diff --git a/lib/galaxy/app.py b/lib/galaxy/app.py index 408de19658d..516a91f53af 100644 --- a/lib/galaxy/app.py +++ b/lib/galaxy/app.py @@ -22,7 +22,7 @@ class UniverseApplication( object ): self.config = config.Configuration( **kwargs ) self.config.check() config.configure_logging( self.config ) - # Set up datatypes registry + # Initialize the datatypes registry to the default data types included in self.config.datatypes_config. self.datatypes_registry = galaxy.datatypes.registry.Registry() self.datatypes_registry.load_datatypes( self.config.root, self.config.datatypes_config ) galaxy.model.set_datatypes_registry( self.datatypes_registry ) @@ -68,6 +68,10 @@ class UniverseApplication( object ): if self.config.get_bool( 'enable_tool_shed_check', False ): from tool_shed import update_manager self.update_manager = update_manager.UpdateManager( self ) + # Manage installed tool shed repositories + self.installed_repository_manager = galaxy.tool_shed.InstalledRepositoryManager( self ) + # Add additional datatypes from installed tool shed repositories to the datatypes registry. + self.installed_repository_manager.load_datatypes() # Load datatype converters self.datatypes_registry.load_datatype_converters( self.toolbox ) # Load history import/export tools diff --git a/lib/galaxy/tool_shed/__init__.py b/lib/galaxy/tool_shed/__init__.py index 422c3577184..b37d90de34f 100644 --- a/lib/galaxy/tool_shed/__init__.py +++ b/lib/galaxy/tool_shed/__init__.py @@ -1,3 +1,22 @@ """ -Classes encapsulating the relationships between Galaxy and Galaxy tool sheds. -""" \ No newline at end of file +Classes encapsulating the management of repositories installed from Galaxy tool sheds. +""" +import os, logging +from galaxy.model.orm import * + +log = logging.getLogger(__name__) + +class InstalledRepositoryManager( object ): + def __init__( self, app ): + self.app = app + self.model = self.app.model + self.sa_session = self.model.context.current + def load_datatypes( self ): + for tool_shed_repository in self.sa_session.query( self.model.ToolShedRepository ) \ + .filter( and_( self.model.ToolShedRepository.table.c.includes_datatypes==True, + self.model.ToolShedRepository.table.c.deleted==False ) ): + metadata = tool_shed_repository.metadata + datatypes_config = metadata[ 'datatypes_config' ] + full_path = os.path.abspath( datatypes_config ) + self.app.datatypes_registry.load_datatypes( self.app.config.root, full_path ) + \ No newline at end of file diff --git a/lib/galaxy/tool_shed/install_manager.py b/lib/galaxy/tool_shed/install_manager.py index 1f182f98c7c..e114a7d71d9 100644 --- a/lib/galaxy/tool_shed/install_manager.py +++ b/lib/galaxy/tool_shed/install_manager.py @@ -158,4 +158,13 @@ class InstallManager( object ): if os.path.exists( clone_dir ): installed = True break + if not installed: + full_path = os.path.abspath( clone_dir ) + # We may have a repository that contains no tools. + if os.path.exists( full_path ): + for root, dirs, files in os.walk( full_path ): + if '.hg' in dirs: + # Assume that the repository has been installed if we find a .hg directory. + installed = True + break return installed diff --git a/lib/galaxy/util/shed_util.py b/lib/galaxy/util/shed_util.py index 1ac108ab04c..2e7ee898a24 100644 --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -109,6 +109,7 @@ def generate_datatypes_metadata( datatypes_config, metadata_dict ): Update the received metadata_dict with changes that have been applied to the received datatypes_config. This method is used by the InstallManager, which does not have access to trans. + TODO: Handle converters, indexers, sniffers, etc... """ # Parse datatypes_config. tree = ElementTree.parse( datatypes_config ) @@ -125,13 +126,29 @@ def generate_datatypes_metadata( datatypes_config, metadata_dict ): registration = root.find( 'registration' ) if registration: for elem in registration.findall( 