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commit/galaxy-central: greg: Fixes for handling tool shed repositories that include tool_data_table_conf.xml.sample files. The fixes apply to determining if the tool is valid in the tool shed and also to the Galaxy environment when the tool shed repository is installed.
by Bitbucket 30 May '12

30 May '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/ec4584a0e500/ changeset: ec4584a0e500 user: greg date: 2012-05-30 22:00:18 summary: Fixes for handling tool shed repositories that include tool_data_table_conf.xml.sample files. The fixes apply to determining if the tool is valid in the tool shed and also to the Galaxy environment when the tool shed repository is installed. affected #: 6 files diff -r 16a93eb6eaf6b2f9b73bbe10d0e4fab1d1142b9f -r ec4584a0e500e755aa5436691318d442831d8787 lib/galaxy/tool_shed/install_manager.py --- a/lib/galaxy/tool_shed/install_manager.py +++ b/lib/galaxy/tool_shed/install_manager.py @@ -152,7 +152,12 @@ if repository_tools_tups: sample_files = metadata_dict.get( 'sample_files', [] ) # Handle missing data table entries for tool parameters that are dynamically generated select lists. - repository_tools_tups = handle_missing_data_table_entry( self.app, self.tool_path, sample_files, repository_tools_tups ) + repository_tools_tups = handle_missing_data_table_entry( self.app, + tool_shed_repository, + changeset_revision, + self.tool_path, + repository_tools_tups, + work_dir ) # Handle missing index files for tool parameters that are dynamically generated select lists. repository_tools_tups, sample_files_copied = handle_missing_index_file( self.app, self.tool_path, sample_files, repository_tools_tups ) # Copy remaining sample files included in the repository to the ~/tool-data directory of the local Galaxy instance. diff -r 16a93eb6eaf6b2f9b73bbe10d0e4fab1d1142b9f -r ec4584a0e500e755aa5436691318d442831d8787 lib/galaxy/tools/data/__init__.py --- a/lib/galaxy/tools/data/__init__.py +++ b/lib/galaxy/tools/data/__init__.py @@ -6,7 +6,7 @@ to modify the tool configurations. """ -import logging, sys, os.path +import logging, sys, os, os.path, tempfile, shutil from galaxy import util log = logging.getLogger( __name__ ) @@ -15,6 +15,9 @@ """Manages a collection of tool data tables""" def __init__( self, config_filename=None ): self.data_tables = {} + # Store config elements for on-the-fly persistence. + self.data_table_elems = [] + self.data_table_elem_names = [] if config_filename: self.load_from_config_file( config_filename ) def __getitem__( self, key ): @@ -29,14 +32,19 @@ type = table_elem.get( 'type', 'tabular' ) assert type in tool_data_table_types, "Unknown data table type '%s'" % type table_elems.append( table_elem ) + table_elem_name = table_elem.get( 'name', None ) + if table_elem_name and table_elem_name not in self.data_table_elem_names: + self.data_table_elem_names.append( table_elem_name ) + self.data_table_elems.append( table_elem ) table = tool_data_table_types[ type ]( table_elem ) if table.name not in self.data_tables: self.data_tables[ table.name ] = table log.debug( "Loaded tool data table '%s'", table.name ) return table_elems - def add_new_entries_from_config_file( self, config_filename ): + def add_new_entries_from_config_file( self, config_filename, tool_data_table_config_path ): """ - We have 2 cases to handle, files whose root tag is <tables>, for example: + This method is called when a tool shed repository that includes a tool_data_table_conf.xml.sample file is being + installed into a local galaxy instance. We have 2 cases to handle, files whose root tag is <tables>, for example: <tables><table name="tmap_indexes" comment_char="#"> @@ -53,6 +61,8 @@ """ tree = util.parse_xml( config_filename ) root = tree.getroot() + # Make a copy of the current list of data_table_elem_names so we can persist later if changes to the config file are necessary. + original_data_table_elem_names = [ name for name in self.data_table_elem_names ] if root.tag == 'tables': table_elems = self.load_from_config_file( config_filename ) else: @@ -60,11 +70,31 @@ type = root.get( 'type', 'tabular' ) assert type in tool_data_table_types, "Unknown data table type '%s'" % type table_elems.append( root ) + table_elem_name = root.get( 'name', None ) + if table_elem_name and table_elem_name not in self.data_table_elem_names: + self.data_table_elem_names.append( table_elem_name ) + self.data_table_elems.append( root ) table = tool_data_table_types[ type ]( root ) if table.name not in self.data_tables: self.data_tables[ table.name ] = table - log.debug( "Loaded tool data table '%s", table.name ) + log.debug( "Added new tool data table '%s'", table.name ) + if self.data_table_elem_names != original_data_table_elem_names: + # Persist Galaxy's version of the changed tool_data_table_conf.xml file. + self.to_xml_file( tool_data_table_config_path ) return table_elems + def to_xml_file( self, tool_data_table_config_path ): + """Write the current in-memory version of the tool_data-table_conf.xml file to disk.""" + full_path = os.path.abspath( tool_data_table_config_path ) + fd, filename = tempfile.mkstemp() + os.write( fd, '<?xml version="1.0"?>\n' ) + os.write( fd, "\n" ) + os.write( fd, '<tables>\n' ) + for elem in self.data_table_elems: + os.write( fd, '%s' % util.xml_to_string( elem ) ) + os.write( fd, '</tables>\n' ) + os.close( fd ) + shutil.move( filename, full_path ) + os.chmod( full_path, 0644 ) class ToolDataTable( object ): def __init__( self, config_element ): diff -r 16a93eb6eaf6b2f9b73bbe10d0e4fab1d1142b9f -r ec4584a0e500e755aa5436691318d442831d8787 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -1003,10 +1003,10 @@ return shed_url # The tool shed from which the repository was originally installed must no longer be configured in tool_sheds_conf.xml. return None -def handle_missing_data_table_entry( app, tool_path, sample_files, repository_tools_tups ): +def handle_missing_data_table_entry( app, repository, changeset_revision, tool_path, repository_tools_tups, dir ): """ Inspect each tool to see if any have input parameters that are dynamically generated select lists that require entries in the - tool_data_table_conf.xml file. This method is not called only from Galaxy (not the tool shed) when a repository is being installed. + tool_data_table_conf.xml file. This method is called only from Galaxy (not the tool shed) when a repository is being installed. """ missing_data_table_entry = False for index, repository_tools_tup in enumerate( repository_tools_tups ): @@ -1015,13 +1015,11 @@ missing_data_table_entry = True break if missing_data_table_entry: - sample_file = None # The repository must contain a tool_data_table_conf.xml.sample file that includes all required entries for all tools in the repository. - for sample_file in sample_files: - sample_file_name = strip_path( sample_file ) - if sample_file_name == 'tool_data_table_conf.xml.sample': - break - error, correction_msg = handle_sample_tool_data_table_conf_file( app, sample_file ) + sample_tool_data_table_conf = get_config_from_repository( app, 'tool_data_table_conf.xml.sample', repository, changeset_revision, dir ) + # Add entries to the ToolDataTableManager's in-memory data_tables dictionary as well as the list of data_table_elems and the list of + # data_table_elem_names. + error, correction_msg = handle_sample_tool_data_table_conf_file( app, sample_tool_data_table_conf ) if error: # TODO: Do more here than logging an exception. log.debug( correction_msg ) @@ -1059,47 +1057,16 @@ return repository_tools_tups, sample_files_copied def handle_sample_tool_data_table_conf_file( app, filename ): """ - Parse the incoming filename and add new entries to the in-memory app.tool_data_tables dictionary as well as appending them to the - shed's tool_data_table_conf.xml file on disk. + Parse the incoming filename and add new entries to the in-memory app.tool_data_tables dictionary as well as appending them to + Galaxy's tool_data_table_conf.xml file on disk. """ - # TODO: Load an in-memory version of the tool_data_table_conf.xml file, and write it to disk - # from the in-memory version only when changes are made. error = False message = '' try: - new_table_elems = app.tool_data_tables.add_new_entries_from_config_file( filename ) + new_table_elems = app.tool_data_tables.add_new_entries_from_config_file( filename, app.config.tool_data_table_config_path ) except Exception, e: message = str( e ) error = True - """ - # TODO: eliminate this - the shed should not need to write this to disk... - if not error: - # Add an entry to the end of the tool_data_table_conf.xml file. - tdt_config = "%s/tool_data_table_conf.xml" % app.config.root - if os.path.exists( tdt_config ): - # Make a backup of the file since we're going to be changing it. - today = date.today() - backup_date = today.strftime( "%Y_%m_%d" ) - tdt_config_copy = '%s/tool_data_table_conf.xml_%s_backup' % ( app.config.root, backup_date ) - shutil.copy( os.path.abspath( tdt_config ), os.path.abspath( tdt_config_copy ) ) - # Write each line of the tool_data_table_conf.xml file, except the last line to a temp file. - fh = tempfile.NamedTemporaryFile( 'wb' ) - tmp_filename = fh.name - fh.close() - new_tdt_config = open( tmp_filename, 'wb' ) - for i, line in enumerate( open( tdt_config, 'rb' ) ): - if line.find( '</tables>' ) >= 0: - for new_table_elem in new_table_elems: - new_tdt_config.write( ' %s\n' % util.xml_to_string( new_table_elem ).rstrip( '\n' ) ) - new_tdt_config.write( '</tables>\n' ) - else: - new_tdt_config.write( line ) - new_tdt_config.close() - shutil.move( tmp_filename, os.path.abspath( tdt_config ) ) - else: - message = "The required file named tool_data_table_conf.xml does not exist in the Galaxy install directory." - error = True - """ return error, message def handle_tool_dependencies( app, tool_shed_repository, installed_changeset_revision, tool_dependencies_config ): """ @@ -1208,11 +1175,20 @@ tool_panel_dict = generate_tool_panel_dict_for_new_install( metadata_dict[ 'tools' ], tool_section ) repository_tools_tups = get_repository_tools_tups( trans.app, metadata_dict ) if repository_tools_tups: + # Handle missing data table entries for tool parameters that are dynamically generated select lists. work_dir = make_tmp_directory() + repository_tools_tups = handle_missing_data_table_entry( trans.app, + tool_shed_repository, + changeset_revision, + tool_path, + repository_tools_tups, + work_dir ) + try: + shutil.rmtree( work_dir ) + except: + pass + # Handle missing index files for tool parameters that are dynamically generated select lists. sample_files = metadata_dict.get( 'sample_files', [] ) - # Handle missing data table entries for tool parameters that are dynamically generated select lists. - repository_tools_tups = handle_missing_data_table_entry( trans.app, tool_path, sample_files, repository_tools_tups ) - # Handle missing index files for tool parameters that are dynamically generated select lists. repository_tools_tups, sample_files_copied = handle_missing_index_file( trans.app, tool_path, sample_files, repository_tools_tups ) # Copy remaining sample files included in the repository to the ~/tool-data directory of the local Galaxy instance. copy_sample_files( trans.app, sample_files, sample_files_copied=sample_files_copied ) @@ -1406,7 +1382,7 @@ trans.app.toolbox.write_integrated_tool_panel_config_file() def reset_tool_data_tables( app ): # Reset the tool_data_tables to an empty dictionary. - app.tool_data_tables = galaxy.tools.data.ToolDataTableManager() + app.tool_data_tables.data_tables = {} def strip_path( fpath ): file_path, file_name = os.path.split( fpath ) return file_name diff -r 16a93eb6eaf6b2f9b73bbe10d0e4fab1d1142b9f -r ec4584a0e500e755aa5436691318d442831d8787 lib/galaxy/web/controllers/admin_toolshed.py --- a/lib/galaxy/web/controllers/admin_toolshed.py +++ b/lib/galaxy/web/controllers/admin_toolshed.py @@ -613,6 +613,7 @@ else: ctx_rev = repository.ctx_rev clone_repository( repository_clone_url, os.path.abspath( relative_install_dir ), ctx_rev ) + tool_section = None if repository.includes_tools: # Get the location in the tool panel in which each tool was originally loaded. metadata = repository.metadata @@ -668,19 +669,19 @@ tool_section = trans.app.toolbox.tool_panel[ section_key ] else: tool_section = None - tool_shed_repository, metadata_dict, error_message = load_repository_contents( trans, - repository_name=repository.name, - description=repository.description, - owner=repository.owner, - changeset_revision=repository.installed_changeset_revision, - ctx_rev=ctx_rev, - tool_path=tool_path, - repository_clone_url=repository_clone_url, - relative_install_dir=relative_install_dir, - tool_shed=repository.tool_shed, - tool_section=tool_section, - shed_tool_conf=shed_tool_conf, - install_tool_dependencies=install_tool_dependencies ) + tool_shed_repository, metadata_dict, error_message = load_repository_contents( trans, + repository_name=repository.name, + description=repository.description, + owner=repository.owner, + changeset_revision=repository.installed_changeset_revision, + ctx_rev=ctx_rev, + tool_path=tool_path, + repository_clone_url=repository_clone_url, + relative_install_dir=relative_install_dir, + tool_shed=repository.tool_shed, + tool_section=tool_section, + shed_tool_conf=shed_tool_conf, + install_tool_dependencies=install_tool_dependencies ) if error_message: message += error_message status = 'error' diff -r 16a93eb6eaf6b2f9b73bbe10d0e4fab1d1142b9f -r ec4584a0e500e755aa5436691318d442831d8787 lib/galaxy/webapps/community/app.py --- a/lib/galaxy/webapps/community/app.py +++ b/lib/galaxy/webapps/community/app.py @@ -36,8 +36,8 @@ self.security = security.SecurityHelper( id_secret=self.config.id_secret ) # Tag handler self.tag_handler = CommunityTagHandler() - # Tool data tables - self.tool_data_tables = galaxy.tools.data.ToolDataTableManager( self.config.tool_data_table_config_path ) + # Tool data tables - never pass a config file here because the tool shed should always have an empty dictionary! + self.tool_data_tables = galaxy.tools.data.ToolDataTableManager() # The tool shed has no toolbox, but this attribute is still required. self.toolbox = None # Load security policy diff -r 16a93eb6eaf6b2f9b73bbe10d0e4fab1d1142b9f -r ec4584a0e500e755aa5436691318d442831d8787 lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -201,23 +201,18 @@ if options: if options.tool_data_table or options.missing_tool_data_table_name: # Make sure the repository contains a tool_data_table_conf.xml.sample file. - sample_found = False - for sample_file in sample_files: - sample_file_name = strip_path( sample_file ) - if sample_file_name == 'tool_data_table_conf.xml.sample': - sample_found = True - error, correction_msg = handle_sample_tool_data_table_conf_file( trans.app, sample_file ) - if error: - can_set_metadata = False - invalid_files.append( ( sample_file_name, correction_msg ) ) - else: - options.missing_tool_data_table_name = None - break - if not sample_found: + sample_tool_data_table_conf = get_config( 'tool_data_table_conf.xml.sample', repo, repo_dir, ctx, dir ) + if sample_tool_data_table_conf: + error, correction_msg = handle_sample_tool_data_table_conf_file( trans.app, sample_tool_data_table_conf ) + if error: + can_set_metadata = False + invalid_files.append( ( 'tool_data_table_conf.xml.sample', correction_msg ) ) + else: + options.missing_tool_data_table_name = None + else: can_set_metadata = False - correction_msg = "This file requires an entry in the tool_data_table_conf.xml file. " - correction_msg += "Upload a file named tool_data_table_conf.xml.sample to the repository " - correction_msg += "that includes the required entry to correct this error.<br/>" + 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.append( ( xml_file_in_ctx, correction_msg ) ) if options.index_file or options.missing_index_file: # Make sure the repository contains the required xxx.loc.sample file. @@ -245,8 +240,8 @@ correction_msg = "This file refers to a file named <b>%s</b>. " % str( index_file ) correction_msg += "Upload a file named <b>%s.sample</b> to the repository to correct this error." % str( index_file_name ) invalid_files.append( ( xml_file_in_ctx, correction_msg ) ) - # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. - reset_tool_data_tables( trans.app ) + # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. + reset_tool_data_tables( trans.app ) return sample_files_copied, can_set_metadata, invalid_files def clean_repository_metadata( trans, id, changeset_revisions ): # Delete all repository_metadata reecords associated with the repository that have a changeset_revision that is not in changeset_revisions. 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: Load datatype converters and display appliations included in installed tool shed repositories after the app's toolbox has been inititlaized.
