1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/0ddc03509b24/ changeset: 0ddc03509b24 user: greg date: 2013-03-18 14:55:28 summary: Eliminate a duplicate method from shed_util_common and add missing documentation to several utility methods. affected #: 6 files
diff -r 92275794f6efe2f2e17c2d3785061e88f2f23f84 -r 0ddc03509b24d4d4e9024902546025df185c6a18 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -184,7 +184,7 @@ params = util.Params( kwd ) repository_id = params.get( 'id', None ) repository = suc.get_installed_tool_shed_repository( trans, repository_id ) - tool_shed_url = suc.get_url_from_repository_tool_shed( trans.app, repository ) + tool_shed_url = suc.get_url_from_tool_shed( trans.app, repository.tool_shed ) url = suc.url_join( tool_shed_url, 'repository/check_for_updates?galaxy_url=%s&name=%s&owner=%s&changeset_revision=%s' % \ ( web.url_for( '/', qualified=True ), repository.name, repository.owner, repository.changeset_revision ) ) @@ -314,7 +314,7 @@ need it so that we can derive the tool shed from which it was installed. """ repository = suc.get_installed_tool_shed_repository( trans, repository_id ) - tool_shed_url = suc.get_url_from_repository_tool_shed( trans.app, repository ) + tool_shed_url = suc.get_url_from_tool_shed( trans.app, repository.tool_shed ) url = suc.url_join( tool_shed_url, 'repository/get_repository_dependencies?name=%s&owner=%s&changeset_revision=%s' % \ ( repository_name, repository_owner, changeset_revision ) ) @@ -337,7 +337,7 @@ it so that we can derive the tool shed from which it was installed. """ repository = suc.get_installed_tool_shed_repository( trans, repository_id ) - tool_shed_url = suc.get_url_from_repository_tool_shed( trans.app, repository ) + tool_shed_url = suc.get_url_from_tool_shed( trans.app, repository.tool_shed ) url = suc.url_join( tool_shed_url, 'repository/get_tool_dependencies?name=%s&owner=%s&changeset_revision=%s' % \ ( repository_name, repository_owner, changeset_revision ) ) @@ -359,7 +359,7 @@ uninstalled tool shed repository. """ repository = suc.get_installed_tool_shed_repository( trans, repository_id ) - tool_shed_url = suc.get_url_from_repository_tool_shed( trans.app, repository ) + tool_shed_url = suc.get_url_from_tool_shed( trans.app, repository.tool_shed ) url = suc.url_join( tool_shed_url, 'repository/get_updated_repository_information?name=%s&owner=%s&changeset_revision=%s' % \ ( repository_name, repository_owner, changeset_revision ) ) @@ -654,7 +654,7 @@ suc.update_tool_shed_repository_status( trans.app, tool_shed_repository, trans.model.ToolShedRepository.installation_status.SETTING_TOOL_VERSIONS ) - tool_shed_url = suc.get_url_from_repository_tool_shed( trans.app, tool_shed_repository ) + tool_shed_url = suc.get_url_from_tool_shed( trans.app, tool_shed_repository.tool_shed ) url = suc.url_join( tool_shed_url, '/repository/get_tool_versions?name=%s&owner=%s&changeset_revision=%s' % \ ( tool_shed_repository.name, tool_shed_repository.owner, tool_shed_repository.changeset_revision ) ) @@ -711,7 +711,7 @@ repository = suc.get_installed_tool_shed_repository( trans, repository_id ) if not repository: return trans.show_error_message( 'Invalid repository specified.' ) - tool_shed_url = suc.get_url_from_repository_tool_shed( trans.app, repository ) + tool_shed_url = suc.get_url_from_tool_shed( trans.app, repository.tool_shed ) if repository.status in [ trans.model.ToolShedRepository.installation_status.CLONING ]: tool_shed_repository_ids = [ repository_id ] return trans.response.send_redirect( web.url_for( controller='admin_toolshed', @@ -1172,7 +1172,7 @@ clone_dir = os.path.join( tool_path, suc.generate_tool_shed_repository_install_dir( repository_clone_url, tool_shed_repository.installed_changeset_revision ) ) relative_install_dir = os.path.join( clone_dir, tool_shed_repository.name ) - tool_shed_url = suc.get_url_from_repository_tool_shed( trans.app, tool_shed_repository ) + tool_shed_url = suc.get_url_from_tool_shed( trans.app, tool_shed_repository.tool_shed ) tool_section = None tool_panel_section = kwd.get( 'tool_panel_section', '' ) new_tool_panel_section = kwd.get( 'new_tool_panel_section', '' ) @@ -1317,7 +1317,7 @@ tool_shed_repository = suc.get_installed_tool_shed_repository( trans, repository_id ) repository_clone_url = suc.generate_clone_url_for_installed_repository( trans.app, tool_shed_repository ) metadata = tool_shed_repository.metadata - tool_shed_url = suc.get_url_from_repository_tool_shed( trans.app, tool_shed_repository ) + tool_shed_url = suc.get_url_from_tool_shed( trans.app, tool_shed_repository.tool_shed ) tool_path, relative_install_dir = tool_shed_repository.get_tool_relative_path( trans.app ) if latest_changeset_revision and latest_ctx_rev: # There are updates available in the tool shed for the repository, so use the receieved dependency information which was retrieved from @@ -1481,7 +1481,7 @@ def reset_repository_metadata( self, trans, id ): """Reset all metadata on a single installed tool shed repository.""" repository = suc.get_installed_tool_shed_repository( trans, id ) - tool_shed_url = suc.get_url_from_repository_tool_shed( trans.app, repository ) + tool_shed_url = suc.get_url_from_tool_shed( trans.app, repository.tool_shed ) repository_clone_url = suc.generate_clone_url_for_installed_repository( trans.app, repository ) tool_path, relative_install_dir = repository.get_tool_relative_path( trans.app ) if relative_install_dir: @@ -1560,7 +1560,7 @@ metadata for the repository's revision in the Galaxy database. """ repository = suc.get_installed_tool_shed_repository( trans, kwd[ 'id' ] ) - tool_shed_url = suc.get_url_from_repository_tool_shed( trans.app, repository ) + tool_shed_url = suc.get_url_from_tool_shed( trans.app, repository.tool_shed ) url = suc.url_join( tool_shed_url, 'repository/get_tool_versions?name=%s&owner=%s&changeset_revision=%s' % \ ( repository.name, repository.owner, repository.changeset_revision ) )
diff -r 92275794f6efe2f2e17c2d3785061e88f2f23f84 -r 0ddc03509b24d4d4e9024902546025df185c6a18 lib/tool_shed/galaxy_install/install_manager.py --- a/lib/tool_shed/galaxy_install/install_manager.py +++ b/lib/tool_shed/galaxy_install/install_manager.py @@ -279,7 +279,7 @@ if self.__isinstalled( clone_dir ): print "Skipping automatic install of repository '", name, "' because it has already been installed in location ", clone_dir else: - tool_shed_url = self.__get_url_from_tool_shed( self.tool_shed ) + tool_shed_url = suc.get_url_from_tool_shed( self.app, self.tool_shed ) repository_clone_url = os.path.join( tool_shed_url, 'repos', self.repository_owner, name ) relative_install_dir = os.path.join( relative_clone_dir, name ) install_dir = os.path.join( clone_dir, name ) @@ -351,16 +351,6 @@ @property def non_shed_tool_panel_configs( self ): return common_util.get_non_shed_tool_panel_configs( self.app ) - def __get_url_from_tool_shed( self, tool_shed ): - # The value of 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 self.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 - # The tool shed from which the repository was originally installed must no longer be configured in tool_sheds_conf.xml. - return None def __isinstalled( self, clone_dir ): full_path = os.path.abspath( clone_dir ) if os.path.exists( full_path ):
diff -r 92275794f6efe2f2e17c2d3785061e88f2f23f84 -r 0ddc03509b24d4d4e9024902546025df185c6a18 lib/tool_shed/galaxy_install/repository_util.py --- a/lib/tool_shed/galaxy_install/repository_util.py +++ b/lib/tool_shed/galaxy_install/repository_util.py @@ -77,7 +77,7 @@ def get_update_to_changeset_revision_and_ctx_rev( trans, repository ): """Return the changeset revision hash to which the repository can be updated.""" changeset_revision_dict = {} - tool_shed_url = suc.get_url_from_repository_tool_shed( trans.app, repository ) + tool_shed_url = suc.get_url_from_tool_shed( trans.app, repository.tool_shed ) url = suc.url_join( tool_shed_url, 'repository/get_changeset_revision_and_ctx_rev?name=%s&owner=%s&changeset_revision=%s' % \ ( repository.name, repository.owner, repository.installed_changeset_revision ) ) try:
