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commit/galaxy-central: greg: Only allow a single file named tool_dependencies.xml to be committed to a repository in the tool shed whose type is tool_dependency_definition.
by commits-noreply＠bitbucket.org 15 Jul '13

15 Jul '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1d05c839c1ea/ Changeset: 1d05c839c1ea User: greg Date: 2013-07-15 17:28:41 Summary: Only allow a single file named tool_dependencies.xml to be committed to a repository in the tool shed whose type is tool_dependency_definition. Affected #: 9 files diff -r 320d6f095b810d8c338c5ad5dbc04d6685505c5e -r 1d05c839c1ea7a83112a98734a6887f7ce419567 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 @@ -436,7 +436,7 @@ message = '' tool_shed_repository = tool_dependencies[ 0 ].tool_shed_repository # Get the tool_dependencies.xml file from the repository. - tool_dependencies_config = suc.get_config_from_disk( 'tool_dependencies.xml', tool_shed_repository.repo_path( trans.app ) ) + tool_dependencies_config = suc.get_config_from_disk( suc.TOOL_DEPENDENCY_DEFINITION_FILENAME, tool_shed_repository.repo_path( trans.app ) ) installed_tool_dependencies = common_install_util.handle_tool_dependencies( app=trans.app, tool_shed_repository=tool_shed_repository, tool_dependencies_config=tool_dependencies_config, diff -r 320d6f095b810d8c338c5ad5dbc04d6685505c5e -r 1d05c839c1ea7a83112a98734a6887f7ce419567 lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -1656,7 +1656,7 @@ # to retrieve older versions of the tool-dependencies.xml file from the repository manafest. repo_dir = repository.repo_path( trans.app ) # Get the tool_dependencies.xml file from disk. - tool_dependencies_config = suc.get_config_from_disk( 'tool_dependencies.xml', repo_dir ) + tool_dependencies_config = suc.get_config_from_disk( suc.TOOL_DEPENDENCY_DEFINITION_FILENAME, repo_dir ) # Return the encoded contents of the tool_dependencies.xml file. if tool_dependencies_config: tool_dependencies_config_file = open( tool_dependencies_config, 'rb' ) diff -r 320d6f095b810d8c338c5ad5dbc04d6685505c5e -r 1d05c839c1ea7a83112a98734a6887f7ce419567 lib/galaxy/webapps/tool_shed/controllers/upload.py --- a/lib/galaxy/webapps/tool_shed/controllers/upload.py +++ b/lib/galaxy/webapps/tool_shed/controllers/upload.py @@ -8,6 +8,7 @@ from galaxy import util from galaxy import web from galaxy.datatypes import checkers +import tool_shed.repository_types.util as rt_util import tool_shed.util.shed_util_common as suc from tool_shed.util import commit_util from tool_shed.util import metadata_util @@ -123,50 +124,54 @@ else: if ( isgzip or isbz2 ) and uncompress_file: uploaded_file_filename = commit_util.uncompress( repository, uploaded_file_name, uploaded_file_filename, isgzip, isbz2 ) - if upload_point is not None: - full_path = os.path.abspath( os.path.join( repo_dir, upload_point, uploaded_file_filename ) ) - else: - full_path = os.path.abspath( os.path.join( repo_dir, uploaded_file_filename ) ) - # Move some version of the uploaded file to the load_point within the repository hierarchy. - if uploaded_file_filename in [ 'repository_dependencies.xml' ]: - # Inspect the contents of the file to see if changeset_revision values are missing and if so, set them appropriately. - altered, root_elem = commit_util.handle_repository_dependencies_definition( trans, uploaded_file_name ) - if altered: - tmp_filename = xml_util.create_and_write_tmp_file( root_elem ) - shutil.move( tmp_filename, full_path ) + if repository.type == rt_util.TOOL_DEPENDENCY_DEFINITION and uploaded_file_filename != suc.TOOL_DEPENDENCY_DEFINITION_FILENAME: + ok = False + message = 'Repositories of type <b>Tool dependency definition</b> can only contain a single file named <b>tool_dependencies.xml</b>.' + if ok: + if upload_point is not None: + full_path = os.path.abspath( os.path.join( repo_dir, upload_point, uploaded_file_filename ) ) + else: + full_path = os.path.abspath( os.path.join( repo_dir, uploaded_file_filename ) ) + # Move some version of the uploaded file to the load_point within the repository hierarchy. + if uploaded_file_filename in [ suc.REPOSITORY_DEPENDENCY_DEFINITION_FILENAME ]: + # Inspect the contents of the file to see if changeset_revision values are missing and if so, set them appropriately. + altered, root_elem = commit_util.handle_repository_dependencies_definition( trans, uploaded_file_name ) + if altered: + tmp_filename = xml_util.create_and_write_tmp_file( root_elem ) + shutil.move( tmp_filename, full_path ) + else: + shutil.move( uploaded_file_name, full_path ) + elif uploaded_file_filename in [ suc.TOOL_DEPENDENCY_DEFINITION_FILENAME ]: + # Inspect the contents of the file to see if it defines a complex repository dependency definition whose changeset_revision values + # are missing and if so, set them appropriately. + altered, root_elem = commit_util.handle_tool_dependencies_definition( trans, uploaded_file_name ) + if altered: + tmp_filename = xml_util.create_and_write_tmp_file( root_elem ) + shutil.move( tmp_filename, full_path ) + else: + shutil.move( uploaded_file_name, full_path ) else: shutil.move( uploaded_file_name, full_path ) - elif uploaded_file_filename in [ 'tool_dependencies.xml' ]: - # Inspect the contents of the file to see if it defines a complex repository dependency definition whose changeset_revision values - # are missing and if so, set them appropriately. - altered, root_elem = commit_util.handle_tool_dependencies_definition( trans, uploaded_file_name ) - if altered: - tmp_filename = xml_util.create_and_write_tmp_file( root_elem ) - shutil.move( tmp_filename, full_path ) + # See if any admin users have chosen to receive email alerts when a repository is updated. If so, check every uploaded file to ensure + # content is appropriate. + check_contents = commit_util.check_file_contents_for_email_alerts( trans ) + if check_contents and os.path.isfile( full_path ): + content_alert_str = commit_util.check_file_content_for_html_and_images( full_path ) else: - shutil.move( uploaded_file_name, full_path ) - else: - shutil.move( uploaded_file_name, full_path ) - # See if any admin users have chosen to receive email alerts when a repository is updated. If so, check every uploaded file to ensure - # content is appropriate. - check_contents = commit_util.check_file_contents_for_email_alerts( trans ) - if check_contents and os.path.isfile( full_path ): - content_alert_str = commit_util.check_file_content_for_html_and_images( full_path ) - else: - content_alert_str = '' - commands.add( repo.ui, repo, full_path ) - # Convert from unicode to prevent "TypeError: array item must be char" - full_path = full_path.encode( 'ascii', 'replace' ) - commands.commit( repo.ui, repo, full_path, user=trans.user.username, message=commit_message ) - if full_path.endswith( 'tool_data_table_conf.xml.sample' ): - # Handle the special case where a tool_data_table_conf.xml.sample file is being uploaded by parsing the file and adding new entries - # to the in-memory trans.app.tool_data_tables dictionary. - error, error_message = tool_util.handle_sample_tool_data_table_conf_file( trans.app, full_path ) - if error: - message = '%s<br/>%s' % ( message, error_message ) - # See if the content of the change set was valid. - admin_only = len( repository.downloadable_revisions ) != 1 - suc.handle_email_alerts( trans, repository, content_alert_str=content_alert_str, new_repo_alert=new_repo_alert, admin_only=admin_only ) + content_alert_str = '' + commands.add( repo.ui, repo, full_path ) + # Convert from unicode to prevent "TypeError: array item must be char" + full_path = full_path.encode( 'ascii', 'replace' ) + commands.commit( repo.ui, repo, full_path, user=trans.user.username, message=commit_message ) + if full_path.endswith( 'tool_data_table_conf.xml.sample' ): + # Handle the special case where a tool_data_table_conf.xml.sample file is being uploaded by parsing the file and adding new entries + # to the in-memory trans.app.tool_data_tables dictionary. + error, error_message = tool_util.handle_sample_tool_data_table_conf_file( trans.app, full_path ) + if error: + message = '%s<br/>%s' % ( message, error_message ) + # See if the content of the change set was valid. + admin_only = len( repository.downloadable_revisions ) != 1 + suc.handle_email_alerts( trans, repository, content_alert_str=content_alert_str, new_repo_alert=new_repo_alert, admin_only=admin_only ) if ok: # Update the repository files for browsing. suc.update_repository( repo ) @@ -255,7 +260,10 @@ for root, dirs, files in os.walk( uploaded_directory ): for uploaded_file in files: relative_path = os.path.normpath( os.path.join( os.path.relpath( root, uploaded_directory ), uploaded_file ) ) - ok = os.path.basename( uploaded_file ) not in commit_util.UNDESIRABLE_FILES + if repository.type == rt_util.TOOL_DEPENDENCY_DEFINITION: + ok = os.path.basename( uploaded_file ) == suc.TOOL_DEPENDENCY_DEFINITION_FILENAME + else: + ok = os.path.basename( uploaded_file ) not in commit_util.UNDESIRABLE_FILES if ok: for file_path_item in relative_path.split( '/' ): if file_path_item in commit_util.UNDESIRABLE_DIRS: @@ -264,20 +272,20 @@ break else: undesirable_files_removed += 1 - uploaded_file_name = os.path.abspath( os.path.join( root, uploaded_file ) ) - if os.path.split( uploaded_file_name )[ -1 ] == 'repository_dependencies.xml': - # Inspect the contents of the file to see if changeset_revision values are missing and if so, set them appropriately. - altered, root_elem = commit_util.handle_repository_dependencies_definition( trans, uploaded_file_name ) - if altered: - tmp_filename = xml_util.create_and_write_tmp_file( root_elem ) - shutil.move( tmp_filename, uploaded_file_name ) - elif os.path.split( uploaded_file_name )[ -1 ] == 'tool_dependencies.xml': - # Inspect the contents of the file to see if changeset_revision values are missing and if so, set them appropriately. - altered, root_elem = commit_util.handle_tool_dependencies_definition( trans, uploaded_file_name ) - if altered: - tmp_filename = xml_util.create_and_write_tmp_file( root_elem ) - shutil.move( tmp_filename, uploaded_file_name ) if ok: + uploaded_file_name = os.path.abspath( os.path.join( root, uploaded_file ) ) + if os.path.split( uploaded_file_name )[ -1 ] == suc.REPOSITORY_DEPENDENCY_DEFINITION_FILENAME: + # Inspect the contents of the file to see if changeset_revision values are missing and if so, set them appropriately. + altered, root_elem = commit_util.handle_repository_dependencies_definition( trans, uploaded_file_name ) + if altered: + tmp_filename = xml_util.create_and_write_tmp_file( root_elem ) + shutil.move( tmp_filename, uploaded_file_name ) + elif os.path.split( uploaded_file_name )[ -1 ] == suc.TOOL_DEPENDENCY_DEFINITION_FILENAME: + # Inspect the contents of the file to see if changeset_revision values are missing and if so, set them appropriately. + altered, root_elem = commit_util.handle_tool_dependencies_definition( trans, uploaded_file_name ) + if altered: + tmp_filename = xml_util.create_and_write_tmp_file( root_elem ) + shutil.move( tmp_filename, uploaded_file_name ) repo_path = os.path.join( full_path, relative_path ) repo_basedir = os.path.normpath( os.path.join( repo_path, os.path.pardir ) ) if not os.path.exists( repo_basedir ): @@ -298,7 +306,7 @@ repo = hg.repository( suc.get_configured_ui(), repo_dir ) undesirable_dirs_removed = 0 undesirable_files_removed = 0 - ok, message = commit_util.check_archive( tar ) + ok, message = commit_util.check_archive( repository, tar ) if not ok: tar.close() uploaded_file.close() @@ -327,13 +335,13 @@ uploaded_file.close() for filename in filenames_in_archive: uploaded_file_name = os.path.join( full_path, filename ) - if os.path.split( uploaded_file_name )[ -1 ] == 'repository_dependencies.xml': + if os.path.split( uploaded_file_name )[ -1 ] == suc.REPOSITORY_DEPENDENCY_DEFINITION_FILENAME: # Inspect the contents of the file to see if changeset_revision values are missing and if so, set them appropriately. altered, root_elem = commit_util.handle_repository_dependencies_definition( trans, uploaded_file_name ) if altered: tmp_filename = xml_util.create_and_write_tmp_file( root_elem ) shutil.move( tmp_filename, uploaded_file_name ) - elif os.path.split( uploaded_file_name )[ -1 ] == 'tool_dependencies.xml': + elif os.path.split( uploaded_file_name )[ -1 ] == suc.TOOL_DEPENDENCY_DEFINITION_FILENAME: # Inspect the contents of the file to see if changeset_revision values are missing and if so, set them appropriately. altered, root_elem = commit_util.handle_tool_dependencies_definition( trans, uploaded_file_name ) if altered: diff -r 320d6f095b810d8c338c5ad5dbc04d6685505c5e -r 1d05c839c1ea7a83112a98734a6887f7ce419567 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 @@ -269,7 +269,7 @@ self.app.sa_session.add( tool_shed_repository ) self.app.sa_session.flush() work_dir = tempfile.mkdtemp( prefix="tmp-toolshed-hrc" ) - datatypes_config = suc.get_config_from_disk( 'datatypes_conf.xml', repo_install_dir ) + datatypes_config = suc.get_config_from_disk( suc.DATATYPES_CONFIG_FILENAME, repo_install_dir ) # Load proprietary data types required by tools. The value of override is not important here since the Galaxy server will be started # after this installation completes. converter_path, display_path = datatype_util.alter_config_and_load_prorietary_datatypes( self.app, datatypes_config, repo_install_dir, override=False ) #repo_install_dir was relative_install_dir diff -r 320d6f095b810d8c338c5ad5dbc04d6685505c5e -r 1d05c839c1ea7a83112a98734a6887f7ce419567 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 @@ -448,7 +448,7 @@ files_dir = relative_install_dir if shed_config_dict.get( 'tool_path' ): files_dir = os.path.join( shed_config_dict[ 'tool_path' ], files_dir ) - datatypes_config = suc.get_config_from_disk( 'datatypes_conf.xml', files_dir ) + datatypes_config = suc.get_config_from_disk( suc.DATATYPES_CONFIG_FILENAME, files_dir ) # Load data types required by tools. converter_path, display_path = datatype_util.alter_config_and_load_prorietary_datatypes( trans.app, datatypes_config, files_dir, override=False ) if converter_path or display_path: diff -r 320d6f095b810d8c338c5ad5dbc04d6685505c5e -r 1d05c839c1ea7a83112a98734a6887f7ce419567 lib/tool_shed/util/commit_util.py --- a/lib/tool_shed/util/commit_util.py +++ b/lib/tool_shed/util/commit_util.py @@ -11,6 +11,7 @@ from tool_shed.util import tool_util from tool_shed.util import xml_util from galaxy import eggs +import tool_shed.repository_types.util as rt_util eggs.require( 'mercurial' ) from mercurial import commands @@ -22,7 +23,7 @@ UNDESIRABLE_DIRS = [ '.hg', '.svn', '.git', '.cvs' ] UNDESIRABLE_FILES = [ '.hg_archival.txt', 'hgrc', '.DS_Store' ] -def check_archive( archive ): +def check_archive( repository, archive ): for member in archive.getmembers(): # Allow regular files and directories only if not ( member.isdir() or member.isfile() or member.islnk() ): @@ -35,6 +36,9 @@ if member.name in [ 'hgrc' ]: message = "Uploaded archives cannot contain hgrc files." return False, message + if repository.type == rt_util.TOOL_DEPENDENCY_DEFINITION and member.name != suc.TOOL_DEPENDENCY_DEFINITION_FILENAME: + message = 'Repositories of type <b>Tool dependency definition</b> can contain only a single file named <b>tool_dependencies.xml</b>.' + return False, message return True, '' def check_file_contents_for_email_alerts( trans ): diff -r 320d6f095b810d8c338c5ad5dbc04d6685505c5e -r 1d05c839c1ea7a83112a98734a6887f7ce419567 lib/tool_shed/util/datatype_util.py --- a/lib/tool_shed/util/datatype_util.py +++ b/lib/tool_shed/util/datatype_util.py @@ -166,7 +166,7 @@ # Load proprietary datatypes and return information needed for loading proprietary datatypes converters and display applications later. metadata = repository.metadata repository_dict = None - datatypes_config = suc.get_config_from_disk( 'datatypes_conf.xml', relative_install_dir ) + datatypes_config = suc.get_config_from_disk( suc.DATATYPES_CONFIG_FILENAME, relative_install_dir ) if datatypes_config: converter_path, display_path = alter_config_and_load_prorietary_datatypes( app, datatypes_config, relative_install_dir, deactivate=deactivate ) if converter_path or display_path: diff -r 320d6f095b810d8c338c5ad5dbc04d6685505c5e -r 1d05c839c1ea7a83112a98734a6887f7ce419567 lib/tool_shed/util/metadata_util.py --- a/lib/tool_shed/util/metadata_util.py +++ b/lib/tool_shed/util/metadata_util.py @@ -36,8 +36,10 @@ SUBSET = 'subset' SUBSET_VALUES = [ EQUAL, SUBSET ] -REPOSITORY_DATA_MANAGER_CONFIG_FILENAME = 'data_manager_conf.xml' -NOT_TOOL_CONFIGS = [ 'datatypes_conf.xml', 'repository_dependencies.xml', 'tool_dependencies.xml', REPOSITORY_DATA_MANAGER_CONFIG_FILENAME ] +NOT_TOOL_CONFIGS = [ suc.DATATYPES_CONFIG_FILENAME, + suc.REPOSITORY_DEPENDENCY_DEFINITION_FILENAME, + suc.TOOL_DEPENDENCY_DEFINITION_FILENAME, + suc.REPOSITORY_DATA_MANAGER_CONFIG_FILENAME ] def add_tool_versions( trans, id, repository_metadata, changeset_revisions ): # Build a dictionary of { 'tool id' : 'parent tool id' } pairs for each tool in repository_metadata. @@ -604,7 +606,7 @@ app.config.tool_data_path = work_dir #FIXME: Thread safe? app.config.tool_data_table_config_path = work_dir # Handle proprietary datatypes, if any. - datatypes_config = suc.get_config_from_disk( 'datatypes_conf.xml', files_dir ) + datatypes_config = suc.get_config_from_disk( suc.DATATYPES_CONFIG_FILENAME, files_dir ) if datatypes_config: metadata_dict = generate_datatypes_metadata( app, repository, repository_clone_url, files_dir, datatypes_config, metadata_dict ) # Get the relative path to all sample files included in the repository for storage in the repository's metadata. @@ -632,7 +634,7 @@ dirs.remove( '.hg' ) for name in files: # See if we have a repository dependencies defined. - if name == 'repository_dependencies.xml': + if name == suc.REPOSITORY_DEPENDENCY_DEFINITION_FILENAME: path_to_repository_dependencies_config = os.path.join( root, name ) metadata_dict, error_message = generate_repository_dependency_metadata( app, path_to_repository_dependencies_config, metadata_dict ) if error_message: @@ -700,7 +702,7 @@ metadata_dict = generate_data_manager_metadata( app, repository, files_dir, - suc.get_config_from_disk( REPOSITORY_DATA_MANAGER_CONFIG_FILENAME, files_dir ), + suc.get_config_from_disk( suc.REPOSITORY_DATA_MANAGER_CONFIG_FILENAME, files_dir ), metadata_dict, shed_config_dict=shed_config_dict ) diff -r 320d6f095b810d8c338c5ad5dbc04d6685505c5e -r 1d05c839c1ea7a83112a98734a6887f7ce419567 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 @@ -35,6 +35,11 @@ MAX_DISPLAY_SIZE = 32768 VALID_CHARS = set( string.letters + string.digits + "'\"-=_.()/+*^,:?!#[]%\\$@;{}&<>" ) +DATATYPES_CONFIG_FILENAME = 'datatypes_conf.xml' +REPOSITORY_DATA_MANAGER_CONFIG_FILENAME = 'data_manager_conf.xml' +REPOSITORY_DEPENDENCY_DEFINITION_FILENAME = 'repository_dependencies.xml' +TOOL_DEPENDENCY_DEFINITION_FILENAME = 'tool_dependencies.xml' + new_repo_email_alert_template = """ Sharable link: ${sharable_link} Repository name: ${repository_name} Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: greg: Display the new request type in appropriate tool shed girds.
by commits-noreply＠bitbucket.org 15 Jul '13

15 Jul '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/320d6f095b81/ Changeset: 320d6f095b81 User: greg Date: 2013-07-15 16:10:12 Summary: Display the new request type in appropriate tool shed girds. Affected #: 2 files diff -r ea94ef1419d04dc442644edc0090f9d165fad2fd -r 320d6f095b810d8c338c5ad5dbc04d6685505c5e lib/tool_shed/grids/repository_grids.py --- a/lib/tool_shed/grids/repository_grids.py +++ b/lib/tool_shed/grids/repository_grids.py @@ -82,6 +82,13 @@ return escape_html( repository.name ) + class TypeColumn( grids.TextColumn ): + + def get_value( self, trans, grid, repository ): + type_class = repository.get_type_class( trans.app ) + return escape_html( type_class.label ) + + class MetadataRevisionColumn( grids.GridColumn ): def __init__( self, col_name ): @@ -210,8 +217,9 @@ DescriptionColumn( "Synopsis", key="description", attach_popup=False ), - MetadataRevisionColumn( "Metadata Revisions" ), - ToolsFunctionallyCorrectColumn( "Tools Verified" ), + TypeColumn( "Type" ), + MetadataRevisionColumn( "Metadata<br/>Revisions" ), + ToolsFunctionallyCorrectColumn( "Tools<br/>Verified" ), UserColumn( "Owner", model_class=model.User, link=( lambda item: dict( operation="repositories_by_user", id=item.id ) ), @@ -365,8 +373,9 @@ key="name", link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), attach_popup=False ), - RepositoryGrid.MetadataRevisionColumn( "Metadata Revisions" ), - RepositoryGrid.ToolsFunctionallyCorrectColumn( "Tools Verified" ), + RepositoryGrid.TypeColumn( "Type" ), + RepositoryGrid.MetadataRevisionColumn( "Metadata<br/>Revisions" ), + RepositoryGrid.ToolsFunctionallyCorrectColumn( "Tools<br/>Verified" ), RepositoryGrid.UserColumn( "Owner", model_class=model.User, link=( lambda item: dict( operation="repositories_by_user", id=item.id ) ), @@ -412,8 +421,9 @@ RepositoryGrid.DescriptionColumn( "Synopsis", key="description", attach_popup=False ), - RepositoryGrid.MetadataRevisionColumn( "Metadata Revisions" ), - RepositoryGrid.ToolsFunctionallyCorrectColumn( "Tools Verified" ), + RepositoryGrid.TypeColumn( "Type" ), + RepositoryGrid.MetadataRevisionColumn( "Metadata<br/>Revisions" ), + RepositoryGrid.ToolsFunctionallyCorrectColumn( "Tools<br/>Verified" ), RepositoryGrid.CategoryColumn( "Category", model_class=model.Category, key="Category.name", @@ -448,8 +458,9 @@ RepositoryGrid.DescriptionColumn( "Synopsis", key="description", attach_popup=False ), - RepositoryGrid.MetadataRevisionColumn( "Metadata Revisions" ), - RepositoryGrid.ToolsFunctionallyCorrectColumn( "Tools Verified" ), + RepositoryGrid.TypeColumn( "Type" ), + RepositoryGrid.MetadataRevisionColumn( "Metadata<br/>Revisions" ), + RepositoryGrid.ToolsFunctionallyCorrectColumn( "Tools<br/>Verified" ), RepositoryGrid.UserColumn( "Owner", model_class=model.User, link=( lambda item: dict( controller="repository", operation="repositories_by_user", id=item.id ) ), @@ -496,8 +507,9 @@ key="name", link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), attach_popup=False ), - RepositoryGrid.MetadataRevisionColumn( "Metadata Revisions" ), - RepositoryGrid.ToolsFunctionallyCorrectColumn( "Tools Verified" ), + RepositoryGrid.TypeColumn( "Type" ), + RepositoryGrid.MetadataRevisionColumn( "Metadata<br/>Revisions" ), + RepositoryGrid.ToolsFunctionallyCorrectColumn( "Tools<br/>Verified" ), RepositoryGrid.DeprecatedColumn( "Deprecated" ) ] columns.append( grids.MulticolFilterColumn( "Search repository name", @@ -785,8 +797,9 @@ key="name", link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), attach_popup=False ), - RepositoriesIOwnGrid.MetadataRevisionColumn( "Metadata Revisions" ), - RepositoryGrid.ToolsFunctionallyCorrectColumn( "Tools Verified" ), + RepositoryGrid.TypeColumn( "Type" ), + RepositoriesIOwnGrid.MetadataRevisionColumn( "Metadata<br/>Revisions" ), + RepositoryGrid.ToolsFunctionallyCorrectColumn( "Tools<br/>Verified" ), RepositoriesIOwnGrid.CategoryColumn( "Category", model_class=model.Category, key="Category.name", @@ -1100,6 +1113,14 @@ return escape_html( repository.name ) + class RepositoryTypeColumn( grids.TextColumn ): + + def get_value( self, trans, grid, repository_metadata ): + repository = repository_metadata.repository + type_class = repository.get_type_class( trans.app ) + return escape_html( type_class.label ) + + class RepositoryOwnerColumn( grids.TextColumn ): def get_value( self, trans, grid, repository_metadata ): @@ -1201,6 +1222,7 @@ key="Repository.name", link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), attach_popup=False ), + RepositoryNameColumn( "Type" ), RepositoryOwnerColumn( "Owner", model_class=model.User, attach_popup=False, @@ -1598,8 +1620,9 @@ RepositoryGrid.DescriptionColumn( "Synopsis", key="description", attach_popup=False ), + RepositoryGrid.TypeColumn( "Type" ), InstallableRevisionColumn( "Installable Revisions" ), - RepositoryGrid.ToolsFunctionallyCorrectColumn( "Tools Verified" ), + RepositoryGrid.ToolsFunctionallyCorrectColumn( "Tools<br/>Verified" ), RepositoryGrid.UserColumn( "Owner", model_class=model.User, attach_popup=False ), diff -r ea94ef1419d04dc442644edc0090f9d165fad2fd -r 320d6f095b810d8c338c5ad5dbc04d6685505c5e test/tool_shed/functional/test_0000_basic_repository_features.py --- a/test/tool_shed/functional/test_0000_basic_repository_features.py +++ b/test/tool_shed/functional/test_0000_basic_repository_features.py @@ -353,5 +353,5 @@ # Check for the changeset revision, repository name, owner username, 'repos' in the clone url, and the captured # unicode decoding error message. strings_displayed = [ 'Changeset %d:%s' % ( revision_number, revision_hash ), 'filtering_0000', 'user1', 'repos', 'added:', - '+These characters should not' ] + '+These characters should not' ] self.load_changeset_in_tool_shed( repository_id, changeset_revision, strings_displayed=strings_displayed ) \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Change tool shed repository type "generic" to be "unrestricted".
by commits-noreply＠bitbucket.org 15 Jul '13

