s . com*/
    GitRepositoryImpl cloneRepo = new GitRepositoryImpl(cloneGit);

    File testFile = new File(masterRepoDir, "test");
    testFile.createNewFile();

    masterGit.add().addFilepattern("test").call();
    masterGit.commit().setMessage("Test message").call();

    cloneRepo.pull();

    List<RevCommit> commits = IterableUtils.toList(cloneGit.log().all().call());

    assertNotNull(commits);
    assertEquals(1, commits.size());
    assertEquals("Test message", commits.get(0).getFullMessage());

    List<String> committedFiles = getCommittedFiles(cloneGit.getRepository(), commits.get(0));

    assertNotNull(committedFiles);
    assertEquals(1, committedFiles.size());
    assertEquals("test", committedFiles.get(0));
}

---

From source file:org.craftercms.deployer.impl.processors.GitDiffProcessor.java

License:Open Source License

protected ObjectId getLatestCommitId(Git git) throws DeployerException {
    try {/*from w w  w.  j a  v a 2 s  . c  o  m*/
        return git.getRepository().resolve(Constants.HEAD);
    } catch (IOException e) {
        throw new DeployerException("Unable to retrieve HEAD commit ID", e);
    }
}

---

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