1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/changeset/018179ad4c9b/ changeset: 018179ad4c9b user: greg date: 2012-06-01 20:51:41 summary: 1) Enhance the InstallManager to provide the installer the ability to choose to install tool dependenceis (or not) rather than automatically installing them. 2) Persist changes to the tool_data_table_conf.xml file only if within the Galaxy webapp. 3) Apply the 1-liner fix from change set 9ffef0de07f5 in Peter van Heusden's pull request which fixes a problem where the __init__ tests if config.database_connection is None. affected #: 8 files

diff -r 9ae91fb49fdd5762dc9a0374dfc471733da47143 -r 018179ad4c9bcec30baea5aee0918f45d254deb2 lib/galaxy/app.py --- a/lib/galaxy/app.py +++ b/lib/galaxy/app.py @@ -31,6 +31,11 @@ db_url = self.config.database_connection else: db_url = "sqlite:///%s?isolation_level=IMMEDIATE" % self.config.database + # Set up the tool sheds registry + if os.path.isfile( self.config.tool_sheds_config ): + self.tool_shed_registry = galaxy.tool_shed.tool_shed_registry.Registry( self.config.root, self.config.tool_sheds_config ) + else: + self.tool_shed_registry = None # Initialize database / check for appropriate schema version. # If this # is a new installation, we'll restrict the tool migration messaging. from galaxy.model.migrate.check import create_or_verify_database @@ -47,11 +52,6 @@ self.config.database_engine_options, database_query_profiling_proxy = self.config.database_query_profiling_proxy, object_store = self.object_store ) - # Set up the tool sheds registry - if os.path.isfile( self.config.tool_sheds_config ): - self.tool_shed_registry = galaxy.tool_shed.tool_shed_registry.Registry( self.config.root, self.config.tool_sheds_config ) - else: - self.tool_shed_registry = None # Manage installed tool shed repositories. self.installed_repository_manager = galaxy.tool_shed.InstalledRepositoryManager( self ) # Create an empty datatypes registry.

diff -r 9ae91fb49fdd5762dc9a0374dfc471733da47143 -r 018179ad4c9bcec30baea5aee0918f45d254deb2 lib/galaxy/tool_shed/install_manager.py --- a/lib/galaxy/tool_shed/install_manager.py +++ b/lib/galaxy/tool_shed/install_manager.py @@ -7,9 +7,12 @@ from galaxy.util.json import from_json_string, to_json_string from galaxy.util.shed_util import * from galaxy.util.odict import odict +from galaxy.tool_shed.migrate.common import * + +REPOSITORY_OWNER = 'devteam'

class InstallManager( object ): - def __init__( self, app, latest_migration_script_number, tool_shed_install_config, migrated_tools_config ): + def __init__( self, app, latest_migration_script_number, tool_shed_install_config, migrated_tools_config, install_dependencies ): """ Check tool settings in tool_shed_install_config and install all repositories that are not already installed. The tool panel configuration file is the received migrated_tools_config, which is the reserved file named migrated_tools_conf.xml. @@ -30,9 +33,9 @@ tree = util.parse_xml( tool_shed_install_config ) root = tree.getroot() self.tool_shed = clean_tool_shed_url( root.get( 'name' ) ) - self.repository_owner = 'devteam' + self.repository_owner = REPOSITORY_OWNER for repository_elem in root: - self.install_repository( repository_elem ) + self.install_repository( repository_elem, install_dependencies ) def get_guid( self, repository_clone_url, relative_install_dir, tool_config ): found = False for root, dirs, files in os.walk( relative_install_dir ): @@ -117,7 +120,8 @@ if not is_displayed: is_displayed = True return is_displayed, tool_sections - def handle_repository_contents( self, repository_clone_url, relative_install_dir, repository_elem, repository_name, description, changeset_revision, ctx_rev ): + def handle_repository_contents( self, repository_clone_url, relative_install_dir, repository_elem, repository_name, description, changeset_revision, + ctx_rev, install_dependencies ): # Generate the metadata for the installed tool shed repository, among other things. It is critical that the installed repository is # updated to the desired changeset_revision before metadata is set because the process for setting metadata uses the repository files on disk. # The values for the keys in each of the following dictionaries will be a list to allow for the same tool to be displayed in multiple places @@ -162,7 +166,7 @@ repository_tools_tups, sample_files_copied = handle_missing_index_file( self.app, self.tool_path, sample_files, repository_tools_tups ) # Copy remaining sample files included in the repository to the ~/tool-data directory of the local Galaxy instance. copy_sample_files( self.app, sample_files, sample_files_copied=sample_files_copied ) - if 'tool_dependencies' in metadata_dict: + if install_dependencies and 'tool_dependencies' in metadata_dict: # Get the tool_dependencies.xml file from the repository. tool_dependencies_config = get_config_from_repository( self.app, 'tool_dependencies.xml', @@ -220,7 +224,7 @@ except: pass return tool_shed_repository, metadata_dict - def install_repository( self, repository_elem ): + def install_repository( self, repository_elem, install_dependencies ): # Install a single repository, loading contained tools into the tool panel. name = repository_elem.get( 'name' ) description = repository_elem.get( 'description' ) @@ -241,7 +245,8 @@ name, description, changeset_revision, - ctx_rev ) + ctx_rev, + install_dependencies ) if 'tools' in metadata_dict: # Get the tool_versions from the tool shed for each tool in the installed change set. url = '%s/repository/get_tool_versions?name=%s&owner=%s&changeset_revision=%s&webapp=galaxy&no_reset=true' % \

