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commit/galaxy-central: greg: First pass implementation for tool shed repository metadata. This implementation currently provides a baseline metadata collection for tools in a tool shed repository. This change set also includes the implementation for displaying a tool UI for each valid tool config in the tool shed repository. Fixes issue # 565.
by Bitbucket 08 Jul '11

08 Jul '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/8b97f197b759/ changeset: 8b97f197b759 user: greg date: 2011-07-08 22:11:28 summary: First pass implementation for tool shed repository metadata. This implementation currently provides a baseline metadata collection for tools in a tool shed repository. This change set also includes the implementation for displaying a tool UI for each valid tool config in the tool shed repository. Fixes issue # 565. affected #: 16 files (14.8 KB) --- a/lib/galaxy/webapps/community/app.py Fri Jul 08 09:09:02 2011 -0400 +++ b/lib/galaxy/webapps/community/app.py Fri Jul 08 16:11:28 2011 -0400 @@ -1,4 +1,6 @@ import sys, config +import galaxy.tools.data +import galaxy.datatypes.registry import galaxy.webapps.community.model from galaxy.web import security from galaxy.tags.tag_handler import CommunityTagHandler @@ -11,6 +13,8 @@ self.config = config.Configuration( **kwargs ) self.config.check() config.configure_logging( self.config ) + # Set up datatypes registry + self.datatypes_registry = galaxy.datatypes.registry.Registry( self.config.root, self.config.datatypes_config ) # Determine the database url if self.config.database_connection: db_url = self.config.database_connection @@ -28,6 +32,8 @@ self.security = security.SecurityHelper( id_secret=self.config.id_secret ) # Tag handler self.tag_handler = CommunityTagHandler() + # Tool data tables + self.tool_data_tables = galaxy.tools.data.ToolDataTableManager( self.config.tool_data_table_config_path ) # Load security policy self.security_agent = self.model.security_agent def shutdown( self ): --- a/lib/galaxy/webapps/community/config.py Fri Jul 08 09:09:02 2011 -0400 +++ b/lib/galaxy/webapps/community/config.py Fri Jul 08 16:11:28 2011 -0400 @@ -41,6 +41,9 @@ self.cookie_path = kwargs.get( "cookie_path", "/" ) self.test_conf = resolve_path( kwargs.get( "test_conf", "" ), self.root ) self.id_secret = kwargs.get( "id_secret", "USING THE DEFAULT IS NOT SECURE!" ) + self.tool_secret = kwargs.get( "tool_secret", "" ) + self.tool_data_path = resolve_path( kwargs.get( "tool_data_path", "tool-data" ), os.getcwd() ) + self.tool_data_table_config_path = resolve_path( kwargs.get( 'tool_data_table_config_path', 'tool_data_table_conf.xml' ), self.root ) self.use_remote_user = string_as_bool( kwargs.get( "use_remote_user", "False" ) ) self.remote_user_maildomain = kwargs.get( "remote_user_maildomain", None ) self.remote_user_logout_href = kwargs.get( "remote_user_logout_href", None ) @@ -56,7 +59,9 @@ self.smtp_server = kwargs.get( 'smtp_server', None ) self.smtp_username = kwargs.get( 'smtp_username', None ) self.smtp_password = kwargs.get( 'smtp_password', None ) + self.start_job_runners = kwargs.get( 'start_job_runners', None ) self.email_alerts_from = kwargs.get( 'email_alerts_from', None ) + self.nginx_upload_path = kwargs.get( 'nginx_upload_path', False ) self.log_actions = string_as_bool( kwargs.get( 'log_actions', 'False' ) ) self.brand = kwargs.get( 'brand', None ) self.wiki_url = kwargs.get( 'wiki_url', 'http://bitbucket.org/galaxy/galaxy-central/wiki/Home' ) @@ -65,7 +70,7 @@ self.screencasts_url = kwargs.get( 'screencasts_url', None ) self.log_events = False self.cloud_controller_instance = False - self.datatypes_config = kwargs.get( 'datatypes_config_file', 'community_datatypes_conf.xml' ) + self.datatypes_config = kwargs.get( 'datatypes_config_file', 'datatypes_conf.xml' ) # Proxy features self.apache_xsendfile = kwargs.get( 'apache_xsendfile', False ) self.nginx_x_accel_redirect_base = kwargs.get( 'nginx_x_accel_redirect_base', False ) --- a/lib/galaxy/webapps/community/controllers/common.py Fri Jul 08 09:09:02 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/common.py Fri Jul 08 16:11:28 2011 -0400 @@ -1,12 +1,13 @@ import os, string, socket, logging from time import strftime from datetime import * +from galaxy.tools import * from galaxy.util.json import from_json_string, to_json_string from galaxy.web.base.controller import * from galaxy.webapps.community import model from galaxy.model.orm import * from galaxy.model.item_attrs import UsesItemRatings -from mercurial import hg, ui +from mercurial import hg, ui, commands log = logging.getLogger( __name__ ) @@ -68,14 +69,15 @@ def get_repository( trans, id ): """Get a repository from the database via id""" return trans.sa_session.query( trans.model.Repository ).get( trans.security.decode_id( id ) ) +def get_repository_metadata( trans, id, changeset_revision ): + """Get metadata for a specified repository change set from the database""" + return trans.sa_session.query( trans.model.RepositoryMetadata ) \ + .filter( and_( trans.model.RepositoryMetadata.table.c.repository_id == trans.security.decode_id( id ), + trans.model.RepositoryMetadata.table.c.changeset_revision == changeset_revision ) ) \ + .first() def get_repository_by_name( trans, name ): """Get a repository from the database via name""" return trans.sa_session.query( app.model.Repository ).filter_by( name=name ).one() -def get_repository_tip( repository ): - # The received repository must be a mercurial repository, not a db record. - tip_changeset = repository.changelog.tip() - tip_ctx = repository.changectx( tip_changeset ) - return "%s:%s" % ( str( tip_ctx.rev() ), tip_ctx.parents()[0] ) def get_user( trans, id ): """Get a user from the database""" return trans.sa_session.query( trans.model.User ).get( trans.security.decode_id( id ) ) @@ -121,19 +123,138 @@ def update_for_browsing( repository, current_working_dir ): # Make a copy of a repository's files for browsing. repo_dir = repository.repo_path + repo = hg.repository( ui.ui(), repo_dir ) + # The following will delete the disk copy of only the files in the repository. + #os.system( 'hg update -r null > /dev/null 2>&1' ) + repo.ui.pushbuffer() + commands.status( repo.ui, repo, all=True ) + status_and_file_names = repo.ui.popbuffer().strip().split( "\n" ) + # status_and_file_names looks something like: + # ['? MY_README_AGAIN', '? galaxy_tmap_tool/tmap-0.0.9.tar.gz', '? dna_filtering.py', 'C filtering.py', 'C filtering.xml'] + # The codes used to show the status of files are: + # M = modified + # A = added + # R = removed + # C = clean + # ! = deleted, but still tracked + # ? = not tracked + # I = ignored + # We'll remove all files that are not tracked or ignored. + files_to_remove_from_disk = [] + for status_and_file_name in status_and_file_names: + if status_and_file_name.startswith( '?' ) or status_and_file_name.startswith( 'I' ): + files_to_remove_from_disk.append( os.path.abspath( os.path.join( repo_dir, status_and_file_name.split()[1] ) ) ) + for full_path in files_to_remove_from_disk: + if os.path.isdir( full_path ): + try: + os.rmdir( full_path ) + except OSError, e: + # The directory is not empty + pass + elif os.path.isfile( full_path ): + os.remove( full_path ) + dir = os.path.split( full_path )[0] + try: + os.rmdir( dir ) + except OSError, e: + # The directory is not empty + pass os.chdir( repo_dir ) os.system( 'hg update > /dev/null 2>&1' ) os.chdir( current_working_dir ) +def load_tool( trans, config_file ): """ - # TODO: the following is useful if the repository files somehow include missing or - # untracked files. If this happens, we can enhance the following to clean things up. - # We're not currently doing any cleanup though since so far none of the repositories - # have problematic files for browsing. - # Get the tip change set. + Load a single tool from the file named by `config_file` and return + an instance of `Tool`. + """ + # Parse XML configuration file and get the root element + tree = util.parse_xml( config_file ) + root = tree.getroot() + if root.tag == 'tool': + # Allow specifying a different tool subclass to instantiate + if root.find( "type" ) is not None: + type_elem = root.find( "type" ) + module = type_elem.get( 'module', 'galaxy.tools' ) + cls = type_elem.get( 'class' ) + mod = __import__( module, globals(), locals(), [cls]) + ToolClass = getattr( mod, cls ) + elif root.get( 'tool_type', None ) is not None: + ToolClass = tool_types.get( root.get( 'tool_type' ) ) + else: + ToolClass = Tool + return ToolClass( config_file, root, trans.app ) + return None +def set_repository_metadata( trans, id, ctx_str, **kwd ): + """Set repository metadata""" + message = '' + status = 'done' + repository = get_repository( trans, id ) + repo_dir = repository.repo_path repo = hg.repository( ui.ui(), repo_dir ) + found = False + invalid_tool_configs = [] for changeset in repo.changelog: ctx = repo.changectx( changeset ) - ctx_parent = ctx.parents()[0] - break - modified, added, removed, deleted, unknown, ignored, clean = repo.status( node1=ctx_parent.node(), node2=ctx.node() ) - """ + if str( ctx ) == ctx_str: + found = True + break + if found: + for root, dirs, files in os.walk( repo_dir ): + if not root.find( '.hg' ) >= 0 and not root.find( 'hgrc' ) >= 0: + if '.hg' in dirs: + # Don't visit .hg directories - should be impossible since we don't + # allow uploaded archives that contain .hg dirs, but just in case... + dirs.remove( '.hg' ) + if 'hgrc' in files: + # Don't include hgrc files in commit. + files.remove( 'hgrc' ) + for name in files: + # Find all tool configs. + if name.endswith( '.xml' ): + try: + full_path = os.path.abspath( os.path.join( root, name ) ) + tool = load_tool( trans, full_path ) + if tool is not None: + repository_metadata = get_repository_metadata( trans, id, repository.tip ) + # TODO: add more stuff, like requirements + tool_dict = dict( id = tool.id, + name = tool.name, + version = tool.version, + description = tool.description, + tool_config = full_path ) + if repository_metadata: + metadata = repository_metadata.metadata + if metadata and 'tools' in metadata: + metadata_tools = metadata[ 'tools' ] + found = False + for tool_metadata_dict in metadata_tools: + if 'id' in tool_metadata_dict and tool_metadata_dict[ 'id' ] == tool.id and \ + 'version' in tool_metadata_dict and tool_metadata_dict[ 'version' ] == tool.version: + found = True + tool_metadata_dict[ 'name' ] = tool.name + tool_metadata_dict[ 'description' ] = tool.description + tool_metadata_dict[ 'tool_config' ] = os.path.join( root, name ) + # TODO: add more stuff, like tool requirements, code files, etc + if not found: + metadata_tools.append( tool_dict ) + else: + if metadata is None: + repository_metadata.metadata = {} + repository_metadata.metadata[ 'tools' ] = [ tool_dict ] + trans.sa_session.add( repository_metadata ) + else: + metadata_dict = dict( tools = [ tool_dict ] ) + repository_metadata = trans.model.RepositoryMetadata( repository.id, repository.tip, metadata_dict ) + trans.sa_session.add( repository_metadata ) + trans.sa_session.flush() + except Exception, e: + invalid_tool_configs.append( ( name, str( e ) ) ) + else: + message = "Repository does not include changeset revision '%s'." % str( ctx_str ) + status = 'error' + if invalid_tool_configs: + message = "The following tool configs are invalid and were not added to the repository metadata:<br/>" + for itc_tup in invalid_tool_configs: + message += "<b>%s</b> - %s<br/>" % ( itc_tup[0], itc_tup[1] ) + status = 'error' + return message, status --- a/lib/galaxy/webapps/community/controllers/repository.py Fri Jul 08 09:09:02 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/repository.py Fri Jul 08 16:11:28 2011 -0400 @@ -76,8 +76,7 @@ return repository.name class VersionColumn( grids.TextColumn ): def get_value( self, trans, grid, repository ): - repo = hg.repository( ui.ui(), repository.repo_path ) - return get_repository_tip( repo ) + return repository.version class DescriptionColumn( grids.TextColumn ): def get_value( self, trans, grid, repository ): return repository.description @@ -124,7 +123,7 @@ key="name", link=( lambda item: dict( operation="view_or_manage_repository", id=item.id, webapp="community" ) ), attach_popup=False ), - DescriptionColumn( "Description", + DescriptionColumn( "Synopsis", key="description", attach_popup=False ), VersionColumn( "Version", @@ -420,7 +419,7 @@ selected_files_to_delete = selected_files_to_delete.split( ',' ) current_working_dir = os.getcwd() # Get the current repository tip. - tip = repo[ 'tip' ] + tip = repository.tip for selected_file in selected_files_to_delete: repo_file = os.path.abspath( selected_file ) commands.remove( repo.ui, repo, repo_file ) @@ -434,10 +433,19 @@ update_for_browsing( repository, current_working_dir ) # Get the new repository tip. repo = hg.repository( ui.ui(), repo_dir ) - if tip != repo[ 'tip' ]: + if tip != repository.tip: message = "The selected files were deleted from the repository." else: message = 'No changes to repository.' + # Set metadata on the repository tip + error_message, status = set_repository_metadata( trans, id, repository.tip, **kwd ) + if error_message: + message = '%s<br/>%s' % ( message, error_message ) + return trans.response.send_redirect( web.url_for( controller='repository', + action='manage_repository', + id=id, + message=message, + status=status ) ) else: message = "Select at least 1 file to delete from the repository before clicking <b>Delete selected files</b>." status = "error" @@ -454,7 +462,6 @@ status = params.get( 'status', 'done' ) repository = get_repository( trans, id ) repo = hg.repository( ui.ui(), repository.repo_path ) - tip = get_repository_tip( repo ) avg_rating, num_ratings = self.get_ave_item_rating_data( trans.sa_session, repository, webapp_model=trans.model ) display_reviews = util.string_as_bool( params.get( 'display_reviews', False ) ) alerts = params.get( 'alerts', '' ) @@ -481,10 +488,15 @@ trans.sa_session.flush() checked = alerts_checked or ( user and user.email in email_alerts ) alerts_check_box = CheckboxField( 'alerts', checked=checked ) + repository_metadata = get_repository_metadata( trans, id, repository.tip ) + if repository_metadata: + metadata = repository_metadata.metadata + else: + metadata = None return trans.fill_template( '/webapps/community/repository/view_repository.mako', repo=repo, repository=repository, - tip=tip, + metadata=metadata, avg_rating=avg_rating, display_reviews=display_reviews, num_ratings=num_ratings, @@ -499,7 +511,6 @@ status = params.get( 'status', 'done' ) repository = get_repository( trans, id ) repo = hg.repository( ui.ui(), repository.repo_path ) - tip = get_repository_tip( repo ) repo_name = util.restore_text( params.get( 'repo_name', repository.name ) ) description = util.restore_text( params.get( 'description', repository.description ) ) long_description = util.restore_text( params.get( 'long_description', repository.long_description ) ) @@ -577,6 +588,11 @@ allow_push_select_field = self.__build_allow_push_select_field( trans, current_allow_push_list ) checked = alerts_checked or user.email in email_alerts alerts_check_box = CheckboxField( 'alerts', checked=checked ) + repository_metadata = get_repository_metadata( trans, id, repository.tip ) + if repository_metadata: + metadata = repository_metadata.metadata + else: + metadata = None return trans.fill_template( '/webapps/community/repository/manage_repository.mako', repo_name=repo_name, description=description, @@ -585,7 +601,7 @@ allow_push_select_field=allow_push_select_field, repo=repo, repository=repository, - tip=tip, + metadata=metadata, avg_rating=avg_rating, display_reviews=display_reviews, num_ratings=num_ratings, @@ -676,7 +692,6 @@ status='error' ) ) repository = get_repository( trans, id ) repo = hg.repository( ui.ui(), repository.repo_path ) - tip = get_repository_tip( repo ) if repository.user == trans.user: return trans.response.send_redirect( web.url_for( controller='repository', action='browse_repositories', @@ -691,7 +706,6 @@ rra = self.get_user_item_rating( trans.sa_session, trans.user, repository, webapp_model=trans.model ) return trans.fill_template( '/webapps/community/repository/rate_repository.mako', repository=repository, - tip=tip, avg_rating=avg_rating, display_reviews=display_reviews, num_ratings=num_ratings, @@ -736,6 +750,40 @@ action='browse_repositories', **kwd ) ) @web.expose + @web.require_login( "set repository metadata" ) + def set_metadata( self, trans, id, ctx_str, **kwd ): + message, status = set_repository_metadata( trans, id, ctx_str, **kwd ) + return trans.response.send_redirect( web.url_for( controller='repository', + action='manage_repository', + id=id, + message=message, + status=status ) ) + @web.expose + def display_tool( self, trans, repository_id, tool_config, **kwd ): + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + repository = get_repository( trans, repository_id ) + tool = load_tool( trans, os.path.abspath( tool_config ) ) + tool_state = self.__new_state( trans ) + return trans.fill_template( "/webapps/community/repository/tool_form.mako", + repository=repository, + tool=tool, + tool_state=tool_state, + message=message, + status=status ) + def __new_state( self, trans, all_pages=False ): + """ + Create a new `DefaultToolState` for this tool. It will not be initialized + with default values for inputs. + + Only inputs on the first page will be initialized unless `all_pages` is + True, in which case all inputs regardless of page are initialized. + """ + state = DefaultToolState() + state.inputs = {} + return state + @web.expose def download( self, trans, repository_id, file_type, **kwd ): # Download an archive of the repository files compressed as zip, gz or bz2. params = util.Params( kwd ) --- a/lib/galaxy/webapps/community/controllers/upload.py Fri Jul 08 09:09:02 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/upload.py Fri Jul 08 16:11:28 2011 -0400 @@ -33,7 +33,7 @@ uploaded_file = None upload_point = self.__get_upload_point( repository, **kwd ) # Get the current repository tip. - tip = repo[ 'tip' ] + tip = repository.tip if params.get( 'upload_button', False ): current_working_dir = os.getcwd() file_data = params.get( 'file_data', '' ) @@ -89,8 +89,7 @@ # is eliminating unwanted files from the repository directory. update_for_browsing( repository, current_working_dir ) # Get the new repository tip. - repo = hg.repository( ui.ui(), repo_dir ) - if tip != repo[ 'tip' ]: + if tip != repository.tip: if ( isgzip or isbz2 ) and uncompress_file: uncompress_str = ' uncompressed and ' else: @@ -102,12 +101,22 @@ else: message += " %d files were removed from the repository root." % len( files_to_remove ) else: - message = 'No changes to repository.' + message = 'No changes to repository.' + # Set metadata on the repository tip + error_message, status = set_repository_metadata( trans, repository_id, repository.tip, **kwd ) + if error_message: + message = '%s<br/>%s' % ( message, error_message ) + return trans.response.send_redirect( web.url_for( controller='repository', + action='manage_repository', + id=repository_id, + message=message, + status=status ) ) trans.response.send_redirect( web.url_for( controller='repository', action='browse_repository', + id=repository_id, commit_message='Deleted selected files', message=message, - id=trans.security.encode_id( repository.id ) ) ) + status=status ) ) else: status = 'error' selected_categories = [ trans.security.decode_id( id ) for id in category_ids ] --- a/lib/galaxy/webapps/community/model/__init__.py Fri Jul 08 09:09:02 2011 -0400 +++ b/lib/galaxy/webapps/community/model/__init__.py Fri Jul 08 16:11:28 2011 -0400 @@ -114,6 +114,15 @@ return config.get( "paths", option ) raise Exception( "Entry for repository %s missing in %s/hgweb.config file." % ( lhs, os.getcwd() ) ) @property + def version( self ): + repo = hg.repository( ui.ui(), self.repo_path ) + tip_ctx = repo.changectx( repo.changelog.tip() ) + return "%s:%s" % ( str( tip_ctx.rev() ), str( repo.changectx( repo.changelog.tip() ) ) ) + @property + def tip( self ): + repo = hg.repository( ui.ui(), self.repo_path ) + return str( repo.changectx( repo.changelog.tip() ) ) + @property def is_new( self ): repo = hg.repository( ui.ui(), self.repo_path ) tip_ctx = repo.changectx( repo.changelog.tip() ) @@ -143,6 +152,12 @@ fp.write( line ) fp.close() +class RepositoryMetadata( object ): + def __init__( self, repository_id=None, changeset_revision=None, metadata=None ): + self.repository_id = repository_id + self.changeset_revision = changeset_revision + self.metadata = metadata or dict() + class ItemRatingAssociation( object ): def __init__( self, id=None, user=None, item=None, rating=0, comment='' ): self.id = id --- a/lib/galaxy/webapps/community/model/mapping.py Fri Jul 08 09:09:02 2011 -0400 +++ b/lib/galaxy/webapps/community/model/mapping.py Fri Jul 08 16:11:28 2011 -0400 @@ -111,6 +111,14 @@ Column( "email_alerts", JSONType, nullable=True ), Column( "times_downloaded", Integer ) ) +RepositoryMetadata.table = Table( "repository_metadata", metadata, + Column( "id", Integer, primary_key=True ), + Column( "create_time", DateTime, default=now ), + Column( "update_time", DateTime, default=now, onupdate=now ), + Column( "repository_id", Integer, ForeignKey( "repository.id" ), index=True ), + Column( "changeset_revision", TrimmedString( 255 ), index=True ), + Column( "metadata", JSONType, nullable=True ) ) + RepositoryRatingAssociation.table = Table( "repository_rating_association", metadata, Column( "id", Integer, primary_key=True ), Column( "create_time", DateTime, default=now ), @@ -186,6 +194,9 @@ ratings=relation( RepositoryRatingAssociation, order_by=desc( RepositoryRatingAssociation.table.c.update_time ), backref="repositories" ), user=relation( User.mapper ) ) ) +assign_mapper( context, RepositoryMetadata, RepositoryMetadata.table, + properties=dict( repository=relation( Repository ) ) ) + assign_mapper( context, RepositoryRatingAssociation, RepositoryRatingAssociation.table, properties=dict( repository=relation( Repository ), user=relation( User ) ) ) --- a/templates/webapps/community/repository/browse_repository.mako Fri Jul 08 09:09:02 2011 -0400 +++ b/templates/webapps/community/repository/browse_repository.mako Fri Jul 08 16:11:28 2011 -0400 @@ -5,12 +5,13 @@ <% from galaxy.web.framework.helpers import time_ago + is_admin = trans.user_is_admin() is_new = repository.is_new can_push = trans.app.security_agent.can_push( trans.user, repository ) can_upload = can_push can_browse_contents = not is_new can_rate = trans.user and repository.user != trans.user - can_manage = repository.user == trans.user + can_manage = is_admin or repository.user == trans.user can_view_change_log = not is_new %> --- a/templates/webapps/community/repository/manage_repository.mako Fri Jul 08 09:09:02 2011 -0400 +++ b/templates/webapps/community/repository/manage_repository.mako Fri Jul 08 16:11:28 2011 -0400 @@ -121,9 +121,9 @@ <div class="form-row"><label>Version:</label> %if can_view_change_log: - <a href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">${tip}</a> + <a href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">${repository.version}</a> %else: - ${tip} + ${repository.version} %endif </div><div class="form-row"> @@ -150,6 +150,40 @@ </form></div></div> +<p/> +<div class="toolForm"> + <div class="toolFormTitle">Repository metadata</div> + <div class="toolFormBody"> + %if metadata: + %if 'tools' in metadata: + <div class="form-row"> + <label>Tools:</label> + <% tool_dicts = metadata[ 'tools' ] %> + <table class="grid"> + %for tool_dict in tool_dicts: + <tr> + <td><a href="${h.url_for( controller='repository', action='display_tool', repository_id=trans.security.encode_id( repository.id ), tool_config=tool_dict[ 'tool_config' ] )}">${tool_dict[ 'name' ]}</a></td> + <td>${tool_dict[ 'description' ]}</td> + <td>version: ${tool_dict[ 'version' ]}</td> + </tr> + %endfor + </table> + </div> + <div style="clear: both"></div> + %endif + %endif + <form name="set_metadata" action="${h.url_for( controller='repository', action='set_metadata', id=trans.security.encode_id( repository.id ), ctx_str=repository.tip )}" method="post"> + <div class="form-row"> + <div style="float: left; width: 250px; margin-right: 10px;"> + <input type="submit" name="set_metadata_button" value="Reset metadata"/> + </div> + <div class="toolParamHelp" style="clear: both;"> + Inspect the repository and reset the above attributes for the repository tip. + </div> + </div> + </form> + </div> +</div> %if trans.app.config.smtp_server: <p/><div class="toolForm"> --- a/templates/webapps/community/repository/rate_repository.mako Fri Jul 08 09:09:02 2011 -0400 +++ b/templates/webapps/community/repository/rate_repository.mako Fri Jul 08 16:11:28 2011 -0400 @@ -4,12 +4,13 @@ <% from galaxy.web.framework.helpers import time_ago from urllib import quote_plus + is_admin = trans.user_is_admin() is_new = repository.is_new can_push = trans.app.security_agent.can_push( trans.user, repository ) can_upload = can_push can_browse_contents = not is_new can_rate = repository.user != trans.user - can_manage = repository.user == trans.user + can_manage = is_admin or repository.user == trans.user can_view_change_log = not is_new if can_push: browse_label = 'Browse or delete repository files' @@ -103,7 +104,7 @@ </div><div class="form-row"><label>Version:</label> - ${tip} + ${repository.version} <div style="clear: both"></div></div><div class="form-row"> --- a/templates/webapps/community/repository/upload.mako Fri Jul 08 09:09:02 2011 -0400 +++ b/templates/webapps/community/repository/upload.mako Fri Jul 08 16:11:28 2011 -0400 @@ -2,11 +2,12 @@ <%namespace file="/webapps/community/repository/common.mako" import="*" /><% + is_admin = trans.user_is_admin() is_new = repository.is_new can_browse_contents = not is_new can_browse_contents = not is_new can_rate = repository.user != trans.user - can_manage = repository.user == trans.user + can_manage = is_admin or repository.user == trans.user can_view_change_log = not is_new %> --- a/templates/webapps/community/repository/view_changelog.mako Fri Jul 08 09:09:02 2011 -0400 +++ b/templates/webapps/community/repository/view_changelog.mako Fri Jul 08 16:11:28 2011 -0400 @@ -5,9 +5,10 @@ <% from galaxy.web.framework.helpers import time_ago + is_admin = trans.user_is_admin() is_new = repository.is_new can_browse_contents = not is_new - can_manage = trans.user == repository.user + can_manage = is_admin or trans.user == repository.user can_push = trans.app.security_agent.can_push( trans.user, repository ) can_rate = trans.user and repository.user != trans.user can_upload = can_push --- a/templates/webapps/community/repository/view_changeset.mako Fri Jul 08 09:09:02 2011 -0400 +++ b/templates/webapps/community/repository/view_changeset.mako Fri Jul 08 16:11:28 2011 -0400 @@ -5,10 +5,11 @@ <% from galaxy.web.framework.helpers import time_ago + is_admin = trans.user_is_admin() is_new = repository.is_new can_browse_contents = not is_new can_rate = trans.user and repository.user != trans.user - can_manage = trans.user == repository.user + can_manage = is_admin or trans.user == repository.user can_push = trans.app.security_agent.can_push( trans.user, repository ) can_view_change_log = not is_new can_upload = can_push --- a/templates/webapps/community/repository/view_repository.mako Fri Jul 08 09:09:02 2011 -0400 +++ b/templates/webapps/community/repository/view_repository.mako Fri Jul 08 16:11:28 2011 -0400 @@ -120,9 +120,9 @@ <div class="form-row"><label>Version:</label> %if can_view_change_log: - <a href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">${tip}</a> + <a href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">${repository.version}</a> %else: - ${tip} + ${repository.version} %endif </div><div class="form-row"> @@ -145,6 +145,30 @@ %endif </div></div> +%if metadata: + <p/> + <div class="toolForm"> + <div class="toolFormTitle">Repository metadata</div> + <div class="toolFormBody"> + %if 'tools' in metadata: + <div class="form-row"> + <label>Tools:</label> + <% tool_dicts = metadata[ 'tools' ] %> + <table class="grid"> + %for tool_dict in tool_dicts: + <tr> + <td><a href="${h.url_for( controller='repository', action='display_tool', repository_id=trans.security.encode_id( repository.id ), tool_config=tool_dict[ 'tool_config' ] )}">${tool_dict[ 'name' ]}</a></td> + <td>${tool_dict[ 'description' ]}</td> + <td>version: ${tool_dict[ 'version' ]}</td> + </tr> + %endfor + </table> + </div> + <div style="clear: both"></div> + %endif + </div> + </div> +%endif %if trans.user and trans.app.config.smtp_server: <p/><div class="toolForm"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Fix a bug when setting default history permissions in the user preferences; receiving method now gets all required params.
