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(""));
}
}
}
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));
}