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

commit/galaxy-central: dan: Do not install Data Managers from the Tool Shed into the Tool Panel.
by Bitbucket 15 Feb '13

15 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2664d904641a/ changeset: 2664d904641a user: dan date: 2013-02-15 19:34:43 summary: Do not install Data Managers from the Tool Shed into the Tool Panel. affected #: 2 files diff -r 0c8763c8d52918ee15f83288d6d7cef153267239 -r 2664d904641abdc1ed6a2f972eb5aeefa8f93703 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -469,13 +469,14 @@ section_name = '' section_version = '' for tool_dict in tool_dicts: - guid = tool_dict[ 'guid' ] - tool_config = tool_dict[ 'tool_config' ] - tool_section_dict = dict( tool_config=tool_config, id=section_id, name=section_name, version=section_version ) - if guid in tool_panel_dict: - tool_panel_dict[ guid ].append( tool_section_dict ) - else: - tool_panel_dict[ guid ] = [ tool_section_dict ] + if tool_dict.get( 'add_to_tool_panel', True ): + guid = tool_dict[ 'guid' ] + tool_config = tool_dict[ 'tool_config' ] + tool_section_dict = dict( tool_config=tool_config, id=section_id, name=section_name, version=section_version ) + if guid in tool_panel_dict: + tool_panel_dict[ guid ].append( tool_section_dict ) + else: + tool_panel_dict[ guid ] = [ tool_section_dict ] return tool_panel_dict def generate_tool_panel_dict_for_tool_config( guid, tool_config, tool_sections=None ): """ diff -r 0c8763c8d52918ee15f83288d6d7cef153267239 -r 2664d904641abdc1ed6a2f972eb5aeefa8f93703 lib/galaxy/util/shed_util_common.py --- a/lib/galaxy/util/shed_util_common.py +++ b/lib/galaxy/util/shed_util_common.py @@ -1614,7 +1614,8 @@ tool_config=tool_config, tool_type=tool.tool_type, requirements=tool_requirements, - tests=tool_tests ) + tests=tool_tests, + add_to_tool_panel=tool.tool_type not in TOOL_TYPES_NOT_IN_TOOL_PANEL ) if 'tools' in metadata_dict: metadata_dict[ 'tools' ].append( tool_dict ) else: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Minor formating fix for 22f7938bfa33.
by Bitbucket 15 Feb '13

15 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0c8763c8d529/ changeset: 0c8763c8d529 user: dan date: 2013-02-15 19:19:30 summary: Minor formating fix for 22f7938bfa33. affected #: 1 file diff -r 22f7938bfa3331e1f4e03b67b85b1f9602fd1e85 -r 0c8763c8d52918ee15f83288d6d7cef153267239 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -705,7 +705,7 @@ new_install=True ) if 'data_manager' in metadata_dict: new_data_managers = shed_util.install_data_managers( trans.app, trans.app.config.shed_data_manager_config_file, metadata_dict, shed_config_dict, relative_install_dir, - tool_shed_repository, repository_tools_tups ) + tool_shed_repository, repository_tools_tups ) if 'datatypes' in metadata_dict: tool_shed_repository.status = trans.model.ToolShedRepository.installation_status.LOADING_PROPRIETARY_DATATYPES if not tool_shed_repository.includes_datatypes: 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: Handle Data Managers when reactivating a deactivated Tool Shed Repository.
by Bitbucket 15 Feb '13

15 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/22f7938bfa33/ changeset: 22f7938bfa33 user: dan date: 2013-02-15 19:18:00 summary: Handle Data Managers when reactivating a deactivated Tool Shed Repository. affected #: 2 files diff -r f53c0039c2c07979b54ce42d680aabbce3be1116 -r 22f7938bfa3331e1f4e03b67b85b1f9602fd1e85 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -42,6 +42,11 @@ shed_tool_conf, tool_panel_dict, new_install=False ) + if repository.includes_data_managers: + tp, data_manager_relative_install_dir = repository.get_tool_relative_path( trans.app ) + data_manager_relative_install_dir = os.path.join( data_manager_relative_install_dir, repository.name ) #hack to add repository.name here, which is actually the root of the installed repository + new_data_managers = install_data_managers( trans.app, trans.app.config.shed_data_manager_config_file, metadata, repository.get_shed_config_dict( trans.app ), data_manager_relative_install_dir, + repository, repository_tools_tups ) trans.sa_session.add( repository ) trans.sa_session.flush() if repository.includes_datatypes: diff -r f53c0039c2c07979b54ce42d680aabbce3be1116 -r 22f7938bfa3331e1f4e03b67b85b1f9602fd1e85 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -704,7 +704,7 @@ tool_panel_dict=tool_panel_dict, new_install=True ) if 'data_manager' in metadata_dict: - rval = shed_util.install_data_managers( trans.app, trans.app.config.shed_data_manager_config_file, metadata_dict, shed_config_dict, relative_install_dir, + new_data_managers = shed_util.install_data_managers( trans.app, trans.app.config.shed_data_manager_config_file, metadata_dict, shed_config_dict, relative_install_dir, tool_shed_repository, repository_tools_tups ) if 'datatypes' in metadata_dict: tool_shed_repository.status = trans.model.ToolShedRepository.installation_status.LOADING_PROPRIETARY_DATATYPES 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: Use strict equality operators.
by Bitbucket 15 Feb '13

15 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f53c0039c2c0/ changeset: f53c0039c2c0 user: jgoecks date: 2013-02-15 18:44:08 summary: Use strict equality operators. affected #: 1 file diff -r 8484a745317e5402e987401c85359e8c7a513445 -r f53c0039c2c07979b54ce42d680aabbce3be1116 static/scripts/viz/visualization.js --- a/static/scripts/viz/visualization.js +++ b/static/scripts/viz/visualization.js @@ -236,8 +236,8 @@ ready_deferred = $.Deferred(), // If requesting raw data, query dataset state; if requesting (converted) data, // need to query converted datasets state. - query_type = (this.get('data_type') == 'raw_data' ? 'state' : - this.get('data_type') == 'data' ? 'converted_datasets_state' : "error" ), + query_type = (this.get('data_type') === 'raw_data' ? 'state' : + this.get('data_type') === 'data' ? 'converted_datasets_state' : "error" ), ss_deferred = new util_mod.ServerStateDeferred({ ajax_settings: { url: this.get('dataset').url(), @@ -575,7 +575,7 @@ */ get_chrom_region: function(chr_name) { var chrom_info = _.find(this.get_chroms_info(), function(chrom_info) { - return chrom_info.chrom == chr_name; + return chrom_info.chrom === chr_name; }); return new GenomeRegion({ chrom: chrom_info.chrom, 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: Give Data Managers from Tool Sheds their own guid.