by Bitbucket 08 Jul '11

08 Jul '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/a787213d08e1/ changeset: a787213d08e1 user: greg date: 2011-07-08 15:09:02 summary: Fix a bug when setting default history permissions in the user preferences; receiving method now gets all required params. affected #: 2 files (470 bytes) --- a/lib/galaxy/web/controllers/user.py Thu Jul 07 12:13:49 2011 -0400 +++ b/lib/galaxy/web/controllers/user.py Fri Jul 08 09:09:02 2011 -0400 @@ -914,6 +914,9 @@ @web.expose def set_default_permissions( self, trans, cntrller, **kwd ): """Sets the user's default permissions for the new histories""" + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) if trans.user: if 'update_roles_button' in kwd: p = util.Params( kwd ) @@ -926,8 +929,11 @@ action = trans.app.security_agent.get_action( v.action ).action permissions[ action ] = in_roles trans.app.security_agent.user_set_default_permissions( trans.user, permissions ) - return trans.show_ok_message( 'Default new history permissions have been changed.' ) - return trans.fill_template( 'user/permissions.mako', cntrller=cntrller ) + message = 'Default new history permissions have been changed.' + return trans.fill_template( 'user/permissions.mako', + cntrller=cntrller, + message=message, + status=status ) else: # User not logged in, history group must be only public return trans.show_error_message( "You must be logged in to change your default permitted actions." ) --- a/templates/user/permissions.mako Thu Jul 07 12:13:49 2011 -0400 +++ b/templates/user/permissions.mako Fri Jul 08 09:09:02 2011 -0400 @@ -1,6 +1,13 @@ <%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> +<%namespace file="/dataset/security_common.mako" import="render_permission_form" /> + <%def name="title()">Change Default Permissions on New Histories</%def> -<%namespace file="/dataset/security_common.mako" import="render_permission_form" /> + +%if message: + ${render_msg( message, status )} +%endif + <br/><br/><ul class="manage-table-actions"><li> @@ -8,5 +15,5 @@ </li></ul> %if trans.user: - ${render_permission_form( trans.user, trans.user.email, h.url_for(), trans.user.all_roles() )} + ${render_permission_form( trans.user, trans.user.email, h.url_for( controller='user', action='set_default_permissions', cntrller=cntrller ), trans.user.all_roles() )} %endif Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Update annotation profiler tool sample configuration file.
by Bitbucket 07 Jul '11

07 Jul '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/4220f8a5c571/ changeset: 4220f8a5c571 user: dan date: 2011-07-07 18:13:49 summary: Update annotation profiler tool sample configuration file. affected #: 2 files (153 bytes) --- a/tool-data/annotation_profiler_options.xml.sample Thu Jul 07 11:55:14 2011 -0400 +++ b/tool-data/annotation_profiler_options.xml.sample Thu Jul 07 12:13:49 2011 -0400 @@ -1,4 +1,4 @@ -<filter type="meta_key" name="dbkey" value="hg18"> +<filter type="data_meta" data_ref="input1" meta_key="dbkey" value="hg18"><options><option name="Mapping and Sequencing Tracks" value="group-map"><option name="STS Markers" value="stsMap"/> --- a/tools/annotation_profiler/annotation_profiler_for_interval.py Thu Jul 07 11:55:14 2011 -0400 +++ b/tools/annotation_profiler/annotation_profiler_for_interval.py Thu Jul 07 12:13:49 2011 -0400 @@ -340,6 +340,8 @@ options, args = parser.parse_args() + assert os.path.isdir( options.path ), IOError( "Configuration error: Table directory is missing (%s)" % options.path ) + #get profiler_info profiler_info = parse_profiler_info( os.path.join( options.path, 'profiler_info.txt' ) ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Trackster: implement broad/wide incremental data fetching and add icons for data fetching.
by Bitbucket 07 Jul '11

07 Jul '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/35c11787e690/ changeset: 35c11787e690 user: jgoecks date: 2011-07-07 17:55:14 summary: Trackster: implement broad/wide incremental data fetching and add icons for data fetching. affected #: 5 files (1.5 KB) --- a/static/june_2007_style/blue/trackster.css Wed Jul 06 22:37:51 2011 -0400 +++ b/static/june_2007_style/blue/trackster.css Thu Jul 07 11:55:14 2011 -0400 @@ -51,3 +51,6 @@ .bookmark{background:white;border:solid #999 1px;border-right:none;margin:0.5em;margin-right:0;padding:0.5em;} .bookmark .position{font-weight:bold;} .delete-icon-container{float:right;} +.icon{display:inline-block;width:16px;height:16px;} +.icon.more-down{background:url('../images/fugue/arrow-transition-270-bw.png') no-repeat 0px 0px;} +.icon.more-across{background:url('../images/fugue/arrow-transition-bw.png') no-repeat 0px 0px;} --- a/static/june_2007_style/trackster.css.tmpl Wed Jul 06 22:37:51 2011 -0400 +++ b/static/june_2007_style/trackster.css.tmpl Thu Jul 07 11:55:14 2011 -0400 @@ -293,3 +293,16 @@ float:right; } +.icon { + display:inline-block; + width:16px; + height:16px; +} +.icon.more-down { + background:url('../images/fugue/arrow-transition-270-bw.png') no-repeat 0px 0px; +} +.icon.more-across{ + background:url('../images/fugue/arrow-transition-bw.png') no-repeat 0px 0px; +} + + --- a/static/scripts/trackster.js Wed Jul 06 22:37:51 2011 -0400 +++ b/static/scripts/trackster.js Thu Jul 07 11:55:14 2011 -0400 @@ -172,7 +172,7 @@ // height of individual features within tracks. Feature height, then, should always be less // than track height. CHAR_HEIGHT_PX = 9, // FIXME: font size may not be static - ERROR_PADDING = 18, // Padding at the top of tracks for error messages + ERROR_PADDING = 20, // Padding at the top of tracks for error messages SUMMARY_TREE_TOP_PADDING = CHAR_HEIGHT_PX + 2, // Maximum number of rows un a slotted track MAX_FEATURE_DEPTH = 100, @@ -369,13 +369,15 @@ // // Set parameters based on request type. // + var query_low = low; if (req_type === this.DEEP_DATA_REQ) { // Use same interval but set start_val to skip data that's already in cur_data. $.extend(extra_params, {start_val: cur_data.data.length + 1}); } else if (req_type === this.BROAD_DATA_REQ) { - // Set low to be past the last feature returned. - low = cur_data.data[cur_data.length-1][2] + 1; + // Set query low to be past the last feature returned so that an area of extreme feature depth + // is bypassed. + query_low = cur_data.data[cur_data.data.length - 1][2] + 1; } // @@ -384,14 +386,19 @@ // var data_manager = this, - new_data_request = this.load_data(low, high, resolution, extra_params) + new_data_request = this.load_data(query_low, high, resolution, extra_params) new_data_available = $.Deferred(); // load_data sets cache to new_data_request, but use custom deferred object so that signal and data // is all data, not just new data. this.set_data(low, high, mode, new_data_available); $.when(new_data_request).then(function(result) { + // Update data and message. if (result.data) { result.data = cur_data.data.concat(result.data); + if (result.message) { + // HACK: replace number in message with current data length. Works but is ugly. + result.message = result.message.replace(/[0-9]+/, result.data.length); + } } data_manager.set_data(low, high, mode, result); new_data_available.resolve(result); @@ -2209,18 +2216,29 @@ message_div = $("<div/>").addClass("tile-message").text(tile.message). // -1 to account for border. css({'height': ERROR_PADDING-1, 'width': tile.canvas.width}).appendTo(container_div), - show_more_data_btn = $("<div/>").text("Show more").addClass("action-button").css({'padding-top': 0, 'padding-bottom':0}).appendTo(message_div); + more_down_icon = $("<a href='javascript:void(0);'/>").addClass("icon more-down").appendTo(message_div), + more_across_icon = $("<a href='javascript:void(0);'/>").addClass("icon more-across").appendTo(message_div); container_div.append(canvas); tile_element = container_div; - // Set up actions for button. - show_more_data_btn.click(function() { + // Set up actions for icons. + more_down_icon.click(function() { // Mark tile as stale, request more data, and redraw track. tile.stale = true; track.data_manager.get_more_data(tile.low, tile.high, tile.resolution, {}, track.data_manager.DEEP_DATA_REQ); track.draw(); }).dblclick(function(e) { - // Do not propogate as this would normal zoom in. + // Do not propogate as this would normally zoom in. + e.stopPropagation(); + }); + + more_across_icon.click(function() { + // Mark tile as stale, request more data, and redraw track. + tile.stale = true; + track.data_manager.get_more_data(tile.low, tile.high, tile.resolution, {}, track.data_manager.BROAD_DATA_REQ); + track.draw(); + }).dblclick(function(e) { + // Do not propogate as this would normally zoom in. e.stopPropagation(); }); } Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: kanwei: Add tool version-string support to tool wrappers. Use the <version_string> tag to denote the command to run for the tool version, such as: tophat --version (see tophat wrapper change for example)
by Bitbucket 07 Jul '11

07 Jul '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/84b20f29dfdf/ changeset: 84b20f29dfdf user: kanwei date: 2011-07-07 04:37:51 summary: Add tool version-string support to tool wrappers. Use the <version_string> tag to denote the command to run for the tool version, such as: tophat --version (see tophat wrapper change for example) The tool version string will currently be appended to the Info string in the history dataset and you will be able to see it in the history pane, although this might be added to the database as well in the future. affected #: 4 files (1.1 KB) --- a/lib/galaxy/jobs/__init__.py Thu Jul 07 10:04:20 2011 +1000 +++ b/lib/galaxy/jobs/__init__.py Wed Jul 06 22:37:51 2011 -0400 @@ -271,7 +271,7 @@ class JobWrapper( object ): """ - Wraps a 'model.Job' with convience methods for running processes and + Wraps a 'model.Job' with convenience methods for running processes and state management. """ def __init__( self, job, queue ): @@ -284,6 +284,9 @@ self.sa_session = self.app.model.context self.extra_filenames = [] self.command_line = None + # Tool versioning variables + self.version_string_cmd = None + self.version_string = "" self.galaxy_lib_dir = None # With job outputs in the working directory, we need the working # directory to be set before prepare is run, or else premature deletion @@ -311,6 +314,9 @@ param_dict = self.tool.params_from_strings( param_dict, self.app ) return param_dict + def get_version_string_path( self ): + return os.path.abspath(os.path.join(self.app.config.new_file_path, "GALAXY_VERSION_STRING_%s" % self.job_id)) + def prepare( self ): """ Prepare the job to run by creating the working directory and the @@ -389,6 +395,7 @@ extra_filenames.append( param_filename ) self.param_dict = param_dict self.extra_filenames = extra_filenames + self.version_string_cmd = self.tool.version_string_cmd return extra_filenames def fail( self, message, exception=False ): @@ -491,6 +498,12 @@ job.state = job.states.ERROR else: job.state = job.states.OK + if self.version_string_cmd: + version_filename = self.get_version_string_path() + if os.path.exists(version_filename): + self.version_string = "Tool version: %s" % open(version_filename).read() + os.unlink(version_filename) + if self.app.config.outputs_to_working_directory: for dataset_path in self.get_output_fnames(): try: @@ -541,7 +554,7 @@ dataset.blurb = 'done' dataset.peek = 'no peek' - dataset.info = context['stdout'] + context['stderr'] + dataset.info = context['stdout'] + context['stderr'] + self.version_string dataset.set_size() if context['stderr']: dataset.blurb = "error" --- a/lib/galaxy/jobs/runners/__init__.py Thu Jul 07 10:04:20 2011 +1000 +++ b/lib/galaxy/jobs/runners/__init__.py Wed Jul 06 22:37:51 2011 -0400 @@ -1,10 +1,9 @@ import os, os.path class BaseJobRunner( object ): - def build_command_line( self, job_wrapper, include_metadata=False ): """ - Compose the sequence of commands neccesary to execute a job. This will + Compose the sequence of commands necessary to execute a job. This will currently include: - environment settings corresponding to any requirement tags - command line taken from job wrapper @@ -15,9 +14,13 @@ # occur if not commands: return None + # Prepend version string + if job_wrapper.version_string_cmd: + commands = "%s &> %s; " % ( job_wrapper.version_string_cmd, job_wrapper.get_version_string_path() ) + commands # Prepend dependency injection if job_wrapper.dependency_shell_commands: commands = "; ".join( job_wrapper.dependency_shell_commands + [ commands ] ) + # Append metadata setting commands, we don't want to overwrite metadata # that was copied over in init_meta(), as per established behavior if include_metadata and self.app.config.set_metadata_externally: --- a/lib/galaxy/tools/__init__.py Thu Jul 07 10:04:20 2011 +1000 +++ b/lib/galaxy/tools/__init__.py Wed Jul 06 22:37:51 2011 -0400 @@ -5,7 +5,7 @@ pkg_resources.require( "simplejson" ) -import logging, os, string, sys, tempfile, glob, shutil, types, urllib +import logging, os, string, sys, tempfile, glob, shutil, types, urllib, subprocess import simplejson import binascii from UserDict import DictMixin @@ -395,6 +395,10 @@ self.redirect_url_params = '' # Short description of the tool self.description = util.xml_text(root, "description") + # Versioning for tools + self.version_string_cmd = None + if root.find("version_string") is not None: + self.version_string_cmd = root.find("version_string").text # Parallelism for tasks, read from tool config. parallelism = root.find("parallelism") if parallelism is not None and parallelism.get("method"): --- a/tools/ngs_rna/tophat_wrapper.xml Thu Jul 07 10:04:20 2011 +1000 +++ b/tools/ngs_rna/tophat_wrapper.xml Wed Jul 06 22:37:51 2011 -0400 @@ -1,5 +1,6 @@ <tool id="tophat" name="Tophat for Illumina" version="1.5.0"><description>Find splice junctions using RNA-seq data</description> + <version_string>tophat --version</version_string><requirements><requirement type="package">tophat</requirement></requirements> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: fubar: More comprehensive error detection for weblogo installation or execution errors
by Bitbucket 07 Jul '11

07 Jul '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/d271dfcdf482/ changeset: d271dfcdf482 user: fubar date: 2011-07-07 02:04:20 summary: More comprehensive error detection for weblogo installation or execution errors affected #: 2 files (431 bytes) --- a/tools/rgenetics/rgWebLogo3.py Wed Jul 06 10:20:57 2011 -0400 +++ b/tools/rgenetics/rgWebLogo3.py Thu Jul 07 10:04:20 2011 +1000 @@ -43,6 +43,11 @@ tlf = open(templog,'w') process = subprocess.Popen(cl, shell=True, stderr=tlf, stdout=tlf) rval = process.wait() + if rval <> 0: + print >> sys.stderr, '## rgWebLogo3.py error - executing %s returned error code %d' % cl + print >> sys.stderr, '## This may be a data problem or a tool dependency (%s) installation problem' % WEBLOGO + print >> sys.stderr, '## Please ensure %s is correctly installed and working on the command line -see http://code.google.com/p/weblogo' % WEBLOGO + sys.exit(1) tlf.close() tlogs = ''.join(open(templog,'r').readlines()) if len(tlogs) > 1: --- a/tools/rgenetics/rgWebLogo3.xml Wed Jul 06 10:20:57 2011 -0400 +++ b/tools/rgenetics/rgWebLogo3.xml Thu Jul 07 10:04:20 2011 +1000 @@ -1,4 +1,4 @@ -<tool id="rgweblogo3" name="Sequence Logo" version="0.3"> +<tool id="rgweblogo3" name="Sequence Logo" version="0.4"><description>generator for fasta (eg Clustal alignments)</description><command interpreter="python"> rgWebLogo3.py -F $outformat -s $size -i $input -o $output -t "$logoname" -c "$colours" -U "$units" Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Trackster: implement start_val parameter for data providers and use parameter to provide incremental fetching of data. Only 'deep' fetching is currently supported.
by Bitbucket 06 Jul '11

06 Jul '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/75eceb82013e/ changeset: 75eceb82013e user: jgoecks date: 2011-07-06 16:20:57 summary: Trackster: implement start_val parameter for data providers and use parameter to provide incremental fetching of data. Only 'deep' fetching is currently supported. affected #: 4 files (1.4 KB) --- a/lib/galaxy/visualization/tracks/data_providers.py Wed Jul 06 09:52:28 2011 -0400 +++ b/lib/galaxy/visualization/tracks/data_providers.py Wed Jul 06 10:20:57 2011 -0400 @@ -72,10 +72,11 @@ # Override. pass - def get_data( self, chrom, start, end, max_vals=None, **kwargs ): + def get_data( self, chrom, start, end, start_val=0, max_vals=None, **kwargs ): """ - Returns data in region defined by chrom, start, and end. If max_vals - is set, returns at most max_vals. + Returns data in region defined by chrom, start, and end. start_val and + max_vals are used to denote the data to return: start_val is the first value to + return and max_vals indicates the number of values to return. """ # Override. pass @@ -215,7 +216,7 @@ # Cleanup. bamfile.close() - def get_data( self, chrom, start, end, max_vals=sys.maxint, **kwargs ): + def get_data( self, chrom, start, end, start_val=0, max_vals=sys.maxint, **kwargs ): """ Fetch reads in the region. @@ -253,8 +254,10 @@ # Encode reads as list of lists. results = [] paired_pending = {} - for read in data: - if len(results) > max_vals: + for count, read in enumerate( data ): + if count < start_val: + continue + if count-start_val >= max_vals: message = ERROR_MAX_VALS % ( max_vals, "reads" ) break qname = read.qname @@ -319,7 +322,7 @@ f.close() return all_dat is not None - def get_data( self, chrom, start, end, max_vals=None, **kwargs ): + def get_data( self, chrom, start, end, start_val=0, max_vals=None, **kwargs ): # Bigwig has the possibility of it being a standalone bigwig file, in which case we use # original_dataset, or coming from wig->bigwig conversion in which we use converted_dataset f, bbi = self._get_dataset() @@ -481,11 +484,14 @@ return tabix.fetch(reference=chrom, start=start, end=end) - def get_data( self, chrom, start, end, max_vals=None, **kwargs ): + def get_data( self, chrom, start, end, start_val=0, max_vals=None, **kwargs ): iterator = self.get_iterator( chrom, start, end ) - return self.process_data( iterator, max_vals, **kwargs ) - + return self.process_data( iterator, start_val, max_vals, **kwargs ) + class IntervalIndexDataProvider( FilterableMixin, TracksDataProvider ): + """ + Interval index files used only for GFF files. + """ col_name_data_attr_mapping = { 4 : { 'index': 4 , 'name' : 'Score' } } def write_data_to_file( self, chrom, start, end, filename ): @@ -501,12 +507,11 @@ out.write(interval.raw_line + '\n') out.close() - def get_data( self, chrom, start, end, max_vals=sys.maxint, **kwargs ): + def get_data( self, chrom, start, end, start_val=0, max_vals=sys.maxint, **kwargs ): start, end = int(start), int(end) source = open( self.original_dataset.file_name ) index = Indexes( self.converted_dataset.file_name ) results = [] - count = 0 message = None # If chrom is not found in indexes, try removing the first three @@ -525,14 +530,15 @@ # filter_cols = from_json_string( kwargs.get( "filter_cols", "[]" ) ) no_detail = ( "no_detail" in kwargs ) - for start, end, offset in index.find(chrom, start, end): - if count >= max_vals: + for count, val in enumerate( index.find(chrom, start, end) ): + start, end, offset = val[0], val[1], val[2] + if count < start_val: + continue + if count-start_val >= max_vals: message = ERROR_MAX_VALS % ( max_vals, "features" ) break - count += 1 source.seek( offset ) # TODO: can we use column metadata to fill out payload? - # TODO: use function to set payload data # GFF dataset. reader = GFFReaderWrapper( source, fix_strand=True ) @@ -549,7 +555,7 @@ Payload format: [ uid (offset), start, end, name, strand, thick_start, thick_end, blocks ] """ - def process_data( self, iterator, max_vals=sys.maxint, **kwargs ): + def process_data( self, iterator, start_val=0, max_vals=sys.maxint, **kwargs ): # # Build data to return. Payload format is: # [ <guid/offset>, <start>, <end>, <name>, <score>, <strand>, <thick_start>, @@ -559,14 +565,14 @@ # filter_cols = from_json_string( kwargs.get( "filter_cols", "[]" ) ) no_detail = ( "no_detail" in kwargs ) - count = 0 rval = [] message = None - for line in iterator: - if count >= max_vals: + for count, line in enumerate( iterator ): + if count < start_val: + continue + if count-start_val >= max_vals: message = ERROR_MAX_VALS % ( max_vals, "features" ) break - count += 1 # TODO: can we use column metadata to fill out payload? # TODO: use function to set payload data @@ -625,16 +631,16 @@ col_name_data_attr_mapping = { 'Qual' : { 'index': 6 , 'name' : 'Qual' } } - def process_data( self, iterator, max_vals=sys.maxint, **kwargs ): + def process_data( self, iterator, start_val=0, max_vals=sys.maxint, **kwargs ): rval = [] - count = 0 message = None - for line in iterator: - if count >= max_vals: + for count, line in enumerate( iterator ): + if count < start_val: + continue + if count-start_val >= max_vals: message = ERROR_MAX_VALS % ( "max_vals", "features" ) break - count += 1 feature = line.split() payload = [ hash(line), int(feature[1])-1, int(feature[1]), @@ -657,22 +663,23 @@ NOTE: this data provider does not use indices, and hence will be very slow for large datasets. """ - def get_data( self, chrom, start, end, max_vals=sys.maxint, **kwargs ): + def get_data( self, chrom, start, end, start_val=0, max_vals=sys.maxint, **kwargs ): start, end = int( start ), int( end ) source = open( self.original_dataset.file_name ) results = [] - count = 0 message = None offset = 0 - for feature in GFFReaderWrapper( source, fix_strand=True ): + for count, feature in enumerate( GFFReaderWrapper( source, fix_strand=True ) ): + if count < start_val: + continue + if count-start_val >= max_vals: + message = ERROR_MAX_VALS % ( max_vals, "reads" ) + break + feature_start, feature_end = convert_gff_coords_to_bed( [ feature.start, feature.end ] ) if feature.chrom != chrom or feature_start < start or feature_end > end: continue - if count >= max_vals: - message = ERROR_MAX_VALS % ( max_vals, "features" ) - break - count += 1 payload = package_gff_feature( feature ) payload.insert( 0, offset ) results.append( payload ) --- a/lib/galaxy/web/controllers/tracks.py Wed Jul 06 09:52:28 2011 -0400 +++ b/lib/galaxy/web/controllers/tracks.py Wed Jul 06 10:20:57 2011 -0400 @@ -469,7 +469,7 @@ return { "status": messages.DATA, "valid_chroms": valid_chroms } @web.json - def data( self, trans, hda_ldda, dataset_id, chrom, low, high, max_vals=5000, **kwargs ): + def data( self, trans, hda_ldda, dataset_id, chrom, low, high, start_val=0, max_vals=5000, **kwargs ): """ Provides a block of data from a dataset. """ @@ -526,7 +526,7 @@ data_provider = data_provider_class( converted_dataset=converted_dataset, original_dataset=dataset, dependencies=deps ) # Get and return data from data_provider. - data = data_provider.get_data( chrom, low, high, max_vals, **kwargs ) + data = data_provider.get_data( chrom, low, high, int(start_val), int(max_vals), **kwargs ) message = None if isinstance(data, dict) and 'message' in data: message = data['message'] --- a/static/scripts/packed/trackster.js Wed Jul 06 09:52:28 2011 -0400 +++ b/static/scripts/packed/trackster.js Wed Jul 06 10:20:57 2011 -0400 @@ -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 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 trackster_module=function(f,T){var n=f("class").extend,p=f("slotting"),I=f("painters");var Z=function(aa,ab){this.document=aa;this.default_font=ab!