1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/2f2870f4f67d/ changeset: 2f2870f4f67d user: greg date: 2012-06-08 17:46:29 summary: Ehancements for automatic installation of tool dependencies when installing tool shed repositories; the enhancements support moving files and changing subdirectories during tool dependency installation. affected #: 5 files
diff -r 2a9c71e1d2209016559b09964c8b5a6f9854a5d5 -r 2f2870f4f67d2198c69b44af688b5b37174459b0 lib/galaxy/tool_shed/tool_dependencies/common_util.py --- a/lib/galaxy/tool_shed/tool_dependencies/common_util.py +++ b/lib/galaxy/tool_shed/tool_dependencies/common_util.py @@ -18,14 +18,16 @@ def iszip( file_path ): return check_zip( file_path ) def tar_extraction_directory( file_path, file_name ): + file_name = file_name.strip() extensions = [ '.tar.gz', '.tgz', '.tar.bz2', '.zip' ] for extension in extensions: - if file_name.endswith( extension ): + if file_name.find( extension ) > 0: dir_name = file_name[ :-len( extension ) ] - full_path = os.path.abspath( os.path.join( file_path, dir_name ) ) - if os.path.exists( full_path ): + if os.path.exists( os.path.abspath( os.path.join( file_path, dir_name ) ) ): return dir_name - raise ValueError( 'Could not find directory %s' % full_path ) + if os.path.exists( os.path.abspath( os.path.join( file_path, file_name ) ) ): + return os.path.abspath( os.path.join( file_path, file_name ) ) + raise ValueError( 'Could not find directory %s' % os.path.abspath( os.path.join( file_path, file_name[ :-len( extension ) ] ) ) ) def url_download( install_dir, downloaded_file_name, download_url ): file_path = os.path.join( install_dir, downloaded_file_name ) src = None
diff -r 2a9c71e1d2209016559b09964c8b5a6f9854a5d5 -r 2f2870f4f67d2198c69b44af688b5b37174459b0 lib/galaxy/tool_shed/tool_dependencies/fabric_util.py --- a/lib/galaxy/tool_shed/tool_dependencies/fabric_util.py +++ b/lib/galaxy/tool_shed/tool_dependencies/fabric_util.py @@ -1,7 +1,7 @@ # For Python 2.5 from __future__ import with_statement
-import os +import os, shutil from contextlib import contextmanager import common_util
@@ -11,7 +11,11 @@ pkg_resources.require('ssh' ) pkg_resources.require( 'Fabric' )
-from fabric.api import env, lcd, local +from fabric.api import env, lcd, local, settings + +DIRECTORY_BUILD_COMMAND_NAMES = [ 'change_directory' ] +MOVE_BUILD_COMMAND_NAMES = [ 'move_directory_files', 'move_file' ] +ALL_BUILD_COMMAND_NAMES = DIRECTORY_BUILD_COMMAND_NAMES + MOVE_BUILD_COMMAND_NAMES
def check_fabric_version(): version = env.version @@ -83,11 +87,39 @@ dir = package_name if build_commands: with lcd( dir ): - for build_command in build_commands: - output = local( build_command, capture=True ) - log_results( build_command, output, os.path.join( install_dir, 'build_commands.log' ) ) - if output.return_code: - return '%s. ' % str( output.stderr ) + current_dir = os.path.abspath( os.path.join( work_dir, dir ) ) + for build_command_tup in build_commands: + build_command_key, build_command_dict = build_command_tup + if build_command_key.find( 'v^v^v' ) >= 0: + build_command_items = build_command_key.split( 'v^v^v' ) + build_command_name = build_command_items[ 0 ] + build_command = build_command_items[ 1 ] + elif build_command_key in ALL_BUILD_COMMAND_NAMES: + build_command_name = build_command_key + else: + build_command_name = None + if build_command_name: + if build_command_name == 'change_directory': + current_dir = os.path.join( current_dir, build_command ) + lcd( current_dir ) + elif build_command_name == 'move_directory_files': + source_directory = os.path.abspath( os.path.join( current_dir, build_command_dict[ 'source_directory' ] ) ) + destination_directory = build_command_dict[ 'destination_directory' ] + for file_name in os.listdir( source_directory ): + source_file = os.path.join( source_directory, file_name ) + destination_file = os.path.join( destination_directory, file_name ) + shutil.move( source_file, destination_file ) + elif build_command_name == 'move_file': + source_file = os.path.abspath( os.path.join( current_dir, build_command_dict[ 'source' ] ) ) + destination = build_command_dict[ 'destination' ] + shutil.move( source_file, destination ) + else: + build_command = build_command_key + with settings( warn_only=True ): + output = local( build_command, capture=True ) + log_results( build_command, output, os.path.join( install_dir, 'build_commands.log' ) ) + if output.return_code: + return '%s. ' % str( output.stderr ) return '' def log_results( command, fabric_AttributeString, file_path ): """ @@ -98,12 +130,12 @@ logfile = open( file_path, 'ab' ) else: logfile = open( file_path, 'wb' ) - logfile.write( "#############################################" ) + logfile.write( "\n#############################################" ) logfile.write( '\n%s\nSTDOUT\n' % command ) - logfile.write( "#############################################" ) + logfile.write( "#############################################\n" ) logfile.write( str( fabric_AttributeString.stdout ) ) - logfile.write( "#############################################" ) + logfile.write( "\n#############################################" ) logfile.write( '\n%s\nSTDERR\n' % command ) - logfile.write( "#############################################" ) + logfile.write( "#############################################\n" ) logfile.write( str( fabric_AttributeString.stderr ) ) logfile.close()
