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import socket
import os
import pybis
from .openbis_command import OpenbisCommand, ContentCopySelector
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from ..checksum import validate_checksum
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from ..command_result import CommandResult
from ..utils import cd
from ..utils import run_shell
from ..utils import complete_openbis_config
from ... import dm
class Clone(OpenbisCommand):
"""
Implements the clone command. Copies a repository from a content copy of a data set
and adds the local copy as a new content copy using the addref command.
"""
def __init__(self, dm, data_set_id, ssh_user, content_copy_index):
self.data_set_id = data_set_id
self.ssh_user = ssh_user
self.content_copy_index = content_copy_index
self.load_global_config(dm)
super(Clone, self).__init__(dm)
def check_configuration(self):
missing_config_settings = []
if self.openbis is None:
missing_config_settings.append('openbis_url')
if self.user() is None:
missing_config_settings.append('user')
if len(missing_config_settings) > 0:
return CommandResult(returncode=-1,
output="Missing configuration settings for {}.".format(missing_config_settings))
return CommandResult(returncode=0, output="")
def run(self):
result = self.prepare_run()
if result.failure():
return result
data_set = self.openbis.get_dataset(self.data_set_id)
content_copy = ContentCopySelector(data_set, self.content_copy_index).select()
host = content_copy['externalDms']['address'].split(':')[0]
path = content_copy['path']
repository_folder = path.split('/')[-1]
result = self.copy_repository(self.ssh_user, host, path)
if result.failure():
return result
result = self.checkout_commit(content_copy, path)
if result.failure():
return result
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data_set = self.openbis.get_dataset(self.data_set_id)
validate_checksum(self.openbis, data_set.file_list, data_set.permId, repository_folder)
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return self.add_content_copy_to_openbis(repository_folder)
def copy_repository(self, ssh_user, host, path):
# abort if local folder already exists
repository_folder = path.split('/')[-1]
if os.path.exists(repository_folder):
return CommandResult(returncode=-1, output="Folder for repository to clone already exists: " + repository_folder)
# check if local or remote
if host == socket.gethostname():
location = path
else:
location = ssh_user + "@" if ssh_user is not None else ""
location += host + ":" + path
# copy repository
return run_shell(["rsync", "--progress", "-av", location, "."])
def checkout_commit(self, content_copy, path):
"""
Checks out the commit of the content copy from which the clone was made
in case there are newer commits / data sets. So the new copy is based on the
data set given as an input.
"""
commit_hash = content_copy['gitCommitHash']
repository_folder = path.split('/')[-1]
with cd(repository_folder):
return self.git_wrapper.git_checkout(commit_hash)
def add_content_copy_to_openbis(self, repository_folder):
with cd(repository_folder):
data_mgmt = dm.DataMgmt(openbis_config={}, git_config={'find_git': True})
return data_mgmt.addref()