==undefined?ab:"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")};n(Z.prototype,{load_pattern:function(aa,ae){var ab=this.patterns,ac=this.dummy_context,ad=new Image();ad.src=image_path+ae;ad.onload=function(){ab[aa]=ac.createPattern(ad,"repeat")}},get_pattern:function(aa){return this.patterns[aa]},new_canvas:function(){var aa=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(aa)}aa.manager=this;return aa}});var C=function(aa,ab){aa.bind("drag",{handle:ab,relative:true},function(af,ag){var ae=$(this).parent();var ad=ae.children();var ac;for(ac=0;ac<ad.length;ac++){if(ag.offsetY<$(ad.get(ac)).position().top){break}}if(ac===ad.length){if(this!==ad.get(ac-1)){ae.append(this)}}else{if(this!==ad.get(ac)){$(this).insertBefore(ad.get(ac))}}}).bind("dragstart",function(){$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css("border","0px")})};T.sortable=C;var D=9,A=18,O=D+2,w=100,F=12000,M=200,z=5,s=10,H=5000,t=100,m="There was an error in indexing this dataset. 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this.tracks[this.tracks.indexOf(aa)];this.num_tracks-=1},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(ah){var ag=this.high-this.low,af=this.low,ab=this.high;if(af<this.max_low){af=this.max_low}if(ab>this.max_high){ab=this.max_high}if(this.high!==0&&ag<this.min_separation){ab=af+this.min_separation}this.low=Math.floor(af);this.high=Math.ceil(ab);this.resolution=Math.pow(z,Math.ceil(Math.log((this.high-this.low)/M)/Math.log(z)));this.zoom_res=Math.pow(s,Math.max(0,Math.ceil(Math.log(this.resolution,s)/Math.log(s))));var aa=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ae=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ai=13;this.overview_box.css({left:aa,width:Math.max(ai,ae)}).show();if(ae<ai){this.overview_box.css("left",aa-(ai-ae)/2)}if(this.overview_highlight){this.overview_highlight.css({left:aa,width:ae})}this.update_location(this.low,this.high);if(!ah){for(var ac=0,ad=this.tracks.length;ac<ad;ac++){if(this.tracks[ac]&&this.tracks[ac].enabled){this.tracks[ac].draw()}}for(ac=0,ad=this.label_tracks.length;ac<ad;ac++){this.label_tracks[ac].draw()}}},zoom_in:function(ab,ac){if(this.max_high===0||this.high-this.low<this.min_separation){return}var ad=this.high-this.low,ae=ad/2+this.low,aa=(ad/this.zoom_factor)/2;if(ab){ae=ab/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ae-aa);this.high=Math.round(ae+aa);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var ab=this.high-this.low,ac=ab/2+this.low,aa=(ab*this.zoom_factor)/2;this.low=Math.round(ac-aa);this.high=Math.round(ac+aa);this.redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.redraw()},reset_overview:function(){this.overview_viewport.find("canvas").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()}});var o=function(ac,ag){this.track=ac;this.name=ag.name;this.params=[];var an=ag.params;for(var ad=0;ad<an.length;ad++){var ai=an[ad],ab=ai.name,am=ai.label,ae=unescape(ai.html),ao=ai.value,ak=ai.type;if(ak==="number"){this.params[this.params.length]=new g(ab,am,ae,ao,ai.min,ai.max)}else{if(ak=="select"){this.params[this.params.length]=new K(ab,am,ae,ao)}else{console.log("WARNING: unrecognized tool parameter type:",ab,ak)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(aq){aq.stopPropagation()}).bind("click",function(aq){aq.stopPropagation()}).bind("dblclick",function(aq){aq.stopPropagation()});var al=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var aj=this.params;var ah=this;$.each(this.params,function(ar,av){var au=$("<div>").addClass("param-row").appendTo(ah.parent_div);var aq=$("<div>").addClass("param-label").text(av.label).appendTo(au);var at=$("<div/>").addClass("slider").html(av.html).appendTo(au);at.find(":input").val(av.value);$("<div style='clear: both;'/>").appendTo(au)});this.parent_div.find("input").click(function(){$(this).select()});var ap=$("<div>").addClass("param-row").appendTo(this.parent_div);var af=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ap);var aa=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(ap);var ah=this;aa.click(function(){ah.run_on_region()});af.click(function(){ah.run_on_dataset()})};n(o.prototype,{get_param_values_dict:function(){var aa={};this.parent_div.find(":input").each(function(){var ab=$(this).attr("name"),ac=$(this).val();aa[ab]=JSON.stringify(ac)});return aa},get_param_values:function(){var ab=[];var aa={};this.parent_div.find(":input").each(function(){var ac=$(this).attr("name"),ad=$(this).val();if(ac){ab[ab.length]=ad}});return ab},run_on_dataset:function(){var aa=this;aa.run({dataset_id:this.track.original_dataset_id,tool_id:aa.name},function(ab){show_modal(aa.name+" is Running",aa.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var aa={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},ac=this.track,ab=aa.tool_id+ac.tool_region_and_parameters_str(aa.chrom,aa.low,aa.high),ad;if(ac instanceof e){ad=new Q(ab,view,ac.hda_ldda,undefined,{},{},ac);ad.change_mode(ac.mode)}this.track.add_track(ad);ad.content_div.text("Starting job.");this.run(aa,function(ae){ad.dataset_id=ae.dataset_id;ad.content_div.text("Running job.");ad.init()})},run:function(ab,ac){$.extend(ab,this.get_param_values_dict());var aa=function(){$.getJSON(rerun_tool_url,ab,function(ad){if(ad==="no converter"){new_track.container_div.addClass("error");new_track.content_div.text(G)}else{if(ad.error){new_track.container_div.addClass("error");new_track.content_div.text(v+ad.message)}else{if(ad==="pending"){new_track.container_div.addClass("pending");new_track.content_div.text("Converting input data so that it can be easily reused.");setTimeout(aa,2000)}else{ac(ad)}}}})};aa()}});var K=function(ab,aa,ac,ad){this.name=ab;this.label=aa;this.html=ac;this.value=ad};var g=function(ac,ab,ae,af,ad,aa){K.call(this,ac,ab,ae,af);this.min=ad;this.max=aa};var h=function(ab,aa,ac,ad){this.name=ab;this.index=aa;this.tool_id=ac;this.tool_exp_name=ad};var R=function(ab,aa,ac,ad){h.call(this,ab,aa,ac,ad);this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.min=Number.MAX_VALUE;this.max=-Number.MAX_VALUE;this.slider=null;this.slider_label=null};n(R.prototype,{applies_to:function(aa){if(aa.length>this.index){return true}return false},keep:function(aa){if(!this.applies_to(aa)){return true}var ab=parseInt(aa[this.index]);return(isNaN(ab)||(ab>=this.low&&ab<=this.high))},update_attrs:function(ab){var aa=false;if(!this.applies_to(ab)){return aa}if(ab[this.index]<this.min){this.min=Math.floor(ab[this.index]);aa=true}if(ab[this.index]>this.max){this.max=Math.ceil(ab[this.index]);aa=true}return aa},update_ui_elt:function(){var ac=function(af,ad){var ae=ad-af;return(ae<=2?0.01:1)};var ab=this.slider.slider("option","min"),aa=this.slider.slider("option","max");if(this.min<ab||this.max>aa){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",ac(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var W=function(ac,al){this.track=ac;this.filters=[];for(var ag=0;ag<al.length;ag++){var aa=al[ag],ab=aa.name,ak=aa.type,ai=aa.index,an=aa.tool_id,ad=aa.tool_exp_name;if(ak==="int"||ak==="float"){this.filters[ag]=new R(ab,ai,an,ad)}else{console.log("ERROR: unsupported filter: ",ab,ak)}}var aj=function(ao,ap,aq){ao.click(function(){var ar=ap.text();max=parseFloat(aq.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(aq.slider("option","values")){input_size=2*input_size+1;multi_value=true}ap.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",ar).appendTo(ap).focus().select().click(function(at){at.stopPropagation()}).blur(function(){$(this).remove();ap.text(ar)}).keyup(function(ax){if(ax.keyCode===27){$(this).trigger("blur")}else{if(ax.keyCode===13){var av=aq.slider("option","min"),at=aq.slider("option","max"),aw=function(ay){return(isNaN(ay)||ay>at||ay<av)},au=$(this).val();if(!multi_value){au=parseFloat(au);if(aw(au)){alert("Parameter value must be in the range ["+av+"-"+at+"]");return $(this)}}else{au=au.split("-");au=[parseFloat(au[0]),parseFloat(au[1])];if(aw(au[0])||aw(au[1])){alert("Parameter value must be in the range ["+av+"-"+at+"]");return $(this)}}aq.slider((multi_value?"values":"value"),au)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(ao){ao.stopPropagation()}).bind("click",function(ao){ao.stopPropagation()}).bind("dblclick",function(ao){ao.stopPropagation()}).bind("keydown",function(ao){ao.stopPropagation()});var ae=this;$.each(this.filters,function(av,ap){var ar=$("<div/>").addClass("slider-row").appendTo(ae.parent_div);var ao=$("<div/>").addClass("slider-label").appendTo(ar);var ax=$("<span/>").addClass("slider-name").text(ap.name+" ").appendTo(ao);var aq=$("<span/>");var at=$("<span/>").addClass("slider-value").appendTo(ao).append("[").append(aq).append("]");var aw=$("<div/>").addClass("slider").appendTo(ar);ap.control_element=$("<div/>").attr("id",ap.name+"-filter-control").appendTo(aw);var au=[0,0];ap.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(ay,az){au=az.values;aq.text(az.values[0]+"-"+az.values[1]);setTimeout(function(){if(az.values[0]==au[0]&&az.values[1]==au[1]){var aA=az.values;aq.text(aA[0]+"-"+aA[1]);ap.low=aA[0];ap.high=aA[1];ae.track.draw(true,true)}},50)},change:function(ay,az){ap.control_element.slider("option","slide").call(ap.control_element,ay,az)}});ap.slider=ap.control_element;ap.slider_label=aq;aj(at,aq,ap.control_element);$("<div style='clear: both;'/>").appendTo(ar)});if(this.filters.length!=0){var am=$("<div>").addClass("param-row").appendTo(this.parent_div);var ah=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(am);var af=this;ah.click(function(){af.run_on_dataset()})}};n(W.prototype,{reset_filters:function(){for(var aa=0;aa<this.filters.length;aa++){filter=this.filters[aa];filter.slider.slider("option","values",[filter.min,filter.max])}},run_on_dataset:function(){var ai=function(am,ak,al){if(!(ak in am)){am[ak]=al}return am[ak]};var ac={},aa,ab,ad;for(var ae=0;ae<this.filters.length;ae++){aa=this.filters[ae];if(aa.tool_id){if(aa.min!=aa.low){ab=ai(ac,aa.tool_id,[]);ab[ab.length]=aa.tool_exp_name+" >= "+aa.low}if(aa.max!=aa.high){ab=ai(ac,aa.tool_id,[]);ab[ab.length]=aa.tool_exp_name+" <= "+aa.high}}}var ag=[];for(var aj in ac){ag[ag.length]=[aj,ac[aj]]}var ah=ag.length;(function af(aq,an){var al=an[0],am=al[0],ap=al[1],ao="("+ap.join(") and (")+")",ak={cond:ao,input:aq,target_dataset_id:aq,tool_id:am},an=an.slice(1);$.getJSON(run_tool_url,ak,function(ar){if(ar.error){show_modal("Filter Dataset","Error running tool "+am,{Close:hide_modal})}else{if(an.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{af(ar.dataset_id,an)}}})})(this.track.dataset_id,ag)}});var V=function(aa){this.track=aa.track;this.params=aa.params;this.values={};if(aa.saved_values){this.restore_values(aa.saved_values)}this.onchange=aa.onchange};n(V.prototype,{restore_values:function(aa){var ab=this;$.each(this.params,function(ac,ad){if(aa[ad.key]!==undefined){ab.values[ad.key]=aa[ad.key]}else{ab.values[ad.key]=ad.default_value}})},build_form:function(){var ab=this;var aa=$("<div />");$.each(this.params,function(af,ad){if(!ad.hidden){var ac="param_"+af;var ak=$("<div class='form-row' />").appendTo(aa);ak.append($("<label />").attr("for",ac).text(ad.label+":"));if(ad.type==="bool"){ak.append($('<input type="checkbox" />').attr("id",ac).attr("name",ac).attr("checked",ab.values[ad.key]))}else{if(ad.type==="color"){var ah=ab.values[ad.key];var ag=$("<input />").attr("id",ac).attr("name",ac).val(ah);var ai=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var ae=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(ai);var aj=$("<div/>").appendTo(ae).farbtastic({width:100,height:100,callback:ag,color:ah});$("<div />").append(ag).append(ai).appendTo(ak).bind("click",function(al){ai.css({left:$(this).position().left+($(ag).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){ai.hide();$(document).unbind("click.color-picker")});al.stopPropagation()})}else{ak.append($("<input />").attr("id",ac).attr("name",ac).val(ab.values[ad.key]))}}}});return aa},update_from_form:function(aa){var ac=this;var ab=false;$.each(this.params,function(ad,af){if(!af.hidden){var ag="param_"+ad;var ae=aa.find("#"+ag).val();if(af.type==="float"){ae=parseFloat(ae)}else{if(af.type==="int"){ae=parseInt(ae)}else{if(af.type==="bool"){ae=aa.find("#"+ag).is(":checked")}}}if(ae!==ac.values[af.key]){ac.values[af.key]=ae;ab=true}}});if(ab){this.onchange()}}});var b=function(ac,ab,aa){this.index=ac;this.resolution=ab;this.canvas=$("<div class='track-tile'/>").append(aa);this.stale=false};var l=function(ac,ab,aa,ad){b.call(this,ac,ab,aa);this.max_val=ad};var L=function(ac,ab,aa,ad){b.call(this,ac,ab,aa);this.message=ad};var j=function(ab,aa,ae,ac,ad){this.name=ab;this.view=aa;this.parent_element=ae;this.data_url=(ac?ac:default_data_url);this.data_url_extra_params={};this.data_query_wait=(ad?ad:H);this.dataset_check_url=converted_datasets_state_url;this.container_div=$("<div />").addClass("track").css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div class='draghandle' />").appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)};n(j.prototype,{get_type:function(){if(this instanceof X){return"LabelTrack"}else{if(this instanceof x){return"ReferenceTrack"}else{if(this instanceof k){return"LineTrack"}else{if(this instanceof S){return"ReadTrack"}else{if(this instanceof Q){return"ToolDataFeatureTrack"}else{if(this instanceof P){return"VcfTrack"}else{if(this instanceof e){return"FeatureTrack"}}}}}}}return""},init:function(){var aa=this;aa.enabled=false;aa.tile_cache.clear();aa.data_cache.clear();aa.initial_canvas=undefined;aa.content_div.css("height","auto");aa.container_div.removeClass("nodata error pending");if(!aa.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:aa.hda_ldda,dataset_id:aa.dataset_id,chrom:aa.view.chrom},function(ab){if(!ab||ab==="error"||ab.kind==="error"){aa.container_div.addClass("error");aa.content_div.text(m);if(ab.message){var ad=aa.view.tracks.indexOf(aa);var ac=$(" <a href='javascript:void(0);'></a>").text("View error").bind("click",function(){show_modal("Trackster Error","<pre>"+ab.message+"</pre>",{Close:hide_modal})});aa.content_div.append(ac)}}else{if(ab==="no converter"){aa.container_div.addClass("error");aa.content_div.text(G)}else{if(ab==="no data"||(ab.data!==undefined&&(ab.data===null||ab.data.length===0))){aa.container_div.addClass("nodata");aa.content_div.text(B)}else{if(ab==="pending"){aa.container_div.addClass("pending");aa.content_div.text(q);setTimeout(function(){aa.init()},aa.data_query_wait)}else{if(ab.status==="data"){if(ab.valid_chroms){aa.valid_chroms=ab.valid_chroms;aa.make_name_popup_menu()}aa.content_div.text(U);if(aa.view.chrom){aa.content_div.text("");aa.content_div.css("height",aa.height_px+"px");aa.enabled=true;$.when(aa.predraw_init()).done(function(){aa.container_div.removeClass("nodata error pending");aa.draw()})}}}}}}})},predraw_init:function(){},update_name:function(aa){this.old_name=this.name;this.name=aa;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)}});var J=function(ah,af,ai){var ab=this,aj=ab.view;this.filters_manager=(ah!==undefined?new W(this,ah):undefined);this.filters_available=false;this.filters_visible=false;this.tool=(af!==undefined&&obj_length(af)>0?new o(this,af):undefined);this.parent_track=ai;this.child_tracks=[];if(ab.hidden){return}if(this.parent_track){this.header_div.find(".draghandle").removeClass("draghandle").addClass("child-track-icon").addClass("icon-button");this.parent_element.addClass("child-track");this.tool=undefined}ab.child_tracks_container=$("<div/>").addClass("child-tracks-container").hide();ab.container_div.append(ab.child_tracks_container);if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}if(ab.display_modes!==undefined){if(ab.mode_div===undefined){ab.mode_div=$("<div class='right-float menubutton popup' />").appendTo(ab.header_div);var ac=(ab.track_config&&ab.track_config.values.mode?ab.track_config.values.mode:ab.display_modes[0]);ab.mode=ac;ab.mode_div.text(ac);var aa={};for(var ad=0,ag=ab.display_modes.length;ad<ag;ad++){var ae=ab.display_modes[ad];aa[ae]=function(ak){return function(){ab.change_mode(ak)}}(ae)}make_popupmenu(ab.mode_div,aa)}else{ab.mode_div.hide()}}this.make_name_popup_menu()};n(J.prototype,j.prototype,{change_mode:function(ab){var aa=this;aa.mode_div.text(ab);aa.mode=ab;aa.track_config.values.mode=ab;aa.tile_cache.clear();aa.draw()},make_name_popup_menu:function(){var ab=this;var aa={};aa["Edit configuration"]=function(){var ah=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},af=function(){ab.track_config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ag=function(ai){if((ai.keyCode||ai.which)===27){ah()}else{if((ai.keyCode||ai.which)===13){af()}}};$(window).bind("keypress.check_enter_esc",ag);show_modal("Configure Track",ab.track_config.build_form(),{Cancel:ah,OK:af})};if(ab.filters_available>0){var ae=(ab.filters_div.is(":visible")?"Hide filters":"Show filters");aa[ae]=function(){ab.filters_visible=(ab.filters_div.is(":visible"));if(ab.filters_visible){ab.filters_manager.reset_filters()}ab.filters_div.toggle();ab.make_name_popup_menu()}}if(ab.tool){var ae=(ab.dynamic_tool_div.is(":visible")?"Hide tool":"Show tool");aa[ae]=function(){if(!ab.dynamic_tool_div.is(":visible")){ab.update_name(ab.name+ab.tool_region_and_parameters_str())}else{menu_option_text="Show dynamic tool";ab.revert_name()}ab.dynamic_tool_div.toggle();ab.make_name_popup_menu()}}if(ab.valid_chroms){aa["List chrom/contigs with data"]=function(){show_modal("Chrom/contigs with data","<p>"+ab.valid_chroms.join("<br/>")+"</p>",{Close:function(){hide_modal()}})}}var ac=view;var ad=function(){$("#no-tracks").show()};if(this.parent_track){ac=this.parent_track;ad=function(){}}aa.Remove=function(){ac.remove_track(ab);if(ac.num_tracks===0){ad()}};make_popupmenu(ab.name_div,aa)},draw:function(aa,ac){if(!this.dataset_id){return}var au=this.view.low,ag=this.view.high,ai=ag-au,ak=this.view.container.width(),ae=ak/ai,al=this.view.resolution,ad=$("<div style='position: relative;'></div>"),am=function(aw,ax,av){return aw+"_"+ax+"_"+av};if(!ac){this.content_div.children().remove()}this.content_div.append(ad);this.max_height=0;var ao=Math.floor(au/al/M);var af=[];var ap=0;while((ao*M*al)<ag){var at=am(ak,ae,ao);var ah=this.tile_cache.get(at);var aq=ao*M*this.view.resolution;var ab=aq+M*this.view.resolution;if(!aa&&ah){af[af.length]=ah;this.show_tile(ah,ad,aq,ab,ae)}else{this.delayed_draw(aa,at,ao,al,ad,ae,af)}ao+=1;ap++}var aj=this;var ar=setInterval(function(){if(af.length===ap){clearInterval(ar);if(ac){var aA=aj.content_div.children();var aB=false;for(var az=aA.length-1,aF=0;az>=aF;az--){var ay=$(aA[az]);if(aB){ay.remove()}else{if(ay.children().length!==0){aB=true}}}}if(aj instanceof e&&aj.mode=="Histogram"){var aE=-1;for(var az=0;az<af.length;az++){var aH=af[az].max_val;if(aH>aE){aE=aH}}for(var az=0;az<af.length;az++){if(af[az].max_val!==aE){var aG=af[az];aG.canvas.remove();aj.delayed_draw(true,am(ak,ae,aG.index),aG.index,aG.resolution,ad,ae,[],{max:aE})}}}if(aj.filters_manager){var ax=aj.filters_manager.filters;for(var aD=0;aD<ax.length;aD++){ax[aD].update_ui_elt()}var aC=false;if(aj.example_feature){for(var aD=0;aD<ax.length;aD++){if(ax[aD].applies_to(aj.example_feature)){aC=true;break}}}if(aj.filters_available!==aC){aj.filters_available=aC;if(!aj.filters_available){aj.filters_div.hide()}aj.make_name_popup_menu()}}var av=false;for(var aw=0;aw<af.length;aw++){if(af[aw].message){av=true;break}}if(av){for(var aw=0;aw<af.length;aw++){aG=af[aw];if(!aG.message){aG.canvas.css("padding-top",A)}}}}},50);for(var an=0;an<this.child_tracks.length;an++){this.child_tracks[an].draw(aa,ac)}},delayed_draw:function(ab,ai,ac,ae,aj,am,ak,af){var ad=this,ag=ac*M*ae,al=ag+M*ae;var ah=function(av,an,ap,ao,at,au,aq){var ar=ad.draw_tile(an,ap,ao,au,aq);ad.tile_cache.set(ai,ar);if(ar===undefined){return}ad.show_tile(ar,at,ag,al,au);ak[ak.length]=ar};var aa=setTimeout(function(){if(ag<=ad.view.high&&al>=ad.view.low){var an=(ab?undefined:ad.tile_cache.get(ai));if(an){ad.show_tile(an,aj,ag,al,am);ak[ak.length]=an}else{$.when(ad.data_cache.get_data(view.chrom,ag,al,ad.mode,ae,ad.data_url_extra_params)).then(function(ao){n(ao,af);if(view.reference_track&&am>view.canvas_manager.char_width_px){$.when(view.reference_track.data_cache.get_data(view.chrom,ag,al,ad.mode,ae,view.reference_track.data_url_extra_params)).then(function(ap){ah(aa,ao,ae,ac,aj,am,ap)})}else{ah(aa,ao,ae,ac,aj,am)}})}}},50)},show_tile:function(ah,aj,ae,ak,am){var ab=this,aa=ah.canvas,af=aa;if(ah.message){var al=$("<div/>"),ai=$("<div/>").addClass("tile-message").text(ah.message).css({height:A-1,width:ah.canvas.width}).appendTo(al),ag=$("<button/>").text("Show more").css("margin-left","0.5em").appendTo(ai);al.append(aa);af=al;ag.click(function(){var an=ab.data_cache.get_data(ab.view.chrom,ae,ak,ab.mode,ah.resolution);an.stale=true;ah.stale=true;ab.data_cache.get_data(ab.view.chrom,ae,ak,ab.mode,ah.resolution,{max_vals:an.data.length*2});ab.draw()}).dblclick(function(an){an.stopPropagation()})}var ad=this.view.high-this.view.low,ac=(ae-this.view.low)*am;if(this.left_offset){ac-=this.left_offset}af.css({position:"absolute",top:0,left:ac,height:""});aj.append(af);ab.max_height=Math.max(ab.max_height,af.height());ab.content_div.css("height",ab.max_height+"px");aj.children().css("height",ab.max_height+"px")},set_overview:function(){var aa=this.view;if(this.initial_canvas&&this.is_overview){aa.overview_close.show();aa.overview_viewport.append(this.initial_canvas);aa.overview_highlight.show().height(this.initial_canvas.height());aa.overview_viewport.height(this.initial_canvas.height()+aa.overview_box.height())}$(window).trigger("resize")},tool_region_and_parameters_str:function(ac,aa,ad){var ab=this,ae=(ac!==undefined&&aa!==undefined&&ad!==undefined?ac+":"+aa+"-"+ad:"all");return" - region=["+ae+"], parameters=["+ab.tool.get_param_values().join(", ")+"]"},add_track:function(aa){aa.track_id=this.track_id+"_"+this.child_tracks.length;aa.container_div.attr("id","track_"+aa.track_id);this.child_tracks_container.append(aa.container_div);C(aa.container_div,".child-track-icon");if(!$(this.child_tracks_container).is(":visible")){this.child_tracks_container.show()}this.child_tracks.push(aa);this.view.has_changes=true},remove_track:function(aa){aa.container_div.fadeOut("slow",function(){$(this).remove()})}});var X=function(aa,ab){this.hidden=true;j.call(this,null,aa,ab);this.container_div.addClass("label-track")};n(X.prototype,j.prototype,{draw:function(){var ac=this.view,ad=ac.high-ac.low,ag=Math.floor(Math.pow(10,Math.floor(Math.log(ad)/Math.log(10)))),aa=Math.floor(ac.low/ag)*ag,ae=this.view.container.width(),ab=$("<div style='position: relative; height: 1.3em;'></div>");while(aa<ac.high){var af=(aa-ac.low)/ad*ae;ab.append($("<div class='label'>"+commatize(aa)+"</div>").css({position:"absolute",left:af-1}));aa+=ag}this.content_div.children(":first").remove();this.content_div.append(ab)}});var x=function(aa){this.hidden=true;j.call(this,null,aa,aa.top_labeltrack);J.call(this);aa.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:aa.dbkey};this.data_cache=new E(y,this,false);this.tile_cache=new c(r)};n(x.prototype,J.prototype,{draw_tile:function(ai,af,ab,ak){var ae=this,ac=M*af;if(ak>this.view.canvas_manager.char_width_px){if(ai===null){ae.content_div.css("height","0px");return}var ad=this.view.canvas_manager.new_canvas();var aj=ad.getContext("2d");ad.width=Math.ceil(ac*ak+ae.left_offset);ad.height=ae.height_px;aj.font=aj.canvas.manager.default_font;aj.textAlign="center";for(var ag=0,ah=ai.length;ag<ah;ag++){var aa=Math.round(ag*ak);aj.fillText(ai[ag],aa+ae.left_offset,10)}return new b(ab,af,ad)}this.content_div.css("height","0px")}});var k=function(ae,ac,af,aa,ad){var ab=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";j.call(this,ae,ac,ac.viewport_container);J.