1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/3f2e8f5f0d7d/ changeset: 3f2e8f5f0d7d user: greg date: 2013-03-16 16:34:03 summary: Add blank lines to shed_util_common.py per new Galaxy dev team standards. affected #: 1 file

diff -r 74da2fbf09633268e1e6b6043bfd7e0515bd8422 -r 3f2e8f5f0d7de7131aa878e867c12c352f1f79b5 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 @@ -107,12 +107,14 @@ option_value = trans.security.encode_id( repository.id ) repositories_select_field.add_option( option_label, option_value ) return repositories_select_field + def changeset_is_malicious( trans, id, changeset_revision, **kwd ): """Check the malicious flag in repository metadata for a specified change set""" repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) if repository_metadata: return repository_metadata.malicious return False + def changeset_is_valid( app, repository, changeset_revision ): repo = hg.repository( get_configured_ui(), repository.repo_path( app ) ) for changeset in repo.changelog: @@ -120,6 +122,7 @@ if changeset_revision == changeset_hash: return True return False + def clean_repository_clone_url( repository_clone_url ): if repository_clone_url.find( '@' ) > 0: # We have an url that includes an authenticated user, something like: @@ -134,11 +137,13 @@ else: tmp_url = repository_clone_url return tmp_url + def clean_tool_shed_url( tool_shed_url ): if tool_shed_url.find( ':' ) > 0: # Eliminate the port, if any, since it will result in an invalid directory name. return tool_shed_url.split( ':' )[ 0 ] return tool_shed_url.rstrip( '/' ) + def clone_repository( repository_clone_url, repository_file_dir, ctx_rev ): """Clone the repository up to the specified changeset_revision. No subsequent revisions will be present in the cloned repository.""" try: @@ -153,6 +158,7 @@ error_message = 'Error cloning repository: %s' % str( e ) log.debug( error_message ) 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. fd, filename = tempfile.mkstemp() @@ -164,6 +170,7 @@ os.close( fd ) shutil.move( filename, os.path.abspath( config_filename ) ) os.chmod( config_filename, 0644 ) + def copy_file_from_manifest( repo, ctx, filename, dir ): """Copy the latest version of the file named filename from the repository manifest to the directory to which dir refers.""" for changeset in reversed_upper_bounded_changelog( repo, ctx ): @@ -176,6 +183,7 @@ fh.close() return file_path return None + def create_or_update_tool_shed_repository( app, name, description, installed_changeset_revision, ctx_rev, repository_clone_url, metadata_dict, status, current_changeset_revision=None, owner='', dist_to_shed=False ): # The received value for dist_to_shed will be True if the InstallManager is installing a repository that contains tools or datatypes that used @@ -231,10 +239,12 @@ sa_session.add( tool_shed_repository ) sa_session.flush() return tool_shed_repository + 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 ) return url_join( tool_shed_url, 'repos', repository.owner, repository.name ) + def generate_clone_url_for_repository_in_tool_shed( trans, repository ): """Generate the URL for cloning a repository that is in the tool shed.""" base_url = url_for( '/', qualified=True ).rstrip( '/' ) @@ -244,12 +254,14 @@ return '%s://%s%s/repos/%s/%s' % ( protocol, username, base, repository.user.username, repository.name ) else: return '%s/repos/%s/%s' % ( base_url, repository.user.username, repository.name ) + def generate_clone_url_from_repo_info_tup( repo_info_tup ): """Generate teh URL for cloning a repositoyr given a tuple of toolshed, name, owner, changeset_revision.""" # Example tuple: ['http://localhost:9009', 'blast_datatypes', 'test', '461a4216e8ab'] toolshed, name, owner, changeset_revision = repo_info_tup # Don't include the changeset_revision in clone urls. return url_join( toolshed, 'repos', owner, name ) + def generate_sharable_link_for_repository_in_tool_shed( trans, repository, changeset_revision=None ): """Generate the URL for sharing a repository that is in