diff -r 9ae91fb49fdd5762dc9a0374dfc471733da47143 -r 018179ad4c9bcec30baea5aee0918f45d254deb2 lib/galaxy/tool_shed/migrate/check.py --- a/lib/galaxy/tool_shed/migrate/check.py +++ b/lib/galaxy/tool_shed/migrate/check.py @@ -6,6 +6,7 @@ from migrate.versioning import repository, schema from sqlalchemy import * from common import * +from galaxy.util.odict import odict

log = logging.getLogger( __name__ )

@@ -44,13 +45,20 @@ if latest_tool_migration_script_number != db_schema.version: if app.new_installation: # New installations will not be missing tools, so we don't need to worry about them. - missing_tool_configs = [] + missing_tool_configs_dict = odict() else: tool_panel_configs = get_non_shed_tool_panel_configs( app ) if tool_panel_configs: - missing_tool_configs = check_for_missing_tools( tool_panel_configs, latest_tool_migration_script_number ) + # The missing_tool_configs_dict contents are something like: + # {'emboss_antigenic.xml': [('emboss', '5.0.0', 'package', '\nreadme blah blah blah\n')]} + missing_tool_configs_dict = check_for_missing_tools( app, tool_panel_configs, latest_tool_migration_script_number ) else: - missing_tool_configs = [] + missing_tool_configs_dict = odict() + have_tool_dependencies = False + for k, v in missing_tool_configs_dict.items(): + if v: + have_tool_dependencies = True + break config_arg = '' if os.path.abspath( os.path.join( os.getcwd(), 'universe_wsgi.ini' ) ) != galaxy_config_file: config_arg = ' -c %s' % galaxy_config_file.replace( os.path.abspath( os.getcwd() ), '.' ) @@ -62,7 +70,7 @@ output = proc.stdout.read( 32768 ) if return_code != 0: raise Exception( "Error attempting to update the value of migrate_tools.version: %s" % output ) - elif missing_tool_configs: + elif missing_tool_configs_dict: if len( tool_panel_configs ) == 1: plural = '' tool_panel_config_file_names = tool_panel_configs[ 0 ] @@ -71,8 +79,8 @@ tool_panel_config_file_names = ', '.join( tool_panel_configs ) msg = "\n>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>" msg += "\n\nThe list of files at the end of this message refers to tools that are configured to load into the tool panel for\n" - msg += "this Galaxy instance, but have been removed from the Galaxy distribution. These tools can be automatically installed\n" - msg += "from the Galaxy tool shed at http://toolshed.g2.bx.psu.edu.%5Cn%5Cn" + msg += "this Galaxy instance, but have been removed from the Galaxy distribution. These tools and their dependencies can be\n" + msg += "automatically installed from the Galaxy tool shed at http://toolshed.g2.bx.psu.edu.%5Cn%5Cn" msg += "To skip this process, attempt to start your Galaxy server again (e.g., sh run.sh or whatever you use). If you do this,\n" msg += "be aware that these tools will no longer be available in your Galaxy tool panel, and entries for each of them should\n" msg += "be removed from your file%s named %s.\n\n" % ( plural, tool_panel_config_file_names ) @@ -87,17 +95,45 @@ msg += "configured could result in undesired behavior when modifying or updating your local Galaxy instance or the tool shed\n" msg += "repositories if they are in directories that pose conflicts. See mercurial's .hgignore documentation at the following\n" msg += "URL for details.\n\nhttp://mercurial.selenic.com/wiki/.hgignore%5Cn%5Cn" - msg += output + if have_tool_dependencies: + msg += "The following tool dependencies can also optionally be installed (see the option flag in the command below). If you\n" + msg += "choose to install them (recommended), they will be installed within the location specified by the 'tool_dependency_dir'\n" + msg += "setting in your main Galaxy configuration file (e.g., uninverse_wsgi.ini).