March 2012 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: dan: In library uploads, allow inheriting the existing datasets metadata when replacing. Allow setting library metadata when adding datasets from a history.
by Bitbucket 05 Mar '12

05 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/8f58413c0937/ changeset: 8f58413c0937 user: dan date: 2012-03-05 19:25:14 summary: In library uploads, allow inheriting the existing datasets metadata when replacing. Allow setting library metadata when adding datasets from a history. affected #: 3 files diff -r e58a87c91bc4bb471b9b6477ef638dc41c4aa4b9 -r 8f58413c09377d25a95ec12e23a5f476fa2a0dd7 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -1582,6 +1582,9 @@ self.library_dataset_dataset_association = library_dataset_dataset_association self.template = form_definition self.info = info + @property + def inheritable( self ): + return True #always allow inheriting, used for replacement class ValidationError( object ): def __init__( self, message=None, err_type=None, attributes=None ): diff -r e58a87c91bc4bb471b9b6477ef638dc41c4aa4b9 -r 8f58413c09377d25a95ec12e23a5f476fa2a0dd7 lib/galaxy/web/controllers/library_common.py --- a/lib/galaxy/web/controllers/library_common.py +++ b/lib/galaxy/web/controllers/library_common.py @@ -746,12 +746,20 @@ roles = params.get( 'roles', '' ) is_admin = trans.user_is_admin() and cntrller in ( 'library_admin', 'api' ) current_user_roles = trans.get_current_user_roles() + widgets = [] + widget_fields_have_contents = False + info_association, inherited = None, None + template_id = "None" if replace_id not in [ '', None, 'None' ]: replace_dataset = trans.sa_session.query( trans.app.model.LibraryDataset ).get( trans.security.decode_id( replace_id ) ) self._check_access( trans, cntrller, is_admin, replace_dataset, current_user_roles, use_panels, library_id, show_deleted ) self._check_modify( trans, cntrller, is_admin, replace_dataset, current_user_roles, use_panels, library_id, show_deleted ) library = replace_dataset.folder.parent_library folder = replace_dataset.folder + info_association, inherited = replace_dataset.library_dataset_dataset_association.get_info_association() + if info_association and ( not( inherited ) or info_association.inheritable ): + widgets = replace_dataset.library_dataset_dataset_association.get_template_widgets( trans ) + widget_fields_have_contents = self.widget_fields_have_contents( widgets ) # The name is stored - by the time the new ldda is created, replace_dataset.name # will point to the new ldda, not the one it's replacing. replace_dataset_name = replace_dataset.name @@ -793,7 +801,8 @@ status='error' ) ) else: # See if we have any inherited templates. - info_association, inherited = folder.get_info_association( inherited=True ) + if not info_association: + info_association, inherited = folder.get_info_association( inherited=True ) if info_association and info_association.inheritable: template_id = str( info_association.template.id ) widgets = folder.get_template_widgets( trans, get_contents=True ) @@ -836,9 +845,6 @@ else: processed_widgets.append( widget_dict ) widgets = processed_widgets - else: - template_id = 'None' - widgets = [] created_outputs_dict = trans.webapp.controllers[ 'library_common' ].upload_dataset( trans, cntrller=cntrller, library_id=trans.security.encode_id( library.id ), @@ -910,13 +916,15 @@ # attribute of the html input file type field is typically ignored by browsers as a security precaution. # See if we have any inherited templates. - info_association, inherited = folder.get_info_association( inherited=True ) - if info_association and info_association.inheritable: - widgets = folder.get_template_widgets( trans, get_contents=True ) + if not info_association: + info_association, inherited = folder.get_info_association( inherited=True ) + if info_association and info_association.inheritable: + widgets = folder.get_template_widgets( trans, get_contents=True ) + if info_association: # Retain contents of widget fields when form was submitted via refresh_on_change. widgets = self.populate_widgets_from_kwd( trans, widgets, **kwd ) - else: - widgets = [] + template_id = str( info_association.template.id ) + # Send list of data formats to the upload form so the "extension" select list can be populated dynamically file_formats = trans.app.datatypes_registry.upload_file_formats # Send list of genome builds to the form so the "dbkey" select list can be populated dynamically @@ -956,6 +964,7 @@ roles_select_list=roles_select_list, history=history, widgets=widgets, + template_id=template_id, space_to_tab=space_to_tab, link_data_only=link_data_only, show_deleted=show_deleted, @@ -1185,6 +1194,10 @@ roles = params.get( 'roles', '' ) is_admin = trans.user_is_admin() and cntrller in ( 'library_admin', 'api' ) current_user_roles = trans.get_current_user_roles() + widgets = [] + widget_fields_have_contents = False + info_association, inherited = None, None + template_id = "None" if replace_id not in [ None, 'None' ]: try: replace_dataset = trans.sa_session.query( trans.app.model.LibraryDataset ).get( trans.security.decode_id( replace_id ) ) @@ -1195,6 +1208,11 @@ library = replace_dataset.folder.parent_library folder = replace_dataset.folder last_used_build = replace_dataset.library_dataset_dataset_association.dbkey + info_association, inherited = replace_dataset.library_dataset_dataset_association.get_info_association() + if info_association and ( not( inherited ) or info_association.inheritable ): + widgets = replace_dataset.library_dataset_dataset_association.get_template_widgets( trans ) + widget_fields_have_contents = self.widget_fields_have_contents( widgets ) + template_id = str( info_association.template.id ) else: folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( trans.security.decode_id( folder_id ) ) self._check_access( trans, cntrller, is_admin, folder, current_user_roles, use_panels, library_id, show_deleted ) @@ -1241,6 +1259,20 @@ # LDDA and LibraryDataset. trans.app.security_agent.copy_library_permissions( trans, folder, ldda ) trans.app.security_agent.copy_library_permissions( trans, folder, ldda.library_dataset ) + else: + library_bunch = upload_common.handle_library_params( trans, params, folder_id, replace_dataset ) + if library_bunch.template and library_bunch.template_field_contents: + # Since information templates are inherited, the template fields can be displayed on the upload form. + # If the user has added field contents, we'll need to create a new form_values and info_association + # for the new library_dataset_dataset_association object. + # Create a new FormValues object, using the template we previously retrieved + form_values = trans.app.model.FormValues( library_bunch.template, library_bunch.template_field_contents ) + trans.sa_session.add( form_values ) + trans.sa_session.flush() + # Create a new info_association between the current ldda and form_values + info_association = trans.app.model.LibraryDatasetDatasetInfoAssociation( ldda, library_bunch.template, form_values ) + trans.sa_session.add( info_association ) + trans.sa_session.flush() # Make sure to apply any defined dataset permissions, allowing the permissions inherited from the folder to # over-ride the same permissions on the dataset, if they exist. dataset_permissions_dict = trans.app.security_agent.get_permissions( hda.dataset ) @@ -1330,6 +1362,7 @@ roles_select_list=roles_select_list, history=history, widgets=widgets, + template_id=template_id, space_to_tab=space_to_tab, link_data_only=link_data_only, show_deleted=show_deleted, diff -r e58a87c91bc4bb471b9b6477ef638dc41c4aa4b9 -r 8f58413c09377d25a95ec12e23a5f476fa2a0dd7 templates/library/common/common.mako --- a/templates/library/common/common.mako +++ b/templates/library/common/common.mako @@ -363,12 +363,6 @@ <div style="clear: both"></div></div> %endif - ## Render hidden template fields so the contents will be associated with the dataset - %if widgets: - %for i, field in enumerate( widgets ): - ${render_template_field( field, render_as_hidden=True )} - %endfor - %endif %for hda in history.visible_datasets: <% encoded_id = trans.security.encode_id( hda.id ) %><div class="form-row"> @@ -376,6 +370,24 @@ <label for="hist_${encoded_id}" style="display: inline;font-weight:normal;">${hda.hid}: ${hda.name}</label></div> %endfor + %if widgets: + <input type="hidden" name="template_id" value="${template_id}"/> + %for i, field in enumerate( widgets ): + <div class="form-row"> + <label>${field[ 'label' ]}</label> + <div class="form-row-input"> + ${field[ 'widget' ].get_html()} + </div> + <div class="toolParamHelp" style="clear: both;"> + %if field[ 'helptext' ]: + ${field[ 'helptext' ]}<br/> + %endif + *Inherited template field + </div> + <div style="clear: both"></div> + </div> + %endfor + %endif <div class="form-row"><input type="submit" name="add_history_datasets_to_library_button" value="Import to library"/></div> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: dannon: Add config option (sanitize_all_html, still enabled by default) to control strict dataset html output sanitization.
by Bitbucket 05 Mar '12

05 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/e58a87c91bc4/ changeset: e58a87c91bc4 user: dannon date: 2012-03-05 18:00:53 summary: Add config option (sanitize_all_html, still enabled by default) to control strict dataset html output sanitization. affected #: 3 files diff -r 6fe4166160f331e99b9d7e799587e0ed95ac9ed4 -r e58a87c91bc4bb471b9b6477ef638dc41c4aa4b9 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -33,7 +33,7 @@ # Database related configuration self.database = resolve_path( kwargs.get( "database_file", "database/universe.sqlite" ), self.root ) self.database_connection = kwargs.get( "database_connection", False ) - self.database_engine_options = get_database_engine_options( kwargs ) + self.database_engine_options = get_database_engine_options( kwargs ) self.database_create_tables = string_as_bool( kwargs.get( "database_create_tables", "True" ) ) self.database_query_profiling_proxy = string_as_bool( kwargs.get( "database_query_profiling_proxy", "False" ) ) # Where dataset files are stored @@ -61,7 +61,7 @@ tcf = kwargs[ 'tool_config_files' ] else: tcf = 'tool_conf.xml' - self.tool_configs = [ resolve_path( p, self.root ) for p in listify( tcf ) ] + self.tool_configs = [ resolve_path( p, self.root ) for p in listify( tcf ) ] self.tool_data_table_config_path = resolve_path( kwargs.get( 'tool_data_table_config_path', 'tool_data_table_conf.xml' ), self.root ) self.enable_tool_shed_check = string_as_bool( kwargs.get( 'enable_tool_shed_check', False ) ) try: @@ -125,6 +125,7 @@ self.use_memdump = string_as_bool( kwargs.get( 'use_memdump', 'False' ) ) self.log_actions = string_as_bool( kwargs.get( 'log_actions', 'False' ) ) self.log_events = string_as_bool( kwargs.get( 'log_events', 'False' ) ) + self.sanitize_all_html = string_as_bool( kwargs.get( 'sanitize_all_html', True ) ) self.ucsc_display_sites = kwargs.get( 'ucsc_display_sites', "main,test,archaea,ucla" ).lower().split(",") self.gbrowse_display_sites = kwargs.get( 'gbrowse_display_sites', "wormbase,tair,modencode_worm,modencode_fly,sgd_yeast" ).lower().split(",") self.genetrack_display_sites = kwargs.get( 'genetrack_display_sites', "main,test" ).lower().split(",") @@ -183,7 +184,7 @@ #Store per-tool runner configs. try: tool_runners_config = global_conf_parser.items("galaxy:tool_runners") - + # Process config to group multiple configs for the same tool. tool_runners = {} for entry in tool_runners_config: @@ -200,17 +201,17 @@ runner_dict[ 'params' ] = param_dict else: tool = tool_config - + # Add runner URL. runner_dict[ 'url' ] = url - + # Create tool entry if necessary. if tool not in tool_runners: tool_runners[ tool ] = [] - + # Add entry to runners. tool_runners[ tool ].append( runner_dict ) - + self.tool_runners = tool_runners except ConfigParser.NoSectionError: self.tool_runners = [] @@ -281,12 +282,12 @@ # Check for deprecated options. for key in self.config_dict.keys(): if key in self.deprecated_options: - log.warning( "Config option '%s' is deprecated and will be removed in a future release. Please consult the latest version of the sample configuration file." % key ) - + log.warning( "Config option '%s' is deprecated and will be removed in a future release. Please consult the latest version of the sample configuration file." % key ) + def is_admin_user( self,user ): """ Determine if the provided user is listed in `admin_users`. - + NOTE: This is temporary, admin users will likely be specified in the database in the future. """ @@ -343,7 +344,7 @@ if level <= logging.DEBUG: logging.getLogger( "paste.httpserver.ThreadPool" ).setLevel( logging.WARN ) # Remove old handlers - for h in root.handlers[:]: + for h in root.handlers[:]: root.removeHandler(h) # Create handler if destination == "stdout": @@ -351,7 +352,7 @@ else: handler = logging.FileHandler( destination ) # Create formatter - formatter = logging.Formatter( format ) + formatter = logging.Formatter( format ) # Hook everything up handler.setFormatter( formatter ) root.addHandler( handler ) diff -r 6fe4166160f331e99b9d7e799587e0ed95ac9ed4 -r e58a87c91bc4bb471b9b6477ef638dc41c4aa4b9 lib/galaxy/web/controllers/dataset.py --- a/lib/galaxy/web/controllers/dataset.py +++ b/lib/galaxy/web/controllers/dataset.py @@ -409,7 +409,7 @@ if isinstance(data.datatype, datatypes.images.Html): max_peek_size = 10000000 # 10 MB for html if not preview or isinstance(data.datatype, datatypes.images.Image) or os.stat( data.file_name ).st_size < max_peek_size: - if trans.response.get_content_type() == "text/html": + if trans.app.config.sanitize_all_html and trans.response.get_content_type() == "text/html": # Sanitize anytime we respond with plain text/html content. return sanitize_html(open( data.file_name ).read()) return open( data.file_name ) diff -r 6fe4166160f331e99b9d7e799587e0ed95ac9ed4 -r e58a87c91bc4bb471b9b6477ef638dc41c4aa4b9 universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -309,6 +309,12 @@ # log_events and log_actions functionality will eventually be merged. #log_actions = True +# Sanitize All HTML Tool Output +# By default, all tool output served as 'text/html' will be sanitized +# thoroughly. This can be disabled if you have special tools that require +# unaltered output. +#sanitize_all_html = True + # Debug enables access to various config options useful for development and # debugging: use_lint, use_profile, use_printdebug and use_interactive. It # also causes the files used by PBS/SGE (submission script, output, and error) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: greg: Keep empty sections in the tool panel when deactivating / uninstalling a repository with tools.
by Bitbucket 02 Mar '12

02 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/6fe4166160f3/ changeset: 6fe4166160f3 user: greg date: 2012-03-02 21:37:35 summary: Keep empty sections in the tool panel when deactivating / uninstalling a repository with tools. affected #: 1 file diff -r 250bbb04b5a4539010100cd56191fbb32c4242a5 -r 6fe4166160f331e99b9d7e799587e0ed95ac9ed4 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -1002,10 +1002,10 @@ if section_key in trans.app.toolbox.tool_panel: tool_section = trans.app.toolbox.tool_panel[ section_key ] tool_key = key = 'tool_%s' % str( tool_elem.get( 'guid' ) ) + # Remove empty sections only from the in-memory config_elems, but leave + # the in-memory tool panel alone. if tool_key in tool_section.elems: del tool_section.elems[ tool_key ] - if not tool_section.elems: - del trans.app.toolbox.tool_panel[ section_key ] if len( config_elem ) < 1: # Keep a list of all empty section elements so they can be removed. config_elems_to_remove.append( config_elem ) 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 02 Mar '12

02 Mar '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/9d5a55bbfcb8/ changeset: 9d5a55bbfcb8 user: jgoecks date: 2012-03-02 20:29:21 summary: Fix custom-build UI bugs. affected #: 2 files diff -r 29f652b9a18cbac444a1c1b68d5ad36f17db7192 -r 9d5a55bbfcb8d9129c3e429098255eee05614930 lib/galaxy/web/controllers/user.py --- a/lib/galaxy/web/controllers/user.py +++ b/lib/galaxy/web/controllers/user.py @@ -1174,6 +1174,8 @@ @web.expose @web.require_login() def dbkeys( self, trans, **kwds ): + """ Handle custom builds. """ + # # Process arguments and add/delete build. # @@ -1298,7 +1300,7 @@ fasta_hdas = trans.sa_session.query( model.HistoryDatasetAssociation ) \ .filter_by( history=trans.history, extension="fasta", deleted=False ) \ .order_by( model.HistoryDatasetAssociation.hid.desc() ) - + return trans.fill_template( 'user/dbkeys.mako', user=user, dbkeys=dbkeys, @@ -1306,7 +1308,7 @@ installed_len_files=self.installed_len_files, lines_skipped=lines_skipped, fasta_hdas=fasta_hdas, - use_panels=kwds.get( 'use_panels', None ) ) + use_panels=kwds.get( 'use_panels', False ) ) @web.expose @web.require_login() def api_keys( self, trans, cntrller, **kwd ): diff -r 29f652b9a18cbac444a1c1b68d5ad36f17db7192 -r 9d5a55bbfcb8d9129c3e429098255eee05614930 templates/user/dbkeys.mako --- a/templates/user/dbkeys.mako +++ b/templates/user/dbkeys.mako @@ -99,7 +99,7 @@ // Before submit, remove inputs not associated with the active tab. $("#submit").click(function() { - var id = $(".active > a").attr("id"); + var id = $(this).parents("form").find(".active > a").attr("id"); $("div.build_definition").children(":input").each(function() { if ( $(this).attr("id") !== (id + "_input") ) { $(this).remove(); @@ -168,6 +168,10 @@ <hr /><h3>Add a Custom Build</h3><form action="dbkeys" method="post" enctype="multipart/form-data"> + ## Include hidden param for panels: + %if use_panels: + <input type="hidden" name="use_panels" value="True"> + %endif ## Custom build via fasta in history. <div class="toolForm" style="float: left;"><div class="toolFormTitle">New Build</div> https://bitbucket.org/galaxy/galaxy-central/changeset/250bbb04b5a4/ changeset: 250bbb04b5a4 user: jgoecks date: 2012-03-02 20:35:57 summary: Merge affected #: 1 file diff -r 9d5a55bbfcb8d9129c3e429098255eee05614930 -r 250bbb04b5a4539010100cd56191fbb32c4242a5 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -599,25 +599,6 @@ if converter_path and display_path: break return converter_path, display_path -def get_in_memory_config_elems_to_remove( shed_tool_conf_dict, guids_to_remove ): - config_elems = shed_tool_conf_dict[ 'config_elems' ] - config_elems_to_remove = [] - for config_elem in config_elems: - if config_elem.tag == 'section': - tool_elems_to_remove = [] - for tool_elem in config_elem: - if tool_elem.get( 'guid' ) in guids_to_remove: - tool_elems_to_remove.append( tool_elem ) - for tool_elem in tool_elems_to_remove: - # Remove all of the appropriate tool sub-elements from the section element. - config_elem.remove( tool_elem ) - if len( config_elem ) < 1: - # Keep a list of all empty section elements so they can be removed. - config_elems_to_remove.append( config_elem ) - elif config_elem.tag == 'tool': - if config_elem.get( 'guid' ) in guids_to_remove: - config_elems_to_remove.append( config_elem ) - return config_elems_to_remove def get_shed_tool_conf_dict( app, shed_tool_conf ): """ Return the in-memory version of the shed_tool_conf file, which is stored in the config_elems entry @@ -1003,18 +984,40 @@ if uninstall: # Remove from the shed_tool_conf file on disk. remove_from_shed_tool_config( trans, shed_tool_conf_dict, guids_to_remove ) - config_elems_to_remove = get_in_memory_config_elems_to_remove( shed_tool_conf_dict, guids_to_remove ) - # Remove from the in-memory list of config_elems. config_elems = shed_tool_conf_dict[ 'config_elems' ] + config_elems_to_remove = [] + for config_elem in config_elems: + if config_elem.tag == 'section': + # Get the section key for the in-memory tool panel. + section_key = 'section_%s' % str( config_elem.get( "id" ) ) + # Generate the list of tool elements to remove. + tool_elems_to_remove = [] + for tool_elem in config_elem: + if tool_elem.get( 'guid' ) in guids_to_remove: + tool_elems_to_remove.append( tool_elem ) + for tool_elem in tool_elems_to_remove: + # Remove the tool sub-element from the section element. + config_elem.remove( tool_elem ) + # Remove the tool from the section in the in-memory tool panel. + if section_key in trans.app.toolbox.tool_panel: + tool_section = trans.app.toolbox.tool_panel[ section_key ] + tool_key = key = 'tool_%s' % str( tool_elem.get( 'guid' ) ) + if tool_key in tool_section.elems: + del tool_section.elems[ tool_key ] + if not tool_section.elems: + del trans.app.toolbox.tool_panel[ section_key ] + if len( config_elem ) < 1: + # Keep a list of all empty section elements so they can be removed. + config_elems_to_remove.append( config_elem ) + elif config_elem.tag == 'tool': + if config_elem.get( 'guid' ) in guids_to_remove: + tool_key = key = 'tool_%s' % str( config_elem.get( 'guid' ) ) + if tool_key in trans.app.toolbox.tool_panel: + del trans.app.toolbox.tool_panel[ tool_key ] + config_elems_to_remove.append( config_elem ) for config_elem in config_elems_to_remove: # Remove the element from the in-memory list of elements. config_elems.remove( config_elem ) - if config_elem.tag == 'section': - key = 'section_%s' % str( config_elem.get( "id" ) ) - del trans.app.toolbox.tool_panel[ key ] - elif config_elem.tag == 'tool': - key = 'tool_%s' % str( config_elem.get( 'guid' ) ) - del trans.app.toolbox.tool_panel[ key ] # Update the config_elems of the in-memory shed_tool_conf_dict. shed_tool_conf_dict[ 'config_elems' ] = config_elems trans.app.toolbox.shed_tool_confs[ index ] = shed_tool_conf_dict Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: greg: Fixes for deactivating / uninstalling a repository containing tools.
by Bitbucket 02 Mar '12

02 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/fc4a31791090/ changeset: fc4a31791090 user: greg date: 2012-03-02 20:30:41 summary: Fixes for deactivating / uninstalling a repository containing tools. affected #: 1 file diff -r 29f652b9a18cbac444a1c1b68d5ad36f17db7192 -r fc4a317910900ba2d17ce1ec25e0316ede0de8be lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -599,25 +599,6 @@ if converter_path and display_path: break return converter_path, display_path -def get_in_memory_config_elems_to_remove( shed_tool_conf_dict, guids_to_remove ): - config_elems = shed_tool_conf_dict[ 'config_elems' ] - config_elems_to_remove = [] - for config_elem in config_elems: - if config_elem.tag == 'section': - tool_elems_to_remove = [] - for tool_elem in config_elem: - if tool_elem.get( 'guid' ) in guids_to_remove: - tool_elems_to_remove.append( tool_elem ) - for tool_elem in tool_elems_to_remove: - # Remove all of the appropriate tool sub-elements from the section element. - config_elem.remove( tool_elem ) - if len( config_elem ) < 1: - # Keep a list of all empty section elements so they can be removed. - config_elems_to_remove.append( config_elem ) - elif config_elem.tag == 'tool': - if config_elem.get( 'guid' ) in guids_to_remove: - config_elems_to_remove.append( config_elem ) - return config_elems_to_remove def get_shed_tool_conf_dict( app, shed_tool_conf ): """ Return the in-memory version of the shed_tool_conf file, which is stored in the config_elems entry @@ -1003,18 +984,40 @@ if uninstall: # Remove from the shed_tool_conf file on disk. remove_from_shed_tool_config( trans, shed_tool_conf_dict, guids_to_remove ) - config_elems_to_remove = get_in_memory_config_elems_to_remove( shed_tool_conf_dict, guids_to_remove ) - # Remove from the in-memory list of config_elems. config_elems = shed_tool_conf_dict[ 'config_elems' ] + config_elems_to_remove = [] + for config_elem in config_elems: + if config_elem.tag == 'section': + # Get the section key for the in-memory tool panel. + section_key = 'section_%s' % str( config_elem.get( "id" ) ) + # Generate the list of tool elements to remove. + tool_elems_to_remove = [] + for tool_elem in config_elem: + if tool_elem.get( 'guid' ) in guids_to_remove: + tool_elems_to_remove.append( tool_elem ) + for tool_elem in tool_elems_to_remove: + # Remove the tool sub-element from the section element. + config_elem.remove( tool_elem ) + # Remove the tool from the section in the in-memory tool panel. + if section_key in trans.app.toolbox.tool_panel: + tool_section = trans.app.toolbox.tool_panel[ section_key ] + tool_key = key = 'tool_%s' % str( tool_elem.get( 'guid' ) ) + if tool_key in tool_section.elems: + del tool_section.elems[ tool_key ] + if not tool_section.elems: + del trans.app.toolbox.tool_panel[ section_key ] + if len( config_elem ) < 1: + # Keep a list of all empty section elements so they can be removed. + config_elems_to_remove.append( config_elem ) + elif config_elem.tag == 'tool': + if config_elem.get( 'guid' ) in guids_to_remove: + tool_key = key = 'tool_%s' % str( config_elem.get( 'guid' ) ) + if tool_key in trans.app.toolbox.tool_panel: + del trans.app.toolbox.tool_panel[ tool_key ] + config_elems_to_remove.append( config_elem ) for config_elem in config_elems_to_remove: # Remove the element from the in-memory list of elements. config_elems.remove( config_elem ) - if config_elem.tag == 'section': - key = 'section_%s' % str( config_elem.get( "id" ) ) - del trans.app.toolbox.tool_panel[ key ] - elif config_elem.tag == 'tool': - key = 'tool_%s' % str( config_elem.get( 'guid' ) ) - del trans.app.toolbox.tool_panel[ key ] # Update the config_elems of the in-memory shed_tool_conf_dict. shed_tool_conf_dict[ 'config_elems' ] = config_elems trans.app.toolbox.shed_tool_confs[ index ] = shed_tool_conf_dict 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: jgoecks: Decode visualization dataset ids before saving them.
by Bitbucket 02 Mar '12

02 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/29f652b9a18c/ changeset: 29f652b9a18c user: jgoecks date: 2012-03-02 19:40:46 summary: Decode visualization dataset ids before saving them. affected #: 1 file diff -r fd2d4e257ee9f8258dbb47ffc4c3a1ca21d49c24 -r 29f652b9a18cbac444a1c1b68d5ad36f17db7192 lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py +++ b/lib/galaxy/web/controllers/tracks.py @@ -649,7 +649,7 @@ def unpack_track( track_json ): """ Unpack a track from its json. """ return { - "dataset_id": track_json['dataset_id'], + "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'], Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: greg: Fixes for managing installed repositories.
by Bitbucket 02 Mar '12

02 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/fd2d4e257ee9/ changeset: fd2d4e257ee9 user: greg date: 2012-03-02 19:33:58 summary: Fixes for managing installed repositories. affected #: 4 files diff -r 80fa0f99e7e21c148900d25689f036de7023e5dc -r fd2d4e257ee9f8258dbb47ffc4c3a1ca21d49c24 lib/galaxy/tool_shed/install_manager.py --- a/lib/galaxy/tool_shed/install_manager.py +++ b/lib/galaxy/tool_shed/install_manager.py @@ -125,24 +125,17 @@ # The values for the keys in each of the following dictionaries will be a list to allow for the same tool to be displayed in multiple places # in the tool panel. tool_panel_dict_for_display = {} - tool_panel_dict_for_metadata = {} for tool_elem in repository_elem: # The tool_elem looks something like this: <tool id="EMBOSS: antigenic1" version="5.0.0" file="emboss_antigenic.xml" /> tool_config = tool_elem.get( 'file' ) guid = self.get_guid( repository_clone_url, relative_install_dir, tool_config ) # See if tool_config is defined inside of a section in self.proprietary_tool_panel_elems. is_displayed, tool_sections = self.get_containing_tool_sections( tool_config ) - tool_panel_dict_for_tool_config = generate_tool_panel_dict_for_tool_config( guid, tool_config, tool_sections=tool_sections ) - # The tool_panel_dict_for_tool_config dictionary contains a single entry that looks something like this. - # {<Tool guid> : [{ tool_config : <tool_config_file>, id: <ToolSection id>, version : <ToolSection version>, name : <TooSection name>}]} - # Add the new entry to the dictionary we're defining to set metadata. - for k, v in tool_panel_dict_for_tool_config.items(): - tool_panel_dict_for_metadata[ k ] = v if is_displayed: - # Add the new entry to the dictionary we're defining to set the tool panel display. + tool_panel_dict_for_tool_config = generate_tool_panel_dict_for_tool_config( guid, tool_config, tool_sections=tool_sections ) for k, v in tool_panel_dict_for_tool_config.items(): tool_panel_dict_for_display[ k ] = v - metadata_dict = generate_metadata( self.toolbox, relative_install_dir, repository_clone_url, tool_panel_dict=tool_panel_dict_for_metadata ) + metadata_dict = generate_metadata( self.toolbox, relative_install_dir, repository_clone_url ) # Add a new record to the tool_shed_repository table if one doesn't already exist. If one exists but is marked # deleted, undelete it. It is critical that this happens before the call to add_to_tool_panel() below because # tools will not be properly loaded if the repository is marked deleted. diff -r 80fa0f99e7e21c148900d25689f036de7023e5dc -r fd2d4e257ee9f8258dbb47ffc4c3a1ca21d49c24 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -175,40 +175,6 @@ if tool_shed_repository: # Only load tools if the repository is not deactivated or uninstalled. can_load = not tool_shed_repository.deleted - if can_load: - metadata = tool_shed_repository.metadata - update_needed = False - if 'tool_panel_section' in metadata: - if panel_entry_per_tool( metadata[ 'tool_panel_section' ] ): - # {<Tool guid> : [{ tool_config : <tool_config_file>, id: <ToolSection id>, version : <ToolSection version>, name : <TooSection name>}]} - tool_panel_dict = metadata[ 'tool_panel_section' ] - else: - # { id: <ToolSection id>, version : <ToolSection version>, name : <TooSection name>} - tool_section_dict = metadata[ 'tool_panel_section' ] - tool_section = generate_tool_section_element_from_dict( tool_section_dict ) - tool_panel_dict = generate_tool_panel_dict_for_repository_tools( metadata, tool_section=tool_section ) - if section: - # This means all tools are loaded into the same tool panel section or are all outside of any sections. - for tool_panel_dict_guid, tool_section_dicts in tool_panel_dict.items(): - for dict_index, tool_section_dict in enumerate( tool_section_dicts ): - if tool_section_dict [ 'id' ] != section.id or \ - tool_section_dict [ 'version' ] != section.version or \ - tool_section_dict [ 'name' ] != section.name: - tool_section_dict [ 'id' ] = section.id - tool_section_dict [ 'version' ] = section.version - tool_section_dict [ 'name' ] = section.name - tool_section_dicts[ dict_index ] = tool_section_dict - tool_panel_dict[ tool_panel_dict_guid ] = tool_section_dicts - update_needed = True - else: - # The tool_panel_section was introduced late, so set it's value if its missing in the metadata. - tool_panel_dict = generate_tool_panel_dict_for_repository_tools( tool_shed_repository.metadata, tool_section=section ) - update_needed = True - if update_needed: - metadata[ 'tool_panel_section' ] = tool_panel_dict - tool_shed_repository.metadata = metadata - self.sa_session.add( tool_shed_repository ) - self.sa_session.flush() else: # If there is not yet a tool_shed_repository record, we're in the process of installing # a new repository, so any included tools can be loaded into the tool panel. diff -r 80fa0f99e7e21c148900d25689f036de7023e5dc -r fd2d4e257ee9f8258dbb47ffc4c3a1ca21d49c24 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -274,7 +274,7 @@ if datatypes: metadata_dict[ 'datatypes' ] = datatypes return metadata_dict -def generate_metadata( toolbox, relative_install_dir, repository_clone_url, tool_section_dict=None, tool_panel_dict=None ): +def generate_metadata( toolbox, relative_install_dir, repository_clone_url ): """ Browse the repository files on disk to generate metadata. Since we are using disk files, it is imperative that the repository is updated to the desired change set revision before metadata is generated. @@ -282,24 +282,6 @@ metadata_dict = {} sample_files = [] datatypes_config = None - new_tool_panel_dict = {} - # Keep track of the section in the tool panel in which this repository's tools will be contained by using the information in either the - # tool_section_dict or the tool_panel_dict (at least 1 of these 2 dictionaries should be None). The tool_section_dict is passed when the - # Admin is manually installing a repository into a single selected section. It looks something like this. - # { id: <ToolSection id>, version : <ToolSection version>, name : <TooSection name>} - # The tool_panel_dict is fully populated with all tools in the repository that should be loaded into the tool panel. It is received when - # this method is called by the InstallManager or when metadata is being reset on an existing repository. This dictionary looks something - # like this. - # {<Tool guid> : [{ tool_config : <tool_config_file>, id: <ToolSection id>, version : <ToolSection version>, name : <TooSection name>}]} - # The tool_panel_dict enables each tool in the repository to be contained inside or outside a specified ToolSection in the tool panel. The - # new_tool_panel_dict with be populated with a subset of the items in the received tool_panel_dict. This will allow for the case where - # repository metadata is being updated where the previous change set revision included more tools than the current change set revision. - if tool_section_dict: - # The received tool_panel_dict must be None, so we'll populate it here. - for k, v in tool_section_dict.items(): - if v is None: - # Coerce None values into empty strings because ElementTree.tostring() throws exceptions on None values. - tool_section_dict[ k ] = '' # Find datatypes_conf.xml if it exists. for root, dirs, files in os.walk( relative_install_dir ): if root.find( '.hg' ) < 0: @@ -336,36 +318,6 @@ tool_config = os.path.join( root, name ) guid = generate_tool_guid( repository_clone_url, tool ) metadata_dict = generate_tool_metadata( tool_config, tool, repository_clone_url, metadata_dict ) - # Populate the tool_section_dict if necessary. - if tool_panel_dict and guid in tool_panel_dict: - # We're updating metadata on a previously installed repository. - old_tool_panel_dicts = tool_panel_dict[ guid ] - for dict_index, old_tool_panel_dict in enumerate( old_tool_panel_dicts ): - # Should we really do this? What if there is more than 1 old_tool_panel_dict in the list? - if 'tool_config' not in old_tool_panel_dict or old_tool_panel_dict[ 'tool_config' ] in [ None, '' ]: - old_tool_panel_dict[ 'tool_config' ] = name - old_tool_panel_dicts[ dict_index ] = old_tool_panel_dict - if guid in new_tool_panel_dict: - for old_tool_panel_dict in old_tool_panel_dicts: - new_tool_panel_dict[ guid ].append( old_tool_panel_dict ) - else: - new_tool_panel_dict[ guid ] = old_tool_panel_dicts - else: - # The admin is manually installing a new repository. - new_tool_section_dict = {} - if tool_section_dict: - for k, v in tool_section_dict.items(): - new_tool_section_dict[ k ] = v - else: - new_tool_section_dict[ 'id' ] = '' - new_tool_section_dict[ 'name' ] = '' - new_tool_section_dict[ 'version' ] = '' - if 'tool_config' not in new_tool_section_dict or new_tool_section_dict[ 'tool_config' ] in [ None, '' ]: - new_tool_section_dict[ 'tool_config' ] = name - if guid in new_tool_panel_dict: - new_tool_panel_dict[ guid ].append( new_tool_section_dict ) - else: - new_tool_panel_dict[ guid ] = [ new_tool_section_dict ] # Find all exported workflows elif name.endswith( '.ga' ): relative_path = os.path.join( root, name ) @@ -375,7 +327,6 @@ exported_workflow_dict = from_json_string( workflow_text ) if 'a_galaxy_workflow' in exported_workflow_dict and exported_workflow_dict[ 'a_galaxy_workflow' ] == 'true': metadata_dict = generate_workflow_metadata( relative_path, exported_workflow_dict, metadata_dict ) - metadata_dict[ 'tool_panel_section' ] = new_tool_panel_dict return metadata_dict def generate_tool_guid( repository_clone_url, tool ): """ @@ -433,7 +384,6 @@ return metadata_dict def generate_tool_panel_elem_list( repository_name, repository_clone_url, changeset_revision, tool_panel_dict, repository_tools_tups, owner='' ): """Generate a list of ElementTree Element objects for each section or tool.""" - # {<Tool guid> : [{ tool_config : <tool_config_file>, id: <ToolSection id>, version : <ToolSection version>, name : <TooSection name>}]} elem_list = [] tool_elem = None tmp_url = clean_repository_clone_url( repository_clone_url ) @@ -487,34 +437,75 @@ else: elem_list.append( tool_elem ) return elem_list -def generate_tool_panel_dict_for_repository_tools( repository_metadata, tool_section=None, tool_section_dict=None ): +def generate_tool_panel_dict_for_new_install( tool_dicts, tool_section=None ): """ - Create a dictionary of the following type for every tool in the repository where the tools are all contained in the same tool section - or no tool section. If tool_section is None, tools will be displayed outside of any sections in the tool panel. - {<Tool guid> : [{ tool_config : <tool_config_file>, id: <ToolSection id>, version : <ToolSection version>, name : <TooSection name>}]} + When installing a repository that contains tools, all tools must curently be defined within the same tool section in the tool + panel or outside of any sections. """ tool_panel_dict = {} - tool_dicts = repository_metadata[ 'tools' ] + if tool_section: + section_id = tool_section.id + section_name = tool_section.name + section_version = tool_section.version + else: + section_id = '' + section_name = '' + section_version = '' for tool_dict in tool_dicts: guid = tool_dict[ 'guid' ] tool_config = tool_dict[ 'tool_config' ] - new_tool_section_dict = {} - if tool_section_dict: - for k, v in tool_section_dict.items(): - new_tool_section_dict[ k ] = v - file_path, file_name = os.path.split( tool_config ) - new_tool_section_dict[ 'tool_config' ] = file_name - if guid in tool_panel_dict: - tool_panel_dict[ guid ].append( new_tool_section_dict ) - else: - tool_panel_dict[ guid ] = [ new_tool_section_dict ] + tool_section_dict = dict( tool_config=tool_config, id=section_id, name=section_name, version=section_version ) + if guid in tool_panel_dict: + tool_panel_dict[ guid ].append( tool_section_dict ) else: - new_tool_section_dicts = generate_tool_section_dicts( tool_config=tool_config, tool_section=tool_section ) - if guid in tool_panel_dict: - for new_tool_section_dict in new_tool_section_dicts: - tool_panel_dict[ guid ].append( new_tool_section_dict ) - else: - tool_panel_dict[ guid ] = new_tool_section_dicts + tool_panel_dict[ guid ] = [ tool_section_dict ] + return tool_panel_dict +def generate_tool_panel_dict_from_shed_tool_conf_entries( trans, repository ): + """ + Keep track of the section in the tool panel in which this repository's tools will be contained by parsing the shed-tool_conf in + which the repository's tools are defined and storing the tool panel definition of each tool in the repository. This method is called + only when the repository is being deactivated or uninstalled and allows for activation or reinstallation using the original layout. + """ + tool_panel_dict = {} + shed_tool_conf, tool_path, relative_install_dir = get_tool_panel_config_tool_path_install_dir( trans.app, repository ) + metadata = repository.metadata + # Create a dictionary of tool guid and tool config file name for each tool in the repository. + guids_and_configs = {} + for tool_dict in metadata[ 'tools' ]: + guid = tool_dict[ 'guid' ] + tool_config = tool_dict[ 'tool_config' ] + file_path, file_name = os.path.split( tool_config ) + guids_and_configs[ guid ] = file_name + # Parse the shed_tool_conf file in which all of this repository's tools are defined and generate the tool_panel_dict. + tree = util.parse_xml( shed_tool_conf ) + root = tree.getroot() + for elem in root: + if elem.tag == 'tool': + guid = elem.get( 'guid' ) + if guid in guids_and_configs: + # The tool is displayed in the tool panel outside of any tool sections. + tool_section_dict = dict( tool_config=guids_and_configs[ guid ], id='', name='', version='' ) + if guid in tool_panel_dict: + tool_panel_dict[ guid ].append( tool_section_dict ) + else: + tool_panel_dict[ guid ] = [ tool_section_dict ] + elif elem.tag == 'section': + section_id = elem.get( 'id' ) or '' + section_name = elem.get( 'name' ) or '' + section_version = elem.get( 'version' ) or '' + for section_elem in elem: + if section_elem.tag == 'tool': + guid = section_elem.get( 'guid' ) + if guid in guids_and_configs: + # The tool is displayed in the tool panel inside the current tool section. + tool_section_dict = dict( tool_config=guids_and_configs[ guid ], + id=section_id, + name=section_name, + version=section_version ) + if guid in tool_panel_dict: + tool_panel_dict[ guid ].append( tool_section_dict ) + else: + tool_panel_dict[ guid ] = [ tool_section_dict ] return tool_panel_dict def generate_tool_panel_dict_for_tool_config( guid, tool_config, tool_sections=None ): """ @@ -611,7 +602,6 @@ def get_in_memory_config_elems_to_remove( shed_tool_conf_dict, guids_to_remove ): config_elems = shed_tool_conf_dict[ 'config_elems' ] config_elems_to_remove = [] - tool_elements_removed = 0 for config_elem in config_elems: if config_elem.tag == 'section': tool_elems_to_remove = [] @@ -621,20 +611,12 @@ for tool_elem in tool_elems_to_remove: # Remove all of the appropriate tool sub-elements from the section element. config_elem.remove( tool_elem ) - log.debug( "Removed tool with guid '%s'." % str( tool_elem.get( 'guid' ) ) ) - tool_elements_removed += 1 if len( config_elem ) < 1: # Keep a list of all empty section elements so they can be removed. config_elems_to_remove.append( config_elem ) - if tool_elements_removed == len( guids_to_remove ): - break elif config_elem.tag == 'tool': if config_elem.get( 'guid' ) in guids_to_remove: config_elems_to_remove.append( config_elem ) - log.debug( "Removed tool with guid '%s'." % str( config_elem.get( 'guid' ) ) ) - tool_elements_removed += 1 - if tool_elements_removed == len( guids_to_remove ): - break return config_elems_to_remove def get_shed_tool_conf_dict( app, shed_tool_conf ): """ @@ -674,6 +656,68 @@ tool = app.toolbox.load_tool( os.path.abspath( relative_path ), guid=guid ) repository_tools_tups.append( ( relative_path, guid, tool ) ) return repository_tools_tups +def get_tool_panel_config_tool_path_install_dir( app, repository ): + # Return shed-related tool panel config, the tool_path configured in it, and the relative path to the directory where the + # repository is installed. This method assumes all repository tools are defined in a single shed-related tool panel config. + tool_shed = clean_tool_shed_url( repository.tool_shed ) + partial_install_dir = '%s/repos/%s/%s/%s' % ( tool_shed, repository.owner, repository.name, repository.installed_changeset_revision ) + # Get the relative tool installation paths from each of the shed tool configs. + relative_install_dir = None + for shed_tool_conf_dict in app.toolbox.shed_tool_confs: + shed_tool_conf = shed_tool_conf_dict[ 'config_filename' ] + if repository.dist_to_shed: + # The repository is owned by devteam and contains tools migrated from the Galaxy distribution to the tool shed, so + # the reserved tool panel config is migrated_tools_conf.xml, to which app.config.migrated_tools_config refers. + if shed_tool_conf == app.config.migrated_tools_config: + tool_path = shed_tool_conf_dict[ 'tool_path' ] + relative_install_dir = os.path.join( tool_path, partial_install_dir ) + if tool_path and relative_install_dir: + return shed_tool_conf, tool_path, relative_install_dir + elif repository.uninstalled: + # Since the repository is uninstalled we don't know what tool panel config was originally used to + # define the tools in the repository, so we'll just make sure not to use the reserved migrated_tools_conf.xml. + if shed_tool_conf != app.config.migrated_tools_config: + tool_path = shed_tool_conf_dict[ 'tool_path' ] + relative_install_dir = os.path.join( tool_path, partial_install_dir ) + if tool_path and relative_install_dir: + return shed_tool_conf, tool_path, relative_install_dir + else: + if repository.includes_tools: + metadata = repository.metadata + for tool_dict in metadata[ 'tools' ]: + # Parse the tool panel config to get the entire set of config_elems. # We'll check config_elems until we + # find an element that matches one of the tools in the repository's metadata. + tool_panel_config = shed_tool_conf_dict[ 'config_filename' ] + tree = util.parse_xml( tool_panel_config ) + root = tree.getroot() + tool_path, relative_install_dir = get_tool_path_install_dir( partial_install_dir, + shed_tool_conf_dict, + tool_dict, + root ) + if tool_path and relative_install_dir: + return shed_tool_conf, tool_path, relative_install_dir + else: + # Nothing will be loaded into the tool panel, so look for the installed repository on disk. + tool_path = shed_tool_conf_dict[ 'tool_path' ] + relative_install_dir = os.path.join( tool_path, partial_install_dir ) + if tool_path and relative_install_dir and os.path.isdir( relative_install_dir ): + return shed_tool_conf, tool_path, relative_install_dir + return None, None, None +def get_tool_path_install_dir( partial_install_dir, shed_tool_conf_dict, tool_dict, config_elems ): + for elem in config_elems: + if elem.tag == 'tool': + if elem.get( 'guid' ) == tool_dict[ 'guid' ]: + tool_path = shed_tool_conf_dict[ 'tool_path' ] + relative_install_dir = os.path.join( tool_path, partial_install_dir ) + return tool_path, relative_install_dir + elif elem.tag == 'section': + for section_elem in elem: + if section_elem.tag == 'tool': + if section_elem.get( 'guid' ) == tool_dict[ 'guid' ]: + tool_path = shed_tool_conf_dict[ 'tool_path' ] + relative_install_dir = os.path.join( tool_path, partial_install_dir ) + return tool_path, relative_install_dir + return None, None def get_tool_version( app, tool_id ): sa_session = app.model.context.current return sa_session.query( app.model.ToolVersion ) \ @@ -829,31 +873,13 @@ if display_path: # Load or deactivate proprietary datatype display applications app.datatypes_registry.load_display_applications( installed_repository_dict=repository_dict, deactivate=deactivate ) -def load_repository_contents( trans, repository_name, description, owner, changeset_revision, tool_path, repository_clone_url, relative_install_dir, - current_working_dir, tmp_name, tool_panel_dict=None, tool_shed=None, tool_section=None, shed_tool_conf=None, - new_install=True ): - """ - Generate the metadata for the installed tool shed repository, among other things. It is critical that the installed repository - is updated to the desired changeset_revision before metadata is set because the process for setting metadata uses the repository - files on disk. If this method is called when a new repository is being installed, the value of tool_panel_dict will be None and - the value of tool_section (a ToolSection or None) will be used. This method is also called when updates have been pulled to a - previously installed repository, in which case the value of tool_panel_dict will be used and the value of new_install will be False. - """ - if tool_panel_dict: - # We're resetting metadata on a previously installed repository. For backward compatibility we have to handle 2 types of dictionaries. - # In the past, all repository tools had to be installed into a single ToolSection (or outside of any sections) in the tool panel. - if panel_entry_per_tool( tool_panel_dict ): - # {<Tool guid> : [{ tool_config : <tool_config_file>, id: <ToolSection id>, version : <ToolSection version>, name : <TooSection name>}]} - metadata_dict = generate_metadata( trans.app.toolbox, relative_install_dir, repository_clone_url, tool_panel_dict=tool_panel_dict ) - else: - # { id: <ToolSection id>, version : <ToolSection version>, name : <TooSection name>} - metadata_dict = generate_metadata( trans.app.toolbox, relative_install_dir, repository_clone_url, tool_section_dict=tool_panel_dict ) - else: - # We're installing a new repository or reinstalling an uninstalled repository where all tools are contained in the same tool panel section - # or outside of any sections in the tool panel. We cannot pass a specific tool_config since we do not yet have one. - tool_section_dicts = generate_tool_section_dicts( tool_config=None, tool_sections=util.listify( tool_section ) ) - metadata_dict = generate_metadata( trans.app.toolbox, relative_install_dir, repository_clone_url, tool_section_dict=tool_section_dicts[ 0 ] ) - tool_panel_dict = metadata_dict[ 'tool_panel_section' ] +def load_repository_contents( trans, repository_name, description, owner, changeset_revision, tool_path, repository_clone_url, + relative_install_dir, current_working_dir, tmp_name, tool_shed=None, tool_section=None, shed_tool_conf=None ): + """Generate the metadata for the installed tool shed repository, among other things.""" + # It is critical that the installed repository is updated to the desired changeset_revision before metadata is set because the + # process for setting metadata uses the repository files on disk. This method is called when an admin is installing a new repository + # or reinstalling an uninstalled repository. + metadata_dict = generate_metadata( trans.app.toolbox, relative_install_dir, repository_clone_url ) # Add a new record to the tool_shed_repository table if one doesn't already exist. If one exists but is marked deleted, undelete it. This # must happen before the call to add_to_tool_panel() below because tools will not be properly loaded if the repository is marked deleted. log.debug( "Adding new row (or updating an existing row) for repository '%s' in the tool_shed_repository table." % repository_name ) @@ -865,6 +891,7 @@ metadata_dict, dist_to_shed=False ) if 'tools' in metadata_dict: + 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: sample_files = metadata_dict.get( 'sample_files', [] ) @@ -874,20 +901,15 @@ repository_tools_tups = handle_missing_index_file( trans.app, tool_path, sample_files, repository_tools_tups ) # Handle tools that use fabric scripts to install dependencies. handle_tool_dependencies( current_working_dir, relative_install_dir, repository_tools_tups ) - if new_install: - add_to_tool_panel( app=trans.app, - repository_name=repository_name, - repository_clone_url=repository_clone_url, - changeset_revision=changeset_revision, - repository_tools_tups=repository_tools_tups, - owner=owner, - shed_tool_conf=shed_tool_conf, - tool_panel_dict=tool_panel_dict, - new_install=new_install ) - elif trans.app.toolbox_search.enabled: - # If search support for tools is enabled, index the new installed tools. In the condition above, this happens in the - # add_to_tool_panel() method. - trans.app.toolbox_search = ToolBoxSearch( trans.app.toolbox ) + add_to_tool_panel( app=trans.app, + repository_name=repository_name, + repository_clone_url=repository_clone_url, + changeset_revision=changeset_revision, + repository_tools_tups=repository_tools_tups, + owner=owner, + shed_tool_conf=shed_tool_conf, + tool_panel_dict=tool_panel_dict, + new_install=True ) # Remove the temporary file try: os.unlink( tmp_name ) @@ -896,8 +918,7 @@ if 'datatypes_config' in metadata_dict: datatypes_config = os.path.abspath( metadata_dict[ 'datatypes_config' ] ) # Load data types required by tools. - override = not new_install - converter_path, display_path = alter_config_and_load_prorietary_datatypes( trans.app, datatypes_config, relative_install_dir, override=override ) + converter_path, display_path = alter_config_and_load_prorietary_datatypes( trans.app, datatypes_config, relative_install_dir, override=False ) if converter_path or display_path: # Create a dictionary of tool shed repository related information. repository_dict = create_repository_dict_for_proprietary_datatypes( tool_shed=tool_shed, @@ -937,7 +958,7 @@ os.chdir( current_working_dir ) tmp_stderr.close() return returncode, tmp_name -def remove_from_shed_tool_config( app, shed_tool_conf_dict, guids_to_remove ): +def remove_from_shed_tool_config( trans, shed_tool_conf_dict, guids_to_remove ): # A tool shed repository is being uninstalled so change the shed_tool_conf file. Parse the config file to generate the entire list # of config_elems instead of using the in-memory list since it will be a subset of the entire list if one or more repositories have # been deactivated. @@ -948,7 +969,6 @@ root = tree.getroot() for elem in root: config_elems.append( elem ) - tool_elements_removed = 0 config_elems_to_remove = [] for config_elem in config_elems: if config_elem.tag == 'section': @@ -959,30 +979,30 @@ for tool_elem in tool_elems_to_remove: # Remove all of the appropriate tool sub-elements from the section element. config_elem.remove( tool_elem ) - tool_elements_removed += 1 if len( config_elem ) < 1: # Keep a list of all empty section elements so they can be removed. config_elems_to_remove.append( config_elem ) - if tool_elements_removed == len( guids_to_remove ): - break elif config_elem.tag == 'tool': if config_elem.get( 'guid' ) in guids_to_remove: config_elems_to_remove.append( config_elem ) - tool_elements_removed += 1 - if tool_elements_removed == len( guids_to_remove ): - break for config_elem in config_elems_to_remove: config_elems.remove( config_elem ) # Persist the altered in-memory version of the tool config. - config_elems_to_xml_file( app, config_elems, shed_tool_conf, tool_path ) -def remove_from_tool_panel( app, shed_tool_conf, tool_panel_dict, uninstall ): + config_elems_to_xml_file( trans.app, config_elems, shed_tool_conf, tool_path ) +def remove_from_tool_panel( trans, repository, shed_tool_conf, uninstall ): """A tool shed repository is being deactivated or uninstalled so handle tool panel alterations accordingly.""" - index, shed_tool_conf_dict = get_shed_tool_conf_dict( app, shed_tool_conf ) + # Determine where the tools are currently defined in the tool panel and store this information so the tools can be displayed + # in the same way when the repository is activated or reinstalled. + tool_panel_dict = generate_tool_panel_dict_from_shed_tool_conf_entries( trans, repository ) + repository.metadata[ 'tool_panel_section' ] = tool_panel_dict + trans.sa_session.add( repository ) + trans.sa_session.flush() # Create a list of guids for all tools that will be removed from the in-memory tool panel and config file on disk. guids_to_remove = [ k for k in tool_panel_dict.keys() ] + index, shed_tool_conf_dict = get_shed_tool_conf_dict( trans.app, shed_tool_conf ) if uninstall: # Remove from the shed_tool_conf file on disk. - remove_from_shed_tool_config( app, shed_tool_conf_dict, guids_to_remove ) + remove_from_shed_tool_config( trans, shed_tool_conf_dict, guids_to_remove ) config_elems_to_remove = get_in_memory_config_elems_to_remove( shed_tool_conf_dict, guids_to_remove ) # Remove from the in-memory list of config_elems. config_elems = shed_tool_conf_dict[ 'config_elems' ] @@ -991,16 +1011,16 @@ config_elems.remove( config_elem ) if config_elem.tag == 'section': key = 'section_%s' % str( config_elem.get( "id" ) ) - del app.toolbox.tool_panel[ key ] + del trans.app.toolbox.tool_panel[ key ] elif config_elem.tag == 'tool': key = 'tool_%s' % str( config_elem.get( 'guid' ) ) - del app.toolbox.tool_panel[ key ] + del trans.app.toolbox.tool_panel[ key ] # Update the config_elems of the in-memory shed_tool_conf_dict. shed_tool_conf_dict[ 'config_elems' ] = config_elems - app.toolbox.shed_tool_confs[ index ] = shed_tool_conf_dict - if app.toolbox_search.enabled: + trans.app.toolbox.shed_tool_confs[ index ] = shed_tool_conf_dict + if trans.app.toolbox_search.enabled: # If search support for tools is enabled, index tools. - app.toolbox_search = ToolBoxSearch( app.toolbox ) + trans.app.toolbox_search = ToolBoxSearch( trans.app.toolbox ) def update_repository( current_working_dir, repo_files_dir, changeset_revision ): # Update the cloned repository to changeset_revision. It is imperative that the # installed repository is updated to the desired changeset_revision before metadata diff -r 80fa0f99e7e21c148900d25689f036de7023e5dc -r fd2d4e257ee9f8258dbb47ffc4c3a1ca21d49c24 lib/galaxy/web/controllers/admin_toolshed.py --- a/lib/galaxy/web/controllers/admin_toolshed.py +++ b/lib/galaxy/web/controllers/admin_toolshed.py @@ -79,48 +79,25 @@ def activate_repository( self, trans, **kwd ): """Activate a repository that was deactivated but not uninstalled.""" repository = get_repository( trans, kwd[ 'id' ] ) - shed_tool_conf, tool_path, relative_install_dir = self.__get_tool_panel_config_tool_path_install_dir( trans, repository ) + shed_tool_conf, tool_path, relative_install_dir = get_tool_panel_config_tool_path_install_dir( trans.app, repository ) repository_clone_url = self.__generate_clone_url( trans, repository ) repository.deleted = False trans.sa_session.add( repository ) trans.sa_session.flush() if repository.includes_tools: + metadata = repository.metadata + repository_tools_tups = get_repository_tools_tups( trans.app, metadata ) # Reload tools into the appropriate tool panel section. - metadata = repository.metadata - if 'tool_panel_section' in metadata: - if panel_entry_per_tool( metadata[ 'tool_panel_section' ] ): - tool_panel_dict = metadata[ 'tool_panel_section' ] - else: - # The value of tool_panel_section is the old dictionary type. - tool_section_dict = metadata[ 'tool_panel_section' ] - tool_panel_dict = generate_tool_panel_dict_for_repository_tools( metadata, tool_section_dict=tool_section_dict ) - repository.metadata[ 'tool_panel_section' ] = tool_panel_dict - trans.sa_session.add( repository ) - trans.sa_session.flush() - else: - # The tool_panel_section was introduced late, so set it's value if its missing in the metadata. - tool_panel_dict = generate_tool_panel_dict_for_repository_tools( metadata ) - repository.metadata[ 'tool_panel_section' ] = tool_panel_dict - trans.sa_session.add( repository ) - trans.sa_session.flush() - repository_tools_tups = get_repository_tools_tups( trans.app, metadata ) - guids_to_activate = [ repository_tool_tup[1] for repository_tool_tup in repository_tools_tups ] - # Make sure we have a tool_version for each guid. - for guid_to_activate in guids_to_activate: - if not get_tool_version( trans.app, guid_to_activate ): - # We're somehow missing a tool_version, so create a new one. - tool_version = trans.model.ToolVersion( tool_id=guid_to_activate, tool_shed_repository=repository ) - trans.sa_session.add( tool_version ) - trans.sa_session.flush() - add_to_tool_panel( trans.app, - repository.name, - repository_clone_url, - repository.changeset_revision, - repository_tools_tups, - repository.owner, - shed_tool_conf, - tool_panel_dict, - new_install=False ) + tool_panel_dict = repository.metadata[ 'tool_panel_section' ] + add_to_tool_panel( trans.app, + repository.name, + repository_clone_url, + repository.changeset_revision, + repository_tools_tups, + repository.owner, + shed_tool_conf, + tool_panel_dict, + new_install=False ) message = 'The <b>%s</b> repository has been activated.' % repository.name status = 'done' return trans.response.send_redirect( web.url_for( controller='admin_toolshed', @@ -197,37 +174,11 @@ remove_from_disk = params.get( 'remove_from_disk', '' ) remove_from_disk_checked = CheckboxField.is_checked( remove_from_disk ) repository = get_repository( trans, kwd[ 'id' ] ) - shed_tool_conf, tool_path, relative_install_dir = self.__get_tool_panel_config_tool_path_install_dir( trans, repository ) + shed_tool_conf, tool_path, relative_install_dir = get_tool_panel_config_tool_path_install_dir( trans.app, repository ) if params.get( 'deactivate_or_uninstall_repository_button', False ): - metadata = repository.metadata if repository.includes_tools: - repository_tools_tups = get_repository_tools_tups( trans.app, metadata ) - # Generate the list of tool panel keys derived from the tools included in the repository. - if repository_tools_tups: - repository_tool_panel_keys = [ 'tool_%s' % repository_tools_tup[ 1 ] for repository_tools_tup in repository_tools_tups ] - else: - repository_tool_panel_keys = [] - if 'tool_panel_section' in metadata: - if panel_entry_per_tool( metadata[ 'tool_panel_section' ] ): - tool_panel_dict = metadata[ 'tool_panel_section' ] - else: - # The tool_panel_section dictionary is the old definition of the tool_panel_section, so update it to the current dictionary. - # All of the repository tools will be installed in the same section or outside of any sections. - tool_section_dict = metadata[ 'tool_panel_section' ] - tool_panel_dict = generate_tool_panel_dict_for_repository_tools( metadata, tool_section_dict=tool_section_dict ) - repository.metadata[ 'tool_panel_section' ] = tool_panel_dict - else: - # The tool_panel_section was introduced late, so set it's value if its missing in the metadata. - tool_panel_dict = generate_tool_panel_dict_for_repository_tools( metadata ) - repository.metadata[ 'tool_panel_section' ] = tool_panel_dict - repository_clone_url = generate_clone_url( trans, repository ) - # The repository is either being deactivated or uninstalled, so handle tool panel alterations accordingly. - # If the repository is being uninstalled, the appropriate tools or tool sections will be removed from the - # appropriate shed-related tool config file on disk. - remove_from_tool_panel( app=trans.app, - shed_tool_conf=shed_tool_conf, - tool_panel_dict=tool_panel_dict, - uninstall=remove_from_disk_checked ) + # Handle tool panel alterations. + 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, relative_install_dir, deactivate=True ) @@ -360,13 +311,9 @@ relative_install_dir=relative_install_dir, current_working_dir=current_working_dir, tmp_name=tmp_name, - tool_panel_dict=None, tool_shed=tool_shed, tool_section=tool_section, - shed_tool_conf=shed_tool_conf, - new_install=True ) - - + shed_tool_conf=shed_tool_conf ) if 'tools' in metadata_dict: # Get the tool_versions from the tool shed for each tool in the installed change set. url = '%s/repository/get_tool_versions?name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % \ @@ -438,7 +385,7 @@ status = params.get( 'status', 'done' ) repository = get_repository( trans, kwd[ 'id' ] ) description = util.restore_text( params.get( 'description', repository.description ) ) - shed_tool_conf, tool_path, relative_install_dir = self.__get_tool_panel_config_tool_path_install_dir( trans, repository ) + shed_tool_conf, tool_path, relative_install_dir = get_tool_panel_config_tool_path_install_dir( trans.app, repository ) repo_files_dir = os.path.abspath( os.path.join( relative_install_dir, repository.name ) ) if params.get( 'edit_repository_button', False ): if description != repository.description: @@ -448,23 +395,7 @@ message = "The repository information has been updated." elif params.get( 'set_metadata_button', False ): repository_clone_url = generate_clone_url( trans, repository ) - # In case metadata was previously generated for this repository, we'll check to see if it has information needed for the tool_section_dict. - metadata = repository.metadata - if 'tool_panel_section' in metadata: - # For backward compatibility we have to handle 2 types of dictionaries. In the past, all repository tools had to be installed into - # a single ToolSection (or outside of any sections) in the tool panel. In this case. the dictionary looks like this. - # { id: <ToolSection id>, version : <ToolSection version>, name : <TooSection name>} - # Later, each tool from a repository could be installed into the tool panel inside or outside a specified ToolSection in the tool panel. - if panel_entry_per_tool( metadata[ 'tool_panel_section' ] ): - tool_panel_dict = metadata[ 'tool_panel_section' ] - metadata_dict = generate_metadata( trans.app.toolbox, relative_install_dir, repository_clone_url, tool_panel_dict=tool_panel_dict ) - else: - tool_section_dict = metadata[ 'tool_panel_section' ] - metadata_dict = generate_metadata( trans.app.toolbox, relative_install_dir, repository_clone_url, tool_section_dict=tool_section_dict ) - else: - # Not sure if we'll ever reach here, but just in case... - tool_section_dict = dict( id='', version='', name='' ) - metadata_dict = generate_metadata( trans.app.toolbox, relative_install_dir, repository_clone_url, tool_section_dict=tool_section_dict ) + metadata_dict = generate_metadata( trans.app.toolbox, relative_install_dir, repository_clone_url ) if metadata_dict: repository.metadata = metadata_dict trans.sa_session.add( repository ) @@ -482,7 +413,7 @@ repository = get_repository( trans, kwd[ 'id' ] ) no_changes = kwd.get( 'no_changes', '' ) no_changes_checked = CheckboxField.is_checked( no_changes ) - shed_tool_conf, tool_path, relative_install_dir = self.__get_tool_panel_config_tool_path_install_dir( trans, repository ) + shed_tool_conf, tool_path, relative_install_dir = get_tool_panel_config_tool_path_install_dir( trans.app, repository ) current_working_dir = os.getcwd() repository_clone_url = generate_clone_url( trans, repository ) clone_dir = os.path.join( tool_path, self.__generate_tool_path( repository_clone_url, repository.installed_changeset_revision ) ) @@ -491,82 +422,58 @@ if returncode == 0: returncode, tmp_name = update_repository( current_working_dir, relative_install_dir, repository.installed_changeset_revision ) if returncode == 0: - # Get the location in the tool panel in which the tool was originally loaded. - metadata = repository.metadata - if 'tool_panel_section' in metadata: - if panel_entry_per_tool( metadata[ 'tool_panel_section' ] ): + if repository.includes_tools: + # Get the location in the tool panel in which each tool was originally loaded. + metadata = repository.metadata + if 'tool_panel_section' in metadata: tool_panel_dict = metadata[ 'tool_panel_section' ] - # TODO: Fix this to handle the case where the tools are distributed across in more than 1 ToolSection. The - # following assumes everything was loaded into 1 section (or no section) in the tool panel. - tool_section_dicts = tool_panel_dict[ tool_panel_dict.keys()[ 0 ] ] - tool_section_dict = tool_section_dicts[ 0 ] else: - tool_section_dict = metadata[ 'tool_panel_section' ] - tool_section = generate_tool_section_element_from_dict( tool_section_dict ) - tool_panel_dict = generate_tool_panel_dict_for_repository_tools( metadata, tool_section=tool_section ) + # This should never happen. + tool_panel_dict = generate_tool_panel_dict_for_new_install( metadata[ 'tools' ] ) + # TODO: Fix this to handle the case where the tools are distributed across in more than 1 ToolSection. The + # following assumes everything was loaded into 1 section (or no section) in the tool panel. + tool_section_dicts = tool_panel_dict[ tool_panel_dict.keys()[ 0 ] ] + tool_section_dict = tool_section_dicts[ 0 ] original_section_id = tool_section_dict[ 'id' ] original_section_name = tool_section_dict[ 'name' ] - else: - tool_panel_dict = generate_tool_panel_dict_for_repository_tools( metadata ) - original_section_id = '' - original_section_name = '' - if no_changes_checked: - if original_section_id in [ '' ]: - tool_section = None + if no_changes_checked: + if original_section_id in [ '' ]: + tool_section = None + else: + section_key = 'section_%s' % str( original_section_id ) + if section_key in trans.app.toolbox.tool_panel: + tool_section = trans.app.toolbox.tool_panel[ section_key ] + else: + # The section in which the tool was originally loaded used to be in the tool panel, but no longer is. + elem = Element( 'section' ) + elem.attrib[ 'name' ] = original_section_name + elem.attrib[ 'id' ] = original_section_id + elem.attrib[ 'version' ] = '' + tool_section = tools.ToolSection( elem ) + trans.app.toolbox.tool_panel[ section_key ] = tool_section else: - section_key = 'section_%s' % str( original_section_id ) - if section_key in trans.app.toolbox.tool_panel: + # The user elected to change the tool panel section to contain the tools. + new_tool_panel_section = kwd.get( 'new_tool_panel_section', '' ) + tool_panel_section = kwd.get( 'tool_panel_section', '' ) + if new_tool_panel_section: + section_id = new_tool_panel_section.lower().replace( ' ', '_' ) + new_section_key = 'section_%s' % str( section_id ) + if new_section_key in trans.app.toolbox.tool_panel: + # Appending a tool to an existing section in trans.app.toolbox.tool_panel + log.debug( "Appending to tool panel section: %s" % new_tool_panel_section ) + tool_section = trans.app.toolbox.tool_panel[ new_section_key ] + else: + # Appending a new section to trans.app.toolbox.tool_panel + log.debug( "Loading new tool panel section: %s" % new_tool_panel_section ) + elem = Element( 'section' ) + elem.attrib[ 'name' ] = new_tool_panel_section + elem.attrib[ 'id' ] = section_id + elem.attrib[ 'version' ] = '' + tool_section = tools.ToolSection( elem ) + trans.app.toolbox.tool_panel[ new_section_key ] = tool_section + elif tool_panel_section: + section_key = 'section_%s' % tool_panel_section tool_section = trans.app.toolbox.tool_panel[ section_key ] - else: - # The section in which the tool was originally loaded used to be in the tool panel, but no longer is. - elem = Element( 'section' ) - elem.attrib[ 'name' ] = original_section_name - elem.attrib[ 'id' ] = original_section_id - elem.attrib[ 'version' ] = '' - tool_section = tools.ToolSection( elem ) - trans.app.toolbox.tool_panel[ section_key ] = tool_section - else: - # The user elected to change the tool panel section to contain the tools. - new_tool_panel_section = kwd.get( 'new_tool_panel_section', '' ) - tool_panel_section = kwd.get( 'tool_panel_section', '' ) - if new_tool_panel_section: - section_id = new_tool_panel_section.lower().replace( ' ', '_' ) - # Update each tool_section dictionary in tool_panel_dict with the new section attributes. - for guid, tool_section_dicts in tool_panel_dict.items(): - for dict_index, tool_section_dict in enumerate( tool_section_dicts ): - tool_section_dict[ 'id' ] = section_id - tool_section_dict[ 'name' ] = new_tool_panel_section - tool_section_dict[ 'version' ] = '' - tool_section_dicts[ dict_index ] = tool_section_dict - tool_panel_dict[ guid ] = tool_section_dicts - new_section_key = 'section_%s' % str( section_id ) - if new_section_key in trans.app.toolbox.tool_panel: - # Appending a tool to an existing section in trans.app.toolbox.tool_panel - log.debug( "Appending to tool panel section: %s" % new_tool_panel_section ) - tool_section = trans.app.toolbox.tool_panel[ new_section_key ] - else: - # Appending a new section to trans.app.toolbox.tool_panel - log.debug( "Loading new tool panel section: %s" % new_tool_panel_section ) - elem = Element( 'section' ) - elem.attrib[ 'name' ] = new_tool_panel_section - elem.attrib[ 'id' ] = section_id - elem.attrib[ 'version' ] = '' - tool_section = tools.ToolSection( elem ) - trans.app.toolbox.tool_panel[ new_section_key ] = tool_section - elif tool_panel_section: - section_key = 'section_%s' % tool_panel_section - tool_section = trans.app.toolbox.tool_panel[ section_key ] - else: - # Update each tool_section dictionary in tool_panel_dict in case the tools used to be contained in a panel section - # but are now being moved outside of any panel sections. - for guid, tool_section_dicts in tool_panel_dict.items(): - for dict_index, tool_section_dict in enumerate( tool_section_dicts ): - tool_section_dict[ 'id' ] = '' - tool_section_dict[ 'name' ] = '' - tool_section_dict[ 'version' ] = '' - tool_section_dicts[ dict_index ] = tool_section_dict - tool_panel_dict[ guid ] = tool_section_dicts - tool_section = None tool_shed_repository, metadata_dict = load_repository_contents( trans, repository_name=repository.name, description=repository.description, @@ -577,11 +484,9 @@ relative_install_dir=relative_install_dir, current_working_dir=current_working_dir, tmp_name=tmp_name, - tool_panel_dict=tool_panel_dict, tool_shed=repository.tool_shed, tool_section=tool_section, - shed_tool_conf=shed_tool_conf, - new_install=True ) + shed_tool_conf=shed_tool_conf ) repository.uninstalled = False repository.deleted = False trans.sa_session.add( repository ) @@ -595,36 +500,6 @@ @web.expose @web.require_admin def reselect_tool_panel_section( self, trans, **kwd ): - """ - INSIDE SECTION: - "{"tool_panel_section": {"gvk.bx.psu.edu:9009/repos/test/grouping/Grouping1/1.9.0": {"id": "group", - "name": "Group", - "tool_config": "grouping.xml", - "version": ""}}, - "tools": [{"description": "data by a column and perform aggregate operation on other columns.", - "guid": "gvk.bx.psu.edu:9009/repos/test/grouping/Grouping1/1.9.0", - "id": "Grouping1", - "name": "Group", - "requirements": [{"fabfile": null, "method": null, "name": "rpy", "type": "python-module", "version": null}], - "tests": [{"inputs": [["input1", "1.bed", {"children": [], "value": "1.bed"}], ["groupcol", "1", {"children": [], "value": "1"}], ["ignorecase", "true", {"children": [], "value": "true"}], ["optype", "mean", {"children": [], "value": "mean"}], ["opcol", "2", {"children": [], "value": "2"}], ["opround", "no", {"children": [], "value": "no"}]], "name": "Test-1", "outputs": [["out_file1", "groupby_out1.dat", {"assert_list": null, "compare": "diff", "delta": 10000, "extra_files": [], "lines_diff": 0, "sort": false}]], "required_files": [["1.bed", {"children": [], "value": "1.bed"}]]}, {"inputs": [["input1", "1.tabular", {"children": [], "value": "1.tabular"}], ["groupcol", "1", {"children": [], "value": "1"}], ["ignorecase", "true", {"children": [], "value": "true"}], ["optype", "mean", {"children": [], "value": "mean"}], ["opcol", "2", {"children": [], "value": "2"}], ["opround", "no", {"children": [], "value": "no"}]], "name": "Test-2", "outputs": [["out_file1", "groupby_out2.dat", {"assert_list": null, "compare": "diff", "delta": 10000, "extra_files": [], "lines_diff": 0, "sort": false}]], "required_files": [["1.tabular", {"children": [], "value": "1.tabular"}]]}], - "tool_config": "../shed_tools/gvk.bx.psu.edu/repos/test/grouping/935f00105de8/grouping/grouping.xml", - "version": "1.9.0", - "version_string_cmd": null}]}" - OUTSIDE SECTION: - "{"tool_panel_section": {"gvk.bx.psu.edu:9009/repos/test/filter/Filter1/1.0.1": {"id": "", - "name": "", - "tool_config": "filtering.xml", - "version": ""}}, - "tools": [{"description": "data on any column using simple expressions", - "guid": "gvk.bx.psu.edu:9009/repos/test/filter/Filter1/1.0.1", - "id": "Filter1", - "name": "Filter", - "requirements": [], - "tests": [{"inputs": [["input", "1.bed", {"children": [], "value": "1.bed"}], ["cond", "c1=='chr22'", {"children": [], "value": "c1=='chr22'"}]], "name": "Test-1", "outputs": [["out_file1", "filter1_test1.bed", {"assert_list": null, "compare": "diff", "delta": 10000, "extra_files": [], "lines_diff": 0, "sort": false}]], "required_files": [["1.bed", {"children": [], "value": "1.bed"}]]}, {"inputs": [["input", "7.bed", {"children": [], "value": "7.bed"}], ["cond", "c1=='chr1' and c3-c2>=2000 and c6=='+'", {"children": [], "value": "c1=='chr1' and c3-c2>=2000 and c6=='+'"}]], "name": "Test-2", "outputs": [["out_file1", "filter1_test2.bed", {"assert_list": null, "compare": "diff", "delta": 10000, "extra_files": [], "lines_diff": 0, "sort": false}]], "required_files": [["7.bed", {"children": [], "value": "7.bed"}]]}], - "tool_config": "../shed_tools/gvk.bx.psu.edu/repos/test/filter/b2df18d723c5/filter/filtering.xml", - "version": "1.0.1", - "version_string_cmd": null}]}" - """ repository = get_repository( trans, kwd[ 'id' ] ) # Get the location in the tool panel in which the tool was originally loaded. metadata = repository.metadata @@ -679,7 +554,7 @@ message += "Reset all of this reppository's metadata in the tool shed, then set the installed tool versions " message ++ "from the installed repository's <b>Repository Actions</b> menu. " status = 'error' - shed_tool_conf, tool_path, relative_install_dir = self.__get_tool_panel_config_tool_path_install_dir( trans, repository ) + shed_tool_conf, tool_path, relative_install_dir = get_tool_panel_config_tool_path_install_dir( trans.app, repository ) repo_files_dir = os.path.abspath( os.path.join( relative_install_dir, repository.name ) ) return trans.fill_template( '/admin/tool_shed_repository/manage_repository.mako', repository=repository, @@ -700,23 +575,12 @@ changeset_revision = params.get( 'changeset_revision', None ) latest_changeset_revision = params.get( 'latest_changeset_revision', None ) repository = get_repository_by_shed_name_owner_changeset_revision( trans.app, tool_shed_url, name, owner, changeset_revision ) - # Get the location in the tool panel in which the tool was originally loaded. - metadata = repository.metadata - if 'tool_panel_section' in metadata: - if panel_entry_per_tool( metadata[ 'tool_panel_section' ] ): - tool_panel_dict = metadata[ 'tool_panel_section' ] - else: - tool_section_dict = metadata[ 'tool_panel_section' ] - tool_section = generate_tool_section_element_from_dict( tool_section_dict ) - tool_panel_dict = generate_tool_panel_dict_for_repository_tools( metadata, tool_section=tool_section ) - else: - tool_panel_dict = generate_tool_panel_dict_for_repository_tools( metadata ) if changeset_revision and latest_changeset_revision: if changeset_revision == latest_changeset_revision: message = "The cloned tool shed repository named '%s' is current (there are no updates available)." % name else: current_working_dir = os.getcwd() - shed_tool_conf, tool_path, relative_install_dir = self.__get_tool_panel_config_tool_path_install_dir( trans, repository ) + shed_tool_conf, tool_path, relative_install_dir = get_tool_panel_config_tool_path_install_dir( trans.app, repository ) if relative_install_dir: repo_files_dir = os.path.join( relative_install_dir, name ) returncode, tmp_name = pull_repository( current_working_dir, repo_files_dir, name ) @@ -726,21 +590,8 @@ # Update the repository metadata. repository_clone_url = os.path.join( tool_shed_url, 'repos', owner, name ) tool_shed = clean_tool_shed_url( tool_shed_url ) - tool_shed_repository, metadata_dict = load_repository_contents( trans, - repository_name=name, - description=repository.description, - owner=owner, - changeset_revision=changeset_revision, - tool_path=tool_path, - repository_clone_url=repository_clone_url, - relative_install_dir=relative_install_dir, - current_working_dir=current_working_dir, - tmp_name=tmp_name, - tool_panel_dict=tool_panel_dict, - tool_shed=tool_shed, - tool_section=None, - shed_tool_conf=None, - new_install=False ) + metadata_dict = generate_metadata( trans.app.toolbox, relative_install_dir, repository_clone_url ) + repository.metadata = metadata_dict # Update the repository changeset_revision in the database. repository.changeset_revision = latest_changeset_revision repository.update_available = False @@ -809,77 +660,6 @@ repo_path = items[ 1 ] tool_shed_url = clean_tool_shed_url( tool_shed_url ) return '%s/repos%s/%s' % ( tool_shed_url, repo_path, changeset_revision ) - def __get_tool_panel_config_tool_path_install_dir( self, trans, repository ): - # Return shed-related tool panel config, the tool_path configured in it, and the relative path to the directory where the - # repository is installed. This method assumes all repository tools are defined in a single shed-related tool panel config. - tool_shed = clean_tool_shed_url( repository.tool_shed ) - partial_install_dir = '%s/repos/%s/%s/%s' % ( tool_shed, repository.owner, repository.name, repository.installed_changeset_revision ) - # Get the relative tool installation paths from each of the shed tool configs. - relative_install_dir = None - for shed_tool_conf_dict in trans.app.toolbox.shed_tool_confs: - shed_tool_conf = shed_tool_conf_dict[ 'config_filename' ] - if repository.dist_to_shed: - # The repository is owned by devteam and contains tools migrated from the Galaxy distribution to the tool shed, so - # the reserved tool panel config is migrated_tools_conf.xml, to which trans.app.config.migrated_tools_config refers. - if shed_tool_conf == trans.app.config.migrated_tools_config: - tool_path = shed_tool_conf_dict[ 'tool_path' ] - relative_install_dir = os.path.join( tool_path, partial_install_dir ) - if tool_path and relative_install_dir: - return shed_tool_conf, tool_path, relative_install_dir - elif repository.uninstalled: - # Since the repository is uninstalled we don't know what tool panel config was originally used to - # define the tools in the repository, so we'll just make sure not to use the reserved migrated_tools_conf.xml. - if shed_tool_conf != trans.app.config.migrated_tools_config: - tool_path = shed_tool_conf_dict[ 'tool_path' ] - relative_install_dir = os.path.join( tool_path, partial_install_dir ) - if tool_path and relative_install_dir: - return shed_tool_conf, tool_path, relative_install_dir - else: - if repository.includes_tools: - # We'll check config_elems until we find an element that matches one of the tools in the repository's metadata. - metadata = repository.metadata - tool_dict = metadata[ 'tools' ][ 0 ] - config_elems = shed_tool_conf_dict[ 'config_elems' ] - if config_elems: - tool_path, relative_install_dir = self.__get_tool_path_install_dir( partial_install_dir, - shed_tool_conf_dict, - tool_dict, - config_elems ) - if tool_path and relative_install_dir: - return shed_tool_conf, tool_path, relative_install_dir - else: - # Parse the tool panel config since we have no in-memory config_elems (not sure if this will ever occur). - tool_panel_config = shed_tool_conf_dict[ 'config_filename' ] - tree = util.parse_xml( tool_panel_config ) - root = tree.getroot() - tool_path, relative_install_dir = self.__get_tool_path_install_dir( partial_install_dir, - shed_tool_conf_dict, - tool_dict, - root ) - if tool_path and relative_install_dir: - return shed_tool_conf, tool_path, relative_install_dir - else: - # Nothing will be loaded into the tool panel, so look for the installed repository on disk. - tool_path = shed_tool_conf_dict[ 'tool_path' ] - relative_install_dir = os.path.join( tool_path, partial_install_dir ) - if tool_path and relative_install_dir and os.path.isdir( relative_install_dir ): - return shed_tool_conf, tool_path, relative_install_dir - return None, None, None - def __get_tool_path_install_dir( self, partial_install_dir, shed_tool_conf_dict, tool_dict, config_elems ): - for elem in config_elems: - if elem.tag == 'tool': - if elem.get( 'guid' ) == tool_dict[ 'guid' ]: - tool_path = shed_tool_conf_dict[ 'tool_path' ] - relative_install_dir = os.path.join( tool_path, partial_install_dir ) - return tool_path, relative_install_dir - elif elem.tag == 'section': - for section_elem in elem: - if section_elem.tag == 'tool': - if section_elem.get( 'guid' ) == tool_dict[ 'guid' ]: - tool_path = shed_tool_conf_dict[ 'tool_path' ] - relative_install_dir = os.path.join( tool_path, partial_install_dir ) - return tool_path, relative_install_dir - return None, None ## ---- Utility methods ------------------------------------------------------- Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: greg: Allow installed tools to have more than 1 entry in the tool panel, and several fixes for deactivating / activating / uninstalling / reinstalling repositories.
