def rename(self, oldpath, newpath):
oldpath = self._realpath(oldpath)
newpath = self._realpath(newpath)
try:
os.rename(oldpath, newpath)
except OSError, e:
return SFTPServer.convert_errno(e.errno)
def list_folder(self, path):
""" List contents of a folder. """
self.log.debug('list_folder({0!r})'.format(path))
rpath = self._realpath(path)
if not self.user.is_sysop and self._is_uploaddir(path):
return []
try:
out = []
if path == u'/':
out.append(self._dummy_dir_stat())
elif flagged_dirname in path:
self.flagged = self.user.get('flaggedfiles', set())
for fname in self.flagged:
rname = fname
attr = SFTPAttributes.from_stat(os.stat(rname))
attr.filename = fname[fname.rindex('/') + 1:]
out.append(attr)
return out
flist = os.listdir(rpath)
for fname in flist:
attr = SFTPAttributes.from_stat(
os.stat(os.path.join(rpath, fname)))
attr.filename = fname
out.append(attr)
return out
except OSError as err:
return SFTPServer.convert_errno(err.errno)
def lstat(self, path):
path = self._realpath(path)
try:
return SFTPAttributes.from_stat(os.lstat(path))
except OSError:
e = sys.exc_info()[1]
return SFTPServer.convert_errno(e.errno)
def stat(self):
""" Stat the file descriptor. """
self.log.debug('stat')
try:
return SFTPAttributes.from_stat(os.fstat(self.readfile.fileno()))
except OSError as err:
return SFTPServer.convert_errno(err.errno)
def rmdir(self, path):
path = self._realpath(path)
try:
os.rmdir(path)
except OSError as e:
return SFTPServer.convert_errno(e.errno)
return SFTP_OK
def chattr(self, path, attr):
path = self._realpath(path)
try:
SFTPServer.set_file_attr(path, attr)
except OSError as e:
return SFTPServer.convert_errno(e.errno)
return SFTP_OK
def rmdir(self, path):
path = self._realpath(path)
try:
os.rmdir(path)
except OSError:
e = sys.exc_info()[1]
return SFTPServer.convert_errno(e.errno)
return SFTP_OK
def chattr(self, attr):
# python doesn't have equivalents to fchown or fchmod, so we have to
# use the stored filename
mutter('Changing permissions on %s to %s', self.filename, attr)
try:
SFTPServer.set_file_attr(self.filename, attr)
except OSError, e:
return SFTPServer.convert_errno(e.errno)
def chattr(self, attr):
# python doesn't have equivalents to fchown or fchmod, so we have to
# use the stored filename
try:
SFTPServer.set_file_attr(self.filename, attr)
return SFTP_OK
except OSError as e:
return SFTPServer.convert_errno(e.errno)
def mkdir(self, path, attr):
path = self._realpath(path)
try:
os.mkdir(path)
if attr is not None:
SFTPServer.set_file_attr(path, attr)
except OSError, e:
return SFTPServer.convert_errno(e.errno)
def stat(self):
"""
This method performs the stat attributes
return path SFTPAttributes or error
"""
try:
return SFTPAttributes.from_stat(os.fstat(self.readfile.fileno()))
except OSError, e:
return SFTPServer.convert_errno(e.errno)
def rename(self, oldpath, newpath):
oldpath = self._realpath(oldpath)
newpath = self._realpath(newpath)
try:
os.rename(oldpath, newpath)
except OSError:
e = sys.exc_info()[1]
return SFTPServer.convert_errno(e.errno)
return SFTP_OK
def open(self, path, flags, attr):
""" Up/download the given path. """
self.log.debug('lstat({0!r}, {1!r}, {2!r})'
.format(path, flags, attr))
path = self._realpath(path)
if (flags & os.O_CREAT and (uploads_dirname not in path and
not self.user.is_sysop) or
(uploads_dirname in path and os.path.exists(path))):
return SFTP_PERMISSION_DENIED
try:
binary_flag = getattr(os, 'O_BINARY', 0)
flags |= binary_flag
filedesc = os.open(path, flags, self.mode)
except OSError as err:
return SFTPServer.convert_errno(err.errno)
if (flags & os.O_CREAT) and (attr is not None):
attr._flags &= ~attr.FLAG_PERMISSIONS
SFTPServer.set_file_attr(path, attr)
if flags & os.O_WRONLY:
if flags & os.O_APPEND:
fstr = 'ab'
else:
fstr = 'wb'
