[galaxy-commits] commit/galaxy-central: greg: When installing a new repository from the too shed repository to Galaxy or reinstalling an uninstalled repository, handle tool dependencies defined for repository dependencies defined for the repository being installed.

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2ec609faae49/ changeset: 2ec609faae49 user: greg date: 2013-01-08 19:50:16 summary: When installing a new repository from the too shed repository to Galaxy or reinstalling an uninstalled repository, handle tool dependencies defined for repository dependencies defined for the repository being installed. affected #: 6 files diff -r 530fb4f8204f2106e11f419c381fd53d2319ce24 -r 2ec609faae49b4ab32190403669849f1af0b68f6 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -653,6 +653,22 @@ tool_dependencies = None missing_tool_dependencies = None return tool_dependencies, missing_tool_dependencies +def get_installed_and_missing_tool_dependencies_for_new_install( trans, all_tool_dependencies ): + """Return the lists of installed tool dependencies and missing tool dependencies for a set of repositories being installed into Galaxy.""" + # FIXME: this method currently populates and returns only missing tool dependencies since tool dependencies defined for complex repository dependency + # relationships is not currently supported. This method should be enhanced to search for installed tool dependencies defined as complex repository + # dependency relationships when that feature is implemented. + if all_tool_dependencies: + tool_dependencies = {} + missing_tool_dependencies = {} + for td_key, val in all_tool_dependencies.items(): + # Since we have a new install, missing tool dependencies have never been installed. + val[ 'status' ] = trans.model.ToolDependency.installation_status.NEVER_INSTALLED + missing_tool_dependencies[ td_key ] = val + else: + tool_dependencies = None + missing_tool_dependencies = None + return tool_dependencies, missing_tool_dependencies def get_repository_owner( cleaned_repository_url ): items = cleaned_repository_url.split( 'repos' ) repo_path = items[ 1 ] @@ -667,7 +683,7 @@ """ Inspect the list of repo_info_dicts for repository dependencies and append a repo_info_dict for each of them to the list. All repository_dependencies entries in each of the received repo_info_dicts includes all required repositories, so only one pass through - this methid is required to retrieve all repository dependencies. + this method is required to retrieve all repository dependencies. """ all_repo_info_dicts = [] if repo_info_dicts: @@ -1035,7 +1051,7 @@ if k not in [ 'id', 'version', 'name' ]: return True return False -def populate_containers_dict_from_repository_metadata( trans, tool_shed_url, tool_path, repository, reinstalling=False ): +def populate_containers_dict_from_repository_metadata( trans, tool_shed_url, tool_path, repository, reinstalling=False, required_repo_info_dicts=None ): """ Retrieve necessary information from the received repository's metadata to populate the containers_dict for display. This method is called only from Galaxy (not the tool shed) when displaying repository dependencies for installed repositories and when displaying them for uninstalled @@ -1064,15 +1080,51 @@ readme_files_dict = None # Handle repository dependencies. installed_repository_dependencies, missing_repository_dependencies = get_installed_and_missing_repository_dependencies( trans, repository ) - # Handle tool dependencies. - all_tool_dependencies = metadata.get( 'tool_dependencies', None ) - installed_tool_dependencies, missing_tool_dependencies = get_installed_and_missing_tool_dependencies( trans, repository, all_tool_dependencies ) + # Handle the current repository's tool dependencies. + repository_tool_dependencies = metadata.get( 'tool_dependencies', None ) + repository_installed_tool_dependencies, repository_missing_tool_dependencies = \ + get_installed_and_missing_tool_dependencies( trans, repository, repository_tool_dependencies ) if reinstalling: - # All tool dependencies will be considered missing since we are reinstalling the repository. - if installed_tool_dependencies: - for td in installed_tool_dependencies: - missing_tool_dependencies.append( td ) - installed_tool_dependencies = None + installed_tool_dependencies = None + missing_tool_dependencies = None + if repository_installed_tool_dependencies is None: + repository_installed_tool_dependencies = {} + if repository_missing_tool_dependencies is None: + repository_missing_tool_dependencies = {} + if required_repo_info_dicts: + # Handle the