by Bitbucket 01 Mar '12

01 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/80fa0f99e7e2/ changeset: 80fa0f99e7e2 user: greg date: 2012-03-01 21:04:51 summary: Allow installed tools to have more than 1 entry in the tool panel, and several fixes for deactivating / activating / uninstalling / reinstalling repositories. affected #: 4 files diff -r c116768aa0e003f579a2bc0cf7da09149305fbea -r 80fa0f99e7e21c148900d25689f036de7023e5dc lib/galaxy/tool_shed/install_manager.py --- a/lib/galaxy/tool_shed/install_manager.py +++ b/lib/galaxy/tool_shed/install_manager.py @@ -88,11 +88,13 @@ if elem not in tool_panel_elems: tool_panel_elems.append( elem ) return tool_panel_elems - def get_containing_tool_section( self, tool_config ): + def get_containing_tool_sections( self, tool_config ): """ - If tool_config is defined somewhere in self.proprietary_tool_panel_elems, return True and the ToolSection in which the tool is - displayed or None if it is displayed outside of any sections. + If tool_config is defined somewhere in self.proprietary_tool_panel_elems, return True and a list of ToolSections in which the + tool is displayed. If the tool is displayed outside of any sections, None is appended to the list. """ + tool_sections = [] + is_displayed = False for proprietary_tool_panel_elem in self.proprietary_tool_panel_elems: if proprietary_tool_panel_elem.tag == 'tool': # The proprietary_tool_panel_elem looks something like <tool file="emboss_5/emboss_antigenic.xml" />. @@ -100,7 +102,9 @@ proprietary_path, proprietary_name = os.path.split( proprietary_tool_config ) if tool_config == proprietary_name: # The tool is loaded outside of any sections. - return True, None + tool_sections.append( None ) + if not is_displayed: + is_displayed = True if proprietary_tool_panel_elem.tag == 'section': # The proprietary_tool_panel_elem looks something like <section name="EMBOSS" id="EMBOSSLite">. for section_elem in proprietary_tool_panel_elem: @@ -110,27 +114,31 @@ proprietary_path, proprietary_name = os.path.split( proprietary_tool_config ) if tool_config == proprietary_name: # The tool is loaded inside of the section_elem. - return True, ToolSection( proprietary_tool_panel_elem ) - return False, None + tool_sections.append( ToolSection( proprietary_tool_panel_elem ) ) + if not is_displayed: + is_displayed = True + return is_displayed, tool_sections def handle_repository_contents( self, current_working_dir, repository_clone_url, relative_install_dir, repository_elem, repository_name, description, changeset_revision, tmp_name ): # Generate the metadata for the installed tool shed repository, among other things. It is critical that the installed repository is # updated to the desired changeset_revision before metadata is set because the process for setting metadata uses the repository files on disk. + # The values for the keys in each of the following dictionaries will be a list to allow for the same tool to be displayed in multiple places + # in the tool panel. tool_panel_dict_for_display = {} tool_panel_dict_for_metadata = {} for tool_elem in repository_elem: # The tool_elem looks something like this: <tool id="EMBOSS: antigenic1" version="5.0.0" file="emboss_antigenic.xml" /> tool_config = tool_elem.get( 'file' ) guid = self.get_guid( repository_clone_url, relative_install_dir, tool_config ) - # See if tool_config is defined somewhere in self.proprietary_tool_panel_elems. - is_loaded, tool_section = self.get_containing_tool_section( tool_config ) - tool_panel_dict_for_tool_config = generate_tool_panel_dict_for_tool_config( guid, tool_config, tool_section=tool_section ) + # See if tool_config is defined inside of a section in self.proprietary_tool_panel_elems. + is_displayed, tool_sections = self.get_containing_tool_sections( tool_config ) + tool_panel_dict_for_tool_config = generate_tool_panel_dict_for_tool_config( guid, tool_config, tool_sections=tool_sections ) # The tool_panel_dict_for_tool_config dictionary contains a single entry that looks something like this. - # {<Tool guid> : { tool_config : <tool_config_file>, id: <ToolSection id>, version : <ToolSection version>, name : <TooSection name>}} + # {<Tool guid> : [{ tool_config : <tool_config_file>, id: <ToolSection id>, version : <ToolSection version>, name : <TooSection name>}]} # Add the new entry to the dictionary we're defining to set metadata. for k, v in tool_panel_dict_for_tool_config.items(): tool_panel_dict_for_metadata[ k ] = v - if is_loaded: + if is_displayed: # Add the new entry to the dictionary we're defining to set the tool panel display. for k, v in tool_panel_dict_for_tool_config.items(): tool_panel_dict_for_display[ k ] = v diff -r c116768aa0e003f579a2bc0cf7da09149305fbea -r 80fa0f99e7e21c148900d25689f036de7023e5dc lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -92,7 +92,7 @@ # We're parsing a shed_tool_conf file since we have a tool_path attribute. parsing_shed_tool_conf = True # Keep an in-memory list of xml elements to enable persistence of the changing tool config. - config_elems=[] + config_elems = [] else: parsing_shed_tool_conf = False # Default to backward compatible config setting. @@ -180,7 +180,7 @@ update_needed = False if 'tool_panel_section' in metadata: if panel_entry_per_tool( metadata[ 'tool_panel_section' ] ): - # {<Tool guid> : { tool_config : <tool_config_file>, id: <ToolSection id>, version : <ToolSection version>, name : <TooSection name>}} + # {<Tool guid> : [{ tool_config : <tool_config_file>, id: <ToolSection id>, version : <ToolSection version>, name : <TooSection name>}]} tool_panel_dict = metadata[ 'tool_panel_section' ] else: # { id: <ToolSection id>, version : <ToolSection version>, name : <TooSection name>} @@ -189,15 +189,17 @@ tool_panel_dict = generate_tool_panel_dict_for_repository_tools( metadata, tool_section=tool_section ) if section: # This means all tools are loaded into the same tool panel section or are all outside of any sections. - for tool_panel_dict_guid, tool_section_dict in tool_panel_dict.items(): - if tool_section_dict [ 'id' ] != section.id or \ - tool_section_dict [ 'version' ] != section.version or \ - tool_section_dict [ 'name' ] != section.name: - tool_section_dict [ 'id' ] = section.id - tool_section_dict [ 'version' ] = section.version - tool_section_dict [ 'name' ] = section.name - tool_panel_dict[ tool_panel_dict_guid ] = tool_section_dict - update_needed = True + for tool_panel_dict_guid, tool_section_dicts in tool_panel_dict.items(): + for dict_index, tool_section_dict in enumerate( tool_section_dicts ): + if tool_section_dict [ 'id' ] != section.id or \ + tool_section_dict [ 'version' ] != section.version or \ + tool_section_dict [ 'name' ] != section.name: + tool_section_dict [ 'id' ] = section.id + tool_section_dict [ 'version' ] = section.version + tool_section_dict [ 'name' ] = section.name + tool_section_dicts[ dict_index ] = tool_section_dict + tool_panel_dict[ tool_panel_dict_guid ] = tool_section_dicts + update_needed = True else: # The tool_panel_section was introduced late, so set it's value if its missing in the metadata. tool_panel_dict = generate_tool_panel_dict_for_repository_tools( tool_shed_repository.metadata, tool_section=section ) diff -r c116768aa0e003f579a2bc0cf7da09149305fbea -r 80fa0f99e7e21c148900d25689f036de7023e5dc lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -11,13 +11,28 @@ from elementtree.ElementTree import Element, SubElement log = logging.getLogger( __name__ ) - -def add_to_tool_panel( app, repository_name, repository_clone_url, changeset_revision, repository_tools_tups, owner, shed_tool_conf, tool_panel_dict, new_install=True ): +def add_to_shed_tool_config( app, shed_tool_conf_dict, elem_list ): + # A tool shed repository is being installed so change the shed_tool_conf file. Parse the config file to generate the entire list + # of config_elems instead of using the in-memory list since it will be a subset of the entire list if one or more repositories have + # been deactivated. + shed_tool_conf = shed_tool_conf_dict[ 'config_filename' ] + tool_path = shed_tool_conf_dict[ 'tool_path' ] + config_elems = [] + tree = util.parse_xml( shed_tool_conf ) + root = tree.getroot() + for elem in root: + config_elems.append( elem ) + # Add the elements to the in-memory list of config_elems. + for elem_entry in elem_list: + config_elems.append( elem_entry ) + # Persist the altered shed_tool_config file. + config_elems_to_xml_file( app, config_elems, shed_tool_conf, tool_path ) +def add_to_tool_panel( app, repository_name, repository_clone_url, changeset_revision, repository_tools_tups, owner, shed_tool_conf, tool_panel_dict, + new_install=True ): """A tool shed repository is being installed or updated so handle tool panel alterations accordingly.""" # We need to change the in-memory version and the file system version of the shed_tool_conf file. index, shed_tool_conf_dict = get_shed_tool_conf_dict( app, shed_tool_conf ) tool_path = shed_tool_conf_dict[ 'tool_path' ] - config_elems = shed_tool_conf_dict[ 'config_elems' ] # Generate the list of ElementTree Element objects for each section or tool. elem_list = generate_tool_panel_elem_list( repository_name, repository_clone_url, @@ -25,22 +40,22 @@ tool_panel_dict, repository_tools_tups, owner=owner ) - # Load the tools into the tool panel. + if new_install: + # Add the new elements to the shed_tool_conf file on disk. + add_to_shed_tool_config( app, shed_tool_conf_dict, elem_list ) + config_elems = shed_tool_conf_dict[ 'config_elems' ] for config_elem in elem_list: + # Add the new elements to the in-memory list of config_elems. + config_elems.append( config_elem ) + # Load the tools into the in-memory tool panel. if config_elem.tag == 'section': app.toolbox.load_section_tag_set( config_elem, app.toolbox.tool_panel, tool_path ) elif config_elem.tag == 'tool': guid = config_elem.get( 'guid' ) app.toolbox.load_tool_tag_set( config_elem, app.toolbox.tool_panel, tool_path=tool_path, guid=guid ) - if new_install: - # Add the elements to the in-memory list of config_elems. - for elem_entry in elem_list: - config_elems.append( elem_entry ) - # Replace the old list of config_elems with the new list. + # Replace the old list of in-memory config_elems with the new list for this shed_tool_conf_dict. shed_tool_conf_dict[ 'config_elems' ] = config_elems app.toolbox.shed_tool_confs[ index ] = shed_tool_conf_dict - # Append the new entry (either section or list of tools) to the shed_tool_config file. - config_elems_to_xml_file( app, shed_tool_conf_dict ) if app.toolbox_search.enabled: # If search support for tools is enabled, index the new installed tools. app.toolbox_search = ToolBoxSearch( app.toolbox ) @@ -122,12 +137,8 @@ except: pass return converter_path, display_path -def config_elems_to_xml_file( app, shed_tool_conf_dict ): - # Persist the current in-memory list of config_elems in the received shed_tool_conf_dict - # to a file named by the value of config_filename in the received shed_tool_conf_dict. - config_filename = shed_tool_conf_dict[ 'config_filename' ] - tool_path = shed_tool_conf_dict[ 'tool_path' ] - config_elems = shed_tool_conf_dict[ 'config_elems' ] +def config_elems_to_xml_file( app, config_elems, config_filename, tool_path ): + # Persist the current in-memory list of config_elems to a file named by the value of config_filename. fd, filename = tempfile.mkstemp() os.write( fd, '<?xml version="1.0"?>\n' ) os.write( fd, '<toolbox tool_path="%s">\n' % str( tool_path ) ) @@ -278,14 +289,13 @@ # { id: <ToolSection id>, version : <ToolSection version>, name : <TooSection name>} # The tool_panel_dict is fully populated with all tools in the repository that should be loaded into the tool panel. It is received when # this method is called by the InstallManager or when metadata is being reset on an existing repository. This dictionary looks something - # like this. - # {<Tool guid> : { tool_config : <tool_config_file>, id: <ToolSection id>, version : <ToolSection version>, name : <TooSection name>}} + # like this. + # {<Tool guid> : [{ tool_config : <tool_config_file>, id: <ToolSection id>, version : <ToolSection version>, name : <TooSection name>}]} # The tool_panel_dict enables each tool in the repository to be contained inside or outside a specified ToolSection in the tool panel. The # new_tool_panel_dict with be populated with a subset of the items in the received tool_panel_dict. This will allow for the case where # repository metadata is being updated where the previous change set revision included more tools than the current change set revision. if tool_section_dict: - # The received tool_panel_dict must be None, so we'll populate it here. Currently tools must all be installed in a single - # section or outside any sections. + # The received tool_panel_dict must be None, so we'll populate it here. for k, v in tool_section_dict.items(): if v is None: # Coerce None values into empty strings because ElementTree.tostring() throws exceptions on None values. @@ -329,10 +339,17 @@ # Populate the tool_section_dict if necessary. if tool_panel_dict and guid in tool_panel_dict: # We're updating metadata on a previously installed repository. - old_tool_panel_dict = tool_panel_dict[ guid ] - if 'tool_config' not in old_tool_panel_dict or old_tool_panel_dict[ 'tool_config' ] in [ None, '' ]: - old_tool_panel_dict[ 'tool_config' ] = name - new_tool_panel_dict[ guid ] = old_tool_panel_dict + old_tool_panel_dicts = tool_panel_dict[ guid ] + for dict_index, old_tool_panel_dict in enumerate( old_tool_panel_dicts ): + # Should we really do this? What if there is more than 1 old_tool_panel_dict in the list? + if 'tool_config' not in old_tool_panel_dict or old_tool_panel_dict[ 'tool_config' ] in [ None, '' ]: + old_tool_panel_dict[ 'tool_config' ] = name + old_tool_panel_dicts[ dict_index ] = old_tool_panel_dict + if guid in new_tool_panel_dict: + for old_tool_panel_dict in old_tool_panel_dicts: + new_tool_panel_dict[ guid ].append( old_tool_panel_dict ) + else: + new_tool_panel_dict[ guid ] = old_tool_panel_dicts else: # The admin is manually installing a new repository. new_tool_section_dict = {} @@ -345,7 +362,10 @@ new_tool_section_dict[ 'version' ] = '' if 'tool_config' not in new_tool_section_dict or new_tool_section_dict[ 'tool_config' ] in [ None, '' ]: new_tool_section_dict[ 'tool_config' ] = name - new_tool_panel_dict[ guid ] = new_tool_section_dict + if guid in new_tool_panel_dict: + new_tool_panel_dict[ guid ].append( new_tool_section_dict ) + else: + new_tool_panel_dict[ guid ] = [ new_tool_section_dict ] # Find all exported workflows elif name.endswith( '.ga' ): relative_path = os.path.join( root, name ) @@ -413,66 +433,65 @@ return metadata_dict def generate_tool_panel_elem_list( repository_name, repository_clone_url, changeset_revision, tool_panel_dict, repository_tools_tups, owner='' ): """Generate a list of ElementTree Element objects for each section or tool.""" - # Each entry in the tool_panel_dict looks like this. - # {<Tool guid> : { tool_config : <tool_config_file>, id: <ToolSection id>, version : <ToolSection version>, name : <TooSection name>}} + # {<Tool guid> : [{ tool_config : <tool_config_file>, id: <ToolSection id>, version : <ToolSection version>, name : <TooSection name>}]} elem_list = [] tool_elem = None tmp_url = clean_repository_clone_url( repository_clone_url ) if not owner: owner = get_repository_owner( tmp_url ) - for guid, tool_section_dict in tool_panel_dict.items(): - tool_section = None - inside_section = False - section_in_elem_list = False - if tool_section_dict[ 'id' ]: - inside_section = True - # Create a new section element only if we haven't already created it. - for index, elem in enumerate( elem_list ): - if elem.tag == 'section': - section_id = elem.get( 'id', None ) - if section_id == tool_section_dict[ 'id' ]: - section_in_elem_list = True - tool_section = elem - break - if tool_section is None: - tool_section = generate_tool_section_element_from_dict( tool_section_dict ) - # Find the tuple containing the current guid from the list of repository_tools_tups. - for repository_tool_tup in repository_tools_tups: - tool_file_path, tup_guid, tool = repository_tool_tup - if tup_guid == guid: - break - if inside_section: - tool_elem = SubElement( tool_section, 'tool' ) - else: - tool_elem = Element( 'tool' ) - tool_elem.attrib[ 'file' ] = tool_file_path - tool_elem.attrib[ 'guid' ] = guid - tool_shed_elem = SubElement( tool_elem, 'tool_shed' ) - tool_shed_elem.text = tmp_url.split( 'repos' )[ 0 ].rstrip( '/' ) - repository_name_elem = SubElement( tool_elem, 'repository_name' ) - repository_name_elem.text = repository_name - repository_owner_elem = SubElement( tool_elem, 'repository_owner' ) - repository_owner_elem.text = owner - changeset_revision_elem = SubElement( tool_elem, 'installed_changeset_revision' ) - changeset_revision_elem.text = changeset_revision - id_elem = SubElement( tool_elem, 'id' ) - id_elem.text = tool.id - version_elem = SubElement( tool_elem, 'version' ) - version_elem.text = tool.version - if inside_section: - if section_in_elem_list: - elem_list[ index ] = tool_section + for guid, tool_section_dicts in tool_panel_dict.items(): + for tool_section_dict in tool_section_dicts: + tool_section = None + inside_section = False + section_in_elem_list = False + if tool_section_dict[ 'id' ]: + inside_section = True + # Create a new section element only if we haven't already created it. + for index, elem in enumerate( elem_list ): + if elem.tag == 'section': + section_id = elem.get( 'id', None ) + if section_id == tool_section_dict[ 'id' ]: + section_in_elem_list = True + tool_section = elem + break + if tool_section is None: + tool_section = generate_tool_section_element_from_dict( tool_section_dict ) + # Find the tuple containing the current guid from the list of repository_tools_tups. + for repository_tool_tup in repository_tools_tups: + tool_file_path, tup_guid, tool = repository_tool_tup + if tup_guid == guid: + break + if inside_section: + tool_elem = SubElement( tool_section, 'tool' ) else: - elem_list.append( tool_section ) - else: - elem_list.append( tool_elem ) + tool_elem = Element( 'tool' ) + tool_elem.attrib[ 'file' ] = tool_file_path + tool_elem.attrib[ 'guid' ] = guid + tool_shed_elem = SubElement( tool_elem, 'tool_shed' ) + tool_shed_elem.text = tmp_url.split( 'repos' )[ 0 ].rstrip( '/' ) + repository_name_elem = SubElement( tool_elem, 'repository_name' ) + repository_name_elem.text = repository_name + repository_owner_elem = SubElement( tool_elem, 'repository_owner' ) + repository_owner_elem.text = owner + changeset_revision_elem = SubElement( tool_elem, 'installed_changeset_revision' ) + changeset_revision_elem.text = changeset_revision + id_elem = SubElement( tool_elem, 'id' ) + id_elem.text = tool.id + version_elem = SubElement( tool_elem, 'version' ) + version_elem.text = tool.version + if inside_section: + if section_in_elem_list: + elem_list[ index ] = tool_section + else: + elem_list.append( tool_section ) + else: + elem_list.append( tool_elem ) return elem_list def generate_tool_panel_dict_for_repository_tools( repository_metadata, tool_section=None, tool_section_dict=None ): """ - Create a dictionary of the following type for every tool in the repository where the tools are all - contained in the same tool section or no tool section. If tool_section is None, tools will be displayed - outside of any sections in the tool panel. - {<Tool guid> : { tool_config : <tool_config_file>, id: <ToolSection id>, version : <ToolSection version>, name : <TooSection name>}} + Create a dictionary of the following type for every tool in the repository where the tools are all contained in the same tool section + or no tool section. If tool_section is None, tools will be displayed outside of any sections in the tool panel. + {<Tool guid> : [{ tool_config : <tool_config_file>, id: <ToolSection id>, version : <ToolSection version>, name : <TooSection name>}]} """ tool_panel_dict = {} tool_dicts = repository_metadata[ 'tools' ] @@ -485,33 +504,49 @@ new_tool_section_dict[ k ] = v file_path, file_name = os.path.split( tool_config ) new_tool_section_dict[ 'tool_config' ] = file_name + if guid in tool_panel_dict: + tool_panel_dict[ guid ].append( new_tool_section_dict ) + else: + tool_panel_dict[ guid ] = [ new_tool_section_dict ] else: - new_tool_section_dict = generate_tool_section_dict( tool_config=tool_config, tool_section=tool_section ) - tool_panel_dict[ guid ] = tool_section_dict + new_tool_section_dicts = generate_tool_section_dicts( tool_config=tool_config, tool_section=tool_section ) + if guid in tool_panel_dict: + for new_tool_section_dict in new_tool_section_dicts: + tool_panel_dict[ guid ].append( new_tool_section_dict ) + else: + tool_panel_dict[ guid ] = new_tool_section_dicts return tool_panel_dict -def generate_tool_panel_dict_for_tool_config( guid, tool_config, tool_section=None ): +def generate_tool_panel_dict_for_tool_config( guid, tool_config, tool_sections=None ): """ Create a dictionary of the following type for a single tool config file name. The intent is to call this method for every tool config in a repository and append each of these as entries to a tool panel dictionary for the repository. This allows for each tool to be loaded into a different section in the tool panel. - {<Tool guid> : { tool_config : <tool_config_file>, id: <ToolSection id>, version : <ToolSection version>, name : <TooSection name>}} + {<Tool guid> : [{ tool_config : <tool_config_file>, id: <ToolSection id>, version : <ToolSection version>, name : <TooSection name>}]} """ tool_panel_dict = {} file_path, file_name = os.path.split( tool_config ) - tool_section_dict = generate_tool_section_dict( tool_config=file_name, tool_section=tool_section ) - tool_panel_dict[ guid ] = tool_section_dict + tool_section_dicts = generate_tool_section_dicts( tool_config=file_name, tool_sections=tool_sections ) + tool_panel_dict[ guid ] = tool_section_dicts return tool_panel_dict -def generate_tool_section_dict( tool_config=None, tool_section=None ): +def generate_tool_section_dicts( tool_config=None, tool_sections=None ): + tool_section_dicts = [] if tool_config is None: tool_config = '' - if tool_section: - section_id = tool_section.id or '' - section_version = tool_section.version or '' - section_name = tool_section.name or '' - tool_section_dict = dict( tool_config=tool_config, id=section_id, version=section_version, name=section_name ) + if tool_sections: + for tool_section in tool_sections: + # The value of tool_section will be None if the tool is displayed outside of any sections in the tool panel. + if tool_section: + section_id = tool_section.id or '' + section_version = tool_section.version or '' + section_name = tool_section.name or '' + else: + section_id = '' + section_version = '' + section_name = '' + tool_section_dicts.append( dict( tool_config=tool_config, id=section_id, version=section_version, name=section_name ) ) else: - tool_section_dict = dict( tool_config=tool_config, id='', version='', name='' ) - return tool_section_dict + tool_section_dicts.append( dict( tool_config=tool_config, id='', version='', name='' ) ) + return tool_section_dicts def generate_tool_section_element_from_dict( tool_section_dict ): # The value of tool_section_dict looks like the following. # { id: <ToolSection id>, version : <ToolSection version>, name : <TooSection name>} @@ -573,6 +608,34 @@ if converter_path and display_path: break return converter_path, display_path +def get_in_memory_config_elems_to_remove( shed_tool_conf_dict, guids_to_remove ): + config_elems = shed_tool_conf_dict[ 'config_elems' ] + config_elems_to_remove = [] + tool_elements_removed = 0 + for config_elem in config_elems: + if config_elem.tag == 'section': + tool_elems_to_remove = [] + for tool_elem in config_elem: + if tool_elem.get( 'guid' ) in guids_to_remove: + tool_elems_to_remove.append( tool_elem ) + for tool_elem in tool_elems_to_remove: + # Remove all of the appropriate tool sub-elements from the section element. + config_elem.remove( tool_elem ) + log.debug( "Removed tool with guid '%s'." % str( tool_elem.get( 'guid' ) ) ) + tool_elements_removed += 1 + if len( config_elem ) < 1: + # Keep a list of all empty section elements so they can be removed. + config_elems_to_remove.append( config_elem ) + if tool_elements_removed == len( guids_to_remove ): + break + elif config_elem.tag == 'tool': + if config_elem.get( 'guid' ) in guids_to_remove: + config_elems_to_remove.append( config_elem ) + log.debug( "Removed tool with guid '%s'." % str( config_elem.get( 'guid' ) ) ) + tool_elements_removed += 1 + if tool_elements_removed == len( guids_to_remove ): + break + return config_elems_to_remove def get_shed_tool_conf_dict( app, shed_tool_conf ): """ Return the in-memory version of the shed_tool_conf file, which is stored in the config_elems entry @@ -780,7 +843,7 @@ # We're resetting metadata on a previously installed repository. For backward compatibility we have to handle 2 types of dictionaries. # In the past, all repository tools had to be installed into a single ToolSection (or outside of any sections) in the tool panel. if panel_entry_per_tool( tool_panel_dict ): - # {<Tool guid> : { tool_config : <tool_config_file>, id: <ToolSection id>, version : <ToolSection version>, name : <TooSection name>}} + # {<Tool guid> : [{ tool_config : <tool_config_file>, id: <ToolSection id>, version : <ToolSection version>, name : <TooSection name>}]} metadata_dict = generate_metadata( trans.app.toolbox, relative_install_dir, repository_clone_url, tool_panel_dict=tool_panel_dict ) else: # { id: <ToolSection id>, version : <ToolSection version>, name : <TooSection name>} @@ -788,8 +851,8 @@ else: # We're installing a new repository or reinstalling an uninstalled repository where all tools are contained in the same tool panel section # or outside of any sections in the tool panel. We cannot pass a specific tool_config since we do not yet have one. - tool_section_dict = generate_tool_section_dict( tool_config=None, tool_section=tool_section ) - metadata_dict = generate_metadata( trans.app.toolbox, relative_install_dir, repository_clone_url, tool_section_dict=tool_section_dict ) + tool_section_dicts = generate_tool_section_dicts( tool_config=None, tool_sections=util.listify( tool_section ) ) + metadata_dict = generate_metadata( trans.app.toolbox, relative_install_dir, repository_clone_url, tool_section_dict=tool_section_dicts[ 0 ] ) tool_panel_dict = metadata_dict[ 'tool_panel_section' ] # Add a new record to the tool_shed_repository table if one doesn't already exist. If one exists but is marked deleted, undelete it. This # must happen before the call to add_to_tool_panel() below because tools will not be properly loaded if the repository is marked deleted. @@ -853,7 +916,7 @@ return tool_shed_repository, metadata_dict def panel_entry_per_tool( tool_section_dict ): # Return True if tool_section_dict looks like this. - # {<Tool guid> : { tool_config : <tool_config_file>, id: <ToolSection id>, version : <ToolSection version>, name : <TooSection name>}} + # {<Tool guid> : [{ tool_config : <tool_config_file>, id: <ToolSection id>, version : <ToolSection version>, name : <TooSection name>}]} # But not like this. # { id: <ToolSection id>, version : <ToolSection version>, name : <TooSection name>} if len( tool_section_dict ) != 3: @@ -874,19 +937,20 @@ os.chdir( current_working_dir ) tmp_stderr.close() return returncode, tmp_name -def remove_from_tool_panel( app, shed_tool_conf, tool_panel_dict, uninstall=False ): - # A tool shed repository is being deactivated or uninstalled so handle tool panel alterations accordingly. We need to change the - # in-memory version and the file system version of the shed_tool_conf file. The value of tool_panel_dict is a dictionary of entries - # that look like this. - # {<Tool guid> : { tool_config : <tool_config_file>, id: <ToolSection id>, version : <ToolSection version>, name : <TooSection name>}} - index, shed_tool_conf_dict = get_shed_tool_conf_dict( app, shed_tool_conf ) - config_elems = shed_tool_conf_dict[ 'config_elems' ] +def remove_from_shed_tool_config( app, shed_tool_conf_dict, guids_to_remove ): + # A tool shed repository is being uninstalled so change the shed_tool_conf file. Parse the config file to generate the entire list + # of config_elems instead of using the in-memory list since it will be a subset of the entire list if one or more repositories have + # been deactivated. + shed_tool_conf = shed_tool_conf_dict[ 'config_filename' ] + tool_path = shed_tool_conf_dict[ 'tool_path' ] + config_elems = [] + tree = util.parse_xml( shed_tool_conf ) + root = tree.getroot() + for elem in root: + config_elems.append( elem ) tool_elements_removed = 0 config_elems_to_remove = [] - # Create a list of guids for all tools that will be removed from the tool panel config. - guids_to_remove = [ k for k in tool_panel_dict.keys() ] for config_elem in config_elems: - config_elems_to_remove = [] if config_elem.tag == 'section': tool_elems_to_remove = [] for tool_elem in config_elem: @@ -895,7 +959,6 @@ for tool_elem in tool_elems_to_remove: # Remove all of the appropriate tool sub-elements from the section element. config_elem.remove( tool_elem ) - log.debug( "Removed tool with guid '%s'." % str( tool_elem.get( 'guid' ) ) ) tool_elements_removed += 1 if len( config_elem ) < 1: # Keep a list of all empty section elements so they can be removed. @@ -905,28 +968,38 @@ elif config_elem.tag == 'tool': if config_elem.get( 'guid' ) in guids_to_remove: config_elems_to_remove.append( config_elem ) - log.debug( "Removed tool with guid '%s'." % str( config_elem.get( 'guid' ) ) ) tool_elements_removed += 1 if tool_elements_removed == len( guids_to_remove ): break for config_elem in config_elems_to_remove: - # Remove the element from the in-menory tool panel. + config_elems.remove( config_elem ) + # Persist the altered in-memory version of the tool config. + config_elems_to_xml_file( app, config_elems, shed_tool_conf, tool_path ) +def remove_from_tool_panel( app, shed_tool_conf, tool_panel_dict, uninstall ): + """A tool shed repository is being deactivated or uninstalled so handle tool panel alterations accordingly.""" + index, shed_tool_conf_dict = get_shed_tool_conf_dict( app, shed_tool_conf ) + # Create a list of guids for all tools that will be removed from the in-memory tool panel and config file on disk. + guids_to_remove = [ k for k in tool_panel_dict.keys() ] + if uninstall: + # Remove from the shed_tool_conf file on disk. + remove_from_shed_tool_config( app, shed_tool_conf_dict, guids_to_remove ) + config_elems_to_remove = get_in_memory_config_elems_to_remove( shed_tool_conf_dict, guids_to_remove ) + # Remove from the in-memory list of config_elems. + config_elems = shed_tool_conf_dict[ 'config_elems' ] + for config_elem in config_elems_to_remove: + # Remove the element from the in-memory list of elements. + config_elems.remove( config_elem ) if config_elem.tag == 'section': key = 'section_%s' % str( config_elem.get( "id" ) ) del app.toolbox.tool_panel[ key ] elif config_elem.tag == 'tool': key = 'tool_%s' % str( config_elem.get( 'guid' ) ) del app.toolbox.tool_panel[ key ] - # Remove the element from the in-memory list of elements. - config_elems.remove( config_elem ) # Update the config_elems of the in-memory shed_tool_conf_dict. shed_tool_conf_dict[ 'config_elems' ] = config_elems app.toolbox.shed_tool_confs[ index ] = shed_tool_conf_dict - if uninstall: - # Persist the altered in-memory version of the tool config. - config_elems_to_xml_file( app, shed_tool_conf_dict ) if app.toolbox_search.enabled: - # If search support for tools is enabled, index the new installed tools. + # If search support for tools is enabled, index tools. app.toolbox_search = ToolBoxSearch( app.toolbox ) def update_repository( current_working_dir, repo_files_dir, changeset_revision ): # Update the cloned repository to changeset_revision. It is imperative that the diff -r c116768aa0e003f579a2bc0cf7da09149305fbea -r 80fa0f99e7e21c148900d25689f036de7023e5dc lib/galaxy/web/controllers/admin_toolshed.py --- a/lib/galaxy/web/controllers/admin_toolshed.py +++ b/lib/galaxy/web/controllers/admin_toolshed.py @@ -80,6 +80,7 @@ """Activate a repository that was deactivated but not uninstalled.""" repository = get_repository( trans, kwd[ 'id' ] ) shed_tool_conf, tool_path, relative_install_dir = self.__get_tool_panel_config_tool_path_install_dir( trans, repository ) + repository_clone_url = self.