diff -r 92275794f6efe2f2e17c2d3785061e88f2f23f84 -r 0ddc03509b24d4d4e9024902546025df185c6a18 lib/tool_shed/galaxy_install/update_manager.py --- a/lib/tool_shed/galaxy_install/update_manager.py +++ b/lib/tool_shed/galaxy_install/update_manager.py @@ -34,7 +34,7 @@ self.sleeper.sleep( self.seconds_to_sleep ) log.info( 'Transfer job restarter shutting down...' ) def check_for_update( self, repository ): - tool_shed_url = suc.get_url_from_repository_tool_shed( self.app, repository ) + tool_shed_url = suc.get_url_from_tool_shed( self.app, repository.tool_shed ) url = '%s/repository/check_for_updates?name=%s&owner=%s&changeset_revision=%s&from_update_manager=True' % \ ( tool_shed_url, repository.name, repository.owner, repository.changeset_revision ) try:
diff -r 92275794f6efe2f2e17c2d3785061e88f2f23f84 -r 0ddc03509b24d4d4e9024902546025df185c6a18 lib/tool_shed/util/metadata_util.py --- a/lib/tool_shed/util/metadata_util.py +++ b/lib/tool_shed/util/metadata_util.py @@ -1432,7 +1432,7 @@ def reset_all_metadata_on_installed_repository( trans, id ): """Reset all metadata on a single tool shed repository installed into a Galaxy instance.""" repository = suc.get_installed_tool_shed_repository( trans, id ) - tool_shed_url = suc.get_url_from_repository_tool_shed( trans.app, repository ) + tool_shed_url = suc.get_url_from_tool_shed( trans.app, repository.tool_shed ) repository_clone_url = suc.generate_clone_url_for_installed_repository( trans.app, repository ) tool_path, relative_install_dir = repository.get_tool_relative_path( trans.app ) if relative_install_dir:
diff -r 92275794f6efe2f2e17c2d3785061e88f2f23f84 -r 0ddc03509b24d4d4e9024902546025df185c6a18 lib/tool_shed/util/shed_util_common.py --- a/lib/tool_shed/util/shed_util_common.py +++ b/lib/tool_shed/util/shed_util_common.py @@ -160,7 +160,7 @@ return False, error_message
def config_elems_to_xml_file( app, config_elems, config_filename, tool_path ): - # Persist the current in-memory list of config_elems to a file named by the value of config_filename. + """Persist the current in-memory list of config_elems to a file named by the value of config_filename.""" fd, filename = tempfile.mkstemp() os.write( fd, '<?xml version="1.0"?>\n' ) os.write( fd, '<toolbox tool_path="%s">\n' % str( tool_path ) ) @@ -242,7 +242,7 @@
def generate_clone_url_for_installed_repository( app, repository ): """Generate the URL for cloning a repository that has been installed into a Galaxy instance.""" - tool_shed_url = get_url_from_repository_tool_shed( app, repository ) + tool_shed_url = get_url_from_tool_shed( app, repository.tool_shed ) return url_join( tool_shed_url, 'repos', repository.owner, repository.name )
def generate_clone_url_for_repository_in_tool_shed( trans, repository ): @@ -469,7 +469,7 @@ return None
def get_installed_tool_shed_repository( trans, id ): - """Get a repository on the Galaxy side from the database via id""" + """Get a tool shed repository record from the Galaxy database defined by the id.""" return trans.sa_session.query( trans.model.ToolShedRepository ).get( trans.security.decode_id( id ) )
def get_named_tmpfile_from_ctx( ctx, filename, dir ): @@ -516,6 +516,11 @@ return None
def get_or_create_tool_shed_repository( trans, tool_shed, name, owner, changeset_revision ): + """ + Return a tool shed repository database record defined by the combination of tool shed, repository name, repository owner and changeset_revision + or installed_changeset_revision. A new tool shed repository record will be created if one is not located. + """ + # This method is used only in Galaxy, not the tool shed. repository = get_repository_for_dependency_relationship( trans.app, tool_shed, name, owner, changeset_revision ) if not repository: tool_shed_url = get_url_from_tool_shed( trans.app, tool_shed ) @@ -572,7 +577,7 @@ previous_changeset_revision = changeset_revision
def get_repo_info_tuple_contents( repo_info_tuple ): - # Take care in handling the repo_info_tuple as it evolves over time as new tool shed features are introduced. + """Take care in handling the repo_info_tuple as it evolves over time as new tool shed features are introduced.""" if len( repo_info_tuple ) == 6: description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, tool_dependencies = repo_info_tuple repository_dependencies = None @@ -613,6 +618,8 @@ return None