elif flags & os.O_RDWR:
if flags & os.O_APPEND:
fstr = 'a+b'
else:
fstr = 'r+b'
else:
# O_RDONLY (== 0)
fstr = 'rb'
try:
openfile = os.fdopen(filedesc, fstr)
except OSError as err:
return SFTPServer.convert_errno(err.errno)
fobj = X84SFTPHandle(flags, user=self.user)
fobj.filename = path
fobj.readfile = openfile
fobj.writefile = openfile
if path in self.flagged:
self.flagged.remove(path)
self.user['flaggedfiles'] = self.flagged
return fobj
def rmdir(self, path):
if not self.user.is_sysop or flagged_dirname in path:
return SFTP_PERMISSION_DENIED
self.log.debug('rmdir({0!r})'.format(path))
path = self._realpath(path)
try:
os.rmdir(path)
except OSError as err:
return SFTPServer.convert_errno(err.errno)
return SFTP_OK
def rename(self, oldpath, newpath):
oldpath = self._realpath(oldpath)
newpath = self._realpath(newpath)
if os.path.exists(newpath):
return SFTP_FAILURE
try:
os.rename(oldpath, newpath)
except OSError as e:
return SFTPServer.convert_errno(e.errno)
return SFTP_OK
def readlink(self, path):
"""
This method reads symbolic links.
path - path to be read
return SFTP_OK or error
"""
path = self._realpath(path)
try:
symlink = os.readlink(path)
except OSError, e:
return SFTPServer.convert_errno(e.errno)
def rmdir(self, path):
"""
This method deletes the given folder
path - folder path to be deleted
return SFTP_OK or error
"""
path = self._realpath(path)
try:
os.rmdir(path)
except OSError, e:
return SFTPServer.convert_errno(e.errno)
def remove(self, path):
"""
This method deletes the given path to file
path - file path
return SFTP_OK or error
"""
path = self._realpath(path)
try:
os.remove(path)
except OSError, e:
return SFTPServer.convert_errno(e.errno)
def chattr(self, attr):
if not self.user.is_sysop:
return SFTP_PERMISSION_DENIED
self.log.debug('chattr ({0!r})'.format(attr))
# python doesn't have equivalents to fchown or fchmod, so we have to
# use the stored filename
try:
SFTPServer.set_file_attr(self.filename, attr)
return SFTP_OK
except OSError as err:
return SFTPServer.convert_errno(err.errno)
def symlink(self, target_path, path):
path = self._realpath(path)
if (len(target_path) > 0) and (target_path[0] == '/'):
# absolute symlink
target_path = os.path.join(self.ROOT, target_path[1:])
try:
os.symlink(target_path, path)
except OSError as e:
return SFTPServer.convert_errno(e.errno)
return SFTP_OK
def rename(self, oldpath, newpath):
if not self.user.is_sysop or flagged_dirname in path:
return SFTP_PERMISSION_DENIED
self.log.debug('rename({0!r}, {1!r})'.format(oldpath, newpath))
oldpath = self._realpath(oldpath)
newpath = self._realpath(newpath)
try:
os.rename(oldpath, newpath)
except OSError as err:
return SFTPServer.convert_errno(err.errno)
return SFTP_OK
def lstat(self, path):
"""
This method performs the lstat attributes for the given path
path - file/folder path
return lstat SFTPAttributes or error
"""
path = self._realpath(path)
try:
return SFTPAttributes.from_stat(os.lstat(path))
except OSError, e:
return SFTPServer.convert_errno(e.errno)
def open(self, path, flags, attr):
path = self._realpath(path)
try:
binary_flag = getattr(os, 'O_BINARY', 0)
flags |= binary_flag
mode = getattr(attr, 'st_mode', None)
if mode is not None:
fd = os.open(path, flags, mode)
else:
# os.open() defaults to 0777 which is
# an odd default mode for files
fd = os.open(path, flags, 1638) # 0666
except OSError:
e = sys.exc_info()[1]
return SFTPServer.convert_errno(e.errno)
if (flags & os.O_CREAT) and (attr is not None):
attr._flags &= ~attr.FLAG_PERMISSIONS
SFTPServer.set_file_attr(path, attr)
if flags & os.O_WRONLY:
if flags & os.O_APPEND:
fstr = 'ab'
else:
fstr = 'wb'
elif flags & os.O_RDWR:
if flags & os.O_APPEND:
fstr = 'a+b'
else:
fstr = 'r+b'
else:
# O_RDONLY (== 0)
fstr = 'rb'
try:
f = os.fdopen(fd, fstr)
except OSError:
e = sys.exc_info()[1]
return SFTPServer.convert_errno(e.errno)
fobj = StubSFTPHandle(flags)
fobj.filename = path
fobj.readfile = f
fobj.writefile = f
return fobj
def list_folder(self, path):
path = self._realpath(path)
try:
out = []
flist = os.listdir(path)
for fname in flist:
attr = SFTPAttributes.from_stat(os.stat(os.path.join(path, fname)))
attr.filename = fname
out.append(attr)
return out
except OSError as e:
return SFTPServer.convert_errno(e.errno)
def mkdir(self, path, attr):
if not self.user.is_sysop or flagged_dirname in path:
return SFTP_PERMISSION_DENIED
self.log.debug('mkdir({0!r}, {1!r})'.format(path, attr))
path = self._realpath(path)
try:
os.mkdir(path)
if attr is not None:
SFTPServer.set_file_attr(path, attr)
except OSError as err:
return SFTPServer.convert_errno(err.errno)
return SFTP_OK
def chattr(self, path, attr):
"""
This method changes the attributes of a given path
path - the path
attr - file attributes to be set
return SFTP_OK or error
"""
path = self._realpath(path)
try:
SFTPServer.set_file_attr(path, attr)
except OSError, e:
return SFTPServer.convert_errno(e.errno)
def open(self, path, flags, attr):
path = self._realpath(path)
try:
flags |= getattr(os, 'O_BINARY', 0)
if getattr(attr, 'st_mode', None):
fd = os.open(path, flags, attr.st_mode)
else:
# os.open() defaults to 0777 which is
# an odd default mode for files
fd = os.open(path, flags, 0666)
except OSError, e:
return SFTPServer.convert_errno(e.errno)
def rename(self, oldpath, newpath):
"""
This method renames oldpath into newpath
oldpath - old file path
newpath - new file path
return SFTP_OK or error
"""
oldpath = self._realpath(oldpath)
newpath = self._realpath(newpath)
try:
os.rename(oldpath, newpath)
except OSError, e:
return SFTPServer.convert_errno(e.errno)
def chattr(self, attr):
"""
This method performs the stat attributes for the given path
path - file/folder path
return path SFTPAttributes or error
"""
# python doesn't have equivalents to fchown or fchmod, so we have to
# use the stored filename
try:
SFTPServer.set_file_attr(self.filename, attr)
return SFTP_OK
except OSError, e:
return SFTPServer.convert_errno(e.errno)
def open(self, path, flags, attr):
path = self._realpath(path)
try:
binary_flag = getattr(os, "O_BINARY", 0)
flags |= binary_flag
mode = getattr(attr, "st_mode", None)
if mode is not None:
fd = os.open(path, flags, mode)
else:
# os.open() defaults to 0777 which is
# an odd default mode for files
fd = os.open(path, flags, o666)
except OSError as e:
return SFTPServer.convert_errno(e.errno)
if (flags & os.O_CREAT) and (attr is not None):
attr._flags &= ~attr.FLAG_PERMISSIONS
SFTPServer.set_file_attr(path, attr)
if flags & os.O_WRONLY:
if flags & os.O_APPEND:
fstr = "ab"
else:
fstr = "wb"
elif flags & os.O_RDWR:
if flags & os.O_APPEND:
fstr = "a+b"
else:
fstr = "r+b"
else:
# O_RDONLY (== 0)
fstr = "rb"
try:
f = os.fdopen(fd, fstr)
except OSError as e:
return SFTPServer.convert_errno(e.errno)
fobj = StubSFTPHandle(flags)
fobj.filename = path
fobj.readfile = f
fobj.writefile = f
return fobj
def rmdir(self, path):
return SFTPServer.convert_errno(errno.E_ACCES)
def chattr(self, path, attr):
return SFTPServer.convert_errno(errno.E_ACCES)
def list_folder(self, path):
self.opt.o("sftpserver", 'list', path)
try:
return self.docker_client.listdir_attr(path)
except IOError as e:
return SFTPServer.convert_errno(e.errno)
def stat(self, path):
self.opt.o("sftpserver", 'stat', path)
try:
return self.docker_client.stat(path)
except IOError as e:
return SFTPServer.convert_errno(e.errno)
def list_folder(self, path):
logging.debug(repr(path))
out = []
try:
cursor = self.mysql_conn.cursor()
logging.debug("list_folder PATH: {}".format(path))
if path == "/":