__generate_clone_url( trans, repository ) repository.deleted = False trans.sa_session.add( repository ) trans.sa_session.flush() @@ -88,19 +89,20 @@ metadata = repository.metadata if 'tool_panel_section' in metadata: if panel_entry_per_tool( metadata[ 'tool_panel_section' ] ): - # {<Tool guid> : { tool_config : <tool_config_file>, id: <ToolSection id>, version : <ToolSection version>, name : <TooSection name>}} tool_panel_dict = metadata[ 'tool_panel_section' ] - # TODO: Fix this to handle the case where the tools are distributed across in more than 1 section. The - # following assumes everything was loaded into 1 section (or no section) in the tool panel. - tool_section_dict = tool_panel_dict[ tool_panel_dict.keys()[ 0 ] ] else: - # The value of tool_panel_section is the old dictionary type like this, so update to the new dictionary type like that above. - # { id: <ToolSection id>, version : <ToolSection version>, name : <TooSection name>} + # The value of tool_panel_section is the old dictionary type. tool_section_dict = metadata[ 'tool_panel_section' ] - original_section_id = tool_section_dict[ 'id' ] + tool_panel_dict = generate_tool_panel_dict_for_repository_tools( metadata, tool_section_dict=tool_section_dict ) + repository.metadata[ 'tool_panel_section' ] = tool_panel_dict + trans.sa_session.add( repository ) + trans.sa_session.flush() else: - # Tools were loaded outside of any panel sections. - original_section_id = '' + # The tool_panel_section was introduced late, so set it's value if its missing in the metadata. + tool_panel_dict = generate_tool_panel_dict_for_repository_tools( metadata ) + repository.metadata[ 'tool_panel_section' ] = tool_panel_dict + trans.sa_session.add( repository ) + trans.sa_session.flush() repository_tools_tups = get_repository_tools_tups( trans.app, metadata ) guids_to_activate = [ repository_tool_tup[1] for repository_tool_tup in repository_tools_tups ] # Make sure we have a tool_version for each guid. @@ -110,53 +112,15 @@ tool_version = trans.model.ToolVersion( tool_id=guid_to_activate, tool_shed_repository=repository ) trans.sa_session.add( tool_version ) trans.sa_session.flush() - if original_section_id in [ '' ]: - # If the repository includes tools, reload them into the tool panel outside of any sections. - self.__add_tools_to_tool_panel( trans, repository, repository_tools_tups, tool_section=None, section_key=None ) - else: - original_section_name = tool_section_dict[ 'name' ] - original_section_version = tool_section_dict[ 'version' ] - section_key = 'section_%s' % str( original_section_id ) - if section_key in trans.app.toolbox.tool_panel: - # Load the repository tools into a section that still exists in the tool panel. - tool_section = trans.app.toolbox.tool_panel[ section_key ] - self.__add_tools_to_tool_panel( trans, repository, repository_tools_tups, tool_section=tool_section, section_key=section_key ) - else: - # Load the repository tools into a section that no longer exists in the tool panel. The section must - # still exist in the tool config since the repository was only deactivated and not uninstalled. - sections_to_load = [] - tool_elems_found = 0 - # Only inspect tool configs that contain installed tool shed repositories. - for shed_tool_conf_dict in trans.app.toolbox.shed_tool_confs: - config_filename = shed_tool_conf_dict[ 'config_filename' ] - log.info( "Parsing the tool configuration %s" % config_filename ) - tree = util.parse_xml( config_filename ) - root = tree.getroot() - tool_path = root.get( 'tool_path' ) - if tool_path is not None: - # Tool configs that contain tools installed from tool shed repositories must have a tool_path attribute. - for elem in root: - if elem.tag == 'section' and \ - elem.get( 'id' ) == original_section_id and \ - elem.get( 'name' ) == original_section_name and \ - elem.get( 'version' ) == original_section_version: - # We've found the section, but we have to make sure it contains the - # correct tool tag set. This is necessary because the shed tool configs - # can include multiple sections of the same id, name and version, each - # containing one or more tool tag sets. - for tool_elem in elem: - if tool_elem.get( 'guid' ) in guids_to_activate: - tool_elems_found += 1 - if elem not in sections_to_load: - sections_to_load.append( elem ) - if tool_elems_found == len( guids_to_activate ): - break - if tool_elems_found == len( guids_to_activate ): - break - if tool_elems_found == len( guids_to_activate ): - break - for elem in sections_to_load: - trans.app.toolbox.load_section_tag_set( elem, trans.app.toolbox.tool_panel, tool_path ) + add_to_tool_panel( trans.app, + repository.name, + repository_clone_url, + repository.changeset_revision, + repository_tools_tups, + repository.owner, + shed_tool_conf, + tool_panel_dict, + new_install=False ) message = 'The <b>%s</b> repository has been activated.' % repository.name status = 'done' return trans.response.send_redirect( web.url_for( controller='admin_toolshed', @@ -245,14 +209,10 @@ repository_tool_panel_keys = [] if 'tool_panel_section' in metadata: if panel_entry_per_tool( metadata[ 'tool_panel_section' ] ): - # The tool_panel_section dictionary contains entries that look like this. - # {<Tool guid> : { tool_config : <tool_config_file>, id: <ToolSection id>, version : <ToolSection version>, name : <TooSection name>}} tool_panel_dict = metadata[ 'tool_panel_section' ] else: - # The tool_panel_section dictionary looks like the following. This is the old definition of the tool_panel_section, - # so update it to the current dictionary like that above. All of the repository tools will be installed in the same - # section or outside of any sections. - # { id: <ToolSection id>, version : <ToolSection version>, name : <TooSection name>} + # The tool_panel_section dictionary is the old definition of the tool_panel_section, so update it to the current dictionary. + # All of the repository tools will be installed in the same section or outside of any sections. tool_section_dict = metadata[ 'tool_panel_section' ] tool_panel_dict = generate_tool_panel_dict_for_repository_tools( metadata, tool_section_dict=tool_section_dict ) repository.metadata[ 'tool_panel_section' ] = tool_panel_dict @@ -496,11 +456,9 @@ # { id: <ToolSection id>, version : <ToolSection version>, name : <TooSection name>} # Later, each tool from a repository could be installed into the tool panel inside or outside a specified ToolSection in the tool panel. if panel_entry_per_tool( metadata[ 'tool_panel_section' ] ): - # {<Tool guid> : { tool_config : <tool_config_file>, id: <ToolSection id>, version : <ToolSection version>, name : <TooSection name>}} tool_panel_dict = metadata[ 'tool_panel_section' ] metadata_dict = generate_metadata( trans.app.toolbox, relative_install_dir, repository_clone_url, tool_panel_dict=tool_panel_dict ) else: - # { id: <ToolSection id>, version : <ToolSection version>, name : <TooSection name>} tool_section_dict = metadata[ 'tool_panel_section' ] metadata_dict = generate_metadata( trans.app.toolbox, relative_install_dir, repository_clone_url, tool_section_dict=tool_section_dict ) else: @@ -537,13 +495,12 @@ metadata = repository.metadata if 'tool_panel_section' in metadata: if panel_entry_per_tool( metadata[ 'tool_panel_section' ] ): - # {<Tool guid> : { tool_config : <tool_config_file>, id: <ToolSection id>, version : <ToolSection version>, name : <TooSection name>}} tool_panel_dict = metadata[ 'tool_panel_section' ] # TODO: Fix this to handle the case where the tools are distributed across in more than 1 ToolSection. The # following assumes everything was loaded into 1 section (or no section) in the tool panel. - tool_section_dict = tool_panel_dict[ tool_panel_dict.keys()[ 0 ] ] + tool_section_dicts = tool_panel_dict[ tool_panel_dict.keys()[ 0 ] ] + tool_section_dict = tool_section_dicts[ 0 ] else: - # { id: <ToolSection id>, version : <ToolSection version>, name : <TooSection name>} tool_section_dict = metadata[ 'tool_panel_section' ] tool_section = generate_tool_section_element_from_dict( tool_section_dict ) tool_panel_dict = generate_tool_panel_dict_for_repository_tools( metadata, tool_section=tool_section ) @@ -575,11 +532,13 @@ if new_tool_panel_section: section_id = new_tool_panel_section.lower().replace( ' ', '_' ) # Update each tool_section dictionary in tool_panel_dict with the new section attributes. - for guid, tool_section_dict in tool_panel_dict.items(): - tool_section_dict[ 'id' ] = section_id - tool_section_dict[ 'name' ] = new_tool_panel_section - tool_section_dict[ 'version' ] = '' - tool_panel_dict[ guid ] = tool_section_dict + for guid, tool_section_dicts in tool_panel_dict.items(): + for dict_index, tool_section_dict in enumerate( tool_section_dicts ): + tool_section_dict[ 'id' ] = section_id + tool_section_dict[ 'name' ] = new_tool_panel_section + tool_section_dict[ 'version' ] = '' + tool_section_dicts[ dict_index ] = tool_section_dict + tool_panel_dict[ guid ] = tool_section_dicts new_section_key = 'section_%s' % str( section_id ) if new_section_key in trans.app.toolbox.tool_panel: # Appending a tool to an existing section in trans.app.toolbox.tool_panel @@ -600,11 +559,13 @@ else: # Update each tool_section dictionary in tool_panel_dict in case the tools used to be contained in a panel section # but are now being moved outside of any panel sections. - for guid, tool_section_dict in tool_panel_dict.items(): - tool_section_dict[ 'id' ] = '' - tool_section_dict[ 'name' ] = '' - tool_section_dict[ 'version' ] = '' - tool_panel_dict[ guid ] = tool_section_dict + for guid, tool_section_dicts in tool_panel_dict.items(): + for dict_index, tool_section_dict in enumerate( tool_section_dicts ): + tool_section_dict[ 'id' ] = '' + tool_section_dict[ 'name' ] = '' + tool_section_dict[ 'version' ] = '' + tool_section_dicts[ dict_index ] = tool_section_dict + tool_panel_dict[ guid ] = tool_section_dicts tool_section = None tool_shed_repository, metadata_dict = load_repository_contents( trans, repository_name=repository.name, @@ -670,13 +631,12 @@ if 'tool_panel_section' in metadata: tool_panel_dict = metadata[ 'tool_panel_section' ] if panel_entry_per_tool( tool_panel_dict ): - # {<Tool guid> : { tool_config : <tool_config_file>, id: <ToolSection id>, version : <ToolSection version>, name : <TooSection name>}} # TODO: Fix this to handle the case where the tools are distributed across in more than 1 ToolSection. The # following assumes everything was loaded into 1 section (or no section) in the tool panel. - tool_panel_dict = tool_panel_dict[ tool_panel_dict.keys()[ 0 ] ] - original_section_name = tool_panel_dict[ 'name' ] + tool_section_dicts = tool_panel_dict[ tool_panel_dict.keys()[ 0 ] ] + tool_section_dict = tool_section_dicts[ 0 ] + original_section_name = tool_section_dict[ 'name' ] else: - # { id: <ToolSection id>, version : <ToolSection version>, name : <TooSection name>} original_section_name = tool_panel_dict[ 'name' ] else: original_section_name = '' @@ -744,10 +704,8 @@ metadata = repository.metadata if 'tool_panel_section' in metadata: if panel_entry_per_tool( metadata[ 'tool_panel_section' ] ): - # {<Tool guid> : { tool_config : <tool_config_file>, id: <ToolSection id>, version : <ToolSection version>, name : <TooSection name>}} tool_panel_dict = metadata[ 'tool_panel_section' ] else: - # { id: <ToolSection id>, version : <ToolSection version>, name : <TooSection name>} tool_section_dict = metadata[ 'tool_panel_section' ] tool_section = generate_tool_section_element_from_dict( tool_section_dict ) tool_panel_dict = generate_tool_panel_dict_for_repository_tools( metadata, tool_section=tool_section ) @@ -833,34 +791,6 @@ metadata=metadata, message=message, status=status ) - def __add_tools_to_tool_panel( self, trans, repository, repository_tools_tups, tool_section=None, section_key=None ): - # Load tools. - if tool_section: - elems = tool_section.elems - for repository_tools_tup in repository_tools_tups: - relative_path, guid, tool = repository_tools_tup - tool.tool_shed = repository.tool_shed - tool.repository_name = repository.name - tool.repository_owner = repository.owner - tool.installed_changeset_revision = repository.installed_changeset_revision - tool.guid = guid - # Set the tool's old_id to the id used before the tool shed existed. - tool.old_id = tool.id - # Set the tool's id to the tool shed guid. - tool.id = guid - if tool_section: - if tool.id not in elems: - elems[ 'tool_%s' % tool.id ] = tool - log.debug( "Reactivated tool id: %s, version: %s" % ( tool.id, tool.version ) ) - else: - if tool.id not in trans.app.toolbox.tools_by_id: - # Allow for the same tool to be loaded into multiple places in the tool panel. - trans.app.toolbox.tools_by_id[ tool.id ] = tool - trans.app.toolbox.tool_panel[ 'tool_%s' % tool.id ] = tool - log.debug( "Reactivated tool id: %s, version: %s" % ( tool.id, tool.version ) ) - if tool_section: - trans.app.toolbox.tool_panel[ section_key ] = tool_section - log.debug( "Appended reactivated tool to section: %s" % tool_section.name ) def __generate_clone_url( self, trans, repository ): """Generate the URL for cloning a repository.""" tool_shed_url = get_url_from_repository_tool_shed( trans.app, repository ) 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: jgoecks: Fix CSS bugs in displaying feature popups in embedded visualizations.
by Bitbucket 01 Mar '12

01 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/c116768aa0e0/ changeset: c116768aa0e0 user: jgoecks date: 2012-03-01 20:19:17 summary: Fix CSS bugs in displaying feature popups in embedded visualizations. affected #: 1 file diff -r f7b12bed396920f2f5908c423b06231653564469 -r c116768aa0e003f579a2bc0cf7da09149305fbea templates/page/display.mako --- a/templates/page/display.mako +++ b/templates/page/display.mako @@ -95,7 +95,7 @@ margin: 0px; } ## Format tables in pages so that they look like they do in the page editor. - .page-body table { + .page-body > table { padding: 8px 5px 5px; min-width: 500px; border: none; @@ -108,7 +108,7 @@ padding: 5px; font-weight: bold; } - .page-body td { + .page-body > table td { width: 25%; padding: 0.2em 0.8em; } 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: jgoecks: Fix bug in embedded visualization drag-zoom.
by Bitbucket 01 Mar '12

01 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/f7b12bed3969/ changeset: f7b12bed3969 user: jgoecks date: 2012-03-01 18:19:28 summary: Fix bug in embedded visualization drag-zoom. affected #: 2 files diff -r 35be930b21bea104bd574d4e9854c6e9c1a58cdb -r f7b12bed396920f2f5908c423b06231653564469 static/scripts/packed/trackster.js --- a/static/scripts/packed/trackster.js +++ b/static/scripts/packed/trackster.js @@ -1,1 +1,1 @@ -var class_module=function(b,a){var c=function(){var f=arguments[0];for(var e=1;e<arguments.length;e++){var d=arguments[e];for(key in d){f[key]=d[key]}}return f};a.extend=c};var requestAnimationFrame=(function(){return window.requestAnimationFrame||window.webkitRequestAnimationFrame||window.mozRequestAnimationFrame||window.oRequestAnimationFrame||window.msRequestAnimationFrame||function(b,a){window.setTimeout(b,1000/60)}})();var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=BEFORE}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=AFTER}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a};var is_overlap=function(c,b){var a=compute_overlap(c,b);return(a!==BEFORE&&a!==AFTER)};var is_deferred=function(a){return("isResolved" in a)};var get_random_color=function(a){if(!a){a="#ffffff"}if(typeof(a)==="string"){a=[a]}for(var j=0;j<a.length;j++){a[j]=parseInt(a[j].slice(1),16)}var n=function(t,s,i){return((t*299)+(s*587)+(i*114))/1000};var e=function(v,u,w,s,i,t){return(Math.max(v,s)-Math.min(v,s))+(Math.max(u,i)-Math.min(u,i))+(Math.max(w,t)-Math.min(w,t))};var g,o,f,k,q,h,r,c,d,b,p,m=false,l=0;do{g=Math.round(Math.random()*16777215);o=(g&16711680)>>16;f=(g&65280)>>8;k=g&255;d=n(o,f,k);m=true;for(var j=0;j<a.length;j++){q=a[j];h=(q&16711680)>>16;r=(q&65280)>>8;c=q&255;b=n(h,r,c);p=e(o,f,k,h,r,c);if((Math.abs(d-b)<40)||(p<200)){m=false;break}}l++}while(!m&&l<=10);return"#"+(16777216+g).toString(16).substr(1,6)};var create_action_icon=function(c,b,a){return $("<a/>").attr("href","javascript:void(0);").attr("title",c).addClass("icon-button").addClass(b).tipsy({gravity:"s"}).click(a)};var trackster_module=function(e,U){var p=e("class").extend,s=e("slotting"),J=e("painters");var ab=function(ac,ad){this.document=ac;this.default_font=ad!==undefined?ad:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};p(ab.prototype,{load_pattern:function(ac,ag){var ad=this.patterns,ae=this.dummy_context,af=new Image();af.src=image_path+ag;af.onload=function(){ad[ac]=ae.createPattern(af,"repeat")}},get_pattern:function(ac){return this.patterns[ac]},new_canvas:function(){var ac=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(ac)}ac.manager=this;return ac}});var n={};var l=function(ac,ad){n[ac.attr("id")]=ad};var m=function(ac,ae,ag,af){ag=".group";var ad={};n[ac.attr("id")]=af;ac.bind("drag",{handle:"."+ae,relative:true},function(ao,ap){var an=$(this);var at=$(this).parent(),ak=at.children(),am=n[$(this).attr("id")],aj,ai,aq,ah,al;ai=$(this).parents(ag);if(ai.length!==0){aq=ai.position().top;ah=aq+ai.outerHeight();if(ap.offsetY<aq){$(this).insertBefore(ai);var ar=n[ai.attr("id")];ar.remove_drawable(am);ar.container.add_drawable_before(am,ar);return}else{if(ap.offsetY>ah){$(this).insertAfter(ai);var ar=n[ai.attr("id")];ar.remove_drawable(am);ar.container.add_drawable(am);return}}}ai=null;for(al=0;al<ak.length;al++){aj=$(ak.get(al));aq=aj.position().top;ah=aq+aj.outerHeight();if(aj.is(ag)&&this!==aj.get(0)&&ap.offsetY>=aq&&ap.offsetY<=ah){if(ap.offsetY-aq<ah-ap.offsetY){aj.find(".content-div").prepend(this)}else{aj.find(".content-div").append(this)}if(am.container){am.container.remove_drawable(am)}n[aj.attr("id")].add_drawable(am);return}}var aj;for(al=0;al<ak.length;al++){aj=$(ak.get(al));if(ap.offsetY<aj.position().top&&!(aj.hasClass("reference-track")||aj.hasClass("intro"))){break}}if(al===ak.length){if(this!==ak.get(al-1)){at.append(this);n[at.attr("id")].move_drawable(am,al)}}else{if(this!==ak.get(al)){$(this).insertBefore(ak.get(al));n[at.attr("id")].move_drawable(am,(ap.deltaY>0?al-1:al))}}}).bind("dragstart",function(){ad["border-top"]=ac.css("border-top");ad["border-bottom"]=ac.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ad)})};U.moveable=m;var aa=16,D=9,A=20,x=100,G=12000,R=400,I=5000,u=100,o="There was an error in indexing this dataset. ",H="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",B="No data for this chrom/contig.",t="Currently indexing... please wait",v="Tool cannot be rerun: ",a="Loading data...",V="Ready for display",O=10,F=20;function W(ad,ac){if(!ac){ac=0}var ae=Math.pow(10,ac);return Math.round(ad*ae)/ae}var c=function(ac){this.num_elements=ac;this.clear()};p(c.prototype,{get:function(ad){var ac=this.key_ary.indexOf(ad);if(ac!==-1){if(this.obj_cache[ad].stale){this.key_ary.splice(ac,1);delete this.obj_cache[ad]}else{this.move_key_to_end(ad,ac)}}return this.obj_cache[ad]},set:function(ad,ae){if(!this.obj_cache[ad]){if(this.key_ary.length>=this.num_elements){var ac=this.key_ary.shift();delete this.obj_cache[ac]}this.key_ary.push(ad)}this.obj_cache[ad]=ae;return ae},move_key_to_end:function(ad,ac){this.key_ary.splice(ac,1);this.key_ary.push(ad)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var P=function(ad,ac){c.call(this,ad);this.track=ac};p(P.prototype,c.prototype,{load_data:function(al,ag,aj,ad,ai){var ak=this.track.view.chrom,af={chrom:ak,low:al,high:ag,mode:aj,resolution:ad,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(af,ai);if(this.track.filters_manager){var am=[];var ac=this.track.filters_manager.filters;for(var ah=0;ah<ac.length;ah++){am.push(ac[ah].name)}af.filter_cols=JSON.stringify(am)}var ae=this;return $.getJSON(this.track.data_url,af,function(an){ae.set_data(al,ag,an)})},get_data:function(ak,ae,ai,ad,ah){var al=this.get(ak,ae);if(al&&(is_deferred(al)||this.track.data_and_mode_compatible(al,ai))){return al}var am,aj,ac,ag,ai,al;for(var af=0;af<this.key_ary.length;af++){am=this.key_ary[af];aj=this.split_key(am);ac=aj[0];ag=aj[1];if(ak>=ac&&ae<=ag){var al=this.obj_cache[am];if(is_deferred(al)||(this.track.data_and_mode_compatible(al,ai)&&this.track.can_subset(al))){this.move_key_to_end(am,af);return al}}}al=this.load_data(ak,ae,ai,ad,ah);this.set_data(ak,ae,al);return al},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(ak,af,aj,ae,ai,ag){var al=this.get(ak,af);if(!(al&&this.track.data_and_mode_compatible(al,aj))){console.log("ERROR: no current data for: ",this.track,ak,af,aj,ae,ai);return}al.stale=true;var ad=ak;if(ag===this.DEEP_DATA_REQ){$.extend(ai,{start_val:al.data.length+1})}else{if(ag===this.BROAD_DATA_REQ){ad=(al.max_high?al.max_high:al.data[al.data.length-1][2])+1}}var ac=this,ah=this.load_data(ad,af,aj,ae,ai);new_data_available=$.Deferred();this.set_data(ak,af,new_data_available);$.when(ah).then(function(am){if(am.data){am.data=al.data.concat(am.data);if(am.max_low){am.max_low=al.max_low}if(am.message){am.message=am.message.replace(/[0-9]+/,am.data.length)}}ac.set_data(ak,af,am);new_data_available.resolve(am)});return new_data_available},get:function(ac,ad){return c.prototype.get.call(this,this.gen_key(ac,ad))},set_data:function(ad,ae,ac){return this.set(this.gen_key(ad,ae),ac)},gen_key:function(ac,ae){var ad=ac+"_"+ae;return ad},split_key:function(ac){return ac.split("_")}});var E=function(ad,ac,ae){P.call(this,ad,ac,ae)};p(E.prototype,P.prototype,c.prototype,{get:P.prototype.get,load_data:function(ac,af,ag,ad,ae){if(ad>1){return{data:null}}return P.prototype.load_data.call(this,ac,af,ag,ad,ae)}});var q=function(ad,ac,af){if(!q.id_counter){q.id_counter=0}this.id=q.id_counter++;this.name=af.name;this.view=ad;this.container=ac;this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name}],saved_values:af.prefs,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=af.drag_handle_class;this.is_overview=false;this.action_icons={};this.content_visible=true;this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(ag){ag.stopPropagation()});var ae=this;this.container_div.hover(function(){ae.icons_div.show()},function(){ae.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};q.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ac){if(ac.content_visible){ac.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ac.hide_contents();ac.content_visible=false}else{ac.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ac.content_visible=true;ac.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(ad){var af=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ac=function(){ad.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ae=function(ag){if((ag.keyCode||ag.which)===27){af()}else{if((ag.keyCode||ag.which)===13){ac()}}};$(window).bind("keypress.check_enter_esc",ae);show_modal("Configure",ad.config.build_form(),{Cancel:af,OK:ac})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ac){$(".tipsy").remove();ac.remove()}}];p(q.prototype,{init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.content_visible){return true}return false},request_draw:function(){},_draw:function(){},to_dict:function(){},update_icons:function(){},set_name:function(ac){this.old_name=this.name;this.name=ac;this.name_div.text(this.name)},revert_name:function(){if(this.old_name){this.name=this.old_name;this.name_div.text(this.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ac=this.view;this.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ad,ai,ah,ag,ac,af){var ae=this;this.action_icons[ad]=$("<a/>").attr("href","javascript:void(0);").attr("title",ai).addClass("icon-button").addClass(ah).tipsy({gravity:"s"}).click(function(){ag(ae)}).appendTo(this.icons_div);if(af){this.action_icons[ad].hide()}},build_action_icons:function(ac){var ae;for(var ad=0;ad<ac.length;ad++){ae=ac[ad];this.add_action_icon(ae.name,ae.title,ae.css_class,ae.on_click_fn,ae.prepend,ae.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){}});var w=function(ad,ac,ae){q.call(this,ad,ac,ae);this.obj_type=ae.obj_type;this.drawables=[]};p(w.prototype,q.prototype,{unpack_drawables:function(ae){this.drawables=[];var ad;for(var ac=0;ac<ae.length;ac++){ad=object_from_template(ae[ac],this);this.add_drawable(ad)}},init:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].init()}},_draw:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac]._draw()}},to_dict:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ad}},add_drawable:function(ac){this.drawables.push(ac);ac.container=this;this.changed()},add_drawable_before:function(ae,ac){this.changed();var ad=this.drawables.indexOf(ac);if(ad!==-1){this.drawables.splice(ad,0,ae);return true}return false},replace_drawable:function(ae,ac,ad){var af=this.drawables.indexOf(ae);if(af!==-1){this.drawables[af]=ac;if(ad){ae.container_div.replaceWith(ac.container_div)}this.changed()}return af},remove_drawable:function(ad){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);ad.container=null;this.changed();return true}return false},move_drawable:function(ad,ae){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);this.drawables.splice(ae,0,ad);this.changed();return true}return false}});var N=function(ad,ac,af){p(af,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});w.call(this,ad,ac,af);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);l(this.container_div,this);l(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new X(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in af){this.unpack_drawables(af.drawables)}if("filters" in af){var ae=this.filters_manager;this.filters_manager=new X(this,af.filters);ae.parent_div.replaceWith(this.filters_manager.parent_div);if(af.filters.visible){this.setup_multitrack_filtering()}}};p(N.prototype,q.prototype,w.prototype,{action_icons_def:[q.prototype.action_icons_def[0],q.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ac){$(".tipsy").remove();ac.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters();ac._restore_filter_managers()}else{ac.setup_multitrack_filtering();ac.request_draw(true)}ac.filters_manager.toggle()}},q.prototype.action_icons_def[2]],build_container_div:function(){var ac=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ac)}return ac},build_header_div:function(){var ac=$("<div/>").addClass("track-header");ac.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(ac);return ac},hide_contents:function(){this.content_div.hide()},show_contents:function(){this.content_div.show();this.request_draw()},update_icons:function(){var ae=this.drawables.length;if(ae===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ae===1){if(this.drawables[0] instanceof h){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var ai,ao=true,ag=this.drawables[0].get_type(),ac=0;for(var al=0;al<ae;al++){ai=this.drawables[al];if(ai.get_type()!==ag){can_composite=false;break}if(ai instanceof d){ac++}}if(ao||ac===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tipsy").remove()}if(ac>1&&ac===this.drawables.length){var ap={},ad;ai=this.drawables[0];for(var ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];ap[ad.name]=[ad]}for(var al=1;al<this.drawables.length;al++){ai=this.drawables[al];for(var ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];if(ad.name in ap){ap[ad.name].push(ad)}}}this.filters_manager.remove_all();var af,ah,aj,am;for(var an in ap){af=ap[an];if(af.length===ac){ah=new S({name:af[0].name,index:af[0].index});this.filters_manager.add_filter(ah)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].filters_manager=this.saved_filters_managers[ac]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ac=0;ac<this.drawables.length;ac++){drawable=this.drawables[ac];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ag=[];for(var ad=0;ad<this.drawables.length;ad++){ag.push(this.drawables[ad].name)}var ae="Composite Track of "+this.drawables.length+" tracks ("+ag.join(", ")+")";var af=new h(this.view,this.view,{name:ae,drawables:this.drawables});var ac=this.container.replace_drawable(this,af,true);af.request_draw()},add_drawable:function(ac){w.prototype.add_drawable.call(this,ac);this.update_icons()},remove_drawable:function(ac){w.prototype.remove_drawable.call(this,ac);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ac=p(w.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ac},request_draw:function(ac,ae){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].request_draw(ac,ae)}}});var Z=function(ac){p(ac,{obj_type:"View"});w.call(this,"View",ac.container,ac);this.chrom=null;this.vis_id=ac.vis_id;this.dbkey=ac.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.init();this.canvas_manager=new ab(this.container.get(0).ownerDocument);this.reset()};p(Z.prototype,w.prototype,{init:function(){var ae=this.container,ac=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ae);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ae);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ae);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;l(this.viewport_container,ac);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var af=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ad=function(ag){if(ag.type==="focusout"||(ag.keyCode||ag.which)===13||(ag.keyCode||ag.which)===27){if((ag.keyCode||ag.which)!==27){ac.go_to($(this).val())}$(this).hide();$(this).val("");ac.location_span.show();ac.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ad).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tipsy({gravity:"n"}).appendTo(this.nav_controls);this.location_span.click(function(){ac.location_span.hide();ac.chrom_select.hide();ac.nav_input.val(ac.chrom+":"+ac.low+"-"+ac.high);ac.nav_input.css("display","inline-block");ac.nav_input.select();ac.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tipsy({gravity:"n"}).click(function(){ac.zoom_out();ac.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tipsy({gravity:"n"}).click(function(){ac.zoom_in();ac.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ac.change_chrom(ac.chrom_select.val())});this.browser_content_div.click(function(ag){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ag){ac.zoom_in(ag.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ag,ah){this.current_x=ah.offsetX}).bind("drag",function(ag,ai){var aj=ai.offsetX-this.current_x;this.current_x=ai.offsetX;var ah=Math.round(aj/ac.viewport_container.width()*(ac.max_high-ac.max_low));ac.move_delta(-ah)});this.overview_close.click(function(){ac.reset_overview()});this.viewport_container.bind("draginit",function(ag,ah){if(ag.clientX>ac.viewport_container.width()-16){return false}}).bind("dragstart",function(ag,ah){ah.original_low=ac.low;ah.current_height=ag.clientY;ah.current_x=ah.offsetX}).bind("drag",function(ai,ak){var ag=$(this);var al=ak.offsetX-ak.current_x;var ah=ag.scrollTop()-(ai.clientY-ak.current_height);ag.scrollTop(ah);ak.current_height=ai.clientY;ak.current_x=ak.offsetX;var aj=Math.round(al/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}).bind("mousewheel",function(ai,ak,ah,ag){if(ah){ah*=50;var aj=Math.round(-ah/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}});this.top_labeltrack.bind("dragstart",function(ag,ah){return $("<div />").css({height:ac.browser_content_div.height()+ac.top_labeltrack.height()+ac.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ak,al){$(al.proxy).css({left:Math.min(ak.pageX,al.startX),width:Math.abs(ak.pageX-al.startX)});var ah=Math.min(ak.pageX,al.startX)-ac.container.offset().left,ag=Math.max(ak.pageX,al.startX)-ac.container.offset().left,aj=(ac.high-ac.low),ai=ac.viewport_container.width();ac.update_location(Math.round(ah/ai*aj)+ac.low,Math.round(ag/ai*aj)+ac.low)}).bind("dragend",function(al,am){var ah=Math.min(al.pageX,am.startX),ag=Math.max(al.pageX,am.startX),aj=(ac.high-ac.low),ai=ac.viewport_container.width(),ak=ac.low;ac.low=Math.round(ah/ai*aj)+ak;ac.high=Math.round(ag/ai*aj)+ak;$(am.proxy).remove();ac.request_redraw()});this.add_label_track(new Y(this,{content_div:this.top_labeltrack}));this.add_label_track(new Y(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){ac.resize_window()});$(document).bind("redraw",function(){ac.redraw()});this.reset();$(window).trigger("resize")},changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},update_location:function(ac,ad){this.location_span.text(commatize(ac)+" - "+commatize(ad));this.nav_input.val(this.chrom+":"+commatize(ac)+"-"+commatize(ad))},load_chroms:function(ae){ae.num=u;ae.dbkey=this.dbkey;var ac=this,ad=$.Deferred();$.ajax({url:chrom_url,data:ae,dataType:"json",success:function(ag){if(ag.chrom_info.length===0){alert("Invalid chromosome: "+ae.chrom);return}if(ag.reference){ac.add_label_track(new y(ac))}ac.chrom_data=ag.chrom_info;var aj='<option value="">Select Chrom/Contig</option>';for(var ai=0,af=ac.chrom_data.length;ai<af;ai++){var ah=ac.chrom_data[ai].chrom;aj+='<option value="'+ah+'">'+ah+"</option>"}if(ag.prev_chroms){aj+='<option value="previous">Previous '+u+"</option>"}if(ag.next_chroms){aj+='<option value="next">Next '+u+"</option>"}ac.chrom_select.html(aj);ac.chrom_start_index=ag.start_index;ad.resolve(ag)},error:function(){alert("Could not load chroms for this dbkey:",ac.dbkey)}});return ad},change_chrom:function(ah,ad,aj){if(!ah||ah==="None"){return}var ae=this;if(ah==="previous"){ae.load_chroms({low:this.chrom_start_index-u});return}if(ah==="next"){ae.load_chroms({low:this.chrom_start_index+u});return}var ai=$.grep(ae.chrom_data,function(ak,al){return ak.chrom===ah})[0];if(ai===undefined){ae.load_chroms({chrom:ah},function(){ae.change_chrom(ah,ad,aj)});return}else{if(ah!==ae.chrom){ae.chrom=ah;ae.chrom_select.val(ae.chrom);ae.max_high=ai.len-1;ae.reset();ae.request_redraw(true);for(var ag=0,ac=ae.drawables.length;ag<ac;ag++){var af=ae.drawables[ag];if(af.init){af.init()}}if(ae.reference_track){ae.reference_track.init()}}if(ad!==undefined&&aj!==undefined){ae.low=Math.max(ad,0);ae.high=Math.min(aj,ae.max_high)}ae.reset_overview();ae.request_redraw()}},go_to:function(ag){ag=ag.replace(/ |,/g,"");var ak=this,ac,af,ad=ag.split(":"),ai=ad[0],aj=ad[1];if(aj!==undefined){try{var ah=aj.split("-");ac=parseInt(ah[0],10);af=parseInt(ah[1],10)}catch(ae){return false}}ak.change_chrom(ai,ac,af)},move_fraction:function(ae){var ac=this;var ad=ac.high-ac.low;this.move_delta(ae*ad)},move_delta:function(ae){var ac=this;var ad=ac.high-ac.low;if(ac.low-ae<ac.max_low){ac.low=ac.max_low;ac.high=ac.max_low+ad}else{if(ac.high-ae>ac.max_high){ac.high=ac.max_high;ac.low=ac.max_high-ad}else{ac.high-=ae;ac.low-=ae}}ac.request_redraw()},add_drawable:function(ac){w.prototype.add_drawable.call(this,ac);ac.init();this.changed();this.update_intro_div()},add_label_track:function(ac){ac.view=this;ac.init();this.label_tracks.push(ac)},remove_drawable:function(ae,ad){w.prototype.remove_drawable.call(this,ae);if(ad){var ac=this;ae.