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=af;this.dataset_id=aa;this.original_dataset_id=aa;this.data_cache=new N(y,this);this.tile_cache=new c(r);this.track_config=new V({track:this,params:[{key:"color",label:"Color",type:"color",default_value:"black"},{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:ad,onchange:function(){ab.vertical_range=ab.prefs.max_value-ab.prefs.min_value;$("#linetrack_"+ab.track_id+"_minval").text(ab.prefs.min_value);$("#linetrack_"+ab.track_id+"_maxval").text(ab.prefs.max_value);ab.tile_cache.clear();ab.draw()}});this.prefs=this.track_config.values;this.height_px=this.track_config.values.height;this.vertical_range=this.track_config.values.max_value-this.track_config.values.min_value;this.add_resize_handle()};n(k.prototype,J.prototype,{add_resize_handle:function(){var aa=this;var ad=false;var ac=false;var ab=$("<div class='track-resize'>");$(aa.container_div).hover(function(){ad=true;ab.show()},function(){ad=false;if(!ac){ab.hide()}});ab.hide().bind("dragstart",function(ae,af){ac=true;af.original_height=$(aa.content_div).height()}).bind("drag",function(af,ag){var ae=Math.min(Math.max(ag.original_height+ag.deltaY,aa.min_height_px),aa.max_height_px);$(aa.content_div).css("height",ae);aa.height_px=ae;aa.draw(true)}).bind("dragend",function(ae,af){aa.tile_cache.clear();ac=false;if(!ad){ab.hide()}aa.track_config.values.height=aa.height_px}).appendTo(aa.container_div)},predraw_init:function(){var aa=this,ab=aa.view.tracks.indexOf(aa);aa.vertical_range=undefined;return $.getJSON(aa.data_url,{stats:true,chrom:aa.view.chrom,low:null,high:null,hda_ldda:aa.hda_ldda,dataset_id:aa.dataset_id},function(ac){aa.container_div.addClass("line-track");var ae=ac.data;if(isNaN(parseFloat(aa.prefs.min_value))||isNaN(parseFloat(aa.prefs.max_value))){aa.prefs.min_value=ae.min;aa.prefs.max_value=ae.max;$("#track_"+ab+"_minval").val(aa.prefs.min_value);$("#track_"+ab+"_maxval").val(aa.prefs.max_value)}aa.vertical_range=aa.prefs.max_value-aa.prefs.min_value;aa.total_frequency=ae.total_frequency;aa.container_div.find(".yaxislabel").remove();var af=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ab+"_minval").text(u(aa.prefs.min_value));var ad=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ab+"_maxval").text(u(aa.prefs.max_value));ad.css({position:"absolute",top:"24px",left:"10px"});ad.prependTo(aa.container_div);af.css({position:"absolute",bottom:"2px",left:"10px"});af.prependTo(aa.container_div)})},draw_tile:function(ak,ae,ab,aj){if(this.vertical_range===undefined){return}var af=ab*M*ae,ad=M*ae,aa=Math.ceil(ad*aj),ah=this.height_px;var ac=this.view.canvas_manager.new_canvas();ac.width=aa,ac.height=ah;var ai=ac.getContext("2d");var ag=new I.LinePainter(ak.data,af,af+ad,this.prefs,this.mode);ag.draw(ai,aa,ah);return new b(ad,ae,ac)}});var e=function(aa,af,ae,ai,ah,ac,ad,ag){var ab=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];this.track_config=new V({track:this,params:[{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ah,onchange:function(){ab.tile_cache.clear();ab.draw()}});this.prefs=this.track_config.values;j.call(this,aa,af,af.viewport_container);J.call(this,ac,ad,ag);this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=ae;this.dataset_id=ai;this.original_dataset_id=ai;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_cache=new N(20,this);this.left_offset=200;this.painter=I.LinkedFeaturePainter};n(e.prototype,J.prototype,{update_auto_mode:function(aa){if(this.mode=="Auto"){if(aa=="no_detail"){aa="feature spans"}else{if(aa=="summary_tree"){aa="coverage histogram"}}this.mode_div.text("Auto ("+aa+")")}},incremental_slots:function(ae,ab,ad){var ac=this.view.canvas_manager.dummy_context,aa=this.inc_slots[ae];if(!aa||(aa.mode!==ad)){aa=new (p.FeatureSlotter)(ae,ad==="Pack",w,function(af){return ac.measureText(af)});aa.mode=ad;this.inc_slots[ae]=aa}return aa.slot_features(ab)},get_summary_tree_data:function(ae,ah,ac,ap){if(ap>ac-ah){ap=ac-ah}var al=Math.floor((ac-ah)/ap),ao=[],ad=0;var af=0,ag=0,ak,an=0,ai=[],am,aj;var ab=function(at,ar,au,aq){at[0]=ar+au*aq;at[1]=ar+(au+1)*aq};while(an<ap&&af!==ae.length){var aa=false;for(;an<ap&&!aa;an++){ab(ai,ah,an,al);for(ag=af;ag<ae.length;ag++){ak=ae[ag].slice(1,3);if(is_overlap(ak,ai)){aa=true;break}}if(aa){break}}data_start_index=ag;ao[ao.length]=am=[ai[0],0];for(;ag<ae.length;ag++){ak=ae[ag].slice(1,3);if(is_overlap(ak,ai)){am[1]++}else{break}}if(am[1]>ad){ad=am[1]}an++}return{max:ad,delta:al,data:ao}},draw_tile:function(an,av,az,aj,ad){var ar=this,aB=az*M*av,ab=(az+1)*M*av,ap=ab-aB,at=Math.ceil(ap*aj),aq=this.mode,aF=25,ae=this.left_offset,ao,af;if(aq==="Auto"){if(an.dataset_type==="summary_tree"){aq=an.dataset_type}else{if(an.extra_info==="no_detail"){aq="no_detail"}else{var aE=an.data;if(this.view.high-this.view.low>F){aq="Squish"}else{aq="Pack"}}}this.update_auto_mode(aq)}if(aq==="summary_tree"||aq==="Histogram"){af=this.summary_draw_height;this.container_div.find(".yaxislabel").remove();var aa=$("<div />").addClass("yaxislabel");aa.text(an.max);aa.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});aa.prependTo(this.container_div);var ac=this.view.canvas_manager.new_canvas();ac.width=at+ae;ac.height=af+O;if(an.dataset_type!="summary_tree"){var ak=this.get_summary_tree_data(an.data,aB,ab,200);if(an.max){ak.max=an.max}an=ak}var aC=new I.SummaryTreePainter(an,aB,ab,this.prefs);var au=ac.getContext("2d");au.translate(ae,O);aC.draw(au,at,af);return new l(az,av,ac,an.max)}var ao,ah=1;if(aq==="no_detail"||aq==="Squish"||aq==="Pack"){ah=this.incremental_slots(aj,an.data,aq);ao=this.inc_slots[aj].slots}var ai=[];if(an.data){var al=this.filters_manager.filters;for(var aw=0,ay=an.data.length;aw<ay;aw++){var ag=an.data[aw];var ax=false;var am;for(var aA=0,aD=al.length;aA<aD;aA++){am=al[aA];am.update_attrs(ag);if(!am.keep(ag)){ax=true;break}}if(!ax){ai.push(ag)}}}var aC=new (this.painter)(ai,aB,ab,this.prefs,aq,ad);var af=aC.get_required_height(ah);var ac=this.view.canvas_manager.new_canvas();ac.width=at+ae;ac.height=af;var au=ac.getContext("2d");au.fillStyle=this.prefs.block_color;au.font=au.canvas.manager.default_font;au.textAlign="right";this.container_div.find(".yaxislabel").remove();if(an.data){this.example_feature=(an.data.length?an.data[0]:undefined);au.translate(ae,0);aC.draw(au,at,af,ao)}return new L(az,av,ac,an.message)}});var P=function(ad,ab,af,aa,ac,ae){e.call(this,ad,ab,af,aa,ac,ae);this.painter=I.VariantPainter};n(P.prototype,J.prototype,e.prototype);var S=function(ad,ab,af,aa,ac,ae){e.call(this,ad,ab,af,aa,ac,ae);this.track_config=new V({track:this,params:[{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{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:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ac,onchange:function(){this.track.tile_cache.clear();this.track.draw()}});this.prefs=this.track_config.values;this.painter=I.ReadPainter;this.make_name_popup_menu()};n(S.prototype,J.prototype,e.prototype);var Q=function(ae,ac,ag,aa,ad,af,ab){e.call(this,ae,ac,ag,aa,ad,af,{},ab);this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};n(Q.prototype,J.prototype,e.prototype,{predraw_init:function(){var ab=this;var aa=function(){if(ab.data_cache.size()===0){setTimeout(aa,300)}else{ab.data_url=default_data_url;ab.data_query_wait=H;ab.dataset_state_url=converted_datasets_state_url;$.getJSON(ab.dataset_state_url,{dataset_id:ab.dataset_id,hda_ldda:ab.hda_ldda},function(ac){})}};aa()}});T.View=Y;T.LineTrack=k;T.FeatureTrack=e;T.ReadTrack=S};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(j,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=j;this.include_label=h;this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,s=this.slots,h=this.start_end_dct,y=[],A=[],n=0,z=this.max_rows;for(var w=0,x=m.length;w<x;w++){var l=m[w],o=l[0];if(s[o]!==undefined){n=Math.max(n,s[o]);A.push(s[o])}else{y.push(w)}}var q=function(G,H){for(var F=0;F<=z;F++){var D=false,I=h[F];if(I!==undefined){for(var C=0,E=I.length;C<E;C++){var B=I[C];if(H>B[0]&&G<B[1]){D=true;break}}}if(!D){return F}}return -1};for(var w=0,x=y.length;w<x;w++){var l=m[y[w]],o=l[0],u=l[1],f=l[2],r=l[3],g=Math.floor(u*p),k=Math.ceil(f*p),v=this.measureText(r).width,j;if(r!==undefined&&this.include_label){v+=(d+a);if(g-v>=0){g-=v;j="left"}else{k+=v;j="right"}}var t=q(g,k);if(t>=0){if(h[t]===undefined){h[t]=[]}h[t].push([g,k]);s[o]=t;n=Math.max(n,t)}else{}}return n+1}})};var painters_module=function(j,w){var t=j("class").extend;var o=function(H,z,F,y,E,C){if(C===undefined){C=4}var B=y-z;var A=E-F;var D=Math.floor(Math.sqrt(B*B+A*A)/C);var I=B/D;var G=A/D;var x;for(x=0;x<D;x++,z+=I,F+=G){if(x%2!==0){continue}H.fillRect(z,F,C,1)}};var p=function(A,z,x,D){var C=z-D/2,B=z+D/2,E=x-Math.sqrt(D*3/2);A.beginPath();A.moveTo(C,E);A.lineTo(B,E);A.lineTo(z,x);A.lineTo(C,E);A.strokeStyle=this.fillStyle;A.fill();A.stroke();A.closePath()};var m=function(z,B,x,y,A){this.data=z;this.view_start=B;this.view_end=x;this.prefs=t({},this.default_prefs,y);this.mode=A};m.prototype.default_prefs={};var u=function(z,B,x,y,A){m.call(this,z,B,x,y,A)};u.prototype.default_prefs={show_counts:false};u.prototype.draw=function(M,z,L){var E=this.view_start,O=this.view_end-this.view_start,N=z/O;var J=this.data.data,I=this.data.delta,G=this.data.max,B=L;delta_x_px=Math.ceil(I*N);M.save();for(var C=0,D=J.length;C<D;C++){var H=Math.floor((J[C][0]-E)*N);var F=J[C][1];if(!F){continue}var K=F/G*L;if(F!==0&&K<1){K=1}M.fillStyle=this.prefs.block_color;M.fillRect(H,B-K,delta_x_px,K);var A=4;if(this.prefs.show_counts&&(M.measureText(F).width+A)<delta_x_px){M.fillStyle=this.prefs.label_color;M.textAlign="center";M.fillText(F,H+(delta_x_px/2),10)}}M.restore()};var c=function(x,B,D,E,z){m.call(this,x,B,D,E,z);if(this.prefs.min_value===undefined){var F=Infinity;for(var y=0,A=this.data.length;y<A;y++){F=Math.min(F,this.data[y][1])}this.prefs.min_value=F}if(this.prefs.max_value===undefined){var C=-Infinity;for(var y=0,A=this.data.length;y<A;y++){C=Math.max(C,this.data[y][1])}this.prefs.max_value=C}};c.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};c.prototype.draw=function(M,L,J){var E=false,G=this.prefs.min_value,C=this.prefs.max_value,I=C-G,x=J,z=this.view_start,K=this.view_end-this.view_start,A=L/K,H=this.mode,S=this.data;M.save();var T=Math.round(J+G/I*J);if(H!=="Intensity"){M.fillStyle="#aaa";M.fillRect(0,T,L,1)}M.beginPath();var Q,D,B;if(S.length>1){B=Math.ceil((S[1][0]-S[0][0])*A)}else{B=10}for(var N=0,O=S.length;N<O;N++){M.fillStyle=this.prefs.color;Q=Math.round((S[N][0]-z)*A);D=S[N][1];var 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focusout",ab).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").appendTo(this.nav_controls);this.location_span.bind("click",function(){aa.location_span.hide();aa.chrom_select.hide();aa.nav_input.val(aa.chrom+":"+aa.low+"-"+aa.high);aa.nav_input.css("display","inline-block");aa.nav_input.select();aa.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 id='zoom-out' />").click(function(){aa.zoom_out();aa.redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a id='zoom-in' />").click(function(){aa.zoom_in();aa.redraw()}).appendTo(this.nav_controls);this.load_chroms({low:0},ad);this.chrom_select.bind("change",function(){aa.change_chrom(aa.chrom_select.val())});this.intro_div.show();this.content_div.bind("click",function(ae){$(this).find("input").trigger("blur")});this.content_div.bind("dblclick",function(ae){aa.zoom_in(ae.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ae,af){this.current_x=af.offsetX}).bind("drag",function(ae,ag){var ah=ag.offsetX-this.current_x;this.current_x=ag.offsetX;var af=Math.round(ah/aa.viewport_container.width()*(aa.max_high-aa.max_low));aa.move_delta(-af)});this.overview_close.bind("click",function(){for(var af=0,ae=aa.tracks.length;af<ae;af++){aa.tracks[af].is_overview=false}$(this).siblings().filter("canvas").remove();$(this).parent().css("height",aa.overview_box.height());aa.overview_highlight.hide();$(this).hide()});this.viewport_container.bind("draginit",function(ae,af){if(ae.clientX>aa.viewport_container.width()-16){return false}}).bind("dragstart",function(ae,af){af.original_low=aa.low;af.current_height=ae.clientY;af.current_x=af.offsetX}).bind("drag",function(ag,ai){var ae=$(this);var aj=ai.offsetX-ai.current_x;var af=ae.scrollTop()-(ag.clientY-ai.current_height);ae.scrollTop(af);ai.current_height=ag.clientY;ai.current_x=ai.offsetX;var ah=Math.round(aj/aa.viewport_container.width()*(aa.high-aa.low));aa.move_delta(ah)}).bind("mousewheel",function(ag,ai,af,ae){if(af){var ah=Math.round(-af/aa.viewport_container.width()*(aa.high-aa.low));aa.move_delta(ah)}});this.top_labeltrack.bind("dragstart",function(ae,af){return $("<div />").css({height:aa.content_div.height()+aa.top_labeltrack.height()+aa.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ai,aj){$(aj.proxy).css({left:Math.min(ai.pageX,aj.startX),width:Math.abs(ai.pageX-aj.startX)});var af=Math.min(ai.pageX,aj.startX)-aa.container.offset().left,ae=Math.max(ai.pageX,aj.startX)-aa.container.offset().left,ah=(aa.high-aa.low),ag=aa.viewport_container.width();aa.update_location(Math.round(af/ag*ah)+aa.low,Math.round(ae/ag*ah)+aa.low)}).bind("dragend",function(aj,ak){var af=Math.min(aj.pageX,ak.startX),ae=Math.max(aj.pageX,ak.startX),ah=(aa.high-aa.low),ag=aa.viewport_container.width(),ai=aa.low;aa.low=Math.round(af/ag*ah)+ai;aa.high=Math.round(ae/ag*ah)+ai;$(ak.proxy).remove();aa.redraw()});this.add_label_track(new X(this,this.top_labeltrack));this.add_label_track(new X(this,this.nav_labeltrack));$(window).bind("resize",function(){aa.resize_window()});$(document).bind("redraw",function(){aa.redraw()});this.reset();$(window).trigger("resize")},update_location:function(aa,ab){this.location_span.text(commatize(aa)+" - "+commatize(ab));this.nav_input.val(this.chrom+":"+commatize(aa)+"-"+commatize(ab))},load_chroms:function(ab,ac){ab.num=t;$.extend(ab,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var aa=this;$.ajax({url:chrom_url,data:ab,dataType:"json",success:function(ae){if(ae.chrom_info.length===0){alert("Invalid chromosome: "+ab.chrom);return}if(ae.reference){aa.add_label_track(new x(aa))}aa.chrom_data=ae.chrom_info;var ah='<option value="">Select Chrom/Contig</option>';for(var ag=0,ad=aa.chrom_data.length;ag<ad;ag++){var af=aa.chrom_data[ag].chrom;ah+='<option value="'+af+'">'+af+"</option>"}if(ae.prev_chroms){ah+='<option value="previous">Previous '+t+"</option>"}if(ae.next_chroms){ah+='<option value="next">Next '+t+"</option>"}aa.chrom_select.html(ah);if(ac){ac()}aa.chrom_start_index=ae.start_index},error:function(){alert("Could not load chroms for this dbkey:",aa.dbkey)}})},change_chrom:function(ae,ab,ag){if(!ae||ae==="None"){return}var ad=this;if(ae==="previous"){ad.load_chroms({low:this.chrom_start_index-t});return}if(ae==="next"){ad.load_chroms({low:this.chrom_start_index+t});return}var af=$.grep(ad.chrom_data,function(ai,aj){return ai.chrom===ae})[0];if(af===undefined){ad.load_chroms({chrom:ae},function(){ad.change_chrom(ae,ab,ag)});return}else{if(ae!==ad.chrom){ad.chrom=ae;if(!ad.chrom){ad.intro_div.show()}else{ad.intro_div.hide()}ad.chrom_select.val(ad.chrom);ad.max_high=af.len-1;ad.reset();ad.redraw(true);for(var ah=0,aa=ad.tracks.length;ah<aa;ah++){var ac=ad.tracks[ah];if(ac.init){ac.init()}}}if(ab!==undefined&&ag!==undefined){ad.low=Math.max(ab,0);ad.high=Math.min(ag,ad.max_high)}ad.reset_overview();ad.redraw()}},go_to:function(ae){var ai=this,aa,ad,ab=ae.split(":"),ag=ab[0],ah=ab[1];if(ah!==undefined){try{var af=ah.split("-");aa=parseInt(af[0].replace(/,/g,""),10);ad=parseInt(af[1].replace(/,/g,""),10)}catch(ac){return false}}ai.change_chrom(ag,aa,ad)},move_fraction:function(ac){var aa=this;var ab=aa.high-aa.low;this.move_delta(ac*ab)},move_delta:function(ac){var aa=this;var ab=aa.high-aa.low;if(aa.low-ac<aa.max_low){aa.low=aa.max_low;aa.high=aa.max_low+ab}else{if(aa.high-ac>aa.max_high){aa.high=aa.max_high;aa.low=aa.max_high-ab}else{aa.high-=ac;aa.low-=ac}}aa.redraw()},add_track:function(aa){aa.view=this;aa.track_id=this.track_id_counter;this.tracks.push(aa);if(aa.init){aa.init()}aa.container_div.attr("id","track_"+aa.track_id);C(aa.container_div,".draghandle");this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(aa){aa.view=this;this.label_tracks.push(aa)},remove_track:function(aa){this.has_changes=true;aa.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[this.tracks.indexOf(aa)];this.num_tracks-=1},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(ah){var ag=this.high-this.low,af=this.low,ab=this.high;if(af<this.max_low){af=this.max_low}if(ab>this.max_high){ab=this.max_high}if(this.high!==0&&ag<this.min_separation){ab=af+this.min_separation}this.low=Math.floor(af);this.high=Math.ceil(ab);this.resolution=Math.pow(z,Math.ceil(Math.log((this.high-this.low)/M)/Math.log(z)));this.zoom_res=Math.pow(s,Math.max(0,Math.ceil(Math.log(this.resolution,s)/Math.log(s))));var aa=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ae=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ai=13;this.overview_box.css({left:aa,width:Math.max(ai,ae)}).show();if(ae<ai){this.overview_box.css("left",aa-(ai-ae)/2)}if(this.overview_highlight){this.overview_highlight.css({left:aa,width:ae})}this.update_location(this.low,this.high);if(!ah){for(var ac=0,ad=this.tracks.length;ac<ad;ac++){if(this.tracks[ac]&&this.tracks[ac].enabled){this.tracks[ac].draw()}}for(ac=0,ad=this.label_tracks.length;ac<ad;ac++){this.label_tracks[ac].draw()}}},zoom_in:function(ab,ac){if(this.max_high===0||this.high-this.low<this.min_separation){return}var ad=this.high-this.low,ae=ad/2+this.low,aa=(ad/this.zoom_factor)/2;if(ab){ae=ab/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ae-aa);this.high=Math.round(ae+aa);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var ab=this.high-this.low,ac=ab/2+this.low,aa=(ab*this.zoom_factor)/2;this.low=Math.round(ac-aa);this.high=Math.round(ac+aa);this.redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.redraw()},reset_overview:function(){this.overview_viewport.find("canvas").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()}});var o=function(ac,ag){this.track=ac;this.name=ag.name;this.params=[];var an=ag.params;for(var ad=0;ad<an.length;ad++){var ai=an[ad],ab=ai.name,am=ai.label,ae=unescape(ai.html),ao=ai.value,ak=ai.type;if(ak==="number"){this.params[this.params.length]=new g(ab,am,ae,ao,ai.min,ai.max)}else{if(ak=="select"){this.params[this.params.length]=new K(ab,am,ae,ao)}else{console.log("WARNING: unrecognized tool parameter 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ah=this;aa.click(function(){ah.run_on_region()});af.click(function(){ah.run_on_dataset()})};n(o.prototype,{get_param_values_dict:function(){var aa={};this.parent_div.find(":input").each(function(){var ab=$(this).attr("name"),ac=$(this).val();aa[ab]=JSON.stringify(ac)});return aa},get_param_values:function(){var ab=[];var aa={};this.parent_div.find(":input").each(function(){var ac=$(this).attr("name"),ad=$(this).val();if(ac){ab[ab.length]=ad}});return ab},run_on_dataset:function(){var aa=this;aa.run({dataset_id:this.track.original_dataset_id,tool_id:aa.name},function(ab){show_modal(aa.name+" is Running",aa.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var aa={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},ac=this.track,ab=aa.tool_id+ac.tool_region_and_parameters_str(aa.chrom,aa.low,aa.high),ad;if(ac instanceof e){ad=new Q(ab,view,ac.hda_ldda,undefined,{},{},ac);ad.change_mode(ac.mode)}this.track.add_track(ad);ad.content_div.text("Starting job.");this.run(aa,function(ae){ad.dataset_id=ae.dataset_id;ad.content_div.text("Running job.");ad.init()})},run:function(ab,ac){$.extend(ab,this.get_param_values_dict());var aa=function(){$.getJSON(rerun_tool_url,ab,function(ad){if(ad==="no converter"){new_track.container_div.addClass("error");new_track.content_div.text(G)}else{if(ad.error){new_track.container_div.addClass("error");new_track.content_div.text(v+ad.message)}else{if(ad==="pending"){new_track.container_div.addClass("pending");new_track.content_div.text("Converting input data so that it can be easily reused.");setTimeout(aa,2000)}else{ac(ad)}}}})};aa()}});var K=function(ab,aa,ac,ad){this.name=ab;this.label=aa;this.html=ac;this.value=ad};var g=function(ac,ab,ae,af,ad,aa){K.call(this,ac,ab,ae,af);this.min=ad;this.max=aa};var h=function(ab,aa,ac,ad){this.name=ab;this.index=aa;this.tool_id=ac;this.tool_exp_name=ad};var R=function(ab,aa,ac,ad){h.call(this,ab,aa,ac,ad);this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.min=Number.MAX_VALUE;this.max=-Number.MAX_VALUE;this.slider=null;this.slider_label=null};n(R.prototype,{applies_to:function(aa){if(aa.length>this.index){return true}return false},keep:function(aa){if(!this.applies_to(aa)){return true}var ab=parseInt(aa[this.index]);return(isNaN(ab)||(ab>=this.low&&ab<=this.high))},update_attrs:function(ab){var aa=false;if(!this.applies_to(ab)){return aa}if(ab[this.index]<this.min){this.min=Math.floor(ab[this.index]);aa=true}if(ab[this.index]>this.max){this.max=Math.ceil(ab[this.index]);aa=true}return aa},update_ui_elt:function(){var ac=function(af,ad){var ae=ad-af;return(ae<=2?0.01:1)};var ab=this.slider.slider("option","min"),aa=this.slider.slider("option","max");if(this.min<ab||this.max>aa){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",ac(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var W=function(ac,al){this.track=ac;this.filters=[];for(var ag=0;ag<al.length;ag++){var aa=al[ag],ab=aa.name,ak=aa.type,ai=aa.index,an=aa.tool_id,ad=aa.tool_exp_name;if(ak==="int"||ak==="float"){this.filters[ag]=new R(ab,ai,an,ad)}else{console.log("ERROR: unsupported filter: ",ab,ak)}}var aj=function(ao,ap,aq){ao.click(function(){var ar=ap.text();max=parseFloat(aq.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(aq.slider("option","values")){input_size=2*input_size+1;multi_value=true}ap.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",ar).appendTo(ap).focus().select().click(function(at){at.stopPropagation()}).blur(function(){$(this).remove();ap.text(ar)}).keyup(function(ax){if(ax.keyCode===27){$(this).trigger("blur")}else{if(ax.keyCode===13){var av=aq.slider("option","min"),at=aq.slider("option","max"),aw=function(ay){return(isNaN(ay)||ay>at||ay<av)},au=$(this).val();if(!multi_value){au=parseFloat(au);if(aw(au)){alert("Parameter value must be in the range ["+av+"-"+at+"]");return $(this)}}else{au=au.split("-");au=[parseFloat(au[0]),parseFloat(au[1])];if(aw(au[0])||aw(au[1])){alert("Parameter value must be in the range ["+av+"-"+at+"]");return $(this)}}aq.slider((multi_value?"values":"value"),au)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(ao){ao.stopPropagation()}).bind("click",function(ao){ao.stopPropagation()}).bind("dblclick",function(ao){ao.stopPropagation()}).bind("keydown",function(ao){ao.stopPropagation()});var ae=this;$.each(this.filters,function(av,ap){var ar=$("<div/>").addClass("slider-row").appendTo(ae.parent_div);var ao=$("<div/>").addClass("slider-label").appendTo(ar);var ax=$("<span/>").addClass("slider-name").text(ap.name+" ").appendTo(ao);var aq=$("<span/>");var at=$("<span/>").addClass("slider-value").appendTo(ao).append("[").append(aq).append("]");var aw=$("<div/>").addClass("slider").appendTo(ar);ap.control_element=$("<div/>").attr("id",ap.name+"-filter-control").appendTo(aw);var au=[0,0];ap.