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Merge pull request #2025 from jmchilton/ts_tool_data_table_config

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Don't setup a default tool_data_table_config_path in the shed.
This commit is contained in:
Björn Grüning
2016-03-29 06:22:28 +02:00
parent 71d8b4a6c1 a9d51f6dfe
commit ad12042f5f
1 changed files with 2 additions and 21 deletions
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lib/galaxy/webapps/tool_shed/config.py
+2 -21
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@@ -7,7 +7,7 @@ import sys
import logging
import logging.config
import ConfigParser
from galaxy.util import string_as_bool, listify
from galaxy.util import string_as_bool
from galaxy.web.formatting import expand_pretty_datetime_format
from galaxy.version import VERSION, VERSION_MAJOR
@@ -72,6 +72,7 @@ class Configuration( object ):
self.tool_path = resolve_path( kwargs.get( "tool_path", "tools" ), self.root )
self.tool_secret = kwargs.get( "tool_secret", "" )
self.tool_data_path = resolve_path( kwargs.get( "tool_data_path", "shed-tool-data" ), os.getcwd() )
self.tool_data_table_config_path = None
self.integrated_tool_panel_config = resolve_path( kwargs.get( 'integrated_tool_panel_config', 'integrated_tool_panel.xml' ), self.root )
self.builds_file_path = resolve_path( kwargs.get( "builds_file_path", os.path.join( self.tool_data_path, 'shared', 'ucsc', 'builds.txt') ), self.root )
self.len_file_path = resolve_path( kwargs.get( "len_file_path", os.path.join( self.tool_data_path, 'shared', 'ucsc', 'chrom') ), self.root )
@@ -175,10 +176,6 @@ class Configuration( object ):
shed_tool_data_table_config=[ 'shed_tool_data_table_conf.xml', 'config/shed_tool_data_table_conf.xml' ],
)
listify_defaults = dict(
tool_data_table_config_path=[ 'config/tool_data_table_conf.xml', 'tool_data_table_conf.xml', 'config/tool_data_table_conf.xml.sample' ],
)
for var, defaults in defaults.items():
if kwargs.get( var, None ) is not None:
path = kwargs.get( var )
@@ -191,22 +188,6 @@ class Configuration( object ):
path = defaults[-1]
setattr( self, var, resolve_path( path, self.root ) )
for var, defaults in listify_defaults.items():
paths = []
if kwargs.get( var, None ) is not None:
paths = listify( kwargs.get( var ) )
else:
for default in defaults:
for path in listify( default ):
if not os.path.exists( resolve_path( path, self.root ) ):
break
else:
paths = listify( default )
break
else:
paths = listify( defaults[-1] )
setattr( self, var, [ resolve_path( x, self.root ) for x in paths ] )
# Backwards compatibility for names used in too many places to fix
self.datatypes_config = self.datatypes_config_file