def get_repository_for_dependency_relationship( app, tool_shed, name, owner, changeset_revision ): + """Return a tool shed repository database record that is defined by either the current changeset revision or the installed_changeset_revision.""" + # This method is used only in Galaxy, not the tool shed. repository = get_tool_shed_repository_by_shed_name_owner_installed_changeset_revision( app=app, tool_shed=tool_shed, name=name, @@ -627,6 +634,7 @@ return repository
def get_repository_file_contents( file_path ): + """Return the display-safe contents of a repository file.""" if checkers.is_gzip( file_path ): safe_str = to_safe_string( '\ngzip compressed file\n' ) elif checkers.is_bz2( file_path ): @@ -646,6 +654,7 @@ return safe_str
def get_repository_files( trans, folder_path ): + """Return the file hierarchy of a tool shed repository.""" contents = [] for item in os.listdir( folder_path ): # Skip .hg directories @@ -684,6 +693,7 @@ return None
def get_repository_owner( cleaned_repository_url ): + """Gvien a "cleaned" repository clone URL, return the owner of the repository.""" items = cleaned_repository_url.split( '/repos/' ) repo_path = items[ 1 ] if repo_path.startswith( '/' ): @@ -691,11 +701,13 @@ return repo_path.lstrip( '/' ).split( '/' )[ 0 ]
def get_repository_owner_from_clone_url( repository_clone_url ): + """Given a repository clone URL, return the owner of the repository.""" tmp_url = clean_repository_clone_url( repository_clone_url ) tool_shed = tmp_url.split( '/repos/' )[ 0 ].rstrip( '/' ) return get_repository_owner( tmp_url )
def get_repository_tools_tups( app, metadata_dict ): + """Return a list of tuples of the form (relative_path, guid, tool) for each tool defined in the received tool shed repository metadata.""" repository_tools_tups = [] index, shed_conf_dict = get_shed_tool_conf_dict( app, metadata_dict.get( 'shed_config_filename' ) ) if 'tools' in metadata_dict: @@ -713,6 +725,7 @@ return repository_tools_tups
def get_reversed_changelog_changesets( repo ): + """Return a list of changesets in reverse order from that provided by the repository manifest.""" reversed_changelog = [] for changeset in repo.changelog: reversed_changelog.insert( 0, changeset ) @@ -728,6 +741,7 @@ return "-1:%s" % changeset_revision
def get_rev_label_from_changeset_revision( repo, changeset_revision ): + """Given a changeset revision hash, return two strings, the changeset rev and the changeset revision hash.""" ctx = get_changectx_for_changeset( repo, changeset_revision ) if ctx: rev = '%04d' % ctx.rev() @@ -748,8 +762,10 @@ return index, shed_tool_conf_dict
def get_tool_panel_config_tool_path_install_dir( app, repository ): - # Return shed-related tool panel config, the tool_path configured in it, and the relative path to the directory where the - # repository is installed. This method assumes all repository tools are defined in a single shed-related tool panel config. + """ + Return shed-related tool panel config, the tool_path configured in it, and the relative path to the directory where the repository is installed. + This method assumes all repository tools are defined in a single shed-related tool panel config. + """ tool_shed = clean_tool_shed_url( repository.tool_shed ) partial_install_dir = '%s/repos/%s/%s/%s' % ( tool_shed, repository.owner, repository.name, repository.installed_changeset_revision ) # Get the relative tool installation paths from each of the shed tool configs. @@ -782,11 +798,14 @@ return None
def get_tool_shed_repository_by_id( trans, repository_id ): + """Return a tool shed repository database record defined by the id.""" + # This method is used only in Galaxy, not the tool shed. return trans.sa_session.query( trans.model.ToolShedRepository ) \ .filter( trans.model.ToolShedRepository.table.c.id == trans.security.decode_id( repository_id ) ) \ .first()