\n" + processed_tool_dependencies = [] + for missing_tool_config, tool_dependencies in missing_tool_configs_dict.items(): + for tool_dependencies_tup in tool_dependencies: + if tool_dependencies_tup not in processed_tool_dependencies: + msg += "------------------------------------\n" + msg += "Tool Dependency\n" + msg += "------------------------------------\n" + msg += "Name: %s, Version: %s, Type: %s\n" % ( tool_dependencies_tup[ 0 ], + tool_dependencies_tup[ 1 ], + tool_dependencies_tup[ 2 ] ) + if tool_dependencies_tup[ 3 ]: + msg += "Requirements and installation information:\n" + msg += "%s\n" % tool_dependencies_tup[ 3 ] + else: + msg += "\n" + msg += "------------------------------------\n" + processed_tool_dependencies.append( tool_dependencies_tup ) + msg += "\n" + msg += "%s" % output.replace( 'done', '' ) + msg += "vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv\n" + msg += "sh ./scripts/migrate_tools/%04d_tools.sh\n" % latest_tool_migration_script_number + msg += "^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n" + if have_tool_dependencies: + msg += "The tool dependencies listed above will be installed along with the repositories if you add the 'install_dependencies'\n" + msg += "option to the above command like this:\n\n" + msg += "vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv\n" + msg += "sh ./scripts/migrate_tools/%04d_tools.sh install_dependencies\n" % latest_tool_migration_script_number + msg += "^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n" + msg += "Tool dependencies can be installed after the repositories have been installed, but installing them now is better.\n\n" msg += "After the installation process finishes, you can start your Galaxy server. As part of this installation process,\n" msg += "entries for each of the following tool config files will be added to the file named ./migrated_tool_conf.xml, so these\n" msg += "tools will continue to be loaded into your tool panel. Because of this, existing entries for these files should be\n" msg += "removed from your file%s named %s, but only after the installation process finishes.\n\n" % ( plural, tool_panel_config_file_names ) - for i, missing_tool_config in enumerate( missing_tool_configs ): + for missing_tool_config, tool_dependencies in missing_tool_configs_dict.items(): msg += "%s\n" % missing_tool_config - # Should we do the following? - #if i > 10: - # msg += "\n...and %d more tools...\n" % ( len( missing_tool_configs ) - ( i + 1 ) ) - # break msg += "<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<\n" raise Exception( msg ) else:

diff -r 9ae91fb49fdd5762dc9a0374dfc471733da47143 -r 018179ad4c9bcec30baea5aee0918f45d254deb2 lib/galaxy/tool_shed/migrate/common.py --- a/lib/galaxy/tool_shed/migrate/common.py +++ b/lib/galaxy/tool_shed/migrate/common.py @@ -1,4 +1,4 @@ -import sys, os, ConfigParser +import sys, os, ConfigParser, urllib2 import galaxy.config import galaxy.datatypes.registry from galaxy import util, tools @@ -7,39 +7,63 @@ from galaxy.objectstore import build_object_store_from_config import galaxy.tool_shed.tool_shed_registry from galaxy.tool_shed import install_manager -from galaxy.tool_shed.migrate.common import * +from galaxy.tool_shed.encoding_util import * +from galaxy.util.odict import odict