15 Jul '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ea94ef1419d0/ Changeset: ea94ef1419d0 User: greg Date: 2013-07-15 15:40:43 Summary: Change tool shed repository type "generic" to be "unrestricted". Affected #: 10 files diff -r d3832bec213c031ea12eaf3d2292a5363e9e88b9 -r ea94ef1419d04dc442644edc0090f9d165fad2fd lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -964,7 +964,7 @@ long_description = kwd.get( 'long_description', '' ) category_ids = util.listify( kwd.get( 'category_id', '' ) ) selected_categories = [ trans.security.decode_id( id ) for id in category_ids ] - repository_type = kwd.get( 'repository_type', rt_util.GENERIC ) + repository_type = kwd.get( 'repository_type', rt_util.UNRESTRICTED ) if kwd.get( 'create_repository_button', False ): error = False message = self.__validate_repository_name( name, trans.user ) diff -r d3832bec213c031ea12eaf3d2292a5363e9e88b9 -r ea94ef1419d04dc442644edc0090f9d165fad2fd lib/galaxy/webapps/tool_shed/model/migrate/versions/0020_add_repository_type_column.py --- a/lib/galaxy/webapps/tool_shed/model/migrate/versions/0020_add_repository_type_column.py +++ b/lib/galaxy/webapps/tool_shed/model/migrate/versions/0020_add_repository_type_column.py @@ -31,8 +31,8 @@ assert c is Repository_table.c.type except Exception, e: print "Adding type column to the repository table failed: %s" % str( e ) - # Update the type column to have the default generic value. - cmd = "UPDATE repository SET type = 'generic'" + # Update the type column to have the default unrestricted value. + cmd = "UPDATE repository SET type = 'unrestricted'" migrate_engine.execute( cmd ) def downgrade( migrate_engine ): diff -r d3832bec213c031ea12eaf3d2292a5363e9e88b9 -r ea94ef1419d04dc442644edc0090f9d165fad2fd lib/galaxy/webapps/tool_shed/model/migrate/versions/0021_change_repository_type_value.py --- /dev/null +++ b/lib/galaxy/webapps/tool_shed/model/migrate/versions/0021_change_repository_type_value.py @@ -0,0 +1,35 @@ +"""Migration script to change repository.type column value from generic to unrestricted.""" + +from sqlalchemy import * +from sqlalchemy.orm import * +from migrate import * +from migrate.changeset import * + +# Need our custom types, but don't import anything else from model +from galaxy.model.custom_types import * + +import sys, logging +log = logging.getLogger( __name__ ) +log.setLevel(logging.DEBUG) +handler = logging.StreamHandler( sys.stdout ) +format = "%(name)s %(levelname)s %(asctime)s %(message)s" +formatter = logging.Formatter( format ) +handler.setFormatter( formatter ) +log.addHandler( handler ) + +metadata = MetaData() + +def upgrade( migrate_engine ): + print __doc__ + metadata.bind = migrate_engine + metadata.reflect() + # Update the type column to have the default unrestricted value. + cmd = "UPDATE repository SET type = 'unrestricted' WHERE type = 'generic'" + migrate_engine.execute( cmd ) + +def downgrade( migrate_engine ): + metadata.bind = migrate_engine + metadata.reflect() + # Update the type column to have the default generic value. + cmd = "UPDATE repository SET type = 'generic' WHERE type = 'unrestricted'" + migrate_engine.execute( cmd ) diff -r d3832bec213c031ea12eaf3d2292a5363e9e88b9 -r ea94ef1419d04dc442644edc0090f9d165fad2fd lib/tool_shed/repository_types/generic.py --- a/lib/tool_shed/repository_types/generic.py +++ /dev/null @@ -1,20 +0,0 @@ -import logging -import tool_shed.repository_types.util as rt_util -from tool_shed.repository_types.metadata import Metadata - -log = logging.getLogger( __name__ ) - - -class Generic( Metadata ): - - def __init__( self ): - self.type = rt_util.GENERIC - self.label = 'Generic' - - def is_valid_for_type( self, app, repository, revisions_to_check=None ): - """A repository's type can only be changed to the generic type if it is new or has never been installed.""" - if repository.is_new( app ): - return True - if repository.times_downloaded == 0: - return True - return False diff -r d3832bec213c031ea12eaf3d2292a5363e9e88b9 -r ea94ef1419d04dc442644edc0090f9d165fad2fd lib/tool_shed/repository_types/registry.py --- a/lib/tool_shed/repository_types/registry.py +++ b/lib/tool_shed/repository_types/registry.py @@ -1,5 +1,5 @@ import logging -import generic +import unrestricted import tool_dependency_definition from galaxy.util.odict import odict @@ -10,7 +10,7 @@ def __init__( self ): self.repository_types_by_label = odict() - self.repository_types_by_label[ 'generic' ] = generic.Generic() + self.repository_types_by_label[ 'unrestricted' ] = unrestricted.Unrestricted() self.repository_types_by_label[ 'tool_dependency_definition' ] = tool_dependency_definition.ToolDependencyDefinition() def get_class_by_label( self, label ): diff -r d3832bec213c031ea12eaf3d2292a5363e9e88b9 -r ea94ef1419d04dc442644edc0090f9d165fad2fd lib/tool_shed/repository_types/unrestricted.py --- /dev/null +++ b/lib/tool_shed/repository_types/unrestricted.py @@ -0,0 +1,20 @@ +import logging +import tool_shed.repository_types.util as rt_util +from tool_shed.repository_types.metadata import Metadata + +log = logging.getLogger( __name__ ) + + +class Unrestricted( Metadata ): + + def __init__( self ): + self.type = rt_util.UNRESTRICTED + self.label = 'Unrestricted' + + def is_valid_for_type( self, app, repository, revisions_to_check=None ): + """A repository's type can only be changed to the unrestricted type if it is new or has never been installed.""" + if repository.is_new( app ): + return True + if repository.times_downloaded == 0: + return True + return False diff -r d3832bec213c031ea12eaf3d2292a5363e9e88b9 -r ea94ef1419d04dc442644edc0090f9d165fad2fd lib/tool_shed/repository_types/util.py --- a/lib/tool_shed/repository_types/util.py +++ b/lib/tool_shed/repository_types/util.py @@ -3,10 +3,10 @@ log = logging.getLogger( __name__ ) -GENERIC = 'generic' +UNRESTRICTED = 'unrestricted' TOOL_DEPENDENCY_DEFINITION = 'tool_dependency_definition' -types = [ GENERIC, TOOL_DEPENDENCY_DEFINITION ] +types = [ UNRESTRICTED, TOOL_DEPENDENCY_DEFINITION ] def build_repository_type_select_field( trans, repository=None, name='repository_type' ): """Called from the Tool Shed to generate the current list of supported repository types.""" diff -r d3832bec213c031ea12eaf3d2292a5363e9e88b9 -r ea94ef1419d04dc442644edc0090f9d165fad2fd lib/tool_shed/util/metadata_util.py --- a/lib/tool_shed/util/metadata_util.py +++ b/lib/tool_shed/util/metadata_util.py @@ -1237,7 +1237,7 @@ if 'datatypes' in metadata: ancestor_datatypes = metadata[ 'datatypes' ] # The saved metadata must be a subset of the new metadata. - datatype_comparison = compare_datatypes( ancestor_datatypes, current_datatypes ) + datatype_comparison = compare_datatypes( trans, ancestor_datatypes, current_datatypes ) if datatype_comparison == NOT_EQUAL_AND_NOT_SUBSET: return True else: diff -r d3832bec213c031ea12eaf3d2292a5363e9e88b9 -r ea94ef1419d04dc442644edc0090f9d165fad2fd templates/webapps/tool_shed/repository/common.mako --- a/templates/webapps/tool_shed/repository/common.mako +++ b/templates/webapps/tool_shed/repository/common.mako @@ -189,8 +189,8 @@ <div class="toolParamHelp" style="clear: both;"> Select the repository type based on the following criteria. <ul> - %if util.GENERIC in repository_types: - <li><b>Generic</b> - contents can be any set of valid Galaxy utilities + %if util.UNRESTRICTED in repository_types: + <li><b>Unrestricted</b> - contents can be any set of valid Galaxy utilities or files %endif %if util.TOOL_DEPENDENCY_DEFINITION in repository_types: <li><b>Tool dependency definition</b> - contents will always be restricted to one file named tool_dependencies.xml diff -r d3832bec213c031ea12eaf3d2292a5363e9e88b9 -r ea94ef1419d04dc442644edc0090f9d165fad2fd test/tool_shed/functional/test_0000_basic_repository_features.py --- a/test/tool_shed/functional/test_0000_basic_repository_features.py +++ b/test/tool_shed/functional/test_0000_basic_repository_features.py @@ -151,7 +151,7 @@ commit_message="Uploaded filtering.txt", strings_displayed=[], strings_not_displayed=[] ) - self.display_manage_repository_page( repository, strings_displayed=[ 'Readme file for filtering 1.1.0' ] ) + self.display_manage_repository_page( repository, strings_displayed=[ 'Readme file for filtering 1.1.0' ] ) def test_0055_upload_filtering_test_data( self ): '''Upload filtering test data.''' @@ -219,19 +219,19 @@ commit_message="Uploaded readme.txt", strings_displayed=[], strings_not_displayed=[] ) - self.display_manage_repository_page( repository, strings_displayed=[ 'This is a readme file.' ] ) + self.display_manage_repository_page( repository, strings_displayed=[ 'This is a readme file.' ] ) # Verify that there is a different readme file for each metadata revision. metadata_revisions = self.get_repository_metadata_revisions( repository ) self.display_manage_repository_page( repository, - strings_displayed=[ 'Readme file for filtering 1.1.0', - 'This is a readme file.' ] ) + strings_displayed=[ 'Readme file for filtering 1.1.0', + 'This is a readme file.' ] ) def test_0075_delete_readme_txt_file( self ): '''Delete the readme.txt file.''' repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) self.delete_files_from_repository( repository, filenames=[ 'readme.txt' ] ) self.check_count_of_metadata_revisions_associated_with_repository( repository, metadata_count=2 ) - self.display_manage_repository_page( repository, strings_displayed=[ 'Readme file for filtering 1.1.0' ] ) + self.display_manage_repository_page( repository, strings_displayed=[ 'Readme file for filtering 1.1.0' ] ) def test_0080_search_for_valid_filter_tool( self ): '''Search for the filtering tool by tool ID, name, and version.''' @@ -335,7 +335,7 @@ commit_message="Uploaded new readme.txt with invalid ascii characters.", strings_displayed=[], strings_not_displayed=[] ) - self.display_manage_repository_page( repository, strings_displayed=[ 'These characters should not' ] ) + self.display_manage_repository_page( repository, strings_displayed=[ 'These characters should not' ] ) def test_0130_verify_handling_of_invalid_characters( self ): '''Load the above changeset in the change log and confirm that there is no server error displayed.''' @@ -353,5 +353,5 @@ # Check for the changeset revision, repository name, owner username, 'repos' in the clone url, and the captured # unicode decoding error message. strings_displayed = [ 'Changeset %d:%s' % ( revision_number, revision_hash ), 'filtering_0000', 'user1', 'repos', 'added:', - '+These characters should not' ] + '+These characters should not' ] self.load_changeset_in_tool_shed( repository_id, changeset_revision, strings_displayed=strings_displayed ) \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Eliminate check for more than 1 file in a changeset when determining if a repository can be of type tool_dependency_definition since mercurial will sometimes have the same file name twice in the changeset depending upon the operation being performed. Also enhance the error message process when loading invalid tools in the tool shed to not display the same error more than once for a specific tool.
by commits-noreply＠bitbucket.org 13 Jul '13

13 Jul '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d3832bec213c/ Changeset: d3832bec213c User: greg Date: 2013-07-13 14:56:33 Summary: Eliminate check for more than 1 file in a changeset when determining if a repository can be of type tool_dependency_definition since mercurial will sometimes have the same file name twice in the changeset depending upon the operation being performed. Also enhance the error message process when loading invalid tools in the tool shed to not display the same error more than once for a specific tool. Affected #: 2 files diff -r a0ea8ac5583cd295266eac38a12da4d9fd7613ac -r d3832bec213c031ea12eaf3d2292a5363e9e88b9 lib/tool_shed/repository_types/tool_dependency_definition.py --- a/lib/tool_shed/repository_types/tool_dependency_definition.py +++ b/lib/tool_shed/repository_types/tool_dependency_definition.py @@ -33,8 +33,6 @@ ctx = repo.changectx( changeset ) # Inspect all files in the changeset (in sorted order) to make sure there is only one and it is named tool_dependencies.xml. files_changed_in_changeset = ctx.files() - if len( files_changed_in_changeset ) > 1: - return False for file_path in files_changed_in_changeset: file_name = suc.strip_path( file_path ) if file_name not in self.valid_file_names: diff -r a0ea8ac5583cd295266eac38a12da4d9fd7613ac -r d3832bec213c031ea12eaf3d2292a5363e9e88b9 lib/tool_shed/util/tool_util.py --- a/lib/tool_shed/util/tool_util.py +++ b/lib/tool_shed/util/tool_util.py @@ -157,7 +157,9 @@ else: correction_msg = "This file requires an entry in the tool_data_table_conf.xml file. Upload a file named tool_data_table_conf.xml.sample " correction_msg += "to the repository that includes the required entry to correct this error.<br/>" - invalid_files_and_errors_tups.append( ( tool_config_name, correction_msg ) ) + invalid_tup = ( tool_config_name, correction_msg ) + if invalid_tup not in invalid_files_and_errors_tups: + invalid_files_and_errors_tups.append( invalid_tup ) if options.index_file or options.missing_index_file: # Make sure the repository contains the required xxx.loc.sample file. index_file = options.index_file or options.missing_index_file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Fix inadvertently committed Galaxy upload tool config setting ajax upload to false.
by commits-noreply＠bitbucket.org 12 Jul '13

12 Jul '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a0ea8ac5583c/ Changeset: a0ea8ac5583c User: greg Date: 2013-07-12 17:13:27 Summary: Fix inadvertently committed Galaxy upload tool config setting ajax upload to false. Affected #: 1 file diff -r af1c29ddf98ac92fc92393af150be73409f63f0b -r a0ea8ac5583cd295266eac38a12da4d9fd7613ac tools/data_source/upload.xml --- a/tools/data_source/upload.xml +++ b/tools/data_source/upload.xml @@ -33,7 +33,7 @@ </param><param name="async_datasets" type="hidden" value="None"/><upload_dataset name="files" title="Specify Files for Dataset" file_type_name="file_type" metadata_ref="files_metadata"> - <param name="file_data" type="file" size="30" label="File" ajax-upload="false" help="TIP: Due to browser limitations, uploading files larger than 2GB is guaranteed to fail. To upload large files, use the URL method (below) or FTP (if enabled by the site administrator)."> + <param name="file_data" type="file" size="30" label="File" ajax-upload="true" help="TIP: Due to browser limitations, uploading files larger than 2GB is guaranteed to fail. To upload large files, use the URL method (below) or FTP (if enabled by the site administrator)."><validator type="expression" message="You will need to reselect the file you specified (%s)." substitute_value_in_message="True">not ( ( isinstance( value, unicode ) or isinstance( value, str ) ) and value != "" )</validator></param><param name="url_paste" type="text" area="true" size="5x35" label="URL/Text" help="Here you may specify a list of URLs (one per line) or paste the contents of a file."/> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Fix for determining if the only difference between rd_tup and a dependency definition in the list of repository_dependencies is the changeset_revision value.
by commits-noreply＠bitbucket.org 12 Jul '13

12 Jul '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/af1c29ddf98a/ Changeset: af1c29ddf98a User: greg Date: 2013-07-12 16:15:50 Summary: Fix for determining if the only difference between rd_tup and a dependency definition in the list of repository_dependencies is the changeset_revision value. Affected #: 1 file diff -r a7edac403b6c7befb1721f06c99dd1ced30b45c3 -r af1c29ddf98ac92fc92393af150be73409f63f0b lib/tool_shed/util/metadata_util.py --- a/lib/tool_shed/util/metadata_util.py +++ b/lib/tool_shed/util/metadata_util.py @@ -214,7 +214,7 @@ if not found_in_current: # In some cases, the only difference between a dependency definition in the lists is the changeset_revision value. We'll # check to see if this is the case, and if the defined dependency is a repository that has metadata set only on it's tip. - if not different_revision_defines_tip_only_repository_dependency( ancestor_tup, current_repository_dependencies ): + if not different_revision_defines_tip_only_repository_dependency( trans, ancestor_tup, current_repository_dependencies ): return NOT_EQUAL_AND_NOT_SUBSET return SUBSET if len( ancestor_repository_dependencies ) == len( current_repository_dependencies ): @@ -346,7 +346,7 @@ break return repository_metadata -def different_revision_defines_tip_only_repository_dependency( rd_tup, repository_dependencies ): +def different_revision_defines_tip_only_repository_dependency( trans, rd_tup, repository_dependencies ): """ Determine if the only difference between rd_tup and a dependency definition in the list of repository_dependencies is the changeset_revision value. """ @@ -1331,7 +1331,7 @@ if saved_repository_dependency not in new_repository_dependencies: # In some cases, the only difference between a dependency definition in the lists is the changeset_revision value. We'll # check to see if this is the case, and if the defined dependency is a repository that has metadata set only on it's tip. - if not different_revision_defines_tip_only_repository_dependency( saved_repository_dependency, new_repository_dependencies ): + if not different_revision_defines_tip_only_repository_dependency( trans, saved_repository_dependency, new_repository_dependencies ): return True return False else: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Contribution from Bjorn Gruning that renders readme files as restructured text. in the tool shed.
by commits-noreply＠bitbucket.org 12 Jul '13

12 Jul '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a7edac403b6c/ Changeset: a7edac403b6c User: greg Date: 2013-07-12 04:33:17 Summary: Contribution from Bjorn Gruning that renders readme files as restructured text. in the tool shed. Affected #: 1 file diff -r 01850fa1b8aa2706c5b6cf67d8d7099b2093aa36 -r a7edac403b6c7befb1721f06c99dd1ced30b45c3 templates/webapps/tool_shed/repository/common.mako --- a/templates/webapps/tool_shed/repository/common.mako +++ b/templates/webapps/tool_shed/repository/common.mako @@ -600,7 +600,7 @@ <%def name="render_readme( readme, pad, parent, row_counter )"><% - from tool_shed.util.shed_util_common import to_safe_string + from galaxy.util import rst_to_html encoded_id = trans.security.encode_id( readme.id ) %><style type="text/css"> @@ -620,7 +620,7 @@ id="libraryItem-${encoded_id}"><td style="padding-left: ${pad+20}px;"><table id="readme_table"> - <tr><td>${ to_safe_string( readme.text, to_html=True ) }</td></tr> + <tr><td>${ rst_to_html( readme.text ) }</td></tr></table></td></tr> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Contribution from Bjorn Gruning to extend the valid list of readme files in tool shed repositories to include .rst files.
by commits-noreply＠bitbucket.org 12 Jul '13

12 Jul '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/01850fa1b8aa/ Changeset: 01850fa1b8aa User: greg Date: 2013-07-12 04:24:35 Summary: Contribution from Bjorn Gruning to extend the valid list of readme files in tool shed repositories to include .rst files. Affected #: 1 file diff -r 43bfb43ed4b508cfa9a611edc71caf531a0c1a2a -r 01850fa1b8aa2706c5b6cf67d8d7099b2093aa36 lib/tool_shed/util/metadata_util.py --- a/lib/tool_shed/util/metadata_util.py +++ b/lib/tool_shed/util/metadata_util.py @@ -982,10 +982,11 @@ return old_id def get_readme_file_names( repository_name ): + """Creates a list of valid filenames.""" readme_files = [ 'readme', 'read_me', 'install' ] - valid_filenames = [ r for r in readme_files ] - for r in readme_files: - valid_filenames.append( '%s.txt' % r ) + valid_filenames = map( lambda f: '%s.txt' % f, readme_files ) + valid_filenames.extend( map( lambda f: '%s.rst' % f, readme_files ) ) + valid_filenames.extend( readme_files ) valid_filenames.append( '%s.txt' % repository_name ) return valid_filenames Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Contribution from Bjorn Gruning allowing installation of a repository to progress even if a repository dependency is not available. This will handle the case where a repository depnedency's env.sh file is not available due to an error in it's installation, but if possible, the dependent repository will proceed with it's installation.
by commits-noreply＠bitbucket.org 12 Jul '13

