July 2013 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: carlfeberhard: api/histories.delete: wrap purge in try/catch, raise HTTPForbidden if config.allow_user_dataset_purge == False and purge == True
by commits-noreply＠bitbucket.org 17 Jul '13

17 Jul '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ef5cc1d272d2/ Changeset: ef5cc1d272d2 User: carlfeberhard Date: 2013-07-17 17:42:14 Summary: api/histories.delete: wrap purge in try/catch, raise HTTPForbidden if config.allow_user_dataset_purge == False and purge == True Affected #: 1 file diff -r 1d05c839c1ea7a83112a98734a6887f7ce419567 -r ef5cc1d272d2805d1c6597b200f9df58a291d863 lib/galaxy/webapps/galaxy/api/histories.py --- a/lib/galaxy/webapps/galaxy/api/histories.py +++ b/lib/galaxy/webapps/galaxy/api/histories.py @@ -4,7 +4,7 @@ import pkg_resources pkg_resources.require( "Paste" ) -from paste.httpexceptions import HTTPBadRequest +from paste.httpexceptions import HTTPBadRequest, HTTPForbidden from galaxy import web from galaxy.util import string_as_bool, restore_text @@ -126,30 +126,39 @@ try: history = self.get_history( trans, history_id, check_ownership=True, check_accessible=False ) + history.deleted = True + + if purge: + if not trans.app.config.allow_user_dataset_purge: + raise HTTPForbidden( detail='This instance does not allow user dataset purging' ) + + # First purge all the datasets + for hda in history.datasets: + if hda.purged: + continue + hda.purged = True + trans.sa_session.add( hda ) + trans.sa_session.flush() + + if hda.dataset.user_can_purge: + try: + hda.dataset.full_delete() + trans.sa_session.add( hda.dataset ) + except: + pass + # flush now to preserve deleted state in case of later interruption + trans.sa_session.flush() + + # Now mark the history as purged + history.purged = True + self.sa_session.add( history ) + + trans.sa_session.flush() + + #TODO: better feedback than this... except Exception, e: return str( e ) - history.deleted = True - if purge and trans.app.config.allow_user_dataset_purge: - # First purge all the datasets - for hda in history.datasets: - if hda.purged: - continue - hda.purged = True - trans.sa_session.add( hda ) - trans.sa_session.flush() - if hda.dataset.user_can_purge: - try: - hda.dataset.full_delete() - trans.sa_session.add( hda.dataset ) - except: - pass - trans.sa_session.flush() - # Now mark the history as purged - history.purged = True - self.sa_session.add( history ) - - trans.sa_session.flush() return 'OK' @web.expose_api 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: 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 Tool dependency definition can only contain a single file named tool_dependencies.xml.' + 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 %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 %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 Tool dependency definition can contain only a single file named tool_dependencies.xml.' + 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.

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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 Revisions" ), + ToolsFunctionallyCorrectColumn( "Tools 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 Revisions" ), + RepositoryGrid.ToolsFunctionallyCorrectColumn( "Tools 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 Revisions" ), + RepositoryGrid.ToolsFunctionallyCorrectColumn( "Tools 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 Revisions" ), + RepositoryGrid.ToolsFunctionallyCorrectColumn( "Tools 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 Revisions" ), + RepositoryGrid.ToolsFunctionallyCorrectColumn( "Tools 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 Revisions" ), + RepositoryGrid.ToolsFunctionallyCorrectColumn( "Tools 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 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>Generic - contents can be any set of valid Galaxy utilities + %if util.UNRESTRICTED in repository_types: + <li>Unrestricted - contents can be any set of valid Galaxy utilities or files %endif %if util.TOOL_DEPENDENCY_DEFINITION in repository_types: <li>Tool dependency definition - 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. " - 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 11 Jul '13

11 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 11 Jul '13

11 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 11 Jul '13

11 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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