tool dependencies defined for each of the repository's repository dependencies. + for rid in required_repo_info_dicts: + for name, repo_info_tuple in rid.items(): + description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = \ + suc.get_repo_info_tuple_contents( repo_info_tuple ) + if tool_dependencies: + tool_shed = suc.get_tool_shed_from_clone_url( repository_clone_url ) + required_repository = suc.get_repository_for_dependency_relationship( trans.app, tool_shed, name, repository_owner, changeset_revision ) + if not required_repository: + # The required_repository may have been installed with a different changeset revision. + required_repository, installed_changeset_revision = repository_was_previously_installed( trans, + tool_shed_url, + name, + repo_info_tuple, + clone_dir ) + if required_repository: + required_repository_installed_tool_dependencies, required_repository_missing_tool_dependencies = \ + get_installed_and_missing_tool_dependencies( trans, required_repository, tool_dependencies ) + if required_repository_installed_tool_dependencies: + for td_key, td_dict in required_repository_installed_tool_dependencies.items(): + if td_key not in repository_installed_tool_dependencies: + repository_installed_tool_dependencies[ td_key ] = td_dict + if required_repository_missing_tool_dependencies: + for td_key, td_dict in required_repository_missing_tool_dependencies.items(): + if td_key not in repository_missing_tool_dependencies: + repository_missing_tool_dependencies[ td_key ] = td_dict + if repository_installed_tool_dependencies: + installed_tool_dependencies = repository_installed_tool_dependencies + if repository_missing_tool_dependencies: + missing_tool_dependencies = repository_missing_tool_dependencies + else: + installed_tool_dependencies = repository_installed_tool_dependencies + missing_tool_dependencies = repository_missing_tool_dependencies # Handle valid tools. valid_tools = metadata.get( 'tools', None ) # Handle workflows. @@ -1092,7 +1144,8 @@ tool_dependencies=installed_tool_dependencies, valid_tools=valid_tools, workflows=workflows, - new_install=False ) + new_install=False, + reinstalling=reinstalling ) else: containers_dict = dict( datatypes=None, invalid_tools=None, diff -r 530fb4f8204f2106e11f419c381fd53d2319ce24 -r 2ec609faae49b4ab32190403669849f1af0b68f6 lib/galaxy/util/shed_util_common.py --- a/lib/galaxy/util/shed_util_common.py +++ b/lib/galaxy/util/shed_util_common.py @@ -78,7 +78,7 @@ return readme_files_dict def build_repository_containers_for_galaxy( trans, toolshed_base_url, repository_name, repository_owner, changeset_revision, repository, datatypes, invalid_tools, missing_repository_dependencies, missing_tool_dependencies, readme_files_dict, - repository_dependencies, tool_dependencies, valid_tools, workflows, new_install=False ): + repository_dependencies, tool_dependencies, valid_tools, workflows, new_install=False, reinstalling=False ): """Return a dictionary of containers for the received repository's dependencies and readme files for display during installation to Galaxy.""" containers_dict = dict( datatypes=None, invalid_tools=None, @@ -160,7 +160,8 @@ tool_dependencies, label=label, missing=False, - new_install=new_install ) + new_install=new_install, + reinstalling=reinstalling ) containers_dict[ 'tool_dependencies' ] = tool_dependencies_root_folder # Missing tool dependencies container. if missing_tool_dependencies: @@ -170,7 +171,8 @@ missing_tool_dependencies, label='Missing tool dependencies', missing=True, - new_install=new_install ) + new_install=new_install, + reinstalling=reinstalling ) containers_dict[ 'missing_tool_dependencies' ] = missing_tool_dependencies_root_folder # Valid tools container. if valid_tools: @@ -790,7 +792,7 @@ Return a dictionary that includes all of the information needed to install a repository into a local Galaxy instance. The dictionary will also contain the recursive list of repository dependencies defined for the repository, as well as the defined tool dependencies. - This method is called from Galaxy from two places: + This method is called from Galaxy in two places: 1. During the tool shed repository installation process (via the tool shed's get_repository_information() method)- in this case both the received repository and repository_metadata will be objects. 