-def check_for_missing_tools( tool_panel_configs, latest_tool_migration_script_number ): +REPOSITORY_OWNER = 'devteam' + +def check_for_missing_tools( app, tool_panel_configs, latest_tool_migration_script_number ): # Get the 000x_tools.xml file associated with the current migrate_tools version number. tools_xml_file_path = os.path.abspath( os.path.join( 'scripts', 'migrate_tools', '%04d_tools.xml' % latest_tool_migration_script_number ) ) # Parse the XML and load the file attributes for later checking against the proprietary tool_panel_config. - migrated_tool_configs = [] + migrated_tool_configs_dict = odict() tree = util.parse_xml( tools_xml_file_path ) root = tree.getroot() + tool_shed = root.get( 'name' ) + tool_shed_url = get_tool_shed_url_from_tools_xml_file_path( app, tool_shed ) for elem in root: if elem.tag == 'repository': + tool_dependencies = [] + tool_dependencies_dict = {} + repository_name = elem.get( 'name' ) + changeset_revision = elem.get( 'changeset_revision' ) + url = '%s/repository/get_tool_dependencies?name=%s&owner=%s&changeset_revision=%s&webapp=install_manager&no_reset=true' % \ + ( tool_shed_url, repository_name, REPOSITORY_OWNER, changeset_revision ) + response = urllib2.urlopen( url ) + text = response.read() + response.close() + if text: + tool_dependencies_dict = tool_shed_decode( text ) + for dependency_key, requirements_dict in tool_dependencies_dict.items(): + tool_dependency_name = requirements_dict[ 'name' ] + tool_dependency_version = requirements_dict[ 'version' ] + tool_dependency_type = requirements_dict[ 'type' ] + tool_dependency_readme = requirements_dict.get( 'readme', '' ) + tool_dependencies.append( ( tool_dependency_name, tool_dependency_version, tool_dependency_type, tool_dependency_readme ) ) for tool_elem in elem.findall( 'tool' ): - migrated_tool_configs.append( tool_elem.get( 'file' ) ) + migrated_tool_configs_dict[ tool_elem.get( 'file' ) ] = tool_dependencies # Parse the proprietary tool_panel_configs (the default is tool_conf.xml) and generate the list of missing tool config file names. - missing_tool_configs = [] + missing_tool_configs_dict = odict() for tool_panel_config in tool_panel_configs: tree = util.parse_xml( tool_panel_config ) root = tree.getroot() for elem in root: + missing_tool_dependencies = [] if elem.tag == 'tool': - missing_tool_configs = check_tool_tag_set( elem, migrated_tool_configs, missing_tool_configs ) + missing_tool_configs_dict = check_tool_tag_set( elem, migrated_tool_configs_dict, missing_tool_configs_dict ) elif elem.tag == 'section': for section_elem in elem: if section_elem.tag == 'tool': - missing_tool_configs = check_tool_tag_set( section_elem, migrated_tool_configs, missing_tool_configs ) - return missing_tool_configs -def check_tool_tag_set( elem, migrated_tool_configs, missing_tool_configs ): + missing_tool_configs_dict = check_tool_tag_set( section_elem, migrated_tool_configs_dict, missing_tool_configs_dict ) + return missing_tool_configs_dict +def check_tool_tag_set( elem, migrated_tool_configs_dict, missing_tool_configs_dict ): file_path = elem.get( 'file', None ) if file_path: path, name = os.path.split( file_path ) - if name in migrated_tool_configs: - missing_tool_configs.append( name ) - return missing_tool_configs + if name in migrated_tool_configs_dict: + tool_dependencies = migrated_tool_configs_dict[ name ] + missing_tool_configs_dict[ name ] = tool_dependencies + return missing_tool_configs_dict def get_non_shed_tool_panel_configs( app ): # Get the non-shed related tool panel configs - there can be more than one, and the default is tool_conf.xml. config_filenames = [] @@ -52,9 +76,18 @@ if tool_path is None: config_filenames.append( config_filename ) return config_filenames +def get_tool_shed_url_from_tools_xml_file_path( app, tool_shed ): + for shed_name, shed_url in app.tool_shed_registry.tool_sheds.items(): + if shed_url.find( tool_shed ) >= 0: + if shed_url.endswith( '/' ): + shed_url = shed_url.rstrip( '/' ) + return shed_url + return None + class MigrateToolsApplication( object ): """Encapsulates the state of a basic Galaxy Universe application in order to initiate the Install Manager""" def __init__( self, tools_migration_config ): + install_dependencies = 'install_dependencies' in sys.argv galaxy_config_file = 'universe_wsgi.ini' if '-c' in sys.argv: pos = sys.argv.index( '-c' ) @@ -69,7 +102,7 @@ for key, value in config_parser.items( "app:main" ): galaxy_config_dict[ key ] = value self.config = galaxy.config.Configuration( **galaxy_config_dict ) - if self.config.database_connection is None: + if not self.config.database_connection: self.config.database_connection = "sqlite:///%s?isolation_level=IMMEDIATE" % self.config.database self.config.update_integrated_tool_panel = True self.object_store = build_object_store_from_config( self.config ) @@ -106,7 +139,8 @@ 'scripts', 'migrate_tools', tools_migration_config ), - migrated_tools_config=self.config.migrated_tools_config ) + migrated_tools_config=self.config.migrated_tools_config, + install_dependencies=install_dependencies ) @property def sa_session( self ): return self.model.context.current