# This is the root path. Print a list of projects.
query = """SELECT p.projectid,UNIX_TIMESTAMP(MAX(r.release_date)) FROM project_membership p
JOIN project_files f ON(f.projectid = p.projectid) JOIN project_release r ON(r.releaseid = f.releaseid)
WHERE p.userid=%s GROUP BY p.projectid"""
cursor.execute(query, (self.userid, ))
for (projectid, m_time) in cursor:
attr = self._dir_attr(m_time)
project = self.arv.groups().get(uuid=projectid).execute()
filename = "{} ({})".format(project['name'], projectid)
attr.filename = filename
logging.debug("Folder attrs: {}".format(str(attr)))
out.append(attr)
else:
parts = path.strip("/").split("/", 3)
logging.debug("list_folder PARTS: {}".format(repr(parts)))
parts[0] = self._get_project_id(parts[0])
logging.debug("Project ID:{}".format(parts[0]))
self._is_allowed(parts[0])
if len(parts) == 1:
# If there is only one part to the path then list the datatypes for the collection
# Perhaps may change this to a release view? Will need to decide how to make paths within the project unique.
query = """SELECT f.type,UNIX_TIMESTAMP(MAX(r.release_date)) FROM project_files f
JOIN project_release r ON(f.releaseid = r.releaseid) WHERE f.projectid=%s
GROUP BY f.type ORDER BY f.type"""
cursor.execute(query, (str(parts[0]), ))
for (filetype, mtime) in cursor:
attr = self._dir_attr(mtime)
attr.filename = filetype
out.append(attr)
else:
# Otherwise find the subpath and files
pathquery = "/" + ("/".join(parts[2:]) +
"/" if len(parts) > 2 else "")
# First check if this a real directory
query = """SELECT COUNT(filename) FROM project_files WHERE projectid=%s AND type=%s AND filepath=%s"""
cursor.execute(query,
(str(parts[0]), str(parts[1]), pathquery))
row = cursor.fetchone()
if row is None:
raise OSError(errno.ENOENT, "No such directory")
# First find the subdirectories and list them
query = """SELECT SUBSTRING_INDEX(SUBSTR(f.filepath, LENGTH(%s)+1),'/',1) as subpath, UNIX_TIMESTAMP(MAX(r.release_date))
FROM project_files f JOIN project_release r ON(f.releaseid = r.releaseid)
WHERE f.projectid=%s AND f.type=%s AND f.filepath LIKE %s AND LENGTH(f.filepath) > LENGTH(%s) GROUP BY subpath ORDER BY f.filepath"""
cursor.execute(query, (pathquery, str(
parts[0]), str(parts[1]), pathquery + '%', pathquery))
logging.debug(cursor.statement)
for (dirname, mtime) in cursor:
attr = self._dir_attr(mtime)
attr.filename = dirname
out.append(attr)
logging.debug("DIR: {}".format(str(attr)))
# Then find the files and list those
query = """SELECT f.filename, UNIX_TIMESTAMP(r.release_date), f.fileid
FROM project_files f JOIN project_release r ON (f.releaseid = r.releaseid)
WHERE f.projectid=%s AND f.type=%s AND f.filepath=%s"""
cursor.execute(query,
(str(parts[0]), str(parts[1]), pathquery))
for (filename, mtime, fileid) in cursor:
file_parts = fileid.split('/', 1)
arv_file = self._get_file(file_parts[0], file_parts[1])
attr = self._file_attr(mtime)
attr.filename = os.path.basename(filename)
attr.st_size = arv_file.size()
out.append(attr)
logging.debug("FILE: {}".format(str(attr)))
cursor.close()
return out
except OSError as e:
return SFTPServer.convert_errno(e.errno)
def lstat(self, path):
path = self._realpath(path)
try:
return SFTPAttributes.from_stat(os.lstat(path))
except OSError, e:
return SFTPServer.convert_errno(e.errno)
def stat(self):
try:
return SFTPAttributes.from_stat(os.fstat(self.readfile.fileno()))
except OSError, e:
return SFTPServer.convert_errno(e.errno)
def readlink(self, path):
path = self._realpath(path)
try:
symlink = os.readlink(path)
except OSError, e:
return SFTPServer.convert_errno(e.errno)
def chattr(self, path, attr):
path = self._realpath(path)
try:
SFTPServer.set_file_attr(path, attr)
except OSError, e:
return SFTPServer.convert_errno(e.errno)
def rmdir(self, path):
path = self._realpath(path)
try:
os.rmdir(path)
except OSError, e:
return SFTPServer.convert_errno(e.errno)
def open(self, path, flags, attr):
path = self._realpath(path)
try:
fd = os.open(path, flags)
except OSError, e:
return SFTPServer.convert_errno(e.errno)
def _SFTPHandle_stat(self):
try:
return paramiko.SFTPAttributes.from_stat(os.fstat(self.readfile.fileno()))
except OSError as e:
return SFTPServer.convert_errno(e.errno)
def rename(self, oldpath, newpath):
return SFTPServer.convert_errno(errno.E_ACCES)
def stat(self, path):
try:
if path == "/":
cursor = self.mysql_conn.cursor()
query = """SELECT UNIX_TIMESTAMP(MAX(r.release_date)) FROM project_membership p
JOIN project_files f ON(f.projectid = p.projectid) JOIN project_release r ON(r.releaseid = f.releaseid)
WHERE p.userid=%s"""
cursor.execute(query, (self.userid, ))
row = cursor.fetchone()
return self._dir_attr(row[0])
else:
logging.debug("stat PATH: {}".format(path))
parts = str(path).strip("/").split("/", 2)
if parts[len(parts) - 1] == "..":
parts.pop()
parts[0] = self._get_project_id(parts[0])
logging.debug("stat PARTS: {}".format(repr(parts)))
cursor = self.mysql_conn.cursor()
# First check if this is a file
if len(parts) > 2:
parts[2] = '/' + parts[2]
query = """SELECT UNIX_TIMESTAMP(r.release_date) FROM project_files f
JOIN project_release r ON(r.releaseid = f.releaseid)
WHERE f.projectid=%s AND f.type=%s AND CONCAT(f.filepath,f.filename)=%s"""
cursor.execute(query, (parts[0], parts[1], parts[2]))
row = cursor.fetchone()
if cursor.with_rows and row is not None:
# this is a file. Return a file attr
attr = self._file_attr(row[0])
logging.debug("STAT: {}".format(repr(attr)))
cursor.close()
return attr
logging.debug("STAT: is directory")
query = """SELECT UNIX_TIMESTAMP(MAX(r.release_date)) FROM project_files f
JOIN project_release r ON(r.releaseid = f.releaseid)
WHERE f.projectid=%s"""
if len(parts) == 3:
logging.debug(repr(parts))
query = query + " AND f.type=%s AND f.filepath=%s"
if not parts[2].endswith('/'):
parts[2] = parts[2] + "/"
cursor.execute(query, (parts[0], parts[1], parts[2]))
elif len(parts) > 1:
query = query + " AND f.type=%s"
cursor.execute(query, (parts[0], parts[1]))
else:
cursor.execute(query, (parts[0], ))
row = cursor.fetchone()
logging.debug("STAT return: {} {}".format(
repr(cursor.statement), repr(row)))
if cursor.with_rows and row[0] is not None:
mtime = row[0]
cursor.close()
return self._dir_attr(mtime)
else:
cursor.close()
raise OSError(errno.ENOENT, "No such file or directory")
except OSError as e:
return SFTPServer.convert_errno(e.errno)
if flags & os.O_APPEND:
fstr = 'ab'
else:
fstr = 'wb'
elif flags & os.O_RDWR:
if flags & os.O_APPEND:
fstr = 'a+b'
else:
fstr = 'r+b'
else:
# O_RDONLY (== 0)
fstr = 'rb'
try:
f = os.fdopen(fd, fstr)
except OSError, e:
return SFTPServer.convert_errno(e.errno)