2. When a tool shed repository that was uninstalled from a Galaxy instance is being re-installed - in this case, both repository and @@ -2414,6 +2416,47 @@ removed = True error_message = '' return removed, error_message +def repository_dependencies_have_tool_dependencies( trans, repository_dependencies ): + """ + repository_dependencies': + {'http://localhost:9009__ESEP__emboss_6__ESEP__test__ESEP__92bedb60b0c9': + [['http://localhost:9009', 'emboss_datatypes', 'test', '27df73fe48a6']], + 'root_key': 'http://localhost:9009__ESEP__emboss__ESEP__test__ESEP__06d729cb3f34', + 'description': 'required to enable emboss 6 tools', + 'http://localhost:9009__ESEP__emboss__ESEP__test__ESEP__06d729cb3f34': + [['http://localhost:9009', 'emboss_6', 'test', '92bedb60b0c9']]}} + """ + rd_tups_processed = [] + for key, rd_tups in repository_dependencies.items(): + if key in [ 'root_key', 'description' ]: + continue + rd_tup = container_util.get_components_from_key( key ) + if rd_tup not in rd_tups_processed: + toolshed, name, owner, changeset_revision = rd_tup + repository = get_repository_by_name_and_owner( trans, name, owner ) + repository_metadata = get_repository_metadata_by_repository_id_changset_revision( trans, + trans.security.encode_id( repository.id ), + changeset_revision ) + if repository_metadata: + metadata = repository_metadata.metadata + if metadata: + if 'tool_dependencies' in metadata: + return True + rd_tups_processed.append( rd_tup ) + for rd_tup in rd_tups: + if rd_tup not in rd_tups_processed: + toolshed, name, owner, changeset_revision = rd_tup + repository = get_repository_by_name_and_owner( trans, name, owner ) + repository_metadata = get_repository_metadata_by_repository_id_changset_revision( trans, + trans.security.encode_id( repository.id ), + changeset_revision ) + if repository_metadata: + metadata = repository_metadata.metadata + if metadata: + if 'tool_dependencies' in metadata: + return True + rd_tups_processed.append( rd_tup ) + return False def reset_all_metadata_on_installed_repository( trans, id ): """Reset all metadata on a single tool shed repository installed into a Galaxy instance.""" repository = get_installed_tool_shed_repository( trans, id ) diff -r 530fb4f8204f2106e11f419c381fd53d2319ce24 -r 2ec609faae49b4ab32190403669849f1af0b68f6 lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -786,9 +786,9 @@ operation='preview_tools_in_changeset', repository_id=repository_id ) self.valid_repository_grid.operations = [ grids.GridOperation( "Preview and install", - url_args=url_args, - allow_multiple=False, - async_compatible=False ) ] + url_args=url_args, + allow_multiple=False, + async_compatible=False ) ] return self.valid_repository_grid( trans, **kwd ) def __build_allow_push_select_field( self, trans, current_push_list, selected_value='none' ): options = [] @@ -1410,7 +1410,10 @@ repo_info_dicts=repo_info_dicts ) @web.json def get_required_repo_info_dict( self, trans, encoded_str ): - """Retrive a list of dictionaries that each contain all of the information needed to install the list of repositories defined by encoded_str.""" + """ + Retrieve and return a dictionary that includes a list of dictionaries that each contain all of the information needed to install the list of + repositories defined by the received encoded_str. + """ encoded_required_repository_str = encoding_util.tool_shed_decode( encoded_str ) encoded_required_repository_tups = encoded_required_repository_str.split( encoding_util.encoding_sep2 ) decoded_required_repository_tups = [] @@ -1430,7 +1433,7 @@ return repo_info_dict @web.expose def get_tool_dependencies( self, trans, **kwd ): - """Handle a request from the InstallManager of a local Galaxy instance.""" + """Handle a request from a Galaxy instance.""" params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) diff -r 530fb4f8204f2106e11f419c381fd53d2319ce24 -r 2ec609faae49b4ab32190403669849f1af0b68f6 lib/galaxy/webapps/community/util/container_util.py --- a/lib/galaxy/webapps/community/util/container_util.py +++ b/lib/galaxy/webapps/community/util/container_util.py @@ -291,7 +291,7 @@ else: tools_root_folder = None return folder_id, tools_root_folder -def build_tool_dependencies_folder( trans, folder_id, tool_dependencies, label='Tool dependencies', missing=False, new_install=False ): +def build_tool_dependencies_folder( trans, folder_id, tool_dependencies, label='Tool dependencies', missing=False, new_install=False, reinstalling=False ): """Return a folder hierarchy containing tool dependencies.""" # The status will be displayed only if the received value for missing is True. When this is the case, we're in Galaxy (not the tool shed) # and the tool dependencies are not installed or are in an error state, so they are considered missing. The tool dependency status will be @@ -304,7 +304,9 @@ folder_id += 1 folder = Folder( id=folder_id, key='tool_dependencies', label=label, parent=tool_dependencies_root_folder ) if trans.webapp.name == 'galaxy': - if missing: + if reinstalling: + folder.description = "this repository's tools require handling of these dependencies" + elif missing and not reinstalling: folder.description = 'click the name to install the missing dependency' else: if new_install: diff -r 530fb4f8204f2106e11f419c381fd53d2319ce24 -r 2ec609faae49b4ab32190403669849f1af0b68f6 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 @@ -1024,6 +1024,8 @@ decoded_kwd = encoding_util.tool_shed_decode( encoded_kwd ) tsr_ids = decoded_kwd[ 'tool_shed_repository_ids' ] tool_panel_section_keys = decoded_kwd[ 'tool_panel_section_keys' ] + repo_info_dicts = decoded_kwd[ 'repo_info_dicts' ] + filtered_repo_info_dicts = [] filtered_tool_panel_section_keys = [] repositories_for_installation = [] for index, tsr_id in enumerate( tsr_ids ): @@ -1031,8 +1033,10 @@ if repository.status in [ trans.model.ToolShedRepository.installation_status.NEW, trans.model.ToolShedRepository.installation_status.UNINSTALLED ]: repositories_for_installation.append( repository ) + filtered_repo_info_dicts.append( repo_info_dicts[ index ] ) filtered_tool_panel_section_keys.append( tool_panel_section_keys[ index ] ) if repositories_for_installation: + decoded_kwd[ 'repo_info_dicts' ] = filtered_repo_info_dicts decoded_kwd[ 'tool_panel_section_keys' ] = filtered_tool_panel_section_keys self.install_tool_shed_repositories( trans, repositories_for_installation, reinstalling=reinstalling, **decoded_kwd ) else: @@ -1152,7 +1156,6 @@ return trans.show_error_message( message ) message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) - includes_tools = util.string_as_bool( kwd.get( 'includes_tools', False ) ) tool_shed_url = kwd[ 'tool_shed_url' ] # Handle repository dependencies. includes_repository_dependencies = util.string_as_bool( kwd.get( 'includes_repository_dependencies', False ) ) @@ -1259,7 +1262,6 @@ shed_tool_conf=shed_tool_conf, status=status, tool_path=tool_path, - tool_panel_section_keys=tool_panel_section_keys, tool_shed_repository_ids=tsrids_list, tool_shed_url=tool_shed_url ) @@ -1300,9 +1302,10 @@ raw_text = response.read() response.close() readme_files_dict = json.from_json_string( raw_text ) - # Handle the scenario where a repository was installed, then uninstalled and an error occurred during the reinstallation process. - # In this case, a record for the repository will exist in the database with the status of 'New'. if repository_dependencies: + missing_tool_dependencies = {} + # Handle the scenario where a repository was installed, then uninstalled and an error occurred during the reinstallation process. + # In this case, a record for the repository will exist in the database with the status of 'New'. repository = suc.get_repository_for_dependency_relationship( trans.app, tool_shed_url, name, repository_owner, changeset_revision ) if repository and repository.metadata: installed_repository_dependencies, missing_repository_dependencies = \ @@ -1310,9 +1313,48 @@ else: installed_repository_dependencies, missing_repository_dependencies = \ shed_util.get_installed_and_missing_repository_dependencies_for_new_install( trans, repository_dependencies ) + # Discover all repository dependencies and retrieve information for installing them. + required_repo_info_dicts = shed_util.get_required_repo_info_dicts( tool_shed_url, util.listify( repo_info_dict ) ) + # Display tool dependencies defined for each of the repository dependencies. + if required_repo_info_dicts: + all_tool_dependencies = {} + for rid in required_repo_info_dicts: + for name, repo_info_tuple in rid.items(): + description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = \ + suc.get_repo_info_tuple_contents( repo_info_tuple ) + if tool_dependencies: + for td_key, td_dict in tool_dependencies.items(): + if td_key not in all_tool_dependencies: + all_tool_dependencies[ td_key ] = td_dict + if all_tool_dependencies: + if tool_dependencies is None: + tool_dependencies = {} + else: + # Move all tool dependencies to the missing_tool_dependencies container. + for td_key, td_dict in tool_dependencies.items(): + if td_key not in missing_tool_dependencies: + missing_tool_dependencies[ td_key ] = td_dict + tool_dependencies = {} + # Discover and categorize all tool dependencies defined this this repository's repository dependencies. + required_tool_dependencies, required_missing_tool_dependencies = \ + shed_util.get_installed_and_missing_tool_dependencies_for_new_install( trans, all_tool_dependencies ) + if required_tool_dependencies: + if not includes_tool_dependencies: + includes_tool_dependencies = True + for td_key, td_dict in required_tool_dependencies.items(): + if td_key not in tool_dependencies: + tool_dependencies[ td_key ] = td_dict + if required_missing_tool_dependencies: + if not includes_tool_dependencies: + includes_tool_dependencies = True + for td_key, td_dict in required_missing_tool_dependencies.items(): + if td_key not in missing_tool_dependencies: + missing_tool_dependencies[ td_key ] = td_dict else: installed_repository_dependencies = None missing_repository_dependencies = None + missing_tool_dependencies = None + required_repo_info_dicts = None # Since we are installing a new repository, no tool dependencies will be considered "missing". Most of the repository contents # are set to None since we don't yet know what they are. containers_dict = suc.build_repository_containers_for_galaxy( trans=trans, @@ -1324,13 +1366,14 @@ datatypes=None, invalid_tools=None, missing_repository_dependencies=missing_repository_dependencies, - missing_tool_dependencies=None, + missing_tool_dependencies=missing_tool_dependencies, readme_files_dict=readme_files_dict, repository_dependencies=installed_repository_dependencies, tool_dependencies=tool_dependencies, valid_tools=None, workflows=None, - new_install=True ) + new_install=True, + reinstalling=False ) # We're handling 1 of 2 scenarios here: (1) we're installing a tool shed repository for the first time, so we're retrieved the list of installed # and missing repository dependencies from the database (2) we're handling the scenario where an error occurred during the installation process, # so we have a tool_shed_repository record in the database with associated repository dependency records. Since we have the repository @@ -1338,6 +1381,7 @@ # each displayed repository dependency will display a status, whether installed or missing. containers_dict = suc.merge_missing_repository_dependencies_to_installed_container( containers_dict ) else: + # FIXME: support the intallation of repository dependencies and tool dependencies for a list of tool shed repositories being installed. containers_dict = dict( datatypes=None, invalid_tools=None, readme_files_dict=None, @@ -1395,6 +1439,8 @@ tool_panel_section_key = None tool_panel_section_keys = [] metadata = tool_shed_repository.metadata + # Keep track of tool dependencies define dfor the current repository or those defined for any of it's repository dependencies. + includes_tool_dependencies = tool_shed_repository.includes_tool_dependencies if tool_shed_repository.includes_tools: # Handle the selected tool panel location for loading tools included in the tool shed repository. tool_section, new_tool_panel_section, tool_panel_section_key = \ @@ -1422,8 +1468,7 @@ if isinstance( repo_info_dict, basestring ): repo_info_dict = encoding_util.tool_shed_decode( repo_info_dict ) else: - # Entering this else block used to happen only if the tool_shed_repository does not include any valid tools. After repository dependencies - # were introduced, it may never happen, but we'll keep the block just in case. + # Entering this else block occurs only if the tool_shed_repository does not include any valid tools. if install_repository_dependencies: repository_dependencies = self.get_repository_dependencies( trans=trans, repository_id=repository_id, @@ -1462,13 +1507,13 @@ filtered_repo_info_dicts = [ repo_info_dict for repo_info_dict in repo_info_dicts ] created_or_updated_tool_shed_repositories = [ tool_shed_repository ] tool_panel_section_keys.append( tool_panel_section_key ) - # Defaulot the selected tool panel location for loading tools included in each newly installed required tool shed repository to the location + # Default the selected tool panel location for loading tools included in each newly installed required tool shed repository to the location # selected for the repository selected for reinstallation. for index, tps_key in enumerate( tool_panel_section_keys ): if tps_key is None: tool_panel_section_keys[ index ] = tool_panel_section_key encoded_repository_ids = [ trans.security.encode_id( r.id ) for r in created_or_updated_tool_shed_repositories ] - new_kwd = dict( includes_tool_dependencies=tool_shed_repository.includes_tool_dependencies, + new_kwd = dict( includes_tool_dependencies=includes_tool_dependencies, includes_tools=tool_shed_repository.includes_tools, install_tool_dependencies=install_tool_dependencies, repo_info_dicts=filtered_repo_info_dicts, @@ -1539,13 +1584,17 @@ repository_metadata=None, metadata=metadata, repository_dependencies=repository_dependencies ) + if includes_repository_dependencies: + # Discover all repository dependencies and retrieve information for installing them. + required_repo_info_dicts = shed_util.get_required_repo_info_dicts( tool_shed_url, util.listify( repo_info_dict ) ) + else: + required_repo_info_dicts = None # Get the location in the tool panel in which the tool was originally loaded. if 'tool_panel_section' in metadata: tool_panel_dict = metadata[ 'tool_panel_section' ] if tool_panel_dict: if shed_util.panel_entry_per_tool( tool_panel_dict ): - # TODO: Fix this to handle the case where the tools are distributed across in more than 1 ToolSection. The - # following assumes everything was loaded into 1 section (or no section) in the tool panel. + # The following forces everything to be loaded into 1 section (or no section) in the tool panel. tool_section_dicts = tool_panel_dict[ tool_panel_dict.keys()[ 0 ] ] tool_section_dict = tool_section_dicts[ 0 ] original_section_name = tool_section_dict[ 'name' ] @@ -1567,7 +1616,14 @@ message += "The tools contained in your <b>%s</b> repository were last loaded into the tool panel outside of any sections. " % tool_shed_repository.name message += "Uncheck the <b>No changes</b> check box and select a tool panel section to load the tools into that section. " status = 'warning' - containers_dict = shed_util.populate_containers_dict_from_repository_metadata( trans, tool_shed_url, tool_path, tool_shed_repository, reinstalling=True ) + # Populate the containers_dict from the metadata for the tool shed repository we're reinstalling, but make sure to include tool dependencies defined for + # all of the repository's repository dependencies. + containers_dict = shed_util.populate_containers_dict_from_repository_metadata( trans=trans, + tool_shed_url=tool_shed_url, + tool_path=tool_path, + repository=tool_shed_repository, + reinstalling=True, + required_repo_info_dicts=required_repo_info_dicts ) # Since we're reinstalling we'll merge the list of missing repository dependencies into the list of installed repository dependencies since each displayed # repository dependency will display a status, whether installed or missing. containers_dict = suc.merge_missing_repository_dependencies_to_installed_container( containers_dict ) diff -r 530fb4f8204f2106e11f419c381fd53d2319ce24 -r 2ec609faae49b4ab32190403669849f1af0b68f6 templates/admin/tool_shed_repository/common.mako --- a/templates/admin/tool_shed_repository/common.mako +++ b/templates/admin/tool_shed_repository/common.mako @@ -91,6 +91,7 @@ repository_dependencies_root_folder = containers_dict[ 'repository_dependencies' ] tool_dependencies_root_folder = containers_dict[ 'tool_dependencies' ] + missing_tool_dependencies_root_folder = containers_dict[ 'missing_tool_dependencies' ] env_settings_heaader_row_displayed = False package_header_row_displayed = False %> @@ -122,7 +123,7 @@ <div style="clear: both"></div></div> %endif - %if tool_dependencies_root_folder: + %if tool_dependencies_root_folder or missing_tool_dependencies_root_folder: %if install_tool_dependencies_check_box is not None: <div class="form-row"><label>Handle tool dependencies?</label> @@ -138,14 +139,26 @@ </div><div style="clear: both"></div> %endif - <div class="form-row"> - <p/> - <% row_counter = RowCounter() %> - <table cellspacing="2" cellpadding="2" border="0" width="100%" class="tables container-table" id="dependency_table"> - ${render_folder( tool_dependencies_root_folder, 0, parent=None, row_counter=row_counter, is_root_folder=True )} - </table> - <div style="clear: both"></div> - </div> + %if tool_dependencies_root_folder: + <div class="form-row"> + <p/> + <% row_counter = RowCounter() %> + <table cellspacing="2" cellpadding="2" border="0" width="100%" class="tables container-table" id="dependency_table"> + ${render_folder( tool_dependencies_root_folder, 0, parent=None, row_counter=row_counter, is_root_folder=True )} + </table> + <div style="clear: both"></div> + </div> + %endif + %if missing_tool_dependencies_root_folder: + <div class="form-row"> + <p/> + <% row_counter = RowCounter() %> + <table cellspacing="2" cellpadding="2" border="0" width="100%" class="tables container-table" id="dependency_table"> + ${render_folder( missing_tool_dependencies_root_folder, 0, parent=None, row_counter=row_counter, is_root_folder=True )} + </table> + <div style="clear: both"></div> + </div> + %endif %endif </%def> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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