12 Jul '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/43bfb43ed4b5/ Changeset: 43bfb43ed4b5 User: greg Date: 2013-07-12 04:06:48 Summary: Contribution from Bjorn Gruning allowing installation of a repository to progress even if a repository dependency is not available. This will handle the case where a repository depnedency's env.sh file is not available due to an error in it's installation, but if possible, the dependent repository will proceed with it's installation. Affected #: 2 files diff -r 0a6c263dd4284d3aed1b59db91c16ca5e4c4a7a0 -r 43bfb43ed4b508cfa9a611edc71caf531a0c1a2a lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py @@ -238,8 +238,11 @@ # in the set_environment action. cmds = [] for env_shell_file_path in env_shell_file_paths: - for i, env_setting in enumerate( open( env_shell_file_path ) ): - cmds.append( env_setting.strip( '\n' ) ) + if os.path.exists( env_shell_file_path ): + for env_setting in open( env_shell_file_path ): + cmds.append( env_setting.strip( '\n' ) ) + else: + log.debug( 'Invalid file %s specified, ignoring set_environment action.', env_shell_file_path ) env_var_dicts = action_dict[ 'environment_variable' ] for env_var_dict in env_var_dicts: # Check for the presence of the $ENV[] key string and populate it if possible. @@ -298,8 +301,11 @@ with settings( warn_only=True ): cmd = '' for env_shell_file_path in env_shell_file_paths: - for env_setting in open( env_shell_file_path ): - cmd += '%s\n' % env_setting + if os.path.exists( env_shell_file_path ): + for env_setting in open( env_shell_file_path ): + cmd += '%s\n' % env_setting + else: + log.debug( 'Invalid file %s specified, ignoring shell_command action.', env_shell_file_path ) cmd += action_dict[ 'command' ] return_code = handle_command( app, tool_dependency, install_dir, cmd ) if return_code: @@ -307,10 +313,13 @@ elif action_type == 'template_command': env_vars = dict() for env_shell_file_path in env_shell_file_paths: - for env_setting in open( env_shell_file_path ): - env_string = env_setting.split( ';' )[ 0 ] - env_name, env_path = env_string.split( '=' ) - env_vars[ env_name ] = env_path + if os.path.exists( env_shell_file_path ): + for env_setting in open( env_shell_file_path ): + env_string = env_setting.split( ';' )[ 0 ] + env_name, env_path = env_string.split( '=' ) + env_vars[ env_name ] = env_path + else: + log.debug( 'Invalid file %s specified, ignoring template_command action.', env_shell_file_path ) env_vars.update( common_util.get_env_var_values( install_dir ) ) language = action_dict[ 'language' ] with settings( warn_only=True, **env_vars ): diff -r 0a6c263dd4284d3aed1b59db91c16ca5e4c4a7a0 -r 43bfb43ed4b508cfa9a611edc71caf531a0c1a2a lib/tool_shed/galaxy_install/tool_dependencies/install_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py @@ -177,15 +177,18 @@ tool_dependency_name=package_name, tool_dependency_version=package_version ) env_sh_file_path = os.path.join( env_sh_file_dir, 'env.sh' ) - for i, line in enumerate( open( env_sh_file_path, 'r' ) ): - env_var_dict = env_var_dicts[ i ] - action = env_var_dict.get( 'action', None ) - name = env_var_dict.get( 'name', None ) - value = env_var_dict.get( 'value', None ) - if action and name and value: - new_value = parse_env_shell_entry( action, name, value, line ) - env_var_dict[ 'value' ] = new_value - new_env_var_dicts.append( env_var_dict ) + if os.path.exists( env_sh_file_path ): + for i, line in enumerate( open( env_sh_file_path, 'r' ) ): + env_var_dict = env_var_dicts[ i ] + action = env_var_dict.get( 'action', None ) + name = env_var_dict.get( 'name', None ) + value = env_var_dict.get( 'value', None ) + if action and name and value: + new_value = parse_env_shell_entry( action, name, value, line ) + env_var_dict[ 'value' ] = new_value + new_env_var_dicts.append( env_var_dict ) + else: + log.debug( 'Invalid file %s specified, ignoring set_environment_for_install action.', env_sh_file_path ) action_dict[ 'environment_variable' ] = new_env_var_dicts else: action_dict[ 'environment_variable' ] = env_var_dicts Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Fix for generating the repository type select list, and fix a related typo in my last commit.
by commits-noreply＠bitbucket.org 11 Jul '13

11 Jul '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0a6c263dd428/ Changeset: 0a6c263dd428 User: greg Date: 2013-07-11 21:16:08 Summary: Fix for generating the repository type select list, and fix a related typo in my last commit. Affected #: 2 files diff -r 5a41d725197d2d42475f80282a57b0b364898671 -r 0a6c263dd4284d3aed1b59db91c16ca5e4c4a7a0 lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -666,7 +666,7 @@ # Update repository files for browsing. suc.update_repository( repo ) metadata = self.get_metadata( trans, id, repository.tip( trans.app ) ) - repository_type_select_field = rt_util.build_repository_type_select_fiels( trans, repository=repository ) + repository_type_select_field = rt_util.build_repository_type_select_field( trans, repository=repository ) return trans.fill_template( '/webapps/tool_shed/repository/browse_repository.mako', repository=repository, metadata=metadata, @@ -1017,7 +1017,7 @@ action='view_repository', message=message, id=trans.security.encode_id( repository.id ) ) ) - repository_type_select_field = rt_util.build_repository_type_select_fiels( trans ) + repository_type_select_field = rt_util.build_repository_type_select_field( trans ) return trans.fill_template( '/webapps/tool_shed/repository/create_repository.mako', name=name, description=description, @@ -2185,7 +2185,7 @@ else: message += malicious_error status = 'error' - repository_type_select_field = rt_util.build_repository_type_select_fiels( trans, repository=repository ) + repository_type_select_field = rt_util.build_repository_type_select_field( trans, repository=repository ) malicious_check_box = CheckboxField( 'malicious', checked=is_malicious ) skip_tool_tests_check_box = CheckboxField( 'skip_tool_tests', checked=skip_tool_tests_checked ) categories = suc.get_categories( trans ) @@ -2365,7 +2365,7 @@ display_reviews = util.string_as_bool( kwd.get( 'display_reviews', False ) ) rra = self.get_user_item_rating( trans.sa_session, trans.user, repository, webapp_model=trans.model ) metadata = self.get_metadata( trans, id, repository.tip( trans.app ) ) - repository_type_select_field = rt_util.build_repository_type_select_fiels( trans, repository=repository ) + repository_type_select_field = rt_util.build_repository_type_select_field( trans, repository=repository ) return trans.fill_template( '/webapps/tool_shed/repository/rate_repository.mako', repository=repository, metadata=metadata, @@ -2565,7 +2565,7 @@ else: message = "Select at least 1 file to delete from the repository before clicking <b>Delete selected files</b>." status = "error" - repository_type_select_field = rt_util.build_repository_type_select_fiels( trans, repository=repository ) + repository_type_select_field = rt_util.build_repository_type_select_field( trans, repository=repository ) return trans.fill_template( '/webapps/tool_shed/repository/browse_repository.mako', repo=repo, repository=repository, @@ -2991,7 +2991,7 @@ message += malicious_error status = 'error' containers_dict = container_util.build_repository_containers_for_tool_shed( trans, repository, changeset_revision, repository_dependencies, repository_metadata ) - repository_type_select_field = rt_util.build_repository_type_select_fiels( trans, repository=repository ) + repository_type_select_field = rt_util.build_repository_type_select_field( trans, repository=repository ) return trans.fill_template( '/webapps/tool_shed/repository/view_repository.mako', repo=repo, repository=repository, diff -r 5a41d725197d2d42475f80282a57b0b364898671 -r 0a6c263dd4284d3aed1b59db91c16ca5e4c4a7a0 lib/tool_shed/repository_types/util.py --- a/lib/tool_shed/repository_types/util.py +++ b/lib/tool_shed/repository_types/util.py @@ -8,13 +8,13 @@ types = [ GENERIC, TOOL_DEPENDENCY_DEFINITION ] -def build_repository_type_select_fiels( trans, repository=None, name='repository_type' ): +def build_repository_type_select_field( trans, repository=None, name='repository_type' ): """Called from the Tool Shed to generate the current list of supported repository types.""" if repository: selected_type = str( repository.type ) else: selected_type = None - repository_type_select_fiels = SelectField( name=name ) + repository_type_select_field = SelectField( name=name ) for type_label, type_class in trans.app.repository_types_registry.repository_types_by_label.items(): option_label = str( type_class.label ) option_value = str( type_class.type ) @@ -23,8 +23,10 @@ else: selected = False if repository: - if type_class.is_valid_for_type( trans.app, repository ): - repository_type_select_fiels.add_option( option_label, option_value, selected=selected ) + if repository.type == option_value: + repository_type_select_field.add_option( option_label, option_value, selected=selected ) + elif type_class.is_valid_for_type( trans.app, repository ): + repository_type_select_field.add_option( option_label, option_value, selected=selected ) else: - repository_type_select_fiels.add_option( option_label, option_value, selected=selected ) - return repository_type_select_fiels + repository_type_select_field.add_option( option_label, option_value, selected=selected ) + return repository_type_select_field Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Add support for categorizing repositories in the tool shed by type, with the first 2 supported types being "generic" and "tool_dependency_definition". Repositories of type "tool_dependency_definition" can always contain only a single file named "tool_dependencies.xml", and the only metadata revision for these types of repositories will be the changelog tip.
by commits-noreply＠bitbucket.org 11 Jul '13