def get_tool_shed_repository_by_shed_name_owner_changeset_revision( app, tool_shed, name, owner, changeset_revision ): + """Return a tool shed repository database record defined by the combination of a tool_shed, repository name, repository owner and current changeet_revision.""" # This method is used only in Galaxy, not the tool shed. sa_session = app.model.context.current if tool_shed.find( '//' ) > 0: @@ -800,6 +819,7 @@ .first()
def get_tool_shed_repository_by_shed_name_owner_installed_changeset_revision( app, tool_shed, name, owner, installed_changeset_revision ): + """Return a tool shed repository database record defined by the combination of a tool_shed, repository name, repository owner and installed_changeet_revision.""" # This method is used only in Galaxy, not the tool shed. sa_session = app.model.context.current if tool_shed.find( '//' ) > 0: @@ -816,23 +836,12 @@ tmp_url = clean_repository_clone_url( repository_clone_url ) return tmp_url.split( '/repos/' )[ 0 ].rstrip( '/' )
-def get_url_from_repository_tool_shed( app, repository ): +def get_url_from_tool_shed( app, tool_shed ): """ - 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 value of 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: - if shed_url.endswith( '/' ): - shed_url = shed_url.rstrip( '/' ) - return shed_url - # The tool shed from which the repository was originally installed must no longer be configured in tool_sheds_conf.xml. - return None - -def get_url_from_tool_shed( app, tool_shed ): - # The value of 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( tool_shed ) >= 0: if shed_url.endswith( '/' ): shed_url = shed_url.rstrip( '/' ) @@ -856,26 +865,28 @@ return None
def handle_email_alerts( trans, repository, content_alert_str='', new_repo_alert=False, admin_only=False ): - # There are 2 complementary features that enable a tool shed user to receive email notification: - # 1. Within User Preferences, they can elect to receive email when the first (or first valid) - # change set is produced for a new repository. - # 2. When viewing or managing a repository, they can check the box labeled "Receive email alerts" - # which caused them to receive email alerts when updates to the repository occur. This same feature - # is available on a per-repository basis on the repository grid within the tool shed. - # - # There are currently 4 scenarios for sending email notification when a change is made to a repository: - # 1. An admin user elects to receive email when the first change set is produced for a new repository - # from User Preferences. The change set does not have to include any valid content. This allows for - # the capture of inappropriate content being uploaded to new repositories. - # 2. A regular user elects to receive email when the first valid change set is produced for a new repository - # from User Preferences. This differs from 1 above in that the user will not receive email until a - # change set tha tincludes valid content is produced. - # 3. An admin user checks the "Receive email alerts" check box on the manage repository page. Since the - # user is an admin user, the email will include information about both HTML and image content that was - # included in the change set. - # 4. A regular user checks the "Receive email alerts" check box on the manage repository page. Since the - # user is not an admin user, the email will not include any information about both HTML and image content - # that was included in the change set. + """ + There are 2 complementary features that enable a tool shed user to receive email notification: + 1. Within User Preferences, they can elect to receive email when the first (or first valid) + change set is produced for a new repository. + 2. When viewing or managing a repository, they can check the box labeled "Receive email alerts" + which caused them to receive email alerts when updates to the repository occur. This same feature + is available on a per-repository basis on the repository grid within the tool shed. + + There are currently 4 scenarios for sending email notification when a change is made to a repository: + 1. An admin user elects to receive email when the first change set is produced for a new repository + from User Preferences. The change set does not have to include