diff -r 2a9c71e1d2209016559b09964c8b5a6f9854a5d5 -r 2f2870f4f67d2198c69b44af688b5b37174459b0 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 @@ -96,7 +96,24 @@ if param_name: if param_name == 'build_commands': for build_command_elem in param_elem: - build_commands.append( build_command_elem.text.replace( '$INSTALL_DIR', install_dir ) ) + build_command_dict = {} + build_command_name = build_command_elem.get( 'name' ) + if build_command_name: + if build_command_name in MOVE_BUILD_COMMAND_NAMES: + build_command_key = build_command_name + for move_elem in build_command_elem: + move_elem_text = move_elem.text.replace( '$INSTALL_DIR', install_dir ) + if move_elem_text: + build_command_dict[ move_elem.tag ] = move_elem_text + elif build_command_elem.text: + build_command_key = '%sv^v^v%s' % ( build_command_name, build_command_elem.text ) + else: + continue + else: + build_command_key = build_command_elem.text.replace( '$INSTALL_DIR', install_dir ) + if not build_command_key: + continue + build_commands.append( ( build_command_key, build_command_dict ) ) if build_commands: params_dict[ 'build_commands' ] = build_commands else: @@ -122,7 +139,6 @@ return message except: return '%s. ' % str( e ) - print package_name, 'installed to', install_dir return '' def run_proprietary_fabric_method( app, elem, fabfile_path, tool_dependency_dir, install_dir, package_name=None, **kwd ): """ @@ -161,7 +177,6 @@ if message: return message else: - print package_name, 'installed to', install_dir return '' def run_subprocess( app, cmd ): env = os.environ
diff -r 2a9c71e1d2209016559b09964c8b5a6f9854a5d5 -r 2f2870f4f67d2198c69b44af688b5b37174459b0 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -485,7 +485,7 @@ requirements_dict[ key ] = fabfiles_dict return requirements_dict def generate_metadata_using_disk_files( toolbox, relative_install_dir, repository_clone_url ): - """generate metadata using only the repository files on disk - files are not retrieved from the repository manifest.""" + """Generate metadata using only the repository files on disk - files are not retrieved from the repository manifest.""" metadata_dict = {} tool_dependencies_config = None datatypes_config = get_config_from_disk( 'datatypes_conf.xml', relative_install_dir ) @@ -1081,9 +1081,8 @@ """ Install and build tool dependencies defined in the tool_dependencies_config. This config's tag sets can refer to installation methods in Galaxy's tool_dependencies module or to proprietary fabric scripts contained in the repository. Future enhancements - to handling tool dependencies may provide installation processes in addition to fabric based processes. - - The dependencies will be installed in: + to handling tool dependencies may provide installation processes in addition to fabric based processes. The dependencies will be + installed in: ~/<app.config.tool_dependency_dir>/<package_name>/<package_version>/<repository_owner>/<repository_name>/<installed_changeset_revision> """ status = 'ok' @@ -1192,10 +1191,6 @@ tool_path, repository_tools_tups, work_dir ) - try: - shutil.rmtree( work_dir ) - except: - pass # Handle missing index files for tool parameters that are dynamically generated select lists. sample_files = metadata_dict.get( 'sample_files', [] ) repository_tools_tups, sample_files_copied = handle_missing_index_file( trans.app, tool_path, sample_files, repository_tools_tups ) @@ -1287,7 +1282,7 @@ commands.pull( get_configured_ui(), repo, source=repository_clone_url, - rev=ctx_rev ) + rev=[ ctx_rev ] ) def remove_from_shed_tool_config( trans, shed_tool_conf_dict, guids_to_remove ): # A tool shed repository is being uninstalled so change the shed_tool_conf file. Parse the config file to generate the entire list # of config_elems instead of using the in-memory list since it will be a subset of the entire list if one or more repositories have
diff -r 2a9c71e1d2209016559b09964c8b5a6f9854a5d5 -r 2f2870f4f67d2198c69b44af688b5b37174459b0 lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -1002,13 +1002,11 @@ metadata_changeset_revision = ancestor_changeset_revision metadata_dict = ancestor_metadata_dict create_or_update_repository_metadata( trans, id, repository, metadata_changeset_revision, metadata_dict ) - # Keep track of the changeset_revisions that we've persisted. changeset_revisions.append( metadata_changeset_revision ) ancestor_changeset_revision = current_changeset_revision ancestor_metadata_dict = current_metadata_dict else: - # We're either at the first change set in the change log or we have just created or updated a repository_metadata record. At - # this point we set the ancestor changeset to the current changeset for comparison in the next iteration. + # We're at the beginning of the change log. ancestor_changeset_revision = current_changeset_revision ancestor_metadata_dict = current_metadata_dict if not ctx.children():
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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