11 Jul '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5a41d725197d/ Changeset: 5a41d725197d User: greg Date: 2013-07-11 20:59:27 Summary: Add support for categorizing repositories in the tool shed by type, with the first 2 supported types being "generic" and "tool_dependency_definition". Repositories of type "tool_dependency_definition" can always contain only a single file named "tool_dependencies.xml", and the only metadata revision for these types of repositories will be the changelog tip. Affected #: 20 files diff -r 92225a7b6e5ecd87410f1da567b9e320b965be50 -r 5a41d725197d2d42475f80282a57b0b364898671 lib/galaxy/webapps/tool_shed/app.py --- a/lib/galaxy/webapps/tool_shed/app.py +++ b/lib/galaxy/webapps/tool_shed/app.py @@ -7,6 +7,7 @@ from galaxy.openid.providers import OpenIDProviders from galaxy.web import security from galaxy.tags.tag_handler import CommunityTagHandler +import tool_shed.repository_types.registry class UniverseApplication( object ): """Encapsulates the state of a Universe application""" @@ -20,6 +21,8 @@ # Set up datatypes registry self.datatypes_registry = galaxy.datatypes.registry.Registry() self.datatypes_registry.load_datatypes( self.config.root, self.config.datatypes_config ) + # Set up the repository_types registry. + self.repository_types_registry = tool_shed.repository_types.registry.Registry() # Determine the database url if self.config.database_connection: db_url = self.config.database_connection diff -r 92225a7b6e5ecd87410f1da567b9e320b965be50 -r 5a41d725197d2d42475f80282a57b0b364898671 lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -35,6 +35,7 @@ import galaxy.tools import tool_shed.grids.repository_grids as repository_grids import tool_shed.grids.util as grids_util +import tool_shed.repository_types.util as rt_util from galaxy import eggs eggs.require('mercurial') @@ -665,10 +666,12 @@ # Update repository files for browsing. suc.update_repository( repo ) metadata = self.get_metadata( trans, id, repository.tip( trans.app ) ) + repository_type_select_field = rt_util.build_repository_type_select_fiels( trans, repository=repository ) return trans.fill_template( '/webapps/tool_shed/repository/browse_repository.mako', repository=repository, metadata=metadata, commit_message=commit_message, + repository_type_select_field=repository_type_select_field, message=message, status=status ) @@ -961,6 +964,7 @@ long_description = kwd.get( 'long_description', '' ) category_ids = util.listify( kwd.get( 'category_id', '' ) ) selected_categories = [ trans.security.decode_id( id ) for id in category_ids ] + repository_type = kwd.get( 'repository_type', rt_util.GENERIC ) if kwd.get( 'create_repository_button', False ): error = False message = self.__validate_repository_name( name, trans.user ) @@ -974,6 +978,7 @@ else: # Add the repository record to the db repository = trans.app.model.Repository( name=name, + type=repository_type, description=description, long_description=long_description, user_id=trans.user.id ) @@ -1001,7 +1006,7 @@ if category_ids: # Create category associations for category_id in category_ids: - category = trans.sa_session.query(model.Category).get( trans.security.decode_id( category_id ) ) + category = trans.sa_session.query( model.Category ).get( trans.security.decode_id( category_id ) ) rca = trans.app.model.RepositoryCategoryAssociation( repository, category ) trans.sa_session.add( rca ) flush_needed = True @@ -1012,12 +1017,14 @@ action='view_repository', message=message, id=trans.security.encode_id( repository.id ) ) ) + repository_type_select_field = rt_util.build_repository_type_select_fiels( trans ) return trans.fill_template( '/webapps/tool_shed/repository/create_repository.mako', name=name, description=description, long_description=long_description, selected_categories=selected_categories, categories=categories, + repository_type_select_field=repository_type_select_field, message=message, status=status ) @@ -1985,6 +1992,7 @@ message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) repository = suc.get_repository_in_tool_shed( trans, id ) + repository_type = kwd.get( 'repository_type', str( repository.type ) ) repo_dir = repository.repo_path( trans.app ) repo = hg.repository( suc.get_configured_ui(), repo_dir ) repo_name = kwd.get( 'repo_name', repository.name ) @@ -2016,6 +2024,9 @@ id=id, message=message, status='error' ) ) + if repository_type != repository.type: + repository.type = repository_type + flush_needed = True if description != repository.description: repository.description = description flush_needed = True @@ -2174,6 +2185,7 @@ else: message += malicious_error status = 'error' + repository_type_select_field = rt_util.build_repository_type_select_fiels( trans, repository=repository ) malicious_check_box = CheckboxField( 'malicious', checked=is_malicious ) skip_tool_tests_check_box = CheckboxField( 'skip_tool_tests', checked=skip_tool_tests_checked ) categories = suc.get_categories( trans ) @@ -2202,6 +2214,7 @@ skip_tool_tests_check_box=skip_tool_tests_check_box, skip_tool_test=skip_tool_test, malicious_check_box=malicious_check_box, + repository_type_select_field=repository_type_select_field, message=message, status=status ) @@ -2352,6 +2365,7 @@ display_reviews = util.string_as_bool( kwd.get( 'display_reviews', False ) ) rra = self.get_user_item_rating( trans.sa_session, trans.user, repository, webapp_model=trans.model ) metadata = self.get_metadata( trans, id, repository.tip( trans.app ) ) + repository_type_select_field = rt_util.build_repository_type_select_fiels( trans, repository=repository ) return trans.fill_template( '/webapps/tool_shed/repository/rate_repository.mako', repository=repository, metadata=metadata, @@ -2359,6 +2373,7 @@ display_reviews=display_reviews, num_ratings=num_ratings, rra=rra, + repository_type_select_field=repository_type_select_field, message=message, status=status ) @@ -2550,10 +2565,12 @@ else: message = "Select at least 1 file to delete from the repository before clicking <b>Delete selected files</b>." status = "error" + repository_type_select_field = rt_util.build_repository_type_select_fiels( trans, repository=repository ) return trans.fill_template( '/webapps/tool_shed/repository/browse_repository.mako', repo=repo, repository=repository, commit_message=commit_message, + repository_type_select_field=repository_type_select_field, message=message, status=status ) @@ -2974,6 +2991,7 @@ message += malicious_error status = 'error' containers_dict = container_util.build_repository_containers_for_tool_shed( trans, repository, changeset_revision, repository_dependencies, repository_metadata ) + repository_type_select_field = rt_util.build_repository_type_select_fiels( trans, repository=repository ) return trans.fill_template( '/webapps/tool_shed/repository/view_repository.mako', repo=repo, repository=repository, @@ -2987,6 +3005,7 @@ changeset_revision=changeset_revision, changeset_revision_select_field=changeset_revision_select_field, revision_label=revision_label, + repository_type_select_field=repository_type_select_field, message=message, status=status ) diff -r 92225a7b6e5ecd87410f1da567b9e320b965be50 -r 5a41d725197d2d42475f80282a57b0b364898671 lib/galaxy/webapps/tool_shed/model/__init__.py --- a/lib/galaxy/webapps/tool_shed/model/__init__.py +++ b/lib/galaxy/webapps/tool_shed/model/__init__.py @@ -5,6 +5,7 @@ from galaxy.util.bunch import Bunch from galaxy.util.hash_util import new_secure_hash from galaxy.model.item_attrs import APIItem +import tool_shed.repository_types.util as rt_util from galaxy import eggs eggs.require( 'mercurial' ) @@ -130,18 +131,20 @@ class Repository( object, APIItem ): - api_collection_visible_keys = ( 'id', 'name', 'description', 'user_id', 'private', 'deleted', 'times_downloaded', 'deprecated' ) - api_element_visible_keys = ( 'id', 'name', 'description', 'long_description', 'user_id', 'private', 'deleted', 'times_downloaded', 'deprecated' ) + api_collection_visible_keys = ( 'id', 'name', 'type', 'description', 'user_id', 'private', 'deleted', 'times_downloaded', 'deprecated' ) + api_element_visible_keys = ( 'id', 'name', 'type', 'description', 'long_description', 'user_id', 'private', 'deleted', 'times_downloaded', + 'deprecated' ) file_states = Bunch( NORMAL = 'n', NEEDS_MERGING = 'm', MARKED_FOR_REMOVAL = 'r', MARKED_FOR_ADDITION = 'a', NOT_TRACKED = '?' ) - def __init__( self, id=None, name=None, description=None, long_description=None, user_id=None, private=False, deleted=None, email_alerts=None, - times_downloaded=0, deprecated=False ): + def __init__( self, id=None, name=None, type=None, description=None, long_description=None, user_id=None, private=False, deleted=None, + email_alerts=None, times_downloaded=0, deprecated=False ): self.id = id self.name = name or "Unnamed repository" + self.type = type self.description = description self.long_description = long_description self.user_id = user_id @@ -154,6 +157,24 @@ def as_dict( self, value_mapper=None ): return self.get_api_value( view='element', value_mapper=value_mapper ) + def can_change_type( self, app ): + # Allow changing the type only if the repository has no contents, has never been installed, or has never been changed from + # the default type. + if self.is_new( app ): + return True + if self.times_downloaded == 0: + return True + if self.type == rt_util.DEFAULT: + return True + return False + + def can_change_type_to( self, app, new_type_label ): + if self.can_change_type( app ): + new_type = app.repository_types_registry.get_class_by_label( new_type_label ) + if new_type.is_valid_for_type( self ): + return True + return False + def get_api_value( self, view='collection', value_mapper=None ): if value_mapper is None: value_mapper = {} @@ -173,6 +194,13 @@ rval[ 'owner' ] = self.user.username return rval + def get_changesets_for_setting_metadata( self, app ): + type_class = self.get_type_class( app ) + return type_class.get_changesets_for_setting_metadata( app, self ) + + def get_type_class( self, app ): + return app.repository_types_registry.get_class_by_label( self.type ) + def repo_path( self, app ): return app.hgweb_config_manager.get_entry( os.path.join( "repos", self.user.username, self.name ) ) diff -r 92225a7b6e5ecd87410f1da567b9e320b965be50 -r 5a41d725197d2d42475f80282a57b0b364898671 lib/galaxy/webapps/tool_shed/model/mapping.py --- a/lib/galaxy/webapps/tool_shed/model/mapping.py +++ b/lib/galaxy/webapps/tool_shed/model/mapping.py @@ -106,6 +106,7 @@ Column( "create_time", DateTime, default=now ), Column( "update_time", DateTime, default=now, onupdate=now ), Column( "name", TrimmedString( 255 ), index=True ), + Column( "type", TrimmedString( 255 ), index=True ), Column( "description" , TEXT ), Column( "long_description" , TEXT ), Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), diff -r 92225a7b6e5ecd87410f1da567b9e320b965be50 -r 5a41d725197d2d42475f80282a57b0b364898671 lib/galaxy/webapps/tool_shed/model/migrate/versions/0020_add_repository_type_column.py --- /dev/null +++ b/lib/galaxy/webapps/tool_shed/model/migrate/versions/0020_add_repository_type_column.py @@ -0,0 +1,46 @@ +"""Migration script to add the type column to the repository table.""" + +from sqlalchemy import * +from sqlalchemy.orm import * +from migrate import * +from migrate.changeset import * + +# Need our custom types, but don't import anything else from model +from galaxy.model.custom_types import * + +import sys, logging +log = logging.getLogger( __name__ ) +log.setLevel(logging.DEBUG) +handler = logging.StreamHandler( sys.stdout ) +format = "%(name)s %(levelname)s %(asctime)s %(message)s" +formatter = logging.Formatter( format ) +handler.setFormatter( formatter ) +log.addHandler( handler ) + +metadata = MetaData() + +def upgrade( migrate_engine ): + print __doc__ + metadata.bind = migrate_engine + metadata.reflect() + Repository_table = Table( "repository", metadata, autoload=True ) + c = Column( "type", TrimmedString( 255 ), index=True ) + try: + # Create + c.create( Repository_table, index_name="ix_repository_type" ) + assert c is Repository_table.c.type + except Exception, e: + print "Adding type column to the repository table failed: %s" % str( e ) + # Update the type column to have the default generic value. + cmd = "UPDATE repository SET type = 'generic'" + migrate_engine.execute( cmd ) + +def downgrade( migrate_engine ): + metadata.bind = migrate_engine + metadata.reflect() + # Drop type column from repository table. + Repository_table = Table( "repository", metadata, autoload=True ) + try: + Repository_table.c.type.drop() + except Exception, e: + print "Dropping column type from the repository table failed: %s" % str( e ) diff -r 92225a7b6e5ecd87410f1da567b9e320b965be50 -r 5a41d725197d2d42475f80282a57b0b364898671 lib/tool_shed/repository_types/generic.py --- /dev/null +++ b/lib/tool_shed/repository_types/generic.py @@ -0,0 +1,20 @@ +import logging +import tool_shed.repository_types.util as rt_util +from tool_shed.repository_types.metadata import Metadata + +log = logging.getLogger( __name__ ) + + +class Generic( Metadata ): + + def __init__( self ): + self.type = rt_util.GENERIC + self.label = 'Generic' + + def is_valid_for_type( self, app, repository, revisions_to_check=None ): + """A repository's type can only be changed to the generic type if it is new or has never been installed.""" + if repository.is_new( app ): + return True + if repository.times_downloaded == 0: + return True + return False diff -r 92225a7b6e5ecd87410f1da567b9e320b965be50 -r 5a41d725197d2d42475f80282a57b0b364898671 lib/tool_shed/repository_types/metadata.py --- /dev/null +++ b/lib/tool_shed/repository_types/metadata.py @@ -0,0 +1,32 @@ +import logging +import tool_shed.repository_types.util as rt_util + +from galaxy import eggs +eggs.require( 'mercurial' ) +from mercurial import hg +from mercurial import ui + +log = logging.getLogger( __name__ ) + + +class Metadata( object ): + + def __init__( self ): + self.type = None + + def get_changesets_for_setting_metadata( self, app, repository ): + repo = hg.repository( ui.ui(), repository.repo_path( app ) ) + return repo.changelog + + def is_valid_for_type( self, repository, revisions_to_check=None ): + raise "Unimplemented Method" + + +class TipOnly( Metadata ): + + def __init__( self ): + self.type = None + + def get_changesets_for_setting_metadata( self, app, repository ): + repo = hg.repository( ui.ui(), repository.repo_path( app ) ) + return [ repo.changelog.tip() ] diff -r 92225a7b6e5ecd87410f1da567b9e320b965be50 -r 5a41d725197d2d42475f80282a57b0b364898671 lib/tool_shed/repository_types/registry.py --- /dev/null +++ b/lib/tool_shed/repository_types/registry.py @@ -0,0 +1,17 @@ +import logging +import generic +import tool_dependency_definition +from galaxy.util.odict import odict + +log = logging.getLogger( __name__ ) + + +class Registry( object ): + + def __init__( self ): + self.repository_types_by_label = odict() + self.repository_types_by_label[ 'generic' ] = generic.Generic() + self.repository_types_by_label[ 'tool_dependency_definition' ] = tool_dependency_definition.ToolDependencyDefinition() + + def get_class_by_label( self, label ): + return self.repository_types_by_label.get( label, None ) diff -r 92225a7b6e5ecd87410f1da567b9e320b965be50 -r 5a41d725197d2d42475f80282a57b0b364898671 lib/tool_shed/repository_types/tool_dependency_definition.py --- /dev/null +++ b/lib/tool_shed/repository_types/tool_dependency_definition.py @@ -0,0 +1,43 @@ +import logging +from tool_shed.repository_types.metadata import TipOnly +import tool_shed.repository_types.util as rt_util +import tool_shed.util.shed_util_common as suc + +from galaxy import eggs +eggs.require( 'mercurial' ) +from mercurial import hg +from mercurial import ui + +log = logging.getLogger( __name__ ) + +class ToolDependencyDefinition( TipOnly ): + + def __init__( self ): + self.type = rt_util.TOOL_DEPENDENCY_DEFINITION + self.label = 'Tool dependency definition' + self.valid_file_names = [ 'tool_dependencies.xml' ] + + def is_valid_for_type( self, app, repository, revisions_to_check=None ): + """ + Inspect the received repository's contents to determine if they abide by the rules defined for the contents of this type. + If the received revisions_to_check is a list of changeset revisions, then inspection will be restricted to the revisions + in the list. + """ + repo = hg.repository( ui.ui(), repository.repo_path( app ) ) + if revisions_to_check: + changeset_revisions = revisions_to_check + else: + changeset_revisions = repo.changelog + for changeset in changeset_revisions: + changeset_revision = str( repo.changectx( changeset ) ) + ctx = repo.changectx( changeset ) + # Inspect all files in the changeset (in sorted order) to make sure there is only one and it is named tool_dependencies.xml. + files_changed_in_changeset = ctx.files() + if len( files_changed_in_changeset ) > 1: + return False + for file_path in files_changed_in_changeset: + file_name = suc.strip_path( file_path ) + if file_name not in self.valid_file_names: + return False + return True + \ No newline at end of file diff -r 92225a7b6e5ecd87410f1da567b9e320b965be50 -r 5a41d725197d2d42475f80282a57b0b364898671 lib/tool_shed/repository_types/util.py --- /dev/null +++ b/lib/tool_shed/repository_types/util.py @@ -0,0 +1,30 @@ +import logging +from galaxy.web.form_builder import SelectField + +log = logging.getLogger( __name__ ) + +GENERIC = 'generic' +TOOL_DEPENDENCY_DEFINITION = 'tool_dependency_definition' + +types = [ GENERIC, TOOL_DEPENDENCY_DEFINITION ] + +def build_repository_type_select_fiels( trans, repository=None, name='repository_type' ): + """Called from the Tool Shed to generate the current list of supported repository types.""" + if repository: + selected_type = str( repository.type ) + else: + selected_type = None + repository_type_select_fiels = SelectField( name=name ) + for type_label, type_class in trans.app.repository_types_registry.repository_types_by_label.items(): + option_label = str( type_class.label ) + option_value = str( type_class.type ) + if selected_type and selected_type == option_value: + selected = True + else: + selected = False + if repository: + if type_class.is_valid_for_type( trans.app, repository ): + repository_type_select_fiels.add_option( option_label, option_value, selected=selected ) + else: + repository_type_select_fiels.add_option( option_label, option_value, selected=selected ) + return repository_type_select_fiels diff -r 92225a7b6e5ecd87410f1da567b9e320b965be50 -r 5a41d725197d2d42475f80282a57b0b364898671 lib/tool_shed/util/metadata_util.py --- a/lib/tool_shed/util/metadata_util.py +++ b/lib/tool_shed/util/metadata_util.py @@ -12,6 +12,7 @@ from galaxy.web import url_for from galaxy.webapps.tool_shed.util import container_util import tool_shed.util.shed_util_common as suc +from tool_shed.repository_types.metadata import TipOnly from tool_shed.util import common_util from tool_shed.util import common_install_util from tool_shed.util import readme_util @@ -65,7 +66,7 @@ trans.sa_session.delete( repository_metadata ) trans.sa_session.flush() -def compare_changeset_revisions( ancestor_changeset_revision, ancestor_metadata_dict, current_changeset_revision, current_metadata_dict ): +def compare_changeset_revisions( trans, ancestor_changeset_revision, ancestor_metadata_dict, current_changeset_revision, current_metadata_dict ): """Compare the contents of two changeset revisions to determine if a new repository metadata revision should be created.""" # The metadata associated with ancestor_changeset_revision is ancestor_metadata_dict. This changeset_revision is an ancestor of # current_changeset_revision which is associated with current_metadata_dict. A new repository_metadata record will be created only @@ -104,11 +105,11 @@ # Uncomment the following if we decide that README files should affect how installable repository revisions are defined. See the NOTE in the # compare_readme_files() method. # readme_file_comparision = compare_readme_files( ancestor_readme_files, current_readme_files ) - repository_dependency_comparison = compare_repository_dependencies( ancestor_repository_dependencies, current_repository_dependencies ) - tool_dependency_comparison = compare_tool_dependencies( ancestor_tool_dependencies, current_tool_dependencies ) - workflow_comparison = compare_workflows( ancestor_workflows, current_workflows ) - datatype_comparison = compare_datatypes( ancestor_datatypes, current_datatypes ) - data_manager_comparison = compare_data_manager( ancestor_data_manager, current_data_manager ) + repository_dependency_comparison = compare_repository_dependencies( trans, ancestor_repository_dependencies, current_repository_dependencies ) + tool_dependency_comparison = compare_tool_dependencies( trans, ancestor_tool_dependencies, current_tool_dependencies ) + workflow_comparison = compare_workflows( trans, ancestor_workflows, current_workflows ) + datatype_comparison = compare_datatypes( trans, ancestor_datatypes, current_datatypes ) + data_manager_comparison = compare_data_manager( trans, ancestor_data_manager, current_data_manager ) # Handle case where all metadata is the same. if ancestor_guids == current_guids and \ repository_dependency_comparison == EQUAL and \ @@ -134,7 +135,7 @@ return SUBSET return NOT_EQUAL_AND_NOT_SUBSET -def compare_data_manager( ancestor_metadata, current_metadata ): +def compare_data_manager( trans, ancestor_metadata, current_metadata ): """Determine if ancestor_metadata is the same as or a subset of current_metadata for data_managers.""" def __data_manager_dict_to_tuple_list( metadata_dict ): # we do not check tool_guid or tool conf file name @@ -149,7 +150,7 @@ return SUBSET return NOT_EQUAL_AND_NOT_SUBSET -def compare_datatypes( ancestor_datatypes, current_datatypes ): +def compare_datatypes( trans, ancestor_datatypes, current_datatypes ): """Determine if ancestor_datatypes is the same as or a subset of current_datatypes.""" # Each datatype dict looks something like: {"dtype": "galaxy.datatypes.images:Image", "extension": "pdf", "mimetype": "application/pdf"} if len( ancestor_datatypes ) <= len( current_datatypes ): @@ -193,7 +194,7 @@ return SUBSET return NOT_EQUAL_AND_NOT_SUBSET -def compare_repository_dependencies( ancestor_repository_dependencies, current_repository_dependencies ): +def compare_repository_dependencies( trans, ancestor_repository_dependencies, current_repository_dependencies ): """Determine if ancestor_repository_dependencies is the same as or a subset of current_repository_dependencies.""" # The list of repository_dependencies looks something like: [["http://localhost:9009", "emboss_datatypes", "test", "ab03a2a5f407", False]]. # Create a string from each tuple in the list for easier comparison. @@ -211,14 +212,18 @@ found_in_current = True break if not found_in_current: - return NOT_EQUAL_AND_NOT_SUBSET + # In some cases, the only difference between a dependency definition in the lists is the changeset_revision value. We'll + # check to see if this is the case, and if the defined dependency is a repository that has metadata set only on it's tip. + if not different_revision_defines_tip_only_repository_dependency( ancestor_tup, current_repository_dependencies ): + return NOT_EQUAL_AND_NOT_SUBSET + return SUBSET if len( ancestor_repository_dependencies ) == len( current_repository_dependencies ): return EQUAL else: return SUBSET return NOT_EQUAL_AND_NOT_SUBSET -def compare_tool_dependencies( ancestor_tool_dependencies, current_tool_dependencies ): +def compare_tool_dependencies( trans, ancestor_tool_dependencies, current_tool_dependencies ): """Determine if ancestor_tool_dependencies is the same as or a subset of current_tool_dependencies.""" # The tool_dependencies dictionary looks something like: # {'bwa/0.5.9': {'readme': 'some string', 'version': '0.5.9', 'type': 'package', 'name': 'bwa'}} @@ -238,7 +243,7 @@ return SUBSET return NOT_EQUAL_AND_NOT_SUBSET -def compare_workflows( ancestor_workflows, current_workflows ): +def compare_workflows( trans, ancestor_workflows, current_workflows ): """Determine if ancestor_workflows is the same as current_workflows or if ancestor_workflows is a subset of current_workflows.""" if len( ancestor_workflows ) <= len( current_workflows ): for ancestor_workflow_tup in ancestor_workflows: @@ -341,6 +346,21 @@ break return repository_metadata +def different_revision_defines_tip_only_repository_dependency( rd_tup, repository_dependencies ): + """ + Determine if the only difference between rd_tup and a dependency definition in the list of repository_dependencies is the changeset_revision value. + """ + new_metadata_required = False + rd_tool_shed, rd_name, rd_owner, rd_changeset_revision, rd_prior_installation_required = suc.parse_repository_dependency_tuple( rd_tup ) + for repository_dependency in repository_dependencies: + tool_shed, name, owner, changeset_revision, prior_installation_required = suc.parse_repository_dependency_tuple( repository_dependency ) + if rd_tool_shed == tool_shed and rd_name == name and rd_owner == owner: + # Determine if the repository represented by the dependency tuple is an instance of the repository type TipOnly. + required_repository = suc.get_repository_by_name_and_owner( trans.app, name, owner ) + repository_type_class = trans.app.repository_types_registry.get_class_by_label( required_repository.type ) + return isinstance( repository_type_class, TipOnly ) + return False + def generate_data_manager_metadata( app, repository, repo_dir, data_manager_config_filename, metadata_dict, shed_config_dict=None ): """Update the received metadata_dict with information from the parsed data_manager_config_filename.""" if data_manager_config_filename is None: @@ -1308,7 +1328,10 @@ # The saved metadata must be a subset of the new metadata. for saved_repository_dependency in saved_repository_dependencies: if saved_repository_dependency not in new_repository_dependencies: - return True + # In some cases, the only difference between a dependency definition in the lists is the changeset_revision value. We'll + # check to see if this is the case, and if the defined dependency is a repository that has metadata set only on it's tip. + if not different_revision_defines_tip_only_repository_dependency( saved_repository_dependency, new_repository_dependencies ): + return True return False else: # The repository_dependencies.xml file must have been deleted, so create a new repository_metadata record so we always have @@ -1588,7 +1611,7 @@ ancestor_metadata_dict = None invalid_file_tups = [] home_dir = os.getcwd() - for changeset in repo.changelog: + for changeset in repository.get_changesets_for_setting_metadata( trans.app ): work_dir = tempfile.mkdtemp( prefix="tmp-toolshed-ramorits" ) current_changeset_revision = str( repo.changectx( changeset ) ) ctx = repo.changectx( changeset ) @@ -1619,7 +1642,8 @@ # EQUAL - ancestor metadata is equivalent to current metadata, so continue from current # SUBSET - ancestor metadata is a subset of current metadata, so continue from current # NOT_EQUAL_AND_NOT_SUBSET - ancestor metadata is neither equal to nor a subset of current metadata, so persist ancestor metadata. - comparison = compare_changeset_revisions( ancestor_changeset_revision, + comparison = compare_changeset_revisions( trans, + ancestor_changeset_revision, ancestor_metadata_dict, current_changeset_revision, current_metadata_dict ) @@ -1752,7 +1776,9 @@ persist=False ) if metadata_dict: repository_metadata = None - if new_metadata_required_for_utilities( trans, repository, metadata_dict ): + repository_type_class = trans.app.repository_types_registry.get_class_by_label( repository.type ) + tip_only = isinstance( repository_type_class, TipOnly ) + if not tip_only and new_metadata_required_for_utilities( trans, repository, metadata_dict ): # Create a new repository_metadata table row. repository_metadata = create_or_update_repository_metadata( trans, encoded_id, repository, repository.tip( trans.app ), metadata_dict ) # If this is the first record stored for this repository, see if we need to send any email alerts. diff -r 92225a7b6e5ecd87410f1da567b9e320b965be50 -r 5a41d725197d2d42475f80282a57b0b364898671 templates/webapps/tool_shed/admin/index.mako --- a/templates/webapps/tool_shed/admin/index.mako +++ b/templates/webapps/tool_shed/admin/index.mako @@ -46,7 +46,7 @@ <div class="unified-panel-header" unselectable="on"><div class='unified-panel-header-inner'>Administration</div></div> - <div class="unified-panel-body" style="padding: 10px; overflow: auto;"> + <div class="unified-panel-body"><div class="toolMenu"><div class="toolSectionList"><div class="toolSectionTitle"> diff -r 92225a7b6e5ecd87410f1da567b9e320b965be50 -r 5a41d725197d2d42475f80282a57b0b364898671 templates/webapps/tool_shed/index.mako --- a/templates/webapps/tool_shed/index.mako +++ b/templates/webapps/tool_shed/index.mako @@ -46,7 +46,7 @@ <div class="unified-panel-header" unselectable="on"><div class='unified-panel-header-inner'>${trans.app.shed_counter.valid_tools | h} valid tools on ${trans.app.shed_counter.generation_time | h}</div></div> - <div class="unified-panel-body" style="padding: 10px; overflow: auto;"> + <div class="unified-panel-body"><div class="toolMenu"><div class="toolSectionList"> %if user_id or repository_id: diff -r 92225a7b6e5ecd87410f1da567b9e320b965be50 -r 5a41d725197d2d42475f80282a57b0b364898671 templates/webapps/tool_shed/repository/browse_repository.mako --- a/templates/webapps/tool_shed/repository/browse_repository.mako +++ b/templates/webapps/tool_shed/repository/browse_repository.mako @@ -46,6 +46,7 @@ ${render_clone_str( repository )} </div> %endif + ${render_repository_type_select_field( repository_type_select_field, render_help=False )} %if can_push: <form name="select_files_to_delete" id="select_files_to_delete" action="${h.url_for( controller='repository', action='select_files_to_delete', id=trans.security.encode_id( repository.id ))}" method="post" ><div class="form-row" > diff -r 92225a7b6e5ecd87410f1da567b9e320b965be50 -r 5a41d725197d2d42475f80282a57b0b364898671 templates/webapps/tool_shed/repository/common.mako --- a/templates/webapps/tool_shed/repository/common.mako +++ b/templates/webapps/tool_shed/repository/common.mako @@ -163,6 +163,46 @@ </script></%def> +<%def name="render_repository_type_select_field( repository_type_select_field, render_help=True )"> + <div class="form-row"> + <label>Repository type:</label> + <% + from tool_shed.repository_types import util + options = repository_type_select_field.options + repository_types = [] + for option_tup in options: + repository_types.append( option_tup[ 1 ] ) + render_as_text = len( options ) == 1 + if render_as_text: + repository_type = options[ 0 ][ 0 ] + %> + %if render_as_text: + ${repository_type | h} + %if render_help: + <div class="toolParamHelp" style="clear: both;"> + This repository's type cannot be changed because it's contents are valid only for it's current type or it has been cloned. + </div> + %endif + %else: + ${repository_type_select_field.get_html()} + %if render_help: + <div class="toolParamHelp" style="clear: both;"> + Select the repository type based on the following criteria. + <ul> + %if util.GENERIC in repository_types: + <li><b>Generic</b> - contents can be any set of valid Galaxy utilities + %endif + %if util.TOOL_DEPENDENCY_DEFINITION in repository_types: + <li><b>Tool dependency definition</b> - contents will always be restricted to one file named tool_dependencies.xml + %endif + </ul> + </div> + %endif + %endif + <div style="clear: both"></div> + </div> +</%def> + <%def name="render_sharable_str( repository, changeset_revision=None )"><% from tool_shed.util.shed_util_common import generate_sharable_link_for_repository_in_tool_shed diff -r 92225a7b6e5ecd87410f1da567b9e320b965be50 -r 5a41d725197d2d42475f80282a57b0b364898671 templates/webapps/tool_shed/repository/create_repository.mako --- a/templates/webapps/tool_shed/repository/create_repository.mako +++ b/templates/webapps/tool_shed/repository/create_repository.mako @@ -1,5 +1,6 @@ <%inherit file="/base.mako"/><%namespace file="/message.mako" import="render_msg" /> +<%namespace file="/webapps/tool_shed/repository/common.mako" import="render_repository_type_select_field" /><%def name="javascripts()"> ${parent.javascripts()} @@ -23,6 +24,7 @@ <input name="name" type="textfield" value="${name | h}" size="40"/><div style="clear: both"></div></div> + ${render_repository_type_select_field( repository_type_select_field, render_help=True )} <div class="form-row"><label>Synopsis:</label><input name="description" type="textfield" value="${description | h}" size="80"/> diff -r 92225a7b6e5ecd87410f1da567b9e320b965be50 -r 5a41d725197d2d42475f80282a57b0b364898671 templates/webapps/tool_shed/repository/manage_repository.mako --- a/templates/webapps/tool_shed/repository/manage_repository.mako +++ b/templates/webapps/tool_shed/repository/manage_repository.mako @@ -151,6 +151,7 @@ </div><div style="clear: both"></div></div> + ${render_repository_type_select_field( repository_type_select_field, render_help=True )} <div class="form-row"><label>Synopsis:</label><input name="description" type="textfield" value="${description | h}" size="80"/> diff -r 92225a7b6e5ecd87410f1da567b9e320b965be50 -r 5a41d725197d2d42475f80282a57b0b364898671 templates/webapps/tool_shed/repository/rate_repository.mako --- a/templates/webapps/tool_shed/repository/rate_repository.mako +++ b/templates/webapps/tool_shed/repository/rate_repository.mako @@ -44,6 +44,7 @@ ${render_clone_str( repository )} </div> %endif + ${render_repository_type_select_field( repository_type_select_field, render_help=False )} <div class="toolFormBody"><div class="form-row"><label>Description:</label> diff -r 92225a7b6e5ecd87410f1da567b9e320b965be50 -r 5a41d725197d2d42475f80282a57b0b364898671 templates/webapps/tool_shed/repository/view_repository.mako --- a/templates/webapps/tool_shed/repository/view_repository.mako +++ b/templates/webapps/tool_shed/repository/view_repository.mako @@ -100,6 +100,7 @@ ${repository.name | h} %endif </div> + ${render_repository_type_select_field( repository_type_select_field, render_help=False )} <div class="form-row"><label>Synopsis:</label> ${repository.description | h} Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: Admin left panel: small bump down
by commits-noreply＠bitbucket.org 11 Jul '13

11 Jul '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/92225a7b6e5e/ Changeset: 92225a7b6e5e User: carlfeberhard Date: 2013-07-11 18:25:34 Summary: Admin left panel: small bump down Affected #: 1 file diff -r 238988fc5d2a963685e7ab12a0282f89a8bca430 -r 92225a7b6e5ecd87410f1da567b9e320b965be50 templates/webapps/galaxy/admin/index.mako --- a/templates/webapps/galaxy/admin/index.mako +++ b/templates/webapps/galaxy/admin/index.mako @@ -22,7 +22,7 @@ overflow: auto; } .toolMenu { - margin-left: 10px; + margin: 8px 0 0 10px; } </style></%def> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: carlfeberhard: Fix deleted check in api/histories.delete, better error reporting in base controller get_object
by commits-noreply＠bitbucket.org 11 Jul '13

11 Jul '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/238988fc5d2a/ Changeset: 238988fc5d2a User: carlfeberhard Date: 2013-07-11 18:18:51 Summary: Fix deleted check in api/histories.delete, better error reporting in base controller get_object Affected #: 2 files diff -r 4cc057df762c219406af27dd04ac725a07a5a6eb -r 238988fc5d2a963685e7ab12a0282f89a8bca430 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -113,21 +113,25 @@ try: decoded_id = trans.security.decode_id( id ) except: - raise MessageException( "Malformed %s id ( %s ) specified, unable to decode" % ( class_name, str( id ) ), type='error' ) + raise MessageException( "Malformed %s id ( %s ) specified, unable to decode" + % ( class_name, str( id ) ), type='error' ) try: item_class = self.get_class( class_name ) assert item_class is not None item = trans.sa_session.query( item_class ).get( decoded_id ) assert item is not None - except: - log.exception( "Invalid %s id ( %s ) specified" % ( class_name, id ) ) + except Exception, exc: + log.exception( "Invalid %s id ( %s ) specified: %s" % ( class_name, id, str( exc ) ) ) raise MessageException( "Invalid %s id ( %s ) specified" % ( class_name, id ), type="error" ) + if check_ownership or check_accessible: self.security_check( trans, item, check_ownership, check_accessible ) if deleted == True and not item.deleted: - raise ItemDeletionException( '%s "%s" is not deleted' % ( class_name, getattr( item, 'name', id ) ), type="warning" ) + raise ItemDeletionException( '%s "%s" is not deleted' + % ( class_name, getattr( item, 'name', id ) ), type="warning" ) elif deleted == False and item.deleted: - raise ItemDeletionException( '%s "%s" is deleted' % ( class_name, getattr( item, 'name', id ) ), type="warning" ) + raise ItemDeletionException( '%s "%s" is deleted' + % ( class_name, getattr( item, 'name', id ) ), type="warning" ) return item # this should be here - but catching errors from sharable item controllers that *should* have SharableItemMixin @@ -190,11 +194,11 @@ check_ownership=check_ownership, check_accessible=check_accessible, deleted=deleted ) except ItemDeletionException, e: - raise HTTPBadRequest( detail="Invalid %s id ( %s ) specified" % ( class_name, str( id ) ) ) + raise HTTPBadRequest( detail="Invalid %s id ( %s ) specified: %s" % ( class_name, str( id ), str( e ) ) ) except MessageException, e: raise HTTPBadRequest( detail=e.err_msg ) except Exception, e: - log.exception( "Execption in get_object check for %s %s:" % ( class_name, str( id ) ) ) + log.exception( "Execption in get_object check for %s %s: %s" % ( class_name, str( id ), str( e ) ) ) raise HTTPInternalServerError( comment=str( e ) ) def validate_in_users_and_groups( self, trans, payload ): @@ -280,8 +284,10 @@ def get_history( self, trans, id, check_ownership=True, check_accessible=False, deleted=None ): """Get a History from the database by id, verifying ownership.""" - history = self.get_object( trans, id, 'History', check_ownership=check_ownership, check_accessible=check_accessible, deleted=deleted ) - return self.security_check( trans, history, check_ownership, check_accessible ) + history = self.get_object( trans, id, 'History', + check_ownership=check_ownership, check_accessible=check_accessible, deleted=deleted ) + history = self.security_check( trans, history, check_ownership, check_accessible ) + return history def get_history_datasets( self, trans, history, show_deleted=False, show_hidden=False, show_purged=False ): """ Returns history's datasets. """ diff -r 4cc057df762c219406af27dd04ac725a07a5a6eb -r 238988fc5d2a963685e7ab12a0282f89a8bca430 lib/galaxy/webapps/galaxy/api/histories.py --- a/lib/galaxy/webapps/galaxy/api/histories.py +++ b/lib/galaxy/webapps/galaxy/api/histories.py @@ -2,6 +2,10 @@ API operations on a history. """ +import pkg_resources +pkg_resources.require( "Paste" ) +from paste.httpexceptions import HTTPBadRequest + from galaxy import web from galaxy.util import string_as_bool, restore_text from galaxy.util.sanitize_html import sanitize_html @@ -75,9 +79,13 @@ history_data = self.get_history_dict( trans, history ) history_data[ 'contents_url' ] = url_for( 'history_contents', history_id=history_id ) + except HTTPBadRequest, bad_req: + trans.response.status = 400 + return str( bad_req ) + except Exception, e: msg = "Error in history API at showing history detail: %s" % ( str( e ) ) - log.error( msg, exc_info=True ) + log.exception( msg, exc_info=True ) trans.response.status = 500 return msg @@ -117,7 +125,7 @@ purge = string_as_bool( kwd['payload'].get( 'purge', False ) ) try: - history = self.get_history( trans, history_id, check_ownership=True, check_accessible=False, deleted=True ) + history = self.get_history( trans, history_id, check_ownership=True, check_accessible=False ) except Exception, e: return str( e ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: Fix unified-panel css in history/view.mako when used with/without 'use_panels'
by commits-noreply＠bitbucket.org 09 Jul '13