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(ay,az){au=az.values;aq.text(az.values[0]+"-"+az.values[1]);setTimeout(function(){if(az.values[0]==au[0]&&az.values[1]==au[1]){var aA=az.values;aq.text(aA[0]+"-"+aA[1]);ap.low=aA[0];ap.high=aA[1];ae.track.draw(true,true)}},50)},change:function(ay,az){ap.control_element.slider("option","slide").call(ap.control_element,ay,az)}});ap.slider=ap.control_element;ap.slider_label=aq;aj(at,aq,ap.control_element);$("<div style='clear: both;'/>").appendTo(ar)});if(this.filters.length!=0){var am=$("<div>").addClass("param-row").appendTo(this.parent_div);var ah=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(am);var af=this;ah.click(function(){af.run_on_dataset()})}};n(W.prototype,{reset_filters:function(){for(var aa=0;aa<this.filters.length;aa++){filter=this.filters[aa];filter.slider.slider("option","values",[filter.min,filter.max])}},run_on_dataset:function(){var ai=function(am,ak,al){if(!(ak in am)){am[ak]=al}return am[ak]};var ac={},aa,ab,ad;for(var ae=0;ae<this.filters.length;ae++){aa=this.filters[ae];if(aa.tool_id){if(aa.min!=aa.low){ab=ai(ac,aa.tool_id,[]);ab[ab.length]=aa.tool_exp_name+" >= "+aa.low}if(aa.max!=aa.high){ab=ai(ac,aa.tool_id,[]);ab[ab.length]=aa.tool_exp_name+" <= "+aa.high}}}var ag=[];for(var aj in ac){ag[ag.length]=[aj,ac[aj]]}var ah=ag.length;(function af(aq,an){var al=an[0],am=al[0],ap=al[1],ao="("+ap.join(") and (")+")",ak={cond:ao,input:aq,target_dataset_id:aq,tool_id:am},an=an.slice(1);$.getJSON(run_tool_url,ak,function(ar){if(ar.error){show_modal("Filter Dataset","Error running tool "+am,{Close:hide_modal})}else{if(an.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{af(ar.dataset_id,an)}}})})(this.track.dataset_id,ag)}});var V=function(aa){this.track=aa.track;this.params=aa.params;this.values={};if(aa.saved_values){this.restore_values(aa.saved_values)}this.onchange=aa.onchange};n(V.prototype,{restore_values:function(aa){var ab=this;$.each(this.params,function(ac,ad){if(aa[ad.key]!==undefined){ab.values[ad.key]=aa[ad.key]}else{ab.values[ad.key]=ad.default_value}})},build_form:function(){var ab=this;var aa=$("<div />");$.each(this.params,function(af,ad){if(!ad.hidden){var ac="param_"+af;var ak=$("<div class='form-row' />").appendTo(aa);ak.append($("<label />").attr("for",ac).text(ad.label+":"));if(ad.type==="bool"){ak.append($('<input type="checkbox" />').attr("id",ac).attr("name",ac).attr("checked",ab.values[ad.key]))}else{if(ad.type==="color"){var ah=ab.values[ad.key];var ag=$("<input />").attr("id",ac).attr("name",ac).val(ah);var ai=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var ae=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(ai);var aj=$("<div/>").appendTo(ae).farbtastic({width:100,height:100,callback:ag,color:ah});$("<div />").append(ag).append(ai).appendTo(ak).bind("click",function(al){ai.css({left:$(this).position().left+($(ag).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){ai.hide();$(document).unbind("click.color-picker")});al.stopPropagation()})}else{ak.append($("<input />").attr("id",ac).attr("name",ac).val(ab.values[ad.key]))}}}});return aa},update_from_form:function(aa){var ac=this;var ab=false;$.each(this.params,function(ad,af){if(!af.hidden){var ag="param_"+ad;var ae=aa.find("#"+ag).val();if(af.type==="float"){ae=parseFloat(ae)}else{if(af.type==="int"){ae=parseInt(ae)}else{if(af.type==="bool"){ae=aa.find("#"+ag).is(":checked")}}}if(ae!==ac.values[af.key]){ac.values[af.key]=ae;ab=true}}});if(ab){this.onchange()}}});var b=function(ac,ab,aa){this.index=ac;this.low=ac*M*ab;this.high=(ac+1)*M*ab;this.resolution=ab;this.canvas=$("<div class='track-tile'/>").append(aa);this.stale=false};var l=function(ac,ab,aa,ad){b.call(this,ac,ab,aa);this.max_val=ad};var L=function(ac,ab,aa,ad){b.call(this,ac,ab,aa);this.message=ad};var j=function(ab,aa,ae,ac,ad){this.name=ab;this.view=aa;this.parent_element=ae;this.data_url=(ac?ac:default_data_url);this.data_url_extra_params={};this.data_query_wait=(ad?ad:H);this.dataset_check_url=converted_datasets_state_url;this.container_div=$("<div />").addClass("track").css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div class='draghandle' />").appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)};n(j.prototype,{get_type:function(){if(this instanceof X){return"LabelTrack"}else{if(this instanceof x){return"ReferenceTrack"}else{if(this instanceof k){return"LineTrack"}else{if(this instanceof S){return"ReadTrack"}else{if(this instanceof Q){return"ToolDataFeatureTrack"}else{if(this instanceof P){return"VcfTrack"}else{if(this instanceof e){return"FeatureTrack"}}}}}}}return""},init:function(){var aa=this;aa.enabled=false;aa.tile_cache.clear();aa.data_manager.clear();aa.initial_canvas=undefined;aa.content_div.css("height","auto");aa.container_div.removeClass("nodata error pending");if(!aa.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:aa.hda_ldda,dataset_id:aa.dataset_id,chrom:aa.view.chrom},function(ab){if(!ab||ab==="error"||ab.kind==="error"){aa.container_div.addClass("error");aa.content_div.text(m);if(ab.message){var ad=aa.view.tracks.indexOf(aa);var ac=$(" <a href='javascript:void(0);'></a>").text("View error").bind("click",function(){show_modal("Trackster Error","<pre>"+ab.message+"</pre>",{Close:hide_modal})});aa.content_div.append(ac)}}else{if(ab==="no converter"){aa.container_div.addClass("error");aa.content_div.text(G)}else{if(ab==="no data"||(ab.data!==undefined&&(ab.data===null||ab.data.length===0))){aa.container_div.addClass("nodata");aa.content_div.text(B)}else{if(ab==="pending"){aa.container_div.addClass("pending");aa.content_div.text(q);setTimeout(function(){aa.init()},aa.data_query_wait)}else{if(ab.status==="data"){if(ab.valid_chroms){aa.valid_chroms=ab.valid_chroms;aa.make_name_popup_menu()}aa.content_div.text(U);if(aa.view.chrom){aa.content_div.text("");aa.content_div.css("height",aa.height_px+"px");aa.enabled=true;$.when(aa.predraw_init()).done(function(){aa.container_div.removeClass("nodata error pending");aa.draw()})}}}}}}})},predraw_init:function(){},update_name:function(aa){this.old_name=this.name;this.name=aa;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)}});var J=function(ah,af,ai){var ab=this,aj=ab.view;this.filters_manager=(ah!==undefined?new W(this,ah):undefined);this.filters_available=false;this.filters_visible=false;this.tool=(af!==undefined&&obj_length(af)>0?new o(this,af):undefined);this.parent_track=ai;this.child_tracks=[];if(ab.hidden){return}if(this.parent_track){this.header_div.find(".draghandle").removeClass("draghandle").addClass("child-track-icon").addClass("icon-button");this.parent_element.addClass("child-track");this.tool=undefined}ab.child_tracks_container=$("<div/>").addClass("child-tracks-container").hide();ab.container_div.append(ab.child_tracks_container);if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}if(ab.display_modes!==undefined){if(ab.mode_div===undefined){ab.mode_div=$("<div class='right-float menubutton popup' />").appendTo(ab.header_div);var ac=(ab.track_config&&ab.track_config.values.mode?ab.track_config.values.mode:ab.display_modes[0]);ab.mode=ac;ab.mode_div.text(ac);var aa={};for(var ad=0,ag=ab.display_modes.length;ad<ag;ad++){var ae=ab.display_modes[ad];aa[ae]=function(ak){return function(){ab.change_mode(ak)}}(ae)}make_popupmenu(ab.mode_div,aa)}else{ab.mode_div.hide()}}this.make_name_popup_menu()};n(J.prototype,j.prototype,{change_mode:function(ab){var aa=this;aa.mode_div.text(ab);aa.mode=ab;aa.track_config.values.mode=ab;aa.tile_cache.clear();aa.draw()},make_name_popup_menu:function(){var ab=this;var aa={};aa["Edit configuration"]=function(){var ah=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},af=function(){ab.track_config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ag=function(ai){if((ai.keyCode||ai.which)===27){ah()}else{if((ai.keyCode||ai.which)===13){af()}}};$(window).bind("keypress.check_enter_esc",ag);show_modal("Configure Track",ab.track_config.build_form(),{Cancel:ah,OK:af})};if(ab.filters_available>0){var ae=(ab.filters_div.is(":visible")?"Hide filters":"Show filters");aa[ae]=function(){ab.filters_visible=(ab.filters_div.is(":visible"));if(ab.filters_visible){ab.filters_manager.reset_filters()}ab.filters_div.toggle();ab.make_name_popup_menu()}}if(ab.tool){var ae=(ab.dynamic_tool_div.is(":visible")?"Hide tool":"Show tool");aa[ae]=function(){if(!ab.dynamic_tool_div.is(":visible")){ab.update_name(ab.name+ab.tool_region_and_parameters_str())}else{menu_option_text="Show dynamic tool";ab.revert_name()}ab.dynamic_tool_div.toggle();ab.make_name_popup_menu()}}if(ab.valid_chroms){aa["List chrom/contigs with data"]=function(){show_modal("Chrom/contigs with data","<p>"+ab.valid_chroms.join("<br/>")+"</p>",{Close:function(){hide_modal()}})}}var ac=view;var ad=function(){$("#no-tracks").show()};if(this.parent_track){ac=this.parent_track;ad=function(){}}aa.Remove=function(){ac.remove_track(ab);if(ac.num_tracks===0){ad()}};make_popupmenu(ab.name_div,aa)},draw:function(aa,ac){if(!this.dataset_id){return}var au=this.view.low,ag=this.view.high,ai=ag-au,ak=this.view.container.width(),ae=ak/ai,al=this.view.resolution,ad=$("<div style='position: relative;'></div>"),am=function(aw,ax,av){return aw+"_"+ax+"_"+av};if(!ac){this.content_div.children().remove()}this.content_div.append(ad);this.max_height=0;var ao=Math.floor(au/al/M);var af=[];var ap=0;while((ao*M*al)<ag){var at=am(ak,ae,ao);var ah=this.tile_cache.get(at);var aq=ao*M*this.view.resolution;var ab=aq+M*this.view.resolution;if(!aa&&ah){af[af.length]=ah;this.show_tile(ah,ad,ae)}else{this.delayed_draw(aa,at,ao,al,ad,ae,af)}ao+=1;ap++}var aj=this;var ar=setInterval(function(){if(af.length===ap){clearInterval(ar);if(ac){var aA=aj.content_div.children();var aB=false;for(var az=aA.length-1,aF=0;az>=aF;az--){var ay=$(aA[az]);if(aB){ay.remove()}else{if(ay.children().length!==0){aB=true}}}}if(aj instanceof e&&aj.mode=="Histogram"){var aE=-1;for(var az=0;az<af.length;az++){var aH=af[az].max_val;if(aH>aE){aE=aH}}for(var az=0;az<af.length;az++){if(af[az].max_val!==aE){var aG=af[az];aG.canvas.remove();aj.delayed_draw(true,am(ak,ae,aG.index),aG.index,aG.resolution,ad,ae,[],{max:aE})}}}if(aj.filters_manager){var ax=aj.filters_manager.filters;for(var aD=0;aD<ax.length;aD++){ax[aD].update_ui_elt()}var aC=false;if(aj.example_feature){for(var aD=0;aD<ax.length;aD++){if(ax[aD].applies_to(aj.example_feature)){aC=true;break}}}if(aj.filters_available!==aC){aj.filters_available=aC;if(!aj.filters_available){aj.filters_div.hide()}aj.make_name_popup_menu()}}var av=false;for(var aw=0;aw<af.length;aw++){if(af[aw].message){av=true;break}}if(av){for(var aw=0;aw<af.length;aw++){aG=af[aw];if(!aG.message){aG.canvas.css("padding-top",A)}}}}},50);for(var an=0;an<this.child_tracks.length;an++){this.child_tracks[an].draw(aa,ac)}},delayed_draw:function(ab,ai,ac,ae,aj,am,ak,af){var ad=this,ag=ac*M*ae,al=ag+M*ae;var ah=function(av,an,ap,ao,at,au,aq){var ar=ad.draw_tile(an,ap,ao,au,aq);ad.tile_cache.set(ai,ar);if(ar===undefined){return}ad.show_tile(ar,at,au);ak[ak.length]=ar};var aa=setTimeout(function(){if(ag<=ad.view.high&&al>=ad.view.low){var an=(ab?undefined:ad.tile_cache.get(ai));if(an){ad.show_tile(an,aj,am);ak[ak.length]=an}else{$.when(ad.data_manager.get_data(ag,al,ae,ad.data_url_extra_params)).then(function(ao){n(ao,af);if(view.reference_track&&am>view.canvas_manager.char_width_px){$.when(view.reference_track.data_manager.get_data(ag,al,ae,view.reference_track.data_url_extra_params)).then(function(ap){ah(aa,ao,ae,ac,aj,am,ap)})}else{ah(aa,ao,ae,ac,aj,am)}})}}},50)},show_tile:function(ag,ai,aj){var ab=this,aa=ag.canvas,ae=aa;if(ag.message){var ak=$("<div/>"),ah=$("<div/>").addClass("tile-message").text(ag.message).css({height:A-1,width:ag.canvas.width}).appendTo(ak),af=$("<div/>").text("Show more").addClass("action-button").css({"padding-top":0,"padding-bottom":0}).appendTo(ah);ak.append(aa);ae=ak;af.click(function(){ag.stale=true;ab.data_manager.get_more_data(ag.low,ag.high,ag.resolution,{},ab.data_manager.DEEP_DATA_REQ);ab.draw()}).dblclick(function(al){al.stopPropagation()})}var ad=this.view.high-this.view.low,ac=(ag.low-this.view.low)*aj;if(this.left_offset){ac-=this.left_offset}ae.css({position:"absolute",top:0,left:ac,height:""});ai.append(ae);ab.max_height=Math.max(ab.max_height,ae.height());ab.content_div.css("height",ab.max_height+"px");ai.children().css("height",ab.max_height+"px")},set_overview:function(){var aa=this.view;if(this.initial_canvas&&this.is_overview){aa.overview_close.show();aa.overview_viewport.append(this.initial_canvas);aa.overview_highlight.show().height(this.initial_canvas.height());aa.overview_viewport.height(this.initial_canvas.height()+aa.overview_box.height())}$(window).trigger("resize")},tool_region_and_parameters_str:function(ac,aa,ad){var ab=this,ae=(ac!==undefined&&aa!==undefined&&ad!==undefined?ac+":"+aa+"-"+ad:"all");return" - region=["+ae+"], parameters=["+ab.tool.get_param_values().join(", ")+"]"},add_track:function(aa){aa.track_id=this.track_id+"_"+this.child_tracks.length;aa.container_div.attr("id","track_"+aa.track_id);this.child_tracks_container.append(aa.container_div);C(aa.container_div,".child-track-icon");if(!$(this.child_tracks_container).is(":visible")){this.child_tracks_container.show()}this.child_tracks.push(aa);this.view.has_changes=true},remove_track:function(aa){aa.container_div.fadeOut("slow",function(){$(this).remove()})}});var X=function(aa,ab){this.hidden=true;j.call(this,null,aa,ab);this.container_div.addClass("label-track")};n(X.prototype,j.prototype,{draw:function(){var ac=this.view,ad=ac.high-ac.low,ag=Math.floor(Math.pow(10,Math.floor(Math.log(ad)/Math.log(10)))),aa=Math.floor(ac.low/ag)*ag,ae=this.view.container.width(),ab=$("<div style='position: relative; height: 1.3em;'></div>");while(aa<ac.high){var af=(aa-ac.low)/ad*ae;ab.append($("<div class='label'>"+commatize(aa)+"</div>").css({position:"absolute",left:af-1}));aa+=ag}this.content_div.children(":first").remove();this.content_div.append(ab)}});var x=function(aa){this.hidden=true;j.call(this,null,aa,aa.top_labeltrack);J.call(this);aa.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:aa.dbkey};this.data_manager=new E(y,this,false);this.tile_cache=new c(r)};n(x.prototype,J.prototype,{draw_tile:function(ai,af,ab,ak){var ae=this,ac=M*af;if(ak>this.view.canvas_manager.char_width_px){if(ai===null){ae.content_div.css("height","0px");return}var ad=this.view.canvas_manager.new_canvas();var aj=ad.getContext("2d");ad.width=Math.ceil(ac*ak+ae.left_offset);ad.height=ae.height_px;aj.font=aj.canvas.manager.default_font;aj.textAlign="center";for(var ag=0,ah=ai.length;ag<ah;ag++){var aa=Math.round(ag*ak);aj.fillText(ai[ag],aa+ae.left_offset,10)}return new b(ab,af,ad)}this.content_div.css("height","0px")}});var k=function(ae,ac,af,aa,ad){var ab=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";j.call(this,ae,ac,ac.viewport_container);J.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=af;this.dataset_id=aa;this.original_dataset_id=aa;this.data_manager=new N(y,this);this.tile_cache=new c(r);this.track_config=new V({track:this,params:[{key:"color",label:"Color",type:"color",default_value:"black"},{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:ad,onchange:function(){ab.vertical_range=ab.prefs.max_value-ab.prefs.min_value;$("#linetrack_"+ab.track_id+"_minval").text(ab.prefs.min_value);$("#linetrack_"+ab.track_id+"_maxval").text(ab.prefs.max_value);ab.tile_cache.clear();ab.draw()}});this.prefs=this.track_config.values;this.height_px=this.track_config.values.height;this.vertical_range=this.track_config.values.max_value-this.track_config.values.min_value;this.add_resize_handle()};n(k.prototype,J.prototype,{add_resize_handle:function(){var aa=this;var ad=false;var ac=false;var ab=$("<div class='track-resize'>");$(aa.container_div).hover(function(){ad=true;ab.show()},function(){ad=false;if(!ac){ab.hide()}});ab.hide().bind("dragstart",function(ae,af){ac=true;af.original_height=$(aa.content_div).height()}).bind("drag",function(af,ag){var ae=Math.min(Math.max(ag.original_height+ag.deltaY,aa.min_height_px),aa.max_height_px);$(aa.content_div).css("height",ae);aa.height_px=ae;aa.draw(true)}).bind("dragend",function(ae,af){aa.tile_cache.clear();ac=false;if(!ad){ab.hide()}aa.track_config.values.height=aa.height_px}).appendTo(aa.container_div)},predraw_init:function(){var aa=this,ab=aa.view.tracks.indexOf(aa);aa.vertical_range=undefined;return $.getJSON(aa.data_url,{stats:true,chrom:aa.view.chrom,low:null,high:null,hda_ldda:aa.hda_ldda,dataset_id:aa.dataset_id},function(ac){aa.container_div.addClass("line-track");var ae=ac.data;if(isNaN(parseFloat(aa.prefs.min_value))||isNaN(parseFloat(aa.prefs.max_value))){aa.prefs.min_value=ae.min;aa.prefs.max_value=ae.max;$("#track_"+ab+"_minval").val(aa.prefs.min_value);$("#track_"+ab+"_maxval").val(aa.prefs.max_value)}aa.vertical_range=aa.prefs.max_value-aa.prefs.min_value;aa.total_frequency=ae.total_frequency;aa.container_div.find(".yaxislabel").remove();var af=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ab+"_minval").text(u(aa.prefs.min_value));var ad=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ab+"_maxval").text(u(aa.prefs.max_value));ad.css({position:"absolute",top:"24px",left:"10px"});ad.prependTo(aa.container_div);af.css({position:"absolute",bottom:"2px",left:"10px"});af.prependTo(aa.container_div)})},draw_tile:function(ak,ae,ab,aj){if(this.vertical_range===undefined){return}var af=ab*M*ae,ad=M*ae,aa=Math.ceil(ad*aj),ah=this.height_px;var ac=this.view.canvas_manager.new_canvas();ac.width=aa,ac.height=ah;var ai=ac.getContext("2d");var ag=new I.LinePainter(ak.data,af,af+ad,this.prefs,this.mode);ag.draw(ai,aa,ah);return new b(ab,ae,ac)}});var e=function(aa,af,ae,ai,ah,ac,ad,ag){var ab=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];this.track_config=new V({track:this,params:[{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ah,onchange:function(){ab.tile_cache.clear();ab.draw()}});this.prefs=this.track_config.values;j.call(this,aa,af,af.viewport_container);J.call(this,ac,ad,ag);this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=ae;this.dataset_id=ai;this.original_dataset_id=ai;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_manager=new N(20,this);this.left_offset=200;this.painter=I.LinkedFeaturePainter};n(e.prototype,J.prototype,{update_auto_mode:function(aa){if(this.mode=="Auto"){if(aa=="no_detail"){aa="feature spans"}else{if(aa=="summary_tree"){aa="coverage histogram"}}this.mode_div.text("Auto ("+aa+")")}},incremental_slots:function(ae,ab,ad){var ac=this.view.canvas_manager.dummy_context,aa=this.inc_slots[ae];if(!aa||(aa.mode!==ad)){aa=new (p.FeatureSlotter)(ae,ad==="Pack",w,function(af){return ac.measureText(af)});aa.mode=ad;this.inc_slots[ae]=aa}return aa.slot_features(ab)},get_summary_tree_data:function(ae,ah,ac,ap){if(ap>ac-ah){ap=ac-ah}var al=Math.floor((ac-ah)/ap),ao=[],ad=0;var af=0,ag=0,ak,an=0,ai=[],am,aj;var ab=function(at,ar,au,aq){at[0]=ar+au*aq;at[1]=ar+(au+1)*aq};while(an<ap&&af!==ae.length){var aa=false;for(;an<ap&&!aa;an++){ab(ai,ah,an,al);for(ag=af;ag<ae.length;ag++){ak=ae[ag].slice(1,3);if(is_overlap(ak,ai)){aa=true;break}}if(aa){break}}data_start_index=ag;ao[ao.length]=am=[ai[0],0];for(;ag<ae.length;ag++){ak=ae[ag].slice(1,3);if(is_overlap(ak,ai)){am[1]++}else{break}}if(am[1]>ad){ad=am[1]}an++}return{max:ad,delta:al,data:ao}},draw_tile:function(an,av,az,aj,ad){var ar=this,aB=az*M*av,ab=(az+1)*M*av,ap=ab-aB,at=Math.ceil(ap*aj),aq=this.mode,aF=25,ae=this.left_offset,ao,af;if(aq==="Auto"){if(an.dataset_type==="summary_tree"){aq=an.dataset_type}else{if(an.extra_info==="no_detail"){aq="no_detail"}else{var aE=an.data;if(this.view.high-this.view.low>F){aq="Squish"}else{aq="Pack"}}}this.update_auto_mode(aq)}if(aq==="summary_tree"||aq==="Histogram"){af=this.summary_draw_height;this.container_div.find(".yaxislabel").remove();var aa=$("<div />").addClass("yaxislabel");aa.text(an.max);aa.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});aa.prependTo(this.container_div);var ac=this.view.canvas_manager.new_canvas();ac.width=at+ae;ac.height=af+O;if(an.dataset_type!="summary_tree"){var ak=this.get_summary_tree_data(an.data,aB,ab,200);if(an.max){ak.max=an.max}an=ak}var aC=new I.SummaryTreePainter(an,aB,ab,this.prefs);var au=ac.getContext("2d");au.translate(ae,O);aC.draw(au,at,af);return new l(az,av,ac,an.max)}var ao,ah=1;if(aq==="no_detail"||aq==="Squish"||aq==="Pack"){ah=this.incremental_slots(aj,an.data,aq);ao=this.inc_slots[aj].slots}var ai=[];if(an.data){var al=this.filters_manager.filters;for(var aw=0,ay=an.data.length;aw<ay;aw++){var ag=an.data[aw];var ax=false;var am;for(var aA=0,aD=al.length;aA<aD;aA++){am=al[aA];am.update_attrs(ag);if(!am.keep(ag)){ax=true;break}}if(!ax){ai.push(ag)}}}var aC=new (this.painter)(ai,aB,ab,this.prefs,aq,ad);var af=aC.get_required_height(ah);var ac=this.view.canvas_manager.new_canvas();ac.width=at+ae;ac.height=af;var au=ac.getContext("2d");au.fillStyle=this.prefs.block_color;au.font=au.canvas.manager.default_font;au.textAlign="right";this.container_div.find(".yaxislabel").remove();if(an.data){this.example_feature=(an.data.length?an.data[0]:undefined);au.translate(ae,0);aC.draw(au,at,af,ao)}return new L(az,av,ac,an.message)}});var P=function(ad,ab,af,aa,ac,ae){e.call(this,ad,ab,af,aa,ac,ae);this.painter=I.VariantPainter};n(P.prototype,J.prototype,e.prototype);var S=function(ad,ab,af,aa,ac,ae){e.call(this,ad,ab,af,aa,ac,ae);this.track_config=new V({track:this,params:[{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{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:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ac,onchange:function(){this.track.tile_cache.clear();this.track.draw()}});this.prefs=this.track_config.values;this.painter=I.ReadPainter;this.make_name_popup_menu()};n(S.prototype,J.prototype,e.prototype);var 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c.trackster){d[key]=c.trackster[key]}})(window); \ No newline at end of file --- a/static/scripts/trackster.js Wed Jul 06 09:52:28 2011 -0400 +++ b/static/scripts/trackster.js Wed Jul 06 10:20:57 2011 -0400 @@ -370,10 +370,8 @@ // Set parameters based on request type. // if (req_type === this.DEEP_DATA_REQ) { - // HACK: for now, just up the max vals and request all data; in the future, - // need server to recognize min_vals and max_vals to specify range of data to - // return. - $.extend(extra_params, {max_vals: cur_data.data.length * 2}); + // Use same interval but set start_val to skip data that's already in cur_data. + $.extend(extra_params, {start_val: cur_data.data.length + 1}); } else if (req_type === this.BROAD_DATA_REQ) { // Set low to be past the last feature returned. @@ -393,7 +391,7 @@ this.set_data(low, high, mode, new_data_available); $.when(new_data_request).then(function(result) { if (result.data) { - //result.data.append(cur_data.data); + result.data = cur_data.data.concat(result.data); } data_manager.set_data(low, high, mode, result); new_data_available.resolve(result); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Add patch from Assaf Gordon to fix the cleanup_dataset.py script, correcting the behavior of setting the info_only flag to True when running delete_datasets.sh and purge_datasets.sh.
