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Use an odict instead of a dict when acquuiring elements for generating entries for the migrated_tools_conf.xml from the InstallManager, and handle multiple proprietary non-shed tool panel configs with the InstallManger.

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This commit is contained in:
Greg Von Kuster
2012-03-15 11:47:46 -04:00
parent 19862fd03b
commit 628b6ea82d
3 changed files with 45 additions and 35 deletions
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lib/galaxy/tool_shed/install_manager.py
+36 -32
View File
@@ -6,6 +6,7 @@ import logging, urllib2
from galaxy.tools import ToolSection
from galaxy.util.json import from_json_string, to_json_string
from galaxy.util.shed_util import *
from galaxy.util.odict import odict
log = logging.getLogger( __name__ )
class InstallManager( object ):
@@ -19,7 +20,7 @@ class InstallManager( object ):
self.migrated_tools_config = migrated_tools_config
# Get the local non-shed related tool panel config (the default name is tool_conf.xml). If the user has more than 1
# non-shed tool panel config it could cause problems.
self.proprietary_tool_conf = self.non_shed_tool_panel_config
self.proprietary_tool_confs = self.non_shed_tool_panel_configs
self.proprietary_tool_panel_elems = self.get_proprietary_tool_panel_elems( latest_migration_script_number )
# Set the location where the repositories will be installed by retrieving the tool_path setting from migrated_tools_config.
tree = util.parse_xml( migrated_tools_config )
@@ -50,10 +51,11 @@ class InstallManager( object ):
tool = self.toolbox.load_tool( full_path )
return generate_tool_guid( repository_clone_url, tool )
def get_proprietary_tool_panel_elems( self, latest_tool_migration_script_number ):
# Parse self.proprietary_tool_conf (the default is tool_conf.xml) and generate a list of Elements that are either ToolSection elements
# or Tool elements. These will be used to generate new entries in the migrated_tools_conf.xml file for the installed tools.
# Parse each config in self.proprietary_tool_confs (the default is tool_conf.xml) and generate a list of Elements that are
# either ToolSection elements or Tool elements. These will be used to generate new entries in the migrated_tools_conf.xml
# file for the installed tools.
tools_xml_file_path = os.path.abspath( os.path.join( 'scripts', 'migrate_tools', '%04d_tools.xml' % latest_tool_migration_script_number ) )
# Parse the XML and load the file attributes for later checking against self.proprietary_tool_conf.
# Parse the XML and load the file attributes for later checking against the integrated elements from self.proprietary_tool_confs.
migrated_tool_configs = []
tree = util.parse_xml( tools_xml_file_path )
root = tree.getroot()
@@ -61,30 +63,31 @@ class InstallManager( object ):
if elem.tag == 'repository':
for tool_elem in elem:
migrated_tool_configs.append( tool_elem.get( 'file' ) )
# Parse self.proprietary_tool_conf and generate the list of tool panel Elements that contain them.
# Parse each file in self.proprietary_tool_confs and generate the integrated list of tool panel Elements that contain them.
tool_panel_elems = []
tree = util.parse_xml( self.proprietary_tool_conf )
root = tree.getroot()
for elem in root:
if elem.tag == 'tool':
# Tools outside of sections.
file_path = elem.get( 'file', None )
if file_path:
path, name = os.path.split( file_path )
if name in migrated_tool_configs:
if elem not in tool_panel_elems:
tool_panel_elems.append( elem )
elif elem.tag == 'section':
# Tools contained in a section.
for section_elem in elem:
if section_elem.tag == 'tool':
file_path = section_elem.get( 'file', None )
if file_path:
path, name = os.path.split( file_path )
if name in migrated_tool_configs:
# Append the section, not the tool.
if elem not in tool_panel_elems:
tool_panel_elems.append( elem )
for proprietary_tool_conf in self.proprietary_tool_confs:
tree = util.parse_xml( proprietary_tool_conf )
root = tree.getroot()
for elem in root:
if elem.tag == 'tool':
