Esempio n. 1
0
 public ExportRow(String gene, Set<String> columns) {
   values = new LinkedHashMap<String, ExportValue>();
   for (Iterator<String> i = columns.iterator(); i.hasNext(); ) {
     String columnName = i.next();
     if (columnName.equals("Gene")) {
       values.put(columnName, new ExportValue(gene));
     } else {
       values.put(columnName, new ExportValue(""));
     }
   }
 }
Esempio n. 2
0
  private boolean handlePut(
      HttpServletRequest request, HttpServletResponse response, String pathString)
      throws GitAPIException, CoreException, IOException, JSONException, ServletException {
    IPath path = pathString == null ? Path.EMPTY : new Path(pathString);
    if (path.segment(0).equals("file") && path.segmentCount() > 1) { // $NON-NLS-1$

      // make sure a clone is addressed
      WebProject webProject = GitUtils.projectFromPath(path);
      if (isAccessAllowed(request.getRemoteUser(), webProject)) {
        Map<IPath, File> gitDirs = GitUtils.getGitDirs(path, Traverse.CURRENT);
        if (gitDirs.isEmpty()) {
          String msg = NLS.bind("Request path is not a git repository: {0}", path);
          return statusHandler.handleRequest(
              request,
              response,
              new ServerStatus(IStatus.ERROR, HttpServletResponse.SC_BAD_REQUEST, msg, null));
        }
        File gitDir = gitDirs.values().iterator().next();

        // make sure required fields are set
        JSONObject toCheckout = OrionServlet.readJSONRequest(request);
        JSONArray paths = toCheckout.optJSONArray(ProtocolConstants.KEY_PATH);
        String branch = toCheckout.optString(GitConstants.KEY_BRANCH_NAME, null);
        String tag = toCheckout.optString(GitConstants.KEY_TAG_NAME, null);
        boolean removeUntracked = toCheckout.optBoolean(GitConstants.KEY_REMOVE_UNTRACKED, false);
        if ((paths == null || paths.length() == 0) && branch == null && tag == null) {
          String msg =
              NLS.bind(
                  "Either '{0}' or '{1}' or '{2}' should be provided, got: {3}",
                  new Object[] {
                    ProtocolConstants.KEY_PATH,
                    GitConstants.KEY_BRANCH_NAME,
                    GitConstants.KEY_TAG_NAME,
                    toCheckout
                  });
          return statusHandler.handleRequest(
              request,
              response,
              new ServerStatus(IStatus.ERROR, HttpServletResponse.SC_BAD_REQUEST, msg, null));
        }

        Git git = new Git(new FileRepository(gitDir));
        if (paths != null) {
          Set<String> toRemove = new HashSet<String>();
          CheckoutCommand checkout = git.checkout();
          for (int i = 0; i < paths.length(); i++) {
            String p = paths.getString(i);
            if (removeUntracked && !isInIndex(git.getRepository(), p)) toRemove.add(p);
            checkout.addPath(p);
          }
          checkout.call();
          for (String p : toRemove) {
            File f = new File(git.getRepository().getWorkTree(), p);
            f.delete();
          }
          return true;
        } else if (tag != null && branch != null) {
          CheckoutCommand co = git.checkout();
          try {
            co.setName(branch).setStartPoint(tag).setCreateBranch(true).call();
            return true;
          } catch (RefNotFoundException e) {
            String msg = NLS.bind("Tag not found: {0}", tag);
            return statusHandler.handleRequest(
                request,
                response,
                new ServerStatus(IStatus.ERROR, HttpServletResponse.SC_NOT_FOUND, msg, e));
          } catch (GitAPIException e) {
            if (org.eclipse.jgit.api.CheckoutResult.Status.CONFLICTS.equals(
                co.getResult().getStatus())) {
              return statusHandler.handleRequest(
                  request,
                  response,
                  new ServerStatus(
                      IStatus.ERROR, HttpServletResponse.SC_CONFLICT, "Checkout aborted.", e));
            }
            // TODO: handle other exceptions
          }
        } else if (branch != null) {

          if (!isLocalBranch(git, branch)) {
            String msg = NLS.bind("{0} is not a branch.", branch);
            return statusHandler.handleRequest(
                request,
                response,
                new ServerStatus(IStatus.ERROR, HttpServletResponse.SC_NOT_FOUND, msg, null));
          }

          CheckoutCommand co = git.checkout();
          try {
            co.setName(Constants.R_HEADS + branch).call();
            return true;
          } catch (CheckoutConflictException e) {
            return statusHandler.handleRequest(
                request,
                response,
                new ServerStatus(
                    IStatus.ERROR, HttpServletResponse.SC_CONFLICT, "Checkout aborted.", e));
          } catch (RefNotFoundException e) {
            String msg = NLS.bind("Branch name not found: {0}", branch);
            return statusHandler.handleRequest(
                request,
                response,
                new ServerStatus(IStatus.ERROR, HttpServletResponse.SC_NOT_FOUND, msg, e));
          } // TODO: handle other exceptions
        }
      } else {
        String msg = NLS.bind("Nothing found for the given ID: {0}", path);
        return statusHandler.handleRequest(
            request,
            response,
            new ServerStatus(IStatus.ERROR, HttpServletResponse.SC_NOT_FOUND, msg, null));
      }
    }
    String msg = NLS.bind("Invalid checkout request {0}", pathString);
    return statusHandler.handleRequest(
        request,
        response,
        new ServerStatus(IStatus.ERROR, HttpServletResponse.SC_BAD_REQUEST, msg, null));
  }