by Bitbucket 06 Jul '11

06 Jul '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/a5e0a5d3c0a1/ changeset: a5e0a5d3c0a1 user: greg date: 2011-07-06 15:52:28 summary: Add patch from Assaf Gordon to fix the cleanup_dataset.py script, correcting the behavior of setting the info_only flag to True when running delete_datasets.sh and purge_datasets.sh. affected #: 1 file (265 bytes) --- a/scripts/cleanup_datasets/cleanup_datasets.py Wed Jul 06 09:45:41 2011 +1000 +++ b/scripts/cleanup_datasets/cleanup_datasets.py Wed Jul 06 09:52:28 2011 -0400 @@ -411,10 +411,13 @@ app.sa_session.add( metadata_file ) app.sa_session.flush() print "%s" % metadata_file.file_name - print "Deleting dataset id", dataset.id - dataset.deleted = True - app.sa_session.add( dataset ) - app.sa_session.flush() + if not info_only: + print "Deleting dataset id", dataset.id + dataset.deleted = True + app.sa_session.add( dataset ) + app.sa_session.flush() + else: + print "Dataset %i will be deleted (without 'info_only' mode)" % ( dataset.id ) def _purge_dataset( app, dataset, remove_from_disk, info_only = False ): if dataset.deleted: @@ -433,6 +436,8 @@ dataset.purged = True app.sa_session.add( dataset ) app.sa_session.flush() + else: + print "Dataset %i will be purged (without 'info_only' mode)" % (dataset.id) else: print "This dataset (%i) is not purgable, the file (%s) will not be removed.\n" % ( dataset.id, dataset.file_name ) except OSError, exc: 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 06 Jul '11

06 Jul '11

2 new changesets in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/94e63070cbb1/ changeset: 94e63070cbb1 user: fubar date: 2011-07-06 01:44:56 summary: Backed out changeset 48bbe32beefe which introduced a whole bunch of unintended reversions from a broken hg repository This is a backout of commit 5765 affected #: 250 files (5.2 KB) --- a/lib/galaxy/security/__init__.py Tue Jul 05 12:40:43 2011 +1000 +++ b/lib/galaxy/security/__init__.py Wed Jul 06 09:44:56 2011 +1000 @@ -1005,8 +1005,7 @@ ucsc_main = ( 'hgw1.cse.ucsc.edu', 'hgw2.cse.ucsc.edu', 'hgw3.cse.ucsc.edu', 'hgw4.cse.ucsc.edu', 'hgw5.cse.ucsc.edu', 'hgw6.cse.ucsc.edu', 'hgw7.cse.ucsc.edu', 'hgw8.cse.ucsc.edu' ), ucsc_test = ( 'hgwdev.cse.ucsc.edu', ), - ucsc_archaea = ( 'lowepub.cse.ucsc.edu', ), - ucsc_bhri = ('ucsc.omics.bhri.internal','galaxy.omics.bhri.internal'), + ucsc_archaea = ( 'lowepub.cse.ucsc.edu', ) ) def __init__( self, model, permitted_actions=None ): self.model = model @@ -1037,7 +1036,7 @@ # We're going to search in order, but if the remote site is load # balancing their connections (as UCSC does), this is okay. try: - if socket.gethostbyname( server ) == addr or server == '127.0.0.1' or server == '172.16.0.38': + if socket.gethostbyname( server ) == addr: break # remote host is in the server list except ( socket.error, socket.gaierror ): pass # can't resolve, try next --- a/lib/galaxy/tools/__init__.py Tue Jul 05 12:40:43 2011 +1000 +++ b/lib/galaxy/tools/__init__.py Wed Jul 06 09:44:56 2011 +1000 @@ -922,8 +922,6 @@ if not self.check_values: return for input in self.inputs.itervalues(): - if input.name not in value: - value[input.name] = input.get_initial_value( None, value ) if isinstance( input, ToolParameter ): callback( "", input, value[input.name] ) else: --- a/lib/galaxy/tools/parameters/basic.py Tue Jul 05 12:40:43 2011 +1000 +++ b/lib/galaxy/tools/parameters/basic.py Wed Jul 06 09:44:56 2011 +1000 @@ -748,6 +748,9 @@ # Dependency on a value that does not yet exist if isinstance( dep_value, RuntimeValue ): return True + #dataset not ready yet + if hasattr( self, 'ref_input' ) and isinstance( dep_value, self.tool.app.model.HistoryDatasetAssociation ) and ( dep_value.is_pending or not isinstance( dep_value.datatype, self.ref_input.formats ) ): + return True # Dynamic, but all dependenceis are known and have values return False def get_initial_value( self, trans, context ): @@ -878,6 +881,7 @@ self.force_select = string_as_bool( elem.get( "force_select", True )) self.accept_default = string_as_bool( elem.get( "accept_default", False )) self.data_ref = elem.get( "data_ref", None ) + self.ref_input = None self.default_value = elem.get( "default_value", None ) self.is_dynamic = True def from_html( self, value, trans=None, context={} ): @@ -973,7 +977,7 @@ if not dataset.metadata.columns: # Only allow late validation if the dataset is not yet ready # (since we have reason to expect the metadata to be ready eventually) - if dataset.is_pending: + if dataset.is_pending or not isinstance( dataset.datatype, self.ref_input.formats ): return True # No late validation return False @@ -1353,7 +1357,7 @@ selected = ( value and ( hda in value ) ) field.add_option( "%s: %s" % ( hid, hda_name ), hda.id, selected ) else: - target_ext, converted_dataset = hda.find_conversion_destination( self.formats, converter_safe = self.converter_safe( other_values, trans ) ) + target_ext, converted_dataset = hda.find_conversion_destination( self.formats ) if target_ext: if converted_dataset: hda = converted_dataset @@ -1402,13 +1406,22 @@ pass #no valid options def dataset_collector( datasets ): def is_convertable( dataset ): - target_ext, converted_dataset = dataset.find_conversion_destination( self.formats, converter_safe = self.converter_safe( context, trans ) ) + target_ext, converted_dataset = dataset.find_conversion_destination( self.formats ) if target_ext is not None: return True return False for i, data in enumerate( datasets ): - if data.visible and not data.deleted and data.state not in [data.states.ERROR, data.states.DISCARDED] and ( isinstance( data.datatype, self.formats) or is_convertable( data ) ): - if self.options and self._options_filter_attribute( data ) != filter_value: + if data.visible and not data.deleted and data.state not in [data.states.ERROR, data.states.DISCARDED]: + is_valid = False + if isinstance( data.datatype, self.formats ): + is_valid = True + else: + target_ext, converted_dataset = data.find_conversion_destination( self.formats ) + if target_ext: + is_valid = True + if converted_dataset: + data = converted_dataset + if not is_valid or ( self.options and self._options_filter_attribute( data ) != filter_value ): continue most_recent_dataset[0] = data # Also collect children via association object --- a/lib/galaxy/web/framework/middleware/remoteuser.py Tue Jul 05 12:40:43 2011 +1000 +++ b/lib/galaxy/web/framework/middleware/remoteuser.py Wed Jul 06 09:44:56 2011 +1000 @@ -36,7 +36,6 @@ """ UCSC_MAIN_SERVERS = ( - 'omics.bhri.internal', 'hgw1.cse.ucsc.edu', 'hgw2.cse.ucsc.edu', 'hgw3.cse.ucsc.edu', @@ -50,7 +49,6 @@ 'lowepub.cse.ucsc.edu', ) - class RemoteUser( object ): def __init__( self, app, maildomain=None, ucsc_display_sites=[], admin_users=[] ): self.app = app @@ -58,7 +56,7 @@ self.allow_ucsc_main = False self.allow_ucsc_archaea = False self.admin_users = admin_users - if 'main' in ucsc_display_sites or 'test' in ucsc_display_sites or 'bhri' in ucsc_display_sites: + if 'main' in ucsc_display_sites or 'test' in ucsc_display_sites: self.allow_ucsc_main = True if 'archaea' in ucsc_display_sites: self.allow_ucsc_archaea = True --- a/scripts/cleanup_datasets/purge_libraries.sh Tue Jul 05 12:40:43 2011 +1000 +++ b/scripts/cleanup_datasets/purge_libraries.sh Wed Jul 06 09:44:56 2011 +1000 @@ -1,5 +1,4 @@ #!/bin/sh cd `dirname $0`/../.. -#python ./scripts/cleanup_datasets/cleanup_datasets.py ./universe_wsgi.ini -d 10 -4 -r $@ >> ./scripts/cleanup_datasets/purge_libraries.log -python ./scripts/cleanup_datasets/cleanup_datasets.py ./universe_wsgi.ini -d 2 -4 -r $@ >> ./scripts/cleanup_datasets/purge_libraries.log +python ./scripts/cleanup_datasets/cleanup_datasets.py ./universe_wsgi.ini -d 10 -4 -r $@ >> ./scripts/cleanup_datasets/purge_libraries.log --- a/tool-data/shared/ucsc/ucsc_build_sites.txt Tue Jul 05 12:40:43 2011 +1000 +++ b/tool-data/shared/ucsc/ucsc_build_sites.txt Wed Jul 06 09:44:56 2011 +1000 @@ -1,6 +1,5 @@ #Harvested from http://genome.ucsc.edu/cgi-bin/das/dsn main http://genome.ucsc.edu/cgi-bin/hgTracks? priPac1,danRer4,mm9,mm8,droAna1,mm5,caeRem2,mm7,mm6,panTro1,dm3,panTro2,anoCar1,ce4,galGal3,galGal2,ce1,rn3,rn2,droMoj1,droMoj2,rn4,droYak1,droYak2,dp3,dp2,dm1,canFam1,danRer5,canFam2,danRer3,danRer2,ornAna1,ci2,ci1,tetNig1,bosTau1,bosTau3,bosTau2,equCab1,oryLat1,droAna2,droEre1,ponAbe2,rheMac2,sacCer1,droPer1,droSim1,monDom1,cb1,dm2,droSec1,strPur1,droVir2,droVir1,strPur2,sc1,xenTro1,droGri1,xenTro2,cb3,gasAcu1,caePb1,anoGam1,fr2,fr1,hg15,hg16,hg17,hg18,felCat3,apiMel2,monDom4,apiMel1,ce2 -bhri http://ucsc.omics.bhri.internal/cgi-bin/hgTracks? hg18,hg19,mm8,mm9,rn4 #Harvested from http://archaea.ucsc.edu/cgi-bin/das/dsn archaea http://archaea.ucsc.edu/cgi-bin/hgTracks? alkaEhrl_MLHE_1,shewW318,idioLoih_L2TR,sulSol1,erwiCaro_ATROSEPTICA,symbTher_IAM14863,moorTher_ATCC39073,therFusc_YX,methHung1,bradJapo,therElon,shewPutrCN32,pediPent_ATCC25745,mariMari_MCS10,nanEqu1,baciSubt,chlaTrac,magnMagn_AMB_1,chroViol,ralsSola,acidCryp_JF_5,erytLito_HTCC2594,desuVulg_HILDENBOROUG,pyrAer1,sulfToko1,shewANA3,paraSp_UWE25,geobKaus_HTA426,rhizEtli_CFN_42,uncuMeth_RCI,candBloc_FLORIDANUS,deinRadi,yersPest_CO92,saccEryt_NRRL_2338,rhodRHA1,candCars_RUDDII,burkMall_ATCC23344,eschColi_O157H7,burk383,psycIngr_37,rhodSpha_2_4_1,wolbEndo_OF_DROSOPHIL,burkViet_G4,propAcne_KPA171202,enteFaec_V583,campJeju_81_176,acidJS42,heliPylo_26695,pseuHalo_TAC125,chroSale_DSM3043,methVann1,archFulg1,neisMeni_Z2491_1,fusoNucl,vermEise_EF01_2,anabVari_ATCC29413,tropWhip_TW08_27,heliHepa,acinSp_ADP1,anapMarg_ST_MARIES,natrPhar1,haheChej_KCTC_2396,therPetr_RKU_1,neisGono_FA1090_1,colwPsyc_34H,desuPsyc_LSV54,hyphNept_ATCC15444,vibrChol1,deinGeot_DSM11300,strePyog_M1_GAS,franCcI3,salmTyph,metaSedu,lactSali_UCC118,trepPall,neisMeni_MC58_1,syntWolf_GOETTINGEN,flavJohn_UW101,methBoon1,haemSomn_129PT,shewLoihPV4,igniHosp1,haemInfl_KW20,haloHalo_SL1,ferrAcid1,sphiAlas_RB2256,candPela_UBIQUE_HTCC1,caldSacc_DSM8903,aerPer1,lactPlan,carbHydr_Z_2901,therTher_HB8,vibrVuln_YJ016_1,rhodPalu_CGA009,acidCell_11B,siliPome_DSS_3,therVolc1,haloWals1,rubrXyla_DSM9941,shewAmaz,nocaJS61,vibrVuln_CMCP6_1,sinoMeli,ureaUrea,baciHalo,bartHens_HOUSTON_1,nitrWino_NB_255,hypeButy1,methBurt2,polaJS66,mesoLoti,methMari_C7,caulCres,neisMeni_FAM18_1,acidBact_ELLIN345,caldMaqu1,salmEnte_PARATYPI_ATC,glucOxyd_621H,cytoHutc_ATCC33406,nitrEuro,therMari,coxiBurn,woliSucc,heliPylo_HPAG1,mesoFlor_L1,pyrHor1,methAeol1,procMari_CCMP1375,pyroArse1,oenoOeni_PSU_1,alcaBork_SK2,wiggBrev,actiPleu_L20,lactLact,methJann1,paraDeni_PD1222,borrBurg,pyroIsla1,orieTsut_BORYONG,shewMR4,methKand1,methCaps_BATH,onioYell_PHYTOPLASMA,bordBron,cenaSymb1,burkCeno_HI2424,franTula_TULARENSIS,pyrFur2,mariAqua_VT8,heliPylo_J99,psycArct_273_4,vibrChol_MO10_1,vibrPara1,rickBell_RML369_C,metAce1,buchSp,ehrlRumi_WELGEVONDEN,methLabrZ_1,chlaPneu_CWL029,thioCrun_XCL_2,pyroCali1,chloTepi_TLS,stapAure_MU50,novoArom_DSM12444,magnMC1,zymoMobi_ZM4,salmTyph_TY2,chloChlo_CAD3,azoaSp_EBN1,therTher_HB27,bifiLong,picrTorr1,listInno,bdelBact,gramFors_KT0803,sulfAcid1,geobTher_NG80_2,peloCarb,ralsEutr_JMP134,mannSucc_MBEL55E,syneSp_WH8102,methTherPT1,clavMich_NCPPB_382,therAcid1,syntAcid_SB,porpGing_W83,therNeut0,leifXyli_XYLI_CTCB0,shewFrig,photProf_SS9,thioDeni_ATCC25259,methMaze1,desuRedu_MI_1,burkThai_E264,campFetu_82_40,blocFlor,jannCCS1,nitrMult_ATCC25196,streCoel,soliUsit_ELLIN6076,pastMult,saliRube_DSM13855,methTher1,nostSp,shigFlex_2A,saccDegr_2_40,oceaIhey,dehaEthe_195,rhodRubr_ATCC11170,arthFB24,shewMR7,pireSp,anaeDeha_2CP_C,haloVolc1,dichNodo_VCS1703A,tricEryt_IMS101,mycoGeni,thioDeni_ATCC33889,methSmit1,geobUran_RF4,shewDeni,halMar1,desuHafn_Y51,methStad1,granBeth_CGDNIH1,therPend1,legiPneu_PHILADELPHIA,vibrChol_O395_1,nitrOcea_ATCC19707,campJeju_RM1221,methPetr_PM1,heliAcin_SHEEBA,eschColi_APEC_O1,peloTher_SI,haloHalo1,syntFuma_MPOB,xyleFast,gloeViol,leucMese_ATCC8293,bactThet_VPI_5482,xantCamp,sodaGlos_MORSITANS,geobSulf,roseDeni_OCH_114,coryEffi_YS_314,brucMeli,mycoTube_H37RV,vibrFisc_ES114_1,pyrAby1,burkXeno_LB400,polyQLWP,stapMari1,peloLute_DSM273,burkCeno_AU_1054,shewBalt,nocaFarc_IFM10152,ente638,mculMari1,saliTrop_CNB_440,neorSenn_MIYAYAMA,aquiAeol,dechArom_RCB,myxoXant_DK_1622,burkPseu_1106A,burkCepa_AMMD,methMari_C5_1,azorCaul2,methFlag_KT,leptInte,eschColi_K12,synePCC6,baumCica_HOMALODISCA,methBark1,pseuAeru,geobMeta_GS15,eschColi_CFT073,photLumi,metMar1,hermArse,campJeju,therKoda1,aeroHydr_ATCC7966,baciAnth_AMES,shewOnei,therTeng,lawsIntr_PHE_MN1_00 #Harvested from http://genome-test.cse.ucsc.edu/cgi-bin/das/dsn --- a/tool_conf.xml.sample Tue Jul 05 12:40:43 2011 +1000 +++ b/tool_conf.xml.sample Wed Jul 06 09:44:56 2011 +1000 @@ -368,7 +368,6 @@ </section><section name="NGS: Simulation" id="ngs-simulation"><tool file="ngs_simulation/ngs_simulation.xml" /> - <tool file="rgenetics/EpiD.xml" /></section><section name="SNP/WGA: Data; Filters" id="rgdat"><label text="Data: Import and upload" id="rgimport" /> --- a/tools/data_source/ucsc_tablebrowser.xml Tue Jul 05 12:40:43 2011 +1000 +++ b/tools/data_source/ucsc_tablebrowser.xml Wed Jul 06 09:44:56 2011 +1000 @@ -5,27 +5,27 @@ initial response ( in addition to 'URL' ) will be encoded and appended to URL and a post will be performed. --><tool name="UCSC Main" id="ucsc_table_direct1" tool_type="data_source"> - <description>table browser</description> - <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command> - <inputs action="http://ucsc.omics.bhri.internal/cgi-bin/hgTables" check_values="false" method="get"> - <display>go to UCSC Table Browser $GALAXY_URL</display> - <param name="GALAXY_URL" type="baseurl" value="/tool_runner" /> - <param name="tool_id" type="hidden" value="ucsc_table_direct1" /> - <param name="sendToGalaxy" type="hidden" value="1" /> - <param name="hgta_compressType" type="hidden" value="none" /> - <param name="hgta_outputType" type="hidden" value="bed" /> - </inputs> - <request_param_translation> + <description>table browser</description> + <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command> + <inputs action="http://genome.ucsc.edu/cgi-bin/hgTables" check_values="false" method="get"> + <display>go to UCSC Table Browser $GALAXY_URL</display> + <param name="GALAXY_URL" type="baseurl" value="/tool_runner" /> + <param name="tool_id" type="hidden" value="ucsc_table_direct1" /> + <param name="sendToGalaxy" type="hidden" value="1" /> + <param name="hgta_compressType" type="hidden" value="none" /> + <param name="hgta_outputType" type="hidden" value="bed" /> + </inputs> + <request_param_translation><request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" /><request_param galaxy_name="URL" remote_name="URL" missing="" /><request_param galaxy_name="dbkey" remote_name="db" missing="?" /><request_param galaxy_name="organism" remote_name="org" missing="unknown species" /> - <request_param galaxy_name="table" remote_name="hgta_table" missing="unknown table" /> - <request_param galaxy_name="description" remote_name="hgta_regionType" missing="no description" /> - <request_param galaxy_name="data_type" remote_name="hgta_outputType" missing="tabular" > + <request_param galaxy_name="table" remote_name="hgta_table" missing="unknown table" /> + <request_param galaxy_name="description" remote_name="hgta_regionType" missing="no description" /> + <request_param galaxy_name="data_type" remote_name="hgta_outputType" missing="auto" ><value_translation> - <value galaxy_value="tabular" remote_value="primaryTable" /> - <value galaxy_value="tabular" remote_value="selectedFields" /> + <value galaxy_value="auto" remote_value="primaryTable" /> + <value galaxy_value="auto" remote_value="selectedFields" /><value galaxy_value="wig" remote_value="wigData" /><value galaxy_value="interval" remote_value="tab" /><value galaxy_value="html" remote_value="hyperlinks" /> @@ -33,10 +33,10 @@ <value galaxy_value="gtf" remote_value="gff" /></value_translation></request_param> - </request_param_translation> - <uihints minwidth="800"/> - <outputs> - <data name="output" format="tabular" /> - </outputs> - <options sanitize="False" refresh="True"/> + </request_param_translation> + <uihints minwidth="800"/> + <outputs> + <data name="output" format="tabular" label="${tool.name} on ${organism}: ${table} (#if $description == 'range' then $getVar( 'position', 'unknown position' ) else $description#)"/> + </outputs> + <options sanitize="False" refresh="True"/></tool> --- a/tools/meme/meme.xml Tue Jul 05 12:40:43 2011 +1000 +++ b/tools/meme/meme.xml Wed Jul 06 09:44:56 2011 +1000 @@ -304,7 +304,7 @@ </when></conditional> - <param name="non_commercial_use" label="I certify that I am not using this tool for commercial purposes." type="boolean" truevalue="NON_COMMERCIAL_USE" falsevalue="COMMERCIAL_USE" checked="True"> + <param name="non_commercial_use" label="I certify that I am not using this tool for commercial purposes." type="boolean" truevalue="NON_COMMERCIAL_USE" falsevalue="COMMERCIAL_USE" checked="False"><validator type="expression" message="This tool is only available for non-commercial use.">value == True</validator></param> --- a/tools/peak_calling/macs_wrapper.py Tue Jul 05 12:40:43 2011 +1000 +++ b/tools/peak_calling/macs_wrapper.py Wed Jul 06 09:44:56 2011 +1000 @@ -51,8 +51,7 @@ cmdline = "macs -t %s" % ",".join( options['input_chipseq'] ) if options['input_control']: cmdline = "%s -c %s" % ( cmdline, ",".join( options['input_control'] ) ) - cmdline = "%s --format='%s' --name='%s' --gsize='%s' --tsize='%s' --bw='%s' --pvalue='%s' --mfold='%s' %s %s" %\ - ( cmdline, options['format'], experiment_name, options['gsize'], options['tsize'], options['bw'], options['pvalue'], options['mfold'], options['nolambda'], options['futurefdr'] ) + cmdline = "%s --format='%s' --name='%s' --gsize='%s' --tsize='%s' --bw='%s' --pvalue='%s' --mfold='%s' %s --lambdaset='%s' %s" % ( cmdline, options['format'], experiment_name, options['gsize'], options['tsize'], options['bw'], options['pvalue'], options['mfold'], options['nolambda'], options['lambdaset'], options['futurefdr'] ) if 'wig' in options: wigextend = int( options['wig']['wigextend'] ) if wigextend >= 0: --- a/tools/peak_calling/macs_wrapper.xml Tue Jul 05 12:40:43 2011 +1000 +++ b/tools/peak_calling/macs_wrapper.xml Wed Jul 06 09:44:56 2011 +1000 @@ -28,8 +28,7 @@ <param name="tsize" type="integer" label="Tag size" value="25"/><param name="bw" type="integer" label="Band width" value="300"/><param name="pvalue" type="float" label="Pvalue cutoff for peak detection" value="1e-5" help="default: 1e-5"/> - <param name="mfold" type="text" label="Select the regions with MFOLD high-confidence enrichment ratio against background to build model" value="10,30" - help="Range for high-confidence enrichment ratio against background for model are within this range. DEFAULT:10,30" /> + <param name="mfold" type="integer" label="Select the regions with MFOLD high-confidence enrichment ratio against background to build model" value="32"/><param name="xls_to_interval" label="Parse xls files into into distinct interval files" type="boolean" truevalue="create" falsevalue="do_not_create" checked="False"/><conditional name="wig_type"><param name="wig_type_selector" type="select" label="Save shifted raw tag count at every bp into a wiggle file"> @@ -45,6 +44,7 @@ </when></conditional><param name="nolambda" label="Use fixed background lambda as local lambda for every peak region" type="boolean" truevalue="--nolambda" falsevalue="" checked="False" help="up to 9X more time consuming"/> + <param name="lambdaset" type="text" label="3 levels of regions around the peak region to calculate the maximum lambda as local lambda" value="1000,5000,10000" size="50"/><conditional name="nomodel_type"><param name="nomodel_type_selector" type="select" label="Build Model"><option value="nomodel">Do not build the shifting model</option> @@ -95,7 +95,7 @@ <configfile name="options_file"><% import simplejson %> -#set $__options = { 'experiment_name':str( $experiment_name ), 'gsize':int( float( str( $gsize ) ) ), 'tsize':str( $tsize ), 'bw':str( $bw ), 'pvalue':str( $pvalue ), 'mfold':str( $mfold ), 'nolambda':str( $nolambda ), 'futurefdr':str( $futurefdr ) } +#set $__options = { 'experiment_name':str( $experiment_name ), 'gsize':int( float( str( $gsize ) ) ), 'tsize':str( $tsize ), 'bw':str( $bw ), 'pvalue':str( $pvalue ), 'mfold':str( $mfold ), 'nolambda':str( $nolambda ), 'lambdaset': str( $lambdaset ), 'futurefdr':str( $futurefdr ) } #if str( $xls_to_interval ) == 'create': #set $__options['xls_to_interval'] = { 'peaks_file': str( $output_xls_to_interval_peaks_file ), 'negative_peaks_file': str( $output_xls_to_interval_negative_peaks_file ) } #else: @@ -145,13 +145,14 @@ <param name="input_control_file1" value="chipseq_input.bed.gz" ftype="bed" /><param name="experiment_name" value="Galaxy Test Run" /><param name="tsize" value="36" /> - <param name="mfold" value="10,30" /> + <param name="mfold" value="13" /><param name="gsize" value="2.7e+9" /><param name="bw" value="300" /><param name="pvalue" value="1e-5" /><param name="xls_to_interval" /><param name="wig_type_selector" value="no_wig" /><param name="nolambda"/> + <param name="lambdaset" value="1000,5000,10000"/><param name="nomodel_type_selector" value="create_model" /><param name="diag_type_selector" value="no_diag" /><param name="futurefdr"/> @@ -170,13 +171,14 @@ <param name="input_control_file1" value="chipseq_input.bed.gz" ftype="bed" /><param name="experiment_name" value="Galaxy Test Run" /><param name="tsize" value="36" /> - <param name="mfold" value="10,30" /> + <param name="mfold" value="13" /><param name="gsize" value="2.7e+9" /><param name="bw" value="300" /><param name="pvalue" value="1e-5" /><param name="xls_to_interval" value="true" /><param name="wig_type_selector" value="no_wig" /><param name="nolambda"/> + <param name="lambdaset" value="1000,5000,10000"/><param name="nomodel_type_selector" value="create_model" /><param name="diag_type_selector" value="no_diag" /><param name="futurefdr"/> @@ -193,7 +195,7 @@ <param name="input_control_file1" value="chipseq_input.bed.gz" ftype="bed" /><param name="experiment_name" value="Galaxy Test Run" /><param name="tsize" value="36" /> - <param name="mfold" value="10,30" /> + <param name="mfold" value="13" /><param name="gsize" value="2.7e+9" /><param name="bw" value="300" /><param name="pvalue" value="1e-5" /> @@ -202,6 +204,7 @@ <param name="wigextend" value="-1" /><param name="space" value="10" /><param name="nolambda"/> + <param name="lambdaset" value="1000,5000,10000"/><param name="nomodel_type_selector" value="create_model" /><param name="diag_type_selector" value="no_diag" /><param name="futurefdr"/> --- a/tools/plotting/histogram.py Tue Jul 05 12:40:43 2011 +1000 +++ b/tools/plotting/histogram.py Wed Jul 06 09:44:56 2011 +1000 @@ -73,8 +73,7 @@ if skipped_lines < i: try: - #a = array( matrix ) - a=matrix + a = r.array( matrix ) r.pdf( out_fname, 8, 8 ) histogram = r.hist( a, probability=not