by Bitbucket 30 May '12

30 May '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/16a93eb6eaf6/ changeset: 16a93eb6eaf6 user: greg date: 2012-05-30 15:46:25 summary: Load datatype converters and display appliations included in installed tool shed repositories after the app's toolbox has been inititlaized. affected #: 4 files diff -r 356aa8a00cfdd8c1d29f7065601f55120d241005 -r 16a93eb6eaf6b2f9b73bbe10d0e4fab1d1142b9f lib/galaxy/app.py --- a/lib/galaxy/app.py +++ b/lib/galaxy/app.py @@ -62,7 +62,6 @@ # However, if there is a conflict (2 datatypes with the same extension) between a proprietary datatype and a datatype # in the Galaxy distribution, the datatype in the Galaxy distribution will take precedence. If there is a conflict # between 2 proprietary datatypes, the datatype from the repository that was installed earliest will take precedence. - # This will also load proprietary datatype converters and display applications. self.installed_repository_manager.load_proprietary_datatypes() # Load the data types in the Galaxy distribution, which are defined in self.config.datatypes_config. self.datatypes_registry.load_datatypes( self.config.root, self.config.datatypes_config ) @@ -84,6 +83,8 @@ if self.config.get_bool( 'enable_tool_shed_check', False ): from tool_shed import update_manager self.update_manager = update_manager.UpdateManager( self ) + # Load proprietary datatype converters and display applications. + self.installed_repository_manager.load_proprietary_converters_and_display_applications() # Load datatype display applications defined in local datatypes_conf.xml self.datatypes_registry.load_display_applications() # Load datatype converters defined in local datatypes_conf.xml diff -r 356aa8a00cfdd8c1d29f7065601f55120d241005 -r 16a93eb6eaf6b2f9b73bbe10d0e4fab1d1142b9f lib/galaxy/tool_shed/__init__.py --- a/lib/galaxy/tool_shed/__init__.py +++ b/lib/galaxy/tool_shed/__init__.py @@ -19,6 +19,7 @@ self.tool_configs = self.app.config.tool_configs if self.app.config.migrated_tools_config not in self.tool_configs: self.tool_configs.append( self.app.config.migrated_tools_config ) + self.installed_repository_dicts = [] def get_repository_install_dir( self, tool_shed_repository ): for tool_config in self.tool_configs: tree = ElementTree.parse( tool_config ) @@ -43,5 +44,13 @@ .order_by( self.model.ToolShedRepository.table.c.id ): relative_install_dir = self.get_repository_install_dir( tool_shed_repository ) if relative_install_dir: - galaxy.util.shed_util.load_datatype_items( self.app, tool_shed_repository, relative_install_dir ) + installed_repository_dict = galaxy.util.shed_util.load_installed_datatypes( self.app, tool_shed_repository, relative_install_dir ) + if installed_repository_dict: + self.installed_repository_dicts.append( installed_repository_dict ) + def load_proprietary_converters_and_display_applications( self, deactivate=False ): + for installed_repository_dict in self.installed_repository_dicts: + if installed_repository_dict[ 'converter_path' ]: + galaxy.util.shed_util.load_installed_datatype_converters( self.app, installed_repository_dict, deactivate=deactivate ) + if installed_repository_dict[ 'display_path' ]: + galaxy.util.shed_util.load_installed_display_applications( installed_repository_dict, deactivate=deactivate ) \ No newline at end of file diff -r 356aa8a00cfdd8c1d29f7065601f55120d241005 -r 16a93eb6eaf6b2f9b73bbe10d0e4fab1d1142b9f lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -1152,10 +1152,14 @@ parent_id=tool_version_using_parent_id.id ) sa_session.add( tool_version_association ) sa_session.flush() -def load_datatype_items( app, repository, relative_install_dir, deactivate=False ): - # Load proprietary datatypes. +def load_installed_datatype_converters( app, installed_repository_dict, deactivate=False ): + # Load or deactivate proprietary datatype converters + app.datatypes_registry.load_datatype_converters( app.toolbox, installed_repository_dict=installed_repository_dict, deactivate=deactivate ) +def load_installed_datatypes( app, repository, relative_install_dir, deactivate=False ): + # Load proprietary datatypes and return information needed for loading proprietary datatypes converters and display applications later. metadata = repository.metadata work_dir = make_tmp_directory() + repository_dict = None datatypes_config = get_config_from_repository( app, 'datatypes_conf.xml', repository, @@ -1173,16 +1177,14 @@ tool_dicts=metadata.get( 'tools', [] ), converter_path=converter_path, display_path=display_path ) - if converter_path: - # Load or deactivate proprietary datatype converters - app.datatypes_registry.load_datatype_converters( app.toolbox, installed_repository_dict=repository_dict, deactivate=deactivate ) - if display_path: - # Load or deactivate proprietary datatype display applications - app.datatypes_registry.load_display_applications( installed_repository_dict=repository_dict, deactivate=deactivate ) try: shutil.rmtree( work_dir ) except: pass + return repository_dict +def load_installed_display_applications( installed_repository_dict, deactivate=False ): + # Load or deactivate proprietary datatype display applications + app.datatypes_registry.load_display_applications( installed_repository_dict=installed_repository_dict, deactivate=deactivate ) def load_repository_contents( trans, repository_name, description, owner, changeset_revision, ctx_rev, tool_path, repository_clone_url, relative_install_dir, tool_shed=None, tool_section=None, shed_tool_conf=None, install_tool_dependencies=False ): """ @@ -1403,8 +1405,8 @@ # Write the current in-memory version of the integrated_tool_panel.xml file to disk. trans.app.toolbox.write_integrated_tool_panel_config_file() def reset_tool_data_tables( app ): - # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. - app.tool_data_tables = galaxy.tools.data.ToolDataTableManager( app.config.tool_data_table_config_path ) + # Reset the tool_data_tables to an empty dictionary. + app.tool_data_tables = galaxy.tools.data.ToolDataTableManager() def strip_path( fpath ): file_path, file_name = os.path.split( fpath ) return file_name diff -r 356aa8a00cfdd8c1d29f7065601f55120d241005 -r 16a93eb6eaf6b2f9b73bbe10d0e4fab1d1142b9f lib/galaxy/web/controllers/admin_toolshed.py --- a/lib/galaxy/web/controllers/admin_toolshed.py +++ b/lib/galaxy/web/controllers/admin_toolshed.py @@ -189,7 +189,11 @@ remove_from_tool_panel( trans, repository, shed_tool_conf, uninstall=remove_from_disk_checked ) if repository.includes_datatypes: # Deactivate proprietary datatypes. - load_datatype_items( trans.app, repository, repository_install_dir, deactivate=True ) + installed_repository_dict = load_installed_datatypes( trans.app, repository, repository_install_dir, deactivate=True ) + if installed_repository_dict[ 'converter_path' ]: + load_installed_datatype_converters( trans.app, installed_repository_dict, deactivate=True ) + if installed_repository_dict[ 'display_path' ]: + load_installed_display_applications( installed_repository_dict, deactivate=True ) if remove_from_disk_checked: try: # Remove the repository from disk. 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: Fix bug in showing/hiding filters in Trackster.
by Bitbucket 30 May '12

30 May '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/356aa8a00cfd/ changeset: 356aa8a00cfd user: jgoecks date: 2012-05-30 15:39:59 summary: Fix bug in showing/hiding filters in Trackster. affected #: 1 file diff -r 3dd591f01f6aae374142a62c25db98bacae5c4e3 -r 356aa8a00cfdd8c1d29f7065601f55120d241005 static/scripts/trackster.js --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -2598,8 +2598,10 @@ * Update filter's slider. */ update_ui_elt: function () { - // Only show filter if min != max because filter is not useful otherwise. - if (this.min !== this.max) { + // Only show filter if min < max because filter is not useful otherwise. This + // covers all corner cases, such as when min, max have not been defined and + // when min == max. + if (this.min < this.max) { this.parent_div.show(); } 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: natefoo: Handle spaces between commas in admin_users
by Bitbucket 30 May '12

30 May '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/3dd591f01f6a/ changeset: 3dd591f01f6a user: natefoo date: 2012-05-30 10:31:56 summary: Handle spaces between commas in admin_users affected #: 1 file diff -r 37a28d5134b37b8450d9c266e1a5a6bb261461bf -r 3dd591f01f6aae374142a62c25db98bacae5c4e3 lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py +++ b/lib/galaxy/web/framework/__init__.py @@ -657,7 +657,7 @@ def user_is_admin( self ): if self.api_inherit_admin: return True - admin_users = self.app.config.get( "admin_users", "" ).split( "," ) + admin_users = [ x.strip() for x in self.app.config.get( "admin_users", "" ).split( "," ) ] return self.user and admin_users and self.user.email in admin_users def user_can_do_run_as( self ): run_as_users = self.app.config.get( "api_allow_run_as", "" ).split( "," ) 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 loading a tool in a tool shed repository.
by Bitbucket 29 May '12

29 May '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/37a28d5134b3/ changeset: 37a28d5134b3 user: greg date: 2012-05-29 20:46:02 summary: Fixes for loading a tool in a tool shed repository. affected #: 4 files diff -r 9765176c63f7ada3ee30a649ab3ef13396d9c84b -r 37a28d5134b37b8450d9c266e1a5a6bb261461bf lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -785,14 +785,14 @@ for filename in ctx: ctx_file_name = strip_path( filename ) if ctx_file_name == config_file: - return get_named_tmpfile_from_ctx( ctx, filename, dir=dir ) + return get_named_tmpfile_from_ctx( ctx, filename, dir ) # Finally look in the repository manifest. for changeset in repo.changelog: prev_ctx = repo.changectx( changeset ) for ctx_file in prev_ctx.files(): ctx_file_name = strip_path( ctx_file ) if ctx_file_name == config_file: - return get_named_tmpfile_from_ctx( prev_ctx, filename, dir=dir ) + return get_named_tmpfile_from_ctx( prev_ctx, filename, dir ) return None def get_config_from_disk( config_file, relative_install_dir ): for root, dirs, files in os.walk( relative_install_dir ): diff -r 9765176c63f7ada3ee30a649ab3ef13396d9c84b -r 37a28d5134b37b8450d9c266e1a5a6bb261461bf lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -547,7 +547,7 @@ .filter( trans.model.RepositoryMetadata.table.c.repository_id == trans.security.decode_id( id ) ) \ .order_by( trans.model.RepositoryMetadata.table.c.id.desc() ) \ .first() -def get_named_tmpfile_from_ctx( ctx, filename, dir=None ): +def get_named_tmpfile_from_ctx( ctx, filename, dir ): fctx = ctx[ filename ] fh = tempfile.NamedTemporaryFile( 'wb', dir=dir ) tmp_filename = fh.name @@ -574,6 +574,28 @@ if parent_id is None: # The tool did not change through all of the changeset revisions. return old_id +def get_previous_valid_changset_revision( repository, repo, before_changeset_revision ): + changeset_tups = [] + for repository_metadata in repository.downloadable_revisions: + changeset_revision = repository_metadata.changeset_revision + ctx = get_changectx_for_changeset( repo, changeset_revision ) + if ctx: + rev = '%04d' % ctx.rev() + else: + rev = '-1' + changeset_tups.append( ( rev, changeset_revision ) ) + previous_changeset_revision = None + current_changeset_revision = None + for changeset_tup in sorted( changeset_tups ): + current_changeset_revision = changeset_tup[ 1 ] + if current_changeset_revision == before_changeset_revision: + if previous_changeset_revision: + return previous_changeset_revision + else: + # Return the hash value of an empty repository changlog - note that this will not be a valid changset revision. + return '000000000000' + else: + previous_changeset_revision = current_changeset_revision def get_repository( trans, id ): """Get a repository from the database via id""" return trans.sa_session.query( trans.model.Repository ).get( trans.security.decode_id( id ) ) @@ -743,8 +765,42 @@ ToolClass = Tool return ToolClass( config_file, root, trans.app ) return None -def load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_config ): - tool_config = strip_path( tool_config ) +def load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_config_filename ): + """ + Return a loaded tool whose tool config file name (e.g., filtering.xml) is the value of tool_config_filename. The value of changeset_revision + is a valid (downloadable) changset revision. If changeset_revision is the repository tip, then the tool will be loaded from it's file on disk. + Otherwise, the tool config will be located in the repository manifest between the received valid changeset revision and the previous valid + changeset revision (if one exists) or the first changeset revision in the repository (if one doesn't). + """ + def load_from_tmp_config( ctx, ctx_file, work_dir ): + tool = None + message = '' + tmp_tool_config = get_named_tmpfile_from_ctx( ctx, ctx_file, work_dir ) + element_tree = util.parse_xml( tmp_tool_config ) + element_tree_root = element_tree.getroot() + # Look for code files required by the tool config. + tmp_code_files = [] + for code_elem in element_tree_root.findall( 'code' ): + code_file_name = code_elem.get( 'file' ) + tmp_code_file_name = copy_file_from_manifest( repo, ctx, code_file_name, work_dir ) + if tmp_code_file_name: + tmp_code_files.append( tmp_code_file_name ) + try: + tool = load_tool( trans, tmp_tool_config ) + except Exception, e: + tool = None + message = "Error loading tool: %s. Clicking <b>Reset metadata</b> may correct this error." % str( e ) + for tmp_code_file in tmp_code_files: + try: + os.unlink( tmp_code_file ) + except: + pass + try: + os.unlink( tmp_tool_config ) + except: + pass + return tool, message + tool_config_filename = strip_path( tool_config_filename ) repository = get_repository( trans, repository_id ) repo_files_dir = repository.repo_path repo = hg.repository( get_configured_ui(), repo_files_dir ) @@ -757,48 +813,39 @@ if tool_data_table_config: error, correction_msg = handle_sample_tool_data_table_conf_file( trans.app, tool_data_table_config ) if changeset_revision == repository.tip: + # Load the tool fron it's config file on disk. try: - copied_tool_config = copy_file_from_disk( tool_config, repo_files_dir, work_dir ) + copied_tool_config = copy_file_from_disk( tool_config_filename, repo_files_dir, work_dir ) tool = load_tool( trans, copied_tool_config ) except Exception, e: tool = None - message = "Error loading tool: %s." % str( e ) + message = "Error loading tool from config '%s': %s." % ( tool_config_filename, str( e ) ) else: - # Get the tool config file name from the hgweb url, something like: /repos/test/convert_chars1/file/e58dcf0026c7/convert_characters.xml - old_tool_config_file_name = tool_config.split( '/' )[ -1 ] - in_ctx = False + found = False + tool = None + # Get the tool config from ctx if present. for ctx_file in ctx.files(): ctx_file_name = strip_path( ctx_file ) - if ctx_file_name == old_tool_config_file_name: - in_ctx = True + if ctx_file_name == tool_config_filename: + found = True break - if in_ctx: - tmp_tool_config = get_named_tmpfile_from_ctx( ctx, ctx_file, dir=work_dir ) - element_tree = util.parse_xml( tmp_tool_config ) - element_tree_root = element_tree.getroot() - # Look for code files required by the tool config. - tmp_code_files = [] - for code_elem in