3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b2df443a12d6/ Changeset: b2df443a12d6 Branch: next-stable User: dannon Date: 2014-12-03 14:21:54+00:00 Summary: Bump NO_OUTPUT_TIMEOUT to 60m; Bjoern said it's causing issues w/ some tools for being too short. Affected #: 1 file diff -r eb9d9ab34d23456d58f291b782b42724a83f711e -r b2df443a12d6a721da2a58b56491fbed08ebc4d9 lib/tool_shed/util/basic_util.py --- a/lib/tool_shed/util/basic_util.py +++ b/lib/tool_shed/util/basic_util.py @@ -16,7 +16,7 @@ CHUNK_SIZE = 2**20 # 1Mb INSTALLATION_LOG = 'INSTALLATION.log' # Set no activity timeout to 20 minutes. -NO_OUTPUT_TIMEOUT = 1200.0 +NO_OUTPUT_TIMEOUT = 3600.0 MAXDIFFSIZE = 8000 MAX_DISPLAY_SIZE = 32768 https://bitbucket.org/galaxy/galaxy-central/commits/81d5a494d274/ Changeset: 81d5a494d274 Branch: next-stable User: dannon Date: 2014-12-03 14:23:14+00:00 Summary: Pep8 tool_shed/util/basic_util Affected #: 1 file diff -r b2df443a12d6a721da2a58b56491fbed08ebc4d9 -r 81d5a494d274918192fe92bd3ac9217bcb22ef2c lib/tool_shed/util/basic_util.py --- a/lib/tool_shed/util/basic_util.py +++ b/lib/tool_shed/util/basic_util.py @@ -13,7 +13,7 @@ log = logging.getLogger( __name__ ) -CHUNK_SIZE = 2**20 # 1Mb +CHUNK_SIZE = 2**20 # 1Mb INSTALLATION_LOG = 'INSTALLATION.log' # Set no activity timeout to 20 minutes. NO_OUTPUT_TIMEOUT = 3600.0 @@ -47,6 +47,7 @@ RUN service postgresql start && service apache2 start && ./run.sh --daemon && sleep 120 && python ./scripts/api/install_tool_shed_repositories.py --api admin -l http://localhost:8080 --url ${tool_shed_url} -o ${repository_owner} --name ${repository_name} --tool-deps --repository-deps --panel-section-name 'Docker' ''' + def evaluate_template( text, install_environment ): """ Substitute variables defined in XML blocks from dependencies file. The value of the received @@ -56,6 +57,7 @@ """ return Template( text ).safe_substitute( get_env_var_values( install_environment ) ) + def get_env_var_values( install_environment ): """ Return a dictionary of values, some of which enable substitution of reserved words for the values. @@ -72,6 +74,7 @@ env_var_dict[ '__is64bit__' ] = sys.maxsize > 2**32 return env_var_dict + def get_file_type_str( changeset_revision, file_type ): if file_type == 'zip': file_type_str = '%s.zip' % changeset_revision @@ -83,6 +86,7 @@ file_type_str = '' return file_type_str + def move_file( current_dir, source, destination, rename_to=None ): source_path = os.path.abspath( os.path.join( current_dir, source ) ) source_file = os.path.basename( source_path ) @@ -97,6 +101,7 @@ os.makedirs( destination_directory ) shutil.move( source_path, destination_path ) + def remove_dir( dir ): """Attempt to remove a directory from disk.""" if dir: @@ -106,6 +111,7 @@ except: pass + def size_string( raw_text, size=MAX_DISPLAY_SIZE ): """Return a subset of a string (up to MAX_DISPLAY_SIZE) translated to a safe string for display in a browser.""" if raw_text and len( raw_text ) >= size: @@ -113,11 +119,13 @@ raw_text = '%s%s' % ( raw_text[ 0:size ], large_str ) return raw_text or '' + def stringify( list ): if list: return ','.join( list ) return '' + def strip_path( fpath ): """Attempt to strip the path from a file name.""" if not fpath: @@ -128,6 +136,7 @@ file_name = fpath return file_name + def to_html_string( text ): """Translates the characters in text to an html string""" if text: https://bitbucket.org/galaxy/galaxy-central/commits/f05ed31c1674/ Changeset: f05ed31c1674 Branch: next-stable User: dannon Date: 2014-12-03 14:24:44+00:00 Summary: Fix size_string; this would have thrown an exception on being called due to an unimported 'util'. Affected #: 1 file diff -r 81d5a494d274918192fe92bd3ac9217bcb22ef2c -r f05ed31c16741b5c1a4a43c73697f7ca9a6919d8 lib/tool_shed/util/basic_util.py --- a/lib/tool_shed/util/basic_util.py +++ b/lib/tool_shed/util/basic_util.py @@ -4,7 +4,7 @@ import sys from string import Template -from galaxy.util import unicodify +from galaxy.util import unicodify, nice_size from galaxy import eggs @@ -115,7 +115,7 @@ def size_string( raw_text, size=MAX_DISPLAY_SIZE ): """Return a subset of a string (up to MAX_DISPLAY_SIZE) translated to a safe string for display in a browser.""" if raw_text and len( raw_text ) >= size: - large_str = '\nFile contents truncated because file size is larger than maximum viewing size of %s\n' % util.nice_size( size ) + large_str = '\nFile contents truncated because file size is larger than maximum viewing size of %s\n' % nice_size( size ) raw_text = '%s%s' % ( raw_text[ 0:size ], large_str ) return raw_text or '' Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.