From 3a71a1959224ce64bf06fd4908df08e65735574b Mon Sep 17 00:00:00 2001
From: vermeul <swen@ethz.ch>
Date: Tue, 11 Feb 2020 11:39:09 +0100
Subject: [PATCH] added more instructions for mount(), implemented _password()
method
---
pybis/src/python/pybis/pybis.py | 147 +++++++++++++++++++++++++-------
1 file changed, 114 insertions(+), 33 deletions(-)
diff --git a/pybis/src/python/pybis/pybis.py b/pybis/src/python/pybis/pybis.py
index 4e655b0fe11..5b01f1fd2c2 100644
--- a/pybis/src/python/pybis/pybis.py
+++ b/pybis/src/python/pybis/pybis.py
@@ -565,21 +565,21 @@ def _subcriteria_for_code(code, entity):
Example::
_subcriteria_for_code("username", "space")
- {
- "criteria": [
- {
- "fieldType": "ATTRIBUTE",
- "@type": "as.dto.common.search.CodeSearchCriteria",
- "fieldName": "code",
- "fieldValue": {
- "@type": "as.dto.common.search.StringEqualToValue",
- "value": "USERNAME"
- }
- }
- ],
- "operator": "AND",
- "@type": "as.dto.space.search.SpaceSearchCriteria"
- }
+ {
+ "criteria": [
+ {
+ "fieldType": "ATTRIBUTE",
+ "@type": "as.dto.common.search.CodeSearchCriteria",
+ "fieldName": "code",
+ "fieldValue": {
+ "@type": "as.dto.common.search.StringEqualToValue",
+ "value": "USERNAME"
+ }
+ }
+ ],
+ "operator": "AND",
+ "@type": "as.dto.space.search.SpaceSearchCriteria"
+ }
"""
if code is not None:
if is_permid(code):
@@ -682,6 +682,13 @@ class Openbis:
print("Session is no longer valid. Please log in again.")
+ def _get_username(self):
+ if self.token:
+ username, rest = self.token.split('-')
+ return username
+ return ''
+
+
def __dir__(self):
return [
'url', 'port', 'hostname', 'token',
@@ -689,6 +696,8 @@ class Openbis:
'logout()',
'is_session_active()',
'is_token_valid()',
+ "mount()",
+ "unmount()",
"get_server_information()",
"get_dataset()",
"get_datasets()",
@@ -929,11 +938,26 @@ class Openbis:
if save_token:
self.save_token()
+ self._password(password)
# update the OPENBIS_TOKEN environment variable, if OPENBIS_URL is identical to self.url
if os.environ.get('OPENBIS_URL') == self.url:
os.environ['OPENBIS_TOKEN'] = self.token
return self.token
+ def _password(self, password=None, pstore={} ):
+ """An elegant way to store passwords which are used later
+ without giving the user an easy possibility to retrieve it.
+ """
+ import inspect
+ allowed_methods = ['mount']
+
+ if password is not None:
+ pstore['password'] = password
+ else:
+ if inspect.stack()[1][3] in allowed_methods:
+ return pstore.get('password')
+ else:
+ raise Exception("This method can only be called from these internal methods: {}".format(allowed_methods))
def unmount(self, mountpoint=None):
"""Unmount a given mountpoint or unmount the stored mountpoint.
@@ -979,10 +1003,54 @@ class Openbis:
return os.path.ismount(mountpoint)
+ def get_mountpoint(self):
+ """Returns the path to the active mountpoint.
+ Returns None if no mountpoint is found or if the mountpoint is not mounted anymore.
+ Experimental: Tries to figure out an existing mountpoint for a given hostname.
+ """
+
+ mountpoint = getattr(self, 'mountpoint', None)
+ if mountpoint:
+ if self.is_mounted(mountpoint):
+ return mountpoint
+ else:
+ return None
+
+ # try to find out the mountpoint
+ import subprocess
+ p1 = subprocess.Popen(["mount", "-d"], stdout=subprocess.PIPE)
+ p2 = subprocess.Popen(["grep", "--fixed-strings", self.hostname], stdin=p1.stdout, stdout=subprocess.PIPE)
+ p1.stdout.close() # Allow p1 to receive a SIGPIPE if p2 exits.
