From 7dbebfa59b156bc757f89e92e709aed0a54a3e8e Mon Sep 17 00:00:00 2001
From: vermeul <swen@ethz.ch>
Date: Fri, 20 Dec 2019 15:13:27 +0100
Subject: [PATCH] added datastores attribute to openbis object
---
pybis/src/python/pybis/pybis.py | 41 ++++++++++++++++++++++++++-------
1 file changed, 33 insertions(+), 8 deletions(-)
diff --git a/pybis/src/python/pybis/pybis.py b/pybis/src/python/pybis/pybis.py
index a37d3cdc593..a23eb061d50 100644
--- a/pybis/src/python/pybis/pybis.py
+++ b/pybis/src/python/pybis/pybis.py
@@ -932,14 +932,36 @@ class Openbis:
os.environ['OPENBIS_TOKEN'] = self.token
return self.token
- def mount(self, username, mountpoint, volname, password, port=2222, kex_algorithms ='+diffie-hellman-group1-sha1'):
- """
- echo password | sshfs -o port=2222 -o ssh_command="ssh -oKexAlgorithms=+diffie-hellman-group1-sha1"
- vermeul@openbis-tst.ethz.ch:/SIS_VERMEUL/MY-FIRST-PROJECT/MY-FIRST-PROJECT_EXP_1/20190403133112022-611/original/DEFAULT ~/mnt
- -oauto_cache,reconnect,defer_permissions,noappledouble,negative_vncache,volname=myVolumeName -o password_stdin
- """
- pass
-
+ def mount(self, username, servername, mountpoint, volname, password, path='/', port=2222, kex_algorithms ='+diffie-hellman-group1-sha1', shell=False):
+
+ """Mounts openBIS dataStore without root, using sshfs and fuse.
+ """
+
+ import subprocess
+ args = {
+ "username": username,
+ "password": password,
+ "servername": servername,
+ "port": port,
+ "path": path,
+ "mountpoint": mountpoint,
+ "volname": volname,
+ "kex_algroithms": kex_algroithms,
+ }
+ cmd = (
+ 'echo "{password}" | sshfs -o port={port}'
+ ' -o ssh_command="ssh -oKexAlgorithms={kex_algroithms}+diffie-hellman-group1-sha1"'
+ ' {username}@{servername}:{path} {mountpoint}'
+ ' -oauto_cache,reconnect,defer_permissions,noappledouble,negative_vncache,volname={volname}'
+ ' -o password_stdin'
+ )
+
+ subprocess.run(cmd.format(**args),
+ stdout=subprocess.PIPE,
+ stderr=subprocess.PIPE,
+ input=password,
+ shell=shell
+ )
def get_server_information(self):
@@ -988,6 +1010,8 @@ class Openbis:
there might be multiple servers. If you upload a file, you need to specifiy the datastore you want
the file uploaded to.
"""
+ if hasattr(self, 'datastores'):
+ return self.datastores
request = {
"method": "searchDataStores",
@@ -1009,6 +1033,7 @@ class Openbis:
objects = resp['objects']
parse_jackson(objects)
datastores = DataFrame(objects)
+ self.datastores = datastores[attrs]
return datastores[attrs]
def gen_code(self, entity, prefix=""):
--
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