the tool shed.""" base_url = url_for( '/', qualified=True ).rstrip( '/' ) @@ -258,6 +270,7 @@ if changeset_revision: sharable_url += '/%s' % changeset_revision return sharable_url + def generate_tool_elem( tool_shed, repository_name, changeset_revision, owner, tool_file_path, tool, tool_section ): if tool_section is not None: tool_elem = SubElement( tool_section, 'tool' ) @@ -278,6 +291,7 @@ version_elem = SubElement( tool_elem, 'version' ) version_elem.text = tool.version return tool_elem + def generate_tool_guid( repository_clone_url, tool ): """ Generate a guid for the installed tool. It is critical that this guid matches the guid for @@ -286,6 +300,7 @@ """ tmp_url = clean_repository_clone_url( repository_clone_url ) return '%s/%s/%s' % ( tmp_url, tool.id, tool.version ) + def generate_tool_panel_dict_from_shed_tool_conf_entries( app, repository ): """ Keep track of the section in the tool panel in which this repository's tools will be contained by parsing the shed_tool_conf in @@ -333,6 +348,7 @@ else: tool_panel_dict[ guid ] = [ tool_section_dict ] return tool_panel_dict + def generate_tool_shed_repository_install_dir( repository_clone_url, changeset_revision ): """ Generate a repository installation directory that guarantees repositories with the same name will always be installed in different directories. @@ -345,6 +361,7 @@ repo_path = items[ 1 ] tool_shed_url = clean_tool_shed_url( tool_shed_url ) return url_join( tool_shed_url, 'repos', repo_path, changeset_revision ) + def get_absolute_path_to_file_in_repository( repo_files_dir, file_name ): """Return the absolute path to a specified disk file contained in a repository.""" stripped_file_name = strip_path( file_name ) @@ -355,21 +372,25 @@ if name == stripped_file_name: return os.path.abspath( os.path.join( root, name ) ) return file_path + def get_categories( trans ): """Get all categories from the database.""" return trans.sa_session.query( trans.model.Category ) \ .filter( trans.model.Category.table.c.deleted==False ) \ .order_by( trans.model.Category.table.c.name ) \ .all() + def get_category( trans, id ): """Get a category from the database.""" return trans.sa_session.query( trans.model.Category ).get( trans.security.decode_id( id ) ) + def get_category_by_name( trans, name ): """Get a category from the database via name.""" try: return trans.sa_session.query( trans.model.Category ).filter_by( name=name ).one() except sqlalchemy.orm.exc.NoResultFound: return None + def get_changectx_for_changeset( repo, changeset_revision, **kwd ): """Retrieve a specified changectx from a repository.""" for changeset in repo.changelog: @@ -377,6 +398,7 @@ if str( ctx ) == changeset_revision: return ctx return None + def get_config( config_file, repo, ctx, dir ): """Return the latest version of config_filename from the repository manifest.""" config_file = strip_path( config_file ) @@ -387,6 +409,7 @@ if ctx_file_name == config_file: return get_named_tmpfile_from_ctx( changeset_ctx, ctx_file, dir ) return None + def get_config_from_disk( config_file, relative_install_dir ): for root, dirs, files in os.walk( relative_install_dir ): if root.find( '.hg' ) < 0: @@ -394,6 +417,7 @@ if name == config_file: return os.path.abspath( os.path.join( root, name ) ) return None + def get_configured_ui(): """Configure any desired ui settings.""" _ui = ui.ui() @@ -403,12 +427,14 @@ # quiet = True _ui.setconfig( 'ui', 'quiet', True ) return _ui + def get_ctx_rev( tool_shed_url, name, owner, changeset_revision ): url = url_join( tool_shed_url, 'repository/get_ctx_rev?name=%s&owner=%s&changeset_revision=%s' % ( name, owner, changeset_revision ) ) response = urllib2.urlopen( url ) ctx_rev = response.read() response.close() return ctx_rev + def get_ctx_file_path_from_manifest( filename, repo, changeset_revision ): """Get the ctx file path for the latest revision of filename from the repository manifest up to the value of changeset_revision.""" stripped_filename = strip_path( filename ) @@ -420,6 +446,7 @@ if ctx_file_name == stripped_filename: return manifest_ctx, ctx_file return None, None + def get_file_context_from_ctx( ctx, filename ): # We have to be careful in determining if we found the correct file because multiple files with the same name may be in different directories # within ctx if the files were moved within the change set. For example, in the following ctx.files() list, the former may have been moved to @@ -440,9 +467,11 @@ if deleted: return 'DELETED' return None + def get_installed_tool_shed_repository( trans, id ): """Get a repository on the Galaxy side from the database via id""" return trans.sa_session.query( trans.model.ToolShedRepository ).get( trans.security.decode_id( id ) ) + def get_named_tmpfile_from_ctx( ctx, filename, dir ): filename = strip_path( filename ) for ctx_file in ctx.files(): @@ -464,6 +493,7 @@ fh.close() return tmp_filename return None + def get_next_downloadable_changeset_revision( repository, repo, after_changeset_revision ): """ Return the installable changeset_revision in the repository changelog after the changeset to which after_changeset_revision refers. If there @@ -484,6 +514,7 @@ # We've found the changeset in the changelog for which we need to get the next downloadable changset. found_after_changeset_revision = True return None + def get_or_create_tool_shed_repository( trans, tool_shed, name, owner, changeset_revision ): repository = get_repository_for_dependency_relationship( trans.app, tool_shed, name, owner, changeset_revision ) if not repository: @@ -502,6 +533,7 @@ owner=owner, dist_to_shed=False ) return repository + def get_ordered_downloadable_changeset_revisions( repository, repo ): """Return an ordered list of changeset_revisions defined by a repository changelog.""" changeset_tups = [] @@ -516,6 +548,7 @@ sorted_changeset_tups = sorted( changeset_tups ) sorted_changeset_revisions = [ changeset_tup[ 1 ] for changeset_tup in sorted_changeset_tups ] return sorted_changeset_revisions + def get_previous_downloadable_changeset_revision( repository, repo, before_changeset_revision ): """ Return the installable changeset_revision in the repository changelog prior to the changeset to which before_changeset_revision @@ -537,6 +570,7 @@ return INITIAL_CHANGELOG_HASH else: 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. if len( repo_info_tuple ) == 6: @@ -545,12 +579,14 @@ elif len( repo_info_tuple ) == 7: description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = repo_info_tuple return description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies + def get_repository_by_id( trans, id ): """Get a repository from the database via id.""" if trans.webapp.name == 'galaxy': return trans.sa_session.query( trans.model.ToolShedRepository ).get( trans.security.decode_id( id ) ) else: return trans.sa_session.query( trans.model.Repository ).get( trans.security.decode_id( id ) ) + def get_repository_by_name( app, name ): """Get a repository from the database via name.""" sa_session = app.model.context.current @@ -558,6 +594,7 @@ return sa_session.query( app.model.ToolShedRepository ).filter_by( name=name ).first() else: return sa_session.query( app.model.Repository ).filter_by( name=name ).first() + def get_repository_by_name_and_owner( app, name, owner ): """Get a repository from the database via name and owner""" sa_session = app.model.context.current @@ -574,6 +611,7 @@ app.model.Repository.table.c.user_id == user.id ) ) \ .first() return None + def get_repository_for_dependency_relationship( app, tool_shed, name, owner, changeset_revision ): repository = get_tool_shed_repository_by_shed_name_owner_installed_changeset_revision( app=app, tool_shed=tool_shed, @@ -587,6 +625,7 @@ owner=owner, changeset_revision=changeset_revision ) return repository + def get_repository_file_contents( file_path ): if checkers.is_gzip( file_path ): safe_str = to_safe_string( '\ngzip compressed file\n' ) @@ -605,6 +644,7 @@ safe_str = '%s%s' % ( safe_str, to_safe_string( large_str ) ) break return safe_str + def