1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/142acf3cf8b8/
changeset: 142acf3cf8b8
user: inithello
date: 2013-02-01 19:37:38
summary: Fix for installing a complex dependency that has not been previously installed.
affected #: 1 file
diff -r c42bfba51ea0eb21cf83b19a193104b3ce4fbfd5 -r 142acf3cf8b831038bfb82d877e41168372a773e lib/galaxy/tool_shed/tool_dependencies/install_util.py
--- a/lib/galaxy/tool_shed/tool_dependencies/install_util.py
+++ b/lib/galaxy/tool_shed/tool_dependencies/install_util.py
@@ -227,8 +227,8 @@
tool_dependency_type='package',
tool_dependency_name=package_name,
tool_dependency_version=package_version )
- assert os.path.exists( required_repository_package_install_dir ), \
- 'Missing required tool dependency directory %s' % str( required_repository_package_install_dir )
+ if not os.path.exists( required_repository_package_install_dir ):
+ print 'Missing required tool dependency directory %s' % str( required_repository_package_install_dir )
repo_files_dir = required_repository.repo_files_directory( app )
tool_dependencies_config = get_absolute_path_to_file_in_repository( repo_files_dir, 'tool_dependencies.xml' )
if tool_dependencies_config:
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/c42bfba51ea0/
changeset: c42bfba51ea0
user: greg
date: 2013-02-01 19:13:09
summary: When resetting all metadata on a repository in the tool shed, restrict display of error messages to those associated with the tip.
affected #: 1 file
diff -r 7250bc892ede728688c010493a4019ec27d2decd -r c42bfba51ea0eb21cf83b19a193104b3ce4fbfd5 lib/galaxy/util/shed_util_common.py
--- a/lib/galaxy/util/shed_util_common.py
+++ b/lib/galaxy/util/shed_util_common.py
@@ -3154,7 +3154,9 @@
resetting_all_metadata_on_repository=True,
updating_installed_repository=False,
persist=False )
- invalid_file_tups.extend( invalid_tups )
+ # We'll only display error messages for the repository tip (it may be better to display error messages for each installable changeset revision).
+ if current_metadata_dict == repository.tip( trans.app ):
+ invalid_file_tups.extend( invalid_tups )
if current_metadata_dict:
if not metadata_changeset_revision and not metadata_dict:
# We're at the first change set in the change log.
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/7250bc892ede/
changeset: 7250bc892ede
user: inithello
date: 2013-02-01 17:43:40
summary: Uncommented cleanup method in functional_tests.py.
affected #: 1 file
diff -r cd6d105e5a5ba60e317ca7e194d63e2025272edb -r 7250bc892ede728688c010493a4019ec27d2decd test/tool_shed/functional_tests.py
--- a/test/tool_shed/functional_tests.py
+++ b/test/tool_shed/functional_tests.py
@@ -391,14 +391,14 @@
galaxyapp.shutdown()
galaxyapp = None
log.info( "Embedded galaxy application stopped" )
-# if 'TOOL_SHED_TEST_NO_CLEANUP' not in os.environ:
-# try:
-# for dir in [ tool_shed_test_tmp_dir ]:
-# if os.path.exists( dir ):
-# log.info( "Cleaning up temporary files in %s" % dir )
-# shutil.rmtree( dir )
-# except:
-# pass
+ if 'TOOL_SHED_TEST_NO_CLEANUP' not in os.environ:
+ try:
+ for dir in [ tool_shed_test_tmp_dir ]:
+ if os.path.exists( dir ):
+ log.info( "Cleaning up temporary files in %s" % dir )
+ shutil.rmtree( dir )
+ except:
+ pass
if success:
return 0
else:
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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