any valid content. This allows for + the capture of inappropriate content being uploaded to new repositories. + 2. A regular user elects to receive email when the first valid change set is produced for a new repository + from User Preferences. This differs from 1 above in that the user will not receive email until a + change set tha tincludes valid content is produced. + 3. An admin user checks the "Receive email alerts" check box on the manage repository page. Since the + user is an admin user, the email will include information about both HTML and image content that was + included in the change set. + 4. A regular user checks the "Receive email alerts" check box on the manage repository page. Since the + user is not an admin user, the email will not include any information about both HTML and image content + that was included in the change set. + """ repo_dir = repository.repo_path( trans.app ) repo = hg.repository( get_configured_ui(), repo_dir ) sharable_link = generate_sharable_link_for_repository_in_tool_shed( trans, repository, changeset_revision=None ) @@ -948,6 +959,7 @@ log.exception( "An error occurred sending a tool shed repository update alert by email." )
def open_repository_files_folder( trans, folder_path ): + """Return a list of dictionaries, each of which contains information for a file or directory contained within a directory in a repository file hierarchy.""" try: files_list = get_repository_files( trans, folder_path ) except OSError, e: @@ -957,19 +969,20 @@ folder_contents = [] for filename in files_list: is_folder = False - if filename and filename[-1] == os.sep: + if filename and filename[ -1 ] == os.sep: is_folder = True if filename: full_path = os.path.join( folder_path, filename ) - node = { "title": filename, - "isFolder": is_folder, - "isLazy": is_folder, - "tooltip": full_path, - "key": full_path } + node = { "title" : filename, + "isFolder" : is_folder, + "isLazy" : is_folder, + "tooltip" : full_path, + "key" : full_path } folder_contents.append( node ) return folder_contents
def remove_dir( dir ): + """Attempt to remove a directory from disk.""" if os.path.exists( dir ): try: shutil.rmtree( dir ) @@ -1029,9 +1042,11 @@ return reversed_changelog
def reversed_upper_bounded_changelog( repo, included_upper_bounds_changeset_revision ): + """Return a reversed list of changesets in the repository changelog up to and including the included_upper_bounds_changeset_revision.""" return reversed_lower_upper_bounded_changelog( repo, INITIAL_CHANGELOG_HASH, included_upper_bounds_changeset_revision )
def strip_path( fpath ): + """Attempt to strip the path from a file name.""" if not fpath: return fpath try: @@ -1072,12 +1087,15 @@ return text
def tool_shed_from_repository_clone_url( repository_clone_url ): + """Given a repository clone URL, return the tool shed that contains the repository.""" return clean_repository_clone_url( repository_clone_url ).split( '/repos/' )[ 0 ].rstrip( '/' )
def tool_shed_is_this_tool_shed( toolshed_base_url ): + """Determine if a tool shed is the current tool shed.""" return toolshed_base_url.rstrip( '/' ) == str( url_for( '/', qualified=True ) ).rstrip( '/' )
def translate_string( raw_text, to_html=True ): + """Return a subset of a string (up to MAX_CONTENT_SIZE) translated to a safe string for display in a browser.""" if raw_text: if len( raw_text ) <= MAX_CONTENT_SIZE: translated_string = to_safe_string( raw_text, to_html=to_html ) @@ -1141,12 +1159,14 @@ commands.update( get_configured_ui(), repo, rev=ctx_rev )
def update_tool_shed_repository_status( app, tool_shed_repository, status ): + """Update the status of a tool shed repository in the process of being installed into Galaxy.""" sa_session = app.model.context.current tool_shed_repository.status = status sa_session.add( tool_shed_repository ) sa_session.flush()
def url_join( *args ): + """Return a valid URL produced by appending a base URL and a set of request parameters.""" parts = [] for arg in args: parts.append( arg.strip( '/' ) )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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