get_repository_files( trans, folder_path ): contents = [] for item in os.listdir( folder_path ): @@ -618,9 +658,11 @@ if contents: contents.sort() return contents + def get_repository_in_tool_shed( trans, id ): """Get a repository on the tool shed side from the database via id.""" return trans.sa_session.query( trans.model.Repository ).get( trans.security.decode_id( id ) ) + def get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ): """Get metadata for a specified repository change set from the database.""" # Make sure there are no duplicate records, and return the single unique record for the changeset_revision. Duplicate records were somehow @@ -640,16 +682,19 @@ elif all_metadata_records: return all_metadata_records[ 0 ] return None + def get_repository_owner( cleaned_repository_url ): items = cleaned_repository_url.split( '/repos/' ) repo_path = items[ 1 ] if repo_path.startswith( '/' ): repo_path = repo_path.replace( '/', '', 1 ) return repo_path.lstrip( '/' ).split( '/' )[ 0 ] + def get_repository_owner_from_clone_url( repository_clone_url ): 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 ): repository_tools_tups = [] index, shed_conf_dict = get_shed_tool_conf_dict( app, metadata_dict.get( 'shed_config_filename' ) ) @@ -666,11 +711,13 @@ if tool: repository_tools_tups.append( ( relative_path, guid, tool ) ) return repository_tools_tups + def get_reversed_changelog_changesets( repo ): reversed_changelog = [] for changeset in repo.changelog: reversed_changelog.insert( 0, changeset ) return reversed_changelog + def get_revision_label( trans, repository, changeset_revision ): """Return a string consisting of the human read-able changeset rev and the changeset revision string.""" repo = hg.repository( get_configured_ui(), repository.repo_path( trans.app ) ) @@ -679,6 +726,7 @@ return "%s:%s" % ( str( ctx.rev() ), changeset_revision ) else: return "-1:%s" % changeset_revision + def get_rev_label_from_changeset_revision( repo, changeset_revision ): ctx = get_changectx_for_changeset( repo, changeset_revision ) if ctx: @@ -688,6 +736,7 @@ rev = '-1' label = "-1:%s" % changeset_revision return rev, label + def get_shed_tool_conf_dict( app, shed_tool_conf ): """Return the in-memory version of the shed_tool_conf file, which is stored in the config_elems entry in the shed_tool_conf_dict associated with the file.""" for index, shed_tool_conf_dict in enumerate( app.toolbox.shed_tool_confs ): @@ -697,6 +746,7 @@ file_name = strip_path( shed_tool_conf_dict[ 'config_filename' ] ) if shed_tool_conf == file_name: 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. @@ -715,6 +765,7 @@ tool_path = shed_config_dict[ 'tool_path' ] relative_install_dir = partial_install_dir return shed_tool_conf, tool_path, relative_install_dir + def get_tool_path_by_shed_tool_conf_filename( trans, shed_tool_conf ): """ Return the tool_path config setting for the received shed_tool_conf file by searching the tool box's in-memory list of shed_tool_confs for the @@ -729,10 +780,12 @@ if file_name == shed_tool_conf: return shed_tool_conf_dict[ 'tool_path' ] return None + def get_tool_shed_repository_by_id( trans, repository_id ): 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 ): # This method is used only in Galaxy, not the tool shed. sa_session = app.model.context.current @@ -745,6 +798,7 @@ app.model.ToolShedRepository.table.c.owner == owner, app.model.ToolShedRepository.table.c.changeset_revision == changeset_revision ) ) \ .first() + def get_tool_shed_repository_by_shed_name_owner_installed_changeset_revision( app, tool_shed, name, owner, installed_changeset_revision ): # This method is used only in Galaxy, not the tool shed. sa_session = app.model.context.current @@ -757,9 +811,11 @@ app.model.ToolShedRepository.table.c.owner == owner, app.model.ToolShedRepository.table.c.installed_changeset_revision == installed_changeset_revision ) ) \ .first() + def get_tool_shed_from_clone_url( repository_clone_url ): 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 ): """ 