frequency, main=title, xlab=xlab, breaks=breaks ) if density: --- a/tools/plotting/scatterplot.py Tue Jul 05 12:40:43 2011 +1000 +++ b/tools/plotting/scatterplot.py Wed Jul 06 09:44:56 2011 +1000 @@ -19,14 +19,8 @@ title = sys.argv[5] xlab = sys.argv[6] ylab = sys.argv[7] - out_type = sys.argv[8] - out_width = int(sys.argv[9]) - out_height = int(sys.argv[10]) - point_size = float(sys.argv[11]) - - xvec=[] - yvec=[] + matrix = [] skipped_lines = 0 first_invalid_line = 0 invalid_value = '' @@ -34,19 +28,17 @@ i = 0 for i, line in enumerate( file( in_fname ) ): valid = True - vals = [] line = line.rstrip( '\r\n' ) if line and not line.startswith( '#' ): row = [] fields = line.split( "\t" ) - for c,column in enumerate(columns): + for column in columns: try: val = fields[column] if val.lower() == "na": - v = float( "nan" ) + row.append( float( "nan" ) ) else: - v = float( fields[column] ) - vals.append(val) + row.append( float( fields[column] ) ) except: valid = False skipped_lines += 1 @@ -65,19 +57,12 @@ first_invalid_line = i+1 if valid: - xvec.append(vals[0]) - yvec.append(vals[1]) + matrix.append( row ) + if skipped_lines < i: try: - if out_type == "jpg": - r.jpeg(out_fname,width=out_width,height=out_height) - elif out_type == "png": - # type="cairo" needed to be set for headless servers - r.png(out_fname,type="cairo",width=out_width,height=out_height) - else: - r.pdf(out_fname, out_width, out_height) - - r.plot(xvec,yvec, type="p", main=title, xlab=xlab, ylab=ylab, col="blue", pch=19,cex=point_size ) + r.pdf( out_fname, 8, 8 ) + r.plot( array( matrix ), type="p", main=title, xlab=xlab, ylab=ylab, col="blue", pch=19 ) r.dev_off() except Exception, exc: stop_err( "%s" %str( exc ) ) --- a/tools/plotting/scatterplot.xml Tue Jul 05 12:40:43 2011 +1000 +++ b/tools/plotting/scatterplot.xml Wed Jul 06 09:44:56 2011 +1000 @@ -1,6 +1,6 @@ <tool id="scatterplot_rpy" name="Scatterplot"><description>of two numeric columns</description> - <command interpreter="python">scatterplot.py $input $out_file1 $col1 $col2 "$title" "$xlab" "$ylab" $output_format $out_width $out_height $point_size</command> + <command interpreter="python">scatterplot.py $input $out_file1 $col1 $col2 "$title" "$xlab" "$ylab"</command><inputs><param name="input" type="data" format="tabular" label="Dataset" help="Dataset missing? See TIP below"/><param name="col1" type="data_column" data_ref="input" numerical="True" label="Numerical column for x axis" /> @@ -8,26 +8,15 @@ <param name="title" size="30" type="text" value="Scatterplot" label="Plot title"/><param name="xlab" size="30" type="text" value="V1" label="Label for x axis"/><param name="ylab" size="30" type="text" value="V2" label="Label for y axis"/> - <param name="output_format" type="select" label="Output format"> - <option value="pdf">pdf</option> - <option value="png">png</option> - <option value="jpg">jpg</option> - </param> - <param name="out_width" size="4" type="integer" value="8" label="Width (pdf=inches, image=pixels)"/> - <param name="out_height" size="4" type="integer" value="8" label="Height (pdf=inches, image=pixels)"/> - <param name="point_size" size="4" type="float" value="0.2" label="Point Size"/></inputs><outputs> - <data format="pdf" name="out_file1"> - <change_format> - <when input="output_format" value="png" format="png" /> - <when input="output_format" value="jpg" format="jpg" /> - </change_format> - </data> + <data format="pdf" name="out_file1" /></outputs><requirements><requirement type="python-module">rpy</requirement></requirements> + <help> --- a/tools/samtools/bam_to_sam.py Tue Jul 05 12:40:43 2011 +1000 +++ b/tools/samtools/bam_to_sam.py Wed Jul 06 09:44:56 2011 +1000 @@ -21,6 +21,7 @@ parser = optparse.OptionParser() parser.add_option( '', '--input1', dest='input1', help='The input SAM dataset' ) parser.add_option( '', '--output1', dest='output1', help='The output BAM dataset' ) + parser.add_option( '', '--header', dest='header', action='store_true', default=False, help='Write SAM Header' ) ( options, args ) = parser.parse_args() # output version # of tool @@ -87,7 +88,11 @@ try: # Extract all alignments from the input BAM file to SAM format ( since no region is specified, all the alignments will be extracted ). - command = 'samtools view -o -h %s %s' % ( options.output1, tmp_sorted_aligns_file_name ) + if options.header: + view_options = "-h" + else: + view_options = "" + command = 'samtools view %s -o %s %s' % ( view_options, options.output1, tmp_sorted_aligns_file_name ) tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name tmp_stderr = open( tmp, 'wb' ) proc = subprocess.Popen( args=command, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() ) --- a/tools/samtools/sam_bitwise_flag_filter.py Tue Jul 05 12:40:43 2011 +1000 +++ b/tools/samtools/sam_bitwise_flag_filter.py Wed Jul 06 09:44:56 2011 +1000 @@ -1,6 +1,6 @@ #!/usr/bin/env python # Refactored on 11/13/2010 by Kanwei Li -# Added drop_header option - default is now keep headers for downstream sanity by ross lazarus + import sys import optparse @@ -14,11 +14,7 @@ options (listed below) default to 'None' if omitted """ parser = optparse.OptionParser(usage=usage) - parser.add_option('--drop_header', - action = 'store_true', - dest='drop_header', - help="Remove sam header - you probably NEVER want this for fussy downstream tools") - + parser.add_option( '--0x0001','--is_paired', choices = ( '0','1' ), @@ -133,24 +129,21 @@ opt_map = { '0': False, '1': True } used_indices = [(index, opt_map[opt]) for index, opt in enumerate(opt_ary) if opt is not None] flag_col = int( options.flag_col ) - 1 + for line in infile: line = line.rstrip( '\r\n' ) - if line: - if line.startswith('@'): - if not options.drop_header: - print line # usually want these so add -h if you don't want headers - elif not line.startswith( '#' ) : - fields = line.split( '\t' ) - flags = int( fields[flag_col] ) + if line and not line.startswith( '#' ) and not line.startswith( '@' ) : + fields = line.split( '\t' ) + flags = int( fields[flag_col] ) - valid_line = True - for index, opt_bool in used_indices: - if bool(flags & 0x0001 << index) != opt_bool: - valid_line = False - break + valid_line = True + for index, opt_bool in used_indices: + if bool(flags & 0x0001 << index) != opt_bool: + valid_line = False + break - if valid_line: - print line + if valid_line: + print line if __name__ == "__main__": main() --- a/tools/samtools/sam_bitwise_flag_filter.xml Tue Jul 05 12:40:43 2011 +1000 +++ b/tools/samtools/sam_bitwise_flag_filter.xml Wed Jul 06 09:44:56 2011 +1000 @@ -1,11 +1,8 @@ -<tool id="sam_bw_filter" name="Filter SAM" version="1.0.1"> +<tool id="sam_bw_filter" name="Filter SAM" version="1.0.0"><description>on bitwise flag values</description><parallelism method="basic"></parallelism><command interpreter="python"> sam_bitwise_flag_filter.py - #if $drop_header == "1": - --drop_header - #end if --input_sam_file=$input1 --flag_column=2 #for $bit in $bits @@ -15,11 +12,6 @@ </command><inputs><param format="sam" name="input1" type="data" label="Select dataset to filter"/> - <param name="drop_header" type="select" display="radio" label="DROP sam headers" - help="Set this if you REALLY want to throw away existing sam header metadata - downstream (eg Picard) tools often demand it" > - <option value="0" selected="true">Keep headers (default)</option> - <option value="1">Drop headers</option> - </param><repeat name="bits" title="Flag"><param name="flags" type="select" label="Type"><option value="--0x0001">Read is paired</option> --- a/tools/samtools/sam_to_bam.py Tue Jul 05 12:40:43 2011 +1000 +++ b/tools/samtools/sam_to_bam.py Wed Jul 06 09:44:56 2011 +1000 @@ -68,7 +68,7 @@ # and the equCab2.fa file will contain fasta sequences. seq_path = check_seq_file( options.dbkey, cached_seqs_pointer_file ) tmp_dir = tempfile.mkdtemp() - if options.ref_file == 'None': + if not options.ref_file or options.ref_file == 'None': # We're using locally cached reference sequences( e.g., /galaxy/data/equCab2/sam_index/equCab2.fa ). # The indexes for /galaxy/data/equCab2/sam_index/equCab2.fa will be contained in # a file named /galaxy/data/equCab2/sam_index/equCab2.fa.fai @@ -125,9 +125,7 @@ tmp_aligns_file = tempfile.NamedTemporaryFile( dir=tmp_dir ) tmp_aligns_file_name = tmp_aligns_file.name tmp_aligns_file.close() - # IMPORTANT NOTE: for some reason the samtools view command gzips the resulting bam file without warning, - # and the docs do not currently state that this occurs ( very bad ). - command = 'samtools view -h -bt %s -o %s %s' % ( fai_index_file_path, tmp_aligns_file_name, options.input1 ) + command = 'samtools view -bt %s -o %s %s' % ( fai_index_file_path, tmp_aligns_file_name, options.input1 ) tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name tmp_stderr = open( tmp, 'wb' ) proc = subprocess.Popen( args=command, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() ) @@ -147,8 +145,6 @@ tmp_stderr.close() if returncode != 0: raise Exception, stderr - if len( open( tmp_aligns_file_name ).read() ) == 0: - raise Exception, 'Initial BAM file empty' except Exception, e: #clean up temp files if os.path.exists( tmp_dir ): @@ -188,11 +184,6 @@ stop_err( 'Error sorting alignments from (%s), %s' % ( tmp_aligns_file_name, str( e ) ) ) # Move tmp_aligns_file_name to our output dataset location sorted_bam_file = '%s.bam' % tmp_sorted_aligns_file_name - if os.path.getsize( sorted_bam_file ) == 0: - #clean up temp files - if os.path.exists( tmp_dir ): - shutil.rmtree( tmp_dir ) - stop_err( 'Error creating sorted version of BAM file' ) shutil.move( sorted_bam_file, options.output1 ) #clean up temp files if os.path.exists( tmp_dir ): @@ -201,6 +192,6 @@ if os.path.getsize( options.output1 ) > 0: sys.stdout.write( 'SAM file converted to BAM' ) else: - stop_err( 'The output file is empty, there may be an error with your input file or settings.' ) + stop_err( 'Error creating sorted version of BAM file.' ) if __name__=="__main__": __main__() http://bitbucket.org/galaxy/galaxy-central/changeset/f37951db86e6/ changeset: f37951db86e6 user: fubar date: 2011-07-06 01:45:41 summary: committing backout from 5765 which included reversions from a broken galaxy-central repository affected #: 251 files (5.7 KB) --- a/lib/galaxy/security/__init__.py Tue Jul 05 11:42:56 2011 -0400 +++ b/lib/galaxy/security/__init__.py Wed Jul 06 09:45:41 2011 +1000 @@ -1005,8 +1005,7 @@ ucsc_main = ( 'hgw1.cse.ucsc.edu', 'hgw2.cse.ucsc.edu', 'hgw3.cse.ucsc.edu', 'hgw4.cse.ucsc.edu', 'hgw5.cse.ucsc.edu', 'hgw6.cse.ucsc.edu', 'hgw7.cse.ucsc.edu', 'hgw8.cse.ucsc.edu' ), ucsc_test = ( 'hgwdev.cse.ucsc.edu', ), - ucsc_archaea = ( 'lowepub.cse.ucsc.edu', ), - ucsc_bhri = ('ucsc.omics.bhri.internal','galaxy.omics.bhri.internal'), + ucsc_archaea = ( 'lowepub.cse.ucsc.edu', ) ) def __init__( self, model, permitted_actions=None ): self.model = model @@ -1037,7 +1036,7 @@ # We're going to search in order, but if the remote site is load # balancing their connections (as UCSC does), this is okay. try: - if socket.gethostbyname( server ) == addr or server == '127.0.0.1' or server == '172.16.0.38': + if socket.gethostbyname( server ) == addr: break # remote host is in the server list except ( socket.error, socket.gaierror ): pass # can't resolve, try next --- a/lib/galaxy/tools/__init__.py Tue Jul 05 11:42:56 2011 -0400 +++ b/lib/galaxy/tools/__init__.py Wed Jul 06 09:45:41 2011 +1000 @@ -922,8 +922,6 @@ if not self.check_values: return for input in self.inputs.itervalues(): - if input.name not in value: - value[input.name] = input.get_initial_value( None, value ) if isinstance( input, ToolParameter ): callback( "", input, value[input.name] ) else: --- a/lib/galaxy/tools/parameters/basic.py Tue Jul 05 11:42:56 2011 -0400 +++ b/lib/galaxy/tools/parameters/basic.py Wed Jul 06 09:45:41 2011 +1000 @@ -748,6 +748,9 @@ # Dependency on a value that does not yet exist if isinstance( dep_value, RuntimeValue ): return True + #dataset not ready yet + if hasattr( self, 'ref_input' ) and isinstance( dep_value, self.tool.app.model.HistoryDatasetAssociation ) and ( dep_value.is_pending or not isinstance( dep_value.datatype, self.ref_input.formats ) ): + return True # Dynamic, but all dependenceis are known and have values return False def get_initial_value( self, trans, context ): @@ -878,6 +881,7 @@ self.force_select = string_as_bool( elem.get( "force_select", True )) self.accept_default = string_as_bool( elem.get( "accept_default", False )) self.data_ref = elem.get( "data_ref", None ) + self.ref_input = None self.default_value = elem.get( "default_value", None ) self.is_dynamic = True def from_html( self, value, trans=None, context={} ): @@ -973,7 +977,7 @@ if not dataset.metadata.columns: # Only allow late validation if the dataset is not yet ready # (since we have reason to expect the metadata to be ready eventually) - if dataset.is_pending: + if dataset.is_pending or not isinstance( dataset.datatype, self.ref_input.formats ): return True # No late validation return False @@ -1353,7 +1357,7 @@ selected = ( value and ( hda in value ) ) field.add_option( "%s: %s" % ( hid, hda_name ), hda.id, selected ) else: - target_ext, converted_dataset = hda.find_conversion_destination( self.formats, converter_safe = self.converter_safe( other_values, trans ) ) + target_ext, converted_dataset = hda.find_conversion_destination( self.formats ) if target_ext: if converted_dataset: hda = converted_dataset @@ -1402,13 +1406,22 @@ pass #no valid options def dataset_collector( datasets ): def is_convertable( dataset ): - target_ext, converted_dataset = dataset.find_conversion_destination( self.formats, converter_safe = self.converter_safe( context, trans ) ) + target_ext, converted_dataset = dataset.find_conversion_destination( self.formats ) if target_ext is not None: return True return False for i, data in enumerate( datasets ): - if data.visible and not data.deleted and data.state not in [data.states.ERROR, data.states.DISCARDED] and ( isinstance( data.datatype, self.formats) or is_convertable( data ) ): - if self.options and self._options_filter_attribute( data ) != filter_value: + if data.visible and not data.deleted and data.state not in [data.states.ERROR, data.states.DISCARDED]: + is_valid = False + if isinstance( data.datatype, self.formats ): + is_valid = True + else: + target_ext, converted_dataset = data.find_conversion_destination( self.formats ) + if target_ext: + is_valid = True + if converted_dataset: + data = converted_dataset + if not is_valid or ( self.options and self._options_filter_attribute( data ) != filter_value ): continue most_recent_dataset[0] = data # Also collect children via association object --- a/lib/galaxy/web/framework/middleware/remoteuser.py Tue Jul 05 11:42:56 2011 -0400 +++ b/lib/galaxy/web/framework/middleware/remoteuser.py Wed Jul 06 09:45:41 2011 +1000 @@ -36,7 +36,6 @@ """ UCSC_MAIN_SERVERS = ( - 'omics.bhri.internal', 'hgw1.cse.ucsc.edu', 'hgw2.cse.ucsc.edu', 'hgw3.cse.ucsc.edu', @@ -50,7 +49,6 @@ 'lowepub.cse.ucsc.edu', ) - class RemoteUser( object ): def __init__( self, app, maildomain=None, ucsc_display_sites=[], admin_users=[] ): self.app = app @@ -58,7 +56,7 @@ self.allow_ucsc_main = False self.allow_ucsc_archaea = False self.admin_users = admin_users - if 'main' in ucsc_display_sites or 'test' in ucsc_display_sites or 'bhri' in ucsc_display_sites: + if 'main' in ucsc_display_sites or 'test' in ucsc_display_sites: self.allow_ucsc_main = True if 'archaea' in ucsc_display_sites: self.allow_ucsc_archaea = True --- a/scripts/cleanup_datasets/purge_libraries.sh Tue Jul 05 11:42:56 2011 -0400 +++ b/scripts/cleanup_datasets/purge_libraries.sh Wed Jul 06 09:45:41 2011 +1000 @@ -1,5 +1,4 @@ #!/bin/sh cd `dirname $0`/../.. -#python ./scripts/cleanup_datasets/cleanup_datasets.py ./universe_wsgi.ini -d 10 -4 -r $@ >> ./scripts/cleanup_datasets/purge_libraries.log -python ./scripts/cleanup_datasets/cleanup_datasets.py ./universe_wsgi.ini -d 2 -4 -r $@ >> ./scripts/cleanup_datasets/purge_libraries.log +python ./scripts/cleanup_datasets/cleanup_datasets.py ./universe_wsgi.ini -d 10 -4 -r $@ >> ./scripts/cleanup_datasets/purge_libraries.log --- a/tool-data/shared/ucsc/ucsc_build_sites.txt Tue Jul 05 11:42:56 2011 -0400 +++ b/tool-data/shared/ucsc/ucsc_build_sites.txt Wed Jul 06 09:45:41 2011 +1000 @@ -1,6 +1,5 @@ #Harvested from http://genome.ucsc.edu/cgi-bin/das/dsn main http://genome.ucsc.edu/cgi-bin/hgTracks? priPac1,danRer4,mm9,mm8,droAna1,mm5,caeRem2,mm7,mm6,panTro1,dm3,panTro2,anoCar1,ce4,galGal3,galGal2,ce1,rn3,rn2,droMoj1,droMoj2,rn4,droYak1,droYak2,dp3,dp2,dm1,canFam1,danRer5,canFam2,danRer3,danRer2,ornAna1,ci2,ci1,tetNig1,bosTau1,bosTau3,bosTau2,equCab1,oryLat1,droAna2,droEre1,ponAbe2,rheMac2,sacCer1,droPer1,droSim1,monDom1,cb1,dm2,droSec1,strPur1,droVir2,droVir1,strPur2,sc1,xenTro1,droGri1,xenTro2,cb3,gasAcu1,caePb1,anoGam1,fr2,fr1,hg15,hg16,hg17,hg18,felCat3,apiMel2,monDom4,apiMel1,ce2 -bhri http://ucsc.omics.bhri.internal/cgi-bin/hgTracks? hg18,hg19,mm8,mm9,rn4 #Harvested from http://archaea.ucsc.edu/cgi-bin/das/dsn archaea http://archaea.ucsc.edu/cgi-bin/hgTracks? alkaEhrl_MLHE_1,shewW318,idioLoih_L2TR,sulSol1,erwiCaro_ATROSEPTICA,symbTher_IAM14863,moorTher_ATCC39073,therFusc_YX,methHung1,bradJapo,therElon,shewPutrCN32,pediPent_ATCC25745,mariMari_MCS10,nanEqu1,baciSubt,chlaTrac,magnMagn_AMB_1,chroViol,ralsSola,acidCryp_JF_5,erytLito_HTCC2594,desuVulg_HILDENBOROUG,pyrAer1,sulfToko1,shewANA3,paraSp_UWE25,geobKaus_HTA426,rhizEtli_CFN_42,uncuMeth_RCI,candBloc_FLORIDANUS,deinRadi,yersPest_CO92,saccEryt_NRRL_2338,rhodRHA1,candCars_RUDDII,burkMall_ATCC23344,eschColi_O157H7,burk383,psycIngr_37,rhodSpha_2_4_1,wolbEndo_OF_DROSOPHIL,burkViet_G4,propAcne_KPA171202,enteFaec_V583,campJeju_81_176,acidJS42,heliPylo_26695,pseuHalo_TAC125,chroSale_DSM3043,methVann1,archFulg1,neisMeni_Z2491_1,fusoNucl,vermEise_EF01_2,anabVari_ATCC29413,tropWhip_TW08_27,heliHepa,acinSp_ADP1,anapMarg_ST_MARIES,natrPhar1,haheChej_KCTC_2396,therPetr_RKU_1,neisGono_FA1090_1,colwPsyc_34H,desuPsyc_LSV54,hyphNept_ATCC15444,vibrChol1,deinGeot_DSM11300,strePyog_M1_GAS,franCcI3,salmTyph,metaSedu,lactSali_UCC118,trepPall,neisMeni_MC58_1,syntWolf_GOETTINGEN,flavJohn_UW101,methBoon1,haemSomn_129PT,shewLoihPV4,igniHosp1,haemInfl_KW20,haloHalo_SL1,ferrAcid1,sphiAlas_RB2256,candPela_UBIQUE_HTCC1,caldSacc_DSM8903,aerPer1,lactPlan,carbHydr_Z_2901,therTher_HB8,vibrVuln_YJ016_1,rhodPalu_CGA009,acidCell_11B,siliPome_DSS_3,therVolc1,haloWals1,rubrXyla_DSM9941,shewAmaz,nocaJS61,vibrVuln_CMCP6_1,sinoMeli,ureaUrea,baciHalo,bartHens_HOUSTON_1,nitrWino_NB_255,hypeButy1,methBurt2,polaJS66,mesoLoti,methMari_C7,caulCres,neisMeni_FAM18_1,acidBact_ELLIN345,caldMaqu1,salmEnte_PARATYPI_ATC,glucOxyd_621H,cytoHutc_ATCC33406,nitrEuro,therMari,coxiBurn,woliSucc,heliPylo_HPAG1,mesoFlor_L1,pyrHor1,methAeol1,procMari_CCMP1375,pyroArse1,oenoOeni_PSU_1,alcaBork_SK2,wiggBrev,actiPleu_L20,lactLact,methJann1,paraDeni_PD1222,borrBurg,pyroIsla1,orieTsut_BORYONG,shewMR4,methKand1,methCaps_BATH,onioYell_PHYTOPLASMA,bordBron,cenaSymb1,burkCeno_HI2424,franTula_TULARENSIS,pyrFur2,mariAqua_VT8,heliPylo_J99,psycArct_273_4,vibrChol_MO10_1,vibrPara1,rickBell_RML369_C,metAce1,buchSp,ehrlRumi_WELGEVONDEN,methLabrZ_1,chlaPneu_CWL029,thioCrun_XCL_2,pyroCali1,chloTepi_TLS,stapAure_MU50,novoArom_DSM12444,magnMC1,zymoMobi_ZM4,salmTyph_TY2,chloChlo_CAD3,azoaSp_EBN1,therTher_HB27,bifiLong,picrTorr1,listInno,bdelBact,gramFors_KT0803,sulfAcid1,geobTher_NG80_2,peloCarb,ralsEutr_JMP134,mannSucc_MBEL55E,syneSp_WH8102,methTherPT1,clavMich_NCPPB_382,therAcid1,syntAcid_SB,porpGing_W83,therNeut0,leifXyli_XYLI_CTCB0,shewFrig,photProf_SS9,thioDeni_ATCC25259,methMaze1,desuRedu_MI_1,burkThai_E264,campFetu_82_40,blocFlor,jannCCS1,nitrMult_ATCC25196,streCoel,soliUsit_ELLIN6076,pastMult,saliRube_DSM13855,methTher1,nostSp,shigFlex_2A,saccDegr_2_40,oceaIhey,dehaEthe_195,rhodRubr_ATCC11170,arthFB24,shewMR7,pireSp,anaeDeha_2CP_C,haloVolc1,dichNodo_VCS1703A,tricEryt_IMS101,mycoGeni,thioDeni_ATCC33889,methSmit1,geobUran_RF4,shewDeni,halMar1,desuHafn_Y51,methStad1,granBeth_CGDNIH1,therPend1,legiPneu_PHILADELPHIA,vibrChol_O395_1,nitrOcea_ATCC19707,campJeju_RM1221,methPetr_PM1,heliAcin_SHEEBA,eschColi_APEC_O1,peloTher_SI,haloHalo1,syntFuma_MPOB,xyleFast,gloeViol,leucMese_ATCC8293,bactThet_VPI_5482,xantCamp,sodaGlos_MORSITANS,geobSulf,roseDeni_OCH_114,coryEffi_YS_314,brucMeli,mycoTube_H37RV,vibrFisc_ES114_1,pyrAby1,burkXeno_LB400,polyQLWP,stapMari1,peloLute_DSM273,burkCeno_AU_1054,shewBalt,nocaFarc_IFM10152,ente638,mculMari1,saliTrop_CNB_440,neorSenn_MIYAYAMA,aquiAeol,dechArom_RCB,myxoXant_DK_1622,burkPseu_1106A,burkCepa_AMMD,methMari_C5_1,azorCaul2,methFlag_KT,leptInte,eschColi_K12,synePCC6,baumCica_HOMALODISCA,methBark1,pseuAeru,geobMeta_GS15,eschColi_CFT073,photLumi,metMar1,hermArse,campJeju,therKoda1,aeroHydr_ATCC7966,baciAnth_AMES,shewOnei,therTeng,lawsIntr_PHE_MN1_00 #Harvested from http://genome-test.cse.ucsc.edu/cgi-bin/das/dsn --- a/tool_conf.xml.sample Tue Jul 05 11:42:56 2011 -0400 +++ b/tool_conf.xml.sample Wed Jul 06 09:45:41 2011 +1000 @@ -368,7 +368,6 @@ </section><section name="NGS: Simulation" id="ngs-simulation"><tool file="ngs_simulation/ngs_simulation.xml" /> - <tool file="rgenetics/EpiD.xml" /></section><section name="SNP/WGA: Data; Filters" id="rgdat"><label text="Data: Import and upload" id="rgimport" /> --- a/tools/data_source/ucsc_tablebrowser.xml Tue Jul 05 11:42:56 2011 -0400 +++ b/tools/data_source/ucsc_tablebrowser.xml Wed Jul 06 09:45:41 2011 +1000 @@ -5,27 +5,27 @@ initial response ( in addition to 'URL' ) will be encoded and appended to URL and a post will be performed. --><tool name="UCSC Main" id="ucsc_table_direct1" tool_type="data_source"> - <description>table browser</description> - <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command> - <inputs action="http://ucsc.omics.bhri.internal/cgi-bin/hgTables" check_values="false" method="get"> - <display>go to UCSC Table Browser $GALAXY_URL</display> - <param name="GALAXY_URL" type="baseurl" value="/tool_runner" /> - <param name="tool_id" type="hidden" value="ucsc_table_direct1" /> - <param name="sendToGalaxy" type="hidden" value="1" /> - <param name="hgta_compressType" type="hidden" value="none" /> - <param name="hgta_outputType" type="hidden" value="bed" /> - </inputs> - <request_param_translation> + <description>table browser</description> + <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command> + <inputs action="http://genome.ucsc.edu/cgi-bin/hgTables" check_values="false" method="get"> + <display>go to UCSC Table Browser $GALAXY_URL</display> + <param name="GALAXY_URL" type="baseurl" value="/tool_runner" /> + <param name="tool_id" type="hidden" value="ucsc_table_direct1" /> + <param name="sendToGalaxy" type="hidden" value="1" /> + <param name="hgta_compressType" type="hidden" value="none" /> + <param name="hgta_outputType" type="hidden" value="bed" /> + </inputs> + <request_param_translation><request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" /><request_param