element_tree_root.findall( 'code' ): - code_file_name = code_elem.get( 'file' ) - tmp_code_file_name = copy_file_from_manifest( repo, ctx, code_file_name, work_dir ) - if tmp_code_file_name: - tmp_code_files.append( tmp_code_file_name ) - try: - tool = load_tool( trans, tmp_tool_config ) - except Exception, e: - tool = None - message = "Error loading tool: %s. Clicking <b>Reset metadata</b> may correct this error." % str( e ) - for tmp_code_file in tmp_code_files: - try: - os.unlink( tmp_code_file ) - except: - pass - try: - os.unlink( tmp_tool_config ) - except: - pass + if found: + if found: + tool, message = load_from_tmp_config( ctx, ctx_file, work_dir ) else: - tool = None + # Get the tool config from the repository manifest between valid changeset revisions. + previous_valid_changset_revision = get_previous_valid_changset_revision( repository, repo, changeset_revision ) + for changeset in reversed_filtered_changelog( repo, previous_valid_changset_revision, changeset_revision ): + manifest_changeset_revision = str( repo.changectx( changeset ) ) + manifest_ctx = repo.changectx( changeset ) + for ctx_file in manifest_ctx.files(): + ctx_file_name = strip_path( ctx_file ) + if ctx_file_name == tool_config_filename: + found = True + break + if found: + tool, message = load_from_tmp_config( manifest_ctx, ctx_file, work_dir ) + break # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. reset_tool_data_tables( trans.app ) try: @@ -811,7 +858,7 @@ tool = None valid = False error_message = '' - tmp_config = get_named_tmpfile_from_ctx( ctx, filename, dir=dir ) + tmp_config = get_named_tmpfile_from_ctx( ctx, filename, dir ) if not ( check_binary( tmp_config ) or check_image( tmp_config ) or check_gzip( tmp_config )[ 0 ] or check_bz2( tmp_config )[ 0 ] or check_zip( tmp_config ) ): try: @@ -979,6 +1026,26 @@ clean_repository_metadata( trans, id, changeset_revisions ) add_repository_metadata_tool_versions( trans, id, changeset_revisions ) return '', 'ok' +def reversed_filtered_changelog( repo, excluded_lower_bounds_changeset_revision, included_upper_bounds_changeset_revision ): + """ + Return a reversed list of changesets in the repository changelog after the excluded_lower_bounds_changeset_revision, but up to and + including the included_upper_bounds_changeset_revision. The value of excluded_lower_bounds_changeset_revision will be '000000000000' + if no valid changesets exist before included_upper_bounds_changeset_revision. + """ + if excluded_lower_bounds_changeset_revision == '000000000000': + appending_started = True + else: + appending_started = False + reversed_changelog = [] + for changeset in repo.changelog: + changeset_hash = str( repo.changectx( changeset ) ) + if appending_started: + reversed_changelog.insert( 0, changeset ) + if changeset_hash == excluded_lower_bounds_changeset_revision and not appending_started: + appending_started = True + if changeset_hash == included_upper_bounds_changeset_revision: + break + return reversed_changelog def set_repository_metadata( trans, id, changeset_revision, content_alert_str='', **kwd ): """ Set repository metadata on the repository tip, returning specific error messages (if any) to alert the repository owner that the changeset diff -r 9765176c63f7ada3ee30a649ab3ef13396d9c84b -r 37a28d5134b37b8450d9c266e1a5a6bb261461bf lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -402,7 +402,6 @@ url_args=url_args, allow_multiple=False, async_compatible=False ) ] - # Render the list view return self.valid_repository_list_grid( trans, **kwd ) @web.expose def browse_invalid_tools( self, trans, **kwd ): @@ -1891,7 +1890,7 @@ for filename in ctx: ctx_file_name = strip_path( filename ) if ctx_file_name == tool_config: - tool_config_path = get_named_tmpfile_from_ctx( ctx, filename, dir=work_dir ) + tool_config_path = get_named_tmpfile_from_ctx( ctx, filename, work_dir ) break metadata_dict, invalid_files = generate_metadata_for_changeset_revision( trans, repo, diff -r 9765176c63f7ada3ee30a649ab3ef13396d9c84b -r 37a28d5134b37b8450d9c266e1a5a6bb261461bf lib/galaxy/webapps/community/controllers/upload.py --- a/lib/galaxy/webapps/community/controllers/upload.py +++ b/lib/galaxy/webapps/community/controllers/upload.py @@ -43,7 +43,6 @@ # See the handle_email_alerts() method for the definition of the scenarios. new_repo_alert = repository.is_new if params.get( 'upload_button', False ): - current_working_dir = os.getcwd() if file_data == '' and url == '': message = 'No files were entered on the upload form.' status = 'error' @@ -270,9 +269,6 @@ error, message = handle_sample_tool_data_table_conf_file( trans.app, filename_in_archive ) if error: return False, message, files_to_remove, content_alert_str, undesirable_dirs_removed, undesirable_files_removed - #if filename_in_archive.endswith( '.loc.sample' ): - # # Handle the special case where a xxx.loc.sample file is being uploaded by copying it to ~/tool-data/xxx.loc. - # copy_sample_file( trans.app, filename_in_archive ) commands.commit( repo.ui, repo, full_path, user=trans.user.username, message=commit_message ) # See if the content of the change set was valid. admin_only = len( repository.downloadable_revisions ) != 1 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 Bitbucket 28 May '12

28 May '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/b129ae3fc035/ changeset: b129ae3fc035 user: jgoecks date: 2012-05-28 18:05:20 summary: Move icons from trackster.css to base.css for general usage. affected #: 5 files diff -r 03cb8ee86726813073913be149516ab10e601e55 -r b129ae3fc0359f08b9f47ae33230249a4ce0975e static/june_2007_style/base_sprites.less.tmpl --- a/static/june_2007_style/base_sprites.less.tmpl +++ b/static/june_2007_style/base_sprites.less.tmpl @@ -102,14 +102,28 @@ -sprite-group: fugue; -sprite-image: silk/chart_curve.png; } - +.icon-button.disk--arrow { + -sprite-group: fugue; + -sprite-image: fugue/disk--arrow-bw.png; +} +.icon-button.disk--arrow:hover { + -sprite-group: fugue; + -sprite-image: fugue/disk--arrow.png; +} +.icon-button.cross-circle { + -sprite-group: fugue; + -sprite-image: fugue/cross-circle-bw.png; +} +.icon-button.cross-circle:hover { + -sprite-group: fugue; + -sprite-image: fugue/cross-circle.png; +} .text-and-autocomplete-select { -sprite-group: fugue; -sprite-image: fugue/control-270.png; -sprite-horiz-position: right; } - div.historyItem-error .state-icon { -sprite-group: history-states; -sprite-image: data_error.png; diff -r 03cb8ee86726813073913be149516ab10e601e55 -r b129ae3fc0359f08b9f47ae33230249a4ce0975e static/june_2007_style/blue/base.css --- a/static/june_2007_style/blue/base.css +++ b/static/june_2007_style/blue/base.css @@ -754,7 +754,11 @@ .icon-button.plus-button:hover{background:url(fugue.png) no-repeat 0px -364px;} .icon-button.gear{background:url(fugue.png) no-repeat 0px -390px;} .icon-button.chart_curve{background:url(fugue.png) no-repeat 0px -416px;} -.text-and-autocomplete-select{background:url(fugue.png) no-repeat right -442px;} +.icon-button.disk--arrow{background:url(fugue.png) no-repeat 0px -442px;} +.icon-button.disk--arrow:hover{background:url(fugue.png) no-repeat 0px -468px;} +.icon-button.cross-circle{background:url(fugue.png) no-repeat 0px -494px;} +.icon-button.cross-circle:hover{background:url(fugue.png) no-repeat 0px -520px;} +.text-and-autocomplete-select{background:url(fugue.png) no-repeat right -546px;} div.historyItem-error .state-icon{background:url(history-states.png) no-repeat 0px 0px;} div.historyItem-empty .state-icon{background:url(history-states.png) no-repeat 0px -25px;} div.historyItem-queued .state-icon{background:url(history-states.png) no-repeat 0px -50px;} diff -r 03cb8ee86726813073913be149516ab10e601e55 -r b129ae3fc0359f08b9f47ae33230249a4ce0975e static/june_2007_style/blue/fugue.png Binary file static/june_2007_style/blue/fugue.png has changed diff -r 03cb8ee86726813073913be149516ab10e601e55 -r b129ae3fc0359f08b9f47ae33230249a4ce0975e static/june_2007_style/blue/trackster.css --- a/static/june_2007_style/blue/trackster.css +++ b/static/june_2007_style/blue/trackster.css @@ -84,16 +84,12 @@ .icon-button.toggle:hover{background:transparent url(../images/fugue/toggle.png) no-repeat;} .icon-button.toggle-expand{background:transparent url(../images/fugue/toggle-expand-bw.png) no-repeat;margin-right:0px;} .icon-button.toggle-expand:hover{background:transparent url(../images/fugue/toggle-expand.png) no-repeat;} -.icon-button.cross-circle{background:transparent url(../images/fugue/cross-circle-bw.png) no-repeat;margin-right:0px;} -.icon-button.cross-circle:hover{background:transparent url(../images/fugue/cross-circle.png) no-repeat;} .icon-button.block--plus{background:transparent url(../images/fugue/block--plus-bw.png) no-repeat;} .icon-button.block--plus:hover{background:transparent url(../images/fugue/block--plus.png) no-repeat;} .icon-button.bookmarks{background:transparent url(../images/fugue/bookmarks-bw.png) no-repeat;} .icon-button.bookmarks:hover{background:transparent url(../images/fugue/bookmarks.png) no-repeat;} .icon-button.toolbox{background:transparent url(../images/fugue/toolbox-bw.png) no-repeat;} .icon-button.toolbox:hover{background:transparent url(../images/fugue/toolbox.png) no-repeat;} -.icon-button.disk--arrow{background:transparent url(../images/fugue/disk--arrow-bw.png) no-repeat;} -.icon-button.disk--arrow:hover{background:transparent url(../images/fugue/disk--arrow.png) no-repeat;} .child-track-icon{background:url('../images/fugue/arrow-000-small-bw.png') no-repeat;width:30px;cursor:move;} .track-resize{background:white url('../images/visualization/draggable_vertical.png') no-repeat top center;position:absolute;right:3px;bottom:-4px;width:14px;height:7px;border:solid #999 1px;z-index:100;} .bookmark{background:white;border:solid #999 1px;border-right:none;margin:0.5em;margin-right:0;padding:0.5em;} diff -r 03cb8ee86726813073913be149516ab10e601e55 -r b129ae3fc0359f08b9f47ae33230249a4ce0975e static/june_2007_style/trackster.css.tmpl --- a/static/june_2007_style/trackster.css.tmpl +++ b/static/june_2007_style/trackster.css.tmpl @@ -405,12 +405,6 @@ .icon-button.toggle-expand:hover { background: transparent url(../images/fugue/toggle-expand.png) no-repeat; } -.icon-button.cross-circle { - background: transparent url(../images/fugue/cross-circle-bw.png) no-repeat;margin-right:0px; -} -.icon-button.cross-circle:hover { - background: transparent url(../images/fugue/cross-circle.png) no-repeat; -} .icon-button.block--plus { background: transparent url(../images/fugue/block--plus-bw.png) no-repeat; } @@ -429,12 +423,6 @@ .icon-button.toolbox:hover { background: transparent url(../images/fugue/toolbox.png) no-repeat; } -.icon-button.disk--arrow { - background: transparent url(../images/fugue/disk--arrow-bw.png) no-repeat; -} -.icon-button.disk--arrow:hover { - background: transparent url(../images/fugue/disk--arrow.png) no-repeat; -} .child-track-icon { background:url('../images/fugue/arrow-000-small-bw.png') no-repeat; width: 30px; https://bitbucket.org/galaxy/galaxy-central/changeset/9765176c63f7/ changeset: 9765176c63f7 user: jgoecks date: 2012-05-28 18:10:04 summary: Visualization: (a) rename circos viz 'circster' and (b) foundational work for circster and backbone-visualization integration. Also pack scripts. affected #: 11 files diff -r b129ae3fc0359f08b9f47ae33230249a4ce0975e -r 9765176c63f7ada3ee30a649ab3ef13396d9c84b lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -277,7 +277,7 @@ class UsesVisualizationMixin( SharableItemSecurityMixin ): """ Mixin for controllers that use Visualization objects. """ - viz_types = [ "trackster", "circos" ] + viz_types = [ "trackster", "circster" ] len_files = None @@ -360,7 +360,7 @@ end = config['viewport']['end'] overview = config['viewport']['overview'] vis_rev.config[ "viewport" ] = { 'chrom': chrom, 'start': start, 'end': end, 'overview': overview } - elif type == 'circos': + elif type == 'circster': # TODO. pass diff -r b129ae3fc0359f08b9f47ae33230249a4ce0975e -r 9765176c63f7ada3ee30a649ab3ef13396d9c84b lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py +++ b/lib/galaxy/web/controllers/tracks.py @@ -758,7 +758,7 @@ @web.expose @web.require_login( "use Galaxy visualizations", use_panels=True ) - def circos( self, trans, hda_ldda, dataset_id ): + def circster( self, trans, hda_ldda, dataset_id ): # Get dataset. dataset = self._get_dataset( trans, hda_ldda, dataset_id ) @@ -777,7 +777,7 @@ summary = indexer.get_summary( chrom_info[ 'chrom' ], 0, chrom_info[ 'len' ], level=4 ) dataset_summary.append( summary ) - return trans.fill_template_mako( "visualization/circos.mako", dataset=dataset, dataset_summary=dataset_summary, genome=genome ) + return trans.fill_template_mako( "visualization/circster.mako", dataset=dataset, dataset_summary=dataset_summary, genome=genome ) # ----------------- # Helper methods. diff -r b129ae3fc0359f08b9f47ae33230249a4ce0975e -r 9765176c63f7ada3ee30a649ab3ef13396d9c84b static/scripts/mvc/tools.js --- a/static/scripts/mvc/tools.js +++ b/static/scripts/mvc/tools.js @@ -181,6 +181,7 @@ * applies search results as they become available. */ var ToolPanel = Backbone.Collection.extend({ + // TODO: need to generate this using url_for url: "/tools", tools: new ToolCollection(), diff -r b129ae3fc0359f08b9f47ae33230249a4ce0975e -r 9765176c63f7ada3ee30a649ab3ef13396d9c84b static/scripts/mvc/ui.js --- a/static/scripts/mvc/ui.js +++ b/static/scripts/mvc/ui.js @@ -1,5 +1,24 @@ /** - * Utility models and views for Galaxy objects. + * -- Functions for creating large UI elements. -- + */ + +/** + * Returns an IconButtonMenuView for the provided configuration. + * Configuration is a list of dictionaries where each dictionary + * defines an icon button. Each dictionary must have the following + * elements: icon_class, title, and on_click. + */ +var create_icon_buttons_menu = function(config) { + // Create and initialize menu. + var buttons = new IconButtonCollection( + _.map(config, function(button_config) { return new IconButton(button_config); }) + ); + + return new IconButtonMenuView( {collection: buttons} ); +}; + +/** + * -- Utility models and views for Galaxy objects. -- */ /** diff -r b129ae3fc0359f08b9f47ae33230249a4ce0975e -r 9765176c63f7ada3ee30a649ab3ef13396d9c84b static/scripts/mvc/visualization.js --- a/static/scripts/mvc/visualization.js +++ b/static/scripts/mvc/visualization.js @@ -26,9 +26,77 @@ }); /** + * A genome browser bookmark. + */ +var BrowserBookmark = Backbone.Model.extend({ + defaults: { + chrom: null, + start: 0, + end: 0, + note: "" + } +}); + +/** + * Bookmarks collection. + */ +var BrowserBookmarks = Backbone.Collection.extend({ + model: BrowserBookmark +}); + +/** + * A visualization. + */ +var Visualization = Backbone.RelationalModel.extend({ + defaults: { + id: "", + title: "", + type: "", + dbkey: "", + datasets: [] + } +}); + +/** + * A Trackster visualization. + */ +var TracksterVisualization = Visualization.extend({ + defaults: { + bookmarks: [], + viewport: {} + } +}); + +/** + * A Circster visualization. + */ +var CircsterVisualization = Visualization.extend({ +}); + +/** + * A dataset. In Galaxy, datasets are associated with a history, so + * this object is also known as a HistoryDatasetAssociation. + */ +var Dataset = Backbone.Model.extend({ + defaults: { + id: "", + type: "", + name: "", + hda_ldda: "" + } +}); + +/** * A histogram dataset. */ var HistogramDataset = Backbone.Model.extend({ + /* + defaults: { + data: [], + dataset: null, + max: 0 + }, + */ initialize: function(data) { // Set max across dataset. @@ -42,9 +110,16 @@ }); /** - * Layout for a histogram dataset in a circos visualization. + * Configuration data for a Trackster track. */ -var CircosHistogramDatasetLayout = Backbone.Model.extend({ +var TrackConfig = Backbone.Model.extend({ + +}); + +/** + * Layout for a histogram dataset in a circster visualization. + */ +var CircsterHistogramDatasetLayout = Backbone.Model.extend({ // TODO: should accept genome and dataset and use these to generate layout data. /** @@ -104,8 +179,8 @@ * -- Views -- */ -var CircosView = Backbone.View.extend({ - className: 'circos', +var CircsterView = Backbone.View.extend({ + className: 'circster', initialize: function(options) { this.width = options.width; @@ -124,7 +199,7 @@ dataset_arc_height = this.dataset_arc_height, // Layout chromosome arcs. - arcs_layout = new CircosHistogramDatasetLayout({ + arcs_layout = new CircsterHistogramDatasetLayout({ genome: this.genome, total_gap: this.total_gap }), @@ -205,3 +280,58 @@ this.view.go_to(new_loc); } }); + +/** + * -- Helper functions. + */ + +/** + * Use a popup grid to add more datasets. + */ +var add_datasets = function(dataset_url, add_track_async_url, success_fn) { + $.ajax({ + url: dataset_url, + data: { "f-dbkey": view.dbkey }, + error: function() { alert( "Grid failed" ); }, + success: function(table_html) { + show_modal( + "Select datasets for new tracks", + table_html, { + "Cancel": function() { + hide_modal(); + }, + "Add": function() { + var requests = []; + $('input[name=id]:checked,input[name=ldda_ids]:checked').each(function() { + var data, + id = $(this).val(); + if ($(this).attr("name") === "id") { + data = { hda_id: id }; + } else { + data = { ldda_id: id}; + } + requests[requests.length] = $.ajax({ + url: add_track_async_url, + data: data, + dataType: "json", + }); + }); + // To preserve order, wait until there are definitions for all tracks and then add + // them sequentially. + $.when.apply($, requests).then(function() { + // jQuery always returns an Array for arguments, so need to look at first element + // to determine whether multiple requests were made and consequently how to + // map arguments to track definitions. + var track_defs = (arguments[0] instanceof Array ? + $.map(arguments, function(arg) { return arg[0]; }) : + [ arguments[0] ] + ); + success_fn(track_defs); + }); + hide_modal(); + } + } + ); + } + }); +}; diff -r b129ae3fc0359f08b9f47ae33230249a4ce0975e -r 9765176c63f7ada3ee30a649ab3ef13396d9c84b static/scripts/packed/mvc/ui.js --- a/static/scripts/packed/mvc/ui.js +++ b/static/scripts/packed/mvc/ui.js @@ -1,1 +1,1 @@ -var GalaxyPaths=Backbone.Model.extend({defaults:{root_path:"",image_path:""}});var IconButton=Backbone.Model.extend({defaults:{title:"",icon_class:"",on_click:null}});var IconButtonCollection=Backbone.Collection.extend({model:IconButton});var IconButtonMenuView=Backbone.View.extend({tagName:"div",render:function(){var a=this;this.collection.each(function(b){$("<a/>").attr("href","javascript:void(0)").attr("title",b.attributes.title).addClass("icon-button menu-button").addClass(b.attributes.icon_class).appendTo(a.$el).click(b.attributes.on_click)});return this}});var Grid=Backbone.Collection.extend({});var GridView=Backbone.View.extend({}); \ No newline at end of file +var create_icon_buttons_menu=function(a){var b=new IconButtonCollection(_.map(a,function(c){return new IconButton(c)}));return new IconButtonMenuView({collection:b})};var GalaxyPaths=Backbone.Model.extend({defaults:{root_path:"",image_path:""}});var IconButton=Backbone.Model.extend({defaults:{title:"",icon_class:"",on_click:null}});var IconButtonCollection=Backbone.Collection.extend({model:IconButton});var IconButtonMenuView=Backbone.View.extend({tagName:"div",render:function(){var a=this;this.collection.each(function(b){$("<a/>").attr("href","javascript:void(0)").attr("title",b.attributes.title).addClass("icon-button menu-button").addClass(b.attributes.icon_class).appendTo(a.$el).click(b.attributes.on_click)});return this}});var Grid=Backbone.Collection.extend({});var GridView=Backbone.View.extend({}); \ No newline at end of file diff -r b129ae3fc0359f08b9f47ae33230249a4ce0975e -r 9765176c63f7ada3ee30a649ab3ef13396d9c84b static/scripts/packed/mvc/visualization.js --- a/static/scripts/packed/mvc/visualization.js +++ b/static/scripts/packed/mvc/visualization.js @@ -1,1 +1,1 @@ -var Genome=Backbone.Model.extend({defaults:{name:null,key:null,chroms_info:null},get_chroms_info:function(){return this.attributes.chroms_info.chrom_info}});var HistogramDataset=Backbone.Model.extend({initialize:function(a){this.attributes.data=a;this.attributes.max=_.max(a,function(b){if(!b||typeof b==="string"){return 0}return b[1]})[1]}});var CircosHistogramDatasetLayout=Backbone.Model.extend({chroms_layout:function(){var b=this.attributes.genome.get_chroms_info(),d=d3.layout.pie().value(function(f){return f.len}).sort(null),e=d(b),a=this.attributes.total_gap/b.length,c=_.map(e,function(h,g){var f=h.endAngle-a;h.endAngle=(f>h.startAngle?f:h.startAngle);return h});return c},chrom_data_layout:function(j,b,g,f,h){if(!b||typeof b==="string"){return null}var d=b[0],i=b[3],c=d3.scale.linear().domain([0,h]).range([g,f]),e=d3.layout.pie().value(function(k){return i}).startAngle(j.startAngle).endAngle(j.endAngle),a=e(d);_.each(d,function(k,l){a[l].outerRadius=c(k[1])});return a}});var CircosView=Backbone.View.extend({className:"circos",initialize:function(a){this.width=a.width;this.height=a.height;this.total_gap=a.total_gap;this.genome=a.genome;this.dataset=a.dataset;this.radius_start=a.radius_start;this.dataset_arc_height=a.dataset_arc_height},render:function(){var d=this.radius_start,e=this.dataset_arc_height,j=new CircosHistogramDatasetLayout({genome:this.genome,total_gap:this.total_gap}),i=j.chroms_layout(),g=_.zip(i,this.dataset.attributes.data),h=this.dataset.attributes.max,b=_.map(g,function(m){var n=m[0],l=m[1];return j.chrom_data_layout(n,l,d,d+e,h)});var c=d3.select(this.$el[0]).append("svg").attr("width",this.width).attr("height",this.height).append("g").attr("transform","translate("+this.width/2+","+this.height/2+")");var k=c.append("g").attr("id","inner-arc"),f=d3.svg.arc().innerRadius(d).outerRadius(d+e),a=k.selectAll("#inner-arc>path").data(i).enter().append("path").attr("d",f).style("stroke","#ccc").style("fill","#ccc").append("title").text(function(l){return l.data.chrom});_.each(b,function(l){if(!l){return}var o=c.append("g"),n=d3.svg.arc().innerRadius(d),m=o.selectAll("path").data(l).enter().append("path").attr("d",n).style("stroke","red").style("fill","red")})}});var TrackBrowserRouter=Backbone.Router.extend({initialize:function(b){this.view=b.view;this.route(/([\w]+)$/,"change_location");this.route(/([\w]+\:[\d,]+-[\d,]+)$/,"change_location");var a=this;a.view.on("navigate",function(c){a.navigate(c)})},change_location:function(a){this.view.go_to(a)}}); \ No newline at end of file +var Genome=Backbone.Model.extend({defaults:{name:null,key:null,chroms_info:null},get_chroms_info:function(){return this.attributes.chroms_info.chrom_info}});var BrowserBookmark=Backbone.Model.extend({defaults:{chrom:null,start:0,end:0,note:""}});var BrowserBookmarks=Backbone.Collection.extend({model:BrowserBookmark});var Visualization=Backbone.RelationalModel.extend({defaults:{id:"",title:"",type:"",dbkey:"",datasets:[]}});var TracksterVisualization=Visualization.extend({defaults:{bookmarks:[],viewport:{}}});var CircsterVisualization=Visualization.extend({});var Dataset=Backbone.Model.extend({defaults:{id:"",type:"",name:"",hda_ldda:""}});var HistogramDataset=Backbone.Model.extend({initialize:function(a){this.attributes.data=a;this.attributes.max=_.max(a,function(b){if(!b||typeof b==="string"){return 0}return b[1]})[1]}});var TrackConfig=Backbone.Model.extend({});var CircsterHistogramDatasetLayout=Backbone.Model.extend({chroms_layout:function(){var b=this.attributes.genome.get_chroms_info(),d=d3.layout.pie().value(function(f){return f.len}).sort(null),e=d(b),a=this.attributes.total_gap/b.length,c=_.map(e,function(h,g){var f=h.endAngle-a;h.endAngle=(f>h.startAngle?f:h.startAngle);return h});return c},chrom_data_layout:function(j,b,g,f,h){if(!b||typeof b==="string"){return null}var d=b[0],i=b[3],c=d3.scale.linear().domain([0,h]).range([g,f]),e=d3.layout.pie().value(function(k){return i}).startAngle(j.startAngle).endAngle(j.endAngle),a=e(d);_.each(d,function(k,l){a[l].outerRadius=c(k[1])});return a}});var CircsterView=Backbone.View.extend({className:"circster",initialize:function(a){this.width=a.width;this.height=a.height;this.total_gap=a.total_gap;this.genome=a.genome;this.dataset=a.dataset;this.radius_start=a.radius_start;this.dataset_arc_height=a.dataset_arc_height},render:function(){var d=this.radius_start,e=this.dataset_arc_height,j=new CircsterHistogramDatasetLayout({genome:this.genome,total_gap:this.total_gap}),i=j.chroms_layout(),g=_.zip(i,this.dataset.attributes.data),h=this.dataset.attributes.max,b=_.map(g,function(m){var n=m[0],l=m[1];return j.chrom_data_layout(n,l,d,d+e,h)});var c=d3.select(this.$el[0]).append("svg").attr("width",this.width).attr("height",this.height).append("g").attr("transform","translate("+this.width/2+","+this.height/2+")");var k=c.append("g").attr("id","inner-arc"),f=d3.svg.arc().innerRadius(d).outerRadius(d+e),a=k.selectAll("#inner-arc>path").data(i).enter().append("path").attr("d",f).style("stroke","#ccc").style("fill","#ccc").append("title").text(function(l){return l.data.chrom});_.each(b,function(l){if(!l){return}var o=c.append("g"),n=d3.svg.arc().innerRadius(d),m=o.selectAll("path").data(l).enter().append("path").attr("d",n).style("stroke","red").style("fill","red")})}});var TrackBrowserRouter=Backbone.Router.extend({initialize:function(b){this.view=b.view;this.route(/([\w]+)$/,"change_location");this.route(/([\w]+\:[\d,]+-[\d,]+)$/,"change_location");var a=this;a.view.on("navigate",function(c){a.navigate(c)})},change_location:function(a){this.view.go_to(a)}});var add_datasets=function(a,c,b){$.ajax({url:a,data:{"f-dbkey":view.dbkey},error:function(){alert("Grid failed")},success:function(d){show_modal("Select datasets for new tracks",d,{Cancel:function(){hide_modal()},Add:function(){var e=[];$("input[name=id]:checked,input[name=ldda_ids]:checked").each(function(){var f,g=$(this).val();if($(this).attr("name")==="id"){f={hda_id:g}}else{f={ldda_id:g}}e[e.length]=$.ajax({url:c,data:f,dataType:"json",})});$.when.apply($,e).then(function(){var f=(arguments[0] instanceof Array?$.map(arguments,function(g){return g[0]}):[arguments[0]]);b(f)});hide_modal()}})}})}; \ No newline at end of file diff -r b129ae3fc0359f08b9f47ae33230249a4ce0975e -r 9765176c63f7ada3ee30a649ab3ef13396d9c84b templates/base_panels.mako --- a/templates/base_panels.mako +++ b/templates/base_panels.mako @@ -61,7 +61,7 @@ <%def name="late_javascripts()"> ## Scripts can be loaded later since they progressively add features to ## the panels, but do not change layout - ${h.js( 'jquery.event.drag', 'jquery.event.hover', 'jquery.form', 'jquery.rating', 'galaxy.base', 'galaxy.panels' )} + ${h.js( 'jquery.event.drag', 'jquery.event.hover', 'jquery.form', 'jquery.rating', 'galaxy.base', 'galaxy.panels', 'jquery.tipsy' )} <script type="text/javascript"> ensure_dd_helper(); diff -r b129ae3fc0359f08b9f47ae33230249a4ce0975e -r 9765176c63f7ada3ee30a649ab3ef13396d9c84b templates/tracks/browser.mako --- a/templates/tracks/browser.mako +++ b/templates/tracks/browser.mako @@ -42,13 +42,16 @@ <script type='text/javascript' src="${h.url_for('/static/scripts/excanvas.js')}"></script><![endif]--> -${h.js( "galaxy.base", "galaxy.panels", "json2", "jquery", "jstorage", "jquery.event.drag", "jquery.event.hover","jquery.mousewheel", "jquery.autocomplete", "trackster", "trackster_ui", "jquery.ui.sortable.slider", "farbtastic", "jquery.tipsy", "mvc/visualization" )} +${h.js( "galaxy.base", "galaxy.panels", "json2", "jquery", "jstorage", "jquery.event.drag", "jquery.event.hover","jquery.mousewheel", "jquery.autocomplete", "trackster", "trackster_ui", "jquery.ui.sortable.slider", "farbtastic", "mvc/visualization" )} <script type="text/javascript"> // // Place URLs here so that url_for can be used to generate them. // - var default_data_url = "${h.url_for( action='data' )}", + var + add_track_async_url = "${h.url_for( action='add_track_async' )}", + add_datasets_url = "${h.url_for( action='list_current_history_datasets' )}", + default_data_url = "${h.url_for( action='data' )}", raw_data_url = "${h.url_for( action='raw_data' )}", run_tool_url = "${h.url_for( action='run_tool' )}", rerun_tool_url = "${h.url_for( action='rerun_tool' )}", @@ -66,60 +69,7 @@ browser_router = new TrackBrowserRouter(options); Backbone.history.start(); }; - - /** - * Use a popup grid to add more tracks. - */ - var add_tracks = function() { - $.ajax({ - url: "${h.url_for( action='list_current_history_datasets' )}", - data: { "f-dbkey": view.dbkey }, - error: function() { alert( "Grid failed" ); }, - success: function(table_html) { - show_modal( - "Select datasets for new tracks", - table_html, { - "Cancel": function() { - hide_modal(); - }, - "Insert": function() { - var requests = []; - $('input[name=id]:checked,input[name=ldda_ids]:checked').each(function() { - var data, - id = $(this).val(); - if ($(this).attr("name") === "id") { - data = { hda_id: id }; - } else { - data = { ldda_id: id}; - } - requests[requests.length] = $.ajax({ - url: "${h.url_for( action='add_track_async' )}", - data: data, - dataType: "json", - }); - }); - // To preserve order, wait until there are definitions for all tracks and then add - // them sequentially. - $.when.apply($, requests).then(function() { - // jQuery always returns an Array for arguments, so need to look at first element - // to determine whether multiple requests were made and consequently how to - // map arguments to track definitions. - var track_defs = (arguments[0] instanceof Array ? - $.map(arguments, function(arg) { return arg[0]; }) : - [ arguments[0] ] - ); - for (var i= 0; i < track_defs.length; i++) { - view.add_drawable( object_from_template(track_defs[i], view) ); - } - }); - hide_modal(); - } - } - ); - } - }); - }; - + /** * Use a popup grid to bookmarks from a dataset. */ @@ -168,23 +118,22 @@ var browser_router; $(function() { // Create and initialize menu. - var - - buttons = new IconButtonCollection([ - new IconButton({icon_class: 'plus-button', title: 'Add tracks', on_click: function() { add_tracks(); } }), - new IconButton({icon_class: 'block--plus', title: 'Add group', on_click: function() { + var menu = create_icon_buttons_menu([ + { icon_class: 'plus-button', title: 'Add tracks', on_click: function() { + add_datasets(add_datasets_url, add_track_async_url, function(tracks) { + _.each(tracks, function(track) { + view.add_drawable( object_from_template(track, view) ); + }); + }); + } }, + { icon_class: 'block--plus', title: 'Add group', on_click: function() { view.add_drawable( new DrawableGroup(view, view, { name: "New Group" }) ); - } }), - /* - new IconButton({icon_class: 'toolbox', title: 'Use tools', on_click: function() { - console.log("toolbox!") - } }), - */ - new IconButton({icon_class: 'bookmarks', title: 'Bookmarks', on_click: function() { + } }, + { icon_class: 'bookmarks', title: 'Bookmarks', on_click: function() { // HACK -- use style to determine if panel is hidden and hide/show accordingly. parent.force_right_panel(($("div#right").css("right") == "0px" ? "hide" : "show")); - } }), - new IconButton({icon_class: 'disk--arrow', title: 'Save', on_click: function() { + } }, + { icon_class: 'disk--arrow', title: 'Save', on_click: function() { // Show saving dialog box show_modal("Saving...", "progress"); @@ -229,15 +178,11 @@ { "Close" : hide_modal } ); } }); - } }), - new IconButton({icon_class: 'cross-circle', title: 'Close', on_click: function() { + } }, + { icon_class: 'cross-circle', title: 'Close', on_click: function() { window.location = "${h.url_for( controller='visualization', action='list' )}"; - } }) - ]), - - menu = new IconButtonMenuView({ - collection: buttons - }); + } } + ]); menu.render(); menu.