by Bitbucket 15 Feb '13

15 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8484a745317e/ changeset: 8484a745317e user: dan date: 2013-02-15 18:01:44 summary: Give Data Managers from Tool Sheds their own guid. affected #: 3 files diff -r ef0e9bf34c0b22dd355759478aa85fc2d46d49d4 -r 8484a745317e5402e987401c85359e8c7a513445 lib/galaxy/tools/data_manager/manager.py --- a/lib/galaxy/tools/data_manager/manager.py +++ b/lib/galaxy/tools/data_manager/manager.py @@ -64,31 +64,38 @@ self.managed_data_tables[ data_table_name ].append( data_manager ) def get_manager( self, *args, **kwds ): return self.data_managers.get( *args, **kwds ) - def remove_manager( self, manager_id ): - data_manager = self.get_manager( manager_id, None ) - if data_manager is not None: - del self.data_managers[ manager_id ] - #remove tool from toolbox - if data_manager.tool: - self.app.toolbox.remove_tool_by_id( data_manager.tool.id ) - #determine if any data_tables are no longer tracked - for data_table_name in data_manager.data_tables.keys(): - remove_data_table_tracking = True - for other_data_manager in self.data_managers.itervalues(): - if data_table_name in other_data_manager.data_tables: - remove_data_table_tracking = False - break - if remove_data_table_tracking and data_table_name in self.managed_data_tables: - del self.managed_data_tables[ data_table_name ] + def remove_manager( self, manager_ids ): + if not isinstance( manager_ids, list ): + manager_ids = [ manager_ids ] + for manager_id in manager_ids: + data_manager = self.get_manager( manager_id, None ) + if data_manager is not None: + del self.data_managers[ manager_id ] + #remove tool from toolbox + if data_manager.tool: + self.app.toolbox.remove_tool_by_id( data_manager.tool.id ) + #determine if any data_tables are no longer tracked + for data_table_name in data_manager.data_tables.keys(): + remove_data_table_tracking = True + for other_data_manager in self.data_managers.itervalues(): + if data_table_name in other_data_manager.data_tables: + remove_data_table_tracking = False + break + if remove_data_table_tracking and data_table_name in self.managed_data_tables: + del self.managed_data_tables[ data_table_name ] class DataManager( object ): + GUID_TYPE = 'data_manager' + DEFAULT_VERSION = "0.0.1" + def __init__( self, data_managers, elem=None, tool_path=None ): self.data_managers = data_managers self.declared_id = None self.name = None self.description = None + self.version = self.DEFAULT_VERSION + self.guid = None self.tool = None - self.tool_guid = None self.data_tables = odict() self.output_ref_by_data_table = {} self.move_by_data_table_column = {} @@ -98,12 +105,14 @@ def load_from_element( self, elem, tool_path ): assert elem.tag == 'data_manager', 'A data manager configuration must have a "data_manager" tag as the root. "%s" is present' % ( root.tag ) self.declared_id = elem.get( 'id', None ) + self.guid = elem.get( 'guid', None ) path = elem.get( 'tool_file', None ) + tool_guid = None if path is None: tool_elem = elem.find( 'tool' ) assert tool_elem is not None, "Error loading tool for data manager. Make sure that a tool_file attribute or a tool tag set has been defined:\n%s" % ( util.xml_to_string( elem ) ) path = tool_elem.get( "file", None ) - self.tool_guid = tool_elem.get( "guid", None ) + tool_guid = tool_elem.get( "guid", None ) #use shed_conf_file to determine tool_path shed_conf_file = elem.get( "shed_conf_file", None ) if shed_conf_file: @@ -111,7 +120,7 @@ if shed_conf: tool_path = shed_conf.get( "tool_path", tool_path ) assert path is not None, "A tool file path could not be determined:\n%s" % ( util.xml_to_string( elem ) ) - self.load_tool( os.path.join( tool_path, path ), guid=self.tool_guid, data_manager_id=self.id ) + self.load_tool( os.path.join( tool_path, path ), guid=tool_guid, data_manager_id=self.id ) self.name = elem.get( 'name', self.tool.name ) self.description = elem.get( 'description', self.tool.description ) @@ -164,7 +173,7 @@ self.move_by_data_table_column[ data_table_name ][ data_table_coumn_name ] = dict( type=move_type, source_base=source_base, source_value=source_value, target_base=target_base, target_value=target_value, relativize_symlinks=relativize_symlinks ) @property def id( self ): - return self.tool_guid or self.declared_id #if we have a tool with a guid, we will use that as the tool_manager id + return self.guid or self.declared_id #if we have a guid, we will use that as the data_manager id def load_tool( self, tool_filename, guid=None, data_manager_id=None ): tool = self.data_managers.app.toolbox.load_tool( tool_filename, guid=guid, data_manager_id=data_manager_id ) self.data_managers.app.toolbox.data_manager_tools[ tool.id ] = tool diff -r ef0e9bf34c0b22dd355759478aa85fc2d46d49d4 -r 8484a745317e5402e987401c85359e8c7a513445 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -1194,7 +1194,11 @@ if data_manager_dict is None: log.error( "Data manager metadata is not defined properly for '%s'." % ( data_manager_id ) ) continue - + guid = data_manager_dict.get( 'guid', None ) + if guid is None: + log.error( "Data manager guid '%s' is not set in metadata for '%s'." % ( guid, data_manager_id ) ) + continue + elem.set( 'guid', guid ) tool_guid = data_manager_dict.get( 'tool_guid', None ) if tool_guid is None: log.error( "Data manager tool guid '%s' is not set in metadata for '%s'." % ( tool_guid, data_manager_id ) ) @@ -1510,27 +1514,18 @@ def remove_from_data_manager( app, repository ): metadata_dict = repository.metadata if metadata_dict and 'data_manager' in metadata_dict: - data_manager_tool_guids = [ data_manager_dict.get( 'tool_guid' ) for data_manager_dict in metadata_dict.get( 'data_manager', {} ).get( 'data_managers', {} ).itervalues() if 'tool_guid' in data_manager_dict ] shed_data_manager_conf_filename = app.config.shed_data_manager_config_file tree = util.parse_xml( shed_data_manager_conf_filename ) root = tree.getroot() assert root.tag == 'data_managers', 'The file provided (%s) for removing data managers from is not a valid data manager xml file.' % ( shed_data_manager_conf_filename ) + guids = [ data_manager_dict.get( 'guid' ) for data_manager_dict in metadata_dict.get( 'data_manager', {} ).get( 'data_managers', {} ).itervalues() if 'guid' in data_manager_dict ] config_elems = [] for elem in root: - keep_elem = True - if elem.tag == 'data_manager': - tool_elem = elem.find( 'tool' ) - if tool_elem is not None: - tool_guid = tool_elem.get( 'guid', None ) - if tool_guid in data_manager_tool_guids: - keep_elem = False - if keep_elem: + if elem.tag != 'data_manager' or elem.get( 'guid', None ) not in guids: config_elems.append( elem ) - #remove data manager from in memory - for data_manager_tool_guids in