# Tools outside of sections.
file_path = elem.get( 'file', None )
if file_path:
path, name = os.path.split( file_path )
if name in migrated_tool_configs:
if elem not in tool_panel_elems:
tool_panel_elems.append( elem )
elif elem.tag == 'section':
# Tools contained in a section.
for section_elem in elem:
if section_elem.tag == 'tool':
file_path = section_elem.get( 'file', None )
if file_path:
path, name = os.path.split( file_path )
if name in migrated_tool_configs:
# Append the section, not the tool.
if elem not in tool_panel_elems:
tool_panel_elems.append( elem )
return tool_panel_elems
def get_containing_tool_sections( self, tool_config ):
"""
@@ -122,7 +125,7 @@ class InstallManager( object ):
# updated to the desired changeset_revision before metadata is set because the process for setting metadata uses the repository files on disk.
# The values for the keys in each of the following dictionaries will be a list to allow for the same tool to be displayed in multiple places
# in the tool panel.
tool_panel_dict_for_display = {}
tool_panel_dict_for_display = odict()
for tool_elem in repository_elem:
# The tool_elem looks something like this: <tool id="EMBOSS: antigenic1" version="5.0.0" file="emboss_antigenic.xml" />
tool_config = tool_elem.get( 'file' )
@@ -264,8 +267,9 @@ class InstallManager( object ):
print "Error cloning repository '", name, "': ", str( tmp_stderr.read() )
tmp_stderr.close()
@property
def non_shed_tool_panel_config( self ):
# Get the non-shed related tool panel config value from the Galaxy config - the default is tool_conf.xml.
def non_shed_tool_panel_configs( self ):
# Get the non-shed related tool panel config file names from the Galaxy config - the default is tool_conf.xml.
config_filenames = []
for config_filename in self.app.config.tool_configs:
# Any config file that includes a tool_path attribute in the root tag set like the following is shed-related.
# <toolbox tool_path="../shed_tools">
@@ -274,8 +278,8 @@ class InstallManager( object ):
tool_path = root.get( 'tool_path', None )
if tool_path is None:
# There will be a problem here if the user has defined 2 non-shed related configs.
return config_filename
return None
config_filenames.append( config_filename )
return config_filenames
def __get_url_from_tool_shed( self, tool_shed ):
# The value of tool_shed is something like: toolshed.g2.bx.psu.edu
# We need the URL to this tool shed, which is something like:
lib/galaxy/tool_shed/migrate/common.py
+1
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@@ -70,6 +70,7 @@ class MigrateToolsApplication( object ):
self.config = galaxy.config.Configuration( **galaxy_config_dict )
if self.config.database_connection is None:
self.config.database_connection = "sqlite:///%s?isolation_level=IMMEDIATE" % self.config.database
self.config.update_integrated_tool_panel = True
self.object_store = build_object_store_from_config( self.config )
# Setup the database engine and ORM
self.model = galaxy.model.mapping.init( self.config.file_path,
scripts/migrate_tools/migrate_tools.py
+8 -3
View File
@@ -19,8 +19,13 @@ from galaxy import eggs
from galaxy.tool_shed.migrate.common import *
app = MigrateToolsApplication( sys.argv[ 1 ] )
non_shed_tool_conf = app.install_manager.proprietary_tool_conf
print "\nThe installation process is finished. You should now remove entries for the installed tools from"
print "your file named %s and start your Galaxy server." % non_shed_tool_conf
non_shed_tool_confs = app.install_manager.proprietary_tool_confs
msg = "\nThe installation process is finished. You should now remove entries for the installed tools from "
if len( non_shed_tool_confs ) == 1:
msg += "your file named %s and start your Galaxy server." % non_shed_tool_conf
else:
file_names = ', '.join( non_shed_tool_confs )
msg += "your files named %s, and start your Galaxy server." % file_names
print msg
app.shutdown()
sys.exit( 0 )