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ak,ac,aj,ad){var ai=this,ag=(ad?[ad]:ai.drawables),ae;var ad;for(var ah=0;ah<ag.length;ah++){ad=ag[ah];ae=-1;for(var af=0;af<ai.tracks_to_be_redrawn.length;af++){if(ai.tracks_to_be_redrawn[af][0]===ad){ae=af;break}}if(ae<0){ai.tracks_to_be_redrawn.push([ad,ac,aj])}else{ai.tracks_to_be_redrawn[ah][1]=ac;ai.tracks_to_be_redrawn[ah][2]=aj}}requestAnimationFrame(function(){ai._redraw(ak)})},_redraw:function(am){var aj=this.low,af=this.high;if(aj<this.max_low){aj=this.max_low}if(af>this.max_high){af=this.max_high}var al=this.high-this.low;if(this.high!==0&&al<this.min_separation){af=aj+this.min_separation}this.low=Math.floor(aj);this.high=Math.ceil(af);this.resolution_b_px=(this.high-this.low)/this.viewport_container.width();this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var ac=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ai=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var an=13;this.overview_box.css({left:ac,width:Math.max(an,ai)}).show();if(ai<an){this.overview_box.css("left",ac-(an-ai)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ac,width:ai})}this.update_location(this.low,this.high);if(!am){var ae,ad,ak;for(var ag=0,ah=this.tracks_to_be_redrawn.length;ag<ah;ag++){ae=this.tracks_to_be_redrawn[ag][0];ad=this.tracks_to_be_redrawn[ag][1];ak=this.tracks_to_be_redrawn[ag][2];if(ae){ae._draw(ad,ak)}}this.tracks_to_be_redrawn=[];for(ag=0,ah=this.label_tracks.length;ag<ah;ag++){this.label_tracks[ag]._draw()}}},zoom_in:function(ad,ae){if(this.max_high===0||this.high-this.low<this.min_separation){return}var af=this.high-this.low,ag=af/2+this.low,ac=(af/this.zoom_factor)/2;if(ad){ag=ad/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ag-ac);this.high=Math.round(ag+ac);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ad=this.high-this.low,ae=ad/2+this.low,ac=(ad*this.zoom_factor)/2;this.low=Math.round(ae-ac);this.high=Math.round(ae+ac);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ae){if(this.overview_drawable){if(this.overview_drawable.dataset_id===ae.dataset_id){return}this.overview_viewport.find(".track").remove()}var ad=ae.copy({content_div:this.overview_viewport}),ac=this;ad.header_div.hide();ad.is_overview=true;ac.overview_drawable=ad;this.overview_drawable.postdraw_actions=function(){ac.overview_highlight.show().height(ac.overview_drawable.content_div.height());ac.overview_viewport.height(ac.overview_drawable.content_div.height()+ac.overview_box.outerHeight());ac.overview_close.show();ac.resize_window()};ac.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".tipsy").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var r=function(ae,aj,af){this.track=ae;this.name=aj.name;this.params=[];var aq=aj.params;for(var ag=0;ag<aq.length;ag++){var al=aq[ag],ad=al.name,ap=al.label,ah=unescape(al.html),ar=al.value,an=al.type;if(an==="number"){this.params.push(new f(ad,ap,ah,(ad in af?af[ad]:ar),al.min,al.max))}else{if(an==="select"){this.params.push(new L(ad,ap,ah,(ad in af?af[ad]:ar)))}else{console.log("WARNING: unrecognized tool parameter type:",ad,an)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(au){au.stopPropagation()}).click(function(au){au.stopPropagation()}).bind("dblclick",function(au){au.stopPropagation()});var ao=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var am=this.params;var ak=this;$.each(this.params,function(av,ay){var ax=$("<div>").addClass("param-row").appendTo(ak.parent_div);var au=$("<div>").addClass("param-label").text(ay.label).appendTo(ax);var aw=$("<div/>").addClass("param-input").html(ay.html).appendTo(ax);aw.find(":input").val(ay.value);$("<div style='clear: both;'/>").appendTo(ax)});this.parent_div.find("input").click(function(){$(this).select()});var at=$("<div>").addClass("param-row").appendTo(this.parent_div);var ai=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(at);var ac=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(at);var ak=this;ac.click(function(){ak.run_on_region()});ai.click(function(){ak.run_on_dataset()});if("visible" in af&&af.visible){this.parent_div.show()}};p(r.prototype,{update_params:function(){for(var ac=0;ac<this.params.length;ac++){this.params[ac].update_value()}},state_dict:function(){var ad={};for(var ac=0;ac<this.params.length;ac++){ad[this.params[ac].name]=this.params[ac].value}ad.visible=this.parent_div.is(":visible");return ad},get_param_values_dict:function(){var ac={};this.parent_div.find(":input").each(function(){var ad=$(this).attr("name"),ae=$(this).val();ac[ad]=JSON.stringify(ae)});return ac},get_param_values:function(){var ad=[];var ac={};this.parent_div.find(":input").each(function(){var ae=$(this).attr("name"),af=$(this).val();if(ae){ad[ad.length]=af}});return ad},run_on_dataset:function(){var ac=this;ac.run({dataset_id:this.track.original_dataset_id,tool_id:ac.name},null,function(ad){show_modal(ac.name+" is Running",ac.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ad={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},ah=this.track,ae=ad.tool_id+ah.tool_region_and_parameters_str(ad.chrom,ad.low,ad.high),ac;if(ah.container===view){var ag=new N(view,view,{name:this.name});var af=ah.container.replace_drawable(ah,ag,false);ag.container_div.insertBefore(ah.view.content_div.children()[af]);ag.add_drawable(ah);ah.container_div.appendTo(ag.content_div);ac=ag}else{ac=ah.container}var ai=new ah.constructor(view,ac,{name:ae,hda_ldda:"hda"});ai.init_for_tool_data();ai.change_mode(ah.mode);ai.set_filters_manager(ah.filters_manager.copy(ai));ai.update_icons();ac.add_drawable(ai);ai.content_div.text("Starting job.");this.update_params();this.run(ad,ai,function(aj){ai.dataset_id=aj.dataset_id;ai.content_div.text("Running job.");ai.init()})},run:function(ad,ae,af){$.extend(ad,this.get_param_values_dict());var ac=function(){$.getJSON(rerun_tool_url,ad,function(ag){if(ag==="no converter"){ae.container_div.addClass("error");ae.content_div.text(H)}else{if(ag.error){ae.container_div.addClass("error");ae.content_div.text(v+ag.message)}else{if(ag==="pending"){ae.container_div.addClass("pending");ae.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(ac,2000)}else{af(ag)}}}})};ac()}});var L=function(ad,ac,ae,af){this.name=ad;this.label=ac;this.html=$(ae);this.value=af};p(L.prototype,{update_value:function(){this.value=$(this.html).val()}});var f=function(ae,ad,ag,ah,af,ac){L.call(this,ae,ad,ag,ah);this.min=af;this.max=ac};p(f.prototype,L.prototype,{update_value:function(){L.prototype.update_value.call(this);this.value=parseFloat(this.value)}});var g=function(ac){this.manager=null;this.name=ac.name;this.index=ac.index;this.tool_id=ac.tool_id;this.tool_exp_name=ac.tool_exp_name};p(g.prototype,{to_dict:function(){return{name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name}}});var S=function(al){g.call(this,al);this.low=("low" in al?al.low:-Number.MAX_VALUE);this.high=("high" in al?al.high:Number.MAX_VALUE);this.min=("min" in al?al.min:Number.MAX_VALUE);this.max=("max" in al?al.max:-Number.MAX_VALUE);this.container=null;this.slider=null;this.slider_label=null;var ah=function(am,an,ao){am.click(function(){var au=an.text(),ar=parseFloat(ao.slider("option","max")),aq=(ar<=1?4:ar<=1000000?ar.toString().length:6),at=false,ap=$(this).parents(".slider-row");ap.addClass("input");if(ao.slider("option","values")){aq=2*aq+1;at=true}an.text("");$("<input type='text'/>").attr("size",aq).attr("maxlength",aq).attr("value",au).appendTo(an).focus().select().click(function(av){av.stopPropagation()}).blur(function(){$(this).remove();an.text(au);ap.removeClass("input")}).keyup(function(az){if(az.keyCode===27){$(this).trigger("blur")}else{if(az.keyCode===13){var ax=ao.slider("option","min"),av=ao.slider("option","max"),ay=function(aA){return(isNaN(aA)||aA>av||aA<ax)},aw=$(this).val();if(!at){aw=parseFloat(aw);if(ay(aw)){alert("Parameter value must be in the range ["+ax+"-"+av+"]");return $(this)}}else{aw=aw.split("-");aw=[parseFloat(aw[0]),parseFloat(aw[1])];if(ay(aw[0])||ay(aw[1])){alert("Parameter value must be in the range ["+ax+"-"+av+"]");return $(this)}}ao.slider((at?"values":"value"),aw);ap.removeClass("input")}}})})};var ad=this;ad.parent_div=$("<div/>").addClass("filter-row slider-row");var ac=$("<div/>").addClass("elt-label").appendTo(ad.parent_div),aj=$("<span/>").addClass("slider-name").text(ad.name+" ").appendTo(ac),ae=$("<span/>").text(this.low+"-"+this.high),af=$("<span/>").addClass("slider-value").appendTo(ac).append("[").append(ae).append("]");ad.values_span=ae;var ai=$("<div/>").addClass("slider").appendTo(ad.parent_div);ad.control_element=$("<div/>").attr("id",ad.name+"-filter-control").appendTo(ai);var ag=[0,0];ad.control_element.slider({range:true,min:this.min,max:this.max,step:this.get_slider_step(this.min,this.max),values:[this.low,this.high],slide:function(am,an){ad.slide(am,an)},change:function(am,an){ad.control_element.slider("option","slide").call(ad.control_element,am,an)}});ad.slider=ad.control_element;ad.slider_label=ae;ah(af,ae,ad.control_element);var ak=$("<div/>").addClass("display-controls").appendTo(ad.parent_div);this.transparency_icon=create_action_icon("Use filter for data transparency","layer-transparent",function(){if(ad.manager.alpha_filter!==ad){ad.manager.alpha_filter=ad;ad.manager.parent_div.find(".layer-transparent").removeClass("active").hide();ad.transparency_icon.addClass("active").show()}else{ad.manager.alpha_filter=null;ad.transparency_icon.removeClass("active")}ad.manager.track.request_draw(true,true)}).appendTo(ak).hide();this.height_icon=create_action_icon("Use filter for data height","arrow-resize-090",function(){if(ad.manager.height_filter!==ad){ad.manager.height_filter=ad;ad.manager.parent_div.find(".arrow-resize-090").removeClass("active").hide();ad.height_icon.addClass("active").show()}else{ad.manager.height_filter=null;ad.height_icon.removeClass("active")}ad.manager.track.request_draw(true,true)}).appendTo(ak).hide();ad.parent_div.hover(function(){ad.transparency_icon.show();ad.height_icon.show()},function(){if(ad.manager.alpha_filter!==ad){ad.transparency_icon.hide()}if(ad.manager.height_filter!==ad){ad.height_icon.hide()}});$("<div style='clear: both;'/>").appendTo(ad.parent_div)};p(S.prototype,{to_dict:function(){var ac=g.prototype.to_dict.call(this);return p(ac,{type:"number",min:this.min,max:this.max,low:this.low,high:this.high})},copy:function(){return new S({name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name})},get_slider_step:function(ae,ac){var ad=ac-ae;return(ad<=2?0.01:1)},slide:function(ad,ae){var ac=ae.values;this.values_span.text(ac[0]+"-"+ac[1]);this.low=ac[0];this.high=ac[1];this.manager.track.request_draw(true,true)},applies_to:function(ac){if(ac.length>this.index){return true}return false},keep:function(ac){if(!this.applies_to(ac)){return true}var ad=ac[this.index];return(isNaN(ad)||(ad>=this.low&&ad<=this.high))},update_attrs:function(ad){var ac=false;if(!this.applies_to(ad)){return ac}if(ad[this.index]<this.min){this.min=Math.floor(ad[this.index]);ac=true}if(ad[this.index]>this.max){this.max=Math.ceil(ad[this.index]);ac=true}return ac},update_ui_elt:function(){if(this.min!==this.max){this.parent_div.show()}else{this.parent_div.hide()}var ad=this.slider.slider("option","min"),ac=this.slider.slider("option","max");if(this.min<ad||this.max>ac){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",this.get_slider_step(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var X=function(ae,ak){this.track=ae;this.alpha_filter=null;this.height_filter=null;this.filters=[];this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(am){am.stopPropagation()}).click(function(am){am.stopPropagation()}).bind("dblclick",function(am){am.stopPropagation()}).bind("keydown",function(am){am.stopPropagation()});if(ak&&"filters" in ak){var ac=("alpha_filter" in ak?ak.alpha_filter:null),af=("height_filter" in ak?ak.height_filter:null),ah=ak.filters,ad;for(var ai=0;ai<ah.length;ai++){if(ah[ai].type==="number"){ad=new S(ah[ai]);this.add_filter(ad);if(ad.name===ac){this.alpha_filter=ad;ad.transparency_icon.addClass("active").show()}if(ad.name===af){this.height_filter=ad;ad.height_icon.addClass("active").show()}}else{console.log("ERROR: unsupported filter: ",name,type)}}if("visible" in ak&&ak.visible){this.parent_div.show()}}if(this.filters.length!==0){var al=$("<div/>").addClass("param-row").appendTo(this.parent_div);var aj=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(al);var ag=this;aj.click(function(){ag.run_on_dataset()})}};p(X.prototype,{show:function(){this.parent_div.show()},hide:function(){this.parent_div.hide()},toggle:function(){this.parent_div.toggle()},visible:function(){return this.parent_div.is(":visible")},to_dict:function(){var af={},ae=[],ad;for(var ac=0;ac<this.filters.length;ac++){ad=this.filters[ac];ae.push(ad.to_dict())}af.filters=ae;af.alpha_filter=(this.alpha_filter?this.alpha_filter.name:null);af.height_filter=(this.height_filter?this.height_filter.name:null);af.visible=this.parent_div.is(":visible");return af},copy:function(ad){var ae=new X(ad);for(var ac=0;ac<this.filters.length;ac++){ae.add_filter(this.filters[ac].copy())}return ae},add_filter:function(ac){ac.manager=this;this.parent_div.append(ac.parent_div);this.filters.push(ac)},remove_all:function(){this.filters=[];this.parent_div.children().remove()},init_filters:function(){for(var ac=0;ac<this.filters.length;ac++){var ad=this.filters[ac];ad.update_ui_elt()}},clear_filters:function(){for(var ac=0;ac<this.filters.length;ac++){var ad=this.filters[ac];ad.slider.slider("option","values",[ad.min,ad.max])}this.alpha_filter=null;this.height_filter=null;this.parent_div.find(".icon-button").hide()},run_on_dataset:function(){var ak=function(ao,am,an){if(!(am in ao)){ao[am]=an}return ao[am]};var ae={},ac,ad,af;for(var ag=0;ag<this.filters.length;ag++){ac=this.filters[ag];if(ac.tool_id){if(ac.min!==ac.low){ad=ak(ae,ac.tool_id,[]);ad[ad.length]=ac.tool_exp_name+" >= "+ac.low}if(ac.max!==ac.high){ad=ak(ae,ac.tool_id,[]);ad[ad.length]=ac.tool_exp_name+" <= "+ac.high}}}var ai=[];for(var al in ae){ai[ai.length]=[al,ae[al]]}var aj=ai.length;(function ah(at,ap){var an=ap[0],ao=an[0],ar=an[1],aq="("+ar.join(") and (")+")",am={cond:aq,input:at,target_dataset_id:at,tool_id:ao},ap=ap.slice(1);$.getJSON(run_tool_url,am,function(au){if(au.error){show_modal("Filter Dataset","Error running tool "+ao,{Close:hide_modal})}else{if(ap.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{ah(au.dataset_id,ap)}}})})(this.track.dataset_id,ai)}});var z=function(ac,ad){J.Scaler.call(this,ad);this.filter=ac};z.prototype.gen_val=function(ac){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ac[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var C=function(ac){this.track=ac.track;this.params=ac.params;this.values={};this.restore_values((ac.saved_values?ac.saved_values:{}));this.onchange=ac.onchange};p(C.prototype,{restore_values:function(ac){var ad=this;$.each(this.params,function(ae,af){if(ac[af.key]!==undefined){ad.values[af.key]=ac[af.key]}else{ad.values[af.key]=af.default_value}})},build_form:function(){var af=this;var ac=$("<div />");var ae;function ad(aj,ag){for(var an=0;an<aj.length;an++){ae=aj[an];if(ae.hidden){continue}var ah="param_"+an;var ar=af.values[ae.key];var av=$("<div class='form-row' />").appendTo(ag);av.append($("<label />").attr("for",ah).text(ae.label+":"));if(ae.type==="bool"){av.append($('<input type="checkbox" />').attr("id",ah).attr("name",ah).attr("checked",ar))}else{if(ae.type==="text"){av.append($('<input type="text"/>').attr("id",ah).val(ar).click(function(){$(this).select()}))}else{if(ae.type==="select"){var ap=$("<select />").attr("id",ah);for(var al=0;al<ae.options.length;al++){$("<option/>").text(ae.options[al].label).attr("value",ae.options[al].value).appendTo(ap)}ap.val(ar);av.append(ap)}else{if(ae.type==="color"){var au=$("<div/>").appendTo(av),ao=$("<input />").attr("id",ah).attr("name",ah).val(ar).css("float","left").appendTo(au).click(function(ax){$(".tipsy").hide();var aw=$(this).siblings(".tipsy");aw.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(aw).height()/2)+($(this).height()/2)}).show();aw.click(function(ay){ay.stopPropagation()});$(document).bind("click.color-picker",function(){aw.hide();$(document).unbind("click.color-picker")});ax.stopPropagation()}),am=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(au).attr("title","Set new random color").tipsy({gravity:"s"}),aq=$("<div class='tipsy tipsy-west' style='position: absolute;' />").appendTo(au).hide(),ai=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(aq),at=$("<div/>").appendTo(ai),ak=$.farbtastic(at,{width:100,height:100,callback:ao,color:ar});au.append($("<div/>").css("clear","both"));(function(aw){am.click(function(){aw.setColor(get_random_color())})})(ak)}else{av.append($("<input />").attr("id",ah).attr("name",ah).val(ar))}}}}if(ae.help){av.append($("<div class='help'/>").text(ae.help))}}}ad(this.params,ac);return ac},update_from_form:function(ac){var ae=this;var ad=false;$.each(this.params,function(af,ah){if(!ah.hidden){var ai="param_"+af;var ag=ac.find("#"+ai).val();if(ah.type==="float"){ag=parseFloat(ag)}else{if(ah.type==="int"){ag=parseInt(ag)}else{if(ah.type==="bool"){ag=ac.find("#"+ai).is(":checked")}}}if(ag!==ae.values[ah.key]){ae.values[ah.key]=ag;ad=true}}});if(ad){this.onchange();this.track.changed()}}});var b=function(ac,af,ae,ad,ag){this.track=ac;this.index=af;var ah=this.track._get_tile_bounds(af,ae);this.low=ah[0];this.high=ah[1];this.resolution=ae;this.html_elt=$("<div class='track-tile'/>").append(ad);this.data=ag;this.stale=false};b.prototype.predisplay_actions=function(){};var k=function(ac,af,ae,ad,ag,ah){b.call(this,ac,af,ae,ad,ag);this.max_val=ah};p(k.prototype,b.prototype);var M=function(af,ak,ag,ae,ai,ao,aj,ap,ad,am){b.call(this,af,ak,ag,ae,ai);this.mode=aj;this.all_slotted=ad;this.feature_mapper=am;this.has_icons=false;if(ap){this.has_icons=true;var al=this;ae=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:A-1,width:ae.width}).prependTo(this.html_elt);var an=ai.length,ah=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+an+" features in this region were obtained from server. Click to get more data including depth").tipsy({gravity:"s"}).appendTo(message_div),ac=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+an+" features in this region were obtained from server. Click to get more data excluding depth").tipsy({gravity:"s"}).appendTo(message_div);ah.click(function(){al.stale=true;af.data_manager.get_more_data(al.low,al.high,af.mode,al.resolution,{},af.data_manager.DEEP_DATA_REQ);$(".tipsy").hide();af.request_draw()}).dblclick(function(aq){aq.stopPropagation()});ac.click(function(){al.stale=true;af.data_manager.get_more_data(al.low,al.high,af.mode,al.resolution,{},af.data_manager.BROAD_DATA_REQ);$(".tipsy").hide();af.request_draw()}).dblclick(function(aq){aq.stopPropagation()})}};p(M.prototype,b.prototype);M.prototype.predisplay_actions=function(){var ad=this,ac={};if(ad.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).siblings(".feature-popup").remove()}).mousemove(function(ao){if(!this.hovered){return}var aj=$(this).offset(),an=ao.pageX-aj.left,am=ao.pageY-aj.top,at=ad.feature_mapper.get_feature_data(an,am),ak=(at?at[0]:null);$(this).siblings(".feature-popup").each(function(){if(!ak||$(this).attr("id")!==ak.toString()){$(this).remove()}});if(at){var af=ac[ak];if(!af){var ak=at[0],ap={name:at[3],start:at[1],end:at[2],strand:at[4]},ai=ad.track.filters_manager.filters,ah;for(var al=0;al<ai.length;al++){ah=ai[al];ap[ah.name]=at[ah.index]}var af=$("<div/>").attr("id",ak).addClass("feature-popup"),au=$("<table/>"),ar,aq,av;for(ar in ap){aq=ap[ar];av=$("<tr/>").appendTo(au);$("<th/>").appendTo(av).text(ar);$("<td/>").attr("align","left").appendTo(av).text(typeof(aq)==="number"?W(aq,2):aq)}af.append($("<div class='feature-popup-inner'>").append(au));ac[ak]=af}af.appendTo($(ad.html_elt).parent());var ag=an+parseInt(ad.html_elt.css("left"))-af.width()/2,ae=am+parseInt(ad.html_elt.css("top"))+7;af.css("left",ag+"px").css("top",ae+"px")}else{if(!ao.isPropagationStopped()){ao.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ao)})}}}).mouseleave(function(){$(this).siblings(".feature-popup").remove()})};var i=function(ad,ac,ae){p(ae,{drag_handle_class:"draghandle"});q.call(this,ad,ac,ae);this.data_url=("data_url" in ae?ae.data_url:default_data_url);this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ae?ae.data_query_wait:I);this.dataset_check_url=converted_datasets_state_url;this.data_manager=("data_manager" in ae?ae.data_manager:new P(F,this));this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div)}};p(i.prototype,q.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},q.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(ac){ac.view.set_overview(ac)}},q.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters()}else{ac.filters_manager.init_filters()}ac.filters_manager.toggle()}},{name:"tools_icon",title:"Tools",css_class:"tools-icon",on_click_fn:function(ac){ac.dynamic_tool_div.toggle();if(ac.dynamic_tool_div.is(":visible")){ac.set_name(ac.name+ac.tool_region_and_parameters_str())}else{ac.revert_name()}$(".tipsy").remove()}},q.prototype.action_icons_def[2]],can_draw:function(){if(this.dataset_id&&q.prototype.can_draw.call(this)){return true}return false},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var ac=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ac)}this.name_div=$("<div/>").addClass("track-name").appendTo(ac).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ac},set_display_modes:function(af,ai){this.display_modes=af;this.mode=(ai?ai:(this.config&&this.config.values.mode?this.config.values.mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ad=this,ag={};for(var ae=0,ac=ad.display_modes.length;ae<ac;ae++){var ah=ad.display_modes[ae];ag[ah]=function(aj){return function(){ad.change_mode(aj);ad.icons_div.show();ad.container_div.mouseleave(function(){ad.icons_div.hide()})}}(ah)}make_popupmenu(this.action_icons.mode_icon,ag)},build_action_icons:function(){q.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.content_div.children().remove();this.content_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.content_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof Y){return"LabelTrack"}else{if(this instanceof y){return"ReferenceTrack"}else{if(this instanceof j){return"LineTrack"}else{if(this instanceof T){return"ReadTrack"}else{if(this instanceof Q){return"VcfTrack"}else{if(this instanceof h){return"CompositeTrack"}else{if(this instanceof d){return"FeatureTrack"}}}}}}}return""},init:function(){var ad=this;ad.enabled=false;ad.tile_cache.clear();ad.data_manager.clear();ad.content_div.css("height","auto");ad.content_div.children().remove();ad.container_div.removeClass("nodata error pending");if(!ad.dataset_id){return}var ac=$.Deferred();$.getJSON(converted_datasets_state_url,{hda_ldda:ad.hda_ldda,dataset_id:ad.dataset_id,chrom:ad.view.chrom},function(ae){if(!ae||ae==="error"||ae.kind==="error"){ad.container_div.addClass("error");ad.content_div.text(o);if(ae.message){var af=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ae.message+"</pre>",{Close:hide_modal})});ad.content_div.append(af)}}else{if(ae==="no converter"){ad.container_div.addClass("error");ad.content_div.text(H)}else{if(ae==="no data"||(ae.data!==undefined&&(ae.data===null||ae.data.length===0))){ad.container_div.addClass("nodata");ad.content_div.text(B)}else{if(ae==="pending"){ad.container_div.addClass("pending");ad.content_div.text(t);setTimeout(function(){ad.init()},ad.data_query_wait)}else{if(ae.status==="data"){if(ae.valid_chroms){ad.valid_chroms=ae.valid_chroms;ad.update_icons()}ad.content_div.text(V);if(ad.view.chrom){ad.content_div.text("");ad.content_div.css("height",ad.height_px+"px");ad.enabled=true;$.when(ad.predraw_init()).done(function(){ac.resolve();ad.container_div.removeClass("nodata error pending");ad.request_draw()})}else{ac.resolve()}}}}}}});this.update_icons();return ac},predraw_init:function(){}});var K=function(ae,ad,af){i.call(this,ae,ad,af);var ac=this,ae=ac.view;m(ac.container_div,ac.drag_handle_class,".group",ac);this.filters_manager=new X(this,("filters" in af?af.filters:null));this.filters_available=false;this.tool=("tool" in af&&af.tool?new r(this,af.tool,af.tool_state):null);this.tile_cache=new c(O);if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}if(af.mode){this.change_mode(af.mode)}};p(K.prototype,q.prototype,i.prototype,{action_icons_def:i.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ac){$(".tipsy").remove();ac.slotters[ac.view.resolution_px_b].max_rows*=2;ac.request_draw(true)},hide:true}]),copy:function(ac){var ad=this.to_dict();p(ad,{data_manager:this.data_manager});var ae=new this.constructor(this.view,ac,ad);ae.change_mode(this.mode);ae.enabled=this.enabled;return ae},set_filters_manager:function(ac){this.filters_manager=ac;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},change_mode:function(ad){var ac=this;ac.mode=ad;ac.config.values.mode=ad;ac.tile_cache.clear();ac.request_draw();this.action_icons.mode_icon.attr("title","Set display mode (now: "+ac.mode+")");return ac},update_icons:function(){var ac=this;if(ac.filters_available){ac.action_icons.filters_icon.show()}else{ac.action_icons.filters_icon.hide()}if(ac.tool){ac.action_icons.tools_icon.show()}else{ac.action_icons.tools_icon.hide()}},_gen_tile_cache_key:function(ad,ae,ac){return ad+"_"+ae+"_"+ac},request_draw:function(ad,ac){this.view.request_redraw(false,ad,ac,this)},_draw:function(ad,an){if(!this.can_draw()){return}var al=this.view.low,ah=this.view.high,aj=ah-al,ae=this.view.container.width(),ap=this.view.resolution_px_b,ag=this.view.resolution_b_px;if(this.is_overview){al=this.view.max_low;ah=this.view.max_high;ag=Math.pow(RESOLUTION,Math.ceil(Math.log((view.max_high-view.max_low)/R)/Math.log(RESOLUTION)));ap=ae/(view.max_high-view.max_low)}this.content_div.children().addClass("remove");this.max_height=0;var ac=Math.floor(al/(ag*R)),ak=true,ao=[],ai=function(aq){return(aq&&"track" in aq)};while((ac*R*ag)<ah){var am=this.draw_helper(ad,ae,ac,ag,this.content_div,ap);if(ai(am)){ao.push(am)}else{ak=false}ac+=1}if(!an){this.content_div.children(".remove").remove()}var af=this;if(ak){this.content_div.children(".remove").remove();af.postdraw_actions(ao,ae,ap,an)}},postdraw_actions:function(af,ag,ai,ac){var ae=this;var ah=false;for(var ad=0;ad<af.length;ad++){if(af[ad].has_icons){ah=true;break}}if(ah){for(var ad=0;ad<af.length;ad++){tile=af[ad];if(!tile.has_icons){tile.html_elt.css("padding-top",A)}}}},draw_helper:function(ac,ao,au,ar,ah,ai,ap){var an=this,ax=this._gen_tile_cache_key(ao,ai,au),af=this._get_tile_bounds(au,ar),av=af[0],ad=af[1];if(!ap){ap={}}var aw=(ac?undefined:an.tile_cache.get(ax));if(aw){an.show_tile(aw,ah,ai);return aw}var al=true;var at=an.data_manager.get_data(av,ad,an.mode,ar,an.data_url_extra_params);if(is_deferred(at)){al=false}var aj;if(view.reference_track&&ai>view.canvas_manager.char_width_px){aj=view.reference_track.data_manager.get_data(av,ad,an.mode,ar,view.reference_track.data_url_extra_params);if(is_deferred(aj)){al=false}}if(al){p(at,ap.more_tile_data);var ak=an.mode;if(ak==="Auto"){ak=an.get_mode(at);an.update_auto_mode(ak)}var ae=an.view.canvas_manager.new_canvas(),af=an._get_tile_bounds(au,ar),av=af[0],ad=af[1],ao=Math.ceil((ad-av)*ai)+an.left_offset,am=an.get_canvas_height(at,ak,ai,ao);ae.width=ao;ae.height=am;var aq=ae.getContext("2d");aq.translate(this.left_offset,0);var aw=an.draw_tile(at,aq,ak,ar,au,ai,aj);if(aw!==undefined){an.tile_cache.set(ax,aw);an.show_tile(aw,ah,ai)}return aw}var ag=$.Deferred();$.when(at,aj).then(function(){view.request_redraw(false,false,false,an);ag.resolve()});return ag},get_canvas_height:function(ac,ae,af,ad){return this.height_px},draw_tile:function(ac,ae,ah,ag,ad,ai,af){console.log("Warning: TiledTrack.draw_tile() not implemented.")},show_tile:function(ae,ag,ah){var ad=this,ac=ae.html_elt;ae.predisplay_actions();var af=(ae.low-(this.is_overview?this.view.max_low:this.view.low))*ah;if(this.left_offset){af-=this.left_offset}ac.css({position:"absolute",top:0,left:af,height:""});if(ac.hasClass("remove")){ac.removeClass("remove")}else{ag.append(ac)}ad.max_height=Math.max(ad.max_height,ac.height());ad.content_div.css("height",ad.max_height+"px");ag.children().css("height",ad.max_height+"px")},_get_tile_bounds:function(ac,ad){var af=Math.floor(ac*R*ad),ag=Math.ceil(R*ad),ae=(af+ag<=this.view.max_high?af+ag:this.view.max_high);return[af,ae]},tool_region_and_parameters_str:function(ae,ac,af){var ad=this,ag=(ae!==undefined&&ac!==undefined&&af!==undefined?ae+":"+ac+"-"+af:"all");return" - region=["+ag+"], parameters=["+ad.tool.get_param_values().join(", ")+"]"},data_and_mode_compatible:function(ac,ad){return true},can_subset:function(ac){return false},init_for_tool_data:function(){this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url;this.predraw_init=function(){var ad=this;var ac=function(){if(ad.data_manager.size()===0){setTimeout(ac,300)}else{ad.data_url=default_data_url;ad.data_query_wait=I;ad.dataset_state_url=converted_datasets_state_url;$.getJSON(ad.dataset_state_url,{dataset_id:ad.dataset_id,hda_ldda:ad.hda_ldda},function(ae){})}};ac()}}});var Y=function(ad,ac){var ae={todo:"label",todo:false};i.call(this,ad,ac,ae);this.container_div.addClass("label-track")};p(Y.prototype,i.prototype,{build_header_div:function(){},init:function(){this.enabled=true},_draw:function(){var ae=this.view,af=ae.high-ae.low,ai=Math.floor(Math.pow(10,Math.floor(Math.log(af)/Math.log(10)))),ac=Math.floor(ae.low/ai)*ai,ag=this.view.container.width(),ad=$("<div style='position: relative; height: 1.3em;'></div>");while(ac<ae.high){var ah=(ac-ae.low)/af*ag;ad.append($("<div class='label'>"+commatize(ac)+"</div>").css({position:"absolute",left:ah-1}));ac+=ai}this.content_div.children(":first").remove();this.content_div.append(ad)}});var h=function(ad,ac,ag){K.call(this,ad,ac,ag);this.drawables=[];this.left_offset=0;if("drawables" in ag){var af;for(var ae=0;ae<ag.drawables.length;ae++){af=ag.drawables[ae];this.drawables[ae]=object_from_template(af);if(af.left_offset>this.left_offset){this.left_offset=af.left_offset}}this.enabled=true}if(this.drawables.length!==0){this.set_display_modes(this.drawables[0].display_modes,this.drawables[0].mode)}this.update_icons();this.obj_type="CompositeTrack"};p(h.prototype,K.prototype,{action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ac){$(".tipsy").remove();ac.show_group()}}].concat(K.prototype.action_icons_def),to_dict:w.prototype.to_dict,add_drawable:w.prototype.add_drawable,unpack_drawables:w.prototype.unpack_drawables,change_mode:function(ac){K.prototype.change_mode.call(this,ac);for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].change_mode(ac)}},init:function(){var ae=[];for(var ad=0;ad<this.drawables.length;ad++){ae.push(this.drawables[ad].init())}var ac=this;$.when.apply($,ae).then(function(){ac.enabled=true;ac.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide()},can_draw:q.prototype.can_draw,draw_helper:function(ad,ar,ay,av,aj,al,at){var aq=this,aC=this._gen_tile_cache_key(ar,al,ay),ah=this._get_tile_bounds(ay,av),az=ah[0],ae=ah[1];if(!at){at={}}var aB=(ad?undefined:aq.tile_cache.get(aC));if(aB){aq.show_tile(aB,aj,al);return aB}var ak=[],aq,ao=true,aw,am;for(var ax=0;ax<this.drawables.length;ax++){aq=this.drawables[ax];aw=aq.data_manager.get_data(az,ae,aq.mode,av,aq.data_url_extra_params);if(is_deferred(aw)){ao=false}ak.push(aw);am=null;if(view.reference_track&&al>view.canvas_manager.char_width_px){am=view.reference_track.data_manager.get_data(az,ae,aq.mode,av,view.reference_track.data_url_extra_params);if(is_deferred(am)){ao=false}}ak.push(am)}if(ao){p(aw,at.more_tile_data);this.tile_predraw_init();var ag=aq.view.canvas_manager.new_canvas(),ah=aq._get_tile_bounds(ay,av),az=ah[0],ae=ah[1],aA=0,ar=Math.ceil((ae-az)*al)+this.left_offset,ap=0,af=[];var ac=0;for(var ax=0;ax<this.drawables.length;ax++,aA+=2){aq=this.drawables[ax];aw=ak[aA];var an=aq.mode;if(an==="Auto"){an=aq.get_mode(aw);aq.update_auto_mode(an)}af.push(an);ac=aq.get_canvas_height(aw,an,al,ar);if(ac>ap){ap=ac}}ag.width=ar;ag.height=(at.height?at.height:ap);aA=0;var au=ag.getContext("2d");au.translate(this.left_offset,0);au.globalAlpha=0.5;au.globalCompositeOperation="source-over";for(var ax=0;ax<this.drawables.length;ax++,aA+=2){aq=this.drawables[ax];aw=ak[aA];am=ak[aA+1];aB=aq.draw_tile(aw,au,af[ax],av,ay,al,am)}this.tile_cache.set(aC,aB);this.show_tile(aB,aj,al);return aB}var ai=$.Deferred(),aq=this;$.when.apply($,ak).then(function(){view.request_redraw(false,false,false,aq);ai.resolve()});return ai},show_group:function(){var af=new N(this.view,this.container,{name:this.name}),ac;for(var ae=0;ae<this.drawables.length;ae++){ac=this.drawables[ae];af.add_drawable(ac);ac.container=af;af.content_div.append(ac.container_div)}var ad=this.container.replace_drawable(this,af,true);af.request_draw()},tile_predraw_init:function(){var af=Number.MAX_VALUE,ac=-af,ad;for(var ae=0;ae<this.drawables.length;ae++){ad=this.drawables[ae];if(ad instanceof j){if(ad.prefs.min_value<af){af=ad.prefs.min_value}if(ad.prefs.max_value>ac){ac=ad.prefs.max_value}}}for(var ae=0;ae<this.drawables.length;ae++){ad=this.drawables[ae];ad.prefs.min_value=af;ad.prefs.max_value=ac}},postdraw_actions:function(ae,ah,aj,ad){K.prototype.postdraw_actions.call(this,ae,ah,aj,ad);var ag=-1;for(var af=0;af<ae.length;af++){var ac=ae[af].html_elt.find("canvas").height();if(ac>ag){ag=ac}}for(var af=0;af<ae.length;af++){var ai=ae[af];if(ai.html_elt.find("canvas").height()!