diff -r 9ae91fb49fdd5762dc9a0374dfc471733da47143 -r 018179ad4c9bcec30baea5aee0918f45d254deb2 lib/galaxy/tool_shed/migrate/versions/0002_tools.py --- a/lib/galaxy/tool_shed/migrate/versions/0002_tools.py +++ b/lib/galaxy/tool_shed/migrate/versions/0002_tools.py @@ -3,10 +3,6 @@ datatypes_conf.xml.sample. You should remove the Emboss datatypes from your version of datatypes_conf.xml. The repositories named emboss_5 and emboss_datatypes from the main Galaxy tool shed at http://toolshed.g2.bx.psu.edu will be installed into your local Galaxy instance at the location discussed above by running the following command. - -vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv -sh ./scripts/migrate_tools/0002_tools.sh -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ """

import sys

diff -r 9ae91fb49fdd5762dc9a0374dfc471733da47143 -r 018179ad4c9bcec30baea5aee0918f45d254deb2 lib/galaxy/tools/data/__init__.py --- a/lib/galaxy/tools/data/__init__.py +++ b/lib/galaxy/tools/data/__init__.py @@ -41,7 +41,7 @@ self.data_tables[ table.name ] = table log.debug( "Loaded tool data table '%s'", table.name ) return table_elems - def add_new_entries_from_config_file( self, config_filename, tool_data_table_config_path ): + def add_new_entries_from_config_file( self, config_filename, tool_data_table_config_path, persist=False ): """ This method is called when a tool shed repository that includes a tool_data_table_conf.xml.sample file is being installed into a local galaxy instance. We have 2 cases to handle, files whose root tag is <tables>, for example: @@ -78,7 +78,7 @@ if table.name not in self.data_tables: self.data_tables[ table.name ] = table log.debug( "Added new tool data table '%s'", table.name ) - if self.data_table_elem_names != original_data_table_elem_names: + if persist and self.data_table_elem_names != original_data_table_elem_names: # Persist Galaxy's version of the changed tool_data_table_conf.xml file. self.to_xml_file( tool_data_table_config_path ) return table_elems