galaxy_name="URL" remote_name="URL" missing="" /><request_param galaxy_name="dbkey" remote_name="db" missing="?" /><request_param galaxy_name="organism" remote_name="org" missing="unknown species" /> - <request_param galaxy_name="table" remote_name="hgta_table" missing="unknown table" /> - <request_param galaxy_name="description" remote_name="hgta_regionType" missing="no description" /> - <request_param galaxy_name="data_type" remote_name="hgta_outputType" missing="tabular" > + <request_param galaxy_name="table" remote_name="hgta_table" missing="unknown table" /> + <request_param galaxy_name="description" remote_name="hgta_regionType" missing="no description" /> + <request_param galaxy_name="data_type" remote_name="hgta_outputType" missing="auto" ><value_translation> - <value galaxy_value="tabular" remote_value="primaryTable" /> - <value galaxy_value="tabular" remote_value="selectedFields" /> + <value galaxy_value="auto" remote_value="primaryTable" /> + <value galaxy_value="auto" remote_value="selectedFields" /><value galaxy_value="wig" remote_value="wigData" /><value galaxy_value="interval" remote_value="tab" /><value galaxy_value="html" remote_value="hyperlinks" /> @@ -33,10 +33,10 @@ <value galaxy_value="gtf" remote_value="gff" /></value_translation></request_param> - </request_param_translation> - <uihints minwidth="800"/> - <outputs> - <data name="output" format="tabular" /> - </outputs> - <options sanitize="False" refresh="True"/> + </request_param_translation> + <uihints minwidth="800"/> + <outputs> + <data name="output" format="tabular" label="${tool.name} on ${organism}: ${table} (#if $description == 'range' then $getVar( 'position', 'unknown position' ) else $description#)"/> + </outputs> + <options sanitize="False" refresh="True"/></tool> --- a/tools/meme/meme.xml Tue Jul 05 11:42:56 2011 -0400 +++ b/tools/meme/meme.xml Wed Jul 06 09:45:41 2011 +1000 @@ -304,7 +304,7 @@ </when></conditional> - <param name="non_commercial_use" label="I certify that I am not using this tool for commercial purposes." type="boolean" truevalue="NON_COMMERCIAL_USE" falsevalue="COMMERCIAL_USE" checked="True"> + <param name="non_commercial_use" label="I certify that I am not using this tool for commercial purposes." type="boolean" truevalue="NON_COMMERCIAL_USE" falsevalue="COMMERCIAL_USE" checked="False"><validator type="expression" message="This tool is only available for non-commercial use.">value == True</validator></param> --- a/tools/peak_calling/macs_wrapper.py Tue Jul 05 11:42:56 2011 -0400 +++ b/tools/peak_calling/macs_wrapper.py Wed Jul 06 09:45:41 2011 +1000 @@ -51,8 +51,7 @@ cmdline = "macs -t %s" % ",".join( options['input_chipseq'] ) if options['input_control']: cmdline = "%s -c %s" % ( cmdline, ",".join( options['input_control'] ) ) - cmdline = "%s --format='%s' --name='%s' --gsize='%s' --tsize='%s' --bw='%s' --pvalue='%s' --mfold='%s' %s %s" %\ - ( cmdline, options['format'], experiment_name, options['gsize'], options['tsize'], options['bw'], options['pvalue'], options['mfold'], options['nolambda'], options['futurefdr'] ) + cmdline = "%s --format='%s' --name='%s' --gsize='%s' --tsize='%s' --bw='%s' --pvalue='%s' --mfold='%s' %s --lambdaset='%s' %s" % ( cmdline, options['format'], experiment_name, options['gsize'], options['tsize'], options['bw'], options['pvalue'], options['mfold'], options['nolambda'], options['lambdaset'], options['futurefdr'] ) if 'wig' in options: wigextend = int( options['wig']['wigextend'] ) if wigextend >= 0: --- a/tools/peak_calling/macs_wrapper.xml Tue Jul 05 11:42:56 2011 -0400 +++ b/tools/peak_calling/macs_wrapper.xml Wed Jul 06 09:45:41 2011 +1000 @@ -28,8 +28,7 @@ <param name="tsize" type="integer" label="Tag size" value="25"/><param name="bw" type="integer" label="Band width" value="300"/><param name="pvalue" type="float" label="Pvalue cutoff for peak detection" value="1e-5" help="default: 1e-5"/> - <param name="mfold" type="text" label="Select the regions with MFOLD high-confidence enrichment ratio against background to build model" value="10,30" - help="Range for high-confidence enrichment ratio against background for model are within this range. DEFAULT:10,30" /> + <param name="mfold" type="integer" label="Select the regions with MFOLD high-confidence enrichment ratio against background to build model" value="32"/><param name="xls_to_interval" label="Parse xls files into into distinct interval files" type="boolean" truevalue="create" falsevalue="do_not_create" checked="False"/><conditional name="wig_type"><param name="wig_type_selector" type="select" label="Save shifted raw tag count at every bp into a wiggle file"> @@ -45,6 +44,7 @@ </when></conditional><param name="nolambda" label="Use fixed background lambda as local lambda for every peak region" type="boolean" truevalue="--nolambda" falsevalue="" checked="False" help="up to 9X more time consuming"/> + <param name="lambdaset" type="text" label="3 levels of regions around the peak region to calculate the maximum lambda as local lambda" value="1000,5000,10000" size="50"/><conditional name="nomodel_type"><param name="nomodel_type_selector" type="select" label="Build Model"><option value="nomodel">Do not build the shifting model</option> @@ -95,7 +95,7 @@ <configfile name="options_file"><% import simplejson %> -#set $__options = { 'experiment_name':str( $experiment_name ), 'gsize':int( float( str( $gsize ) ) ), 'tsize':str( $tsize ), 'bw':str( $bw ), 'pvalue':str( $pvalue ), 'mfold':str( $mfold ), 'nolambda':str( $nolambda ), 'futurefdr':str( $futurefdr ) } +#set $__options = { 'experiment_name':str( $experiment_name ), 'gsize':int( float( str( $gsize ) ) ), 'tsize':str( $tsize ), 'bw':str( $bw ), 'pvalue':str( $pvalue ), 'mfold':str( $mfold ), 'nolambda':str( $nolambda ), 'lambdaset': str( $lambdaset ), 'futurefdr':str( $futurefdr ) } #if str( $xls_to_interval ) == 'create': #set $__options['xls_to_interval'] = { 'peaks_file': str( $output_xls_to_interval_peaks_file ), 'negative_peaks_file': str( $output_xls_to_interval_negative_peaks_file ) } #else: @@ -145,13 +145,14 @@ <param name="input_control_file1" value="chipseq_input.bed.gz" ftype="bed" /><param name="experiment_name" value="Galaxy Test Run" /><param name="tsize" value="36" /> - <param name="mfold" value="10,30" /> + <param name="mfold" value="13" /><param name="gsize" value="2.7e+9" /><param name="bw" value="300" /><param name="pvalue" value="1e-5" /><param name="xls_to_interval" /><param name="wig_type_selector" value="no_wig" /><param name="nolambda"/> + <param name="lambdaset" value="1000,5000,10000"/><param name="nomodel_type_selector" value="create_model" /><param name="diag_type_selector" value="no_diag" /><param name="futurefdr"/> @@ -170,13 +171,14 @@ <param name="input_control_file1" value="chipseq_input.bed.gz" ftype="bed" /><param name="experiment_name" value="Galaxy Test Run" /><param name="tsize" value="36" /> - <param name="mfold" value="10,30" /> + <param name="mfold" value="13" /><param name="gsize" value="2.7e+9" /><param name="bw" value="300" /><param name="pvalue" value="1e-5" /><param name="xls_to_interval" value="true" /><param name="wig_type_selector" value="no_wig" /><param name="nolambda"/> + <param name="lambdaset" value="1000,5000,10000"/><param name="nomodel_type_selector" value="create_model" /><param name="diag_type_selector" value="no_diag" /><param name="futurefdr"/> @@ -193,7 +195,7 @@ <param name="input_control_file1" value="chipseq_input.bed.gz" ftype="bed" /><param name="experiment_name" value="Galaxy Test Run" /><param name="tsize" value="36" /> - <param name="mfold" value="10,30" /> + <param name="mfold" value="13" /><param name="gsize" value="2.7e+9" /><param name="bw" value="300" /><param name="pvalue" value="1e-5" /> @@ -202,6 +204,7 @@ <param name="wigextend" value="-1" /><param name="space" value="10" /><param name="nolambda"/> + <param name="lambdaset" value="1000,5000,10000"/><param name="nomodel_type_selector" value="create_model" /><param name="diag_type_selector" value="no_diag" /><param name="futurefdr"/> --- a/tools/plotting/histogram.py Tue Jul 05 11:42:56 2011 -0400 +++ b/tools/plotting/histogram.py Wed Jul 06 09:45:41 2011 +1000 @@ -73,8 +73,7 @@ if skipped_lines < i: try: - #a = array( matrix ) - a=matrix + a = r.array( matrix ) r.pdf( out_fname, 8, 8 ) histogram = r.hist( a, probability=not frequency, main=title, xlab=xlab, breaks=breaks ) if density: --- a/tools/plotting/scatterplot.py Tue Jul 05 11:42:56 2011 -0400 +++ b/tools/plotting/scatterplot.py Wed Jul 06 09:45:41 2011 +1000 @@ -19,14 +19,8 @@ title = sys.argv[5] xlab = sys.argv[6] ylab = sys.argv[7] - out_type = sys.argv[8] - out_width = int(sys.argv[9]) - out_height = int(sys.argv[10]) - point_size = float(sys.argv[11]) - - xvec=[] - yvec=[] + matrix = [] skipped_lines = 0 first_invalid_line = 0 invalid_value = '' @@ -34,19 +28,17 @@ i = 0 for i, line in enumerate( file( in_fname ) ): valid = True - vals = [] line = line.rstrip( '\r\n' ) if line and not line.startswith( '#' ): row = [] fields = line.split( "\t" ) - for c,column in enumerate(columns): + for column in columns: try: val = fields[column] if val.lower() == "na": - v = float( "nan" ) + row.append( float( "nan" ) ) else: - v = float( fields[column] ) - vals.append(val) + row.append( float( fields[column] ) ) except: valid = False skipped_lines += 1 @@ -65,19 +57,12 @@ first_invalid_line = i+1 if valid: - xvec.append(vals[0]) - yvec.append(vals[1]) + matrix.append( row ) + if skipped_lines < i: try: - if out_type == "jpg": - r.jpeg(out_fname,width=out_width,height=out_height) - elif out_type == "png": - # type="cairo" needed to be set for headless servers - r.png(out_fname,type="cairo",width=out_width,height=out_height) - else: - r.pdf(out_fname, out_width, out_height) - - r.plot(xvec,yvec, type="p", main=title, xlab=xlab, ylab=ylab, col="blue", pch=19,cex=point_size ) + r.pdf( out_fname, 8, 8 ) + r.plot( array( matrix ), type="p", main=title, xlab=xlab, ylab=ylab, col="blue", pch=19 ) r.dev_off() except Exception, exc: stop_err( "%s" %str( exc ) ) --- a/tools/plotting/scatterplot.xml Tue Jul 05 11:42:56 2011 -0400 +++ b/tools/plotting/scatterplot.xml Wed Jul 06 09:45:41 2011 +1000 @@ -1,6 +1,6 @@ <tool id="scatterplot_rpy" name="Scatterplot"><description>of two numeric columns</description> - <command interpreter="python">scatterplot.py $input $out_file1 $col1 $col2 "$title" "$xlab" "$ylab" $output_format $out_width $out_height $point_size</command> + <command interpreter="python">scatterplot.py $input $out_file1 $col1 $col2 "$title" "$xlab" "$ylab"</command><inputs><param name="input" type="data" format="tabular" label="Dataset" help="Dataset missing? See TIP below"/><param name="col1" type="data_column" data_ref="input" numerical="True" label="Numerical column for x axis" /> @@ -8,26 +8,15 @@ <param name="title" size="30" type="text" value="Scatterplot" label="Plot title"/><param name="xlab" size="30" type="text" value="V1" label="Label for x axis"/><param name="ylab" size="30" type="text" value="V2" label="Label for y axis"/> - <param name="output_format" type="select" label="Output format"> - <option value="pdf">pdf</option> - <option value="png">png</option> - <option value="jpg">jpg</option> - </param> - <param name="out_width" size="4" type="integer" value="8" label="Width (pdf=inches, image=pixels)"/> - <param name="out_height" size="4" type="integer" value="8" label="Height (pdf=inches, image=pixels)"/> - <param name="point_size" size="4" type="float" value="0.2" label="Point Size"/></inputs><outputs> - <data format="pdf" name="out_file1"> - <change_format> - <when input="output_format" value="png" format="png" /> - <when input="output_format" value="jpg" format="jpg" /> - </change_format> - </data> + <data format="pdf" name="out_file1" /></outputs><requirements><requirement type="python-module">rpy</requirement></requirements> + <help> --- a/tools/samtools/bam_to_sam.py Tue Jul 05 11:42:56 2011 -0400 +++ b/tools/samtools/bam_to_sam.py Wed Jul 06 09:45:41 2011 +1000 @@ -21,6 +21,7 @@ parser = optparse.OptionParser() parser.add_option( '', '--input1', dest='input1', help='The input SAM dataset' ) parser.add_option( '', '--output1', dest='output1', help='The output BAM dataset' ) + parser.add_option( '', '--header', dest='header', action='store_true', default=False, help='Write SAM Header' ) ( options, args ) = parser.parse_args() # output version # of tool @@ -87,7 +88,11 @@ try: # Extract all alignments from the input BAM file to SAM format ( since no region is specified, all the alignments will be extracted ). - command = 'samtools view -o -h %s %s' % ( options.output1, tmp_sorted_aligns_file_name ) + if options.header: + view_options = "-h" + else: + view_options = "" + command = 'samtools view %s -o %s %s' % ( view_options, options.output1, tmp_sorted_aligns_file_name ) tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name tmp_stderr = open( tmp, 'wb' ) proc = subprocess.Popen( args=command, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() ) --- a/tools/samtools/sam_bitwise_flag_filter.py Tue Jul 05 11:42:56 2011 -0400 +++ b/tools/samtools/sam_bitwise_flag_filter.py Wed Jul 06 09:45:41 2011 +1000 @@ -1,6 +1,6 @@ #!/usr/bin/env python # Refactored on 11/13/2010 by Kanwei Li -# Added drop_header option - default is now keep headers for downstream sanity by ross lazarus + import sys import optparse @@ -14,11 +14,7 @@ options (listed below) default to 'None' if omitted """ parser = optparse.OptionParser(usage=usage) - parser.add_option('--drop_header', - action = 'store_true', - dest='drop_header', - help="Remove sam header - you probably NEVER want this for fussy downstream tools") - + parser.add_option( '--0x0001','--is_paired', choices = ( '0','1' ), @@ -133,24 +129,21 @@ opt_map = { '0': False, '1': True } used_indices = [(index, opt_map[opt]) for index, opt in enumerate(opt_ary) if opt is not None] flag_col = int( options.flag_col ) - 1 + for line in infile: line = line.rstrip( '\r\n' ) - if line: - if line.startswith('@'): - if not options.drop_header: - print line # usually want these so add -h if you don't want headers - elif not line.startswith( '#' ) : - fields = line.split( '\t' ) - flags = int( fields[flag_col] ) + if line and not line.startswith( '#' ) and not line.startswith( '@' ) : + fields = line.split( '\t' ) + flags = int( fields[flag_col] ) - valid_line = True - for index, opt_bool in used_indices: - if bool(flags & 0x0001 << index) != opt_bool: - valid_line = False - break + valid_line = True + for index, opt_bool in used_indices: + if bool(flags & 0x0001 << index) != opt_bool: + valid_line = False + break - if valid_line: - print line + if valid_line: + print line if __name__ == "__main__": main() --- a/tools/samtools/sam_bitwise_flag_filter.xml Tue Jul 05 11:42:56 2011 -0400 +++ b/tools/samtools/sam_bitwise_flag_filter.xml Wed Jul 06 09:45:41 2011 +1000 @@ -1,11 +1,8 @@ -<tool id="sam_bw_filter" name="Filter SAM" version="1.0.1"> +<tool id="sam_bw_filter" name="Filter SAM" version="1.0.0"><description>on bitwise flag values</description><parallelism method="basic"></parallelism><command interpreter="python"> sam_bitwise_flag_filter.py - #if $drop_header == "1": - --drop_header - #end if --input_sam_file=$input1 --flag_column=2 #for $bit in $bits @@ -15,11 +12,6 @@ </command><inputs><param format="sam" name="input1" type="data" label="Select dataset to filter"/> - <param name="drop_header" type="select" display="radio" label="DROP sam headers" - help="Set this if you REALLY want to throw away existing sam header metadata - downstream (eg Picard) tools often demand it" > - <option value="0" selected="true">Keep headers (default)</option> - <option value="1">Drop headers</option> - </param><repeat name="bits" title="Flag"><param name="flags" type="select" label="Type"><option value="--0x0001">Read is paired</option> --- a/tools/samtools/sam_to_bam.py Tue Jul 05 11:42:56 2011 -0400 +++ b/tools/samtools/sam_to_bam.py Wed Jul 06 09:45:41 2011 +1000 @@ -68,7 +68,7 @@ # and the equCab2.fa file will contain fasta sequences. seq_path = check_seq_file( options.dbkey, cached_seqs_pointer_file ) tmp_dir = tempfile.mkdtemp() - if options.ref_file == 'None': + if not options.ref_file or options.ref_file == 'None': # We're using locally cached reference sequences( e.g., /galaxy/data/equCab2/sam_index/equCab2.fa ). # The indexes for /galaxy/data/equCab2/sam_index/equCab2.fa will be contained in # a file named /galaxy/data/equCab2/sam_index/equCab2.fa.fai @@ -125,9 +125,7 @@ tmp_aligns_file = tempfile.NamedTemporaryFile( dir=tmp_dir ) tmp_aligns_file_name = tmp_aligns_file.name tmp_aligns_file.close() - # IMPORTANT NOTE: for some reason the samtools view command gzips the resulting bam file without warning, - # and the docs do not currently state that this occurs ( very bad ). - command = 'samtools view -h -bt %s -o %s %s' % ( fai_index_file_path, tmp_aligns_file_name, options.input1 ) + command = 'samtools view -bt %s -o %s %s' % ( fai_index_file_path, tmp_aligns_file_name, options.input1 ) tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name tmp_stderr = open( tmp, 'wb' ) proc = subprocess.Popen( args=command, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() ) @@ -147,8 +145,6 @@ tmp_stderr.close() if returncode != 0: raise Exception, stderr - if len( open( tmp_aligns_file_name ).read() ) == 0: - raise Exception, 'Initial BAM file empty' except Exception, e: #clean up temp files if os.path.exists( tmp_dir ): @@ -188,11 +184,6 @@ stop_err( 'Error sorting alignments from (%s), %s' % ( tmp_aligns_file_name, str( e ) ) ) # Move tmp_aligns_file_name to our output dataset location sorted_bam_file = '%s.bam' % tmp_sorted_aligns_file_name - if os.path.getsize( sorted_bam_file ) == 0: - #clean up temp files - if os.path.exists( tmp_dir ): - shutil.rmtree( tmp_dir ) - stop_err( 'Error creating sorted version of BAM file' ) shutil.move( sorted_bam_file, options.output1 ) #clean up temp files if os.path.exists( tmp_dir ): @@ -201,6 +192,6 @@ if os.path.getsize( options.output1 ) > 0: sys.stdout.write( 'SAM file converted to BAM' ) else: - stop_err( 'The output file is empty, there may be an error with your input file or settings.' ) + stop_err( 'Error creating sorted version of BAM file.' ) if __name__=="__main__": __main__() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Trackster: add infrastructure for getting data iteratively but, for now, still fetch all data when getting more data. Use Galaxy button styles as well.
by Bitbucket 05 Jul '11

05 Jul '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/9a5c403bb2e5/ changeset: 9a5c403bb2e5 user: jgoecks date: 2011-07-05 17:42:56 summary: Trackster: add infrastructure for getting data iteratively but, for now, still fetch all data when getting more data. Use Galaxy button styles as well. affected #: 1 file (2.2 KB) --- a/static/scripts/trackster.js Tue Jul 05 16:46:21 2011 +1000 +++ b/static/scripts/trackster.js Tue Jul 05 11:42:56 2011 -0400 @@ -305,10 +305,8 @@ // Look for entry and return if found. var mode = this.track.mode, - entry = this.get(this.gen_key(low, high, mode)); - if (entry) { - return entry; - } + entry = this.get_data_from_cache(low, high, mode); + if (entry) { return entry; } // // If data supports subsetting: @@ -348,6 +346,69 @@ this.set_data(low, high, mode, entry); return entry }, + /** "Deep" data request; used as a parameter for DataManager.get_more_data() */ + DEEP_DATA_REQ: "deep", + /** "Broad" data request; used as a parameter for DataManager.get_more_data() */ + BROAD_DATA_REQ: "breadth", + /** + * Gets more data for a region using either a depth-first or a breadth-first approach. + */ + get_more_data: function(low, high, resolution, extra_params, req_type) { + // + // Get current data from cache and mark as stale. + // + var + mode = this.track.mode, + cur_data = this.get_data_from_cache(low, high, mode); + if (!cur_data) { + console.log("ERROR: no current data for: ", this.track, low, high, resolution, extra_params); + return; + } + cur_data.stale = true; + + // + // Set parameters based on request type. + // + if (req_type === this.DEEP_DATA_REQ) { + // HACK: for now, just up the max vals and request all data; in the future, + // need server to recognize min_vals and max_vals to specify range of data to + // return. + $.extend(extra_params, {max_vals: cur_data.data.length * 2}); + } + else if (req_type === this.BROAD_DATA_REQ) { + // Set low to be past the last feature returned. + low = cur_data.data[cur_data.length-1][2] + 1; + } + + // + // Get additional data, append to current data, and set new data. Use a custom deferred object + // to signal when new data is available. + // + var + data_manager = this, + new_data_request = this.load_data(low, high, resolution, extra_params) + new_data_available = $.Deferred(); + // load_data sets cache to new_data_request, but use custom deferred object so that signal and data + // is all data, not just new data. + this.set_data(low, high, mode, new_data_available); + $.when(new_data_request).then(function(result) { + if (result.data) { + //result.data.append(cur_data.data); + } + data_manager.set_data(low, high, mode, result); + new_data_available.resolve(result); + }); + return new_data_available; + }, + /** + * Gets data from the cache. + */ + get_data_from_cache: function(low, high, mode) { + return this.get(this.gen_key(low, high, mode)); + }, + /** + * Sets data in the cache. + */ set_data: function(low, high, mode, result) { //console.log("set_data", low, high, mode, result); return this.set(this.gen_key(low, high, mode), result); @@ -2150,18 +2211,15 @@ message_div = $("<div/>").addClass("tile-message").text(tile.message). // -1 to account for border. css({'height': ERROR_PADDING-1, 'width': tile.canvas.width}).appendTo(container_div), - show_more_data_btn = $("<button/>").text("Show more").css("margin-left", "0.5em").appendTo(message_div); + show_more_data_btn = $("<div/>").text("Show more").addClass("action-button").css({'padding-top': 0, 'padding-bottom':0}).appendTo(message_div); container_div.append(canvas); tile_element = container_div; // Set up actions for button. show_more_data_btn.click(function() { - // Mark data, tile as stale, request more data, and redraw track. - // HACK: get_data used will return object that can be marked as stale, but a better way to this is needed. - var cur_data = track.data_manager.get_data(tile.low, tile.high, tile.resolution); - cur_data.stale = true; + // Mark tile as stale, request more data, and redraw track. tile.stale = true; - track.data_manager.get_data(tile.low, tile.high, tile.resolution, {max_vals: cur_data.data.length * 2}); + track.data_manager.get_more_data(tile.low, tile.high, tile.resolution, {}, track.data_manager.DEEP_DATA_REQ); track.draw(); }).dblclick(function(e) { // Do not propogate as this would normal zoom in. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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