==ag){this.draw_helper(true,ah,ai.index,ai.resolution,ai.html_elt.parent(),aj,{height:ag});ai.html_elt.remove()}}}});var y=function(ac){K.call(this,"reference",ac,{content_div:ac.top_labeltrack},{});ac.reference_track=this;this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:ac.dbkey};this.data_manager=new E(F,this,false)};p(y.prototype,q.prototype,K.prototype,{build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},can_draw:q.prototype.can_draw,draw_tile:function(ak,al,ah,ag,ad,am){var af=this;if(am>this.view.canvas_manager.char_width_px){if(ak.data===null){af.content_div.css("height","0px");return}var ae=al.canvas;al.font=al.canvas.manager.default_font;al.textAlign="center";ak=ak.data;for(var ai=0,aj=ak.length;ai<aj;ai++){var ac=Math.floor(ai*am);al.fillText(ak[ai],ac,10)}return new b(af,ad,ag,ae,ak)}this.content_div.css("height","0px")}});var j=function(ae,ad,af){var ac=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";K.call(this,ae,ad,af);this.min_height_px=16;this.max_height_px=400;this.height_px=32;this.hda_ldda=af.hda_ldda;this.dataset_id=af.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Color",type:"color",default_value:get_random_color()},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:af.prefs,onchange:function(){ac.set_name(ac.prefs.name);ac.vertical_range=ac.prefs.max_value-ac.prefs.min_value;ac.set_min_value(ac.prefs.min_value);ac.set_max_value(ac.prefs.max_value)}});this.prefs=this.config.values;this.height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value;this.add_resize_handle()};p(j.prototype,q.prototype,K.prototype,{set_min_value:function(ac){this.prefs.min_value=ac;$("#linetrack_"+this.dataset_id+"_minval").text(this.prefs.min_value);this.tile_cache.clear();this.request_draw()},set_max_value:function(ac){this.prefs.max_value=ac;$("#linetrack_"+this.dataset_id+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.request_draw()},add_resize_handle:function(){var ac=this;var af=false;var ae=false;var ad=$("<div class='track-resize'>");$(ac.container_div).hover(function(){if(ac.content_visible){af=true;ad.show()}},function(){af=false;if(!ae){ad.hide()}});ad.hide().bind("dragstart",function(ag,ah){ae=true;ah.original_height=$(ac.content_div).height()}).bind("drag",function(ah,ai){var ag=Math.min(Math.max(ai.original_height+ai.deltaY,ac.min_height_px),ac.max_height_px);$(ac.content_div).css("height",ag);ac.height_px=ag;ac.request_draw(true)}).bind("dragend",function(ag,ah){ac.tile_cache.clear();ae=false;if(!af){ad.hide()}ac.config.values.height=ac.height_px}).appendTo(ac.container_div)},predraw_init:function(){var ac=this;ac.vertical_range=undefined;return $.getJSON(ac.data_url,{stats:true,chrom:ac.view.chrom,low:null,high:null,hda_ldda:ac.hda_ldda,dataset_id:ac.dataset_id},function(ad){ac.container_div.addClass("line-track");var ag=ad.data;if(isNaN(parseFloat(ac.prefs.min_value))||isNaN(parseFloat(ac.prefs.max_value))){var ae=ag.min;var ai=ag.max;ae=Math.floor(Math.min(0,Math.max(ae,ag.mean-2*ag.sd)));ai=Math.ceil(Math.max(0,Math.min(ai,ag.mean+2*ag.sd)));ac.prefs.min_value=ae;ac.prefs.max_value=ai;$("#track_"+ac.dataset_id+"_minval").val(ac.prefs.min_value);$("#track_"+ac.dataset_id+"_maxval").val(ac.prefs.max_value)}ac.vertical_range=ac.prefs.max_value-ac.prefs.min_value;ac.total_frequency=ag.total_frequency;ac.container_div.find(".yaxislabel").remove();var ah=get_editable_text_elt(W(ac.prefs.min_value,3),false,6,null,function(aj){var aj=parseFloat(aj);if(!isNaN(aj)){ac.set_min_value(aj)}}).addClass("yaxislabel bottom").attr("id","linetrack_"+ac.dataset_id+"_minval").prependTo(ac.container_div),af=get_editable_text_elt(W(ac.prefs.max_value,3),false,6,null,function(aj){var aj=parseFloat(aj);if(!isNaN(aj)){ac.set_max_value(aj)}}).addClass("yaxislabel top").attr("id","linetrack_"+ac.dataset_id+"_maxval").prependTo(ac.container_div)})},draw_tile:function(am,ak,ah,af,ad,al){var ae=ak.canvas,ac=this._get_tile_bounds(ad,af),ag=ac[0],aj=ac[1],ai=new J.LinePainter(am.data,ag,aj,this.prefs,ah);ai.draw(ak,ae.width,ae.height,al);return new b(this,ad,af,ae,am.data)},can_subset:function(ac){return false},});var d=function(ae,ad,af){var ac=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];K.call(this,ae,ad,af);this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:af.prefs,onchange:function(){ac.set_name(ac.prefs.name);ac.tile_cache.clear();ac.set_painter_from_config();ac.request_draw()}});this.prefs=this.config.values;this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=af.hda_ldda;this.dataset_id=af.dataset_id;this.original_dataset_id=af.dataset_id;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};p(d.prototype,q.prototype,K.prototype,{set_painter_from_config:function(){if(this.config.values.connector_style==="arcs"){this.painter=J.ArcLinkedFeaturePainter}else{this.painter=J.LinkedFeaturePainter}},postdraw_actions:function(ar,am,ah,ag){K.prototype.postdraw_actions.call(this,ar,ag);var al=this;if(al.mode==="Histogram"){var ad=-1;for(var ao=0;ao<ar.length;ao++){var an=ar[ao].max_val;if(an>ad){ad=an}}for(var ao=0;ao<ar.length;ao++){var au=ar[ao];if(au.max_val!==ad){au.html_elt.remove();al.draw_helper(true,am,au.index,au.resolution,au.html_elt.parent(),ah,{more_tile_data:{max:ad}})}}}if(al.filters_manager){var ai=al.filters_manager.filters;for(var aq=0;aq<ai.length;aq++){ai[aq].update_ui_elt()}var at=false,ac,aj;for(var ao=0;ao<ar.length;ao++){if(ar[ao].data.length){ac=ar[ao].data[0];for(var aq=0;aq<ai.length;aq++){aj=ai[aq];if(aj.applies_to(ac)&&aj.min!==aj.max){at=true;break}}}}if(al.filters_available!==at){al.filters_available=at;if(!al.filters_available){al.filters_manager.hide()}al.update_icons()}}this.container_div.find(".yaxislabel").remove();var af=ar[0];if(af instanceof k){var ak=(this.prefs.histogram_max?this.prefs.histogram_max:af.max_val),ae=get_editable_text_elt(ak,false,12,0,function(av){var av=parseFloat(av);al.prefs.histogram_max=(!isNaN(av)?av:null);al.tile_cache.clear();al.request_draw()}).addClass("yaxislabel top").css("color",this.prefs.label_color);this.container_div.prepend(ae)}if(af instanceof M){var ap=true;for(var ao=0;ao<ar.length;ao++){if(!ar[ao].all_slotted){ap=false;break}}if(!ap){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ac){var ac;if(this.mode==="Auto"){if(ac==="no_detail"){ac="feature spans"}else{if(ac==="summary_tree"){ac="coverage histogram"}}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ac+")")}},incremental_slots:function(ag,ac,af){var ad=this.view.canvas_manager.dummy_context,ae=this.slotters[ag];if(!ae||(ae.mode!==af)){ae=new (s.FeatureSlotter)(ag,af,x,function(ah){return ad.measureText(ah)});this.slotters[ag]=ae}return ae.slot_features(ac)},get_summary_tree_data:function(ag,aj,ae,ar){if(ar>ae-aj){ar=ae-aj}var an=Math.floor((ae-aj)/ar),aq=[],af=0;var ah=0,ai=0,am,ap=0,ak=[],ao,al;var ad=function(av,au,aw,at){av[0]=au+aw*at;av[1]=au+(aw+1)*at};while(ap<ar&&ah!==ag.length){var ac=false;for(;ap<ar&&!ac;ap++){ad(ak,aj,ap,an);for(ai=ah;ai<ag.length;ai++){am=ag[ai].slice(1,3);if(is_overlap(am,ak)){ac=true;break}}if(ac){break}}data_start_index=ai;aq[aq.length]=ao=[ak[0],0];for(;ai<ag.length;ai++){am=ag[ai].slice(1,3);if(is_overlap(am,ak)){ao[1]++}else{break}}if(ao[1]>af){af=ao[1]}ap++}return{max:af,delta:an,data:aq}},get_mode:function(ac){if(ac.dataset_type==="summary_tree"){mode="summary_tree"}else{if(ac.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>G){mode="Squish"}else{mode="Pack"}}}return mode},get_canvas_height:function(ac,ag,ah,ad){if(ag==="summary_tree"||ag==="Histogram"){return this.summary_draw_height}else{var af=this.incremental_slots(ah,ac.data,ag);var ae=new (this.painter)(null,null,null,this.prefs,ag);return Math.max(aa,ae.get_required_height(af,ad))}},draw_tile:function(an,ar,ap,at,ax,aj,ae){var aq=this,ad=ar.canvas,ag=this._get_tile_bounds(ax,at),aA=ag[0],ac=ag[1],aF=25,af=this.left_offset;if(ap==="summary_tree"||ap==="Histogram"){if(an.dataset_type!=="summary_tree"){var ak=this.get_summary_tree_data(an.data,aA,ac,200);if(an.max){ak.max=an.max}an=ak}var aC=new J.SummaryTreePainter(an,aA,ac,this.prefs);aC.draw(ar,ad.width,ad.height,aj);return new k(aq,ax,at,ad,an.data,an.max)}var ai=[],ao=this.slotters[aj].slots;all_slotted=true;if(an.data){var al=this.filters_manager.filters;for(var au=0,aw=an.data.length;au<aw;au++){var ah=an.data[au];var av=false;var am;for(var az=0,aE=al.length;az<aE;az++){am=al[az];am.update_attrs(ah);if(!am.keep(ah)){av=true;break}}if(!av){ai.push(ah);if(!(ah[0] in ao)){all_slotted=false}}}}var aD=(this.filters_manager.alpha_filter?new z(this.filters_manager.alpha_filter):null);var aB=(this.filters_manager.height_filter?new z(this.filters_manager.height_filter):null);var aC=new (this.painter)(ai,aA,ac,this.prefs,ap,aD,aB,ae);var ay=null;ar.fillStyle=this.prefs.block_color;ar.font=ar.canvas.manager.default_font;ar.textAlign="right";if(an.data){ay=aC.draw(ar,ad.width,ad.height,aj,ao);ay.translation=-af}return new M(aq,ax,at,ad,an.data,aj,ap,an.message,all_slotted,ay)},data_and_mode_compatible:function(ac,ad){if(ad==="Auto"){return true}else{if(ac.extra_info==="no_detail"||ac.dataset_type==="summary_tree"){return false}else{return true}}},can_subset:function(ac){if(ac.dataset_type==="summary_tree"||ac.message){return false}return true},});var Q=function(ad,ac,ae){d.call(this,ad,ac,ae);this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ae.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=J.ReadPainter};p(Q.prototype,q.prototype,K.prototype,d.prototype);var T=function(ae,ad,ag){d.call(this,ae,ad,ag);var af=get_random_color(),ac=get_random_color([af,"#ffffff"]);this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:af},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ac},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"Clear value to set automatically"},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ag.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=J.ReadPainter;this.update_icons()};p(T.prototype,q.prototype,K.prototype,d.prototype);U.View=Z;U.DrawableGroup=N;U.LineTrack=j;U.FeatureTrack=d;U.ReadTrack=T;U.VcfTrack=Q;U.CompositeTrack=h};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(i,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=i;this.mode=h;this.include_label=(h==="Pack");this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,h=this.start_end_dct,x=[],z=[],n=0,y=this.max_rows;for(var v=0,w=m.length;v<w;v++){var k=m[v],o=k[0];if(this.slots[o]!==undefined){n=Math.max(n,this.slots[o]);z.push(this.slots[o])}else{x.push(v)}}var q=function(E,F){for(var D=0;D<=y;D++){var B=false,G=h[D];if(G!==undefined){for(var A=0,C=G.length;A<C;A++){var i=G[A];if(F>i[0]&&E<i[1]){B=true;break}}}if(!B){return D}}return -1};for(var v=0,w=x.length;v<w;v++){var k=m[x[v]],o=k[0],t=k[1],f=k[2],r=k[3],g=Math.floor(t*p),l=Math.ceil(f*p),u=this.measureText(r).width,j;if(r!==undefined&&this.include_label){u+=(d+a);if(g-u>=0){g-=u;j="left"}else{l+=u;j="right"}}var s=q(g,l);if(s>=0){if(h[s]===undefined){h[s]=[]}h[s].push([g,l]);this.slots[o]=s;n=Math.max(n,s)}}return n+1}})};var painters_module=function(i,x){var u=i("class").extend;var p=function(I,A,G,z,F,D){if(D===undefined){D=4}var C=z-A;var B=F-G;var E=Math.floor(Math.sqrt(C*C+B*B)/D);var J=C/E;var H=B/E;var y;for(y=0;y<E;y++,A+=J,G+=H){if(y%2!==0){continue}I.fillRect(A,G,D,1)}};var q=function(B,A,z,E){var D=A-E/2,C=A+E/2,F=z-Math.sqrt(E*3/2);B.beginPath();B.moveTo(D,F);B.lineTo(C,F);B.lineTo(A,z);B.lineTo(D,F);B.strokeStyle=this.fillStyle;B.fill();B.stroke();B.closePath()};var d=function(y){this.default_val=(y?y:1)};d.prototype.gen_val=function(y){return this.default_val};var l=function(A,C,y,z,B){this.data=A;this.view_start=C;this.view_end=y;this.prefs=u({},this.default_prefs,z);this.mode=B};l.prototype.default_prefs={};l.prototype.draw=function(z,A,y,B){};var v=function(A,C,y,z,B){l.call(this,A,C,y,z,B)};v.prototype.default_prefs={show_counts:false};v.prototype.draw=function(L,z,K,M){var E=this.view_start,N=this.view_end-this.view_start,I=this.data.data,G=(this.prefs.histogram_max?this.prefs.histogram_max:this.data.max),B=K;delta_x_px=Math.ceil(this.data.delta*M);L.save();for(var C=0,D=I.length;C<D;C++){var H=Math.floor((I[C][0]-E)*M);var F=I[C][1];if(!F){continue}var J=F/G*K;if(F!==0&&J<1){J=1}L.fillStyle=this.prefs.block_color;L.fillRect(H,B-J,delta_x_px,J);var A=4;if(this.prefs.show_counts&&(L.measureText(F).width+A)<delta_x_px){L.fillStyle=this.prefs.label_color;L.textAlign="center";L.fillText(F,H+(delta_x_px/2),10)}}L.restore()};var b=function(y,C,E,F,A){l.call(this,y,C,E,F,A);if(this.prefs.min_value===undefined){var G=Infinity;for(var z=0,B=this.data.length;z<B;z++){G=Math.min(G,this.data[z][1])}this.prefs.min_value=G}if(this.prefs.max_value===undefined){var D=-Infinity;for(var z=0,B=this.data.length;z<B;z++){D=Math.max(D,this.data[z][1])}this.prefs.max_value=D}};b.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};b.prototype.draw=function(S,Q,N,D){var I=false,K=this.prefs.min_value,F=this.prefs.max_value,M=F-K,B=N,C=this.view_start,P=this.view_end-this.view_start,L=this.mode,aa=this.data;S.save();var ac=Math.round(N+K/M*N);if(L!=="Intensity"){S.fillStyle="#aaa";S.fillRect(0,ac,Q,1)}S.beginPath();var Y,G,E;if(aa.length>1){E=Math.ceil((aa[1][0]-aa[0][0])*D)}else{E=10}var A=parseInt(this.prefs.color.slice(1),16),H=(A&16711680)>>16,R=(A&65280)>>8,V=A&255;for(var T=0,U=aa.length;T<U;T++){S.fillStyle=S.strokeStyle=this.prefs.color;Y=Math.round((aa[T][0]-C)*D);G=aa[T][1];var W=false,J=false;if(G===null){if(I&&L==="Filled"){S.lineTo(Y,B)}I=false;continue}if(G<K){J=true;G=K}else{if(G>F){W=true;G=F}}if(L==="Histogram"){G=Math.round(G/M*B);S.fillRect(Y,ac,E,-G)}else{if(L==="Intensity"){var z=(G-K)/M,O=Math.round(H+(255-H)*(1-z)),X=Math.round(R+(255-R)*(1-z)),ab=Math.round(V+(255-V)*(1-z));S.fillStyle="rgb("+O+","+X+","+ab+")";S.fillRect(Y,0,E,B)}else{G=Math.round(B-(G-K)/M*B);if(I){S.lineTo(Y,G)}else{I=true;if(L==="Filled"){S.moveTo(Y,B);S.lineTo(Y,G)}else{S.moveTo(Y,G)}}}}S.fillStyle=this.prefs.overflow_color;if(W||J){var Z;if(L==="Histogram"||L==="Intensity"){Z=E}else{Y-=2;Z=4}if(W){S.fillRect(Y,0,Z,3)}if(J){S.fillRect(Y,B-3,Z,3)}}S.fillStyle=this.prefs.color}if(L==="Filled"){if(I){S.lineTo(Y,ac);S.lineTo(0,ac)}S.fill()}else{S.stroke()}S.restore()};var m=function(y){this.feature_positions={};this.slot_height=y;this.translation=0;this.y_translation=0};m.prototype.map_feature_data=function(z,B,y,A){if(!this.feature_positions[B]){this.feature_positions[B]=[]}this.feature_positions[B].push({data:z,x_start:y,x_end:A})};m.prototype.get_feature_data=function(z,D){var C=Math.floor((D-this.y_translation)/this.slot_height),B;if(!this.feature_positions[C]){return null}z+=this.translation;for(var A=0;A<this.feature_positions[C].length;A++){B=this.feature_positions[C][A];if(z>=B.x_start&&z<=B.x_end){return B.data}}};var o=function(A,D,y,z,C,E,B){l.call(this,A,D,y,z,C);this.alpha_scaler=(E?E:new d());this.height_scaler=(B?B:new d())};o.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};u(o.prototype,{get_required_height:function(A,z){var y=y_scale=this.get_row_height(),B=this.mode;if(B==="no_detail"||B==="Squish"||B==="Pack"){y=A*y_scale}return y+this.get_top_padding(z)+this.get_bottom_padding(z)},get_top_padding:function(y){return 0},get_bottom_padding:function(y){return Math.max(Math.round(this.get_row_height()/2),5)},draw:function(K,I,G,E,F){var Q=this.data,D=this.view_start,M=this.view_end;K.save();K.fillStyle=this.prefs.block_color;K.textAlign="right";var H=this.view_end-this.view_start,L=this.get_row_height(),P=new m(L),B;for(var N=0,O=Q.length;N<O;N++){var A=Q[N],C=A[0],J=A[1],y=A[2],z=(F&&F[C]!==undefined?F[C]:null);if((J<M&&y>D)&&(this.mode==="Dense"||z!==null)){B=this.draw_element(K,this.mode,A,z,D,M,E,L,I);P.map_feature_data(A,z,B[0],B[1])}}K.restore();P.y_translation=this.get_top_padding(I);return P},draw_element:function(E,A,G,C,B,D,F,z,y){console.log("WARNING: Unimplemented function.");return[0,0]}});var c=10,h=3,k=5,w=10,f=1,s=9,e=3,a=9,j=2,g="#ccc";var r=function(A,D,y,z,C,E,B){o.call(this,A,D,y,z,C,E,B);this.draw_background_connector=true;this.draw_individual_connectors=false};u(r.prototype,o.prototype,{get_row_height:function(){var z=this.mode,y;if(z==="Dense"){y=c}else{if(z==="no_detail"){y=h}else{if(z==="Squish"){y=k}else{y=w}}}return y},draw_element:function(M,D,X,H,O,aj,an,ap,y){var T=X[0],al=X[1],ad=X[2]-1,Q=X[3],ae=Math.floor(Math.max(0,(al-O)*an)),N=Math.ceil(Math.min(y,Math.max(0,(ad-O)*an))),ac=ae,ao=N,aa=(D==="Dense"?0:(0+H))*ap+this.get_top_padding(y),L,ah,R=null,ar=null,B=this.prefs.block_color,ag=this.prefs.label_color;M.globalAlpha=this.alpha_scaler.gen_val(X);if(D==="Dense"){H=1}if(D==="no_detail"){M.fillStyle=B;M.fillRect(ae,aa+5,N-ae,f)}else{var K=X[4],Z=X[5],af=X[6],C=X[7],V=true;if(Z&&af){R=Math.floor(Math.max(0,(Z-O)*an));ar=Math.ceil(Math.min(y,Math.max(0,(af-O)*an)))}var am,U;if(D==="Squish"){am=1;U=e;V=false}else{if(D==="Dense"){am=5;U=s}else{am=5;U=a}}if(!C){M.fillStyle=B;M.fillRect(ae,aa+1,N-ae,U);if(K&&V){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand_inv")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand_inv")}}M.fillRect(ae,aa+1,N-ae,U)}}else{var J,W;if(D==="Squish"||D==="Dense"){J=aa+Math.floor(e/2)+1;W=1}else{if(K){J=aa;W=U}else{J+=(e/2)+1;W=1}}if(this.draw_background_connector){if(D==="Squish"||D==="Dense"){M.fillStyle=g}else{if(K){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand")}}}else{M.fillStyle=g}}M.fillRect(ae,J,N-ae,W)}var E;for(var ak=0,A=C.length;ak<A;ak++){var F=C[ak],z=Math.floor(Math.max(0,(F[0]-O)*an)),Y=Math.ceil(Math.min(y,Math.max((F[1]-1-O)*an))),S,ab;if(z>Y){continue}M.fillStyle=B;M.fillRect(z,aa+(U-am)/2+1,Y-z,am);if(R!==undefined&&af>Z&&!(z>ar||Y<R)){var ai=Math.max(z,R),I=Math.min(Y,ar);M.fillRect(ai,aa+1,I-ai,U);if(C.length===1&&D==="Pack"){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand_inv")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand_inv")}}if(ai+14<I){ai+=2;I-=2}M.fillRect(ai,aa+1,I-ai,U)}}if(this.draw_individual_connectors&&S){this.draw_connector(M,S,ab,z,Y,aa)}S=z;ab=Y}if(D==="Pack"){M.globalAlpha=1;M.fillStyle="white";var G=this.height_scaler.gen_val(X),P=Math.ceil(U*G),aq=Math.round((U-P)/2);if(G!==1){M.fillRect(ae,J+1,N-ae,aq);M.fillRect(ae,J+U-aq+1,N-ae,aq)}}}M.globalAlpha=1;if(D==="Pack"&&al>O){M.fillStyle=ag;if(O===0&&ae-M.measureText(Q).width<0){M.textAlign="left";M.fillText(Q,N+j,aa+8);ao+=M.measureText(Q).width+j}else{M.textAlign="right";M.fillText(Q,ae-j,aa+8);ac-=M.measureText(Q).width+j}}}M.globalAlpha=1;return[ac,ao]}});var t=function(B,E,y,A,D,F,C,z){o.call(this,B,E,y,A,D,F,C);this.ref_seq=(z?z.data:null)};u(t.prototype,o.prototype,{get_row_height:function(){var y,z=this.mode;if(z==="Dense"){y=c}else{if(z==="Squish"){y=k}else{y=w;if(this.prefs.show_insertions){y*=2}}}return y},draw_read:function(K,A,ag,V,L,aa,ad,C,B,M){K.textAlign="center";var J=this,R=[L,aa],Z=0,W=0,D=0,F=K.canvas.manager.char_width_px,y=(B==="+"?this.prefs.block_color:this.prefs.reverse_strand_color);var O=[];if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){D=Math.round(ag/2)}if(!C){C=[[0,M.length]]}for(var G=0,I=C.length;G<I;G++){var z=C[G],E="MIDNSHP=X"[z[0]],S=z[1];if(E==="H"||E==="S"){Z-=S}var U=ad+Z,Y=Math.floor(Math.max(0,(U-L)*ag)),ab=Math.floor(Math.max(0,(U+S-L)*ag));if(Y===ab){ab+=1}switch(E){case"H":break;case"S":case"M":case"=":if(is_overlap([U,U+S],R)){var N=M.slice(W,W+S);if(D>0){K.fillStyle=y;K.fillRect(Y-D,V+1,ab-Y,9);K.fillStyle=g;for(var af=0,H=N.length;af<H;af++){if(this.prefs.show_differences){if(this.ref_seq){var P=this.ref_seq[U-L+af];if(!P||P.toLowerCase()===N[af].toLowerCase()){continue}}else{continue}}if(U+af>=L&&U+af<=aa){var X=Math.floor(Math.max(0,(U+af-L)*ag));K.fillText(N[af],X,V+9)}}}else{K.fillStyle=y;K.fillRect(Y,V+4,ab-Y,e)}}W+=S;Z+=S;break;case"N":K.fillStyle=g;K.fillRect(Y-D,V+5,ab-Y,1);Z+=S;break;case"D":K.fillStyle="red";K.fillRect(Y-D,V+4,ab-Y,3);Z+=S;break;case"P":break;case"I":var ah=Y-D;if(is_overlap([U,U+S],R)){var N=M.slice(W,W+S);if(this.prefs.show_insertions){var T=Y-(ab-Y)/2;if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){K.fillStyle="yellow";K.fillRect(T-D,V-9,ab-Y,9);O[O.length]={type:"triangle",data:[ah,V+4,5]};K.fillStyle=g;switch(compute_overlap([U,U+S],R)){case (OVERLAP_START):N=N.slice(L-U);break;case (OVERLAP_END):N=N.slice(0,U-aa);break;case (CONTAINED_BY):break;case (CONTAINS):N=N.slice(L-U,U-aa);break}for(var af=0,H=N.length;af<H;af++){var X=Math.floor(Math.max(0,(U+af-L)*ag));K.fillText(N[af],X-(ab-Y)/2,V)}}else{K.fillStyle="yellow";K.fillRect(T,V+(this.mode!=="Dense"?2:5),ab-Y,(A!=="Dense"?e:s))}}else{if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){O.push({type:"text",data:[N.length,ah,V+9]})}else{}}}W+=S;break;case"X":W+=S;break}}K.fillStyle="yellow";var Q,ai,ae;for(var ac=0;ac<O.length;ac++){Q=O[ac];ai=Q.type;ae=Q.data;if(ai==="text"){K.save();K.font="bold "+K.font;K.fillText(ae[0],ae[1],ae[2]);K.restore()}else{if(ai==="triangle"){q(K,ae[0],ae[1],ae[2])}}}},draw_element:function(R,M,E,B,U,z,I,S,P){var H=E[0],Q=E[1],A=E[2],J=E[3],D=Math.floor(Math.max(0,(Q-U)*I)),F=Math.ceil(Math.min(P,Math.max(0,(A-U)*I))),C=(M==="Dense"?0:(0+B))*S,G=this.prefs.label_color,O=0;if((M==="Pack"||this.mode==="Auto")&&I>R.canvas.manager.char_width_px){var O=Math.round(I/2)}if(E[5] instanceof Array){var N=Math.floor(Math.max(0,(E[4][0]-U)*I)),L=Math.ceil(Math.min(P,Math.max(0,(E[4][1]-U)*I))),K=Math.floor(Math.max(0,(E[5][0]-U)*I)),y=Math.ceil(Math.min(P,Math.max(0,(E[5][1]-U)*I)));if(E[4][1]>=U&&E[4][0]<=z&&E[4][2]){this.draw_read(R,M,I,C,U,z,E[4][0],E[4][2],E[4][3],E[4][4])}if(E[5][1]>=U&&E[5][0]<=z&&E[5][2]){this.draw_read(R,M,I,C,U,z,E[5][0],E[5][2],E[5][3],E[5][4])}if(K>L){R.fillStyle=g;p(R,L-O,C+5,K-O,C+5)}}else{this.draw_read(R,M,I,C,U,z,Q,E[4],E[5],E[6])}if(M==="Pack"&&Q>U&&J!=="."){R.fillStyle=this.prefs.label_color;var T=1;if(T===0&&D-R.measureText(J).width<0){R.textAlign="left";R.fillText(J,F+j-O,C+8)}else{R.textAlign="right";R.fillText(J,D-j-O,C+8)}}return[0,0]}});var n=function(A,D,y,z,C,E,B){r.call(this,A,D,y,z,C,E,B);this.longest_feature_length=this.calculate_longest_feature_length();this.draw_background_connector=false;this.draw_individual_connectors=true};u(n.prototype,o.prototype,r.prototype,{calculate_longest_feature_length:function(){var z=0;for(var C=0,y=this.data.length;C<y;C++){var B=this.data[C],A=B[1],D=B[2];z=Math.max(z,D-A)}return z},get_top_padding:function(z){var y=this.view_end-this.view_start,A=z/y;return Math.min(128,Math.ceil((this.longest_feature_length/2)*A))},draw_connector:function(G,B,F,H,E,D){var y=(F+H)/2,C=H-y;var A=Math.PI,z=0;if(C>0){G.beginPath();G.arc(y,D,H-y,Math.PI,0);G.stroke()}}});x.Scaler=d;x.SummaryTreePainter=v;x.LinePainter=b;x.LinkedFeaturePainter=r;x.ReadPainter=t;x.ArcLinkedFeaturePainter=n};(function(d){var c={};var b=function(e){return c[e]};var a=function(f,g){var e={};g(b,e);c[f]=e};a("class",class_module);a("slotting",slotting_module);a("painters",painters_module);a("trackster",trackster_module);for(key in c.trackster){d[key]=c.trackster[key]}})(window); \ No newline at end of file +var class_module=function(b,a){var c=function(){var f=arguments[0];for(var e=1;e<arguments.length;e++){var d=arguments[e];for(key in d){f[key]=d[key]}}return f};a.extend=c};var requestAnimationFrame=(function(){return window.requestAnimationFrame||window.webkitRequestAnimationFrame||window.mozRequestAnimationFrame||window.oRequestAnimationFrame||window.msRequestAnimationFrame||function(b,a){window.setTimeout(b,1000/60)}})();var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=BEFORE}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=AFTER}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a};var is_overlap=function(c,b){var a=compute_overlap(c,b);return(a!==BEFORE&&a!==AFTER)};var is_deferred=function(a){return("isResolved" in a)};var get_random_color=function(a){if(!a){a="#ffffff"}if(typeof(a)==="string"){a=[a]}for(var j=0;j<a.length;j++){a[j]=parseInt(a[j].slice(1),16)}var n=function(t,s,i){return((t*299)+(s*587)+(i*114))/1000};var e=function(v,u,w,s,i,t){return(Math.max(v,s)-Math.min(v,s))+(Math.max(u,i)-Math.min(u,i))+(Math.max(w,t)-Math.min(w,t))};var g,o,f,k,q,h,r,c,d,b,p,m=false,l=0;do{g=Math.round(Math.random()*16777215);o=(g&16711680)>>16;f=(g&65280)>>8;k=g&255;d=n(o,f,k);m=true;for(var j=0;j<a.length;j++){q=a[j];h=(q&16711680)>>16;r=(q&65280)>>8;c=q&255;b=n(h,r,c);p=e(o,f,k,h,r,c);if((Math.abs(d-b)<40)||(p<200)){m=false;break}}l++}while(!m&&l<=10);return"#"+(16777216+g).toString(16).substr(1,6)};var create_action_icon=function(c,b,a){return $("<a/>").attr("href","javascript:void(0);").attr("title",c).addClass("icon-button").addClass(b).tipsy({gravity:"s"}).click(a)};var trackster_module=function(e,U){var p=e("class").extend,s=e("slotting"),J=e("painters");var ab=function(ac,ad){this.document=ac;this.default_font=ad!==undefined?ad:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};p(ab.prototype,{load_pattern:function(ac,ag){var ad=this.patterns,ae=this.dummy_context,af=new Image();af.src=image_path+ag;af.onload=function(){ad[ac]=ae.createPattern(af,"repeat")}},get_pattern:function(ac){return this.patterns[ac]},new_canvas:function(){var ac=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(ac)}ac.manager=this;return ac}});var n={};var l=function(ac,ad){n[ac.attr("id")]=ad};var m=function(ac,ae,ag,af){ag=".group";var ad={};n[ac.attr("id")]=af;ac.bind("drag",{handle:"."+ae,relative:true},function(ao,ap){var an=$(this);var at=$(this).parent(),ak=at.children(),am=n[$(this).attr("id")],aj,ai,aq,ah,al;ai=$(this).parents(ag);if(ai.length!==0){aq=ai.position().top;ah=aq+ai.outerHeight();if(ap.offsetY<aq){$(this).insertBefore(ai);var ar=n[ai.attr("id")];ar.remove_drawable(am);ar.container.add_drawable_before(am,ar);return}else{if(ap.offsetY>ah){$(this).insertAfter(ai);var ar=n[ai.attr("id")];ar.remove_drawable(am);ar.container.add_drawable(am);return}}}ai=null;for(al=0;al<ak.length;al++){aj=$(ak.get(al));aq=aj.position().top;ah=aq+aj.outerHeight();if(aj.is(ag)&&this!==aj.get(0)&&ap.offsetY>=aq&&ap.offsetY<=ah){if(ap.offsetY-aq<ah-ap.offsetY){aj.find(".content-div").prepend(this)}else{aj.find(".content-div").append(this)}if(am.container){am.container.remove_drawable(am)}n[aj.attr("id")].add_drawable(am);return}}var aj;for(al=0;al<ak.length;al++){aj=$(ak.get(al));if(ap.offsetY<aj.position().top&&!(aj.hasClass("reference-track")||aj.hasClass("intro"))){break}}if(al===ak.length){if(this!==ak.get(al-1)){at.append(this);n[at.attr("id")].move_drawable(am,al)}}else{if(this!==ak.get(al)){$(this).insertBefore(ak.get(al));n[at.attr("id")].move_drawable(am,(ap.deltaY>0?al-1:al))}}}).bind("dragstart",function(){ad["border-top"]=ac.css("border-top");ad["border-bottom"]=ac.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ad)})};U.moveable=m;var aa=16,D=9,A=20,x=100,G=12000,R=400,I=5000,u=100,o="There was an error in indexing this dataset. ",H="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",B="No data for this chrom/contig.",t="Currently indexing... please wait",v="Tool cannot be rerun: ",a="Loading data...",V="Ready for display",O=10,F=20;function W(ad,ac){if(!ac){ac=0}var ae=Math.pow(10,ac);return Math.round(ad*ae)/ae}var c=function(ac){this.num_elements=ac;this.clear()};p(c.prototype,{get:function(ad){var ac=this.key_ary.indexOf(ad);if(ac!==-1){if(this.obj_cache[ad].stale){this.key_ary.splice(ac,1);delete this.obj_cache[ad]}else{this.move_key_to_end(ad,ac)}}return this.obj_cache[ad]},set:function(ad,ae){if(!this.obj_cache[ad]){if(this.key_ary.length>=this.num_elements){var ac=this.key_ary.shift();delete this.obj_cache[ac]}this.key_ary.push(ad)}this.obj_cache[ad]=ae;return ae},move_key_to_end:function(ad,ac){this.key_ary.splice(ac,1);this.key_ary.push(ad)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var P=function(ad,ac){c.call(this,ad);this.track=ac};p(P.prototype,c.prototype,{load_data:function(al,ag,aj,ad,ai){var ak=this.track.view.chrom,af={chrom:ak,low:al,high:ag,mode:aj,resolution:ad,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(af,ai);if(this.track.filters_manager){var am=[];var ac=this.track.filters_manager.filters;for(var ah=0;ah<ac.length;ah++){am.push(ac[ah].name)}af.filter_cols=JSON.stringify(am)}var ae=this;return $.getJSON(this.track.data_url,af,function(an){ae.set_data(al,ag,an)})},get_data:function(ak,ae,ai,ad,ah){var al=this.get(ak,ae);if(al&&(is_deferred(al)||this.track.data_and_mode_compatible(al,ai))){return al}var am,aj,ac,ag,ai,al;for(var af=0;af<this.key_ary.length;af++){am=this.key_ary[af];aj=this.split_key(am);ac=aj[0];ag=aj[1];if(ak>=ac&&ae<=ag){var al=this.obj_cache[am];if(is_deferred(al)||(this.track.data_and_mode_compatible(al,ai)&&this.track.can_subset(al))){this.move_key_to_end(am,af);return al}}}al=this.load_data(ak,ae,ai,ad,ah);this.set_data(ak,ae,al);return al},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(ak,af,aj,ae,ai,ag){var al=this.get(ak,af);if(!(al&&this.track.data_and_mode_compatible(al,aj))){console.log("ERROR: no current data for: ",this.track,ak,af,aj,ae,ai);return}al.stale=true;var ad=ak;if(ag===this.DEEP_DATA_REQ){$.extend(ai,{start_val:al.data.length+1})}else{if(ag===this.BROAD_DATA_REQ){ad=(al.max_high?al.max_high:al.data[al.data.length-1][2])+1}}var ac=this,ah=this.load_data(ad,af,aj,ae,ai);new_data_available=$.Deferred();this.set_data(ak,af,new_data_available);$.when(ah).then(function(am){if(am.data){am.data=al.data.concat(am.data);if(am.max_low){am.max_low=al.max_low}if(am.message){am.message=am.message.replace(/[0-9]+/,am.data.length)}}ac.set_data(ak,af,am);new_data_available.resolve(am)});return new_data_available},get:function(ac,ad){return c.prototype.get.call(this,this.gen_key(ac,ad))},set_data:function(ad,ae,ac){return this.set(this.gen_key(ad,ae),ac)},gen_key:function(ac,ae){var ad=ac+"_"+ae;return ad},split_key:function(ac){return ac.split("_")}});var E=function(ad,ac,ae){P.call(this,ad,ac,ae)};p(E.prototype,P.prototype,c.prototype,{get:P.prototype.get,load_data:function(ac,af,ag,ad,ae){if(ad>1){return{data:null}}return P.prototype.load_data.call(this,ac,af,ag,ad,ae)}});var q=function(ad,ac,af){if(!q.id_counter){q.id_counter=0}this.id=q.id_counter++;this.name=af.name;this.view=ad;this.container=ac;this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name}],saved_values:af.prefs,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=af.drag_handle_class;this.is_overview=false;this.action_icons={};this.content_visible=true;this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(ag){ag.stopPropagation()});var ae=this;this.container_div.hover(function(){ae.icons_div.show()},function(){ae.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};q.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ac){if(ac.content_visible){ac.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ac.hide_contents();ac.content_visible=false}else{ac.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ac.content_visible=true;ac.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(ad){var af=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ac=function(){ad.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ae=function(ag){if((ag.keyCode||ag.which)===27){af()}else{if((ag.keyCode||ag.which)===13){ac()}}};$(window).bind("keypress.check_enter_esc",ae);show_modal("Configure",ad.config.build_form(),{Cancel:af,OK:ac})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ac){$(".tipsy").remove();ac.remove()}}];p(q.prototype,{init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.content_visible){return true}return false},request_draw:function(){},_draw:function(){},to_dict:function(){},update_icons:function(){},set_name:function(ac){this.old_name=this.name;this.name=ac;this.name_div.text(this.name)},revert_name:function(){if(this.old_name){this.name=this.old_name;this.name_div.text(this.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ac=this.view;this.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ad,ai,ah,ag,ac,af){var ae=this;this.action_icons[ad]=$("<a/>").attr("href","javascript:void(0);").attr("title",ai).addClass("icon-button").addClass(ah).tipsy({gravity:"s"}).click(function(){ag(ae)}).appendTo(this.icons_div);if(af){this.action_icons[ad].hide()}},build_action_icons:function(ac){var ae;for(var ad=0;ad<ac.length;ad++){ae=ac[ad];this.add_action_icon(ae.name,ae.title,ae.css_class,ae.on_click_fn,ae.prepend,ae.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){}});var w=function(ad,ac,ae){q.call(this,ad,ac,ae);this.obj_type=ae.obj_type;this.drawables=[]};p(w.prototype,q.prototype,{unpack_drawables:function(ae){this.drawables=[];var ad;for(var ac=0;ac<ae.length;ac++){ad=object_from_template(ae[ac],this);this.add_drawable(ad)}},init:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].init()}},_draw:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac]._draw()}},to_dict:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ad}},add_drawable:function(ac){this.drawables.push(ac);ac.container=this;this.changed()},add_drawable_before:function(ae,ac){this.changed();var ad=this.drawables.indexOf(ac);if(ad!==-1){this.drawables.splice(ad,0,ae);return true}return false},replace_drawable:function(ae,ac,ad){var af=this.drawables.indexOf(ae);if(af!