data_manager_tool_guids: - #for shed-based data managers, the data_manager id is the same as the tool guid - app.data_managers.remove_manager( data_manager_tool_guids ) - # Persist the altered shed_tool_config file. + #remove data managers from in memory + app.data_managers.remove_manager( guids ) + # Persist the altered shed_data_manager_config file. suc.data_manager_config_elems_to_xml_file( app, config_elems, shed_data_manager_conf_filename ) def remove_from_shed_tool_config( trans, shed_tool_conf_dict, guids_to_remove ): # A tool shed repository is being uninstalled so change the shed_tool_conf file. Parse the config file to generate the entire list diff -r ef0e9bf34c0b22dd355759478aa85fc2d46d49d4 -r 8484a745317e5402e987401c85359e8c7a513445 lib/galaxy/util/shed_util_common.py --- a/lib/galaxy/util/shed_util_common.py +++ b/lib/galaxy/util/shed_util_common.py @@ -13,6 +13,7 @@ import sqlalchemy.orm.exc from galaxy.tools.parameters import dynamic_options from galaxy.tool_shed import encoding_util +from galaxy.tools.data_manager.manager import DataManager from galaxy import eggs import pkg_resources @@ -1012,7 +1013,7 @@ def generate_clone_url_for_repository_in_tool_shed( trans, repository ): """Generate the URL for cloning a repository that is in the tool shed.""" base_url = url_for( '/', qualified=True ).rstrip( '/' ) - if trans.user: + if trans and trans.user: protocol, base = base_url.split( '://' ) username = '%s@' % trans.user.username return '%s://%s%s/repos/%s/%s' % ( protocol, username, base, repository.user.username, repository.name ) @@ -1038,10 +1039,14 @@ tools[tool_conf_name] = tool repo_path = repository.repo_path( app ) try: + #Galaxy Side repo_files_directory = repository.repo_files_directory( app ) repo_dir = repo_files_directory + repository_clone_url = generate_clone_url_for_installed_repository( app, repository ) except AttributeError: + #Tool Shed side repo_files_directory = repo_path + repository_clone_url = generate_clone_url_for_repository_in_tool_shed( None, repository ) relative_data_manager_dir = util.relpath( os.path.split( data_manager_config_filename )[0], repo_dir ) rel_data_manager_config_filename = os.path.join( relative_data_manager_dir, os.path.split( data_manager_config_filename )[1] ) data_managers = {} @@ -1057,6 +1062,8 @@ if data_manager_id is None: log.error( 'Data Manager entry is missing id attribute in "%s".' % ( data_manager_config_filename ) ) continue + version = data_manager_elem.get( 'version', DataManager.DEFAULT_VERSION ) + guid = generate_guid_for_object( repository_clone_url, DataManager.GUID_TYPE, data_manager_id, version ) data_tables = [] if tool_file is None: log.error( 'Data Manager entry is missing tool_file attribute in "%s".' % ( data_manager_config_filename ) ) @@ -1073,7 +1080,7 @@ if tool is None: log.error( "Unable to determine tools metadata for '%s'." % ( data_manager_metadata_tool_file ) ) continue - data_managers[ data_manager_id ] = { 'tool_config_file': data_manager_metadata_tool_file, 'data_tables': data_tables, 'tool_guid': tool['guid'] } + data_managers[ data_manager_id ] = { 'guid': guid, 'version': version, 'tool_config_file': data_manager_metadata_tool_file, 'data_tables': data_tables, 'tool_guid': tool['guid'] } log.debug( 'Loaded Data Manager tool_files: %s' % ( tool_file ) ) return metadata_dict def generate_datatypes_metadata( datatypes_config, metadata_dict ): @@ -1555,6 +1562,9 @@ version_elem = SubElement( tool_elem, 'version' ) version_elem.text = tool.version return tool_elem +def generate_guid_for_object( repository_clone_url, guid_type, obj_id, version ): + tmp_url = clean_repository_clone_url( repository_clone_url ) + return '%s/%s/%s/%s' % ( tmp_url, guid_type, obj_id, version ) def generate_tool_guid( repository_clone_url, tool ): """ Generate a guid for the installed tool. It is critical that this guid matches the guid for 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: Add missing Data Manager controller.
by Bitbucket 15 Feb '13

15 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ef0e9bf34c0b/ changeset: ef0e9bf34c0b user: dan date: 2013-02-15 17:58:29 summary: Add missing Data Manager controller. affected #: 1 file diff -r d04aa3ad613211d3c88f1daa7e5a9df4d1233597 -r ef0e9bf34c0b22dd355759478aa85fc2d46d49d4 lib/galaxy/webapps/galaxy/controllers/data_manager.py --- /dev/null +++ b/lib/galaxy/webapps/galaxy/controllers/data_manager.py @@ -0,0 +1,79 @@ +from galaxy import web +from galaxy.web.base.controller import BaseUIController +from galaxy.util.json import from_json_string + +import pkg_resources; +pkg_resources.require( "Paste" ) +import paste.httpexceptions + +#set up logger +import logging +log = logging.getLogger( __name__ ) + +class DataManager( BaseUIController ): + + @web.expose + def index( self, trans, **kwd ): + not_is_admin = not trans.user_is_admin() + if not_is_admin and not trans.app.config.enable_data_manager_user_view: + raise paste.httpexceptions.HTTPUnauthorized( "This Galaxy instance is not configured to allow non-admins to view the data manager." ) + message = kwd.get( 'message' ) + status = kwd.get( 'status', 'info' ) + return trans.fill_template( "data_manager/index.mako", data_managers=trans.app.data_managers, view_only=not_is_admin, message=message, status=status ) + + @web.expose + def manage_data_manager( self, trans, **kwd ): + not_is_admin = not trans.user_is_admin() + if not_is_admin and not trans.app.config.enable_data_manager_user_view: + raise paste.httpexceptions.HTTPUnauthorized( "This Galaxy instance is not configured to allow non-admins to view the data manager." ) + message = kwd.get( 'message' ) + status = kwd.get( 'status', 'info' ) + data_manager_id = kwd.get( 'id', None ) + data_manager = trans.app.data_managers.get_manager( data_manager_id ) + if data_manager is None: + return trans.response.send_redirect( web.url_for( controller="data_manager", action="index", message="Invalid Data Manager (%s) was requested" % data_manager_id, status="error" ) ) + jobs = reversed( [ assoc.job for assoc in trans.sa_session.query( trans.app.model.DataManagerJobAssociation ).filter_by( data_manager_id=data_manager_id ) ] ) + return trans.fill_template( "data_manager/manage_data_manager.mako", data_manager=data_manager, jobs=jobs, view_only=not_is_admin, message=message, status=status ) + + @web.expose + def view_job( self, trans, **kwd ): + not_is_admin = not trans.user_is_admin() + if not_is_admin and not trans.app.config.enable_data_manager_user_view: + raise paste.httpexceptions.HTTPUnauthorized( "This Galaxy instance is not configured to allow non-admins to view the data manager." ) + message = kwd.get( 'message' ) + status = kwd.get( 'status', 'info' ) + job_id = kwd.get( 'id', None ) + try: + job_id = trans.security.decode_id( job_id ) + job = trans.app.model.Job.get( job_id ) + except Exception, e: + job = None + log.error( "Bad job id (%s) passed to view_job: %s" % ( job_id, e ) ) + if not job: + return trans.response.send_redirect( web.url_for( controller="data_manager", action="index",message="Invalid job (%s) was requested" % job_id, status="error" ) ) + data_manager_id = job.data_manager_association.data_manager_id + data_manager = trans.app.data_managers.get_manager( data_manager_id ) + hdas = [ assoc.dataset for assoc in job.get_output_datasets() ] + data_manager_output = [] + for hda in hdas: + data_manager_json = from_json_string( open( hda.get_file_name() ).read() ) + values = [] + for key, value in data_manager_json.get( 'data_tables', {} ).iteritems(): + values.append( ( key, value ) ) + data_manager_output.append( values ) + return trans.fill_template( "data_manager/view_job.mako", data_manager=data_manager, job=job, view_only=not_is_admin, hdas=hdas, data_manager_output=data_manager_output, message=message, status=status ) + + @web.expose + def manage_data_table( self, trans, **kwd ): + not_is_admin = not trans.user_is_admin() + if not_is_admin and not trans.app.config.enable_data_manager_user_view: + raise paste.httpexceptions.HTTPUnauthorized( "This Galaxy instance is not configured to allow non-admins to view the data manager." ) + message = kwd.get( 'message' ) + status = kwd.get( 'status', 'info' ) + data_table_name = kwd.get( 'table_name', None ) + if not data_table_name: + return trans.response.send_redirect( web.url_for( controller="data_manager", action="index" ) ) + data_table = trans.app.tool_data_tables.get( data_table_name, None ) + if data_table is None: + return trans.response.send_redirect( web.url_for( controller="data_manager", action="index", message="Invalid Data table (%s) was requested" % data_table_name, status="error" ) ) + return trans.fill_template( "data_manager/manage_data_table.mako", data_table=data_table, view_only=not_is_admin, message=message, status=status ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: inithello: Enhance tool shed functional tests to be more informative when errors occur.
by Bitbucket 15 Feb '13

15 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d04aa3ad6132/ changeset: d04aa3ad6132 user: inithello date: 2013-02-15 17:42:19 summary: Enhance tool shed functional tests to be more informative when errors occur. affected #: 23 files diff -r 359f6fbcde82bbf8aa1d4b932a54882f86121d71 -r d04aa3ad613211d3c88f1daa7e5a9df4d1233597 test/tool_shed/base/twilltestcase.py --- a/test/tool_shed/base/twilltestcase.py +++ b/test/tool_shed/base/twilltestcase.py @@ -941,7 +941,10 @@ for data_table in data_tables: if 'name' in table_elem.attrib and table_elem.attrib[ 'name' ] == data_table: file_elem = table_elem.find( 'file' ) - assert os.path.exists( file_elem.attrib[ 'path' ] ), 'Tool data table file %s not found.' % file_elem.path + file_path = file_elem.get( 'path', None ) + full_path = os.path.join( self.tool_data_path, file_path ) + assert file_path is not None, 'No file path configured for this data table.' + assert os.path.exists( full_path ), 'Tool data table file %s not found.' % full_path found = True break assert found, 'No entry for %s in %s.' % ( data_table, self.shed_tool_data_table_conf ) diff -r 359f6fbcde82bbf8aa1d4b932a54882f86121d71 -r d04aa3ad613211d3c88f1daa7e5a9df4d1233597 test/tool_shed/functional/test_0000_basic_repository_features.py --- a/test/tool_shed/functional/test_0000_basic_repository_features.py +++ b/test/tool_shed/functional/test_0000_basic_repository_features.py @@ -83,7 +83,9 @@ repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) self.logout() self.login( email=common.admin_email, username=common.admin_username ) - self.set_repository_malicious( repository, set_malicious=True, strings_displayed=[ 'The repository tip has been defined as malicious.' ] ) + self.set_repository_malicious( repository, + set_malicious=True, + strings_displayed=[ 'The repository tip has been defined as malicious.' ] ) self.set_repository_malicious( repository, set_malicious=False, strings_displayed=[ 'The repository tip has been defined as not malicious.' ] ) @@ -92,8 +94,8 @@ self.set_repository_deprecated( repository, strings_displayed=[ 'has been marked as deprecated', 'Mark as not deprecated' ] ) self.display_manage_repository_page( repository, - strings_displayed=[ 'This repository has been marked as deprecated' ], - strings_not_displayed=[ 'Upload files', 'Reset all repository metadata' ] ) + strings_displayed=[ 'This repository has been marked as deprecated' ], + strings_not_displayed=[ 'Upload files', 'Reset all repository metadata' ] ) self.browse_repository( repository, strings_not_displayed=[ 'Upload files' ] ) self.set_repository_deprecated( repository, strings_displayed=[ 'has been marked as not deprecated', 'Mark as deprecated' ], @@ -197,16 +199,18 @@ def test_0090_verify_reserved_repository_name_handling( self ): '''Check that reserved repository names are handled correctly.''' category = test_db_util.get_category_by_name( 'Test 0000 Basic Repository Features 1' ) + error_message = 'The term repos is a reserved word in the tool shed, so it cannot be used as a repository name.' self.get_or_create_repository( name='repos', description=repository_description, long_description=repository_long_description, owner=common.test_user_1_name, category_id=self.security.encode_id( category.id ), - strings_displayed=[ 'The term repos is a reserved word in the tool shed, so it cannot be used as a repository name.' ] ) + strings_displayed=[ error_message ] ) def test_0100_verify_reserved_username_handling( self ): '''Check that reserved usernames are handled correctly.''' self.logout() self.login( email='baduser(a)bx.psu.edu', username='repos' ) test_user_1 = test_db_util.get_user( 'baduser(a)bx.psu.edu' ) assert test_user_1 is None, 'Creating user with public name "repos" succeeded.' - self.check_for_strings( strings_displayed=[ 'The term repos is a reserved word in the tool shed, so it cannot be used as a public user name.' ] ) + error_message = 'The term repos is a reserved word in the tool shed, so it cannot be used as a public user name.' + self.check_for_strings( strings_displayed=[ error_message ] ) diff -r 359f6fbcde82bbf8aa1d4b932a54882f86121d71 -r d04aa3ad613211d3c88f1daa7e5a9df4d1233597 test/tool_shed/functional/test_0020_basic_repository_dependencies.py --- a/test/tool_shed/functional/test_0020_basic_repository_dependencies.py +++ b/test/tool_shed/functional/test_0020_basic_repository_dependencies.py @@ -6,8 +6,8 @@ datatypes_repository_long_description = "Galaxy