'datatype' ): - extension = elem.get( 'extension', None ) + datatypes_dict = {} + display_in_upload = elem.get( 'display_in_upload', None ) + if display_in_upload: + datatypes_dict[ 'display_in_upload' ] = display_in_upload dtype = elem.get( 'type', None ) + if dtype: + datatypes_dict[ 'dtype' ] = dtype + extension = elem.get( 'extension', None ) + if extension: + datatypes_dict[ 'extension' ] = extension + max_optional_metadata_filesize = elem.get( 'max_optional_metadata_filesize', None ) + if max_optional_metadata_filesize: + datatypes_dict[ 'max_optional_metadata_filesize' ] = max_optional_metadata_filesize mimetype = elem.get( 'mimetype', None ) - datatypes.append( dict( extension=extension, - dtype=dtype, - mimetype=mimetype ) ) - metadata_dict[ 'datatypes' ] = datatypes + if mimetype: + datatypes_dict[ 'mimetype' ] = mimetype + subclass = elem.get( 'subclass', None ) + if subclass: + datatypes_dict[ 'subclass' ] = subclass + if datatypes_dict: + datatypes.append( datatypes_dict ) + if datatypes: + metadata_dict[ 'datatypes' ] = datatypes return metadata_dict def generate_metadata( toolbox, relative_install_dir, repository_clone_url ): """ @@ -426,46 +443,52 @@ def load_datatypes( app, datatypes_config, relative_intall_dir ): # This method is used by the InstallManager, which does not have access to trans. imported_module = None # Parse datatypes_config. - tree = parse_xml( datatypes_config ) + tree = util.parse_xml( datatypes_config ) datatypes_config_root = tree.getroot() relative_path_to_datatype_file_name = None datatype_files = datatypes_config_root.find( 'datatype_files' ) - # Currently only a single datatype_file is supported. For example: - # - # - # - for elem in datatype_files.findall( 'datatype_file' ): - datatype_file_name = elem.get( 'name', None ) - if datatype_file_name: - # Find the file in the installed repository. - for root, dirs, files in os.walk( relative_intall_dir ): - if root.find( '.hg' ) < 0: - for name in files: - if name == datatype_file_name: - relative_path_to_datatype_file_name = os.path.join( root, name ) - break - break - if relative_path_to_datatype_file_name: - relative_head, relative_tail = os.path.split( relative_path_to_datatype_file_name ) - registration = datatypes_config_root.find( 'registration' ) - # Get the module by parsing the tag. - for elem in registration.findall( 'datatype' ): - # A 'type' attribute is currently required. The attribute - # should be something like: type="gmap:GmapDB". - dtype = elem.get( 'type', None ) - if dtype: - fields = dtype.split( ':' ) - datatype_module = fields[0] - datatype_class_name = fields[1] - # Since we currently support only a single datatype_file, - # we have what we need. + if datatype_files: + # Currently only a single datatype_file is supported. For example: + # + # + # + for elem in datatype_files.findall( 'datatype_file' ): + datatype_file_name = elem.get( 'name', None ) + if datatype_file_name: + # Find the file in the installed repository. + for root, dirs, files in os.walk( relative_intall_dir ): + if root.find( '.hg' ) < 0: + for name in files: + if name == datatype_file_name: + relative_path_to_datatype_file_name = os.path.join( root, name ) + break break - try: - sys.path.insert( 0, relative_head ) - imported_module = __import__( datatype_module ) - sys.path.pop( 0 ) - except Exception, e: - log.debug( "Exception importing datatypes code file included in installed repository: %s" % str( e ) ) + if relative_path_to_datatype_file_name: + relative_head, relative_tail = os.path.split( relative_path_to_datatype_file_name ) + registration = datatypes_config_root.find( 'registration' ) + # Get the module by parsing the tag. + for elem in registration.findall( 'datatype' ): + # A 'type' attribute is currently required. The attribute + # should be something like: type="gmap:GmapDB". + dtype = elem.get( 'type', None ) + if dtype: + fields = dtype.split( ':' ) + datatype_module = fields[0] + datatype_class_name = fields[1] + # Since we currently support only a single datatype_file, + # we have what we need. + break + try: + sys.path.insert( 0, relative_head ) + imported_module = __import__( datatype_module ) + sys.path.pop( 0 ) + except Exception, e: + log.debug( "Exception importing datatypes code file included in installed repository: %s" % str( e ) ) + else: + # The repository includes a datayptes_conf.xml file, but no code file that + # contains data type classes. This implies that the data types in datayptes_conf.xml + # are all subclasses of data types that are in the distribution. + imported_module = None app.datatypes_registry.load_datatypes( root_dir=app.config.root, config=datatypes_config, imported_module=imported_module ) def load_repository_contents( app, name, description, owner, changeset_revision, tool_path, repository_clone_url, relative_install_dir, current_working_dir, tmp_name, tool_section=None, shed_tool_conf=None, new_install=True ): diff --git a/lib/galaxy/web/controllers/admin_toolshed.py b/lib/galaxy/web/controllers/admin_toolshed.py index a5dc6b2bcda..9aa4426d6c3 100644 --- a/lib/galaxy/web/controllers/admin_toolshed.py +++ b/lib/galaxy/web/controllers/admin_toolshed.py @@ -191,13 +191,20 @@ class AdminToolshed( AdminGalaxy ): repo_info_dict = kwd[ 'repo_info_dict' ] new_tool_panel_section = kwd.get( 'new_tool_panel_section', '' ) tool_panel_section = kwd.get( 'tool_panel_section', '' ) - if kwd.get( 'select_tool_panel_section_button', False ): - shed_tool_conf = kwd[ 'shed_tool_conf' ] + includes_tools = util.string_as_bool( kwd.get( 'includes_tools', False ) ) + if not includes_tools or ( includes_tools and kwd.get( 'select_tool_panel_section_button', False ) ): + if includes_tools: + shed_tool_conf = kwd[ 'shed_tool_conf' ] + else: + # If installing a repository that includes no tools, get the relative + # tool_path from the file to which the install_tool_config_file config + # setting points. + shed_tool_conf = trans.app.config.install_tool_config # Get the tool path. for k, tool_path in trans.app.toolbox.shed_tool_confs.items(): if k == shed_tool_conf: break - if new_tool_panel_section or tool_panel_section: + if includes_tools and ( new_tool_panel_section or tool_panel_section ): if new_tool_panel_section: section_id = new_tool_panel_section.lower().replace( ' ', '_' ) new_section_key = 'section_%s' % str( section_id ) @@ -290,6 +297,7 @@ class AdminToolshed( AdminGalaxy ): tool_shed_url=tool_shed_url, repo_info_dict=repo_info_dict, shed_tool_conf=shed_tool_conf, + includes_tools=includes_tools, shed_tool_conf_select_field=shed_tool_conf_select_field, tool_panel_section_select_field=tool_panel_section_select_field, new_tool_panel_section=new_tool_panel_section, diff --git a/lib/galaxy/webapps/community/controllers/common.py b/lib/galaxy/webapps/community/controllers/common.py index fec93f73879..9be25a0325e 100644 --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -4,6 +4,7 @@ from datetime import * from galaxy.tools import * from galaxy.util.json import from_json_string, to_json_string from galaxy.util.hash_util import * +from galaxy.util.shed_util import generate_datatypes_metadata, generate_tool_metadata, generate_workflow_metadata from galaxy.web.base.controller import * from galaxy.webapps.community import model from galaxy.model.orm import * @@ -149,6 +150,7 @@ def get_latest_repository_metadata( trans, id ): .order_by( trans.model.RepositoryMetadata.table.c.id.desc() ) \ .first() def generate_clone_url( trans, repository_id ): + """Generate the URL for cloning a repository.""" repository = get_repository( trans, repository_id ) protocol, base = trans.request.base.split( '://' ) if trans.user: @@ -220,54 +222,6 @@ def check_tool_input_params( trans, name, tool, sample_files, invalid_files ): correction_msg += "Upload a file named %s.sample to the repository to correct this error." % str( index_tail ) invalid_files.append( ( name, correction_msg ) ) return can_set_metadata, invalid_files -def generate_tool_metadata( trans, id, changeset_revision, tool_config, tool, metadata_dict ): - """ - Update the received metadata_dict with changes that have been - applied to the received tool. - """ - repository = get_repository( trans, id ) - # Handle tool.requirements. - tool_requirements = [] - for tr in tool.requirements: - name=tr.name - type=tr.type - if type == 'fabfile': - version = None - fabfile = tr.fabfile - method = tr.method - else: - version = tr.version - fabfile = None - method = None - requirement_dict = dict( name=name, - type=type, - version=version, - fabfile=fabfile, - method=method ) - tool_requirements.append( requirement_dict ) - # Handle tool.tests. - tool_tests = [] - if tool.tests: - for ttb in tool.tests: - test_dict = dict( name=ttb.name, - required_files=ttb.required_files, - inputs=ttb.inputs, - outputs=ttb.outputs ) - tool_tests.append( test_dict ) - tool_dict = dict( id=tool.id, - guid = generate_tool_guid( trans, repository, tool ), - name=tool.name, - version=tool.version, - description=tool.description, - version_string_cmd = tool.version_string_cmd, - tool_config=tool_config, - requirements=tool_requirements, - tests=tool_tests ) - if 'tools' in metadata_dict: - metadata_dict[ 'tools' ].append( tool_dict ) - else: - metadata_dict[ 'tools' ] = [ tool_dict ] - return metadata_dict def new_tool_metadata_required( trans, id, metadata_dict ): """ Compare the last saved metadata for each tool in the repository with the new metadata @@ -309,16 +263,6 @@ def new_tool_metadata_required( trans, id, metadata_dict ): # The received metadata_dict includes no metadata for tools, so a new repository_metadata table # record is not needed. return False -def generate_workflow_metadata( trans, id, changeset_revision, exported_workflow_dict, metadata_dict ): - """ - Update the received metadata_dict with changes that have been applied - to the received exported_workflow_dict. Store everything in the database. - """ - if 'workflows' in metadata_dict: - metadata_dict[ 'workflows' ].append( exported_workflow_dict ) - else: - metadata_dict[ 'workflows' ] = [ exported_workflow_dict ] - return metadata_dict def new_workflow_metadata_required( trans, id, metadata_dict ): """ Currently everything about an exported workflow except the name is hard-coded, so there's @@ -337,34 +281,6 @@ def new_workflow_metadata_required( trans, id, metadata_dict ): # The received metadata_dict includes no metadata for workflows, so a new repository_metadata table # record is not needed. return False -def generate_datatypes_metadata( trans, id, changeset_revision, datatypes_config, metadata_dict ): - """ - Update the received metadata_dict with changes that have been applied - to the received datatypes_config. - """ - # Parse datatypes_config. - tree = ElementTree.parse( datatypes_config ) - root = tree.getroot() - ElementInclude.include( root ) - repository_datatype_code_files = [] - datatype_files = root.find( 'datatype_files' ) - if datatype_files: - for elem in datatype_files.findall( 'datatype_file' ): - name = elem.get( 'name', None ) - repository_datatype_code_files.append( name ) - metadata_dict[ 'datatype_files' ] = repository_datatype_code_files - datatypes = [] - registration = root.find( 'registration' ) - if registration: - for elem in registration.findall( 'datatype' ): - extension = elem.get( 'extension', None ) - dtype = elem.get( 'type', None ) - mimetype = elem.get( 'mimetype', None ) - datatypes.append( dict( extension=extension, - dtype=dtype, - mimetype=mimetype ) ) - metadata_dict[ 'datatypes' ] = datatypes - return metadata_dict def generate_metadata_for_repository_tip( trans, id, ctx, changeset_revision, repo_dir ): # Browse the repository tip files on disk to generate metadata. This is faster than # the generate_metadata_for_changeset_revision() method below because fctx.data() does @@ -382,7 +298,7 @@ def generate_metadata_for_repository_tip( trans, id, ctx, changeset_revision, re datatypes_config = os.path.abspath( os.path.join( root, name ) ) break if datatypes_config: - metadata_dict = generate_datatypes_metadata( trans, id, changeset_revision, datatypes_config, metadata_dict ) + metadata_dict = generate_datatypes_metadata( datatypes_config, metadata_dict ) # Find all special .sample files. for root, dirs, files in os.walk( repo_dir ): if root.find( '.hg' ) < 0: @@ -409,19 +325,19 @@ def generate_metadata_for_repository_tip( trans, id, ctx, changeset_revision, re if can_set_metadata: # Update the list of metadata dictionaries for tools in metadata_dict. tool_config = os.path.join( root, name ) - metadata_dict = generate_tool_metadata( trans, id, changeset_revision, tool_config, tool, metadata_dict ) + repository_clone_url = generate_clone_url( trans, id ) + metadata_dict = generate_tool_metadata( tool_config, tool, repository_clone_url, metadata_dict ) # Find all exported workflows elif name.endswith( '.ga' ): try: - full_path = os.path.abspath( os.path.join( root, name ) ) + relative_path = os.path.join( root, name ) # Convert workflow data from json - fp = open( full_path, 'rb' ) + fp = open( relative_path, 'rb' ) workflow_text = fp.read() fp.close() exported_workflow_dict = from_json_string( workflow_text ) if 'a_galaxy_workflow' in exported_workflow_dict and exported_workflow_dict[ 'a_galaxy_workflow' ] == 'true': - # Update the list of metadata dictionaries for workflows in metadata_dict. - metadata_dict = generate_workflow_metadata( trans, id, changeset_revision, exported_workflow_dict, metadata_dict ) + metadata_dict = generate_workflow_metadata( relative_path, exported_workflow_dict, metadata_dict ) except Exception, e: invalid_files.append( ( name, str( e ) ) ) return metadata_dict, invalid_files @@ -438,7 +354,7 @@ def generate_metadata_for_changeset_revision( trans, id, ctx, changeset_revision datatypes_config = fctx.data() break if datatypes_config: - metadata_dict = generate_datatypes_metadata( trans, id, changeset_revision, datatypes_config, metadata_dict ) + metadata_dict = generate_datatypes_metadata( datatypes_config, metadata_dict ) # Get all tool config file names from the hgweb url, something like: # /repos/test/convert_chars1/file/e58dcf0026c7/convert_characters.xml for filename in ctx: @@ -469,7 +385,8 @@ def generate_metadata_for_changeset_revision( trans, id, ctx, changeset_revision # anything, but may result in a bit of confusion when maintaining the code / data over time. # IMPORTANT NOTE: Here we are assuming that since the current change set is not the repository # tip, we do not have to handle any .loc.sample files since they would have been handled previously. - metadata_dict = generate_tool_metadata( trans, id, changeset_revision, filename, tool, metadata_dict ) + repository_clone_url = generate_clone_url( trans, id ) + metadata_dict = generate_tool_metadata( filename, tool, repository_clone_url, metadata_dict ) try: os.unlink( tmp_filename ) except: @@ -481,8 +398,7 @@ def generate_metadata_for_changeset_revision( trans, id, ctx, changeset_revision workflow_text = fctx.data() exported_workflow_dict = from_json_string( workflow_text ) if 'a_galaxy_workflow' in exported_workflow_dict and exported_workflow_dict[ 'a_galaxy_workflow' ] == 'true': - # Update the list of metadata dictionaries for workflows in metadata_dict. - metadata_dict = generate_workflow_metadata( trans, id, changeset_revision, exported_workflow_dict, metadata_dict ) + metadata_dict = generate_workflow_metadata( '', exported_workflow_dict, metadata_dict ) except Exception, e: invalid_files.append( ( name, str( e ) ) ) return metadata_dict, invalid_files @@ -510,12 +426,18 @@ def set_repository_metadata( trans, id, changeset_revision, content_alert_str='' if len( repository.downloadable_revisions ) == 1: handle_email_alerts( trans, repository, content_alert_str='', new_repo_alert=True, admin_only=False ) else: - # Update the last saved repository_metadata table row. repository_metadata = get_latest_repository_metadata( trans, id ) - repository_metadata.changeset_revision = changeset_revision - repository_metadata.metadata = metadata_dict - trans.sa_session.add( repository_metadata ) - trans.sa_session.flush() + if repository_metadata: + # Update the last saved repository_metadata table row. + repository_metadata.changeset_revision = changeset_revision + repository_metadata.metadata = metadata_dict + trans.sa_session.add( repository_metadata ) + trans.sa_session.flush() + else: + # There are no tools in the repository, and we're setting metadat on the repository tip. + repository_metadata = trans.model.RepositoryMetadata( repository.id, changeset_revision, metadata_dict ) + trans.sa_session.add( repository_metadata ) + trans.sa_session.flush() else: # We're re-generating metadata for an old repository revision. repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) diff --git a/lib/galaxy/webapps/community/controllers/repository.py b/lib/galaxy/webapps/community/controllers/repository.py index 43712752bda..53147bb7853 100644 --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -436,9 +436,9 @@ class RepositoryController( BaseUIController, ItemRatings ): **kwd ) ) if operation == "install": galaxy_url = trans.get_cookie( name='toolshedgalaxyurl' ) - encoded_repo_info_dict = self.__encode_repo_info_dict( trans, webapp, util.listify( item_id ) ) - url = '%s/admin_toolshed/install_repository?tool_shed_url=%s&webapp=%s&repo_info_dict=%s' % \ - ( galaxy_url, url_for( '', qualified=True ), webapp, encoded_repo_info_dict ) + encoded_repo_info_dict, includes_tools = self.__encode_repo_info_dict( trans, webapp, util.listify( item_id ) ) + url = '%s/admin_toolshed/install_repository?tool_shed_url=%s&webapp=%s&repo_info_dict=%s&includes_tools=%s' % \ + ( galaxy_url, url_for( '', qualified=True ), webapp, encoded_repo_info_dict, str( includes_tools ) ) return trans.response.send_redirect( url ) else: # This can only occur when there is a multi-select grid with check boxes and an operation, @@ -512,9 +512,9 @@ class RepositoryController( BaseUIController, ItemRatings ): **kwd ) ) if operation == "install": galaxy_url = trans.get_cookie( name='toolshedgalaxyurl' ) - encoded_repo_info_dict = self.__encode_repo_info_dict( trans, webapp, util.listify( item_id ) ) - url = '%s/admin_toolshed/install_repository?tool_shed_url=%s&webapp=%s&repo_info_dict=%s' % \ - ( galaxy_url, url_for( '', qualified=True ), webapp, encoded_repo_info_dict ) + encoded_repo_info_dict, includes_tools = self.__encode_repo_info_dict( trans, webapp, util.listify( item_id ) ) + url = '%s/admin_toolshed/install_repository?tool_shed_url=%s&webapp=%s&repo_info_dict=%s&includes_tools=%s' % \ + ( galaxy_url, url_for( '', qualified=True ), webapp, encoded_repo_info_dict, str( includes_tools ) ) return trans.response.send_redirect( url ) else: # This can only occur when there is a multi-select grid with check boxes and an operation, @@ -707,14 +707,17 @@ class RepositoryController( BaseUIController, ItemRatings ): return match_tuples def __encode_repo_info_dict( self, trans, webapp, repository_metadata_ids ): repo_info_dict = {} + includes_tools = False for repository_metadata_id in repository_metadata_ids: repository_metadata = get_repository_metadata_by_id( trans, repository_metadata_id ) + if not includes_tools and 'tools' in repository_metadata.metadata: + includes_tools = True repository = get_repository( trans, trans.security.encode_id( repository_metadata.repository_id ) ) repository_id = trans.security.encode_id( repository.id ) changeset_revision = repository_metadata.changeset_revision repository_clone_url = generate_clone_url( trans, repository_id ) repo_info_dict[ repository.name ] = ( repository.description, repository_clone_url, changeset_revision ) - return encode( repo_info_dict ) + return encode( repo_info_dict ), includes_tools @web.expose def preview_tools_in_changeset( self, trans, repository_id, **kwd ): params = util.Params( kwd ) @@ -755,12 +758,16 @@ class RepositoryController( BaseUIController, ItemRatings ): repository_clone_url = generate_clone_url( trans, repository_id ) repository = get_repository( trans, repository_id ) changeset_revision = util.restore_text( params.get( 'changeset_revision', repository.tip ) ) + repository_metadata = get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision ) + # Tell the caller if the repository includes Galaxy tools so the page + # enabling selection of the tool panel section can be displayed. + includes_tools = 'tools' in repository_metadata.metadata repo_info_dict = {} repo_info_dict[ repository.name ] = ( repository.description, repository_clone_url, changeset_revision ) encoded_repo_info_dict = encode( repo_info_dict ) # Redirect back to local Galaxy to perform install. - url = '%s/admin_toolshed/install_repository?tool_shed_url=%s&repo_info_dict=%s' % \ - ( galaxy_url, url_for( '', qualified=True ), encoded_repo_info_dict ) + url = '%s/admin_toolshed/install_repository?tool_shed_url=%s&repo_info_dict=%s&includes_tools=%s' % \ + ( galaxy_url, url_for( '', qualified=True ), encoded_repo_info_dict, str( includes_tools ) ) return trans.response.send_redirect( url ) @web.expose def check_for_updates( self, trans, **kwd ): diff --git a/templates/admin/tool_shed_repository/common.mako b/templates/admin/tool_shed_repository/common.mako index d4455358c91..48f69195818 100644 --- a/templates/admin/tool_shed_repository/common.mako +++ b/templates/admin/tool_shed_repository/common.mako @@ -128,25 +128,22 @@ - + + %for datatypes_dict in datatypes_dicts: - <% - extension = datatypes_dict[ 'extension' ] - dtype = datatypes_dict[ 'dtype' ] - mimetype = datatypes_dict[ 'mimetype' ] + <% + extension = datatypes_dict.get( 'extension', ' ' ) + dtype = datatypes_dict.get( 'dtype', ' ' ) + mimetype = datatypes_dict.get( 'mimetype', ' ' ) + subclass = datatypes_dict.get( 'subclass', ' ' ) %> - + + %endfor
extensiondtypetype mimetypesubclass
${extension} ${dtype} - %if mimetype: - ${mimetype} - %else: -   - %endif - ${mimetype}${subclass}
diff --git a/templates/admin/tool_shed_repository/select_tool_panel_section.mako b/templates/admin/tool_shed_repository/select_tool_panel_section.mako index bf8665af822..5200e7c7f29 100644 --- a/templates/admin/tool_shed_repository/select_tool_panel_section.mako +++ b/templates/admin/tool_shed_repository/select_tool_panel_section.mako @@ -25,7 +25,7 @@
Choose tool panel section to contain installed tools (optional)
-
+ %if shed_tool_conf_select_field:
diff --git a/templates/webapps/community/repository/common.mako b/templates/webapps/community/repository/common.mako index efd69ebaa80..6eb6516cc2b 100644 --- a/templates/webapps/community/repository/common.mako +++ b/templates/webapps/community/repository/common.mako @@ -209,25 +209,22 @@ - + + %for datatypes_dict in datatypes_dicts: - <% - extension = datatypes_dict[ 'extension' ] - dtype = datatypes_dict[ 'dtype' ] - mimetype = datatypes_dict[ 'mimetype' ] + <% + extension = datatypes_dict.get( 'extension', ' ' ) + dtype = datatypes_dict.get( 'dtype', ' ' ) + mimetype = datatypes_dict.get( 'mimetype', ' ' ) + subclass = datatypes_dict.get( 'subclass', ' ' ) %> - + + %endfor
extensiondtypetype mimetypesubclass
${extension} ${dtype} - %if mimetype: - ${mimetype} - %else: -   - %endif - ${mimetype}${subclass}