09 Jul '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4cc057df762c/ Changeset: 4cc057df762c User: carlfeberhard Date: 2013-07-09 21:32:57 Summary: Fix unified-panel css in history/view.mako when used with/without 'use_panels' Affected #: 1 file diff -r 0fa860b8ee41897a63c7c66581a16c360f48b11a -r 4cc057df762c219406af27dd04ac725a07a5a6eb templates/webapps/galaxy/history/view.mako --- a/templates/webapps/galaxy/history/view.mako +++ b/templates/webapps/galaxy/history/view.mako @@ -24,12 +24,9 @@ <%def name="stylesheets()"> ${parent.stylesheets()} ${h.css( "history", "autocomplete_tagging" )} + <style type="text/css"> - .historyItemContainer { - padding-right: 3px; - border-right-style: solid; - border-right-color: #66AA66; - } + .page-body { padding: 10px; @@ -46,9 +43,18 @@ border: 2px solid #DDDDDD; border-top: 4px solid #DDDDDD; } - </style> - <style> + div.unified-panel-body { + position: relative; + top: 0px; + width: auto; + } + + .historyItemContainer { + padding-right: 3px; + border-right-style: solid; + border-right-color: #66AA66; + } .historyItemBody { display: none; } @@ -86,11 +92,13 @@ href_to_user_histories = h.url_for( controller='/history', action='list_published' )##should this instead be be None or empty string? %> + %if context.get( 'use_panels' ): <div class="unified-panel-header" unselectable="on"></div> + %endif <div class="unified-panel-body"> - <div style="overflow: auto; height: 100%;"> + <div class="wrapping" style="overflow: auto; height: 100%;"> ## Render view of history. <div id="top-links" class="historyLinks" style="padding: 0px 0px 5px 0px"> %if not history.purged: @@ -117,11 +125,9 @@ %endif %if not datasets: - <div class="infomessagesmall" id="emptyHistoryMessage"> %else: - ## Render requested datasets, ordered from newest to oldest %for data in datasets: %if data.visible: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Apply changes recently made to the left panel in Galaxy to the left panel in the Tool Shed.
by commits-noreply＠bitbucket.org 09 Jul '13

09 Jul '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0fa860b8ee41/ Changeset: 0fa860b8ee41 User: greg Date: 2013-07-09 20:13:12 Summary: Apply changes recently made to the left panel in Galaxy to the left panel in the Tool Shed. Affected #: 2 files diff -r 1f63dbb2ed28333e0b6ad7f930199dceacf5766a -r 0fa860b8ee41897a63c7c66581a16c360f48b11a templates/webapps/tool_shed/admin/index.mako --- a/templates/webapps/tool_shed/admin/index.mako +++ b/templates/webapps/tool_shed/admin/index.mako @@ -1,7 +1,7 @@ <%inherit file="/webapps/tool_shed/base_panels.mako"/><%namespace file="/message.mako" import="render_msg" /> -<%def name="stylesheets()"> +<%def name="stylesheets()"> ## Include "base.css" for styling tool menu and forms (details) ${h.css( "base", "autocomplete_tagging", "tool_menu" )} @@ -13,6 +13,12 @@ #left { background: #C1C9E5 url(${h.url_for('/static/style/menu_bg.png')}) top repeat-x; } + .unified-panel-body { + overflow: auto; + } + .toolMenu { + margin-left: 10px; + } </style></%def> diff -r 1f63dbb2ed28333e0b6ad7f930199dceacf5766a -r 0fa860b8ee41897a63c7c66581a16c360f48b11a templates/webapps/tool_shed/index.mako --- a/templates/webapps/tool_shed/index.mako +++ b/templates/webapps/tool_shed/index.mako @@ -2,7 +2,6 @@ <%namespace file="/message.mako" import="render_msg" /><%def name="stylesheets()"> - ${parent.stylesheets()} ## Include "base.css" for styling tool menu and forms (details) ${h.css( "base", "autocomplete_tagging", "tool_menu" )} @@ -14,6 +13,12 @@ #left { background: #C1C9E5 url(${h.url_for('/static/style/menu_bg.png')}) top repeat-x; } + .unified-panel-body { + overflow: auto; + } + .toolMenu { + margin-left: 10px; + } </style></%def> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: guerler: Scratchbook: Update, fix tooltip, re-factor code
by commits-noreply＠bitbucket.org 09 Jul '13