+ output = p2.communicate()[0]
+ output = output.decode()
+ # output will either be '' (=not mounted) or a string like this:
+ # {username}@{hostname}:{path} on {mountpoint} (osxfuse, nodev, nosuid, synchronous, mounted by vermeul)
+ try:
+ mountpoint = output.split()[2]
+ self.mountpoint = mountpoint
+ return mountpoint
+ except Exception:
+ return None
+
+
+ def mount(self,
+ username=None, password=None,
+ hostname=None, mountpoint=None,
+ volname=None, path='/', port=2222,
+ kex_algorithms ='+diffie-hellman-group1-sha1'
+ ):
+
+ """Mounts openBIS dataStore without being root, using sshfs and fuse. Both
+ SSHFS and FUSE must be installed on the system (see below)
+
+ Params:
+ username -- default: the currently used username
+ password -- default: the currently used password
+ hostname -- default: the current hostname
+ mountpoint -- default: ~/hostname
- def mount(self, username, password, servername, mountpoint, volname=None, path='/', port=2222, kex_algorithms ='+diffie-hellman-group1-sha1'):
- """Mounts openBIS dataStore without being root, using sshfs and fuse. Both SSHFS and FUSE must be installed on the system (the installation requires root privileges):
+ FUSE / SSHFS Installation (requires root privileges):
Mac OS X
========
@@ -995,7 +1063,11 @@ class Openbis:
$ sudo yum --enablerepo=epel -y install fuse-sshfs
$ user="$(whoami)"
$ usermod -a -G fuse "$user"
+
"""
+ if self.is_mounted():
+ if VERBOSE: print("openBIS dataStore is already mounted on {}".format(self.mountpoint))
+ return
def check_sshfs_is_installed():
import subprocess
@@ -1008,6 +1080,17 @@ class Openbis:
check_sshfs_is_installed()
+ if username is None: username = self._get_username()
+ if not username: raise ValueError("no token available - pleas provide a username")
+ if password is None: password = self._password()
+ if not password: raise ValueError("please provide a password")
+
+ if hostname is None: hostname = self.hostname
+ if not hostname: raise ValueError("please provide a hostname")
+
+ if mountpoint is None: mountpoint = os.path.join('~', self.hostname)
+
+
# check if mountpoint exists, otherwise create it
full_mountpoint_path = os.path.abspath(os.path.expanduser(mountpoint))
if not os.path.exists(full_mountpoint_path):
@@ -1022,18 +1105,18 @@ class Openbis:
os_options = {
- "darwin": "-oauto_cache,reconnect,defer_permissions,noappledouble,negative_vncache,volname={}".format(servername),
+ "darwin": "-oauto_cache,reconnect,defer_permissions,noappledouble,negative_vncache,volname={}".format(hostname),
"linux": "-oauto_cache,reconnect",
}
if volname is None:
- volname = servername
+ volname = hostname
import subprocess
args = {
"username": username,
"password": password,
- "servername": servername,
+ "hostname": hostname,
"port": port,
"path": path,
"mountpoint": mountpoint,
@@ -1043,7 +1126,7 @@ class Openbis:
}
cmd = 'echo "{password}" | sshfs'\
- ' {username}@{servername}:{path} {mountpoint}' \
+ ' {username}@{hostname}:{path} {mountpoint}' \
' -o port={port} -o ssh_command="ssh -oKexAlgorithms={kex_algorithms}" -o password_stdin'\
' {os_options}'.format(**args)
@@ -1403,18 +1486,16 @@ class Openbis:
"method": "createRoleAssignments",
"params": [
self.token,
- [
- {
- "role": role,
- "userId": userId,
- "authorizationGroupId": groupId,
- "spaceId": spaceId,
- "projectId": projectId,
- "@type": "as.dto.roleassignment.create.RoleAssignmentCreation",
- }
- ]
- ]
- }
+ [ {
+ "role": role,
+ "userId": userId,
+ "authorizationGroupId": groupId,
+ "spaceId": spaceId,
+ "projectId": projectId,
+ "@type": "as.dto.roleassignment.create.RoleAssignmentCreation",
+ } ]
+ ]
+ }
resp = self._post_request(self.as_v3, request)
return
--
GitLab