1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/b5ce9451c5d1/ changeset: b5ce9451c5d1 user: greg date: 2012-11-08 16:01:08 summary: Attempt to make sure .sample files included in an installed tool shed repository are only copied to ~/tool-data if they are sample data index files. affected #: 1 file
diff -r 5ff899b77dffce59580991a4b1d4dfbcdc091090 -r b5ce9451c5d190f0507f3b2c484afe937f12a045 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -7,6 +7,7 @@ from galaxy.web.form_builder import SelectField from galaxy.tools import parameters from galaxy.datatypes.checkers import * +from galaxy.datatypes.sniff import is_column_based from galaxy.util.json import * from galaxy.util import inflector from galaxy.tools.search import ToolBoxSearch @@ -546,15 +547,20 @@ shutil.copy( full_source_path, os.path.join( dest_path, copied_file ) ) def copy_sample_files( app, sample_files, tool_path=None, sample_files_copied=None, dest_path=None ): """ - Copy all files to dest_path in the local Galaxy environment that have not already been copied. Those that have been copied - are contained in sample_files_copied. The default value for dest_path is ~/tool-data. + Copy all appropriate files to dest_path in the local Galaxy environment that have not already been copied. Those that have been copied + are contained in sample_files_copied. The default value for dest_path is ~/tool-data. We need to be careful to copy only appropriate + files here because tool shed repositories can contain files ending in .sample that should not be copied to the ~/tool-data directory. """ + filenames_not_to_copy = [ 'tool_data_table_conf.xml.sample' ] sample_files_copied = util.listify( sample_files_copied ) for filename in sample_files: - if filename not in sample_files_copied: + filename_sans_path = os.path.split( filename )[ 1 ] + if filename_sans_path not in filenames_not_to_copy and filename not in sample_files_copied: if tool_path: filename=os.path.join( tool_path, filename ) - copy_sample_file( app, filename, dest_path=dest_path ) + # Attempt to ensure we're copying an appropriate file. + if is_data_index_sample_file( filename ): + copy_sample_file( app, filename, dest_path=dest_path ) def create_repo_info_dict( repository, owner, repository_clone_url, changeset_revision, ctx_rev, metadata ): repo_info_dict = {} repo_info_dict[ repository.name ] = ( repository.description, @@ -1539,9 +1545,11 @@ if shed_tool_conf == file_name: return index, shed_tool_conf_dict def get_tool_index_sample_files( sample_files ): + """Try to return the list of all appropriate tool data sample files included in the repository.""" tool_index_sample_files = [] for s in sample_files: - if s.endswith( '.loc.sample' ): + # The problem with this is that Galaxy does not follow a standard naming convention for file names. + if s.endswith( '.loc.sample' ) or s.endswith( '.xml.sample' ) or s.endswith( '.txt.sample' ): tool_index_sample_files.append( s ) return tool_index_sample_files def get_tool_dependency( trans, id ): @@ -1846,6 +1854,29 @@ parent_id=tool_version_using_parent_id.id ) sa_session.add( tool_version_association ) sa_session.flush() +def is_data_index_sample_file( file_path ): + """ + Attempt to determine if a .sample file is appropriate for copying to ~/tool-data when a tool shed repository is being installed + into a Galaxy instance. + """ + # Currently most data index files are tabular, so check that first. We'll assume that if the file is tabular, it's ok to copy. + if is_column_based( file_path ): + return True + # If the file is any of the following, don't copy it. + if check_html( file_path ): + return False + if check_image( file_path ): + return False + if check_binary( name=file_path ): + return False + if is_bz2( file_path ): + return False + if is_gzip( file_path ): + return False + if check_zip( file_path ): + return False + # Default to copying the file if none of the above are true. + return True def is_downloadable( metadata_dict ): return 'datatypes' in metadata_dict or 'tools' in metadata_dict or 'workflows' in metadata_dict def load_installed_datatype_converters( app, installed_repository_dict, deactivate=False ):
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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