09 Jul '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1f63dbb2ed28/ Changeset: 1f63dbb2ed28 User: guerler Date: 2013-07-09 19:32:58 Summary: Scratchbook: Update, fix tooltip, re-factor code Affected #: 7 files diff -r 62d88237b1f23c26ff76565ee047b5c9f6ca1cb1 -r 1f63dbb2ed28333e0b6ad7f930199dceacf5766a static/scripts/galaxy.frame.js --- a/static/scripts/galaxy.frame.js +++ b/static/scripts/galaxy.frame.js @@ -123,8 +123,8 @@ this.event_initialize(); // add - //$(".galaxy-frame-active").tooltip({title: "Enable/Disable Scratchbook"}); - //$(".galaxy-frame-load").tooltip({title: "Show/Hide Scratchbook"}); + $(".galaxy-frame-active").tooltip({title: "Enable/Disable Scratchbook"}); + $(".galaxy-frame-load").tooltip({title: "Show/Hide Scratchbook"}); // catch window resize event var self = this; @@ -731,8 +731,7 @@ this.visible = false; // hide - for (var i in this.frame_list) - $(this.frame_list[i].id).fadeOut('fast'); + $(".galaxy-frame").fadeOut('fast'); // add class $(".galaxy-frame-load .icon").addClass("fa-icon-eye-close"); @@ -748,8 +747,7 @@ this.visible = true; // show - for (var i in this.frame_list) - $(this.frame_list[i].id).fadeIn('fast'); + $(".galaxy-frame").fadeIn('fast'); // add class $(".galaxy-frame-load .icon").addClass("fa-icon-eye-open"); @@ -800,59 +798,68 @@ if (!this.active) { // load frame in main window - if (options.center) + if (options.location == 'center') { var galaxy_main = $( window.parent.document ).find( 'iframe#galaxy_main' ); galaxy_main.attr( 'src', options.content ); } else window.location = options.content; - + // stop return; } - + + // check for number of frames + if (this.frame_counter > this.options.frame_max) + { + alert("You have reached the maximum number of allowed frames (" + this.options.frame_max + ")."); + return; + } + // generate frame identifier var frame_id = '#galaxy-frame-' + (this.frame_counter_id++); // check if frame exists - if ($(frame_id).length === 0 && this.options.frame_max > this.frame_counter) + if ($(frame_id).length !== 0) { - // reset top - this.top = this.options.top_min; + alert("This frame already exists. This page might contain multiple frame managers."); + return; + } + + // reset top + this.top = this.options.top_min; + + // append + $(this.el).append(this.frame_template(frame_id.substring(1), options.title, options.type, options.content)); - // set dimensions - options.width = this.to_pixel_coord('width', this.options.frame.cols); - options.height = this.to_pixel_coord('height', this.options.frame.rows); + // construct a new frame + var frame = { + id : frame_id, + screen_location : {}, + grid_location : {}, + grid_rank : null, + grid_lock : false + }; + + // set dimensions + options.width = this.to_pixel_coord('width', this.options.frame.cols); + options.height = this.to_pixel_coord('height', this.options.frame.rows); + + // add to frame list + this.frame_list[frame_id] = frame; + + // increase frame counter + this.frame_counter++; + + // resize + this.frame_resize(frame, {width: options.width, height: options.height}); - // append - $(this.el).append(this.frame_template(frame_id.substring(1), options.title, options.type, options.content)); + // place frame + this.frame_insert(frame, {top: 0, left: 0}, true); - // construct a new frame - var frame = { - id : frame_id, - screen_location : {}, - grid_location : {}, - grid_rank : null, - grid_lock : false - }; - - // increase frame counter - this.frame_counter++; - - // add to frame list - this.frame_list[frame_id] = frame; - - // resize - this.frame_resize(frame, {width: options.width, height: options.height}); - - // place frame - this.frame_insert(frame, {top: 0, left: 0}, true); - - // show frames if hidden - if (!this.visible) - this.panel_show_hide(); - } else - alert("You have reached the maximum number of allowed frames (" + this.options.frame_max + ")."); + // show frames if hidden + if (!this.visible) + this.panel_show_hide(); }, // frame insert at given location @@ -922,7 +929,7 @@ // panel menu this.menu_refresh(); }, - + // naive frame place frame_place: function(frame, animate) { @@ -1052,7 +1059,7 @@ '<span class="f-title">' + title + '</span>' + '<span class="f-icon f-pin fa-icon-pushpin"></span>' + '<span class="f-icon f-close fa-icon-trash"></span>' + - '</div>' + + '</div>' + '<div class="f-content f-corner">' + content + '<div class="f-cover"></div>' + '</div>' + diff -r 62d88237b1f23c26ff76565ee047b5c9f6ca1cb1 -r 1f63dbb2ed28333e0b6ad7f930199dceacf5766a static/scripts/mvc/dataset/hda-base.js --- a/static/scripts/mvc/dataset/hda-base.js +++ b/static/scripts/mvc/dataset/hda-base.js @@ -237,7 +237,7 @@ } else { displayBtnData.title = _l( 'View data' ); - displayBtnData.href = "javascript:parent.frame_manager.frame_new({title: 'Data Viewer', type: 'url', center: true, content: '" + this.urls.display + "'});"; + displayBtnData.href = "javascript:parent.frame_manager.frame_new({title: 'Data Viewer', type: 'url', location: 'center', content: '" + this.urls.display + "'});"; } this.displayButton = new IconButtonView({ model : new IconButton( displayBtnData ) }); diff -r 62d88237b1f23c26ff76565ee047b5c9f6ca1cb1 -r 1f63dbb2ed28333e0b6ad7f930199dceacf5766a static/scripts/packed/galaxy.frame.js --- a/static/scripts/packed/galaxy.frame.js +++ b/static/scripts/packed/galaxy.frame.js @@ -1,1 +1,1 @@ -define(["utils/galaxy.css","libs/backbone/backbone-relational"],function(b){var a=Backbone.View.extend({el:"#everything",el_header:"#masthead",options:{frame:{cols:6,rows:3},rows:1000,cell:130,margin:5,scroll:5,top_min:40,frame_max:10},cols:0,top:0,top_max:0,frame_counter:0,frame_counter_id:0,frame_list:[],galaxy_frame_shadow:null,visible:false,active:false,initialize:function(d){b.load_file(d.url.styles+"/galaxy.frame.css");if(d){this.options=_.defaults(d,this.options)}this.top=this.top_max=this.options.top_min;$(this.el).append(this.frame_template_background());$(this.el).append(this.frame_template_menu());$(this.el_header).append(this.frame_template_header());var e="#galaxy-frame-shadow";$(this.el).append(this.frame_template_shadow(e.substring(1)));this.galaxy_frame_shadow={id:e,screen_location:{},grid_location:{},grid_rank:null,grid_lock:false};this.frame_resize(this.galaxy_frame_shadow,{width:0,height:0});this.frame_list[e]=this.galaxy_frame_shadow;this.panel_refresh();this.event_initialize();var c=this;$(window).resize(function(){c.panel_refresh()});window.onbeforeunload=function(){if(c.frame_counter>0){return"You opened "+c.frame_counter+" frame(s) which will be lost."}}},is_mobile:function(){return navigator.userAgent.match(/mobile|(iPad)|(iPhone)|(iPod)|(android)|(webOS)/i)},event:{type:null,target:null,xy:null},event_initialize:function(){this.events={mousemove:"event_frame_mouse_move",mouseup:"event_frame_mouse_up",mouseleave:"event_frame_mouse_up",mousewheel:"event_panel_scroll",DOMMouseScroll:"event_panel_scroll","mousedown .galaxy-frame":"event_frame_mouse_down","mousedown .galaxy-frame-active":"event_panel_active","mousedown .galaxy-frame-load":"event_panel_load","mousedown .galaxy-frame-background":"event_panel_load","mousedown .galaxy-frame-scroll-up":"event_panel_scroll_up","mousedown .galaxy-frame-scroll-down":"event_panel_scroll_down","mousedown .f-close":"event_frame_close","mousedown .f-pin":"event_frame_lock"};this.delegateEvents(this.events)},event_frame_mouse_down:function(c){if(this.event.type!==null){return}if($(c.target).hasClass("f-header")||$(c.target).hasClass("f-title")){this.event.type="drag"}if($(c.target).hasClass("f-resize")){this.event.type="resize"}if(this.event.type===null){return}c.preventDefault();this.event.target=this.event_get_frame(c.target);if(this.event.target.grid_lock){this.event.type=null;return}this.event.xy={x:c.originalEvent.pageX,y:c.originalEvent.pageY};this.frame_drag_start(this.event.target)},event_frame_mouse_move:function(i){if(this.event.type!="drag"&&this.event.type!="resize"){return}var g={x:i.originalEvent.pageX,y:i.originalEvent.pageY};var d={x:g.x-this.event.xy.x,y:g.y-this.event.xy.y};this.event.xy=g;var h=this.frame_screen(this.event.target);if(this.event.type=="resize"){h.width+=d.x;h.height+=d.y;var f=this.options.cell-this.options.margin-1;h.width=Math.max(h.width,f);h.height=Math.max(h.height,f);this.frame_resize(this.event.target,h);h.width=this.to_grid_coord("width",h.width)+1;h.height=this.to_grid_coord("height",h.height)+1;h.width=this.to_pixel_coord("width",h.width);h.height=this.to_pixel_coord("height",h.height);this.frame_resize(this.galaxy_frame_shadow,h);this.frame_insert(this.galaxy_frame_shadow,{top:this.to_grid_coord("top",h.top),left:this.to_grid_coord("left",h.left)})}if(this.event.type=="drag"){h.left+=d.x;h.top+=d.y;this.frame_offset(this.event.target,h);var c={top:this.to_grid_coord("top",h.top),left:this.to_grid_coord("left",h.left)};if(c.left!==0){c.left++}this.frame_insert(this.galaxy_frame_shadow,c)}},event_frame_mouse_up:function(c){if(this.event.type!="drag"&&this.event.type!="resize"){return}this.frame_drag_stop(this.event.target);this.event.type=null},event_frame_close:function(d){if(this.event.type!==null){return}d.preventDefault();var f=this.event_get_frame(d.target);var c=this;$(f.id).fadeOut("fast",function(){$(f.id).remove();delete c.frame_list[f.id];c.frame_counter--;c.panel_refresh(true);c.panel_animation_complete();if(c.visible&&c.frame_counter==0){c.panel_show_hide()}})},event_frame_lock:function(c){if(this.event.type!==null){return}c.preventDefault();var d=this.event_get_frame(c.target);if(d.grid_lock){d.grid_lock=false;$(d.id).find(".f-pin").removeClass("f-toggle");$(d.id).find(".f-header").removeClass("f-not-allowed");$(d.id).find(".f-title").removeClass("f-not-allowed");$(d.id).find(".f-resize").show();$(d.id).find(".f-close").show()}else{d.grid_lock=true;$(d.id).find(".f-pin").addClass("f-toggle");$(d.id).find(".f-header").addClass("f-not-allowed");$(d.id).find(".f-title").addClass("f-not-allowed");$(d.id).find(".f-resize").hide();$(d.id).find(".f-close").hide()}},event_panel_load:function(c){if(this.event.type!==null){return}c.preventDefault();this.panel_show_hide()},event_panel_active:function(c){if(this.event.type!==null){return}c.preventDefault();this.panel_active_disable()},event_panel_scroll:function(c){if(this.event.type!==null||!this.visible){return}c.preventDefault();var d=c.originalEvent.detail?c.originalEvent.detail:c.originalEvent.wheelDelta/-3;this.panel_scroll(d)},event_panel_scroll_up:function(c){if(this.event.type!==null){return}c.preventDefault();this.panel_scroll(-this.options.scroll)},event_panel_scroll_down:function(c){if(this.event.type!==null){return}c.preventDefault();this.panel_scroll(this.options.scroll)},event_get_frame:function(c){return this.frame_list["#"+$(c).closest(".galaxy-frame").attr("id")]},frame_drag_start:function(d){this.frame_focus(d,true);var c=this.frame_screen(d);this.frame_resize(this.galaxy_frame_shadow,c);this.frame_grid(this.galaxy_frame_shadow,d.grid_location);d.grid_location=null;$(this.galaxy_frame_shadow.id).show();$(".f-cover").show()},frame_drag_stop:function(d){this.frame_focus(d,false);var c=this.frame_screen(this.galaxy_frame_shadow);this.frame_resize(d,c);this.frame_grid(d,this.galaxy_frame_shadow.grid_location,true);this.galaxy_frame_shadow.grid_location=null;$(this.galaxy_frame_shadow.id).hide();$(".f-cover").hide();this.panel_animation_complete()},to_grid_coord:function(e,d){var c=(e=="width"||e=="height")?1:-1;if(e=="top"){d-=this.top}return parseInt((d+c*this.options.margin)/this.options.cell,10)},to_pixel_coord:function(e,f){var c=(e=="width"||e=="height")?1:-1;var d=(f*this.options.cell)-c*this.options.margin;if(e=="top"){d+=this.top}return d},to_grid:function(c){return{top:this.to_grid_coord("top",c.top),left:this.to_grid_coord("left",c.left),width:this.to_grid_coord("width",c.width),height:this.to_grid_coord("height",c.height)}},to_pixel:function(c){return{top:this.to_pixel_coord("top",c.top),left:this.to_pixel_coord("left",c.left),width:this.to_pixel_coord("width",c.width),height:this.to_pixel_coord("height",c.height)}},is_collision:function(e){function c(h,g){return !(h.left>g.left+g.width-1||h.left+h.width-1<g.left||h.top>g.top+g.height-1||h.top+h.height-1<g.top)}for(var d in this.frame_list){var f=this.frame_list[d];if(f.grid_location===null){continue}if(c(e,f.grid_location)){return true}}return false},location_rank:function(c){return(c.top*this.cols)+c.left},menu_refresh:function(){$(".galaxy-frame-load .number").text(this.frame_counter);if(this.frame_counter==0){$(".galaxy-frame-load").hide()}else{$(".galaxy-frame-load").show()}if(this.top==this.options.top_min){$(".galaxy-frame-scroll-up").hide()}else{$(".galaxy-frame-scroll-up").show()}if(this.top==this.top_max){$(".galaxy-frame-scroll-down").hide()}else{$(".galaxy-frame-scroll-down").show()}},panel_animation_complete:function(){var c=this;$(".galaxy-frame").promise().done(function(){c.panel_scroll(0,true)})},panel_refresh:function(c){this.cols=parseInt($(window).width()/this.options.cell,10)+1;this.frame_insert(null,null,c)},panel_scroll:function(h,c){var e=this.top-this.options.scroll*h;e=Math.max(e,this.top_max);e=Math.min(e,this.options.top_min);if(this.top!=e){for(var d in this.frame_list){var g=this.frame_list[d];if(g.grid_location!==null){var f={top:g.screen_location.top-(this.top-e),left:g.screen_location.left};this.frame_offset(g,f,c)}}this.top=e}this.menu_refresh()},panel_show_hide:function(){if(this.visible){this.visible=false;for(var c in this.frame_list){$(this.frame_list[c].id).fadeOut("fast")}$(".galaxy-frame-load .icon").addClass("fa-icon-eye-close");$(".galaxy-frame-load .icon").removeClass("fa-icon-eye-open");$(".galaxy-frame-background").hide();$(".galaxy-frame-menu").hide()}else{this.visible=true;for(var c in this.frame_list){$(this.frame_list[c].id).fadeIn("fast")}$(".galaxy-frame-load .icon").addClass("fa-icon-eye-open");$(".galaxy-frame-load .icon").removeClass("fa-icon-eye-close");$(this.galaxy_frame_shadow.id).hide();$(".galaxy-frame-background").show();this.menu_refresh()}},panel_active_disable:function(){if(this.active){this.active=false;$(".galaxy-frame-active .icon").removeClass("f-toggle");if(this.visible){this.panel_show_hide()}}else{this.active=true;$(".galaxy-frame-active .icon").addClass("f-toggle")}},frame_new:function(d){if(!this.active){if(d.center){var c=$(window.parent.document).find("iframe#galaxy_main");c.attr("src",d.content)}else{window.location=d.content}return}var e="#galaxy-frame-"+(this.frame_counter_id++);if($(e).length===0&&this.options.frame_max>this.frame_counter){this.top=this.options.top_min;d.width=this.to_pixel_coord("width",this.options.frame.cols);d.height=this.to_pixel_coord("height",this.options.frame.rows);$(this.el).append(this.frame_template(e.substring(1),d.title,d.type,d.content));var f={id:e,screen_location:{},grid_location:{},grid_rank:null,grid_lock:false};this.frame_counter++;this.frame_list[e]=f;this.frame_resize(f,{width:d.width,height:d.height});this.frame_insert(f,{top:0,left:0},true);if(!this.visible){this.panel_show_hide()}}else{alert("You have reached the maximum number of allowed frames ("+this.options.frame_max+").")}},frame_insert:function(j,c,e){var d=[];if(j){j.grid_location=null;d.push([j,this.location_rank(c)])}var g=null;for(g in this.frame_list){var h=this.frame_list[g];if(h.grid_location!==null&&!h.grid_lock){h.grid_location=null;d.push([h,h.grid_rank])}}d.sort(function(k,f){var m=k[1];var l=f[1];return m<l?-1:(m>l?1:0)});for(g=0;g<d.length;g++){this.frame_place(d[g][0],e)}this.top_max=0;for(var g in this.frame_list){var j=this.frame_list[g];if(j.grid_location!==null){this.top_max=Math.max(this.top_max,j.grid_location.top+j.grid_location.height)}}this.top_max=$(window).height()-this.top_max*this.options.cell-2*this.options.margin;this.top_max=Math.min(this.top_max,this.options.top_min);this.menu_refresh()},frame_place:function(k,d){k.grid_location=null;var h=this.to_grid(this.frame_screen(k));var c=false;for(var f=0;f<this.options.rows;f++){for(var e=0;e<Math.max(1,this.cols-h.width);e++){h.top=f;h.left=e;if(!this.is_collision(h)){c=true;break}}if(c){break}}if(c){this.frame_grid(k,h,d)}else{console.log("Grid dimensions exceeded.")}},frame_focus:function(e,c){var d=parseInt(b.get_attribute("galaxy-frame","z-index"))+(c?1:0);$(e.id).css("z-index",d)},frame_offset:function(f,e,d){f.screen_location.left=e.left;f.screen_location.top=e.top;if(d){this.frame_focus(f,true);var c=this;$(f.id).animate({top:e.top,left:e.left},"fast",function(){c.frame_focus(f,false)})}else{$(f.id).css({top:e.top,left:e.left})}},frame_resize:function(d,c){$(d.id).css({width:c.width,height:c.height});d.screen_location.width=c.width;d.screen_location.height=c.height},frame_grid:function(e,c,d){e.grid_location=c;this.frame_offset(e,this.to_pixel(c),d);e.grid_rank=this.location_rank(c)},frame_screen:function(d){var c=d.screen_location;return{top:c.top,left:c.left,width:c.width,height:c.height}},frame_template:function(f,e,c,d){if(!e){e=""}if(c=="url"){d='<iframe scrolling="auto" class="f-iframe" src="'+d+'"></iframe>'}return'<div id="'+f+'" class="galaxy-frame f-corner"><div class="f-header f-corner"><span class="f-title">'+e+'</span><span class="f-icon f-pin fa-icon-pushpin"></span><span class="f-icon f-close fa-icon-trash"></span></div><div class="f-content f-corner">'+d+'<div class="f-cover"></div></div><span class="f-resize f-icon f-corner fa-icon-resize-full"></span></div>'},frame_template_shadow:function(c){return'<div id="'+c+'" class="galaxy-frame-shadow f-corner"></div>'},frame_template_background:function(){return'<div class="galaxy-frame-background"></div>'},frame_template_header:function(){return'<div class="galaxy-frame-load f-corner"><div class="number f-corner">0</div><div class="icon fa-icon-2x"></div></div><div class="galaxy-frame-active f-corner" style="position: absolute; top: 8px;"><div class="icon fa-icon-2x fa-icon-th"></div></div>'},frame_template_menu:function(){return'<div class="galaxy-frame-scroll-up galaxy-frame-menu fa-icon-chevron-up fa-icon-2x"></div><div class="galaxy-frame-scroll-down galaxy-frame-menu fa-icon-chevron-down fa-icon-2x"></div>'}});return{GalaxyFrameManager:a}}); \ No newline at end of file +define(["utils/galaxy.css","libs/backbone/backbone-relational"],function(b){var a=Backbone.View.extend({el:"#everything",el_header:"#masthead",options:{frame:{cols:6,rows:3},rows:1000,cell:130,margin:5,scroll:5,top_min:40,frame_max:10},cols:0,top:0,top_max:0,frame_counter:0,frame_counter_id:0,frame_list:[],galaxy_frame_shadow:null,visible:false,active:false,initialize:function(d){b.load_file(d.url.styles+"/galaxy.frame.css");if(d){this.options=_.defaults(d,this.options)}this.top=this.top_max=this.options.top_min;$(this.el).append(this.frame_template_background());$(this.el).append(this.frame_template_menu());$(this.el_header).append(this.frame_template_header());var e="#galaxy-frame-shadow";$(this.el).append(this.frame_template_shadow(e.substring(1)));this.galaxy_frame_shadow={id:e,screen_location:{},grid_location:{},grid_rank:null,grid_lock:false};this.frame_resize(this.galaxy_frame_shadow,{width:0,height:0});this.frame_list[e]=this.galaxy_frame_shadow;this.panel_refresh();this.event_initialize();$(".galaxy-frame-active").tooltip({title:"Enable/Disable Scratchbook"});$(".galaxy-frame-load").tooltip({title:"Show/Hide Scratchbook"});var c=this;$(window).resize(function(){c.panel_refresh()});window.onbeforeunload=function(){if(c.frame_counter>0){return"You opened "+c.frame_counter+" frame(s) which will be lost."}}},is_mobile:function(){return navigator.userAgent.match(/mobile|(iPad)|(iPhone)|(iPod)|(android)|(webOS)/i)},event:{type:null,target:null,xy:null},event_initialize:function(){this.events={mousemove:"event_frame_mouse_move",mouseup:"event_frame_mouse_up",mouseleave:"event_frame_mouse_up",mousewheel:"event_panel_scroll",DOMMouseScroll:"event_panel_scroll","mousedown .galaxy-frame":"event_frame_mouse_down","mousedown .galaxy-frame-active":"event_panel_active","mousedown .galaxy-frame-load":"event_panel_load","mousedown .galaxy-frame-background":"event_panel_load","mousedown .galaxy-frame-scroll-up":"event_panel_scroll_up","mousedown .galaxy-frame-scroll-down":"event_panel_scroll_down","mousedown .f-close":"event_frame_close","mousedown .f-pin":"event_frame_lock"};this.delegateEvents(this.events)},event_frame_mouse_down:function(c){if(this.event.type!==null){return}if($(c.target).hasClass("f-header")||$(c.target).hasClass("f-title")){this.event.type="drag"}if($(c.target).hasClass("f-resize")){this.event.type="resize"}if(this.event.type===null){return}c.preventDefault();this.event.target=this.event_get_frame(c.target);if(this.event.target.grid_lock){this.event.type=null;return}this.event.xy={x:c.originalEvent.pageX,y:c.originalEvent.pageY};this.frame_drag_start(this.event.target)},event_frame_mouse_move:function(i){if(this.event.type!="drag"&&this.event.type!="resize"){return}var g={x:i.originalEvent.pageX,y:i.originalEvent.pageY};var d={x:g.x-this.event.xy.x,y:g.y-this.event.xy.y};this.event.xy=g;var h=this.frame_screen(this.event.target);if(this.event.type=="resize"){h.width+=d.x;h.height+=d.y;var f=this.options.cell-this.options.margin-1;h.width=Math.max(h.width,f);h.height=Math.max(h.height,f);this.frame_resize(this.event.target,h);h.width=this.to_grid_coord("width",h.width)+1;h.height=this.to_grid_coord("height",h.height)+1;h.width=this.to_pixel_coord("width",h.width);h.height=this.to_pixel_coord("height",h.height);this.frame_resize(this.galaxy_frame_shadow,h);this.frame_insert(this.galaxy_frame_shadow,{top:this.to_grid_coord("top",h.top),left:this.to_grid_coord("left",h.left)})}if(this.event.type=="drag"){h.left+=d.x;h.top+=d.y;this.frame_offset(this.event.target,h);var c={top:this.to_grid_coord("top",h.top),left:this.to_grid_coord("left",h.left)};if(c.left!==0){c.left++}this.frame_insert(this.galaxy_frame_shadow,c)}},event_frame_mouse_up:function(c){if(this.event.type!="drag"&&this.event.type!="resize"){return}this.frame_drag_stop(this.event.target);this.event.type=null},event_frame_close:function(d){if(this.event.type!==null){return}d.preventDefault();var f=this.event_get_frame(d.target);var c=this;$(f.id).fadeOut("fast",function(){$(f.id).remove();delete c.frame_list[f.id];c.frame_counter--;c.panel_refresh(true);c.panel_animation_complete();if(c.visible&&c.frame_counter==0){c.panel_show_hide()}})},event_frame_lock:function(c){if(this.event.type!==null){return}c.preventDefault();var d=this.event_get_frame(c.target);if(d.grid_lock){d.grid_lock=false;$(d.id).find(".f-pin").removeClass("f-toggle");$(d.id).find(".f-header").removeClass("f-not-allowed");$(d.id).find(".f-title").removeClass("f-not-allowed");$(d.id).find(".f-resize").show();$(d.id).find(".f-close").show()}else{d.grid_lock=true;$(d.id).find(".f-pin").addClass("f-toggle");$(d.id).find(".f-header").addClass("f-not-allowed");$(d.id).find(".f-title").addClass("f-not-allowed");$(d.id).find(".f-resize").hide();$(d.id).find(".f-close").hide()}},event_panel_load:function(c){if(this.event.type!==null){return}c.preventDefault();this.panel_show_hide()},event_panel_active:function(c){if(this.event.type!==null){return}c.preventDefault();this.panel_active_disable()},event_panel_scroll:function(c){if(this.event.type!==null||!this.visible){return}c.preventDefault();var d=c.originalEvent.detail?c.originalEvent.detail:c.originalEvent.wheelDelta/-3;this.panel_scroll(d)},event_panel_scroll_up:function(c){if(this.event.type!==null){return}c.preventDefault();this.panel_scroll(-this.options.scroll)},event_panel_scroll_down:function(c){if(this.event.type!==null){return}c.preventDefault();this.panel_scroll(this.options.scroll)},event_get_frame:function(c){return this.frame_list["#"+$(c).closest(".galaxy-frame").attr("id")]},frame_drag_start:function(d){this.frame_focus(d,true);var c=this.frame_screen(d);this.frame_resize(this.galaxy_frame_shadow,c);this.frame_grid(this.galaxy_frame_shadow,d.grid_location);d.grid_location=null;$(this.galaxy_frame_shadow.id).show();$(".f-cover").show()},frame_drag_stop:function(d){this.frame_focus(d,false);var c=this.frame_screen(this.galaxy_frame_shadow);this.frame_resize(d,c);this.frame_grid(d,this.galaxy_frame_shadow.grid_location,true);this.galaxy_frame_shadow.grid_location=null;$(this.galaxy_frame_shadow.id).hide();$(".f-cover").hide();this.panel_animation_complete()},to_grid_coord:function(e,d){var c=(e=="width"||e=="height")?1:-1;if(e=="top"){d-=this.top}return parseInt((d+c*this.options.margin)/this.options.cell,10)},to_pixel_coord:function(e,f){var c=(e=="width"||e=="height")?1:-1;var d=(f*this.options.cell)-c*this.options.margin;if(e=="top"){d+=this.top}return d},to_grid:function(c){return{top:this.to_grid_coord("top",c.top),left:this.to_grid_coord("left",c.left),width:this.to_grid_coord("width",c.width),height:this.to_grid_coord("height",c.height)}},to_pixel:function(c){return{top:this.to_pixel_coord("top",c.top),left:this.to_pixel_coord("left",c.left),width:this.to_pixel_coord("width",c.width),height:this.to_pixel_coord("height",c.height)}},is_collision:function(e){function c(h,g){return !(h.left>g.left+g.width-1||h.left+h.width-1<g.left||h.top>g.top+g.height-1||h.top+h.height-1<g.top)}for(var d in this.frame_list){var f=this.frame_list[d];if(f.grid_location===null){continue}if(c(e,f.grid_location)){return true}}return false},location_rank:function(c){return(c.top*this.cols)+c.left},menu_refresh:function(){$(".galaxy-frame-load .number").text(this.frame_counter);if(this.frame_counter==0){$(".galaxy-frame-load").hide()}else{$(".galaxy-frame-load").show()}if(this.top==this.options.top_min){$(".galaxy-frame-scroll-up").hide()}else{$(".galaxy-frame-scroll-up").show()}if(this.top==this.top_max){$(".galaxy-frame-scroll-down").hide()}else{$(".galaxy-frame-scroll-down").show()}},panel_animation_complete:function(){var c=this;$(".galaxy-frame").promise().done(function(){c.panel_scroll(0,true)})},panel_refresh:function(c){this.cols=parseInt($(window).width()/this.options.cell,10)+1;this.frame_insert(null,null,c)},panel_scroll:function(h,c){var e=this.top-this.options.scroll*h;e=Math.max(e,this.top_max);e=Math.min(e,this.options.top_min);if(this.top!=e){for(var d in this.frame_list){var g=this.frame_list[d];if(g.grid_location!==null){var f={top:g.screen_location.top-(this.top-e),left:g.screen_location.left};this.frame_offset(g,f,c)}}this.top=e}this.menu_refresh()},panel_show_hide:function(){if(this.visible){this.visible=false;$(".galaxy-frame").fadeOut("fast");$(".galaxy-frame-load .icon").addClass("fa-icon-eye-close");$(".galaxy-frame-load .icon").removeClass("fa-icon-eye-open");$(".galaxy-frame-background").hide();$(".galaxy-frame-menu").hide()}else{this.visible=true;$(".galaxy-frame").fadeIn("fast");$(".galaxy-frame-load .icon").addClass("fa-icon-eye-open");$(".galaxy-frame-load .icon").removeClass("fa-icon-eye-close");$(this.galaxy_frame_shadow.id).hide();$(".galaxy-frame-background").show();this.menu_refresh()}},panel_active_disable:function(){if(this.active){this.active=false;$(".galaxy-frame-active .icon").removeClass("f-toggle");if(this.visible){this.panel_show_hide()}}else{this.active=true;$(".galaxy-frame-active .icon").addClass("f-toggle")}},frame_new:function(d){if(!this.active){if(d.location=="center"){var c=$(window.parent.document).find("iframe#galaxy_main");c.attr("src",d.content)}else{window.location=d.content}return}if(this.frame_counter>this.options.frame_max){alert("You have reached the maximum number of allowed frames ("+this.options.frame_max+").");return}var e="#galaxy-frame-"+(this.frame_counter_id++);if($(e).length!==0){alert("This frame already exists. This page might contain multiple frame managers.");return}this.top=this.options.top_min;$(this.el).append(this.frame_template(e.substring(1),d.title,d.type,d.content));var f={id:e,screen_location:{},grid_location:{},grid_rank:null,grid_lock:false};d.width=this.to_pixel_coord("width",this.options.frame.cols);d.height=this.to_pixel_coord("height",this.options.frame.rows);this.frame_list[e]=f;this.frame_counter++;this.frame_resize(f,{width:d.width,height:d.height});this.frame_insert(f,{top:0,left:0},true);if(!this.visible){this.panel_show_hide()}},frame_insert:function(j,c,e){var d=[];if(j){j.grid_location=null;d.push([j,this.location_rank(c)])}var g=null;for(g in this.frame_list){var h=this.frame_list[g];if(h.grid_location!==null&&!h.grid_lock){h.grid_location=null;d.push([h,h.grid_rank])}}d.sort(function(k,f){var m=k[1];var l=f[1];return m<l?-1:(m>l?1:0)});for(g=0;g<d.length;g++){this.frame_place(d[g][0],e)}this.top_max=0;for(var g in this.frame_list){var j=this.frame_list[g];if(j.grid_location!==null){this.top_max=Math.max(this.top_max,j.grid_location.top+j.grid_location.height)}}this.top_max=$(window).height()-this.top_max*this.options.cell-2*this.options.margin;this.top_max=Math.min(this.top_max,this.options.top_min);this.menu_refresh()},frame_place:function(k,d){k.grid_location=null;var h=this.to_grid(this.frame_screen(k));var c=false;for(var f=0;f<this.options.rows;f++){for(var e=0;e<Math.max(1,this.cols-h.width);e++){h.top=f;h.left=e;if(!this.is_collision(h)){c=true;break}}if(c){break}}if(c){this.frame_grid(k,h,d)}else{console.log("Grid dimensions exceeded.")}},frame_focus:function(e,c){var d=parseInt(b.get_attribute("galaxy-frame","z-index"))+(c?1:0);$(e.id).css("z-index",d)},frame_offset:function(f,e,d){f.screen_location.left=e.left;f.screen_location.top=e.top;if(d){this.frame_focus(f,true);var c=this;$(f.id).animate({top:e.top,left:e.left},"fast",function(){c.frame_focus(f,false)})}else{$(f.id).css({top:e.top,left:e.left})}},frame_resize:function(d,c){$(d.id).css({width:c.width,height:c.height});d.screen_location.width=c.width;d.screen_location.height=c.height},frame_grid:function(e,c,d){e.grid_location=c;this.frame_offset(e,this.to_pixel(c),d);e.grid_rank=this.location_rank(c)},frame_screen:function(d){var c=d.screen_location;return{top:c.top,left:c.left,width:c.width,height:c.height}},frame_template:function(f,e,c,d){if(!e){e=""}if(c=="url"){d='<iframe scrolling="auto" class="f-iframe" src="'+d+'"></iframe>'}return'<div id="'+f+'" class="galaxy-frame f-corner"><div class="f-header f-corner"><span class="f-title">'+e+'</span><span class="f-icon f-pin fa-icon-pushpin"></span><span class="f-icon f-close fa-icon-trash"></span></div><div class="f-content f-corner">'+d+'<div class="f-cover"></div></div><span class="f-resize f-icon f-corner fa-icon-resize-full"></span></div>'},frame_template_shadow:function(c){return'<div id="'+c+'" class="galaxy-frame-shadow f-corner"></div>'},frame_template_background:function(){return'<div class="galaxy-frame-background"></div>'},frame_template_header:function(){return'<div class="galaxy-frame-load f-corner"><div class="number f-corner">0</div><div class="icon fa-icon-2x"></div></div><div class="galaxy-frame-active f-corner" style="position: absolute; top: 8px;"><div class="icon fa-icon-2x fa-icon-th"></div></div>'},frame_template_menu:function(){return'<div class="galaxy-frame-scroll-up galaxy-frame-menu fa-icon-chevron-up fa-icon-2x"></div><div class="galaxy-frame-scroll-down galaxy-frame-menu fa-icon-chevron-down fa-icon-2x"></div>'}});return{GalaxyFrameManager:a}}); \ No newline at end of file diff -r 62d88237b1f23c26ff76565ee047b5c9f6ca1cb1 -r 1f63dbb2ed28333e0b6ad7f930199dceacf5766a static/scripts/packed/mvc/dataset/hda-base.js --- a/static/scripts/packed/mvc/dataset/hda-base.js +++ b/static/scripts/packed/mvc/dataset/hda-base.js @@ -1,1 +1,1 @@ -var HDABaseView=Backbone.View.extend(LoggableMixin).extend({tagName:"div",className:"historyItemContainer",initialize:function(a){if(a.logger){this.logger=this.model.logger=a.logger}this.log(this+".initialize:",a);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];if(!a.urlTemplates){throw ("HDAView needs urlTemplates on initialize")}this.urlTemplates=a.urlTemplates;this.expanded=a.expanded||false;this.model.bind("change",function(c,d){var b=_.without(_.keys(d.changes),"display_apps","display_types");if(b.length){this.render()}else{if(this.expanded){this._render_displayApps()}}},this)},render:function(){var b=this,e=this.model.get("id"),c=this.model.get("state"),a=$("<div/>").attr("id","historyItem-"+e),d=(this.$el.children().size()===0);this.$el.attr("id","historyItemContainer-"+e);this.urls=this._renderUrls(this.urlTemplates,this.model.toJSON());a.addClass("historyItemWrapper").addClass("historyItem").addClass("historyItem-"+c);a.append(this._render_warnings());a.append(this._render_titleBar());this._setUpBehaviors(a);this.body=$(this._render_body());a.append(this.body);this.$el.fadeOut("fast",function(){b.$el.children().remove();b.$el.append(a).fadeIn("fast",function(){b.log(b+" rendered:",b.$el);var f="rendered";if(d){f+=":initial"}else{if(b.model.inReadyState()){f+=":ready"}}b.trigger(f)})});return this},_renderUrls:function(d,a){var b=this,c={};_.each(d,function(e,f){if(_.isObject(e)){c[f]=b._renderUrls(e,a)}else{if(f==="meta_download"){c[f]=b._renderMetaDownloadUrls(e,a)}else{try{c[f]=_.template(e,a)}catch(g){throw (b+"._renderUrls error: "+g+"\n rendering:"+e+"\n with "+JSON.stringify(a))}}}});return c},_renderMetaDownloadUrls:function(b,a){return _.map(a.meta_files,function(c){return{url:_.template(b,{id:a.id,file_type:c.file_type}),file_type:c.file_type}})},_setUpBehaviors:function(a){a=a||this.$el;make_popup_menus(a);a.find(".tooltip").tooltip({placement:"bottom"})},_render_warnings:function(){return $(jQuery.trim(HDABaseView.templates.messages(this.model.toJSON())))},_render_titleBar:function(){var a=$('<div class="historyItemTitleBar" style="overflow: hidden"></div>');a.append(this._render_titleButtons());a.append('<span class="state-icon"></span>');a.append(this._render_titleLink());return a},_render_titleButtons:function(){var a=$('<div class="historyItemButtons"></div>');a.append(this._render_displayButton());return a},_render_displayButton:function(){if((this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(this.model.get("state")===HistoryDatasetAssociation.STATES.NEW)||(!this.model.get("accessible"))){this.displayButton=null;return null}var a={icon_class:"display",target:"galaxy_main"};if(this.model.get("purged")){a.enabled=false;a.title=_l("Cannot display datasets removed from disk")}else{a.title=_l("View data");a.href="javascript:parent.frame_manager.frame_new({title: 'Data Viewer', type: 'url', center: true, content: '"+this.urls.display+"'});"}this.displayButton=new IconButtonView({model:new IconButton(a)});return this.displayButton.render().$el},_render_titleLink:function(){return $(jQuery.trim(HDABaseView.templates.titleLink(_.extend(this.model.toJSON(),{urls:this.urls}))))},_render_hdaSummary:function(){var a=_.extend(this.model.toJSON(),{urls:this.urls});return HDABaseView.templates.hdaSummary(a)},_render_primaryActionButtons:function(c){var a=this,b=$("<div/>").attr("id","primary-actions-"+this.model.get("id"));_.each(c,function(d){b.append(d.call(a))});return b},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var a=HDABaseView.templates.downloadLinks(_.extend(this.model.toJSON(),{urls:this.urls}));return $(a.trim())},_render_showParamsButton:function(){this.showParamsButton=new IconButtonView({model:new IconButton({title:_l("View details"),href:this.urls.show_params,target:"galaxy_main",icon_class:"information"})});return this.showParamsButton.render().$el},_render_displayAppArea:function(){return $("<div/>").addClass("display-apps")},_render_displayApps:function(c){c=c||this.$el;var d=c.find("div.display-apps"),a=this.model.get("display_types"),b=this.model.get("display_apps");if((!this.model.hasData())||(!c||!c.length)||(!d.length)){return}d.html(null);if(!_.isEmpty(a)){d.append(HDABaseView.templates.displayApps({displayApps:a}))}if(!_.isEmpty(b)){d.append(HDABaseView.templates.displayApps({displayApps:b}))}},_render_peek:function(){var a=this.model.get("peek");if(!a){return null}return $("<div/>").append($("<pre/>").attr("id","peek"+this.model.get("id")).addClass("peek").append(a))},_render_body:function(){var a=$("<div/>").attr("id","info-"+this.model.get("id")).addClass("historyItemBody").attr("style","display: none");if(this.expanded){this._render_body_html(a);a.css("display","block")}return a},_render_body_html:function(a){a.html("");switch(this.model.get("state")){case HistoryDatasetAssociation.STATES.NEW:this._render_body_new(a);break;case HistoryDatasetAssociation.STATES.NOT_VIEWABLE:this._render_body_not_viewable(a);break;case HistoryDatasetAssociation.STATES.UPLOAD:this._render_body_uploading(a);break;case HistoryDatasetAssociation.STATES.PAUSED:this._render_body_paused(a);break;case HistoryDatasetAssociation.STATES.QUEUED:this._render_body_queued(a);break;case HistoryDatasetAssociation.STATES.RUNNING:this._render_body_running(a);break;case HistoryDatasetAssociation.STATES.ERROR:this._render_body_error(a);break;case HistoryDatasetAssociation.STATES.DISCARDED:this._render_body_discarded(a);break;case HistoryDatasetAssociation.STATES.SETTING_METADATA:this._render_body_setting_metadata(a);break;case HistoryDatasetAssociation.STATES.EMPTY:this._render_body_empty(a);break;case HistoryDatasetAssociation.STATES.FAILED_METADATA:this._render_body_failed_metadata(a);break;case HistoryDatasetAssociation.STATES.OK:this._render_body_ok(a);break;default:a.append($('<div>Error: unknown dataset state "'+this.model.get("state")+'".</div>'))}a.append('<div style="clear: both"></div>');this._setUpBehaviors(a)},_render_body_new:function(b){var a=_l("This is a new dataset and not all of its data are available yet");b.append($("<div>"+_l(a)+"</div>"))},_render_body_not_viewable:function(a){a.append($("<div>"+_l("You do not have permission to view dataset")+"</div>"))},_render_body_uploading:function(a){a.append($("<div>"+_l("Dataset is uploading")+"</div>"))},_render_body_queued:function(a){a.append($("<div>"+_l("Job is waiting to run")+"</div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_paused:function(a){a.append($("<div>"+_l("Job is paused. Use the history menu to resume")+"</div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_running:function(a){a.append("<div>"+_l("Job is currently running")+"</div>");a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_error:function(a){if(!this.model.get("purged")){a.append($("<div>"+this.model.get("misc_blurb")+"</div>"))}a.append((_l("An error occurred with this dataset")+": <i>"+$.trim(this.model.get("misc_info"))+"</i>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers.concat([this._render_downloadButton])))},_render_body_discarded:function(a){a.append("<div>"+_l("The job creating this dataset was cancelled before completion")+".</div>");a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_setting_metadata:function(a){a.append($("<div>"+_l("Metadata is being auto-detected")+".</div>"))},_render_body_empty:function(a){a.append($("<div>"+_l("No data")+": <i>"+this.model.get("misc_blurb")+"</i></div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_failed_metadata:function(a){a.append($(HDABaseView.templates.failedMetadata(_.extend(this.model.toJSON(),{urls:this.urls}))));this._render_body_ok(a)},_render_body_ok:function(a){a.append(this._render_hdaSummary());if(this.model.isDeletedOrPurged()){a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton]));return}a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton]));a.append('<div class="clear"/>');a.append(this._render_displayAppArea());this._render_displayApps(a);a.append(this._render_peek())},events:{"click .historyItemTitle":"toggleBodyVisibility"},toggleBodyVisibility:function(c,a){var b=this;this.expanded=(a===undefined)?(!this.body.is(":visible")):(a);if(this.expanded){b._render_body_html(b.body);this.body.slideDown("fast",function(){b.trigger("body-expanded",b.model.get("id"))})}else{this.body.slideUp("fast",function(){b.trigger("body-collapsed",b.model.get("id"))})}},remove:function(b){var a=this;this.$el.fadeOut("fast",function(){a.$el.remove();a.off();if(b){b()}})},toString:function(){var a=(this.model)?(this.model+""):("(no model)");return"HDABaseView("+a+")"}});HDABaseView.templates={warningMsg:Handlebars.templates["template-warningmessagesmall"],messages:Handlebars.templates["template-hda-warning-messages"],titleLink:Handlebars.templates["template-hda-titleLink"],hdaSummary:Handlebars.templates["template-hda-hdaSummary"],downloadLinks:Handlebars.templates["template-hda-downloadLinks"],failedMetadata:Handlebars.templates["template-hda-failedMetadata"],displayApps:Handlebars.templates["template-hda-displayApps"]}; \ No newline at end of file +var HDABaseView=Backbone.View.extend(LoggableMixin).extend({tagName:"div",className:"historyItemContainer",initialize:function(a){if(a.logger){this.logger=this.model.logger=a.logger}this.log(this+".initialize:",a);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];if(!a.urlTemplates){throw ("HDAView needs urlTemplates on initialize")}this.urlTemplates=a.urlTemplates;this.expanded=a.expanded||false;this.model.bind("change",function(c,d){var b=_.without(_.keys(d.changes),"display_apps","display_types");if(b.length){this.render()}else{if(this.expanded){this._render_displayApps()}}},this)},render:function(){var b=this,e=this.model.get("id"),c=this.model.get("state"),a=$("<div/>").attr("id","historyItem-"+e),d=(this.$el.children().size()===0);this.$el.attr("id","historyItemContainer-"+e);this.urls=this._renderUrls(this.urlTemplates,this.model.toJSON());a.addClass("historyItemWrapper").addClass("historyItem").addClass("historyItem-"+c);a.append(this._render_warnings());a.append(this._render_titleBar());this._setUpBehaviors(a);this.body=$(this._render_body());a.append(this.body);this.$el.fadeOut("fast",function(){b.$el.children().remove();b.$el.append(a).fadeIn("fast",function(){b.log(b+" rendered:",b.$el);var f="rendered";if(d){f+=":initial"}else{if(b.model.inReadyState()){f+=":ready"}}b.trigger(f)})});return this},_renderUrls:function(d,a){var b=this,c={};_.each(d,function(e,f){if(_.isObject(e)){c[f]=b._renderUrls(e,a)}else{if(f==="meta_download"){c[f]=b._renderMetaDownloadUrls(e,a)}else{try{c[f]=_.template(e,a)}catch(g){throw (b+"._renderUrls error: "+g+"\n rendering:"+e+"\n with "+JSON.stringify(a))}}}});return c},_renderMetaDownloadUrls:function(b,a){return _.map(a.meta_files,function(c){return{url:_.template(b,{id:a.id,file_type:c.file_type}),file_type:c.file_type}})},_setUpBehaviors:function(a){a=a||this.$el;make_popup_menus(a);a.find(".tooltip").tooltip({placement:"bottom"})},_render_warnings:function(){return $(jQuery.trim(HDABaseView.templates.messages(this.model.toJSON())))},_render_titleBar:function(){var a=$('<div class="historyItemTitleBar" style="overflow: hidden"></div>');a.append(this._render_titleButtons());a.append('<span class="state-icon"></span>');a.append(this._render_titleLink());return a},_render_titleButtons:function(){var a=$('<div class="historyItemButtons"></div>');a.append(this._render_displayButton());return a},_render_displayButton:function(){if((this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(this.model.get("state")===HistoryDatasetAssociation.STATES.NEW)||(!this.model.get("accessible"))){this.displayButton=null;return null}var a={icon_class:"display",target:"galaxy_main"};if(this.model.get("purged")){a.enabled=false;a.title=_l("Cannot display datasets removed from disk")}else{a.title=_l("View data");a.href="javascript:parent.frame_manager.frame_new({title: 'Data Viewer', type: 'url', location: 'center', content: '"+this.urls.display+"'});"}this.displayButton=new IconButtonView({model:new IconButton(a)});return this.displayButton.render().$el},_render_titleLink:function(){return $(jQuery.trim(HDABaseView.templates.titleLink(_.extend(this.model.toJSON(),{urls:this.urls}))))},_render_hdaSummary:function(){var a=_.extend(this.model.toJSON(),{urls:this.urls});return HDABaseView.templates.hdaSummary(a)},_render_primaryActionButtons:function(c){var a=this,b=$("<div/>").attr("id","primary-actions-"+this.model.get("id"));_.each(c,function(d){b.append(d.call(a))});return b},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var a=HDABaseView.templates.downloadLinks(_.extend(this.model.toJSON(),{urls:this.urls}));return $(a.trim())},_render_showParamsButton:function(){this.showParamsButton=new IconButtonView({model:new IconButton({title:_l("View details"),href:this.urls.show_params,target:"galaxy_main",icon_class:"information"})});return this.showParamsButton.render().$el},_render_displayAppArea:function(){return $("<div/>").addClass("display-apps")},_render_displayApps:function(c){c=c||this.$el;var d=c.find("div.display-apps"),a=this.model.get("display_types"),b=this.model.get("display_apps");if((!this.model.hasData())||(!c||!c.length)||(!d.length)){return}d.html(null);if(!_.isEmpty(a)){d.append(HDABaseView.templates.displayApps({displayApps:a}))}if(!_.isEmpty(b)){d.append(HDABaseView.templates.displayApps({displayApps:b}))}},_render_peek:function(){var a=this.model.get("peek");if(!a){return null}return $("<div/>").append($("<pre/>").attr("id","peek"+this.model.get("id")).addClass("peek").append(a))},_render_body:function(){var a=$("<div/>").attr("id","info-"+this.model.get("id")).addClass("historyItemBody").attr("style","display: none");if(this.expanded){this._render_body_html(a);a.css("display","block")}return a},_render_body_html:function(a){a.html("");switch(this.model.get("state")){case HistoryDatasetAssociation.STATES.NEW:this._render_body_new(a);break;case HistoryDatasetAssociation.STATES.NOT_VIEWABLE:this._render_body_not_viewable(a);break;case HistoryDatasetAssociation.STATES.UPLOAD:this._render_body_uploading(a);break;case HistoryDatasetAssociation.STATES.PAUSED:this._render_body_paused(a);break;case HistoryDatasetAssociation.STATES.QUEUED:this._render_body_queued(a);break;case HistoryDatasetAssociation.STATES.RUNNING:this._render_body_running(a);break;case HistoryDatasetAssociation.STATES.ERROR:this._render_body_error(a);break;case HistoryDatasetAssociation.STATES.DISCARDED:this._render_body_discarded(a);break;case HistoryDatasetAssociation.STATES.SETTING_METADATA:this._render_body_setting_metadata(a);break;case HistoryDatasetAssociation.STATES.EMPTY:this._render_body_empty(a);break;case HistoryDatasetAssociation.STATES.FAILED_METADATA:this._render_body_failed_metadata(a);break;case HistoryDatasetAssociation.STATES.OK:this._render_body_ok(a);break;default:a.append($('<div>Error: unknown dataset state "'+this.model.get("state")+'".</div>'))}a.append('<div style="clear: both"></div>');this._setUpBehaviors(a)},_render_body_new:function(b){var a=_l("This is a new dataset and not all of its data are available yet");b.append($("<div>"+_l(a)+"</div>"))},_render_body_not_viewable:function(a){a.append($("<div>"+_l("You do not have permission to view dataset")+"</div>"))},_render_body_uploading:function(a){a.append($("<div>"+_l("Dataset is uploading")+"</div>"))},_render_body_queued:function(a){a.append($("<div>"+_l("Job is waiting to run")+"</div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_paused:function(a){a.append($("<div>"+_l("Job is paused. Use the history menu to resume")+"</div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_running:function(a){a.append("<div>"+_l("Job is currently running")+"</div>");a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_error:function(a){if(!this.model.get("purged")){a.append($("<div>"+this.model.get("misc_blurb")+"</div>"))}a.append((_l("An error occurred with this dataset")+": <i>"+$.trim(this.model.get("misc_info"))+"</i>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers.concat([this._render_downloadButton])))},_render_body_discarded:function(a){a.append("<div>"+_l("The job creating this dataset was cancelled before completion")+".</div>");a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_setting_metadata:function(a){a.append($("<div>"+_l("Metadata is being auto-detected")+".</div>"))},_render_body_empty:function(a){a.append($("<div>"+_l("No data")+": <i>"+this.model.get("misc_blurb")+"</i></div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_failed_metadata:function(a){a.append($(HDABaseView.templates.failedMetadata(_.extend(this.model.toJSON(),{urls:this.urls}))));this._render_body_ok(a)},_render_body_ok:function(a){a.append(this._render_hdaSummary());if(this.model.isDeletedOrPurged()){a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton]));return}a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton]));a.append('<div class="clear"/>');a.append(this._render_displayAppArea());this._render_displayApps(a);a.append(this._render_peek())},events:{"click .historyItemTitle":"toggleBodyVisibility"},toggleBodyVisibility:function(c,a){var b=this;this.expanded=(a===undefined)?(!this.body.is(":visible")):(a);if(this.expanded){b._render_body_html(b.body);this.body.slideDown("fast",function(){b.trigger("body-expanded",b.model.get("id"))})}else{this.body.slideUp("fast",function(){b.trigger("body-collapsed",b.model.get("id"))})}},remove:function(b){var a=this;this.$el.fadeOut("fast",function(){a.$el.remove();a.off();if(b){b()}})},toString:function(){var a=(this.model)?(this.model+""):("(no model)");return"HDABaseView("+a+")"}});HDABaseView.templates={warningMsg:Handlebars.templates["template-warningmessagesmall"],messages:Handlebars.templates["template-hda-warning-messages"],titleLink:Handlebars.templates["template-hda-titleLink"],hdaSummary:Handlebars.templates["template-hda-hdaSummary"],downloadLinks:Handlebars.templates["template-hda-downloadLinks"],failedMetadata:Handlebars.templates["template-hda-failedMetadata"],displayApps:Handlebars.templates["template-hda-displayApps"]}; \ No newline at end of file diff -r 62d88237b1f23c26ff76565ee047b5c9f6ca1cb1 -r 1f63dbb2ed28333e0b6ad7f930199dceacf5766a static/style/blue/galaxy.frame.css --- a/static/style/blue/galaxy.frame.css +++ b/static/style/blue/galaxy.frame.css @@ -13,6 +13,11 @@ color: #BCC800; } +.bs-tooltip +{ + z-index: 34010; +} + /* galaxy-frames */ diff -r 62d88237b1f23c26ff76565ee047b5c9f6ca1cb1 -r 1f63dbb2ed28333e0b6ad7f930199dceacf5766a static/style/blue/galaxy.frame.masthead.css --- a/static/style/blue/galaxy.frame.masthead.css +++ b/static/style/blue/galaxy.frame.masthead.css @@ -16,4 +16,9 @@ #right { top: 0 !important; +} + +#left +{ + top: 0 !important; } \ No newline at end of file diff -r 62d88237b1f23c26ff76565ee047b5c9f6ca1cb1 -r 1f63dbb2ed28333e0b6ad7f930199dceacf5766a templates/webapps/galaxy/base_panels.mako --- a/templates/webapps/galaxy/base_panels.mako +++ b/templates/webapps/galaxy/base_panels.mako @@ -117,8 +117,8 @@ ${tab( "analysis", _("Analyze Data"), h.url_for( controller='/root', action='index' ) )} ## Workflow tab. - ${tab( "workflow", _("Workflow"), h.url_for( controller='/workflow', action='index' ) )} - + ${tab( "workflow", _("Workflow"), "javascript:frame_manager.frame_new({title: 'Workflow', type: 'url', content: '" + h.url_for( controller='/workflow', action='index' ) + "'});")} + ## 'Shared Items' or Libraries tab. <% menu_options = [ Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: carlfeberhard: Fix admin left panel scrollbar
by commits-noreply＠bitbucket.org 09 Jul '13

