I had to make slight changes because in my version Repository does not have
@property repo_path anymore (or not yet).
It now also assigns one category (which has to exist before).
thank you very much,
ido
#!/usr/bin/env python
'''
This script requires the Galaxy instance to use Postgres for database storage.
To run this script, use "sh copy_repository.sh" from this directory
'''
import sys, os, ConfigParser
assert sys.version_info[:2] >= ( 2, 4 )
new_path = [ os.path.join( os.getcwd(), "lib" ) ]
new_path.extend( sys.path[1:] ) # remove scripts/ from the path
sys.path = new_path
from galaxy import eggs
import pkg_resources
pkg_resources.require( "psycopg2" )
import psycopg2
pkg_resources.require( 'elementtree' )
from elementtree import ElementTree, ElementInclude
import galaxy.webapps.community.app
from galaxy import util
from mercurial import hg, ui, httprepo, commands
def directory_hash_id( id ):
s = str( id )
l = len( s )
# Shortcut -- ids 0-999 go under ../000/
if l < 4:
return [ "000" ]
# Pad with zeros until a multiple of three
padded = ( ( ( 3 - len( s ) ) % 3 ) * "0" ) + s
# Drop the last three digits -- 1000 files per directory
padded = padded[:-3]
# Break into chunks of three
return [ padded[i*3:(i+1)*3] for i in range( len( padded ) // 3 ) ]
def add_hgweb_config_entry( repository, repository_path ):
# Add an entry in the hgweb.config file for a new repository. This enables calls to repository.repo_path.
# An entry looks something like: repos/test/mira_assembler = database/community_files/000/repo_123
hgweb_config = "%s/hgweb.config" % os.getcwd()
entry = "repos/%s/%s = %s" % ( repository.user.username, repository.name, repository_path.lstrip( './' ) )
if os.path.exists( hgweb_config ):
output = open( hgweb_config, 'a' )
else:
output = open( hgweb_config, 'w' )
output.write( '[paths]\n' )
output.write( "%s\n" % entry )
output.close()
def create_hgrc_file( repo_path, username, reponame ):
# At this point, an entry for the repository is required to be in the hgweb.config
# file so we can call repository.repo_path.
# Create a .hg/hgrc file that looks something like this:
# [web]
# allow_push = test
# name = convert_characters1
# push_ssl = False
# Upon repository creation, only the owner can push to it ( allow_push setting ),
# and since we support both http and https, we set push_ssl to False to override
# the default (which is True) in the mercurial api.
hgrc_file = os.path.abspath( os.path.join( repo_path, ".hg", "hgrc" ) )
output = open( hgrc_file, 'w' )
output.write( '[web]\n' )
output.write( 'allow_push = %s\n' % username )
output.write( 'name = %s\n' % reponame )
output.write( 'push_ssl = false\n' )
output.flush()
output.close()
def clone_repository( repository_clone_url, repository_path ):
"""Clone the repository up to the specified changeset_revision. No subsequent revisions will be present in the cloned repository."""
print( str( repository_clone_url )+" "+str( repository_path ))
commands.clone( get_configured_ui(),
str( repository_clone_url ),
dest=str( repository_path ),
pull=True,
noupdate=False,
rev=[] )
def contains( containing_str, contained_str ):
return containing_str.lower().find( contained_str.lower() ) >= 0
def copy_repository( app, repository_clone_url, name, description, user_id, username, catname ):
sa_session = app.model.context
# Add the repository record to the db
print "Adding new database record for repository: ", name
repository = app.model.Repository( name=name,
description=description,
long_description=description,
user_id=user_id )
# repopath = app.hgweb_config_manager.get_entry( os.path.join( "repos", username, name ) )
# Flush to get the id
sa_session.add( repository )
sa_session.flush()
category = sa_session.query( app.model.Category ).filter( app.model.Category.table.c.name == catname ).all()[0]
assoc = app.model.RepositoryCategoryAssociation(repository, category)
sa_session.add(assoc)
sa_session.flush()
# Determine the repository's repo_path on disk
clone_dir = os.path.join( app.config.file_path, *directory_hash_id( repository.id ) )
# Create directory if it does not exist
if not os.path.exists( clone_dir ):
os.makedirs( clone_dir )
# Define repo name inside hashed directory
repository_path = os.path.join( clone_dir, "repo_%d" % repository.id )
# Create local repository directory
if not os.path.exists( repository_path ):
os.makedirs( repository_path )
print "Creating local repository at: ", repository_path
# Clone the repository
clone_repository( repository_clone_url, os.path.abspath( repository_path ) )
repo = hg.repository( get_configured_ui(), repository_path )
# Update the repository files for browsing.
print "Updating repository"
update_repository( repo )
# Add an entry in the hgweb.config file for the local repository. This enables calls to repository.repo_path
print "Adding entry to hgweb.config"
add_hgweb_config_entry( repository, repository_path )
# Create a .hg/hgrc file for the local repository
print "Creating hgrc file"
create_hgrc_file( repository_path, username, name )
print "Repository '%s' has been copied." % repository.name
def create_user( app, email, password, username ):
sa_session = app.model.context
user = app.model.User( email=email )
user.set_password_cleartext( password )
user.username = username
sa_session.add( user )
sa_session.flush()
return user
def get_configured_ui():