$el.attr("style", "float: right"); diff -r b129ae3fc0359f08b9f47ae33230249a4ce0975e -r 9765176c63f7ada3ee30a649ab3ef13396d9c84b templates/visualization/circos.mako --- a/templates/visualization/circos.mako +++ /dev/null @@ -1,39 +0,0 @@ -<%inherit file="/base.mako"/> - -<%def name="stylesheets()"> - ${parent.stylesheets()} -</%def> - -<%def name="javascripts()"> - ${parent.javascripts()} - - ${h.js( "libs/d3", "mvc/visualization" )} - - <script type="text/javascript"> - $(function() { - // -- Viz set up. -- - - var genome = new Genome(JSON.parse('${ h.to_json_string( genome ) }')), - dataset = new HistogramDataset(JSON.parse('${ h.to_json_string( dataset_summary ) }')), - circos = new CircosView({ - width: 600, - height: 600, - // Gap is difficult to set because it very dependent on chromosome size and organization. - total_gap: 2 * Math.PI * 0.5, - genome: genome, - dataset: dataset, - radius_start: 100, - dataset_arc_height: 50 - }); - - // -- Render viz. -- - - circos.render(); - $('body').append(circos.$el); - }); - </script> -</%def> - -<%def name="body()"> - <h1>Circos plot for '${dataset.name}'</h1> -</%def> diff -r b129ae3fc0359f08b9f47ae33230249a4ce0975e -r 9765176c63f7ada3ee30a649ab3ef13396d9c84b templates/visualization/circster.mako --- /dev/null +++ b/templates/visualization/circster.mako @@ -0,0 +1,97 @@ +<%inherit file="/webapps/galaxy/base_panels.mako"/> + +<%def name="init()"> +<% + self.has_left_panel=False + self.has_right_panel=False + self.active_view="visualization" + self.message_box_visible=False +%> +</%def> + +<%def name="stylesheets()"> + ${parent.stylesheets()} +</%def> + +<%def name="javascripts()"> + ${parent.javascripts()} + + ${h.js( "libs/d3", "mvc/visualization" )} + + <script type="text/javascript"> + $(function() { + // -- Visualization menu and set up. + var menu = create_icon_buttons_menu([ + { icon_class: 'plus-button', title: 'Add tracks', on_click: function() { add_tracks(); } }, + { icon_class: 'disk--arrow', title: 'Save', on_click: function() { + // Show saving dialog box + show_modal("Saving...", "progress"); + + $.ajax({ + url: "${h.url_for( action='save' )}", + type: "POST", + data: { + 'id': view.vis_id, + 'title': view.name, + 'dbkey': view.dbkey, + 'type': 'trackster', + 'config': JSON.stringify(payload) + }, + dataType: "json", + success: function(vis_info) { + hide_modal(); + view.vis_id = vis_info.vis_id; + view.has_changes = false; + + // Needed to set URL when first saving a visualization. + window.history.pushState({}, "", vis_info.url + window.location.hash); + }, + error: function() { + show_modal( "Could Not Save", "Could not save visualization. Please try again later.", + { "Close" : hide_modal } ); + } + }); + } }, + { icon_class: 'cross-circle', title: 'Close', on_click: function() { + window.location = "${h.url_for( controller='visualization', action='list' )}"; + } } + ]); + + menu.render(); + menu.$el.attr("style", "float: right"); + $("#center .unified-panel-header-inner").append(menu.$el); + // Manual tipsy config because default gravity is S and cannot be changed. + $(".menu-button").tipsy( {gravity: 'n'} ); + + // -- Viz set up. -- + + var genome = new Genome(JSON.parse('${ h.to_json_string( genome ) }')), + dataset = new HistogramDataset(JSON.parse('${ h.to_json_string( dataset_summary ) }')), + circster = new CircsterView({ + width: 600, + height: 600, + // Gap is difficult to set because it very dependent on chromosome size and organization. + total_gap: 2 * Math.PI * 0.5, + genome: genome, + dataset: dataset, + radius_start: 100, + dataset_arc_height: 50 + }); + + // -- Render viz. -- + + circster.render(); + $('#vis').append(circster.$el); + }); + </script> +</%def> + +<%def name="center_panel()"> + <div class="unified-panel-header" unselectable="on"> + <div class="unified-panel-header-inner"> + <div style="float:left;" id="title"></div> + </div> + <div style="clear: both"></div> + </div> + <div id="vis" class="unified-panel-body"></div> +</%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: 2 new changesets
by Bitbucket 27 May '12

27 May '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/c5ba3065b82e/ changeset: c5ba3065b82e user: jgoecks date: 2012-05-27 21:54:32 summary: Support for saving and validating different visualization types. affected #: 3 files diff -r fdc3f20a46d3af6ac89bd02baef3db09eed3f235 -r c5ba3065b82ee8a9d165c164f1f864526baf18e4 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -305,60 +305,64 @@ decoded_id = trans.security.decode_id( id ) vis = session.query( trans.model.Visualization ).get( decoded_id ) - # Decode the payload - decoded_payload = config # Create new VisualizationRevision that will be attached to the viz vis_rev = trans.model.VisualizationRevision() vis_rev.visualization = vis vis_rev.title = vis.title vis_rev.dbkey = dbkey + + # -- Validate config. -- + + if vis.type == 'trackster': + def unpack_track( track_json ): + """ Unpack a track from its json. """ + return { + "dataset_id": trans.security.decode_id( track_json['dataset_id'] ), + "hda_ldda": track_json.get('hda_ldda', 'hda'), + "name": track_json['name'], + "track_type": track_json['track_type'], + "prefs": track_json['prefs'], + "mode": track_json['mode'], + "filters": track_json['filters'], + "tool_state": track_json['tool_state'] + } - def unpack_track( track_json ): - """ Unpack a track from its json. """ - return { - "dataset_id": trans.security.decode_id( track_json['dataset_id'] ), - "hda_ldda": track_json.get('hda_ldda', 'hda'), - "name": track_json['name'], - "track_type": track_json['track_type'], - "prefs": track_json['prefs'], - "mode": track_json['mode'], - "filters": track_json['filters'], - "tool_state": track_json['tool_state'] - } + def unpack_collection( collection_json ): + """ Unpack a collection from its json. """ + unpacked_drawables = [] + drawables = collection_json[ 'drawables' ] + for drawable_json in drawables: + if 'track_type' in drawable_json: + drawable = unpack_track( drawable_json ) + else: + drawable = unpack_collection( drawable_json ) + unpacked_drawables.append( drawable ) + return { + "name": collection_json.get( 'name', '' ), + "obj_type": collection_json[ 'obj_type' ], + "drawables": unpacked_drawables, + "prefs": collection_json.get( 'prefs' , [] ), + "filters": collection_json.get( 'filters', None ) + } - def unpack_collection( collection_json ): - """ Unpack a collection from its json. """ - unpacked_drawables = [] - drawables = collection_json[ 'drawables' ] - for drawable_json in drawables: - if 'track_type' in drawable_json: - drawable = unpack_track( drawable_json ) - else: - drawable = unpack_collection( drawable_json ) - unpacked_drawables.append( drawable ) - return { - "name": collection_json.get( 'name', '' ), - "obj_type": collection_json[ 'obj_type' ], - "drawables": unpacked_drawables, - "prefs": collection_json.get( 'prefs' , [] ), - "filters": collection_json.get( 'filters', None ) - } + # TODO: unpack and validate bookmarks: + def unpack_bookmarks( bookmarks_json ): + return bookmarks_json - # TODO: unpack and validate bookmarks: - def unpack_bookmarks( bookmarks_json ): - return bookmarks_json - - # Unpack and validate view content. - view_content = unpack_collection( decoded_payload[ 'view' ] ) - bookmarks = unpack_bookmarks( decoded_payload[ 'bookmarks' ] ) - vis_rev.config = { "view": view_content, "bookmarks": bookmarks } - # Viewport from payload - if 'viewport' in decoded_payload: - chrom = decoded_payload['viewport']['chrom'] - start = decoded_payload['viewport']['start'] - end = decoded_payload['viewport']['end'] - overview = decoded_payload['viewport']['overview'] - vis_rev.config[ "viewport" ] = { 'chrom': chrom, 'start': start, 'end': end, 'overview': overview } + # Unpack and validate view content. + view_content = unpack_collection( config[ 'view' ] ) + bookmarks = unpack_bookmarks( config[ 'bookmarks' ] ) + vis_rev.config = { "view": view_content, "bookmarks": bookmarks } + # Viewport from payload + if 'viewport' in config: + chrom = config['viewport']['chrom'] + start = config['viewport']['start'] + end = config['viewport']['end'] + overview = config['viewport']['overview'] + vis_rev.config[ "viewport" ] = { 'chrom': chrom, 'start': start, 'end': end, 'overview': overview } + elif type == 'circos': + # TODO. + pass vis.latest_revision = vis_rev session.add( vis_rev ) diff -r fdc3f20a46d3af6ac89bd02baef3db09eed3f235 -r c5ba3065b82ee8a9d165c164f1f864526baf18e4 lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py +++ b/lib/galaxy/web/controllers/tracks.py @@ -234,6 +234,15 @@ rows.append( [location, name] ) return { 'data': rows } + # TODO: this is duplicated from visualization controller; remove it once + # routing incompatibilities have been resolved. + @web.json + def save( self, trans, config, type, id=None, title=None, dbkey=None, annotation=None ): + """ + Save a visualization; if visualization does not have an ID, a new + visualization is created. Returns JSON of visualization. + """ + return self.save_visualization( trans, from_json_string( config ), type, id, title, dbkey, annotation ) @web.expose @web.require_login() @@ -409,11 +418,7 @@ result = data_provider.get_data( chrom, low, high, int( start_val ), int( max_vals ), **kwargs ) result.update( { 'dataset_type': tracks_dataset_type, 'extra_info': extra_info } ) return result - - @web.json - def save( self, trans, config, type, id=None, title=None, dbkey=None, annotation=None ): - return self.save_visualization( trans, from_json_string( config ), type, id, title, dbkey, annotation ) - + @web.expose @web.require_login( "see all available libraries" ) def list_libraries( self, trans, **kwargs ): diff -r fdc3f20a46d3af6ac89bd02baef3db09eed3f235 -r c5ba3065b82ee8a9d165c164f1f864526baf18e4 lib/galaxy/web/controllers/visualization.py --- a/lib/galaxy/web/controllers/visualization.py +++ b/lib/galaxy/web/controllers/visualization.py @@ -349,7 +349,7 @@ def create( self, trans, visualization_title="", visualization_slug="", visualization_annotation="", visualization_dbkey="", visualization_type="" ): """ - Create a new visualization + Creates a new visualization or returns a form for creating visualization. """ visualization_title_err = visualization_slug_err = visualization_annotation_err = "" if trans.request.method == "POST": @@ -381,6 +381,14 @@ .add_text( "visualization_annotation", "Visualization annotation", value=visualization_annotation, error=visualization_annotation_err, help="A description of the visualization; annotation is shown alongside published visualizations."), template="visualization/create.mako" ) + + @web.json + def save( self, trans, config, type, id=None, title=None, dbkey=None, annotation=None ): + """ + Save a visualization; if visualization does not have an ID, a new + visualization is created. Returns JSON of visualization. + """ + return self.save_visualization( trans, from_json_string( config ), type, id, title, dbkey, annotation ) @web.expose @web.require_login( "edit visualizations" ) https://bitbucket.org/galaxy/galaxy-central/changeset/03cb8ee86726/ changeset: 03cb8ee86726 user: jgoecks date: 2012-05-27 22:09:16 summary: Include 'mixin' in names of many common controller mixins. affected #: 22 files diff -r c5ba3065b82ee8a9d165c164f1f864526baf18e4 -r 03cb8ee86726813073913be149516ab10e601e55 lib/galaxy/tools/genome_index/__init__.py --- a/lib/galaxy/tools/genome_index/__init__.py +++ b/lib/galaxy/tools/genome_index/__init__.py @@ -3,7 +3,7 @@ from galaxy.web.framework.helpers import to_unicode from galaxy.model.item_attrs import UsesAnnotations from galaxy.util.json import * -from galaxy.web.base.controller import UsesHistory +from galaxy.web.base.controller import UsesHistoryMixin from galaxy.tools.data import ToolDataTableManager log = logging.getLogger(__name__) @@ -63,8 +63,6 @@ if gitd: destination = None - alldone = True - indexjobs = gitd.deferred.params[ 'indexjobs' ] tdtman = ToolDataTableManager() xmltree = tdtman.load_from_config_file(app.config.tool_data_table_config_path) for node in xmltree: @@ -165,14 +163,6 @@ self._check_link( fasta, target ) for line in location: self._add_line( line[ 'file' ], line[ 'line' ] ) - for indexjob in indexjobs: - js = sa_session.query( model.Job ).filter_by( id=indexjob ).first() - if js.state not in [ 'ok', 'done', 'error' ]: - alldone = False - if alldone: - gitd.deferred.state = 'ok' - sa_session.add( gitd.deferred ) - sa_session.flush() def _check_link( self, targetfile, symlink ): target = os.path.relpath( targetfile, os.path.dirname( symlink ) ) diff -r c5ba3065b82ee8a9d165c164f1f864526baf18e4 -r 03cb8ee86726813073913be149516ab10e601e55 lib/galaxy/tools/imp_exp/__init__.py --- a/lib/galaxy/tools/imp_exp/__init__.py +++ b/lib/galaxy/tools/imp_exp/__init__.py @@ -4,7 +4,7 @@ from galaxy.web.framework.helpers import to_unicode from galaxy.model.item_attrs import UsesAnnotations from galaxy.util.json import * -from galaxy.web.base.controller import UsesHistory +from galaxy.web.base.controller import UsesHistoryMixin log = logging.getLogger(__name__) @@ -42,7 +42,7 @@ toolbox.tools_by_id[ history_imp_tool.id ] = history_imp_tool log.debug( "Loaded history import tool: %s", history_imp_tool.id ) -class JobImportHistoryArchiveWrapper( object, UsesHistory, UsesAnnotations ): +class JobImportHistoryArchiveWrapper( object, UsesHistoryMixin, UsesAnnotations ): """ Class provides support for performing jobs that import a history from an archive. @@ -263,7 +263,7 @@ jiha.job.stderr += "Error cleaning up history import job: %s" % e db_session.flush() -class JobExportHistoryArchiveWrapper( object, UsesHistory, UsesAnnotations ): +class JobExportHistoryArchiveWrapper( object, UsesHistoryMixin, UsesAnnotations ): """ Class provides support for performing jobs that export a history to an archive. diff -r c5ba3065b82ee8a9d165c164f1f864526baf18e4 -r 03cb8ee86726813073913be149516ab10e601e55 lib/galaxy/web/api/datasets.py --- a/lib/galaxy/web/api/datasets.py +++ b/lib/galaxy/web/api/datasets.py @@ -10,7 +10,7 @@ log = logging.getLogger( __name__ ) -class DatasetsController( BaseAPIController, UsesHistoryDatasetAssociation ): +class DatasetsController( BaseAPIController, UsesHistoryMixinDatasetAssociationMixin ): @web.expose_api def index( self, trans, hda_id, **kwd ): diff -r c5ba3065b82ee8a9d165c164f1f864526baf18e4 -r 03cb8ee86726813073913be149516ab10e601e55 lib/galaxy/web/api/histories.py --- a/lib/galaxy/web/api/histories.py +++ b/lib/galaxy/web/api/histories.py @@ -12,7 +12,7 @@ log = logging.getLogger( __name__ ) -class HistoriesController( BaseAPIController, UsesHistory ): +class HistoriesController( BaseAPIController, UsesHistoryMixin ): @web.expose_api def index( self, trans, deleted='False', **kwd ): @@ -153,7 +153,7 @@ POST /api/histories/deleted/{encoded_quota_id}/undelete Undeletes a quota """ - history = self.get_history( trans, id, check_ownership=True, check_accessible=False, deleted=True ) + history = self.get_history( trans, history_id, check_ownership=True, check_accessible=False, deleted=True ) history.deleted = False trans.sa_session.add( history ) trans.sa_session.flush() diff -r c5ba3065b82ee8a9d165c164f1f864526baf18e4 -r 03cb8ee86726813073913be149516ab10e601e55 lib/galaxy/web/api/history_contents.py --- a/lib/galaxy/web/api/history_contents.py +++ b/lib/galaxy/web/api/history_contents.py @@ -12,7 +12,7 @@ log = logging.getLogger( __name__ ) -class HistoryContentsController( BaseAPIController, UsesHistoryDatasetAssociation, UsesHistory, UsesLibrary, UsesLibraryItems ): +class HistoryContentsController( BaseAPIController, UsesHistoryMixinDatasetAssociationMixin, UsesHistoryMixin, UsesLibraryMixin, UsesLibraryMixinItems ): @web.expose_api def index( self, trans, history_id, **kwd ): diff -r c5ba3065b82ee8a9d165c164f1f864526baf18e4 -r 03cb8ee86726813073913be149516ab10e601e55 lib/galaxy/web/api/library_contents.py --- a/lib/galaxy/web/api/library_contents.py +++ b/lib/galaxy/web/api/library_contents.py @@ -10,7 +10,7 @@ log = logging.getLogger( __name__ ) -class LibraryContentsController( BaseAPIController, UsesLibrary, UsesLibraryItems ): +class LibraryContentsController( BaseAPIController, UsesLibraryMixin, UsesLibraryMixinItems ): @web.expose_api def index( self, trans, library_id, **kwd ): diff -r c5ba3065b82ee8a9d165c164f1f864526baf18e4 -r 03cb8ee86726813073913be149516ab10e601e55 lib/galaxy/web/api/quotas.py --- a/lib/galaxy/web/api/quotas.py +++ b/lib/galaxy/web/api/quotas.py @@ -2,7 +2,7 @@ API operations on Quota objects. """ import logging -from galaxy.web.base.controller import BaseAPIController, Admin, UsesQuota, url_for +from galaxy.web.base.controller import BaseAPIController, Admin, UsesQuotaMixin, url_for from galaxy import web, util from elementtree.ElementTree import XML @@ -14,7 +14,7 @@ log = logging.getLogger( __name__ ) -class QuotaAPIController( BaseAPIController, Admin, AdminActions, UsesQuota, QuotaParamParser ): +class QuotaAPIController( BaseAPIController, Admin, AdminActions, UsesQuotaMixin, QuotaParamParser ): @web.expose_api @web.require_admin def index( self, trans, deleted='False', **kwd ): diff -r c5ba3065b82ee8a9d165c164f1f864526baf18e4 -r 03cb8ee86726813073913be149516ab10e601e55 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -177,7 +177,11 @@ def not_implemented( self, trans, **kwd ): raise HTTPNotImplemented() -class SharableItemSecurity: +# +# -- Mixins for working with Galaxy objects. -- +# + +class SharableItemSecurityMixin: """ Mixin for handling security for sharable items. """ def security_check( self, trans, item, check_ownership=False, check_accessible=False ): """ Security checks for an item: checks if (a) user owns item or (b) item is accessible to user. """ @@ -197,11 +201,7 @@ raise ItemAccessibilityException( "%s is not accessible to the current user" % item.__class__.__name__, type='error' ) return item -# -# TODO: need to move UsesHistory, etc. mixins to better location - perhaps lib/galaxy/model/XXX ? -# - -class UsesHistoryDatasetAssociation: +class UsesHistoryMixinDatasetAssociationMixin: """ Mixin for controllers that use HistoryDatasetAssociation objects. """ def get_dataset( self, trans, dataset_id, check_ownership=True, check_accessible=False ): """ Get an HDA object by id. """ @@ -259,14 +259,14 @@ truncated = False return truncated, dataset_data -class UsesLibrary: +class UsesLibraryMixin: def get_library( self, trans, id, check_ownership=False, check_accessible=True ): l = self.get_object( trans, id, 'Library' ) if check_accessible and not ( trans.user_is_admin() or trans.app.security_agent.can_access_library( trans.get_current_user_roles(), l ) ): error( "LibraryFolder is not accessible to the current user" ) return l -class UsesLibraryItems( SharableItemSecurity ): +class UsesLibraryMixinItems( SharableItemSecurityMixin ): def get_library_folder( self, trans, id, check_ownership=False, check_accessible=True ): return self.get_object( trans, id, 'LibraryFolder', check_ownership=False, check_accessible=check_accessible ) def get_library_dataset_dataset_association( self, trans, id, check_ownership=False, check_accessible=True ): @@ -274,7 +274,7 @@ def get_library_dataset( self, trans, id, check_ownership=False, check_accessible=True ): return self.get_object( trans, id, 'LibraryDataset', check_ownership=False, check_accessible=check_accessible ) -class UsesVisualization( SharableItemSecurity ): +class UsesVisualizationMixin( SharableItemSecurityMixin ): """ Mixin for controllers that use Visualization objects. """ viz_types = [ "trackster", "circos" ] @@ -522,7 +522,7 @@ return visualization -class UsesStoredWorkflow( SharableItemSecurity ): +class UsesStoredWorkflowMixin( SharableItemSecurityMixin ): """ Mixin for controllers that use StoredWorkflow objects. """ def get_stored_workflow( self, trans, id, check_ownership=True, check_accessible=False ): """ Get a StoredWorkflow from the database by id, verifying ownership. """ @@ -560,7 +560,7 @@ # Connections by input name step.input_connections_by_name = dict( ( conn.input_name, conn ) for conn in step.input_connections ) -class UsesHistory( SharableItemSecurity ): +class UsesHistoryMixin( SharableItemSecurityMixin ): """ Mixin for controllers that use History objects. """ def get_history( self, trans, id, check_ownership=True, check_accessible=False, deleted=None ): """Get a History from the database by id, verifying ownership.""" @@ -580,7 +580,7 @@ query = query.filter( trans.model.Dataset.purged == False ) return query.all() -class UsesFormDefinitions: +class UsesFormDefinitionsMixin: """Mixin for controllers that use Galaxy form objects.""" def get_all_forms( self, trans, all_versions=False, filter=None, form_type='All' ): """ @@ -1342,7 +1342,7 @@ selected_value=selected_value, refresh_on_change=True ) -class Sharable: +class SharableMixin: """ Mixin for a controller that manages an item that can be shared. """ # -- Implemented methods. -- @@ -1433,7 +1433,7 @@ """ Return item based on id. """ raise "Unimplemented Method" -class UsesQuota( object ): +class UsesQuotaMixin( object ): def get_quota( self, trans, id, check_ownership=False, check_accessible=False, deleted=None ): return self.get_object( trans, id, 'Quota', check_ownership=False, check_accessible=False, deleted=deleted ) diff -r c5ba3065b82ee8a9d165c164f1f864526baf18e4 -r 03cb8ee86726813073913be149516ab10e601e55 lib/galaxy/web/controllers/admin.py --- a/lib/galaxy/web/controllers/admin.py +++ b/lib/galaxy/web/controllers/admin.py @@ -428,7 +428,7 @@ def build_initial_query( self, trans, **kwd ): return trans.sa_session.query( self.model_class ) -class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuota, QuotaParamParser ): +class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuotaMixin, QuotaParamParser ): user_list_grid = UserListGrid() role_list_grid = RoleListGrid() diff -r c5ba3065b82ee8a9d165c164f1f864526baf18e4 -r 03cb8ee86726813073913be149516ab10e601e55 lib/galaxy/web/controllers/dataset.py --- a/lib/galaxy/web/controllers/dataset.py +++ b/lib/galaxy/web/controllers/dataset.py @@ -150,7 +150,7 @@ .filter( model.History.deleted==False ) \ .filter( self.model_class.visible==True ) -class DatasetInterface( BaseUIController, UsesAnnotations, UsesHistory, UsesHistoryDatasetAssociation, UsesItemRatings ): +class DatasetInterface( BaseUIController, UsesAnnotations, UsesHistoryMixin, UsesHistoryMixinDatasetAssociationMixin, UsesItemRatings ): stored_list_grid = HistoryDatasetAssociationListGrid() diff -r c5ba3065b82ee8a9d165c164f1f864526baf18e4 -r 03cb8ee86726813073913be149516ab10e601e55 lib/galaxy/web/controllers/external_service.py --- a/lib/galaxy/web/controllers/external_service.py +++ b/lib/galaxy/web/controllers/external_service.py @@ -63,7 +63,7 @@ grids.GridAction( "Create new external service", dict( controller='external_service', action='create_external_service' ) ) ] -class ExternalService( BaseUIController, UsesFormDefinitions ): +class ExternalService( BaseUIController, UsesFormDefinitionsMixin ): external_service_grid = ExternalServiceGrid() @web.expose diff -r c5ba3065b82ee8a9d165c164f1f864526baf18e4 -r 03cb8ee86726813073913be149516ab10e601e55 lib/galaxy/web/controllers/history.py --- a/lib/galaxy/web/controllers/history.py +++ b/lib/galaxy/web/controllers/history.py @@ -190,7 +190,7 @@ # A public history is published, has a slug, and is not deleted. return query.filter( self.model_class.published == True ).filter( self.model_class.slug != None ).filter( self.model_class.deleted == False ) -class HistoryController( BaseUIController, Sharable, UsesAnnotations, UsesItemRatings, UsesHistory ): +class HistoryController( BaseUIController, SharableMixin, UsesAnnotations, UsesItemRatings, UsesHistoryMixin ): @web.expose def index( self, trans ): return "" diff -r c5ba3065b82ee8a9d165c164f1f864526baf18e4 -r 03cb8ee86726813073913be149516ab10e601e55 lib/galaxy/web/controllers/library_common.py --- a/lib/galaxy/web/controllers/library_common.py +++ b/lib/galaxy/web/controllers/library_common.py @@ -68,7 +68,7 @@ pass os.rmdir( tmpd ) -class LibraryCommon( BaseUIController, UsesFormDefinitions ): +class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin ): @web.json def library_item_updates( self, trans, ids=None, states=None ): # Avoid caching diff -r c5ba3065b82ee8a9d165c164f1f864526baf18e4 -r 03cb8ee86726813073913be149516ab10e601e55 lib/galaxy/web/controllers/page.py --- a/lib/galaxy/web/controllers/page.py +++ b/lib/galaxy/web/controllers/page.py @@ -272,8 +272,8 @@ # Default behavior: _BaseHTMLProcessor.unknown_endtag( self, tag ) -class PageController( BaseUIController, Sharable, UsesAnnotations, UsesHistory, - UsesStoredWorkflow, UsesHistoryDatasetAssociation, UsesVisualization, UsesItemRatings ): +class PageController( BaseUIController, SharableMixin, UsesAnnotations, UsesHistoryMixin, + UsesStoredWorkflowMixin, UsesHistoryMixinDatasetAssociationMixin, UsesVisualizationMixin, UsesItemRatings ): _page_list = PageListGrid() _all_published_list = PageAllPublishedGrid() diff -r c5ba3065b82ee8a9d165c164f1f864526baf18e4 -r 03cb8ee86726813073913be149516ab10e601e55 lib/galaxy/web/controllers/request_type.py --- a/lib/galaxy/web/controllers/request_type.py +++ b/lib/galaxy/web/controllers/request_type.py @@ -72,7 +72,7 @@ grids.GridAction( "Create new request type", dict( controller='request_type', action='create_request_type' ) ) ] -class RequestType( BaseUIController, UsesFormDefinitions ): +class RequestType( BaseUIController, UsesFormDefinitionsMixin ): request_type_grid = RequestTypeGrid() @web.expose diff -r c5ba3065b82ee8a9d165c164f1f864526baf18e4 -r 03cb8ee86726813073913be149516ab10e601e55 lib/galaxy/web/controllers/requests_admin.py --- a/lib/galaxy/web/controllers/requests_admin.py +++ b/lib/galaxy/web/controllers/requests_admin.py @@ -94,7 +94,7 @@ return query return query.filter_by( sample_id=trans.security.decode_id( sample_id ) ) -class RequestsAdmin( BaseUIController, UsesFormDefinitions ): +class RequestsAdmin( BaseUIController, UsesFormDefinitionsMixin ): request_grid = AdminRequestsGrid() datatx_grid = DataTransferGrid() diff -r c5ba3065b82ee8a9d165c164f1f864526baf18e4 -r 03cb8ee86726813073913be149516ab10e601e55 lib/galaxy/web/controllers/requests_common.py --- a/lib/galaxy/web/controllers/requests_common.py +++ b/lib/galaxy/web/controllers/requests_common.py @@ -93,7 +93,7 @@ confirm="Samples cannot be added to this request after it is submitted. Click OK to submit." ) ] -class RequestsCommon( BaseUIController, UsesFormDefinitions ): +class RequestsCommon( BaseUIController, UsesFormDefinitionsMixin ): @web.json def sample_state_updates( self, trans, ids=None, states=None ): # Avoid caching diff -r c5ba3065b82ee8a9d165c164f1f864526baf18e4 -r 03cb8ee86726813073913be149516ab10e601e55 lib/galaxy/web/controllers/root.py --- a/lib/galaxy/web/controllers/root.py +++ b/lib/galaxy/web/controllers/root.py @@ -11,7 +11,7 @@ log = logging.getLogger( __name__ ) -class RootController( BaseUIController, UsesHistory, UsesAnnotations ): +class RootController( BaseUIController, UsesHistoryMixin, UsesAnnotations ): @web.expose def default(self, trans, target1=None, target2=None, **kwd): diff -r c5ba3065b82ee8a9d165c164f1f864526baf18e4 -r 03cb8ee86726813073913be149516ab10e601e55 lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py +++ b/lib/galaxy/web/controllers/tracks.py @@ -163,7 +163,7 @@ def apply_query_filter( self, trans, query, **kwargs ): return query.filter( self.model_class.user_id == trans.user.id ) -class TracksController( BaseUIController, UsesVisualization, UsesHistoryDatasetAssociation, Sharable ): +class TracksController( BaseUIController, UsesVisualizationMixin, UsesHistoryMixinDatasetAssociationMixin, SharableMixin ): """ Controller for track browser interface. Handles building a new browser from datasets in the current history, and display of the resulting browser. diff -r c5ba3065b82ee8a9d165c164f1f864526baf18e4 -r 03cb8ee86726813073913be149516ab10e601e55 lib/galaxy/web/controllers/user.py --- a/lib/galaxy/web/controllers/user.py +++ b/lib/galaxy/web/controllers/user.py @@ -38,7 +38,7 @@ def build_initial_query( self, trans, **kwd ): return trans.sa_session.query( self.model_class ).filter( self.model_class.user_id == trans.user.id ) -class User( BaseUIController, UsesFormDefinitions ): +class User( BaseUIController, UsesFormDefinitionsMixin ): user_openid_grid = UserOpenIDGrid() installed_len_files = None diff -r c5ba3065b82ee8a9d165c164f1f864526baf18e4 -r 03cb8ee86726813073913be149516ab10e601e55 lib/galaxy/web/controllers/visualization.py --- a/lib/galaxy/web/controllers/visualization.py +++ b/lib/galaxy/web/controllers/visualization.py @@ -68,8 +68,8 @@ return query.filter( self.model_class.deleted==False ).filter( self.model_class.published==True ) -class VisualizationController( BaseUIController, Sharable, UsesAnnotations, - UsesHistoryDatasetAssociation, UsesVisualization, +class VisualizationController( BaseUIController, SharableMixin, UsesAnnotations, + UsesHistoryMixinDatasetAssociationMixin, UsesVisualizationMixin, UsesItemRatings ): _user_list_grid = VisualizationListGrid() _published_list_grid = VisualizationAllPublishedGrid() diff -r c5ba3065b82ee8a9d165c164f1f864526baf18e4 -r 03cb8ee86726813073913be149516ab10e601e55 lib/galaxy/web/controllers/workflow.py --- a/lib/galaxy/web/controllers/workflow.py +++ b/lib/galaxy/web/controllers/workflow.py @@ -105,7 +105,7 @@ if self.cur_tag == self.target_tag: self.tag_content += text -class WorkflowController( BaseUIController, Sharable, UsesStoredWorkflow, UsesAnnotations, UsesItemRatings ): +class WorkflowController( BaseUIController, SharableMixin, UsesStoredWorkflowMixin, UsesAnnotations, UsesItemRatings ): stored_list_grid = StoredWorkflowListGrid() published_list_grid = StoredWorkflowAllPublishedGrid() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Provide generic support for saving visualizations.