09 Jul '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/62d88237b1f2/ Changeset: 62d88237b1f2 User: carlfeberhard Date: 2013-07-09 18:20:19 Summary: Fix admin left panel scrollbar Affected #: 1 file diff -r 5e9d00b4d205b834fffd9568fde2055032267499 -r 62d88237b1f23c26ff76565ee047b5c9f6ca1cb1 templates/webapps/galaxy/admin/index.mako --- a/templates/webapps/galaxy/admin/index.mako +++ b/templates/webapps/galaxy/admin/index.mako @@ -17,6 +17,13 @@ #left { background: #C1C9E5 url(${h.url_for('/static/style/menu_bg.png')}) top repeat-x; } + + .unified-panel-body { + overflow: auto; + } + .toolMenu { + margin-left: 10px; + } </style></%def> @@ -36,7 +43,7 @@ <div class="unified-panel-header" unselectable="on"><div class='unified-panel-header-inner'>Administration</div></div> - <div class="unified-panel-body" style="padding: 10px; overflow: auto;"> + <div class="unified-panel-body"><div class="toolMenu"><div class="toolSectionList"><div class="toolSectionTitle">Security</div> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: carlfeberhard: Fix form url in history permissions form
by commits-noreply＠bitbucket.org 09 Jul '13

09 Jul '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5e9d00b4d205/ Changeset: 5e9d00b4d205 User: carlfeberhard Date: 2013-07-09 18:10:59 Summary: Fix form url in history permissions form Affected #: 1 file diff -r 9e985bee20419c0cdbf76fadbe2448400820cbb9 -r 5e9d00b4d205b834fffd9568fde2055032267499 templates/webapps/galaxy/history/permissions.mako --- a/templates/webapps/galaxy/history/permissions.mako +++ b/templates/webapps/galaxy/history/permissions.mako @@ -4,5 +4,6 @@ %if trans.user: <% history = trans.get_history() %> - ${render_permission_form( history, history.name, h.url_for(controller='root'), trans.user.all_roles() )} + ${render_permission_form( history, history.name, + h.url_for( controller='root', action='history_set_default_permissions' ), trans.user.all_roles() )} %endif Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Fixes for repairing an installed tool shed repository.
by commits-noreply＠bitbucket.org 09 Jul '13

09 Jul '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9e985bee2041/ Changeset: 9e985bee2041 User: greg Date: 2013-07-09 17:54:49 Summary: Fixes for repairing an installed tool shed repository. Affected #: 4 files diff -r 86efa5ac1fae6fb46e7af9804e036a7ab44b0e26 -r 9e985bee20419c0cdbf76fadbe2448400820cbb9 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 @@ -589,14 +589,6 @@ else: kwd[ 'message' ] = 'All selected tool shed repositories are already installed.' kwd[ 'status' ] = 'error' - elif operation == "repair": - # In this case, tsridslist is ordered. - repositories_for_repair = [] - for tsr_id in tsridslist: - repository = trans.sa_session.query( trans.model.ToolShedRepository ).get( trans.security.decode_id( tsr_id ) ) - repositories_for_repair.append( repository ) - ordered_repo_info_dicts = kwd.get( 'ordered_repo_info_dicts', [] ) - self.repair_tool_shed_repositories( trans, repositories_for_repair, ordered_repo_info_dicts ) return self.repository_installation_grid( trans, **kwd ) @web.expose @@ -1159,23 +1151,29 @@ status=status ) ) tool_shed_repository = suc.get_installed_tool_shed_repository( trans, repository_id ) if kwd.get( 'repair_repository_button', False ): - repair_dict = kwd.get( 'repair_dict', None ) + encoded_repair_dict = kwd.get( 'repair_dict', None ) + if encoded_repair_dict: + repair_dict = encoding_util.tool_shed_decode( encoded_repair_dict ) + else: + repair_dict = None if not repair_dict: repair_dict = repository_util.get_repair_dict( trans, tool_shed_repository ) - ordered_tsr_ids = repair_dict.get( 'ordered_tsr_ids', [] ) - ordered_repo_info_dicts = repair_dict.get( 'ordered_repo_info_dicts', [] ) - if ordered_tsr_ids and ordered_repo_info_dicts: - return trans.response.send_redirect( web.url_for( controller='admin_toolshed', - action='manage_repositories', - operation='repair', - ordered_tsr_ids=ordered_tsr_ids, - ordered_repo_info_dicts=ordered_repo_info_dicts ) ) + ordered_tsr_ids = repair_dict.get( 'ordered_tsr_ids', [] ) + ordered_repo_info_dicts = repair_dict.get( 'ordered_repo_info_dicts', [] ) + if ordered_tsr_ids and ordered_repo_info_dicts: + repositories_for_repair = [] + for tsr_id in ordered_tsr_ids: + repository = trans.sa_session.query( trans.model.ToolShedRepository ).get( trans.security.decode_id( tsr_id ) ) + repositories_for_repair.append( repository ) + return self.repair_tool_shed_repositories( trans, repositories_for_repair, ordered_repo_info_dicts ) tool_shed_repository = suc.get_installed_tool_shed_repository( trans, repository_id ) repair_dict = repository_util.get_repair_dict( trans, tool_shed_repository ) + encoded_repair_dict = encoding_util.tool_shed_encode( repair_dict ) ordered_tsr_ids = repair_dict.get( 'ordered_tsr_ids', [] ) ordered_repo_info_dicts = repair_dict.get( 'ordered_repo_info_dicts', [] ) return trans.fill_template( 'admin/tool_shed_repository/repair_repository.mako', repository=tool_shed_repository, + encoded_repair_dict=encoded_repair_dict, repair_dict=repair_dict, message=message, status=status ) diff -r 86efa5ac1fae6fb46e7af9804e036a7ab44b0e26 -r 9e985bee20419c0cdbf76fadbe2448400820cbb9 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 @@ -110,9 +110,9 @@ installed_repositories.append( installed_repository ) for rd_val in rd_vals: try: - tool_shed, name, owner, changeset_revision, prior_installation_required = container_util.get_components_from_key( rd_key ) + tool_shed, name, owner, changeset_revision, prior_installation_required = rd_val except: - tool_shed, name, owner, changeset_revision = container_util.get_components_from_key( rd_val ) + tool_shed, name, owner, changeset_revision = rd_val installed_repository = suc.get_tool_shed_repository_by_shed_name_owner_changeset_revision( trans.app, tool_shed, name, owner, changeset_revision ) if installed_repository not in installed_repositories: installed_repositories.append( installed_repository ) @@ -182,6 +182,7 @@ # tsr_ids to ensure all repositories are repaired in the required order. tsr_ids = [] repo_info_dicts = [] + tool_panel_section_keys = [] for installed_repository in installed_repositories: tsr_ids.append( trans.security.encode_id( installed_repository.id ) ) repository_clone_url = suc.generate_clone_url_for_installed_repository( trans.app, installed_repository ) @@ -189,8 +190,36 @@ metadata = installed_repository.metadata if metadata: tool_dependencies = metadata.get( 'tool_dependencies', None ) + tool_panel_section_dict = metadata.get( 'tool_panel_section', None ) + if tool_panel_section_dict: + # The installed_repository must be in the uninstalled state. The structure of tool_panel_section_dict is: + # {<tool guid> : [{ 'id':<section id>, 'name':<section name>, 'version':<section version>, 'tool_config':<tool config file name> }]} + # Here is an example: + # {"localhost:9009/repos/test/filter/Filter1/1.1.0": + # [{"id": "filter_and_sort", "name": "Filter and Sort", "tool_config": "filtering.xml", "version": ""}]} + # Currently all tools contained within an installed tool shed repository must be loaded into the same section in the tool panel, so we can + # get the section id of the first guid in the tool_panel_section_dict. In the future, we'll have to handle different sections per guid. + guid = tool_panel_section_dict.keys()[ 0 ] + section_dicts = tool_panel_section_dict[ guid ] + section_dict = section_dicts[ 0 ] + tool_panel_section_id = section_dict[ 'id' ] + tool_panel_section_name = section_dict[ 'name' ] + if tool_panel_section_id: + tool_panel_section_key, tool_panel_section = tool_util.get_or_create_tool_section( trans, + tool_panel_section_id=tool_panel_section_id, + new_tool_panel_section=tool_panel_section_name ) + tool_panel_section_keys.append( tool_panel_section_key ) + else: + # The tools will be loaded outside of any sections in the tool panel. + tool_panel_section_keys.append( None ) + else: + # The installed_repository must be in the installed state, so we can skip determining if it has tools that are displayed in a tool panel section + # since no changes will be made to it. + tool_panel_section_keys.append( None ) else: tool_dependencies = None + # The tools will be loaded outside of any sections in the tool panel. + tool_panel_section_keys.append( None ) repo_info_dict = create_repo_info_dict( trans=trans, repository_clone_url=repository_clone_url, changeset_revision=installed_repository.changeset_revision, @@ -202,11 +231,11 @@ tool_dependencies=tool_dependencies, repository_dependencies=repository_dependencies ) repo_info_dicts.append( repo_info_dict ) - # We don't consider tool_panel_section_keys since the repository database records already exist. - ordered_tsr_ids, ordered_repo_info_dicts, ordered_tool_panel_section_keys = order_components_for_installation( trans, - tsr_ids, - repo_info_dicts, - tool_panel_section_keys=None ) + ordered_tsr_ids, ordered_repo_info_dicts, ordered_tool_panel_section_keys = \ + order_components_for_installation( trans, + tsr_ids, + repo_info_dicts, + tool_panel_section_keys=tool_panel_section_keys ) repair_dict[ 'ordered_tsr_ids' ] = ordered_tsr_ids repair_dict[ 'ordered_repo_info_dicts' ] = ordered_repo_info_dicts repair_dict[ 'ordered_tool_panel_section_keys' ] = ordered_tool_panel_section_keys @@ -245,7 +274,7 @@ repository_dependencies=None ) return repo_info_dict, includes_tools, includes_tool_dependencies, includes_tools_for_display_in_tool_panel, has_repository_dependencies -def get_repository_components_for_installation( encoded_tsr_id, encoded_tsr_ids, repo_info_dicts, tool_panel_section_keys=None ): +def get_repository_components_for_installation( encoded_tsr_id, encoded_tsr_ids, repo_info_dicts, tool_panel_section_keys ): """ The received encoded_tsr_ids, repo_info_dicts, and tool_panel_section_keys are 3 lists that contain associated elements at each location in the list. This method will return the elements from repo_info_dicts and tool_panel_section_keys associated with the received encoded_tsr_id @@ -254,10 +283,7 @@ for index, tsr_id in enumerate( encoded_tsr_ids ): if tsr_id == encoded_tsr_id: repo_info_dict = repo_info_dicts[ index ] - if tool_panel_section_keys: - tool_panel_section_key = tool_panel_section_keys[ index ] - else: - tool_panel_section_key = None + tool_panel_section_key = tool_panel_section_keys[ index ] return repo_info_dict, tool_panel_section_key return None, None @@ -684,7 +710,7 @@ lock.release() return new_containers_dict -def order_components_for_installation( trans, tsr_ids, repo_info_dicts, tool_panel_section_keys=None ): +def order_components_for_installation( trans, tsr_ids, repo_info_dicts, tool_panel_section_keys ): """ Some repositories may have repository dependencies that are required to be installed before the dependent repository. This method will inspect the list of repositories about to be installed and make sure to order them appropriately. For each repository about to be installed, if required repositories are not @@ -713,16 +739,14 @@ tool_panel_section_keys=tool_panel_section_keys ) ordered_tsr_ids.append( prior_install_required_id ) ordered_repo_info_dicts.append( prior_repo_info_dict ) - if tool_panel_section_keys: - ordered_tool_panel_section_keys.append( prior_tool_panel_section_key ) + ordered_tool_panel_section_keys.append( prior_tool_panel_section_key ) repo_info_dict, tool_panel_section_key = get_repository_components_for_installation( tsr_id, tsr_ids, repo_info_dicts, tool_panel_section_keys=tool_panel_section_keys ) ordered_tsr_ids.append( tsr_id ) ordered_repo_info_dicts.append( repo_info_dict ) - if tool_panel_section_keys: - ordered_tool_panel_section_keys.append( tool_panel_section_key ) + ordered_tool_panel_section_keys.append( tool_panel_section_key ) return ordered_tsr_ids, ordered_repo_info_dicts, ordered_tool_panel_section_keys def populate_containers_dict_for_new_install( trans, tool_shed_url, tool_path, readme_files_dict, installed_repository_dependencies, missing_repository_dependencies, @@ -785,11 +809,11 @@ shed_tool_conf, tool_path, relative_install_dir = suc.get_tool_panel_config_tool_path_install_dir( trans.app, repository ) # Reset the repository attributes to the New state for installation. if metadata: - tool_panel_section_key = tool_util.handle_tool_panel_selection( trans, - metadata, - no_changes_checked=True, - tool_panel_section=None, - new_tool_panel_section=None ) + tool_section, new_tool_panel_section, tool_panel_section_key = tool_util.handle_tool_panel_selection( trans, + metadata, + no_changes_checked=True, + tool_panel_section=None, + new_tool_panel_section=None ) else: # The tools will be loaded outside of any sections in the tool panel. tool_panel_section_key = None diff -r 86efa5ac1fae6fb46e7af9804e036a7ab44b0e26 -r 9e985bee20419c0cdbf76fadbe2448400820cbb9 lib/tool_shed/util/tool_util.py --- a/lib/tool_shed/util/tool_util.py +++ b/lib/tool_shed/util/tool_util.py @@ -639,8 +639,7 @@ if 'tools' in metadata: # This forces everything to be loaded into the same section (or no section) in the tool panel. if no_changes_checked: - # Make sure the no_changes check box overrides the new_tool_panel_section if the user checked the check box and entered something - # into the field. + # Make sure the no_changes check box overrides the new_tool_panel_section if the user checked the check box and entered something into the field. new_tool_panel_section = None if 'tool_panel_section' in metadata: tool_panel_dict = metadata[ 'tool_panel_section' ] @@ -649,7 +648,7 @@ else: tool_panel_dict = generate_tool_panel_dict_for_new_install( metadata[ 'tools' ] ) if tool_panel_dict: - #tool_panel_dict is empty when tools exist but are not installed into a tool panel + # The tool_panel_dict is empty when tools exist but are not installed into a tool panel section. tool_section_dicts = tool_panel_dict[ tool_panel_dict.keys()[ 0 ] ] tool_section_dict = tool_section_dicts[ 0 ] original_section_id = tool_section_dict[ 'id' ] diff -r 86efa5ac1fae6fb46e7af9804e036a7ab44b0e26 -r 9e985bee20419c0cdbf76fadbe2448400820cbb9 templates/admin/tool_shed_repository/repair_repository.mako --- a/templates/admin/tool_shed_repository/repair_repository.mako +++ b/templates/admin/tool_shed_repository/repair_repository.mako @@ -25,7 +25,7 @@ <div class="toolForm"><div class="toolFormTitle">Repair tool shed repository '${repository.name}'</div><br/><br/> - <form name="repair_repository" id="repair_repository" action="${h.url_for( controller='admin_toolshed', action='repair_repository', id=trans.security.encode_id( repository.id ), repair_dict=repair_dict )}" method="post" > + <form name="repair_repository" id="repair_repository" action="${h.url_for( controller='admin_toolshed', action='repair_repository', id=trans.security.encode_id( repository.id ), repair_dict=encoded_repair_dict )}" method="post" ><% ordered_repo_info_dicts = repair_dict.get( 'ordered_repo_info_dicts', [] ) %><table class="grid"><tr><th bgcolor="#D8D8D8">Name</th><th bgcolor="#D8D8D8">Owner</th><th bgcolor="#D8D8D8">Changeset revision</th></tr> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Raise an exception with a useful message if a dependency definition file being uploaded to a repository in the tool shed is missing a required name or owner attribute for a repository dependency.
by commits-noreply＠bitbucket.org 08 Jul '13