fobj = StubSFTPHandle(flags)
fobj.filename = path
fobj.readfile = f
fobj.writefile = f
return fobj
def remove(self, path):
path = self._realpath(path)
try:
os.remove(path)
except OSError, e:
return SFTPServer.convert_errno(e.errno)
return SFTP_OK
def rename(self, oldpath, newpath):
class SFTPInterface (SFTPServerInterface):
def __init__(self, server):
self.server = server
self.user = server.user
self.shares = {}
self.shares_accessed = set()
self.modified_date = {}
for share in Share.user_queryset(self.user,include_stats=False):
self.shares[share.slug_or_id] = share#{'path':share.get_realpath()}
# print 'user'
# print self.user
# self.ROOT = root
def session_ended(self):
SFTPServerInterface.session_ended(self)
Share.objects.filter(id__in=list(self.shares_accessed)).update(last_data_access=timezone.now())
def _get_share(self,path):
parts = path.split(os.path.sep)
if len(parts) < 2:
print 'bad length'
raise PermissionDenied("Received an invalid path: %s"%path)
if not self.shares.has_key(parts[1]) and self.user.id == -1: #Anonymous users don't yet have a dictionary of shares.
try:
share = Share.get_by_slug_or_id(parts[1])
self.shares[share.slug_or_id] = share
except:
pass
if not self.shares.has_key(parts[1]):
print 'no share exists'
print path
raise PermissionDenied("Share does not exist: %s"%path[1])
return self.shares[parts[1]]
def _path_modified(self,path):
share = self._get_share(path)
previous_date = self.modified_date.get(share.id,None)
current_date = timezone.now()
if not previous_date or (current_date-previous_date).seconds > SFTP_UPDATE_SHARE_MODIFIED_DATE_FREQUENCY_SECONDS:
self.modified_date[share.id] = current_date
Share.objects.filter(id=share.id,updated__lt=current_date).update(updated=current_date)
def _get_bioshare_path_permissions(self,path):
share = self._get_share(path)
self.shares_accessed.add(share.id)
permissions = share.get_user_permissions(self.user)
# print permissions
return permissions
def _get_path_permissions(self,path):
permissions = self._get_bioshare_path_permissions(path)
#translate
# PERMISSION_VIEW = 'view_share_files'
# PERMISSION_DELETE = 'delete_share_files'
# PERMISSION_DOWNLOAD = 'download_share_files'
# PERMISSION_WRITE = 'write_to_share'
# PERMISSION_LINK_TO_PATH = 'link_to_path'
# PERMISSION_ADMIN
return permissions
def _realpath(self, path):
# print 'realpath'
# print path
parts = path.split(os.path.sep)
share = self._get_share(path)
realpath = os.path.realpath(os.path.join(share.get_realpath(),os.path.sep.join(parts[2:])))
if not paths_contain(settings.DIRECTORY_WHITELIST,realpath):
raise PermissionDenied("Encountered a path outside the whitelist")
return realpath
# print self.ROOT + self.canonicalize(path)
# return self.ROOT + self.canonicalize(path)
@sftp_response
def list_shares(self):
# print "LIST SHARES"
if self.user.id == -1:
return []
try:
out = []
for id,share in self.shares.iteritems():
try:
# print id
attr = paramiko.SFTPAttributes.from_stat(os.stat(share.get_realpath()))
attr.filename = id
out.append(attr)
except Exception, e:
pass #directory may be missing
return out
except OSError as e:
return SFTPServer.convert_errno(e.errno)
def stat(self, path):
path = self._realpath(path)
try:
return paramiko.SFTPAttributes.from_stat(os.stat(path))
except OSError as e:
return SFTPServer.convert_errno(e.errno)