by Bitbucket 27 May '12

27 May '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/fdc3f20a46d3/ changeset: fdc3f20a46d3 user: jgoecks date: 2012-05-27 18:34:52 summary: Provide generic support for saving visualizations. affected #: 3 files diff -r f4c4ba7be3d17fbf7924e9f8d6ae005960fcc4c0 -r fdc3f20a46d3af6ac89bd02baef3db09eed3f235 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -280,41 +280,91 @@ viz_types = [ "trackster", "circos" ] len_files = None - + def create_visualization( self, trans, title, slug, type, dbkey, annotation=None, config={} ): - user = trans.get_user() + """ Create visualiation and first revision. """ + visualization = self._create_visualization( trans, title, type, dbkey, slug, annotation ) - # Error checking. - title_err = slug_err = "" - if not title: - title_err = "visualization name is required" - elif not slug: - slug_err = "visualization id is required" - elif not VALID_SLUG_RE.match( slug ): - slug_err = "visualization identifier must consist of only lowercase letters, numbers, and the '-' character" - elif trans.sa_session.query( trans.model.Visualization ).filter_by( user=user, slug=slug, deleted=False ).first(): - slug_err = "visualization id must be unique" - - if title_err or slug_err: - return { 'title_err': title_err, 'slug_err': slug_err } - - # Create visualization - visualization = trans.model.Visualization( user=user, title=title, slug=slug, dbkey=dbkey, type=type ) - if annotation: - annotation = sanitize_html( annotation, 'utf-8', 'text/html' ) - self.add_item_annotation( trans.sa_session, trans.user, visualization, annotation ) - - # And the first visualization revision - revision = trans.model.VisualizationRevision( visualization=visualization, title=title, config={}, dbkey=dbkey ) + # Create and save first visualization revision + revision = trans.model.VisualizationRevision( visualization=visualization, title=title, config=config, dbkey=dbkey ) visualization.latest_revision = revision - - # Persist session = trans.sa_session - session.add(visualization) - session.add(revision) + session.add( revision ) session.flush() return visualization + + def save_visualization( self, trans, config, type, id=None, title=None, dbkey=None, slug=None, annotation=None ): + session = trans.sa_session + + # Create/get visualization. + if not id: + # Create new visualization. + vis = self._create_visualization( trans, title, type, dbkey, slug, annotation ) + else: + decoded_id = trans.security.decode_id( id ) + vis = session.query( trans.model.Visualization ).get( decoded_id ) + + # Decode the payload + decoded_payload = config + # Create new VisualizationRevision that will be attached to the viz + vis_rev = trans.model.VisualizationRevision() + vis_rev.visualization = vis + vis_rev.title = vis.title + vis_rev.dbkey = dbkey + + def unpack_track( track_json ): + """ Unpack a track from its json. """ + return { + "dataset_id": trans.security.decode_id( track_json['dataset_id'] ), + "hda_ldda": track_json.get('hda_ldda', 'hda'), + "name": track_json['name'], + "track_type": track_json['track_type'], + "prefs": track_json['prefs'], + "mode": track_json['mode'], + "filters": track_json['filters'], + "tool_state": track_json['tool_state'] + } + + def unpack_collection( collection_json ): + """ Unpack a collection from its json. """ + unpacked_drawables = [] + drawables = collection_json[ 'drawables' ] + for drawable_json in drawables: + if 'track_type' in drawable_json: + drawable = unpack_track( drawable_json ) + else: + drawable = unpack_collection( drawable_json ) + unpacked_drawables.append( drawable ) + return { + "name": collection_json.get( 'name', '' ), + "obj_type": collection_json[ 'obj_type' ], + "drawables": unpacked_drawables, + "prefs": collection_json.get( 'prefs' , [] ), + "filters": collection_json.get( 'filters', None ) + } + + # TODO: unpack and validate bookmarks: + def unpack_bookmarks( bookmarks_json ): + return bookmarks_json + + # Unpack and validate view content. + view_content = unpack_collection( decoded_payload[ 'view' ] ) + bookmarks = unpack_bookmarks( decoded_payload[ 'bookmarks' ] ) + vis_rev.config = { "view": view_content, "bookmarks": bookmarks } + # Viewport from payload + if 'viewport' in decoded_payload: + chrom = decoded_payload['viewport']['chrom'] + start = decoded_payload['viewport']['start'] + end = decoded_payload['viewport']['end'] + overview = decoded_payload['viewport']['overview'] + vis_rev.config[ "viewport" ] = { 'chrom': chrom, 'start': start, 'end': end, 'overview': overview } + + vis.latest_revision = vis_rev + session.add( vis_rev ) + session.flush() + encoded_id = trans.security.encode_id( vis.id ) + return { "vis_id": encoded_id, "url": url_for( action='browser', id=encoded_id ) } def _get_dbkeys( self, trans ): """ Returns all valid dbkeys that a user can use in a visualization. """ @@ -432,6 +482,41 @@ config['viewport'] = latest_revision.config['viewport'] return config + + # -- Helper functions -- + + def _create_visualization( self, trans, title, type, dbkey, slug=None, annotation=None ): + """ Create visualization but not first revision. Returns Visualization object. """ + user = trans.get_user() + + # Error checking. + title_err = slug_err = "" + if not title: + title_err = "visualization name is required" + elif slug and not VALID_SLUG_RE.match( slug ): + slug_err = "visualization identifier must consist of only lowercase letters, numbers, and the '-' character" + elif slug and trans.sa_session.query( trans.model.Visualization ).filter_by( user=user, slug=slug, deleted=False ).first(): + slug_err = "visualization identifier must be unique" + + if title_err or slug_err: + return { 'title_err': title_err, 'slug_err': slug_err } + + + # Create visualization + visualization = trans.model.Visualization( user=user, title=title, dbkey=dbkey, type=type ) + if slug: + visualization.slug = slug + else: + self.create_item_slug( trans.sa_session, visualization ) + if annotation: + annotation = sanitize_html( annotation, 'utf-8', 'text/html' ) + self.add_item_annotation( trans.sa_session, trans.user, visualization, annotation ) + + session = trans.sa_session + session.add( visualization ) + session.flush() + + return visualization class UsesStoredWorkflow( SharableItemSecurity ): """ Mixin for controllers that use StoredWorkflow objects. """ @@ -1255,7 +1340,9 @@ class Sharable: """ Mixin for a controller that manages an item that can be shared. """ - # Implemented methods. + + # -- Implemented methods. -- + @web.expose @web.require_login( "share Galaxy items" ) def set_public_username( self, trans, id, username, **kwargs ): @@ -1268,42 +1355,50 @@ trans.sa_session.flush return self.sharing( trans, id, **kwargs ) - # Abstract methods. + # -- Abstract methods. -- + @web.expose @web.require_login( "modify Galaxy items" ) def set_slug_async( self, trans, id, new_slug ): """ Set item slug asynchronously. """ raise "Unimplemented Method" + @web.expose @web.require_login( "share Galaxy items" ) def sharing( self, trans, id, **kwargs ): """ Handle item sharing. """ raise "Unimplemented Method" + @web.expose @web.require_login( "share Galaxy items" ) def share( self, trans, id=None, email="", **kwd ): """ Handle sharing an item with a particular user. """ raise "Unimplemented Method" + @web.expose def display_by_username_and_slug( self, trans, username, slug ): """ Display item by username and slug. """ raise "Unimplemented Method" - @web.expose + @web.json @web.require_login( "get item name and link" ) def get_name_and_link_async( self, trans, id=None ): """ Returns item's name and link. """ raise "Unimplemented Method" + @web.expose @web.require_login("get item content asynchronously") def get_item_content_async( self, trans, id ): """ Returns item content in HTML format. """ raise "Unimplemented Method" - # Helper methods. + + # -- Helper methods. -- + def _make_item_accessible( self, sa_session, item ): """ Makes item accessible--viewable and importable--and sets item's slug. Does not flush/commit changes, however. Item must have name, user, importable, and slug attributes. """ item.importable = True self.create_item_slug( sa_session, item ) + def create_item_slug( self, sa_session, item ): """ Create item slug. Slug is unique among user's importable items for item's class. Returns true if item's slug was set; false otherwise. """ if item.slug is None or item.slug == "": @@ -1323,12 +1418,13 @@ slug = slug_base count = 1 while sa_session.query( item.__class__ ).filter_by( user=item.user, slug=slug, importable=True ).count() != 0: - # Slug taken; choose a new slug based on count. This approach can handle numerous histories with the same name gracefully. + # Slug taken; choose a new slug based on count. This approach can handle numerous items with the same name gracefully. slug = '%s-%i' % ( slug_base, count ) count += 1 item.slug = slug return True return False + def get_item( self, trans, id ): """ Return item based on id. """ raise "Unimplemented Method" diff -r f4c4ba7be3d17fbf7924e9f8d6ae005960fcc4c0 -r fdc3f20a46d3af6ac89bd02baef3db09eed3f235 lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py +++ b/lib/galaxy/web/controllers/tracks.py @@ -163,7 +163,7 @@ def apply_query_filter( self, trans, query, **kwargs ): return query.filter( self.model_class.user_id == trans.user.id ) -class TracksController( BaseUIController, UsesVisualization, UsesHistoryDatasetAssociation ): +class TracksController( BaseUIController, UsesVisualization, UsesHistoryDatasetAssociation, Sharable ): """ Controller for track browser interface. Handles building a new browser from datasets in the current history, and display of the resulting browser. @@ -411,83 +411,8 @@ return result @web.json - def save( self, trans, **kwargs ): - session = trans.sa_session - vis_id = "undefined" - if 'vis_id' in kwargs: - vis_id = kwargs['vis_id'].strip('"') - dbkey = kwargs['dbkey'] - # Lookup or create Visualization object - if vis_id == "undefined": # new vis - vis = model.Visualization() - vis.user = trans.user - vis.title = kwargs['title'] - vis.type = "trackster" - vis.dbkey = dbkey - session.add( vis ) - else: - decoded_id = trans.security.decode_id( vis_id ) - vis = session.query( model.Visualization ).get( decoded_id ) - # Decode the payload - decoded_payload = simplejson.loads( kwargs['payload'] ) - # Create new VisualizationRevision that will be attached to the viz - vis_rev = model.VisualizationRevision() - vis_rev.visualization = vis - vis_rev.title = vis.title - vis_rev.dbkey = dbkey - - def unpack_track( track_json ): - """ Unpack a track from its json. """ - return { - "dataset_id": trans.security.decode_id( track_json['dataset_id'] ), - "hda_ldda": track_json.get('hda_ldda', "hda"), - "name": track_json['name'], - "track_type": track_json['track_type'], - "prefs": track_json['prefs'], - "mode": track_json['mode'], - "filters": track_json['filters'], - "tool_state": track_json['tool_state'] - } - - def unpack_collection( collection_json ): - """ Unpack a collection from its json. """ - unpacked_drawables = [] - drawables = collection_json[ 'drawables' ] - for drawable_json in drawables: - if 'track_type' in drawable_json: - drawable = unpack_track( drawable_json ) - else: - drawable = unpack_collection( drawable_json ) - unpacked_drawables.append( drawable ) - return { - "name": collection_json.get( 'name', '' ), - "obj_type": collection_json[ 'obj_type' ], - "drawables": unpacked_drawables, - "prefs": collection_json.get( 'prefs' , [] ), - "filters": collection_json.get( 'filters', None ) - } - - # TODO: unpack and validate bookmarks: - def unpack_bookmarks( bookmarks_json ): - return bookmarks_json - - # Unpack and validate view content. - view_content = unpack_collection( decoded_payload[ 'view' ] ) - bookmarks = unpack_bookmarks( decoded_payload[ 'bookmarks' ] ) - vis_rev.config = { "view": view_content, "bookmarks": bookmarks } - # Viewport from payload - if 'viewport' in decoded_payload: - chrom = decoded_payload['viewport']['chrom'] - start = decoded_payload['viewport']['start'] - end = decoded_payload['viewport']['end'] - overview = decoded_payload['viewport']['overview'] - vis_rev.config[ "viewport" ] = { 'chrom': chrom, 'start': start, 'end': end, 'overview': overview } - - vis.latest_revision = vis_rev - session.add( vis_rev ) - session.flush() - encoded_id = trans.security.encode_id(vis.id) - return { "vis_id": encoded_id, "url": url_for( action='browser', id=encoded_id ) } + def save( self, trans, config, type, id=None, title=None, dbkey=None, annotation=None ): + return self.save_visualization( trans, from_json_string( config ), type, id, title, dbkey, annotation ) @web.expose @web.require_login( "see all available libraries" ) diff -r f4c4ba7be3d17fbf7924e9f8d6ae005960fcc4c0 -r fdc3f20a46d3af6ac89bd02baef3db09eed3f235 templates/tracks/browser.mako --- a/templates/tracks/browser.mako +++ b/templates/tracks/browser.mako @@ -209,10 +209,11 @@ url: "${h.url_for( action='save' )}", type: "POST", data: { - 'vis_id': view.vis_id, + 'id': view.vis_id, 'title': view.name, 'dbkey': view.dbkey, - 'payload': JSON.stringify(payload) + 'type': 'trackster', + 'config': JSON.stringify(payload) }, dataType: "json", success: function(vis_info) { Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: natefoo: Provide a modified check_galaxy.py that is suitable for use with nagios.
by Bitbucket 26 May '12

26 May '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/f4c4ba7be3d1/ changeset: f4c4ba7be3d1 user: natefoo date: 2012-05-26 21:00:36 summary: Provide a modified check_galaxy.py that is suitable for use with nagios. affected #: 3 files diff -r 62bdb265d3007d4f761a1defa82a44d888c30bfd -r f4c4ba7be3d17fbf7924e9f8d6ae005960fcc4c0 contrib/nagios/README --- /dev/null +++ b/contrib/nagios/README @@ -0,0 +1,1 @@ +Nagios checks for Galaxy. check_galaxy is used to call check_galaxy.py. diff -r 62bdb265d3007d4f761a1defa82a44d888c30bfd -r f4c4ba7be3d17fbf7924e9f8d6ae005960fcc4c0 contrib/nagios/check_galaxy --- /dev/null +++ b/contrib/nagios/check_galaxy @@ -0,0 +1,40 @@ +#!/bin/sh + +if [ -z "$3" ]; then + echo "usage: check_galaxy <server><username><password>" + exit 3 +fi + +here=`dirname $0` +var="$HOME/.check_galaxy/$1" + +touch $var/iterations +iterations=`cat $var/iterations` +if [ -z "$iterations" ]; then + iterations=0 +fi + +new_history='' +if [ $iterations -gt 96 ]; then + new_history='-n' + echo 0 > $var/iterations +else + echo `expr $iterations + 1` > $var/iterations +fi + +date >> $var/log +status=`python $here/check_galaxy.py $new_history $1 $2 $3 2>&1 | tee -a $var/log | tail -n 1` + +echo "$status" + +case "$status" in + "Exception: Tool never finished") + exit 1 + ;; + "OK") + exit 0 + ;; + *) + exit 2 + ;; +esac diff -r 62bdb265d3007d4f761a1defa82a44d888c30bfd -r f4c4ba7be3d17fbf7924e9f8d6ae005960fcc4c0 contrib/nagios/check_galaxy.py --- /dev/null +++ b/contrib/nagios/check_galaxy.py @@ -0,0 +1,393 @@ +#!