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Change the implementation for importing proprietary datatype class modules that are included in installed tool shed repositories. This approach will correctly import proprietary datatype classes whose file names conflict with a Python standard library module name (e.g., if a proprietary datatype class file is named xml.py, it will conflict with the Python standard library's xml module when attempting to import it).

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This commit is contained in:
Greg Von Kuster
2012-08-30 14:40:28 -04:00
parent d018ca4734
commit 2d589bd376
1 changed files with 6 additions and 7 deletions
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lib/galaxy/datatypes/registry.py
+6 -7
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@@ -1,7 +1,7 @@
"""
Provides mapping between extensions and datatypes, mime-types, etc.
"""
import os, sys, tempfile, threading, logging
import os, sys, tempfile, threading, logging, imp
import data, tabular, interval, images, sequence, qualityscore, genetics, xml, coverage, tracks, chrominfo, binary, assembly, ngsindex
import galaxy.util
from galaxy.util.odict import odict
@@ -55,10 +55,9 @@ class Registry( object ):
being installed. Since installation is occurring after the datatypes registry has been initialized, its
contents cannot be overridden by new introduced conflicting data types.
"""
def __import_module( full_path, datatype_module ):
sys.path.insert( 0, full_path )
imported_module = __import__( datatype_module )
sys.path.pop( 0 )
def __import_module( full_path, datatype_module, datatype_class_name ):
open_file_obj, file_name, description = imp.find_module( datatype_module, [ full_path ] )
imported_module = imp.load_module( datatype_class_name, open_file_obj, file_name, description )
return imported_module
if root_dir and config:
handling_proprietary_datatypes = False
@@ -130,12 +129,12 @@ class Registry( object ):
datatype_module = fields[0]
datatype_class_name = fields[1]
datatype_class = None
if proprietary_path and proprietary_datatype_module:
if proprietary_path and proprietary_datatype_module and datatype_class_name:
# We need to change the value of sys.path, so do it in a way that is thread-safe.
lock = threading.Lock()
lock.acquire( True )
try:
imported_module = __import_module( proprietary_path, proprietary_datatype_module )
imported_module = __import_module( proprietary_path, proprietary_datatype_module, datatype_class_name )
if imported_module not in self.imported_modules:
self.imported_modules.append( imported_module )
if hasattr( imported_module, datatype_class_name ):