08 Jul '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/86efa5ac1fae/ Changeset: 86efa5ac1fae User: greg Date: 2013-07-08 20:31:15 Summary: Raise an exception with a useful message if a dependency definition file being uploaded to a repository in the tool shed is missing a required name or owner attribute for a repository dependency. Affected #: 3 files diff -r 2accb50ef103b083f053c9550518d75c7527f706 -r 86efa5ac1fae6fb46e7af9804e036a7ab44b0e26 lib/tool_shed/util/commit_util.py --- a/lib/tool_shed/util/commit_util.py +++ b/lib/tool_shed/util/commit_util.py @@ -164,6 +164,18 @@ suc.handle_email_alerts( trans, repository, content_alert_str=content_alert_str, new_repo_alert=new_repo_alert, admin_only=admin_only ) return True, '', files_to_remove, content_alert_str, undesirable_dirs_removed, undesirable_files_removed +def handle_missing_repository_attribute( elem ): + # <repository name="molecule_datatypes" owner="test" /> + error_message = '' + name = elem.get( 'name' ) + if not name: + error_message += 'The tag is missing the required name attribute. ' + owner = elem.get( 'owner' ) + if not owner: + error_message += 'The tag is missing the required owner attribute. ' + log.debug( error_message ) + return error_message + def handle_gzip( repository, uploaded_file_name ): fd, uncompressed = tempfile.mkstemp( prefix='repo_%d_upload_gunzip_' % repository.id, dir=os.path.dirname( uploaded_file_name ), text=False ) gzipped_file = gzip.GzipFile( uploaded_file_name, 'rb' ) @@ -192,7 +204,10 @@ if root.tag == 'repositories': for index, elem in enumerate( root ): # <repository name="molecule_datatypes" owner="test" changeset_revision="1a070566e9c6" /> - populated, elem = handle_repository_dependency_elem( trans, elem ) + populated, elem, error_message = handle_repository_dependency_elem( trans, elem ) + if error_message: + exception_message = 'The repository_dependencies.xml file contains an invalid <repository> tag. %s' % error_message + raise Exception( exception_message ) if populated: root[ index ] = elem if not altered: @@ -202,6 +217,12 @@ def handle_repository_dependency_elem( trans, elem ): # <repository name="molecule_datatypes" owner="test" changeset_revision="1a070566e9c6" /> + error_message = '' + name = elem.get( 'name' ) + owner = elem.get( 'owner' ) + if not name or not owner: + error_message = handle_missing_repository_attribute( elem ) + return False, elem, error_message populated = False toolshed = elem.get( 'toolshed' ) if not toolshed: @@ -209,8 +230,6 @@ toolshed = str( url_for( '/', qualified=True ) ).rstrip( '/' ) elem.attrib[ 'toolshed' ] = toolshed populated = True - name = elem.get( 'name' ) - owner = elem.get( 'owner' ) changeset_revision = elem.get( 'changeset_revision' ) if not changeset_revision: # Populate the changeset_revision attribute with the latest installable metadata revision for the defined repository. @@ -224,7 +243,9 @@ if lastest_installable_changeset_revision != suc.INITIAL_CHANGELOG_HASH: elem.attrib[ 'changeset_revision' ] = lastest_installable_changeset_revision populated = True - return populated, elem + else: + error_message = 'Unable to locate repository with name %s and owner %s. ' % ( str( name ), str( owner ) ) + return populated, elem, error_message def handle_tool_dependencies_definition( trans, tool_dependencies_config ): altered = False @@ -241,7 +262,10 @@ for package_index, package_elem in enumerate( root_elem ): if package_elem.tag == 'repository': # <repository name="package_eigen_2_0" owner="test" changeset_revision="09eb05087cd0" prior_installation_required="True" /> - populated, repository_elem = handle_repository_dependency_elem( trans, package_elem ) + populated, repository_elem, error_message = handle_repository_dependency_elem( trans, package_elem ) + if error_message: + exception_message = 'The tool_dependencies.xml file contains an invalid <repository> tag. %s' % error_message + raise Exception( exception_message ) if populated: root_elem[ package_index ] = repository_elem package_altered = True @@ -259,7 +283,10 @@ # </repository> # </action> for repo_index, repo_elem in enumerate( action_elem ): - populated, repository_elem = handle_repository_dependency_elem( trans, repo_elem ) + populated, repository_elem, error_message = handle_repository_dependency_elem( trans, repo_elem ) + if error_message: + exception_message = 'The tool_dependencies.xml file contains an invalid <repository> tag. %s' % error_message + raise Exception( exception_message ) if populated: action_elem[ repo_index ] = repository_elem package_altered = True diff -r 2accb50ef103b083f053c9550518d75c7527f706 -r 86efa5ac1fae6fb46e7af9804e036a7ab44b0e26 lib/tool_shed/util/common_util.py --- a/lib/tool_shed/util/common_util.py +++ b/lib/tool_shed/util/common_util.py @@ -63,7 +63,7 @@ else: exception_msg = '\n\nThe entry for the main Galaxy tool shed at %s is missing from the %s file. ' % ( tool_shed, app.config.tool_sheds_config ) exception_msg += 'The entry for this tool shed must always be available in this file, so re-add it before attempting to start your Galaxy server.\n' - raise Exception( exception_msg ) + raise Exception( exception_msg ) return tool_shed_accessible, missing_tool_configs_dict def check_tool_tag_set( elem, migrated_tool_configs_dict, missing_tool_configs_dict ): diff -r 2accb50ef103b083f053c9550518d75c7527f706 -r 86efa5ac1fae6fb46e7af9804e036a7ab44b0e26 lib/tool_shed/util/repository_dependency_util.py --- a/lib/tool_shed/util/repository_dependency_util.py +++ b/lib/tool_shed/util/repository_dependency_util.py @@ -249,7 +249,7 @@ if metadata_dict: invalid_repository_dependencies_dict = metadata_dict.get( 'invalid_repository_dependencies', None ) if invalid_repository_dependencies_dict: - invalid_repository_dependencies = invalid_repository_dependencies_dict[ 'invalid_repository_dependencies' ] + invalid_repository_dependencies = invalid_repository_dependencies_dict.get( 'invalid_repository_dependencies', [] ) for repository_dependency_tup in invalid_repository_dependencies: toolshed, name, owner, changeset_revision, prior_installation_required, error = \ suc.parse_repository_dependency_tuple( repository_dependency_tup, contains_error=True ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Fix for checking the Galaxy environment for missing migrated tools at server startup.
by commits-noreply＠bitbucket.org 08 Jul '13

08 Jul '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2accb50ef103/ Changeset: 2accb50ef103 User: greg Date: 2013-07-08 18:03:22 Summary: Fix for checking the Galaxy environment for missing migrated tools at server startup. Affected #: 1 file diff -r afec613d77fa58ad0de7066a2d9b18daad8cdb88 -r 2accb50ef103b083f053c9550518d75c7527f706 lib/tool_shed/util/common_util.py --- a/lib/tool_shed/util/common_util.py +++ b/lib/tool_shed/util/common_util.py @@ -19,6 +19,7 @@ tool_shed_url = get_tool_shed_url_from_tools_xml_file_path( app, tool_shed ) # The default behavior is that the tool shed is down. tool_shed_accessible = False + missing_tool_configs_dict = odict() if tool_shed_url: for elem in root: if elem.tag == 'repository': @@ -48,7 +49,6 @@ migrated_tool_configs_dict[ tool_elem.get( 'file' ) ] = tool_dependencies if tool_shed_accessible: # Parse the proprietary tool_panel_configs (the default is tool_conf.xml) and generate the list of missing tool config file names. - missing_tool_configs_dict = odict() for tool_panel_config in tool_panel_configs: tree, error_message = xml_util.parse_xml( tool_panel_config ) if tree: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Contributions from Bjorn Gruning - add support for a template_command action type in tool dependency definitions for the tool shed. An example of the new action tag is <action type="template_command" language="cheetah">...</action>. This is a slightly modified version of Bjorn's original patch contribution.
by commits-noreply＠bitbucket.org 08 Jul '13

08 Jul '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/afec613d77fa/ Changeset: afec613d77fa User: greg Date: 2013-07-08 17:31:29 Summary: Contributions from Bjorn Gruning - add support for a template_command action type in tool dependency definitions for the tool shed. An example of the new action tag is <action type="template_command" language="cheetah">...</action>. This is a slightly modified version of Bjorn's original patch contribution. Affected #: 4 files diff -r a691d69caa99ec771062d5dd5312a516af5ff6c1 -r afec613d77fa58ad0de7066a2d9b18daad8cdb88 lib/galaxy/util/template.py --- a/lib/galaxy/util/template.py +++ b/lib/galaxy/util/template.py @@ -6,4 +6,4 @@ def fill_template( template_text, context=None, **kwargs ): if not context: context = kwargs - return str( Template( source=template_text, searchList=[context] ) ) \ No newline at end of file + return str( Template( source=template_text, searchList=[context] ) ) diff -r a691d69caa99ec771062d5dd5312a516af5ff6c1 -r afec613d77fa58ad0de7066a2d9b18daad8cdb88 lib/tool_shed/galaxy_install/tool_dependencies/common_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/common_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/common_util.py @@ -80,10 +80,6 @@ tar.extractall( path=file_path ) tar.close() -def format_traceback(): - ex_type, ex, tb = sys.exc_info() - return ''.join( traceback.format_tb( tb ) ) - def extract_zip( archive_path, extraction_path ): # TODO: change this method to use zipfile.Zipfile.extractall() when we stop supporting Python 2.5. if not zipfile_ok( archive_path ): @@ -99,6 +95,10 @@ zip_archive.close() return True +def format_traceback(): + ex_type, ex, tb = sys.exc_info() + return ''.join( traceback.format_tb( tb ) ) + def get_env_shell_file_path( installation_directory ): env_shell_file_name = 'env.sh' default_location = os.path.abspath( os.path.join( installation_directory, env_shell_file_name ) ) @@ -167,6 +167,14 @@ log.debug( error_message ) return env_shell_file_paths +def get_env_var_values( install_dir ): + env_var_dict = {} + env_var_dict[ 'INSTALL_DIR' ] = install_dir + env_var_dict[ 'system_install' ] = install_dir + # If the Python interpreter is 64bit then we can safely assume that the underlying system is also 64bit. + env_var_dict[ '__is64bit__' ] = sys.maxsize > 2**32 + return env_var_dict + def isbz2( file_path ): return checkers.is_bz2( file_path ) diff -r a691d69caa99ec771062d5dd5312a516af5ff6c1 -r afec613d77fa58ad0de7066a2d9b18daad8cdb88 lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py @@ -8,8 +8,9 @@ import tempfile import shutil from contextlib import contextmanager +from galaxy.util.template import fill_template +from galaxy import eggs -from galaxy import eggs import pkg_resources pkg_resources.require('ssh' ) @@ -297,12 +298,28 @@ with settings( warn_only=True ): cmd = '' for env_shell_file_path in env_shell_file_paths: - for i, env_setting in enumerate( open( env_shell_file_path ) ): + for env_setting in open( env_shell_file_path ): cmd += '%s\n' % env_setting cmd += action_dict[ 'command' ] return_code = handle_command( app, tool_dependency, install_dir, cmd ) if return_code: return + elif action_type == 'template_command': + env_vars = dict() + for env_shell_file_path in env_shell_file_paths: + for env_setting in open( env_shell_file_path ): + env_string = env_setting.split( ';' )[ 0 ] + env_name, env_path = env_string.split( '=' ) + env_vars[ env_name ] = env_path + env_vars.update( common_util.get_env_var_values( install_dir ) ) + language = action_dict[ 'language' ] + with settings( warn_only=True, **env_vars ): + if language == 'cheetah': + # We need to import fabric.api.env so that we can access all collected environment variables. + cmd = fill_template( '#from fabric.api import env\n%s' % action_dict[ 'command' ], context=env_vars ) + return_code = handle_command( app, tool_dependency, install_dir, cmd ) + if return_code: + return elif action_type == 'download_file': # Download a single file to the current working directory. url = action_dict[ 'url' ] diff -r a691d69caa99ec771062d5dd5312a516af5ff6c1 -r afec613d77fa58ad0de7066a2d9b18daad8cdb88 lib/tool_shed/galaxy_install/tool_dependencies/install_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py @@ -361,12 +361,8 @@ sa_session = app.model.context.current def evaluate_template( text ): - """ Substitute variables defined in XML blocks obtained loaded from dependencies file. """ - # # Added for compatibility with CloudBioLinux. - # TODO: Add tool_version substitution for compat with CloudBioLinux. - substitutions = { "INSTALL_DIR" : install_dir, - "system_install" : install_dir } - return Template( text ).safe_substitute( substitutions ) + """ Substitute variables defined in XML blocks from dependencies file.""" + return Template( text ).safe_substitute( common_util.get_env_var_values( install_dir ) ) if not os.path.exists( install_dir ): os.makedirs( install_dir ) @@ -387,6 +383,25 @@ action_dict[ 'command' ] = action_elem_text else: continue + elif action_type == 'template_command': + # Default to Cheetah as it's the first template language supported. + language = action_elem.get( 'language', 'cheetah' ).lower() + if language == 'cheetah': + # Cheetah template syntax. + # <action type="template_command" language="cheetah"> + # #if env.PATH: + # make + # #end if + # </action> + action_elem_text = action_elem.text.strip() + if action_elem_text: + action_dict[ 'language' ] = language + action_dict[ 'command' ] = action_elem_text + else: + continue + else: + log.debug( "Unsupported template language '%s'. Not proceeding." % str( language ) ) + raise Exception( "Unsupported template language '%s' in tool dependency definition." % str( language ) ) elif action_type == 'download_by_url': # <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1…</action> if action_elem.text: @@ -690,4 +705,4 @@ parts = [] for arg in args: parts.append( arg.strip( '/' ) ) - return '/'.join( parts ) \ No newline at end of file + return '/'.join( parts ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Allow public usernames in the tool shed to be a minimum of 3 characters.
by commits-noreply＠bitbucket.org 06 Jul '13

06 Jul '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a691d69caa99/ Changeset: a691d69caa99 User: greg Date: 2013-07-07 01:41:10 Summary: Allow public usernames in the tool shed to be a minimum of 3 characters. Affected #: 2 files diff -r a13a9bce1c09319b0c18f287d17cbc2a7cd544ed -r a691d69caa99ec771062d5dd5312a516af5ff6c1 lib/galaxy/security/validate_user_input.py --- a/lib/galaxy/security/validate_user_input.py +++ b/lib/galaxy/security/validate_user_input.py @@ -23,8 +23,12 @@ return '' if user and user.username == publicname: return '' - if len( publicname ) < 4: - return "Public name must be at least 4 characters in length" + if trans.webapp.name == 'tool_shed': + if len( publicname ) < 3: + return "Public name must be at least 3 characters in length" + else: + if len( publicname ) < 4: + return "Public name must be at least 4 characters in length" if len( publicname ) > 255: return "Public name cannot be more than 255 characters in length" if not( VALID_PUBLICNAME_RE.match( publicname ) ): diff -r a13a9bce1c09319b0c18f287d17cbc2a7cd544ed -r a691d69caa99ec771062d5dd5312a516af5ff6c1 tools/data_source/upload.xml --- a/tools/data_source/upload.xml +++ b/tools/data_source/upload.xml @@ -33,7 +33,7 @@ </param><param name="async_datasets" type="hidden" value="None"/><upload_dataset name="files" title="Specify Files for Dataset" file_type_name="file_type" metadata_ref="files_metadata"> - <param name="file_data" type="file" size="30" label="File" ajax-upload="true" help="TIP: Due to browser limitations, uploading files larger than 2GB is guaranteed to fail. To upload large files, use the URL method (below) or FTP (if enabled by the site administrator)."> + <param name="file_data" type="file" size="30" label="File" ajax-upload="false" help="TIP: Due to browser limitations, uploading files larger than 2GB is guaranteed to fail. To upload large files, use the URL method (below) or FTP (if enabled by the site administrator)."><validator type="expression" message="You will need to reselect the file you specified (%s)." substitute_value_in_message="True">not ( ( isinstance( value, unicode ) or isinstance( value, str ) ) and value != "" )</validator></param><param name="url_paste" type="text" area="true" size="5x35" label="URL/Text" help="Here you may specify a list of URLs (one per line) or paste the contents of a file."/> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Make BAM_to_SAM tool write temporary files to job working directory rather than generic temp space.
by commits-noreply＠bitbucket.org 03 Jul '13

03 Jul '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a13a9bce1c09/ Changeset: a13a9bce1c09 User: jgoecks Date: 2013-07-03 16:39:02 Summary: Make BAM_to_SAM tool write temporary files to job working directory rather than generic temp space. Affected #: 1 file diff -r ebe87051fadff5750ec226490b31e49bdd68b070 -r a13a9bce1c09319b0c18f287d17cbc2a7cd544ed tools/samtools/bam_to_sam.py --- a/tools/samtools/bam_to_sam.py +++ b/tools/samtools/bam_to_sam.py @@ -43,7 +43,7 @@ except: sys.stdout.write( 'Could not determine Samtools version\n' ) - tmp_dir = tempfile.mkdtemp() + tmp_dir = tempfile.mkdtemp( dir='.' ) try: # exit if input file empty Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 02 Jul '13

02 Jul '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/fd4113962c32/ Changeset: fd4113962c32 Branch: stable User: dannon Date: 2013-07-02 16:48:31 Summary: Fix two more downgrade invocations to accept the migrate_engine parameter Affected #: 2 files diff -r 0a06df7da177a204c7f3800ee39e5b9fd0956d7a -r fd4113962c32b67ea0623b6cfd37be63e26ef7c6 lib/galaxy/webapps/tool_shed/model/migrate/versions/0005_drop_tool_related_tables.py --- a/lib/galaxy/webapps/tool_shed/model/migrate/versions/0005_drop_tool_related_tables.py +++ b/lib/galaxy/webapps/tool_shed/model/migrate/versions/0005_drop_tool_related_tables.py @@ -94,7 +94,7 @@ Tool_table.drop() except Exception, e: log.debug( "Dropping tool table failed: %s" % str( e ) ) -def downgrade(): +def downgrade(migrate_engine): # Load existing tables metadata.bind = migrate_engine metadata.reflect() diff -r 0a06df7da177a204c7f3800ee39e5b9fd0956d7a -r fd4113962c32b67ea0623b6cfd37be63e26ef7c6 lib/galaxy/webapps/tool_shed/model/migrate/versions/0018_add_repository_metadata_flag_columns.py --- a/lib/galaxy/webapps/tool_shed/model/migrate/versions/0018_add_repository_metadata_flag_columns.py +++ b/lib/galaxy/webapps/tool_shed/model/migrate/versions/0018_add_repository_metadata_flag_columns.py @@ -64,7 +64,7 @@ except Exception, e: print "Adding missing_test_components column to the repository_metadata table failed: %s" % str( e ) -def downgrade(): +def downgrade(migrate_engine): metadata.bind = migrate_engine metadata.reflect() # Drop missing_test_components and tool_test_results from the repository_metadata table and add tool_test_errors to the repository_metadata table. https://bitbucket.org/galaxy/galaxy-central/commits/ebe87051fadf/ Changeset: ebe87051fadf User: dannon Date: 2013-07-02 16:48:31 Summary: Fix two more downgrade invocations to accept the migrate_engine parameter Affected #: 2 files diff -r 8bf64d93370436a9f5e55b6c04990a382f63b3b9 -r ebe87051fadff5750ec226490b31e49bdd68b070 lib/galaxy/webapps/tool_shed/model/migrate/versions/0005_drop_tool_related_tables.py --- a/lib/galaxy/webapps/tool_shed/model/migrate/versions/0005_drop_tool_related_tables.py +++ b/lib/galaxy/webapps/tool_shed/model/migrate/versions/0005_drop_tool_related_tables.py @@ -94,7 +94,7 @@ Tool_table.drop() except Exception, e: log.debug( "Dropping tool table failed: %s" % str( e ) ) -def downgrade(): +def downgrade(migrate_engine): # Load existing tables metadata.bind = migrate_engine metadata.reflect() diff -r 8bf64d93370436a9f5e55b6c04990a382f63b3b9 -r ebe87051fadff5750ec226490b31e49bdd68b070 lib/galaxy/webapps/tool_shed/model/migrate/versions/0018_add_repository_metadata_flag_columns.py --- a/lib/galaxy/webapps/tool_shed/model/migrate/versions/0018_add_repository_metadata_flag_columns.py +++ b/lib/galaxy/webapps/tool_shed/model/migrate/versions/0018_add_repository_metadata_flag_columns.py @@ -64,7 +64,7 @@ except Exception, e: print "Adding missing_test_components column to the repository_metadata table failed: %s" % str( e ) -def downgrade(): +def downgrade(migrate_engine): metadata.bind = migrate_engine metadata.reflect() # Drop missing_test_components and tool_test_results from the repository_metadata table and add tool_test_errors to the repository_metadata table. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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