# Configure any desired ui settings.
_ui = ui.ui()
# The following will suppress all messages. This is
# the same as adding the following setting to the repo
# hgrc file' [ui] section:
# quiet = True
_ui.setconfig( 'ui', 'quiet', True )
return _ui
def get_user( app, email ):
sa_session = app.model.context
return sa_session.query( app.model.User ) \
.filter( app.model.User.table.c.email == email ) \
.first()
def update_repository( repo, ctx_rev=None ):
commands.update( get_configured_ui(),
repo,
rev=ctx_rev )
def main():
if len( sys.argv ) < 3:
print "Usage: python %s <Tool shed config file> copy_repository.xml" % sys.argv[0]
sys.exit( 0 )
email = 'user@changeme'
password = 'password'
username = 'username'
catname = 'category'
# community_wsgi.ini file
ini_file = sys.argv[ 1 ]
repository_xml_file = sys.argv[ 2 ]
conf_parser = ConfigParser.ConfigParser( { 'here' : os.getcwd() } )
conf_parser.read( ini_file )
try:
db_conn_str = conf_parser.get( "app:main", "database_connection" )
except ConfigParser.NoOptionError, e:
db_conn_str = conf_parser.get( "app:main", "database_file" )
print 'DB Connection: ', db_conn_str
# Determine db connection - only postgres is supported
if contains( db_conn_str, '///' ) and contains( db_conn_str, '?' ) and contains( db_conn_str, '&' ):
# postgres:///galaxy_test?user=postgres&password=postgres
db_str = db_conn_str.split( '///' )[ 1 ]
db_name = db_str.split( '?' )[ 0 ]
db_user = db_str.split( '?' )[ 1 ].split( '&' )[ 0 ].split( '=' )[ 1 ]
db_password = db_str.split( '?' )[ 1 ].split( '&' )[ 1 ].split( '=' )[ 1 ]
elif contains( db_conn_str, '//' ) and contains( db_conn_str, ':' ):
# dialect://user:password@host/db_name
db_name = db_conn_str.split( '/' )[ -1 ]
db_user = db_conn_str.split( '//' )[ 1 ].split( ':' )[ 0 ]
# Instantiate app
configuration = {}
for key, value in conf_parser.items( "app:main" ):
configuration[ key ] = value
app = galaxy.webapps.community.app.UniverseApplication( global_conf=dict( __file__=ini_file ), **configuration )
sa_session = app.model.context
# Make sure we have a user.
user = get_user( app, email )
if user is None:
user = create_user( app, email, password, username )
hgweb_config = "%s/hgweb.config" % os.getcwd()
# Parse the copy_repository.xml file to determine what repositories should be copied.
tree = util.parse_xml( repository_xml_file )
root = tree.getroot()
tool_shed_url = root.get( 'url' )
for repository_elem in root:
repository_name = repository_elem.get( 'name' )
repository_description = repository_elem.get( 'description' )
repository_owner = repository_elem.get( 'owner' )
repository_clone_url = os.path.join( tool_shed_url, 'repos', repository_owner, repository_name )
copy_repository( app, repository_clone_url, repository_name, repository_description, user.id, user.username, catname )
app.shutdown()
sys.exit(0)
if __name__ == "__main__":
main()
On Dec 4, 2012, at 5:27 PM, Greg Von Kuster wrote:
> Hi Ido,
>
> On Dec 4, 2012, at 10:26 AM, Ido Tamir wrote:
>
> > Hi,
> > how do I get tools from one local toolshed (or the main galaxy toolshed)
> > into another tool-shed? Is it possible to clone the content of a complete
> > tool-shed - all repositories
> > at once into another tool-shed?
>
> Not at the current time, but I've attached a script that I use in my
> development environment that sort of does what you want.
>
> When you run it for the first time, make sure it installs to a tool shed you
> don't care about destroying just so you can see how it works. It uses the
> configuration settings in commnity_wsgi.ini, so make sure you set things
> accordingly.
>
> here's what you do:
>
> 1. Place the 3 attached files in ~/scripts/tool_shed
> 2. Define the tool shed you want to copy repositories form in
> copy_repository.xml
> 3. Define any number of valid <repository> tags in copy_repository.xml
> 4. run the copy_repositoyr.sh shell script from the ~/scripts/tool_shed
> directory
> 5. When all repositories have been copied into you local tool shed, start it
> up and make sure to reset all metadata on all repositories as the script does
> not do so. You can dfo this from the Tool Shed's admin interface.
>
> I do not have time to support it, so you're on your own if you want to use it
> as is. If you enhance it to the point that it would be useful to the
> community, please contribute it back to me and I'll make sure it is included
> in the Galaxy code base.
>
>
>
>
>
>
>
>
>
> > Can I then import all the tools at once into a local galaxy instance?
>
> Not currently, but this is planned for the near future ( within a few months
> ).
>
> >
> > We have a group with their own tool-shed. Unfortunately, I accessed it
> > directly
> > without a proxy on its port which leads to a problem described in issue 825
> > in galaxy-central.
> >
> > I want to
> > a) clone the tool-shed as it is into my own tool-shed (rsync?)
> > b) selectively or bulk install these tools into my galaxy server.
> >
> > thank you very much,
> > ido
> >
> >
> >
> > ___________________________________________________________
> > Please keep all replies on the list by using "reply all"
> > in your mail client. To manage your subscriptions to this
> > and other Galaxy lists, please use the interface at:
> >
> > http://lists.bx.psu.edu/
>
> <copy_repository.py><copy_repository.sh><copy_repository.xml>
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