diff -r 9ae91fb49fdd5762dc9a0374dfc471733da47143 -r 018179ad4c9bcec30baea5aee0918f45d254deb2 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -993,8 +993,8 @@ .first() def get_url_from_repository_tool_shed( app, repository ): """ - The stored value of repository.tool_shed is something like: toolshed.g2.bx.psu.edu - We need the URL to this tool shed, which is something like: http://toolshed.g2.bx.psu.edu/ + The stored value of repository.tool_shed is something like: toolshed.g2.bx.psu.edu. We need the URL to this tool shed, which is + something like: http://toolshed.g2.bx.psu.edu/. """ for shed_name, shed_url in app.tool_shed_registry.tool_sheds.items(): if shed_url.find( repository.tool_shed ) >= 0: @@ -1019,7 +1019,7 @@ sample_tool_data_table_conf = get_config_from_repository( app, 'tool_data_table_conf.xml.sample', repository, changeset_revision, dir ) # Add entries to the ToolDataTableManager's in-memory data_tables dictionary as well as the list of data_table_elems and the list of # data_table_elem_names. - error, correction_msg = handle_sample_tool_data_table_conf_file( app, sample_tool_data_table_conf ) + error, correction_msg = handle_sample_tool_data_table_conf_file( app, sample_tool_data_table_conf, persist=True ) if error: # TODO: Do more here than logging an exception. log.debug( correction_msg ) @@ -1055,15 +1055,15 @@ repository_tool = app.toolbox.load_tool( os.path.join( tool_path, tup_path ), guid=guid ) repository_tools_tups[ index ] = ( tup_path, guid, repository_tool ) return repository_tools_tups, sample_files_copied -def handle_sample_tool_data_table_conf_file( app, filename ): +def handle_sample_tool_data_table_conf_file( app, filename, persist=False ): """ - Parse the incoming filename and add new entries to the in-memory app.tool_data_tables dictionary as well as appending them to - Galaxy's tool_data_table_conf.xml file on disk. + Parse the incoming filename and add new entries to the in-memory app.tool_data_tables dictionary. If persist is True (should only occur) + if call is from the Galaxy side (not the tool shed), the new entries will be appended to Galaxy's tool_data_table_conf.xml file on disk. """ error = False message = '' try: - new_table_elems = app.tool_data_tables.add_new_entries_from_config_file( filename, app.config.tool_data_table_config_path ) + new_table_elems = app.tool_data_tables.add_new_entries_from_config_file( filename, app.config.tool_data_table_config_path, persist=persist ) except Exception, e: message = str( e ) error = True

diff -r 9ae91fb49fdd5762dc9a0374dfc471733da47143 -r 018179ad4c9bcec30baea5aee0918f45d254deb2 lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -11,6 +11,7 @@ from galaxy.util.json import from_json_string, to_json_string from galaxy.model.orm import * from galaxy.util.shed_util import get_changectx_for_changeset, get_configured_ui, make_tmp_directory, NOT_TOOL_CONFIGS, strip_path +from galaxy.tool_shed.encoding_util import * from common import *

from galaxy import eggs @@ -995,6 +996,30 @@ url += '&latest_ctx_rev=%s' % str( latest_ctx.rev() ) return trans.response.send_redirect( url ) @web.expose + def get_tool_dependencies( self, trans, **kwd ): + # Handle a request from a local Galaxy instance. If the request originated with the Galaxy instances' InstallManager, the value of 'webapp' + # will be 'install_manager'. + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + # If the request originated with the UpdateManager, it will not include a galaxy_url. + galaxy_url = kwd.get( 'galaxy_url', '' ) + name = params.get( 'name', None ) + owner = params.get( 'owner', None ) + changeset_revision = params.get( 'changeset_revision', None ) + webapp = params.get( 'webapp', 'community' ) + repository = get_repository_by_name_and_owner( trans, name, owner ) + for downloadable_revision in repository.downloadable_revisions: + if downloadable_revision.changeset_revision == changeset_revision: + break + metadata = downloadable_revision.metadata + tool_dependencies = metadata.get( 'tool_dependencies', '' ) + if webapp == 'install_manager': + if tool_dependencies: + return tool_shed_encode( tool_dependencies ) + return '' + # TODO: future handler where request comes from some Galaxy admin feature. + @web.expose def browse_repositories( self, trans, **kwd ): # We add params to the keyword dict in this method in order to rename the param # with an "f-" prefix, simulating filtering by clicking a search link. We have

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