/usr/bin/env python +""" +check_galaxy can be run by hand, although it is meant to run from cron +via the check_galaxy.sh script in Galaxy's cron/ directory. +""" + +import socket, sys, os, time, tempfile, filecmp, htmllib, formatter, getopt +from user import home + +import warnings +with warnings.catch_warnings(): + warnings.simplefilter('ignore') + import twill + import twill.commands as tc + +# options +if os.environ.has_key( "DEBUG" ): + debug = os.environ["DEBUG"] +else: + debug = False + +test_data_dir = os.path.join( os.path.dirname( __file__ ), 'check_galaxy_data' ) +# what tools to run - not so pretty +tools = { + "Extract+genomic+DNA+1" : + [ + { + "inputs" : + ( + { + "file_path" : os.path.join( test_data_dir, "1.bed" ), + "dbkey" : "hg17", + }, + + ) + }, + { "check_file" : os.path.join( test_data_dir, "extract_genomic_dna_out1.fasta" ) }, + { + "tool_run_options" : + { + "input" : "1.bed", + "interpret_features" : "yes", + "index_source" : "cached", + "out_format" : "fasta" + } + } + ] +} + +# handle arg(s) +def usage(): + print "usage: check_galaxy.py <server><username><password>" + sys.exit(1) + +try: + opts, args = getopt.getopt( sys.argv[1:], 'n' ) +except getopt.GetoptError, e: + print str(e) + usage() +if len( args ) < 1: + usage() +server = args[0] +username = args[1] +password = args[2] + +if server.endswith(".g2.bx.psu.edu"): + if debug: + print "Checking a PSU Galaxy server, using maint file" + maint = "/errordocument/502/%s/maint" % args[0].split('.', 1)[0] +else: + maint = None + +new_history = False +for o, a in opts: + if o == "-n": + if debug: + print "Specified -n, will create a new history" + new_history = True + else: + usage() + +# state information +var_dir = os.path.join( home, ".check_galaxy", server ) +if not os.access( var_dir, os.F_OK ): + os.makedirs( var_dir, 0700 ) + +# default timeout for twill browser is never +socket.setdefaulttimeout(300) + +# user-agent +tc.agent("Mozilla/5.0 (compatible; check_galaxy/0.1)") +tc.config('use_tidy', 0) + +class Browser: + + def __init__(self): + self.server = server + self.maint = maint + self.tool = None + self.tool_opts = None + self.id = None + self.status = None + self.check_file = None + self.hid = None + self.cookie_jar = os.path.join( var_dir, "cookie_jar" ) + dprint("cookie jar path: %s" % self.cookie_jar) + if not os.access(self.cookie_jar, os.R_OK): + dprint("no cookie jar at above path, creating") + tc.save_cookies(self.cookie_jar) + tc.load_cookies(self.cookie_jar) + + def get(self, path): + tc.go("http://%s%s" % (self.server, path)) + tc.code(200) + + def reset(self): + self.tool = None + self.tool_opts = None + self.id = None + self.status = None + self.check_file = None + self.delete_datasets() + self.get("/root/history") + p = didParser() + p.feed(tc.browser.get_html()) + if len(p.dids) > 0: + print "Remaining datasets ids:", " ".join( p.dids ) + raise Exception, "History still contains datasets after attempting to delete them" + if new_history: + self.get("/history/delete_current") + tc.save_cookies(self.cookie_jar) + + def check_redir(self, url): + try: + tc.get_browser()._browser.set_handle_redirect(False) + tc.go(url) + tc.code(302) + tc.get_browser()._browser.set_handle_redirect(True) + dprint( "%s is returning redirect (302)" % url ) + return(True) + except twill.errors.TwillAssertionError, e: + tc.get_browser()._browser.set_handle_redirect(True) + dprint( "%s is not returning redirect (302): %s" % (url, e) ) + code = tc.browser.get_code() + if code == 502: + is_maint = self.check_maint() + if is_maint: + dprint( "Galaxy is down, but a maint file was found, so not sending alert" ) + sys.exit(0) + else: + print "Galaxy is down (code 502)" + sys.exit(1) + return(False) + + # checks for a maint file + def check_maint(self): + if self.maint is None: + #dprint( "Warning: unable to check maint file for %s" % self.server ) + return(False) + try: + self.get(self.maint) + return(True) + except twill.errors.TwillAssertionError, e: + return(False) + + def login(self, user, pw): + self.get("/user/login") + tc.fv("1", "email", user) + tc.fv("1", "password", pw) + tc.submit("Login") + tc.code(200) + if len(tc.get_browser().get_all_forms()) > 0: + # uh ohs, fail + p = userParser() + p.feed(tc.browser.get_html()) + if p.no_user: + dprint("user does not exist, will try creating") + self.create_user(user, pw) + elif p.bad_pw: + raise Exception, "Password is incorrect" + else: + raise Exception, "Unknown error logging in" + tc.save_cookies(self.cookie_jar) + + def create_user(self, user, pw): + self.get("/user/create") + tc.fv("1", "email", user) + tc.fv("1", "password", pw) + tc.fv("1", "confirm", pw) + tc.submit("Submit") + tc.code(200) + if len(tc.get_browser().get_all_forms()) > 0: + p = userParser() + p.feed(tc.browser.get_html()) + if p.already_exists: + raise Exception, 'The user you were trying to create already exists' + + def upload(self, input): + self.get("/tool_runner/index?tool_id=upload1") + tc.fv("1","file_type", "bed") + tc.fv("1","dbkey", input.get('dbkey', '?')) + tc.formfile("1","file_data", input['file_path']) + tc.submit("runtool_btn") + tc.code(200) + + def runtool(self): + self.get("/tool_runner/index?tool_id=%s" % self.tool) + for k, v in self.tool_opts.items(): + tc.fv("1", k, v) + tc.submit("runtool_btn") + tc.code(200) + + def wait(self): + sleep_amount = 1 + count = 0 + maxiter = 16 + while count < maxiter: + count += 1 + self.get("/root/history") + page = tc.browser.get_html() + if page.find( '' ) > -1: + time.sleep( sleep_amount ) + sleep_amount += 1 + else: + break + if count == maxiter: + raise Exception, "Tool never finished" + + def check_status(self): + self.get("/root/history") + p = historyParser() + p.feed(tc.browser.get_html()) + if p.status != "ok": + self.get("/datasets/%s/stderr" % p.id) + print tc.browser.get_html() + raise Exception, "HDA %s NOT OK: %s" % (p.id, p.status) + self.id = p.id + self.status = p.status + #return((p.id, p.status)) + + def diff(self): + self.get("/datasets/%s/display?to_ext=%s" % (self.id, self.tool_opts.get('out_format', 'fasta'))) + data = tc.browser.get_html() + tmp = tempfile.mkstemp() + dprint("tmp file: %s" % tmp[1]) + tmpfh = os.fdopen(tmp[0], 'w') + tmpfh.write(data) + tmpfh.close() + if filecmp.cmp(tmp[1], self.check_file): + dprint("Tool output is as expected") + else: + if not debug: + os.remove(tmp[1]) + raise Exception, "Tool output differs from expected" + if not debug: + os.remove(tmp[1]) + + def delete_datasets(self): + self.get("/root/history") + p = didParser() + p.feed(tc.browser.get_html()) + dids = p.dids + for did in dids: + self.get("/datasets/%s/delete" % did) + + def check_if_logged_in(self): + self.get("/user?cntrller=user") + p = loggedinParser() + p.feed(tc.browser.get_html()) + return p.logged_in + +class userParser(htmllib.HTMLParser): + def __init__(self): + htmllib.HTMLParser.__init__(self, formatter.NullFormatter()) + self.in_span = False + self.in_div = False + self.no_user = False + self.bad_pw = False + self.already_exists = False + def start_span(self, attrs): + self.in_span = True + def start_div(self, attrs): + self.in_div = True + def end_span(self): + self.in_span = False + def end_div(self): + self.in_div = False + def handle_data(self, data): + if self.in_span or self.in_div: + if data == "No such user (please note that login is case sensitive)": + self.no_user = True + elif data == "Invalid password": + self.bad_pw = True + elif data == "User with that email already exists": + self.already_exists = True + +class historyParser(htmllib.HTMLParser): + def __init__(self): + htmllib.HTMLParser.__init__(self, formatter.NullFormatter()) + self.status = None + self.id = None + def start_div(self, attrs): + # find the top history item + for i in attrs: + if i[0] == "class" and i[1].startswith("historyItemWrapper historyItem historyItem-"): + self.status = i[1].rsplit("historyItemWrapper historyItem historyItem-", 1)[1] + dprint("status: %s" % self.status) + if i[0] == "id" and i[1].startswith("historyItem-"): + self.id = i[1].rsplit("historyItem-", 1)[1] + dprint("id: %s" % self.id) + if self.status is not None: + self.reset() + +class didParser(htmllib.HTMLParser): + def __init__(self): + htmllib.HTMLParser.__init__(self, formatter.NullFormatter()) + self.dids = [] + def start_div(self, attrs): + for i in attrs: + if i[0] == "id" and i[1].startswith("historyItemContainer-"): + self.dids.append( i[1].rsplit("historyItemContainer-", 1)[1] ) + dprint("got a dataset id: %s" % self.dids[-1]) + +class loggedinParser(htmllib.HTMLParser): + def __init__(self): + htmllib.HTMLParser.__init__(self, formatter.NullFormatter()) + self.in_p = False + self.logged_in = False + def start_p(self, attrs): + self.in_p = True + def end_p(self): + self.in_p = False + def handle_data(self, data): + if self.in_p: + if data == "You are currently not logged in.": + self.logged_in = False + elif data.startswith( "You are currently logged in as " ): + self.logged_in = True + +def dprint(str): + if debug: + print str + +# do stuff here +if __name__ == "__main__": + + dprint("checking %s" % server) + + b = Browser() + + # login (or not) + if b.check_if_logged_in(): + dprint("we are already logged in (via cookies), hooray!") + else: + dprint("not logged in... logging in") + b.login(username, password) + + for tool, params in tools.iteritems(): + + check_file = "" + + # make sure history and state is clean + b.reset() + b.tool = tool + + # get all the tool run conditions + for dict in params: + for k, v in dict.items(): + if k == 'inputs': + for input in v: + b.upload(input) + b.wait() + elif k == 'check_file': + b.check_file = v + elif k == 'tool_run_options': + b.tool_opts = v + else: + raise Exception, "Unknown key in tools dict: %s" % k + + b.runtool() + b.wait() + b.check_status() + b.diff() + b.delete_datasets() + + # by this point, everything else has succeeded. there should be no maint. + is_maint = b.check_maint() + if is_maint: + print "Galaxy is up and fully functional, but a maint file is in place." + sys.exit(1) + + print "OK" + sys.exit(0) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Infrastructure for managing visualizations: (a) support for creating multiple types of visualizations; (b) a placeholder visualization API controller; (c) abstract visualization creation so that it can be reused in multiple controllers.
by Bitbucket 25 May '12

25 May '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/62bdb265d300/ changeset: 62bdb265d300 user: jgoecks date: 2012-05-26 00:23:43 summary: Infrastructure for managing visualizations: (a) support for creating multiple types of visualizations; (b) a placeholder visualization API controller; (c) abstract visualization creation so that it can be reused in multiple controllers. affected #: 6 files diff -r 4288ffb1bd16d8f014dc06759c8073919e7347c8 -r 62bdb265d3007d4f761a1defa82a44d888c30bfd lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -2445,12 +2445,13 @@ self.user = None class Visualization( object ): - def __init__( self, user=None, type=None, title=None, dbkey=None, latest_revision=None ): + def __init__( self, user=None, type=None, title=None, dbkey=None, slug=None, latest_revision=None ): self.id = None self.user = user self.type = type self.title = title self.dbkey = dbkey + self.slug = slug self.latest_revision = latest_revision self.revisions = [] if self.latest_revision: diff -r 4288ffb1bd16d8f014dc06759c8073919e7347c8 -r 62bdb265d3007d4f761a1defa82a44d888c30bfd lib/galaxy/visualization/__init__.py --- a/lib/galaxy/visualization/__init__.py +++ b/lib/galaxy/visualization/__init__.py @@ -1,3 +1,3 @@ """ Package for Galaxy visualization plugins. -""" \ No newline at end of file +""" diff -r 4288ffb1bd16d8f014dc06759c8073919e7347c8 -r 62bdb265d3007d4f761a1defa82a44d888c30bfd lib/galaxy/web/api/visualizations.py --- /dev/null +++ b/lib/galaxy/web/api/visualizations.py @@ -0,0 +1,28 @@ +from galaxy import web +from galaxy.web.base.controller import BaseController, BaseAPIController + +class VisualizationsController( BaseAPIController ): + """ + RESTful controller for interactions with visualizations. + """ + + @web.expose_api + def index( self, trans, **kwds ): + """ + GET /api/visualizations: + """ + pass + + @web.json + def show( self, trans, id, **kwd ): + """ + GET /api/visualizations/{viz_id} + """ + pass + + @web.expose_api + def create( self, trans, payload, **kwd ): + """ + POST /api/visualizations + """ + pass \ No newline at end of file diff -r 4288ffb1bd16d8f014dc06759c8073919e7347c8 -r 62bdb265d3007d4f761a1defa82a44d888c30bfd lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -7,6 +7,7 @@ from galaxy import config, tools, web, util from galaxy.util import inflector from galaxy.util.hash_util import * +from galaxy.util.sanitize_html import sanitize_html from galaxy.web import error, form, url_for from galaxy.model.orm import * from galaxy.workflow.modules import * @@ -275,8 +276,45 @@ class UsesVisualization( SharableItemSecurity ): """ Mixin for controllers that use Visualization objects. """ + + viz_types = [ "trackster", "circos" ] len_files = None + + def create_visualization( self, trans, title, slug, type, dbkey, annotation=None, config={} ): + user = trans.get_user() + + # Error checking. + title_err = slug_err = "" + if not title: + title_err = "visualization name is required" + elif not slug: + slug_err = "visualization id is required" + elif not VALID_SLUG_RE.match( slug ): + slug_err = "visualization identifier must consist of only lowercase letters, numbers, and the '-' character" + elif trans.sa_session.query( trans.model.Visualization ).filter_by( user=user, slug=slug, deleted=False ).first(): + slug_err = "visualization id must be unique" + + if title_err or slug_err: + return { 'title_err': title_err, 'slug_err': slug_err } + + # Create visualization + visualization = trans.model.Visualization( user=user, title=title, slug=slug, dbkey=dbkey, type=type ) + if annotation: + annotation = sanitize_html( annotation, 'utf-8', 'text/html' ) + self.add_item_annotation( trans.sa_session, trans.user, visualization, annotation ) + + # And the first visualization revision + revision = trans.model.VisualizationRevision( visualization=visualization, title=title, config={}, dbkey=dbkey ) + visualization.latest_revision = revision + + # Persist + session = trans.sa_session + session.add(visualization) + session.add(revision) + session.flush() + + return visualization def _get_dbkeys( self, trans ): """ Returns all valid dbkeys that a user can use in a visualization. """ diff -r 4288ffb1bd16d8f014dc06759c8073919e7347c8 -r 62bdb265d3007d4f761a1defa82a44d888c30bfd lib/galaxy/web/buildapp.py --- a/lib/galaxy/web/buildapp.py +++ b/lib/galaxy/web/buildapp.py @@ -132,6 +132,7 @@ webapp.api_mapper.resource_with_deleted( 'quota', 'quotas', path_prefix='/api' ) webapp.api_mapper.resource( 'tool', 'tools', path_prefix='/api' ) webapp.api_mapper.resource_with_deleted( 'user', 'users', path_prefix='/api' ) + webapp.api_mapper.resource( 'visualization', 'visualizations', path_prefix='/api' ) webapp.api_mapper.resource( 'workflow', 'workflows', path_prefix='/api' ) webapp.api_mapper.resource_with_deleted( 'history', 'histories', path_prefix='/api' ) #webapp.api_mapper.connect( 'run_workflow', '/api/workflow/{workflow_id}/library/{library_id}', controller='workflows', action='run', workflow_id=None, library_id=None, conditions=dict(method=["GET"]) ) diff -r 4288ffb1bd16d8f014dc06759c8073919e7347c8 -r 62bdb265d3007d4f761a1defa82a44d888c30bfd lib/galaxy/web/controllers/visualization.py --- a/lib/galaxy/web/controllers/visualization.py +++ b/lib/galaxy/web/controllers/visualization.py @@ -4,7 +4,6 @@ from galaxy.web.framework.helpers import time_ago, grids, iff from galaxy.util.sanitize_html import sanitize_html - class VisualizationListGrid( grids.Grid ): # Grid definition title = "Saved Visualizations" @@ -14,6 +13,7 @@ columns = [ grids.TextColumn( "Title", key="title", attach_popup=True, link=( lambda item: dict( controller="tracks", action="browser", id=item.id ) ) ), + grids.TextColumn( "Type", key="type" ), grids.TextColumn( "Dbkey", key="dbkey" ), grids.IndividualTagsColumn( "Tags", key="tags", model_tag_association_class=model.VisualizationTagAssociation, filterable="advanced", grid_name="VisualizationListGrid" ), grids.SharingStatusColumn( "Sharing", key="sharing", filterable="advanced", sortable=False ), @@ -346,51 +346,31 @@ @web.expose @web.require_login( "create visualizations" ) - def create( self, trans, visualization_title="", visualization_slug="", visualization_annotation="", visualization_dbkey="" ): + def create( self, trans, visualization_title="", visualization_slug="", visualization_annotation="", visualization_dbkey="", + visualization_type="" ): """ Create a new visualization """ - user = trans.get_user() visualization_title_err = visualization_slug_err = visualization_annotation_err = "" if trans.request.method == "POST": - if not visualization_title: - visualization_title_err = "visualization name is required" - elif not visualization_slug: - visualization_slug_err = "visualization id is required" - elif not VALID_SLUG_RE.match( visualization_slug ): - visualization_slug_err = "visualization identifier must consist of only lowercase letters, numbers, and the '-' character" - elif trans.sa_session.query( model.Visualization ).filter_by( user=user, slug=visualization_slug, deleted=False ).first(): - visualization_slug_err = "visualization id must be unique" + rval = self.create_visualization( trans, title=visualization_title, + slug=visualization_slug, + annotation=visualization_annotation, + dbkey=visualization_dbkey, + type=visualization_type ) + if isinstance( rval, dict ): + # Found error creating viz. + visualization_title_err = rval[ 'title_err' ] + visualization_slug_err = rval[ 'slug_err' ] else: - # Create the new stored visualization - visualization = model.Visualization() - visualization.title = visualization_title - visualization.slug = visualization_slug - visualization.dbkey = visualization_dbkey - visualization.type = 'trackster' # HACK: set visualization type to trackster since it's the only viz - visualization_annotation = sanitize_html( visualization_annotation, 'utf-8', 'text/html' ) - self.add_item_annotation( trans.sa_session, trans.get_user(), visualization, visualization_annotation ) - visualization.user = user - - # And the first (empty) visualization revision - visualization_revision = model.VisualizationRevision() - visualization_revision.title = visualization_title - visualization_revision.config = {} - visualization_revision.dbkey = visualization_dbkey - visualization_revision.visualization = visualization - visualization.latest_revision = visualization_revision - - # Persist - session = trans.sa_session - session.add(visualization) - session.add(visualization_revision) - session.flush() - + # Successfully created viz. return trans.response.send_redirect( web.url_for( action='list' ) ) - + + viz_type_options = [ ( t, t ) for t in self.viz_types ] return trans.show_form( web.FormBuilder( web.url_for(), "Create new visualization", submit_text="Submit" ) .add_text( "visualization_title", "Visualization title", value=visualization_title, error=visualization_title_err ) + .add_select( "visualization_type", "Type", options=viz_type_options, error=None ) .add_text( "visualization_slug", "Visualization identifier", value=visualization_slug, error=visualization_slug_err, help="""A unique identifier that will be used for public links to this visualization. A default is generated 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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