==-1){this.drawables[af]=ac;if(ad){ae.container_div.replaceWith(ac.container_div)}this.changed()}return af},remove_drawable:function(ad){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);ad.container=null;this.changed();return true}return false},move_drawable:function(ad,ae){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);this.drawables.splice(ae,0,ad);this.changed();return true}return false}});var N=function(ad,ac,af){p(af,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});w.call(this,ad,ac,af);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);l(this.container_div,this);l(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new X(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in af){this.unpack_drawables(af.drawables)}if("filters" in af){var ae=this.filters_manager;this.filters_manager=new X(this,af.filters);ae.parent_div.replaceWith(this.filters_manager.parent_div);if(af.filters.visible){this.setup_multitrack_filtering()}}};p(N.prototype,q.prototype,w.prototype,{action_icons_def:[q.prototype.action_icons_def[0],q.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ac){$(".tipsy").remove();ac.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters();ac._restore_filter_managers()}else{ac.setup_multitrack_filtering();ac.request_draw(true)}ac.filters_manager.toggle()}},q.prototype.action_icons_def[2]],build_container_div:function(){var ac=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ac)}return ac},build_header_div:function(){var ac=$("<div/>").addClass("track-header");ac.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(ac);return ac},hide_contents:function(){this.content_div.hide()},show_contents:function(){this.content_div.show();this.request_draw()},update_icons:function(){var ae=this.drawables.length;if(ae===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ae===1){if(this.drawables[0] instanceof h){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var ai,ao=true,ag=this.drawables[0].get_type(),ac=0;for(var al=0;al<ae;al++){ai=this.drawables[al];if(ai.get_type()!==ag){can_composite=false;break}if(ai instanceof d){ac++}}if(ao||ac===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tipsy").remove()}if(ac>1&&ac===this.drawables.length){var ap={},ad;ai=this.drawables[0];for(var ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];ap[ad.name]=[ad]}for(var al=1;al<this.drawables.length;al++){ai=this.drawables[al];for(var ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];if(ad.name in ap){ap[ad.name].push(ad)}}}this.filters_manager.remove_all();var af,ah,aj,am;for(var an in ap){af=ap[an];if(af.length===ac){ah=new S({name:af[0].name,index:af[0].index});this.filters_manager.add_filter(ah)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].filters_manager=this.saved_filters_managers[ac]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ac=0;ac<this.drawables.length;ac++){drawable=this.drawables[ac];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ag=[];for(var ad=0;ad<this.drawables.length;ad++){ag.push(this.drawables[ad].name)}var ae="Composite Track of "+this.drawables.length+" tracks ("+ag.join(", ")+")";var af=new h(this.view,this.view,{name:ae,drawables:this.drawables});var ac=this.container.replace_drawable(this,af,true);af.request_draw()},add_drawable:function(ac){w.prototype.add_drawable.call(this,ac);this.update_icons()},remove_drawable:function(ac){w.prototype.remove_drawable.call(this,ac);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ac=p(w.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ac},request_draw:function(ac,ae){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].request_draw(ac,ae)}}});var Z=function(ac){p(ac,{obj_type:"View"});w.call(this,"View",ac.container,ac);this.chrom=null;this.vis_id=ac.vis_id;this.dbkey=ac.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.init();this.canvas_manager=new ab(this.container.get(0).ownerDocument);this.reset()};p(Z.prototype,w.prototype,{init:function(){var ae=this.container,ac=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ae);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ae);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ae);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;l(this.viewport_container,ac);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var af=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ad=function(ag){if(ag.type==="focusout"||(ag.keyCode||ag.which)===13||(ag.keyCode||ag.which)===27){if((ag.keyCode||ag.which)!==27){ac.go_to($(this).val())}$(this).hide();$(this).val("");ac.location_span.show();ac.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ad).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tipsy({gravity:"n"}).appendTo(this.nav_controls);this.location_span.click(function(){ac.location_span.hide();ac.chrom_select.hide();ac.nav_input.val(ac.chrom+":"+ac.low+"-"+ac.high);ac.nav_input.css("display","inline-block");ac.nav_input.select();ac.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tipsy({gravity:"n"}).click(function(){ac.zoom_out();ac.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tipsy({gravity:"n"}).click(function(){ac.zoom_in();ac.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ac.change_chrom(ac.chrom_select.val())});this.browser_content_div.click(function(ag){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ag){ac.zoom_in(ag.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ag,ah){this.current_x=ah.offsetX}).bind("drag",function(ag,ai){var aj=ai.offsetX-this.current_x;this.current_x=ai.offsetX;var ah=Math.round(aj/ac.viewport_container.width()*(ac.max_high-ac.max_low));ac.move_delta(-ah)});this.overview_close.click(function(){ac.reset_overview()});this.viewport_container.bind("draginit",function(ag,ah){if(ag.clientX>ac.viewport_container.width()-16){return false}}).bind("dragstart",function(ag,ah){ah.original_low=ac.low;ah.current_height=ag.clientY;ah.current_x=ah.offsetX}).bind("drag",function(ai,ak){var ag=$(this);var al=ak.offsetX-ak.current_x;var ah=ag.scrollTop()-(ai.clientY-ak.current_height);ag.scrollTop(ah);ak.current_height=ai.clientY;ak.current_x=ak.offsetX;var aj=Math.round(al/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}).bind("mousewheel",function(ai,ak,ah,ag){if(ah){ah*=50;var aj=Math.round(-ah/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}});this.top_labeltrack.bind("dragstart",function(ag,ah){return $("<div />").css({height:ac.browser_content_div.height()+ac.top_labeltrack.height()+ac.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ak,al){$(al.proxy).css({left:Math.min(ak.pageX,al.startX)-ac.container.offset().left,width:Math.abs(ak.pageX-al.startX)});var ah=Math.min(ak.pageX,al.startX)-ac.container.offset().left,ag=Math.max(ak.pageX,al.startX)-ac.container.offset().left,aj=(ac.high-ac.low),ai=ac.viewport_container.width();ac.update_location(Math.round(ah/ai*aj)+ac.low,Math.round(ag/ai*aj)+ac.low)}).bind("dragend",function(al,am){var ah=Math.min(al.pageX,am.startX),ag=Math.max(al.pageX,am.startX),aj=(ac.high-ac.low),ai=ac.viewport_container.width(),ak=ac.low;ac.low=Math.round(ah/ai*aj)+ak;ac.high=Math.round(ag/ai*aj)+ak;$(am.proxy).remove();ac.request_redraw()});this.add_label_track(new Y(this,{content_div:this.top_labeltrack}));this.add_label_track(new Y(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){ac.resize_window()});$(document).bind("redraw",function(){ac.redraw()});this.reset();$(window).trigger("resize")},changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},update_location:function(ac,ad){this.location_span.text(commatize(ac)+" - "+commatize(ad));this.nav_input.val(this.chrom+":"+commatize(ac)+"-"+commatize(ad))},load_chroms:function(ae){ae.num=u;ae.dbkey=this.dbkey;var ac=this,ad=$.Deferred();$.ajax({url:chrom_url,data:ae,dataType:"json",success:function(ag){if(ag.chrom_info.length===0){alert("Invalid chromosome: "+ae.chrom);return}if(ag.reference){ac.add_label_track(new y(ac))}ac.chrom_data=ag.chrom_info;var aj='<option value="">Select Chrom/Contig</option>';for(var ai=0,af=ac.chrom_data.length;ai<af;ai++){var ah=ac.chrom_data[ai].chrom;aj+='<option value="'+ah+'">'+ah+"</option>"}if(ag.prev_chroms){aj+='<option value="previous">Previous '+u+"</option>"}if(ag.next_chroms){aj+='<option value="next">Next '+u+"</option>"}ac.chrom_select.html(aj);ac.chrom_start_index=ag.start_index;ad.resolve(ag)},error:function(){alert("Could not load chroms for this dbkey:",ac.dbkey)}});return ad},change_chrom:function(ah,ad,aj){if(!ah||ah==="None"){return}var ae=this;if(ah==="previous"){ae.load_chroms({low:this.chrom_start_index-u});return}if(ah==="next"){ae.load_chroms({low:this.chrom_start_index+u});return}var ai=$.grep(ae.chrom_data,function(ak,al){return ak.chrom===ah})[0];if(ai===undefined){ae.load_chroms({chrom:ah},function(){ae.change_chrom(ah,ad,aj)});return}else{if(ah!==ae.chrom){ae.chrom=ah;ae.chrom_select.val(ae.chrom);ae.max_high=ai.len-1;ae.reset();ae.request_redraw(true);for(var ag=0,ac=ae.drawables.length;ag<ac;ag++){var af=ae.drawables[ag];if(af.init){af.init()}}if(ae.reference_track){ae.reference_track.init()}}if(ad!==undefined&&aj!==undefined){ae.low=Math.max(ad,0);ae.high=Math.min(aj,ae.max_high)}ae.reset_overview();ae.request_redraw()}},go_to:function(ag){ag=ag.replace(/ |,/g,"");var ak=this,ac,af,ad=ag.split(":"),ai=ad[0],aj=ad[1];if(aj!==undefined){try{var ah=aj.split("-");ac=parseInt(ah[0],10);af=parseInt(ah[1],10)}catch(ae){return false}}ak.change_chrom(ai,ac,af)},move_fraction:function(ae){var ac=this;var ad=ac.high-ac.low;this.move_delta(ae*ad)},move_delta:function(ae){var ac=this;var ad=ac.high-ac.low;if(ac.low-ae<ac.max_low){ac.low=ac.max_low;ac.high=ac.max_low+ad}else{if(ac.high-ae>ac.max_high){ac.high=ac.max_high;ac.low=ac.max_high-ad}else{ac.high-=ae;ac.low-=ae}}ac.request_redraw()},add_drawable:function(ac){w.prototype.add_drawable.call(this,ac);ac.init();this.changed();this.update_intro_div()},add_label_track:function(ac){ac.view=this;ac.init();this.label_tracks.push(ac)},remove_drawable:function(ae,ad){w.prototype.remove_drawable.call(this,ae);if(ad){var ac=this;ae.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ak,ac,aj,ad){var ai=this,ag=(ad?[ad]:ai.drawables),ae;var ad;for(var ah=0;ah<ag.length;ah++){ad=ag[ah];ae=-1;for(var af=0;af<ai.tracks_to_be_redrawn.length;af++){if(ai.tracks_to_be_redrawn[af][0]===ad){ae=af;break}}if(ae<0){ai.tracks_to_be_redrawn.push([ad,ac,aj])}else{ai.tracks_to_be_redrawn[ah][1]=ac;ai.tracks_to_be_redrawn[ah][2]=aj}}requestAnimationFrame(function(){ai._redraw(ak)})},_redraw:function(am){var aj=this.low,af=this.high;if(aj<this.max_low){aj=this.max_low}if(af>this.max_high){af=this.max_high}var al=this.high-this.low;if(this.high!==0&&al<this.min_separation){af=aj+this.min_separation}this.low=Math.floor(aj);this.high=Math.ceil(af);this.resolution_b_px=(this.high-this.low)/this.viewport_container.width();this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var ac=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ai=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var an=13;this.overview_box.css({left:ac,width:Math.max(an,ai)}).show();if(ai<an){this.overview_box.css("left",ac-(an-ai)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ac,width:ai})}this.update_location(this.low,this.high);if(!am){var ae,ad,ak;for(var ag=0,ah=this.tracks_to_be_redrawn.length;ag<ah;ag++){ae=this.tracks_to_be_redrawn[ag][0];ad=this.tracks_to_be_redrawn[ag][1];ak=this.tracks_to_be_redrawn[ag][2];if(ae){ae._draw(ad,ak)}}this.tracks_to_be_redrawn=[];for(ag=0,ah=this.label_tracks.length;ag<ah;ag++){this.label_tracks[ag]._draw()}}},zoom_in:function(ad,ae){if(this.max_high===0||this.high-this.low<this.min_separation){return}var af=this.high-this.low,ag=af/2+this.low,ac=(af/this.zoom_factor)/2;if(ad){ag=ad/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ag-ac);this.high=Math.round(ag+ac);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ad=this.high-this.low,ae=ad/2+this.low,ac=(ad*this.zoom_factor)/2;this.low=Math.round(ae-ac);this.high=Math.round(ae+ac);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ae){if(this.overview_drawable){if(this.overview_drawable.dataset_id===ae.dataset_id){return}this.overview_viewport.find(".track").remove()}var ad=ae.copy({content_div:this.overview_viewport}),ac=this;ad.header_div.hide();ad.is_overview=true;ac.overview_drawable=ad;this.overview_drawable.postdraw_actions=function(){ac.overview_highlight.show().height(ac.overview_drawable.content_div.height());ac.overview_viewport.height(ac.overview_drawable.content_div.height()+ac.overview_box.outerHeight());ac.overview_close.show();ac.resize_window()};ac.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".tipsy").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var r=function(ae,aj,af){this.track=ae;this.name=aj.name;this.params=[];var aq=aj.params;for(var ag=0;ag<aq.length;ag++){var al=aq[ag],ad=al.name,ap=al.label,ah=unescape(al.html),ar=al.value,an=al.type;if(an==="number"){this.params.push(new f(ad,ap,ah,(ad in af?af[ad]:ar),al.min,al.max))}else{if(an==="select"){this.params.push(new L(ad,ap,ah,(ad in af?af[ad]:ar)))}else{console.log("WARNING: unrecognized tool parameter type:",ad,an)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(au){au.stopPropagation()}).click(function(au){au.stopPropagation()}).bind("dblclick",function(au){au.stopPropagation()});var ao=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var am=this.params;var ak=this;$.each(this.params,function(av,ay){var ax=$("<div>").addClass("param-row").appendTo(ak.parent_div);var au=$("<div>").addClass("param-label").text(ay.label).appendTo(ax);var aw=$("<div/>").addClass("param-input").html(ay.html).appendTo(ax);aw.find(":input").val(ay.value);$("<div style='clear: both;'/>").appendTo(ax)});this.parent_div.find("input").click(function(){$(this).select()});var at=$("<div>").addClass("param-row").appendTo(this.parent_div);var ai=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(at);var ac=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(at);var ak=this;ac.click(function(){ak.run_on_region()});ai.click(function(){ak.run_on_dataset()});if("visible" in af&&af.visible){this.parent_div.show()}};p(r.prototype,{update_params:function(){for(var ac=0;ac<this.params.length;ac++){this.params[ac].update_value()}},state_dict:function(){var ad={};for(var ac=0;ac<this.params.length;ac++){ad[this.params[ac].name]=this.params[ac].value}ad.visible=this.parent_div.is(":visible");return ad},get_param_values_dict:function(){var ac={};this.parent_div.find(":input").each(function(){var ad=$(this).attr("name"),ae=$(this).val();ac[ad]=JSON.stringify(ae)});return ac},get_param_values:function(){var ad=[];var ac={};this.parent_div.find(":input").each(function(){var ae=$(this).attr("name"),af=$(this).val();if(ae){ad[ad.length]=af}});return ad},run_on_dataset:function(){var ac=this;ac.run({dataset_id:this.track.original_dataset_id,tool_id:ac.name},null,function(ad){show_modal(ac.name+" is Running",ac.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ad={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},ah=this.track,ae=ad.tool_id+ah.tool_region_and_parameters_str(ad.chrom,ad.low,ad.high),ac;if(ah.container===view){var ag=new N(view,view,{name:this.name});var af=ah.container.replace_drawable(ah,ag,false);ag.container_div.insertBefore(ah.view.content_div.children()[af]);ag.add_drawable(ah);ah.container_div.appendTo(ag.content_div);ac=ag}else{ac=ah.container}var ai=new ah.constructor(view,ac,{name:ae,hda_ldda:"hda"});ai.init_for_tool_data();ai.change_mode(ah.mode);ai.set_filters_manager(ah.filters_manager.copy(ai));ai.update_icons();ac.add_drawable(ai);ai.content_div.text("Starting job.");this.update_params();this.run(ad,ai,function(aj){ai.dataset_id=aj.dataset_id;ai.content_div.text("Running job.");ai.init()})},run:function(ad,ae,af){$.extend(ad,this.get_param_values_dict());var ac=function(){$.getJSON(rerun_tool_url,ad,function(ag){if(ag==="no converter"){ae.container_div.addClass("error");ae.content_div.text(H)}else{if(ag.error){ae.container_div.addClass("error");ae.content_div.text(v+ag.message)}else{if(ag==="pending"){ae.container_div.addClass("pending");ae.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(ac,2000)}else{af(ag)}}}})};ac()}});var L=function(ad,ac,ae,af){this.name=ad;this.label=ac;this.html=$(ae);this.value=af};p(L.prototype,{update_value:function(){this.value=$(this.html).val()}});var f=function(ae,ad,ag,ah,af,ac){L.call(this,ae,ad,ag,ah);this.min=af;this.max=ac};p(f.prototype,L.prototype,{update_value:function(){L.prototype.update_value.call(this);this.value=parseFloat(this.value)}});var g=function(ac){this.manager=null;this.name=ac.name;this.index=ac.index;this.tool_id=ac.tool_id;this.tool_exp_name=ac.tool_exp_name};p(g.prototype,{to_dict:function(){return{name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name}}});var S=function(al){g.call(this,al);this.low=("low" in al?al.low:-Number.MAX_VALUE);this.high=("high" in al?al.high:Number.MAX_VALUE);this.min=("min" in al?al.min:Number.MAX_VALUE);this.max=("max" in al?al.max:-Number.MAX_VALUE);this.container=null;this.slider=null;this.slider_label=null;var ah=function(am,an,ao){am.click(function(){var au=an.text(),ar=parseFloat(ao.slider("option","max")),aq=(ar<=1?4:ar<=1000000?ar.toString().length:6),at=false,ap=$(this).parents(".slider-row");ap.addClass("input");if(ao.slider("option","values")){aq=2*aq+1;at=true}an.text("");$("<input type='text'/>").attr("size",aq).attr("maxlength",aq).attr("value",au).appendTo(an).focus().select().click(function(av){av.stopPropagation()}).blur(function(){$(this).remove();an.text(au);ap.removeClass("input")}).keyup(function(az){if(az.keyCode===27){$(this).trigger("blur")}else{if(az.keyCode===13){var ax=ao.slider("option","min"),av=ao.slider("option","max"),ay=function(aA){return(isNaN(aA)||aA>av||aA<ax)},aw=$(this).val();if(!at){aw=parseFloat(aw);if(ay(aw)){alert("Parameter value must be in the range ["+ax+"-"+av+"]");return $(this)}}else{aw=aw.split("-");aw=[parseFloat(aw[0]),parseFloat(aw[1])];if(ay(aw[0])||ay(aw[1])){alert("Parameter value must be in the range ["+ax+"-"+av+"]");return $(this)}}ao.slider((at?"values":"value"),aw);ap.removeClass("input")}}})})};var ad=this;ad.parent_div=$("<div/>").addClass("filter-row slider-row");var ac=$("<div/>").addClass("elt-label").appendTo(ad.parent_div),aj=$("<span/>").addClass("slider-name").text(ad.name+" ").appendTo(ac),ae=$("<span/>").text(this.low+"-"+this.high),af=$("<span/>").addClass("slider-value").appendTo(ac).append("[").append(ae).append("]");ad.values_span=ae;var ai=$("<div/>").addClass("slider").appendTo(ad.parent_div);ad.control_element=$("<div/>").attr("id",ad.name+"-filter-control").appendTo(ai);var ag=[0,0];ad.control_element.slider({range:true,min:this.min,max:this.max,step:this.get_slider_step(this.min,this.max),values:[this.low,this.high],slide:function(am,an){ad.slide(am,an)},change:function(am,an){ad.control_element.slider("option","slide").call(ad.control_element,am,an)}});ad.slider=ad.control_element;ad.slider_label=ae;ah(af,ae,ad.control_element);var ak=$("<div/>").addClass("display-controls").appendTo(ad.parent_div);this.transparency_icon=create_action_icon("Use filter for data transparency","layer-transparent",function(){if(ad.manager.alpha_filter!==ad){ad.manager.alpha_filter=ad;ad.manager.parent_div.find(".layer-transparent").removeClass("active").hide();ad.transparency_icon.addClass("active").show()}else{ad.manager.alpha_filter=null;ad.transparency_icon.removeClass("active")}ad.manager.track.request_draw(true,true)}).appendTo(ak).hide();this.height_icon=create_action_icon("Use filter for data height","arrow-resize-090",function(){if(ad.manager.height_filter!==ad){ad.manager.height_filter=ad;ad.manager.parent_div.find(".arrow-resize-090").removeClass("active").hide();ad.height_icon.addClass("active").show()}else{ad.manager.height_filter=null;ad.height_icon.removeClass("active")}ad.manager.track.request_draw(true,true)}).appendTo(ak).hide();ad.parent_div.hover(function(){ad.transparency_icon.show();ad.height_icon.show()},function(){if(ad.manager.alpha_filter!==ad){ad.transparency_icon.hide()}if(ad.manager.height_filter!==ad){ad.height_icon.hide()}});$("<div style='clear: both;'/>").appendTo(ad.parent_div)};p(S.prototype,{to_dict:function(){var ac=g.prototype.to_dict.call(this);return p(ac,{type:"number",min:this.min,max:this.max,low:this.low,high:this.high})},copy:function(){return new S({name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name})},get_slider_step:function(ae,ac){var ad=ac-ae;return(ad<=2?0.01:1)},slide:function(ad,ae){var ac=ae.values;this.values_span.text(ac[0]+"-"+ac[1]);this.low=ac[0];this.high=ac[1];this.manager.track.request_draw(true,true)},applies_to:function(ac){if(ac.length>this.index){return true}return false},keep:function(ac){if(!this.applies_to(ac)){return true}var ad=ac[this.index];return(isNaN(ad)||(ad>=this.low&&ad<=this.high))},update_attrs:function(ad){var ac=false;if(!this.applies_to(ad)){return ac}if(ad[this.index]<this.min){this.min=Math.floor(ad[this.index]);ac=true}if(ad[this.index]>this.max){this.max=Math.ceil(ad[this.index]);ac=true}return ac},update_ui_elt:function(){if(this.min!==this.max){this.parent_div.show()}else{this.parent_div.hide()}var ad=this.slider.slider("option","min"),ac=this.slider.slider("option","max");if(this.min<ad||this.max>ac){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",this.get_slider_step(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var X=function(ae,ak){this.track=ae;this.alpha_filter=null;this.height_filter=null;this.filters=[];this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(am){am.stopPropagation()}).click(function(am){am.stopPropagation()}).bind("dblclick",function(am){am.stopPropagation()}).bind("keydown",function(am){am.stopPropagation()});if(ak&&"filters" in ak){var ac=("alpha_filter" in ak?ak.alpha_filter:null),af=("height_filter" in ak?ak.height_filter:null),ah=ak.filters,ad;for(var ai=0;ai<ah.length;ai++){if(ah[ai].type==="number"){ad=new S(ah[ai]);this.add_filter(ad);if(ad.name===ac){this.alpha_filter=ad;ad.transparency_icon.addClass("active").show()}if(ad.name===af){this.height_filter=ad;ad.height_icon.addClass("active").show()}}else{console.log("ERROR: unsupported filter: ",name,type)}}if("visible" in ak&&ak.visible){this.parent_div.show()}}if(this.filters.length!==0){var al=$("<div/>").addClass("param-row").appendTo(this.parent_div);var aj=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(al);var ag=this;aj.click(function(){ag.run_on_dataset()})}};p(X.prototype,{show:function(){this.parent_div.show()},hide:function(){this.parent_div.hide()},toggle:function(){this.parent_div.toggle()},visible:function(){return this.parent_div.is(":visible")},to_dict:function(){var af={},ae=[],ad;for(var ac=0;ac<this.filters.length;ac++){ad=this.filters[ac];ae.push(ad.to_dict())}af.filters=ae;af.alpha_filter=(this.alpha_filter?this.alpha_filter.name:null);af.height_filter=(this.height_filter?this.height_filter.name:null);af.visible=this.parent_div.is(":visible");return af},copy:function(ad){var ae=new X(ad);for(var ac=0;ac<this.filters.length;ac++){ae.add_filter(this.filters[ac].copy())}return ae},add_filter:function(ac){ac.manager=this;this.parent_div.append(ac.parent_div);this.filters.push(ac)},remove_all:function(){this.filters=[];this.parent_div.children().remove()},init_filters:function(){for(var ac=0;ac<this.filters.length;ac++){var ad=this.filters[ac];ad.update_ui_elt()}},clear_filters:function(){for(var ac=0;ac<this.filters.length;ac++){var ad=this.filters[ac];ad.slider.slider("option","values",[ad.min,ad.max])}this.alpha_filter=null;this.height_filter=null;this.parent_div.find(".icon-button").hide()},run_on_dataset:function(){var ak=function(ao,am,an){if(!(am in ao)){ao[am]=an}return ao[am]};var ae={},ac,ad,af;for(var ag=0;ag<this.filters.length;ag++){ac=this.filters[ag];if(ac.tool_id){if(ac.min!==ac.low){ad=ak(ae,ac.tool_id,[]);ad[ad.length]=ac.tool_exp_name+" >= "+ac.low}if(ac.max!==ac.high){ad=ak(ae,ac.tool_id,[]);ad[ad.length]=ac.tool_exp_name+" <= "+ac.high}}}var ai=[];for(var al in ae){ai[ai.length]=[al,ae[al]]}var aj=ai.length;(function ah(at,ap){var an=ap[0],ao=an[0],ar=an[1],aq="("+ar.join(") and (")+")",am={cond:aq,input:at,target_dataset_id:at,tool_id:ao},ap=ap.slice(1);$.getJSON(run_tool_url,am,function(au){if(au.error){show_modal("Filter Dataset","Error running tool "+ao,{Close:hide_modal})}else{if(ap.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{ah(au.dataset_id,ap)}}})})(this.track.dataset_id,ai)}});var z=function(ac,ad){J.Scaler.call(this,ad);this.filter=ac};z.prototype.gen_val=function(ac){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ac[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var C=function(ac){this.track=ac.track;this.params=ac.params;this.values={};this.restore_values((ac.saved_values?ac.saved_values:{}));this.onchange=ac.onchange};p(C.prototype,{restore_values:function(ac){var ad=this;$.each(this.params,function(ae,af){if(ac[af.key]!==undefined){ad.values[af.key]=ac[af.key]}else{ad.values[af.key]=af.default_value}})},build_form:function(){var af=this;var ac=$("<div />");var ae;function ad(aj,ag){for(var an=0;an<aj.length;an++){ae=aj[an];if(ae.hidden){continue}var ah="param_"+an;var ar=af.values[ae.key];var av=$("<div class='form-row' />").appendTo(ag);av.append($("<label />").attr("for",ah).text(ae.label+":"));if(ae.type==="bool"){av.append($('<input type="checkbox" />').attr("id",ah).attr("name",ah).attr("checked",ar))}else{if(ae.type==="text"){av.append($('<input type="text"/>').attr("id",ah).val(ar).click(function(){$(this).select()}))}else{if(ae.type==="select"){var ap=$("<select />").attr("id",ah);for(var al=0;al<ae.options.length;al++){$("<option/>").text(ae.options[al].label).attr("value",ae.options[al].value).appendTo(ap)}ap.val(ar);av.append(ap)}else{if(ae.type==="color"){var au=$("<div/>").appendTo(av),ao=$("<input />").attr("id",ah).attr("name",ah).val(ar).css("float","left").appendTo(au).click(function(ax){$(".tipsy").hide();var aw=$(this).siblings(".tipsy");aw.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(aw).height()/2)+($(this).height()/2)}).show();aw.click(function(ay){ay.stopPropagation()});$(document).bind("click.color-picker",function(){aw.hide();$(document).unbind("click.color-picker")});ax.stopPropagation()}),am=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(au).attr("title","Set new random color").tipsy({gravity:"s"}),aq=$("<div class='tipsy tipsy-west' style='position: absolute;' />").appendTo(au).hide(),ai=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(aq),at=$("<div/>").appendTo(ai),ak=$.farbtastic(at,{width:100,height:100,callback:ao,color:ar});au.append($("<div/>").css("clear","both"));(function(aw){am.click(function(){aw.setColor(get_random_color())})})(ak)}else{av.append($("<input />").attr("id",ah).attr("name",ah).val(ar))}}}}if(ae.help){av.append($("<div class='help'/>").text(ae.help))}}}ad(this.params,ac);return ac},update_from_form:function(ac){var ae=this;var ad=false;$.each(this.params,function(af,ah){if(!ah.hidden){var ai="param_"+af;var ag=ac.find("#"+ai).val();if(ah.type==="float"){ag=parseFloat(ag)}else{if(ah.type==="int"){ag=parseInt(ag)}else{if(ah.type==="bool"){ag=ac.find("#"+ai).is(":checked")}}}if(ag!==ae.values[ah.key]){ae.values[ah.key]=ag;ad=true}}});if(ad){this.onchange();this.track.changed()}}});var b=function(ac,af,ae,ad,ag){this.track=ac;this.index=af;var ah=this.track._get_tile_bounds(af,ae);this.low=ah[0];this.high=ah[1];this.resolution=ae;this.html_elt=$("<div class='track-tile'/>").append(ad);this.data=ag;this.stale=false};b.prototype.predisplay_actions=function(){};var k=function(ac,af,ae,ad,ag,ah){b.call(this,ac,af,ae,ad,ag);this.max_val=ah};p(k.prototype,b.prototype);var M=function(af,ak,ag,ae,ai,ao,aj,ap,ad,am){b.call(this,af,ak,ag,ae,ai);this.mode=aj;this.all_slotted=ad;this.feature_mapper=am;this.has_icons=false;if(ap){this.has_icons=true;var al=this;ae=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:A-1,width:ae.width}).prependTo(this.html_elt);var an=ai.length,ah=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+an+" features in this region were obtained from server. Click to get more data including depth").tipsy({gravity:"s"}).appendTo(message_div),ac=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+an+" features in this region were obtained from server. Click to get more data excluding depth").tipsy({gravity:"s"}).appendTo(message_div);ah.click(function(){al.stale=true;af.data_manager.get_more_data(al.low,al.high,af.mode,al.resolution,{},af.data_manager.DEEP_DATA_REQ);$(".tipsy").hide();af.request_draw()}).dblclick(function(aq){aq.stopPropagation()});ac.click(function(){al.stale=true;af.data_manager.get_more_data(al.low,al.high,af.mode,al.resolution,{},af.data_manager.BROAD_DATA_REQ);$(".tipsy").hide();af.request_draw()}).dblclick(function(aq){aq.stopPropagation()})}};p(M.prototype,b.prototype);M.prototype.predisplay_actions=function(){var ad=this,ac={};if(ad.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).siblings(".feature-popup").remove()}).mousemove(function(ao){if(!this.hovered){return}var aj=$(this).offset(),an=ao.pageX-aj.left,am=ao.pageY-aj.top,at=ad.feature_mapper.get_feature_data(an,am),ak=(at?at[0]:null);$(this).siblings(".feature-popup").each(function(){if(!ak||$(this).attr("id")!==ak.toString()){$(this).remove()}});if(at){var af=ac[ak];if(!af){var ak=at[0],ap={name:at[3],start:at[1],end:at[2],strand:at[4]},ai=ad.track.filters_manager.filters,ah;for(var al=0;al<ai.length;al++){ah=ai[al];ap[ah.name]=at[ah.index]}var af=$("<div/>").attr("id",ak).addClass("feature-popup"),au=$("<table/>"),ar,aq,av;for(ar in ap){aq=ap[ar];av=$("<tr/>").appendTo(au);$("<th/>").appendTo(av).text(ar);$("<td/>").attr("align","left").appendTo(av).text(typeof(aq)==="number"?W(aq,2):aq)}af.append($("<div class='feature-popup-inner'>").append(au));ac[ak]=af}af.appendTo($(ad.html_elt).parent());var ag=an+parseInt(ad.html_elt.css("left"))-af.width()/2,ae=am+parseInt(ad.html_elt.css("top"))+7;af.css("left",ag+"px").css("top",ae+"px")}else{if(!ao.isPropagationStopped()){ao.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ao)})}}}).mouseleave(function(){$(this).siblings(".feature-popup").remove()})};var i=function(ad,ac,ae){p(ae,{drag_handle_class:"draghandle"});q.call(this,ad,ac,ae);this.data_url=("data_url" in ae?ae.data_url:default_data_url);this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ae?ae.data_query_wait:I);this.dataset_check_url=converted_datasets_state_url;this.data_manager=("data_manager" in ae?ae.data_manager:new P(F,this));this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div)}};p(i.prototype,q.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},q.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(ac){ac.view.set_overview(ac)}},q.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters()}else{ac.filters_manager.init_filters()}ac.filters_manager.toggle()}},{name:"tools_icon",title:"Tools",css_class:"tools-icon",on_click_fn:function(ac){ac.dynamic_tool_div.toggle();if(ac.dynamic_tool_div.is(":visible")){ac.set_name(ac.name+ac.tool_region_and_parameters_str())}else{ac.revert_name()}$(".tipsy").remove()}},q.prototype.action_icons_def[2]],can_draw:function(){if(this.dataset_id&&q.prototype.can_draw.call(this)){return true}return false},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var ac=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ac)}this.name_div=$("<div/>").addClass("track-name").appendTo(ac).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ac},set_display_modes:function(af,ai){this.display_modes=af;this.mode=(ai?ai:(this.config&&this.config.values.mode?this.config.values.mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ad=this,ag={};for(var ae=0,ac=ad.display_modes.length;ae<ac;ae++){var ah=ad.display_modes[ae];ag[ah]=function(aj){return function(){ad.change_mode(aj);ad.icons_div.show();ad.container_div.mouseleave(function(){ad.icons_div.hide()})}}(ah)}make_popupmenu(this.action_icons.mode_icon,ag)},build_action_icons:function(){q.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.content_div.children().remove();this.content_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.content_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof Y){return"LabelTrack"}else{if(this instanceof y){return"ReferenceTrack"}else{if(this instanceof j){return"LineTrack"}else{if(this instanceof T){return"ReadTrack"}else{if(this instanceof Q){return"VcfTrack"}else{if(this instanceof h){return"CompositeTrack"}else{if(this instanceof d){return"FeatureTrack"}}}}}}}return""},init:function(){var ad=this;ad.enabled=false;ad.tile_cache.clear();ad.data_manager.clear();ad.content_div.css("height","auto");ad.content_div.children().remove();ad.container_div.removeClass("nodata error pending");if(!ad.dataset_id){return}var ac=$.Deferred();$.getJSON(converted_datasets_state_url,{hda_ldda:ad.hda_ldda,dataset_id:ad.dataset_id,chrom:ad.view.chrom},function(ae){if(!ae||ae==="error"||ae.kind==="error"){ad.container_div.addClass("error");ad.content_div.text(o);if(ae.message){var af=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ae.message+"</pre>",{Close:hide_modal})});ad.content_div.append(af)}}else{if(ae==="no converter"){ad.container_div.addClass("error");ad.content_div.text(H)}else{if(ae==="no data"||(ae.data!