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 @@ -772,6 +828,7 @@ 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/ @@ -782,9 +839,11 @@ 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_user( trans, id ): """Get a user from the database by id.""" return trans.sa_session.query( trans.model.User ).get( trans.security.decode_id( id ) ) + def get_user_by_username( app, username ): """Get a user from the database by username.""" sa_session = app.model.context.current @@ -795,6 +854,7 @@ return user except Exception, e: 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) @@ -886,6 +946,7 @@ util.send_mail( frm, to, subject, body, trans.app.config ) except Exception, e: log.exception( "An error occurred sending a tool shed repository update alert by email." ) + def open_repository_files_folder( trans, folder_path ): try: files_list = get_repository_files( trans, folder_path ) @@ -907,12 +968,14 @@ "key": full_path } folder_contents.append( node ) return folder_contents + def remove_dir( dir ): if os.path.exists( dir ): try: shutil.rmtree( dir ) except: pass + def repository_was_previously_installed( trans, tool_shed_url, repository_name, repo_info_tuple ): """ Handle the case where the repository was previously installed using an older changeset_revsion, but later the repository was updated @@ -940,6 +1003,7 @@ if tool_shed_repository and tool_shed_repository.status not in [ trans.model.ToolShedRepository.installation_status.NEW ]: return tool_shed_repository, previous_changeset_revision return None, None + def reversed_lower_upper_bounded_changelog( repo, excluded_lower_bounds_changeset_revision, included_upper_bounds_changeset_revision ): """ Return a reversed list of changesets in the repository changelog after the excluded_lower_bounds_changeset_revision, but up to and @@ -963,8 +1027,10 @@ if changeset_hash == included_upper_bounds_changeset_revision: break return reversed_changelog + def reversed_upper_bounded_changelog( repo, included_upper_bounds_changeset_revision ): return reversed_lower_upper_bounded_changelog( repo, INITIAL_CHANGELOG_HASH, included_upper_bounds_changeset_revision ) + def strip_path( fpath ): if not fpath: return fpath @@ -973,6 +1039,7 @@ except: file_name = fpath return file_name + def to_safe_string( text, to_html=True ): """Translates the characters in text to an html string""" if text: @@ -1003,10 +1070,13 @@ translated.append( '' ) return ''.join( translated ) return text + def tool_shed_from_repository_clone_url( repository_clone_url ): return clean_repository_clone_url( repository_clone_url ).split( '/repos/' )[ 0 ].rstrip( '/' ) + def tool_shed_is_this_tool_shed( toolshed_base_url ): return toolshed_base_url.rstrip( '/' ) == str( url_for( '/', qualified=True ) ).rstrip( '/' ) + def translate_string( raw_text, to_html=True ): if raw_text: if len( raw_text ) <= MAX_CONTENT_SIZE: @@ -1017,6 +1087,7 @@ else: translated_string = '' return translated_string + def update_in_shed_tool_config( app, repository ): """ A tool shed repository is being updated so change the shed_tool_conf file. Parse the config file to generate the entire list @@ -1050,6 +1121,7 @@ elem = guid_to_tool_elem_dict[ guid ] config_elems.append( elem ) config_elems_to_xml_file( app, config_elems, shed_tool_conf, tool_path ) + def update_repository( repo, ctx_rev=None ): """ Update the cloned repository to changeset_revision. It is critical that the installed repository is updated to the desired @@ -1067,11 +1139,13 @@ # It would be nice if we could use mercurial's purge extension to remove untracked files. The problem is that # purging is not supported by the mercurial API. commands.update( get_configured_ui(), repo, rev=ctx_rev ) + def update_tool_shed_repository_status( app, tool_shed_repository, status ): sa_session = app.model.context.current tool_shed_repository.status = status sa_session.add( tool_shed_repository ) sa_session.flush() + def url_join( *args ): parts = [] for arg in args:

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