==undefined&&(ae.data===null||ae.data.length===0))){ad.container_div.addClass("nodata");ad.content_div.text(B)}else{if(ae==="pending"){ad.container_div.addClass("pending");ad.content_div.text(t);setTimeout(function(){ad.init()},ad.data_query_wait)}else{if(ae.status==="data"){if(ae.valid_chroms){ad.valid_chroms=ae.valid_chroms;ad.update_icons()}ad.content_div.text(V);if(ad.view.chrom){ad.content_div.text("");ad.content_div.css("height",ad.height_px+"px");ad.enabled=true;$.when(ad.predraw_init()).done(function(){ac.resolve();ad.container_div.removeClass("nodata error pending");ad.request_draw()})}else{ac.resolve()}}}}}}});this.update_icons();return ac},predraw_init:function(){}});var K=function(ae,ad,af){i.call(this,ae,ad,af);var ac=this,ae=ac.view;m(ac.container_div,ac.drag_handle_class,".group",ac);this.filters_manager=new X(this,("filters" in af?af.filters:null));this.filters_available=false;this.tool=("tool" in af&&af.tool?new r(this,af.tool,af.tool_state):null);this.tile_cache=new c(O);if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}if(af.mode){this.change_mode(af.mode)}};p(K.prototype,q.prototype,i.prototype,{action_icons_def:i.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ac){$(".tipsy").remove();ac.slotters[ac.view.resolution_px_b].max_rows*=2;ac.request_draw(true)},hide:true}]),copy:function(ac){var ad=this.to_dict();p(ad,{data_manager:this.data_manager});var ae=new this.constructor(this.view,ac,ad);ae.change_mode(this.mode);ae.enabled=this.enabled;return ae},set_filters_manager:function(ac){this.filters_manager=ac;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},change_mode:function(ad){var ac=this;ac.mode=ad;ac.config.values.mode=ad;ac.tile_cache.clear();ac.request_draw();this.action_icons.mode_icon.attr("title","Set display mode (now: "+ac.mode+")");return ac},update_icons:function(){var ac=this;if(ac.filters_available){ac.action_icons.filters_icon.show()}else{ac.action_icons.filters_icon.hide()}if(ac.tool){ac.action_icons.tools_icon.show()}else{ac.action_icons.tools_icon.hide()}},_gen_tile_cache_key:function(ad,ae,ac){return ad+"_"+ae+"_"+ac},request_draw:function(ad,ac){this.view.request_redraw(false,ad,ac,this)},_draw:function(ad,an){if(!this.can_draw()){return}var al=this.view.low,ah=this.view.high,aj=ah-al,ae=this.view.container.width(),ap=this.view.resolution_px_b,ag=this.view.resolution_b_px;if(this.is_overview){al=this.view.max_low;ah=this.view.max_high;ag=Math.pow(RESOLUTION,Math.ceil(Math.log((view.max_high-view.max_low)/R)/Math.log(RESOLUTION)));ap=ae/(view.max_high-view.max_low)}this.content_div.children().addClass("remove");this.max_height=0;var ac=Math.floor(al/(ag*R)),ak=true,ao=[],ai=function(aq){return(aq&&"track" in aq)};while((ac*R*ag)<ah){var am=this.draw_helper(ad,ae,ac,ag,this.content_div,ap);if(ai(am)){ao.push(am)}else{ak=false}ac+=1}if(!an){this.content_div.children(".remove").remove()}var af=this;if(ak){this.content_div.children(".remove").remove();af.postdraw_actions(ao,ae,ap,an)}},postdraw_actions:function(af,ag,ai,ac){var ae=this;var ah=false;for(var ad=0;ad<af.length;ad++){if(af[ad].has_icons){ah=true;break}}if(ah){for(var ad=0;ad<af.length;ad++){tile=af[ad];if(!tile.has_icons){tile.html_elt.css("padding-top",A)}}}},draw_helper:function(ac,ao,au,ar,ah,ai,ap){var an=this,ax=this._gen_tile_cache_key(ao,ai,au),af=this._get_tile_bounds(au,ar),av=af[0],ad=af[1];if(!ap){ap={}}var aw=(ac?undefined:an.tile_cache.get(ax));if(aw){an.show_tile(aw,ah,ai);return aw}var al=true;var at=an.data_manager.get_data(av,ad,an.mode,ar,an.data_url_extra_params);if(is_deferred(at)){al=false}var aj;if(view.reference_track&&ai>view.canvas_manager.char_width_px){aj=view.reference_track.data_manager.get_data(av,ad,an.mode,ar,view.reference_track.data_url_extra_params);if(is_deferred(aj)){al=false}}if(al){p(at,ap.more_tile_data);var ak=an.mode;if(ak==="Auto"){ak=an.get_mode(at);an.update_auto_mode(ak)}var ae=an.view.canvas_manager.new_canvas(),af=an._get_tile_bounds(au,ar),av=af[0],ad=af[1],ao=Math.ceil((ad-av)*ai)+an.left_offset,am=an.get_canvas_height(at,ak,ai,ao);ae.width=ao;ae.height=am;var aq=ae.getContext("2d");aq.translate(this.left_offset,0);var aw=an.draw_tile(at,aq,ak,ar,au,ai,aj);if(aw!==undefined){an.tile_cache.set(ax,aw);an.show_tile(aw,ah,ai)}return aw}var ag=$.Deferred();$.when(at,aj).then(function(){view.request_redraw(false,false,false,an);ag.resolve()});return ag},get_canvas_height:function(ac,ae,af,ad){return this.height_px},draw_tile:function(ac,ae,ah,ag,ad,ai,af){console.log("Warning: TiledTrack.draw_tile() not implemented.")},show_tile:function(ae,ag,ah){var ad=this,ac=ae.html_elt;ae.predisplay_actions();var af=(ae.low-(this.is_overview?this.view.max_low:this.view.low))*ah;if(this.left_offset){af-=this.left_offset}ac.css({position:"absolute",top:0,left:af,height:""});if(ac.hasClass("remove")){ac.removeClass("remove")}else{ag.append(ac)}ad.max_height=Math.max(ad.max_height,ac.height());ad.content_div.css("height",ad.max_height+"px");ag.children().css("height",ad.max_height+"px")},_get_tile_bounds:function(ac,ad){var af=Math.floor(ac*R*ad),ag=Math.ceil(R*ad),ae=(af+ag<=this.view.max_high?af+ag:this.view.max_high);return[af,ae]},tool_region_and_parameters_str:function(ae,ac,af){var ad=this,ag=(ae!==undefined&&ac!==undefined&&af!==undefined?ae+":"+ac+"-"+af:"all");return" - region=["+ag+"], parameters=["+ad.tool.get_param_values().join(", ")+"]"},data_and_mode_compatible:function(ac,ad){return true},can_subset:function(ac){return false},init_for_tool_data:function(){this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url;this.predraw_init=function(){var ad=this;var ac=function(){if(ad.data_manager.size()===0){setTimeout(ac,300)}else{ad.data_url=default_data_url;ad.data_query_wait=I;ad.dataset_state_url=converted_datasets_state_url;$.getJSON(ad.dataset_state_url,{dataset_id:ad.dataset_id,hda_ldda:ad.hda_ldda},function(ae){})}};ac()}}});var Y=function(ad,ac){var ae={todo:"label",todo:false};i.call(this,ad,ac,ae);this.container_div.addClass("label-track")};p(Y.prototype,i.prototype,{build_header_div:function(){},init:function(){this.enabled=true},_draw:function(){var ae=this.view,af=ae.high-ae.low,ai=Math.floor(Math.pow(10,Math.floor(Math.log(af)/Math.log(10)))),ac=Math.floor(ae.low/ai)*ai,ag=this.view.container.width(),ad=$("<div style='position: relative; height: 1.3em;'></div>");while(ac<ae.high){var ah=(ac-ae.low)/af*ag;ad.append($("<div class='label'>"+commatize(ac)+"</div>").css({position:"absolute",left:ah-1}));ac+=ai}this.content_div.children(":first").remove();this.content_div.append(ad)}});var h=function(ad,ac,ag){K.call(this,ad,ac,ag);this.drawables=[];this.left_offset=0;if("drawables" in ag){var af;for(var ae=0;ae<ag.drawables.length;ae++){af=ag.drawables[ae];this.drawables[ae]=object_from_template(af);if(af.left_offset>this.left_offset){this.left_offset=af.left_offset}}this.enabled=true}if(this.drawables.length!==0){this.set_display_modes(this.drawables[0].display_modes,this.drawables[0].mode)}this.update_icons();this.obj_type="CompositeTrack"};p(h.prototype,K.prototype,{action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ac){$(".tipsy").remove();ac.show_group()}}].concat(K.prototype.action_icons_def),to_dict:w.prototype.to_dict,add_drawable:w.prototype.add_drawable,unpack_drawables:w.prototype.unpack_drawables,change_mode:function(ac){K.prototype.change_mode.call(this,ac);for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].change_mode(ac)}},init:function(){var ae=[];for(var ad=0;ad<this.drawables.length;ad++){ae.push(this.drawables[ad].init())}var ac=this;$.when.apply($,ae).then(function(){ac.enabled=true;ac.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide()},can_draw:q.prototype.can_draw,draw_helper:function(ad,ar,ay,av,aj,al,at){var aq=this,aC=this._gen_tile_cache_key(ar,al,ay),ah=this._get_tile_bounds(ay,av),az=ah[0],ae=ah[1];if(!at){at={}}var aB=(ad?undefined:aq.tile_cache.get(aC));if(aB){aq.show_tile(aB,aj,al);return aB}var ak=[],aq,ao=true,aw,am;for(var ax=0;ax<this.drawables.length;ax++){aq=this.drawables[ax];aw=aq.data_manager.get_data(az,ae,aq.mode,av,aq.data_url_extra_params);if(is_deferred(aw)){ao=false}ak.push(aw);am=null;if(view.reference_track&&al>view.canvas_manager.char_width_px){am=view.reference_track.data_manager.get_data(az,ae,aq.mode,av,view.reference_track.data_url_extra_params);if(is_deferred(am)){ao=false}}ak.push(am)}if(ao){p(aw,at.more_tile_data);this.tile_predraw_init();var ag=aq.view.canvas_manager.new_canvas(),ah=aq._get_tile_bounds(ay,av),az=ah[0],ae=ah[1],aA=0,ar=Math.ceil((ae-az)*al)+this.left_offset,ap=0,af=[];var ac=0;for(var ax=0;ax<this.drawables.length;ax++,aA+=2){aq=this.drawables[ax];aw=ak[aA];var an=aq.mode;if(an==="Auto"){an=aq.get_mode(aw);aq.update_auto_mode(an)}af.push(an);ac=aq.get_canvas_height(aw,an,al,ar);if(ac>ap){ap=ac}}ag.width=ar;ag.height=(at.height?at.height:ap);aA=0;var au=ag.getContext("2d");au.translate(this.left_offset,0);au.globalAlpha=0.5;au.globalCompositeOperation="source-over";for(var ax=0;ax<this.drawables.length;ax++,aA+=2){aq=this.drawables[ax];aw=ak[aA];am=ak[aA+1];aB=aq.draw_tile(aw,au,af[ax],av,ay,al,am)}this.tile_cache.set(aC,aB);this.show_tile(aB,aj,al);return aB}var ai=$.Deferred(),aq=this;$.when.apply($,ak).then(function(){view.request_redraw(false,false,false,aq);ai.resolve()});return ai},show_group:function(){var af=new N(this.view,this.container,{name:this.name}),ac;for(var ae=0;ae<this.drawables.length;ae++){ac=this.drawables[ae];af.add_drawable(ac);ac.container=af;af.content_div.append(ac.container_div)}var ad=this.container.replace_drawable(this,af,true);af.request_draw()},tile_predraw_init:function(){var af=Number.MAX_VALUE,ac=-af,ad;for(var ae=0;ae<this.drawables.length;ae++){ad=this.drawables[ae];if(ad instanceof j){if(ad.prefs.min_value<af){af=ad.prefs.min_value}if(ad.prefs.max_value>ac){ac=ad.prefs.max_value}}}for(var ae=0;ae<this.drawables.length;ae++){ad=this.drawables[ae];ad.prefs.min_value=af;ad.prefs.max_value=ac}},postdraw_actions:function(ae,ah,aj,ad){K.prototype.postdraw_actions.call(this,ae,ah,aj,ad);var ag=-1;for(var af=0;af<ae.length;af++){var ac=ae[af].html_elt.find("canvas").height();if(ac>ag){ag=ac}}for(var af=0;af<ae.length;af++){var ai=ae[af];if(ai.html_elt.find("canvas").height()!==ag){this.draw_helper(true,ah,ai.index,ai.resolution,ai.html_elt.parent(),aj,{height:ag});ai.html_elt.remove()}}}});var y=function(ac){K.call(this,"reference",ac,{content_div:ac.top_labeltrack},{});ac.reference_track=this;this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:ac.dbkey};this.data_manager=new E(F,this,false)};p(y.prototype,q.prototype,K.prototype,{build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},can_draw:q.prototype.can_draw,draw_tile:function(ak,al,ah,ag,ad,am){var af=this;if(am>this.view.canvas_manager.char_width_px){if(ak.data===null){af.content_div.css("height","0px");return}var ae=al.canvas;al.font=al.canvas.manager.default_font;al.textAlign="center";ak=ak.data;for(var ai=0,aj=ak.length;ai<aj;ai++){var ac=Math.floor(ai*am);al.fillText(ak[ai],ac,10)}return new b(af,ad,ag,ae,ak)}this.content_div.css("height","0px")}});var j=function(ae,ad,af){var ac=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";K.call(this,ae,ad,af);this.min_height_px=16;this.max_height_px=400;this.height_px=32;this.hda_ldda=af.hda_ldda;this.dataset_id=af.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Color",type:"color",default_value:get_random_color()},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:af.prefs,onchange:function(){ac.set_name(ac.prefs.name);ac.vertical_range=ac.prefs.max_value-ac.prefs.min_value;ac.set_min_value(ac.prefs.min_value);ac.set_max_value(ac.prefs.max_value)}});this.prefs=this.config.values;this.height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value;this.add_resize_handle()};p(j.prototype,q.prototype,K.prototype,{set_min_value:function(ac){this.prefs.min_value=ac;$("#linetrack_"+this.dataset_id+"_minval").text(this.prefs.min_value);this.tile_cache.clear();this.request_draw()},set_max_value:function(ac){this.prefs.max_value=ac;$("#linetrack_"+this.dataset_id+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.request_draw()},add_resize_handle:function(){var ac=this;var af=false;var ae=false;var ad=$("<div class='track-resize'>");$(ac.container_div).hover(function(){if(ac.content_visible){af=true;ad.show()}},function(){af=false;if(!ae){ad.hide()}});ad.hide().bind("dragstart",function(ag,ah){ae=true;ah.original_height=$(ac.content_div).height()}).bind("drag",function(ah,ai){var ag=Math.min(Math.max(ai.original_height+ai.deltaY,ac.min_height_px),ac.max_height_px);$(ac.content_div).css("height",ag);ac.height_px=ag;ac.request_draw(true)}).bind("dragend",function(ag,ah){ac.tile_cache.clear();ae=false;if(!af){ad.hide()}ac.config.values.height=ac.height_px}).appendTo(ac.container_div)},predraw_init:function(){var ac=this;ac.vertical_range=undefined;return $.getJSON(ac.data_url,{stats:true,chrom:ac.view.chrom,low:null,high:null,hda_ldda:ac.hda_ldda,dataset_id:ac.dataset_id},function(ad){ac.container_div.addClass("line-track");var ag=ad.data;if(isNaN(parseFloat(ac.prefs.min_value))||isNaN(parseFloat(ac.prefs.max_value))){var ae=ag.min;var ai=ag.max;ae=Math.floor(Math.min(0,Math.max(ae,ag.mean-2*ag.sd)));ai=Math.ceil(Math.max(0,Math.min(ai,ag.mean+2*ag.sd)));ac.prefs.min_value=ae;ac.prefs.max_value=ai;$("#track_"+ac.dataset_id+"_minval").val(ac.prefs.min_value);$("#track_"+ac.dataset_id+"_maxval").val(ac.prefs.max_value)}ac.vertical_range=ac.prefs.max_value-ac.prefs.min_value;ac.total_frequency=ag.total_frequency;ac.container_div.find(".yaxislabel").remove();var ah=get_editable_text_elt(W(ac.prefs.min_value,3),false,6,null,function(aj){var aj=parseFloat(aj);if(!isNaN(aj)){ac.set_min_value(aj)}}).addClass("yaxislabel bottom").attr("id","linetrack_"+ac.dataset_id+"_minval").prependTo(ac.container_div),af=get_editable_text_elt(W(ac.prefs.max_value,3),false,6,null,function(aj){var aj=parseFloat(aj);if(!isNaN(aj)){ac.set_max_value(aj)}}).addClass("yaxislabel top").attr("id","linetrack_"+ac.dataset_id+"_maxval").prependTo(ac.container_div)})},draw_tile:function(am,ak,ah,af,ad,al){var ae=ak.canvas,ac=this._get_tile_bounds(ad,af),ag=ac[0],aj=ac[1],ai=new J.LinePainter(am.data,ag,aj,this.prefs,ah);ai.draw(ak,ae.width,ae.height,al);return new b(this,ad,af,ae,am.data)},can_subset:function(ac){return false},});var d=function(ae,ad,af){var ac=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];K.call(this,ae,ad,af);this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:af.prefs,onchange:function(){ac.set_name(ac.prefs.name);ac.tile_cache.clear();ac.set_painter_from_config();ac.request_draw()}});this.prefs=this.config.values;this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=af.hda_ldda;this.dataset_id=af.dataset_id;this.original_dataset_id=af.dataset_id;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};p(d.prototype,q.prototype,K.prototype,{set_painter_from_config:function(){if(this.config.values.connector_style==="arcs"){this.painter=J.ArcLinkedFeaturePainter}else{this.painter=J.LinkedFeaturePainter}},postdraw_actions:function(ar,am,ah,ag){K.prototype.postdraw_actions.call(this,ar,ag);var al=this;if(al.mode==="Histogram"){var ad=-1;for(var ao=0;ao<ar.length;ao++){var an=ar[ao].max_val;if(an>ad){ad=an}}for(var ao=0;ao<ar.length;ao++){var au=ar[ao];if(au.max_val!==ad){au.html_elt.remove();al.draw_helper(true,am,au.index,au.resolution,au.html_elt.parent(),ah,{more_tile_data:{max:ad}})}}}if(al.filters_manager){var ai=al.filters_manager.filters;for(var aq=0;aq<ai.length;aq++){ai[aq].update_ui_elt()}var at=false,ac,aj;for(var ao=0;ao<ar.length;ao++){if(ar[ao].data.length){ac=ar[ao].data[0];for(var aq=0;aq<ai.length;aq++){aj=ai[aq];if(aj.applies_to(ac)&&aj.min!==aj.max){at=true;break}}}}if(al.filters_available!==at){al.filters_available=at;if(!al.filters_available){al.filters_manager.hide()}al.update_icons()}}this.container_div.find(".yaxislabel").remove();var af=ar[0];if(af instanceof k){var ak=(this.prefs.histogram_max?this.prefs.histogram_max:af.max_val),ae=get_editable_text_elt(ak,false,12,0,function(av){var av=parseFloat(av);al.prefs.histogram_max=(!isNaN(av)?av:null);al.tile_cache.clear();al.request_draw()}).addClass("yaxislabel top").css("color",this.prefs.label_color);this.container_div.prepend(ae)}if(af instanceof M){var ap=true;for(var ao=0;ao<ar.length;ao++){if(!ar[ao].all_slotted){ap=false;break}}if(!ap){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ac){var ac;if(this.mode==="Auto"){if(ac==="no_detail"){ac="feature spans"}else{if(ac==="summary_tree"){ac="coverage histogram"}}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ac+")")}},incremental_slots:function(ag,ac,af){var ad=this.view.canvas_manager.dummy_context,ae=this.slotters[ag];if(!ae||(ae.mode!==af)){ae=new (s.FeatureSlotter)(ag,af,x,function(ah){return ad.measureText(ah)});this.slotters[ag]=ae}return ae.slot_features(ac)},get_summary_tree_data:function(ag,aj,ae,ar){if(ar>ae-aj){ar=ae-aj}var an=Math.floor((ae-aj)/ar),aq=[],af=0;var ah=0,ai=0,am,ap=0,ak=[],ao,al;var ad=function(av,au,aw,at){av[0]=au+aw*at;av[1]=au+(aw+1)*at};while(ap<ar&&ah!==ag.length){var ac=false;for(;ap<ar&&!ac;ap++){ad(ak,aj,ap,an);for(ai=ah;ai<ag.length;ai++){am=ag[ai].slice(1,3);if(is_overlap(am,ak)){ac=true;break}}if(ac){break}}data_start_index=ai;aq[aq.length]=ao=[ak[0],0];for(;ai<ag.length;ai++){am=ag[ai].slice(1,3);if(is_overlap(am,ak)){ao[1]++}else{break}}if(ao[1]>af){af=ao[1]}ap++}return{max:af,delta:an,data:aq}},get_mode:function(ac){if(ac.dataset_type==="summary_tree"){mode="summary_tree"}else{if(ac.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>G){mode="Squish"}else{mode="Pack"}}}return mode},get_canvas_height:function(ac,ag,ah,ad){if(ag==="summary_tree"||ag==="Histogram"){return this.summary_draw_height}else{var af=this.incremental_slots(ah,ac.data,ag);var ae=new (this.painter)(null,null,null,this.prefs,ag);return Math.max(aa,ae.get_required_height(af,ad))}},draw_tile:function(an,ar,ap,at,ax,aj,ae){var aq=this,ad=ar.canvas,ag=this._get_tile_bounds(ax,at),aA=ag[0],ac=ag[1],aF=25,af=this.left_offset;if(ap==="summary_tree"||ap==="Histogram"){if(an.dataset_type!=="summary_tree"){var ak=this.get_summary_tree_data(an.data,aA,ac,200);if(an.max){ak.max=an.max}an=ak}var aC=new J.SummaryTreePainter(an,aA,ac,this.prefs);aC.draw(ar,ad.width,ad.height,aj);return new k(aq,ax,at,ad,an.data,an.max)}var ai=[],ao=this.slotters[aj].slots;all_slotted=true;if(an.data){var al=this.filters_manager.filters;for(var au=0,aw=an.data.length;au<aw;au++){var ah=an.data[au];var av=false;var am;for(var az=0,aE=al.length;az<aE;az++){am=al[az];am.update_attrs(ah);if(!am.keep(ah)){av=true;break}}if(!av){ai.push(ah);if(!(ah[0] in ao)){all_slotted=false}}}}var aD=(this.filters_manager.alpha_filter?new z(this.filters_manager.alpha_filter):null);var aB=(this.filters_manager.height_filter?new z(this.filters_manager.height_filter):null);var aC=new (this.painter)(ai,aA,ac,this.prefs,ap,aD,aB,ae);var ay=null;ar.fillStyle=this.prefs.block_color;ar.font=ar.canvas.manager.default_font;ar.textAlign="right";if(an.data){ay=aC.draw(ar,ad.width,ad.height,aj,ao);ay.translation=-af}return new M(aq,ax,at,ad,an.data,aj,ap,an.message,all_slotted,ay)},data_and_mode_compatible:function(ac,ad){if(ad==="Auto"){return true}else{if(ac.extra_info==="no_detail"||ac.dataset_type==="summary_tree"){return false}else{return true}}},can_subset:function(ac){if(ac.dataset_type==="summary_tree"||ac.message){return false}return true},});var Q=function(ad,ac,ae){d.call(this,ad,ac,ae);this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ae.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=J.ReadPainter};p(Q.prototype,q.prototype,K.prototype,d.prototype);var T=function(ae,ad,ag){d.call(this,ae,ad,ag);var af=get_random_color(),ac=get_random_color([af,"#ffffff"]);this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:af},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ac},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"Clear value to set automatically"},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ag.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=J.ReadPainter;this.update_icons()};p(T.prototype,q.prototype,K.prototype,d.prototype);U.View=Z;U.DrawableGroup=N;U.LineTrack=j;U.FeatureTrack=d;U.ReadTrack=T;U.VcfTrack=Q;U.CompositeTrack=h};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(i,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=i;this.mode=h;this.include_label=(h==="Pack");this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,h=this.start_end_dct,x=[],z=[],n=0,y=this.max_rows;for(var v=0,w=m.length;v<w;v++){var k=m[v],o=k[0];if(this.slots[o]!==undefined){n=Math.max(n,this.slots[o]);z.push(this.slots[o])}else{x.push(v)}}var q=function(E,F){for(var D=0;D<=y;D++){var B=false,G=h[D];if(G!==undefined){for(var A=0,C=G.length;A<C;A++){var i=G[A];if(F>i[0]&&E<i[1]){B=true;break}}}if(!B){return D}}return -1};for(var v=0,w=x.length;v<w;v++){var k=m[x[v]],o=k[0],t=k[1],f=k[2],r=k[3],g=Math.floor(t*p),l=Math.ceil(f*p),u=this.measureText(r).width,j;if(r!==undefined&&this.include_label){u+=(d+a);if(g-u>=0){g-=u;j="left"}else{l+=u;j="right"}}var s=q(g,l);if(s>=0){if(h[s]===undefined){h[s]=[]}h[s].push([g,l]);this.slots[o]=s;n=Math.max(n,s)}}return n+1}})};var painters_module=function(i,x){var u=i("class").extend;var p=function(I,A,G,z,F,D){if(D===undefined){D=4}var C=z-A;var B=F-G;var E=Math.floor(Math.sqrt(C*C+B*B)/D);var J=C/E;var H=B/E;var y;for(y=0;y<E;y++,A+=J,G+=H){if(y%2!==0){continue}I.fillRect(A,G,D,1)}};var q=function(B,A,z,E){var D=A-E/2,C=A+E/2,F=z-Math.sqrt(E*3/2);B.beginPath();B.moveTo(D,F);B.lineTo(C,F);B.lineTo(A,z);B.lineTo(D,F);B.strokeStyle=this.fillStyle;B.fill();B.stroke();B.closePath()};var d=function(y){this.default_val=(y?y:1)};d.prototype.gen_val=function(y){return this.default_val};var l=function(A,C,y,z,B){this.data=A;this.view_start=C;this.view_end=y;this.prefs=u({},this.default_prefs,z);this.mode=B};l.prototype.default_prefs={};l.prototype.draw=function(z,A,y,B){};var v=function(A,C,y,z,B){l.call(this,A,C,y,z,B)};v.prototype.default_prefs={show_counts:false};v.prototype.draw=function(L,z,K,M){var E=this.view_start,N=this.view_end-this.view_start,I=this.data.data,G=(this.prefs.histogram_max?this.prefs.histogram_max:this.data.max),B=K;delta_x_px=Math.ceil(this.data.delta*M);L.save();for(var C=0,D=I.length;C<D;C++){var H=Math.floor((I[C][0]-E)*M);var F=I[C][1];if(!F){continue}var J=F/G*K;if(F!==0&&J<1){J=1}L.fillStyle=this.prefs.block_color;L.fillRect(H,B-J,delta_x_px,J);var A=4;if(this.prefs.show_counts&&(L.measureText(F).width+A)<delta_x_px){L.fillStyle=this.prefs.label_color;L.textAlign="center";L.fillText(F,H+(delta_x_px/2),10)}}L.restore()};var b=function(y,C,E,F,A){l.call(this,y,C,E,F,A);if(this.prefs.min_value===undefined){var G=Infinity;for(var z=0,B=this.data.length;z<B;z++){G=Math.min(G,this.data[z][1])}this.prefs.min_value=G}if(this.prefs.max_value===undefined){var D=-Infinity;for(var z=0,B=this.data.length;z<B;z++){D=Math.max(D,this.data[z][1])}this.prefs.max_value=D}};b.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};b.prototype.draw=function(S,Q,N,D){var I=false,K=this.prefs.min_value,F=this.prefs.max_value,M=F-K,B=N,C=this.view_start,P=this.view_end-this.view_start,L=this.mode,aa=this.data;S.save();var ac=Math.round(N+K/M*N);if(L!=="Intensity"){S.fillStyle="#aaa";S.fillRect(0,ac,Q,1)}S.beginPath();var Y,G,E;if(aa.length>1){E=Math.ceil((aa[1][0]-aa[0][0])*D)}else{E=10}var A=parseInt(this.prefs.color.slice(1),16),H=(A&16711680)>>16,R=(A&65280)>>8,V=A&255;for(var T=0,U=aa.length;T<U;T++){S.fillStyle=S.strokeStyle=this.prefs.color;Y=Math.round((aa[T][0]-C)*D);G=aa[T][1];var W=false,J=false;if(G===null){if(I&&L==="Filled"){S.lineTo(Y,B)}I=false;continue}if(G<K){J=true;G=K}else{if(G>F){W=true;G=F}}if(L==="Histogram"){G=Math.round(G/M*B);S.fillRect(Y,ac,E,-G)}else{if(L==="Intensity"){var z=(G-K)/M,O=Math.round(H+(255-H)*(1-z)),X=Math.round(R+(255-R)*(1-z)),ab=Math.round(V+(255-V)*(1-z));S.fillStyle="rgb("+O+","+X+","+ab+")";S.fillRect(Y,0,E,B)}else{G=Math.round(B-(G-K)/M*B);if(I){S.lineTo(Y,G)}else{I=true;if(L==="Filled"){S.moveTo(Y,B);S.lineTo(Y,G)}else{S.moveTo(Y,G)}}}}S.fillStyle=this.prefs.overflow_color;if(W||J){var Z;if(L==="Histogram"||L==="Intensity"){Z=E}else{Y-=2;Z=4}if(W){S.fillRect(Y,0,Z,3)}if(J){S.fillRect(Y,B-3,Z,3)}}S.fillStyle=this.prefs.color}if(L==="Filled"){if(I){S.lineTo(Y,ac);S.lineTo(0,ac)}S.fill()}else{S.stroke()}S.restore()};var m=function(y){this.feature_positions={};this.slot_height=y;this.translation=0;this.y_translation=0};m.prototype.map_feature_data=function(z,B,y,A){if(!this.feature_positions[B]){this.feature_positions[B]=[]}this.feature_positions[B].push({data:z,x_start:y,x_end:A})};m.prototype.get_feature_data=function(z,D){var C=Math.floor((D-this.y_translation)/this.slot_height),B;if(!this.feature_positions[C]){return null}z+=this.translation;for(var A=0;A<this.feature_positions[C].length;A++){B=this.feature_positions[C][A];if(z>=B.x_start&&z<=B.x_end){return B.data}}};var o=function(A,D,y,z,C,E,B){l.call(this,A,D,y,z,C);this.alpha_scaler=(E?E:new d());this.height_scaler=(B?B:new d())};o.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};u(o.prototype,{get_required_height:function(A,z){var y=y_scale=this.get_row_height(),B=this.mode;if(B==="no_detail"||B==="Squish"||B==="Pack"){y=A*y_scale}return y+this.get_top_padding(z)+this.get_bottom_padding(z)},get_top_padding:function(y){return 0},get_bottom_padding:function(y){return Math.max(Math.round(this.get_row_height()/2),5)},draw:function(K,I,G,E,F){var Q=this.data,D=this.view_start,M=this.view_end;K.save();K.fillStyle=this.prefs.block_color;K.textAlign="right";var H=this.view_end-this.view_start,L=this.get_row_height(),P=new m(L),B;for(var N=0,O=Q.length;N<O;N++){var A=Q[N],C=A[0],J=A[1],y=A[2],z=(F&&F[C]!==undefined?F[C]:null);if((J<M&&y>D)&&(this.mode==="Dense"||z!==null)){B=this.draw_element(K,this.mode,A,z,D,M,E,L,I);P.map_feature_data(A,z,B[0],B[1])}}K.restore();P.y_translation=this.get_top_padding(I);return P},draw_element:function(E,A,G,C,B,D,F,z,y){console.log("WARNING: Unimplemented function.");return[0,0]}});var c=10,h=3,k=5,w=10,f=1,s=9,e=3,a=9,j=2,g="#ccc";var r=function(A,D,y,z,C,E,B){o.call(this,A,D,y,z,C,E,B);this.draw_background_connector=true;this.draw_individual_connectors=false};u(r.prototype,o.prototype,{get_row_height:function(){var z=this.mode,y;if(z==="Dense"){y=c}else{if(z==="no_detail"){y=h}else{if(z==="Squish"){y=k}else{y=w}}}return y},draw_element:function(M,D,X,H,O,aj,an,ap,y){var T=X[0],al=X[1],ad=X[2]-1,Q=X[3],ae=Math.floor(Math.max(0,(al-O)*an)),N=Math.ceil(Math.min(y,Math.max(0,(ad-O)*an))),ac=ae,ao=N,aa=(D==="Dense"?0:(0+H))*ap+this.get_top_padding(y),L,ah,R=null,ar=null,B=this.prefs.block_color,ag=this.prefs.label_color;M.globalAlpha=this.alpha_scaler.gen_val(X);if(D==="Dense"){H=1}if(D==="no_detail"){M.fillStyle=B;M.fillRect(ae,aa+5,N-ae,f)}else{var K=X[4],Z=X[5],af=X[6],C=X[7],V=true;if(Z&&af){R=Math.floor(Math.max(0,(Z-O)*an));ar=Math.ceil(Math.min(y,Math.max(0,(af-O)*an)))}var am,U;if(D==="Squish"){am=1;U=e;V=false}else{if(D==="Dense"){am=5;U=s}else{am=5;U=a}}if(!C){M.fillStyle=B;M.fillRect(ae,aa+1,N-ae,U);if(K&&V){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand_inv")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand_inv")}}M.fillRect(ae,aa+1,N-ae,U)}}else{var J,W;if(D==="Squish"||D==="Dense"){J=aa+Math.floor(e/2)+1;W=1}else{if(K){J=aa;W=U}else{J+=(e/2)+1;W=1}}if(this.draw_background_connector){if(D==="Squish"||D==="Dense"){M.fillStyle=g}else{if(K){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand")}}}else{M.fillStyle=g}}M.fillRect(ae,J,N-ae,W)}var E;for(var ak=0,A=C.length;ak<A;ak++){var F=C[ak],z=Math.floor(Math.max(0,(F[0]-O)*an)),Y=Math.ceil(Math.min(y,Math.max((F[1]-1-O)*an))),S,ab;if(z>Y){continue}M.fillStyle=B;M.fillRect(z,aa+(U-am)/2+1,Y-z,am);if(R!==undefined&&af>Z&&!(z>ar||Y<R)){var ai=Math.max(z,R),I=Math.min(Y,ar);M.fillRect(ai,aa+1,I-ai,U);if(C.length===1&&D==="Pack"){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand_inv")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand_inv")}}if(ai+14<I){ai+=2;I-=2}M.fillRect(ai,aa+1,I-ai,U)}}if(this.draw_individual_connectors&&S){this.draw_connector(M,S,ab,z,Y,aa)}S=z;ab=Y}if(D==="Pack"){M.globalAlpha=1;M.fillStyle="white";var G=this.height_scaler.gen_val(X),P=Math.ceil(U*G),aq=Math.round((U-P)/2);if(G!==1){M.fillRect(ae,J+1,N-ae,aq);M.fillRect(ae,J+U-aq+1,N-ae,aq)}}}M.globalAlpha=1;if(D==="Pack"&&al>O){M.fillStyle=ag;if(O===0&&ae-M.measureText(Q).width<0){M.textAlign="left";M.fillText(Q,N+j,aa+8);ao+=M.measureText(Q).width+j}else{M.textAlign="right";M.fillText(Q,ae-j,aa+8);ac-=M.measureText(Q).width+j}}}M.globalAlpha=1;return[ac,ao]}});var t=function(B,E,y,A,D,F,C,z){o.call(this,B,E,y,A,D,F,C);this.ref_seq=(z?z.data:null)};u(t.prototype,o.prototype,{get_row_height:function(){var y,z=this.mode;if(z==="Dense"){y=c}else{if(z==="Squish"){y=k}else{y=w;if(this.prefs.show_insertions){y*=2}}}return y},draw_read:function(K,A,ag,V,L,aa,ad,C,B,M){K.textAlign="center";var J=this,R=[L,aa],Z=0,W=0,D=0,F=K.canvas.manager.char_width_px,y=(B==="+"?this.prefs.block_color:this.prefs.reverse_strand_color);var O=[];if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){D=Math.round(ag/2)}if(!C){C=[[0,M.length]]}for(var G=0,I=C.length;G<I;G++){var z=C[G],E="MIDNSHP=X"[z[0]],S=z[1];if(E==="H"||E==="S"){Z-=S}var U=ad+Z,Y=Math.floor(Math.max(0,(U-L)*ag)),ab=Math.floor(Math.max(0,(U+S-L)*ag));if(Y===ab){ab+=1}switch(E){case"H":break;case"S":case"M":case"=":if(is_overlap([U,U+S],R)){var N=M.slice(W,W+S);if(D>0){K.fillStyle=y;K.fillRect(Y-D,V+1,ab-Y,9);K.fillStyle=g;for(var af=0,H=N.length;af<H;af++){if(this.prefs.show_differences){if(this.ref_seq){var P=this.ref_seq[U-L+af];if(!P||P.toLowerCase()===N[af].toLowerCase()){continue}}else{continue}}if(U+af>=L&&U+af<=aa){var X=Math.floor(Math.max(0,(U+af-L)*ag));K.fillText(N[af],X,V+9)}}}else{K.fillStyle=y;K.fillRect(Y,V+4,ab-Y,e)}}W+=S;Z+=S;break;case"N":K.fillStyle=g;K.fillRect(Y-D,V+5,ab-Y,1);Z+=S;break;case"D":K.fillStyle="red";K.fillRect(Y-D,V+4,ab-Y,3);Z+=S;break;case"P":break;case"I":var ah=Y-D;if(is_overlap([U,U+S],R)){var N=M.slice(W,W+S);if(this.prefs.show_insertions){var T=Y-(ab-Y)/2;if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){K.fillStyle="yellow";K.fillRect(T-D,V-9,ab-Y,9);O[O.length]={type:"triangle",data:[ah,V+4,5]};K.fillStyle=g;switch(compute_overlap([U,U+S],R)){case (OVERLAP_START):N=N.slice(L-U);break;case (OVERLAP_END):N=N.slice(0,U-aa);break;case (CONTAINED_BY):break;case (CONTAINS):N=N.slice(L-U,U-aa);break}for(var af=0,H=N.length;af<H;af++){var X=Math.floor(Math.max(0,(U+af-L)*ag));K.fillText(N[af],X-(ab-Y)/2,V)}}else{K.fillStyle="yellow";K.fillRect(T,V+(this.mode!=="Dense"?2:5),ab-Y,(A!=="Dense"?e:s))}}else{if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){O.push({type:"text",data:[N.length,ah,V+9]})}else{}}}W+=S;break;case"X":W+=S;break}}K.fillStyle="yellow";var Q,ai,ae;for(var ac=0;ac<O.length;ac++){Q=O[ac];ai=Q.type;ae=Q.data;if(ai==="text"){K.save();K.font="bold "+K.font;K.fillText(ae[0],ae[1],ae[2]);K.restore()}else{if(ai==="triangle"){q(K,ae[0],ae[1],ae[2])}}}},draw_element:function(R,M,E,B,U,z,I,S,P){var H=E[0],Q=E[1],A=E[2],J=E[3],D=Math.floor(Math.max(0,(Q-U)*I)),F=Math.ceil(Math.min(P,Math.max(0,(A-U)*I))),C=(M==="Dense"?0:(0+B))*S,G=this.prefs.label_color,O=0;if((M==="Pack"||this.mode==="Auto")&&I>R.canvas.manager.char_width_px){var O=Math.round(I/2)}if(E[5] instanceof Array){var N=Math.floor(Math.max(0,(E[4][0]-U)*I)),L=Math.ceil(Math.min(P,Math.max(0,(E[4][1]-U)*I))),K=Math.floor(Math.max(0,(E[5][0]-U)*I)),y=Math.ceil(Math.min(P,Math.max(0,(E[5][1]-U)*I)));if(E[4][1]>=U&&E[4][0]<=z&&E[4][2]){this.draw_read(R,M,I,C,U,z,E[4][0],E[4][2],E[4][3],E[4][4])}if(E[5][1]>=U&&E[5][0]<=z&&E[5][2]){this.draw_read(R,M,I,C,U,z,E[5][0],E[5][2],E[5][3],E[5][4])}if(K>L){R.fillStyle=g;p(R,L-O,C+5,K-O,C+5)}}else{this.draw_read(R,M,I,C,U,z,Q,E[4],E[5],E[6])}if(M==="Pack"&&Q>U&&J!=="."){R.fillStyle=this.prefs.label_color;var T=1;if(T===0&&D-R.measureText(J).width<0){R.textAlign="left";R.fillText(J,F+j-O,C+8)}else{R.textAlign="right";R.fillText(J,D-j-O,C+8)}}return[0,0]}});var n=function(A,D,y,z,C,E,B){r.call(this,A,D,y,z,C,E,B);this.longest_feature_length=this.calculate_longest_feature_length();this.draw_background_connector=false;this.draw_individual_connectors=true};u(n.prototype,o.prototype,r.prototype,{calculate_longest_feature_length:function(){var z=0;for(var C=0,y=this.data.length;C<y;C++){var B=this.data[C],A=B[1],D=B[2];z=Math.max(z,D-A)}return z},get_top_padding:function(z){var y=this.view_end-this.view_start,A=z/y;return Math.min(128,Math.ceil((this.longest_feature_length/2)*A))},draw_connector:function(G,B,F,H,E,D){var y=(F+H)/2,C=H-y;var A=Math.PI,z=0;if(C>0){G.beginPath();G.arc(y,D,H-y,Math.PI,0);G.stroke()}}});x.Scaler=d;x.SummaryTreePainter=v;x.LinePainter=b;x.LinkedFeaturePainter=r;x.ReadPainter=t;x.ArcLinkedFeaturePainter=n};(function(d){var c={};var b=function(e){return c[e]};var a=function(f,g){var e={};g(b,e);c[f]=e};a("class",class_module);a("slotting",slotting_module);a("painters",painters_module);a("trackster",trackster_module);for(key in c.trackster){d[key]=c.trackster[key]}})(window); \ No newline at end of file diff -r 35be930b21bea104bd574d4e9854c6e9c1a58cdb -r f7b12bed396920f2f5908c423b06231653564469 static/scripts/trackster.js --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -1474,7 +1474,7 @@ "z-index": 1000 } ).appendTo( $(this) ); }).bind( "drag", function( e, d ) { - $( d.proxy ).css({ left: Math.min( e.pageX, d.startX ), width: Math.abs( e.pageX - d.startX ) }); + $( d.proxy ).css({ left: Math.min( e.pageX, d.startX ) - view.container.offset().left, width: Math.abs( e.pageX - d.startX ) }); var min = Math.min(e.pageX, d.startX ) - view.container.offset().left, max = Math.max(e.pageX, d.startX ) - view.container.offset().left, span = (view.high - view.low), 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