applicable data formats used by Emboss tools. This repository contains no tools." emboss_repository_name = 'emboss_0020' -emboss_repository_description = 'Galaxy wrappers for Emboss version 5.0.0 tools' -emboss_repository_long_description = 'Galaxy wrappers for Emboss version 5.0.0 tools' +emboss_repository_description = 'Galaxy wrappers for Emboss version 5.0.0 tools for test 0020' +emboss_repository_long_description = 'Galaxy wrappers for Emboss version 5.0.0 tools for test 0020' class TestBasicRepositoryDependencies( ShedTwillTestCase ): '''Testing emboss 5 with repository dependencies.''' @@ -93,8 +93,8 @@ 'emboss', '5.0.0', 'package', - datatypes_repository_name, - common.test_user_1_name, + 'emboss_datatypes_0020', + 'user1', changeset_revision, 'Repository dependencies' ] self.display_manage_repository_page( repository, strings_displayed=strings_displayed ) diff -r 359f6fbcde82bbf8aa1d4b932a54882f86121d71 -r d04aa3ad613211d3c88f1daa7e5a9df4d1233597 test/tool_shed/functional/test_0030_repository_dependency_revisions.py --- a/test/tool_shed/functional/test_0030_repository_dependency_revisions.py +++ b/test/tool_shed/functional/test_0030_repository_dependency_revisions.py @@ -1,6 +1,7 @@ from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os import tool_shed.base.test_db_util as test_db_util - +import logging +log = logging.getLogger(__name__) datatypes_repository_name = 'emboss_datatypes_0030' datatypes_repository_description = "Galaxy applicable data formats used by Emboss tools." datatypes_repository_long_description = "Galaxy applicable data formats used by Emboss tools. This repository contains no tools." @@ -8,8 +9,8 @@ emboss_repository_name = 'emboss_0030' emboss_5_repository_name = 'emboss_5_0030' emboss_6_repository_name = 'emboss_6_0030' -emboss_repository_description = 'Galaxy wrappers for Emboss version 5.0.0 tools' -emboss_repository_long_description = 'Galaxy wrappers for Emboss version 5.0.0 tools' +emboss_repository_description = 'Galaxy wrappers for Emboss version 5.0.0 tools for test 0030' +emboss_repository_long_description = 'Galaxy wrappers for Emboss version 5.0.0 tools for test 0030' class TestRepositoryDependencyRevisions( ShedTwillTestCase ): '''Test dependencies on different revisions of a repository.''' @@ -91,10 +92,10 @@ self.login( email=common.test_user_1_email, username=common.test_user_1_name ) category = test_db_util.get_category_by_name( 'Test 0030 Repository Dependency Revisions' ) repository = self.get_or_create_repository( name=emboss_repository_name, - description=emboss_repository_description, - long_description=emboss_repository_long_description, - owner=common.test_user_1_name, - category_id=self.security.encode_id( category.id ) ) + description=emboss_repository_description, + long_description=emboss_repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ) ) self.upload_file( repository, filename='emboss/emboss.tar', filepath=None, @@ -175,14 +176,8 @@ datatypes_tip = self.get_repository_tip( datatypes_repository ) # Iterate through all metadata revisions and check for repository dependencies. for metadata, changeset_revision in repository_metadata: - strings_displayed = [ str( metadata_elem ) for metadata_elem in metadata[ 'repository_dependencies' ][ 'repository_dependencies' ][ 0 ] ] - # Remove the tool shed URL, because that's not displayed on the page (yet?) - strings_displayed.pop( strings_displayed.index( self.url ) ) # Add the dependency description and datatypes repository details to the strings to check. - strings_displayed.extend( [ metadata[ 'repository_dependencies' ][ 'description' ], - datatypes_repository_name, - datatypes_repository.user.username, - datatypes_tip ] ) + strings_displayed.extend( [ 'Emboss requires the Emboss', 'emboss_datatypes_0030', 'user1', datatypes_tip ] ) strings_displayed.extend( [ 'Tool dependencies', 'emboss', '5.0.0', 'package' ] ) self.display_manage_repository_page( repository, changeset_revision=changeset_revision, diff -r 359f6fbcde82bbf8aa1d4b932a54882f86121d71 -r d04aa3ad613211d3c88f1daa7e5a9df4d1233597 test/tool_shed/functional/test_0040_repository_circular_dependencies.py --- a/test/tool_shed/functional/test_0040_repository_circular_dependencies.py +++ b/test/tool_shed/functional/test_0040_repository_circular_dependencies.py @@ -2,12 +2,12 @@ import tool_shed.base.test_db_util as test_db_util freebayes_repository_name = 'freebayes_0040' -freebayes_repository_description = "Galaxy's freebayes tool" -freebayes_repository_long_description = "Long description of Galaxy's freebayes tool" +freebayes_repository_description = "Galaxy's freebayes tool for test 0040" +freebayes_repository_long_description = "Long description of Galaxy's freebayes tool for test 0040" filtering_repository_name = 'filtering_0040' -filtering_repository_description = "Galaxy's filtering tool" -filtering_repository_long_description = "Long description of Galaxy's filtering tool" +filtering_repository_description = "Galaxy's filtering tool for test 0040" +filtering_repository_long_description = "Long description of Galaxy's filtering tool for test 0040" class TestRepositoryCircularDependencies( ShedTwillTestCase ): '''Verify that the code correctly displays repositories with circular repository dependencies.''' diff -r 359f6fbcde82bbf8aa1d4b932a54882f86121d71 -r d04aa3ad613211d3c88f1daa7e5a9df4d1233597 test/tool_shed/functional/test_0400_repository_component_reviews.py --- a/test/tool_shed/functional/test_0400_repository_component_reviews.py +++ b/test/tool_shed/functional/test_0400_repository_component_reviews.py @@ -474,7 +474,7 @@ valid_tools_only=True, uncompress_file=True, remove_repo_files_not_in_tar=False, - commit_message='Uploaded filtering 1.1.0 tarball.', + commit_message='Uploaded filtering test data.', strings_displayed=[], strings_not_displayed=[] ) def test_0110_review_new_changeset_functional_tests( self ): diff -r 359f6fbcde82bbf8aa1d4b932a54882f86121d71 -r d04aa3ad613211d3c88f1daa7e5a9df4d1233597 test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py --- a/test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py +++ b/test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py @@ -111,10 +111,10 @@ install_tool_dependencies=False, new_tool_panel_section='test_1010' ) installed_repository = test_db_util.get_installed_repository_by_name_owner( repository_name, common.test_user_1_name ) - strings_displayed = [ installed_repository.name, - installed_repository.description, - installed_repository.owner, - installed_repository.tool_shed, + strings_displayed = [ 'freebayes_0010', + "Galaxy's freebayes tool", + 'user1', + self.url.replace( 'http://', '' ), installed_repository.installed_changeset_revision ] self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed ) self.display_installed_repository_manage_page( installed_repository, diff -r 359f6fbcde82bbf8aa1d4b932a54882f86121d71 -r d04aa3ad613211d3c88f1daa7e5a9df4d1233597 test/tool_shed/functional/test_1020_install_repository_with_repository_dependencies.py --- a/test/tool_shed/functional/test_1020_install_repository_with_repository_dependencies.py +++ b/test/tool_shed/functional/test_1020_install_repository_with_repository_dependencies.py @@ -6,8 +6,8 @@ datatypes_repository_long_description = "Galaxy applicable data formats used by Emboss tools. This repository contains no tools." emboss_repository_name = 'emboss_0020' -emboss_repository_description = 'Galaxy wrappers for Emboss version 5.0.0 tools' -emboss_repository_long_description = 'Galaxy wrappers for Emboss version 5.0.0 tools' +emboss_repository_description = 'Galaxy wrappers for Emboss version 5.0.0 tools for test 0020' +emboss_repository_long_description = 'Galaxy wrappers for Emboss version 5.0.0 tools for test 0020' base_datatypes_count = 0 repository_datatypes_count = 0 @@ -103,10 +103,10 @@ install_tool_dependencies=False, new_tool_panel_section='test_1020' ) installed_repository = test_db_util.get_installed_repository_by_name_owner( 'emboss_0020', common.test_user_1_name ) - strings_displayed = [ installed_repository.name, - installed_repository.description, - installed_repository.owner, - installed_repository.tool_shed, + strings_displayed = [ 'emboss_0020', + 'Galaxy wrappers for Emboss version 5.0.0 tools for test 0020', + 'user1', + self.url.replace( 'http://', '' ), installed_repository.installed_changeset_revision ] self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed ) self.display_installed_repository_manage_page( installed_repository, diff -r 359f6fbcde82bbf8aa1d4b932a54882f86121d71 -r d04aa3ad613211d3c88f1daa7e5a9df4d1233597 test/tool_shed/functional/test_1030_install_repository_with_dependency_revisions.py --- a/test/tool_shed/functional/test_1030_install_repository_with_dependency_revisions.py +++ b/test/tool_shed/functional/test_1030_install_repository_with_dependency_revisions.py @@ -8,8 +8,8 @@ emboss_repository_name = 'emboss_0030' emboss_5_repository_name = 'emboss_5_0030' emboss_6_repository_name = 'emboss_6_0030' -emboss_repository_description = 'Galaxy wrappers for Emboss version 5.0.0 tools' -emboss_repository_long_description = 'Galaxy wrappers for Emboss version 5.0.0 tools' +emboss_repository_description = 'Galaxy wrappers for Emboss version 5.0.0 tools for test 0030' +emboss_repository_long_description = 'Galaxy wrappers for Emboss version 5.0.0 tools for test 0030' base_datatypes_count = 0 repository_datatypes_count = 0 @@ -173,8 +173,8 @@ install_tool_dependencies=False, new_tool_panel_section='test_1030' ) installed_repository = test_db_util.get_installed_repository_by_name_owner( 'emboss_0030', common.test_user_1_name ) - strings_displayed = [ installed_repository.name, - installed_repository.description, + strings_displayed = [ 'emboss_0030', + 'Galaxy wrappers for Emboss version 5.0.0 tools for test 0030', installed_repository.owner, installed_repository.tool_shed, installed_repository.installed_changeset_revision ] diff -r 359f6fbcde82bbf8aa1d4b932a54882f86121d71 -r d04aa3ad613211d3c88f1daa7e5a9df4d1233597 test/tool_shed/functional/test_1040_install_repository_basic_circular_dependencies.py --- a/test/tool_shed/functional/test_1040_install_repository_basic_circular_dependencies.py +++ b/test/tool_shed/functional/test_1040_install_repository_basic_circular_dependencies.py @@ -2,12 +2,12 @@ import tool_shed.base.test_db_util as test_db_util freebayes_repository_name = 'freebayes_0040' -freebayes_repository_description = "Galaxy's freebayes tool" -freebayes_repository_long_description = "Long description of Galaxy's freebayes tool" +freebayes_repository_description = "Galaxy's freebayes tool for test 0040" +freebayes_repository_long_description = "Long description of Galaxy's freebayes tool for test 0040" filtering_repository_name = 'filtering_0040' -filtering_repository_description = "Galaxy's filtering tool" -filtering_repository_long_description = "Long description of Galaxy's filtering tool" +filtering_repository_description = "Galaxy's filtering tool for test 0040" +filtering_repository_long_description = "Long description of Galaxy's filtering tool for test 0040" category_name = 'test_0040_repository_circular_dependencies' @@ -164,6 +164,6 @@ self.check_galaxy_repository_tool_panel_section( installed_freebayes_repository, 'freebayes' ) strings_displayed = [ 'Missing repository', 'freebayes' ] self.display_installed_repository_manage_page( installed_filtering_repository, strings_displayed=strings_displayed ) - self.check_galaxy_repository_db_status( freebayes_repository_name, - common.test_user_1_name, + self.check_galaxy_repository_db_status( 'freebayes_0040', + 'user1', 'Uninstalled' ) diff -r 359f6fbcde82bbf8aa1d4b932a54882f86121d71 -r d04aa3ad613211d3c88f1daa7e5a9df4d1233597 test/tool_shed/functional/test_1050_circular_dependencies_4_levels.py --- a/test/tool_shed/functional/test_1050_circular_dependencies_4_levels.py +++ b/test/tool_shed/functional/test_1050_circular_dependencies_4_levels.py @@ -343,9 +343,9 @@ assert original_datatypes < self.get_datatypes_count(), 'Installing a repository that depends on emboss_datatypes did not add datatypes.' emboss_repository = test_db_util.get_installed_repository_by_name_owner( emboss_repository_name, common.test_user_1_name ) datatypes_repository = test_db_util.get_installed_repository_by_name_owner( emboss_datatypes_repository_name, common.test_user_1_name ) - strings_displayed = [ emboss_repository.name, + strings_displayed = [ 'emboss_0050', + 'emboss_datatypes_0050', emboss_repository.installed_changeset_revision, - datatypes_repository.name, datatypes_repository.installed_changeset_revision ] self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed ) # Installing freebayes should automatically reinstall emboss and reactivate emboss_datatypes. diff -r 359f6fbcde82bbf8aa1d4b932a54882f86121d71 -r d04aa3ad613211d3c88f1daa7e5a9df4d1233597 test/tool_shed/functional/test_1060_install_repository_with_workflow.py --- a/test/tool_shed/functional/test_1060_install_repository_with_workflow.py +++ b/test/tool_shed/functional/test_1060_install_repository_with_workflow.py @@ -84,6 +84,6 @@ workflow_name, strings_displayed=[ '#EBD9B2' ], strings_not_displayed=[ '#EBBCB2' ] ) - self.display_all_workflows( strings_not_displayed=[ workflow_name ] ) + self.display_all_workflows( strings_not_displayed=[ 'Workflow for 0060_filter_workflow_repository' ] ) self.import_workflow( installed_repository, workflow_name ) - self.display_all_workflows( strings_displayed=[ workflow_name ] ) + self.display_all_workflows( strings_displayed=[ 'Workflow for 0060_filter_workflow_repository' ] ) diff -r 359f6fbcde82bbf8aa1d4b932a54882f86121d71 -r d04aa3ad613211d3c88f1daa7e5a9df4d1233597 test/tool_shed/functional/test_1070_invalid_tool.py --- a/test/tool_shed/functional/test_1070_invalid_tool.py +++ b/test/tool_shed/functional/test_1070_invalid_tool.py @@ -73,10 +73,10 @@ install_tool_dependencies=False, new_tool_panel_section='test_1070' ) installed_repository = test_db_util.get_installed_repository_by_name_owner( repository_name, common.test_user_1_name ) - strings_displayed = [ installed_repository.name, - installed_repository.description, - installed_repository.owner, - installed_repository.tool_shed, + strings_displayed = [ 'bismark_0070', + "Galaxy's bismark wrapper", + 'user1', + self.url.replace( 'http://', '' ), installed_repository.installed_changeset_revision ] self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed ) self.display_installed_repository_manage_page( installed_repository, diff -r 359f6fbcde82bbf8aa1d4b932a54882f86121d71 -r d04aa3ad613211d3c88f1daa7e5a9df4d1233597 test/tool_shed/functional/test_1080_advanced_circular_dependency_installation.py --- a/test/tool_shed/functional/test_1080_advanced_circular_dependency_installation.py +++ b/test/tool_shed/functional/test_1080_advanced_circular_dependency_installation.py @@ -131,15 +131,15 @@ common.test_user_1_name ) installed_column_repository = test_db_util.get_installed_repository_by_name_owner( column_repository_name, common.test_user_1_name ) - browse_strings_displayed = [ installed_convert_repository.name, - installed_convert_repository.description, - installed_convert_repository.tool_shed, + browse_strings_displayed = [ 'convert_chars_0080', + 'Convert delimiters', + self.url.replace( 'http://', '' ), installed_convert_repository.installed_changeset_revision ] - strings_displayed = [ installed_convert_repository.name, - installed_convert_repository.description, - installed_convert_repository.tool_shed, + strings_displayed = [ 'convert_chars_0080', + 'Convert delimiters', + self.url.replace( 'http://', '' ), installed_convert_repository.installed_changeset_revision, - installed_column_repository.name, + 'column_maker_0080', installed_column_repository.installed_changeset_revision, 'Missing repository dependencies' ] self.display_galaxy_browse_repositories_page( strings_displayed=browse_strings_displayed ) @@ -157,18 +157,18 @@ common.test_user_1_name ) installed_column_repository = test_db_util.get_installed_repository_by_name_owner( column_repository_name, common.test_user_1_name ) - browse_strings_displayed = [ installed_convert_repository.name, - installed_convert_repository.description, - installed_convert_repository.tool_shed, + browse_strings_displayed = [ 'convert_chars_0080', + 'Convert delimiters', + self.url.replace( 'http://', '' ), installed_convert_repository.installed_changeset_revision, - installed_column_repository.name, - installed_column_repository.description, + 'column_maker_0080', + 'Add column', installed_column_repository.installed_changeset_revision ] - strings_displayed = [ installed_column_repository.name, - installed_column_repository.description, - installed_column_repository.tool_shed, + strings_displayed = [ 'column_maker_0080', + 'Add column', + self.url.replace( 'http://', '' ), installed_column_repository.installed_changeset_revision, - installed_convert_repository.name, + 'convert_chars_0080', installed_convert_repository.installed_changeset_revision, 'Installed repository dependencies' ] self.display_galaxy_browse_repositories_page( strings_displayed=browse_strings_displayed ) @@ -181,11 +181,11 @@ installed_column_repository = test_db_util.get_installed_repository_by_name_owner( column_repository_name, common.test_user_1_name ) self.uninstall_repository( installed_convert_repository, remove_from_disk=False ) - strings_displayed = [ installed_column_repository.name, - installed_column_repository.description, - installed_column_repository.tool_shed, + strings_displayed = [ 'column_maker_0080', + 'Add column', + self.url.replace( 'http://', '' ), installed_column_repository.installed_changeset_revision, - installed_convert_repository.name, + 'convert_chars_0080', installed_convert_repository.installed_changeset_revision, 'Missing repository dependencies', 'Deactivated' ] @@ -198,11 +198,11 @@ installed_column_repository = test_db_util.get_installed_repository_by_name_owner( column_repository_name, common.test_user_1_name ) self.reactivate_repository( installed_convert_repository ) - strings_displayed = [ installed_convert_repository.name, - installed_convert_repository.description, - installed_convert_repository.tool_shed, + strings_displayed = [ 'convert_chars_0080', + 'Convert delimiters', + self.url.replace( 'http://', '' ), installed_convert_repository.installed_changeset_revision, - installed_column_repository.name, + 'column_maker_0080', installed_column_repository.installed_changeset_revision, 'Installed repository dependencies' ] def test_0040_deactivate_column_repository( self ): @@ -212,11 +212,11 @@ installed_column_repository = test_db_util.get_installed_repository_by_name_owner( column_repository_name, common.test_user_1_name ) self.uninstall_repository( installed_column_repository, remove_from_disk=False ) - strings_displayed = [ installed_convert_repository.name, - installed_convert_repository.description, - installed_convert_repository.tool_shed, + strings_displayed = [ 'convert_chars_0080', + 'Convert delimiters', + self.url.replace( 'http://', '' ), installed_convert_repository.installed_changeset_revision, - installed_column_repository.name, + 'column_maker_0080', installed_column_repository.installed_changeset_revision, 'Missing repository dependencies', 'Deactivated' ] @@ -229,9 +229,9 @@ installed_column_repository = test_db_util.get_installed_repository_by_name_owner( column_repository_name, common.test_user_1_name ) self.uninstall_repository( installed_convert_repository, remove_from_disk=False ) - strings_not_displayed = [ installed_column_repository.name, + strings_not_displayed = [ 'column_maker_0080', installed_column_repository.installed_changeset_revision, - installed_convert_repository.name, + 'convert_chars_0080', installed_convert_repository.installed_changeset_revision ] self.display_galaxy_browse_repositories_page( strings_not_displayed=strings_not_displayed ) def test_0050_reactivate_column_repository( self ): @@ -241,11 +241,11 @@ installed_column_repository = test_db_util.get_installed_repository_by_name_owner( column_repository_name, common.test_user_1_name ) self.reactivate_repository( installed_column_repository ) - strings_displayed = [ installed_column_repository.name, - installed_column_repository.description, - installed_column_repository.tool_shed, + strings_displayed = [ 'column_maker_0080', + 'Add column', + self.url.replace( 'http://', '' ), installed_column_repository.installed_changeset_revision, - installed_convert_repository.name, + 'convert_chars_0080', installed_convert_repository.installed_changeset_revision, 'Missing repository dependencies', 'Deactivated' ] @@ -258,20 +258,20 @@ installed_column_repository = test_db_util.get_installed_repository_by_name_owner( column_repository_name, common.test_user_1_name ) self.reactivate_repository( installed_convert_repository ) - strings_displayed = [ installed_column_repository.name, - installed_column_repository.description, - installed_column_repository.tool_shed, + strings_displayed = [ 'column_maker_0080', + 'Add column', + self.url.replace( 'http://', '' ), installed_column_repository.installed_changeset_revision, - installed_convert_repository.name, + 'convert_chars_0080', installed_convert_repository.installed_changeset_revision, 'Installed repository dependencies' ] self.display_installed_repository_manage_page( installed_column_repository, strings_displayed=strings_displayed ) - strings_displayed = [ installed_convert_repository.name, - installed_convert_repository.description, - installed_convert_repository.tool_shed, + strings_displayed = [ 'convert_chars_0080', + 'Convert delimiters', + self.url.replace( 'http://', '' ), installed_convert_repository.installed_changeset_revision, - installed_column_repository.name, + 'column_maker_0080', installed_column_repository.installed_changeset_revision, 'Installed repository dependencies' ] self.display_installed_repository_manage_page( installed_convert_repository, @@ -283,11 +283,11 @@ installed_column_repository = test_db_util.get_installed_repository_by_name_owner( column_repository_name, common.test_user_1_name ) self.uninstall_repository( installed_column_repository, remove_from_disk=True ) - strings_displayed = [ installed_convert_repository.name, - installed_convert_repository.description, - installed_convert_repository.tool_shed, + strings_displayed = [ 'convert_chars_0080', + 'Convert delimiters', + self.url.replace( 'http://', '' ), installed_convert_repository.installed_changeset_revision, - installed_column_repository.name, + 'column_maker_0080', installed_column_repository.installed_changeset_revision, 'Missing repository dependencies', 'Uninstalled' ] @@ -301,20 +301,20 @@ installed_column_repository = test_db_util.get_installed_repository_by_name_owner( column_repository_name, common.test_user_1_name ) self.reinstall_repository( installed_column_repository, install_repository_dependencies=False ) - strings_displayed = [ installed_column_repository.name, - installed_column_repository.description, - installed_column_repository.tool_shed, + strings_displayed = [ 'column_maker_0080', + 'Add column', + self.url.replace( 'http://', '' ), installed_column_repository.installed_changeset_revision, - installed_convert_repository.name, + 'convert_chars_0080', installed_convert_repository.installed_changeset_revision, 'Installed repository dependencies' ] self.display_installed_repository_manage_page( installed_column_repository, strings_displayed=strings_displayed ) - strings_displayed = [ installed_convert_repository.name, - installed_convert_repository.description, - installed_convert_repository.tool_shed, + strings_displayed = [ 'convert_chars_0080', + 'Convert delimiters', + self.url.replace( 'http://', '' ), installed_convert_repository.installed_changeset_revision, - installed_column_repository.name, + 'column_maker_0080', installed_column_repository.installed_changeset_revision, 'Installed repository dependencies' ] self.display_installed_repository_manage_page( installed_convert_repository, @@ -326,11 +326,11 @@ installed_column_repository = test_db_util.get_installed_repository_by_name_owner( column_repository_name, common.test_user_1_name ) self.uninstall_repository( installed_convert_repository, remove_from_disk=True ) - strings_displayed = [ installed_column_repository.name, - installed_column_repository.description, - installed_column_repository.tool_shed, + strings_displayed = [ 'column_maker_0080', + 'Add column', + self.url.replace( 'http://', '' ), installed_column_repository.installed_changeset_revision, - installed_convert_repository.name, + 'convert_chars_0080', installed_convert_repository.installed_changeset_revision, 'Missing repository dependencies', 'Uninstalled' ] @@ -344,11 +344,11 @@ installed_column_repository = test_db_util.get_installed_repository_by_name_owner( column_repository_name, common.test_user_1_name ) self.uninstall_repository( installed_column_repository, remove_from_disk=True ) - strings_displayed = [ installed_convert_repository.name, - installed_convert_repository.description, - installed_convert_repository.tool_shed, + strings_displayed = [ 'convert_chars_0080', + 'Convert delimiters', + self.url.replace( 'http://', '' ), installed_convert_repository.installed_changeset_revision, - installed_column_repository.name, + 'column_maker_0080', installed_column_repository.installed_changeset_revision, 'Missing repository dependencies', 'Activate or reinstall repository', @@ -365,20 +365,20 @@ install_repository_dependencies=True, no_changes=False, new_tool_panel_section='convert_maker' ) - strings_displayed = [ installed_column_repository.name, - installed_column_repository.description, - installed_column_repository.tool_shed, + strings_displayed = [ 'column_maker_0080', + 'Add column', + self.url.replace( 'http://', '' ), installed_column_repository.installed_changeset_revision, - installed_convert_repository.name, + 'convert_chars_0080', installed_convert_repository.installed_changeset_revision, 'Installed repository dependencies' ] self.display_installed_repository_manage_page( installed_column_repository, strings_displayed=strings_displayed ) - strings_displayed = [ installed_convert_repository.name, - installed_convert_repository.description, - installed_convert_repository.tool_shed, + strings_displayed = [ 'convert_chars_0080', + 'Convert delimiters', + self.url.replace( 'http://', '' ), installed_convert_repository.installed_changeset_revision, - installed_column_repository.name, + 'column_maker_0080', installed_column_repository.installed_changeset_revision, 'Installed repository dependencies' ] self.display_installed_repository_manage_page( installed_convert_repository, diff -r 359f6fbcde82bbf8aa1d4b932a54882f86121d71 -r d04aa3ad613211d3c88f1daa7e5a9df4d1233597 test/tool_shed/functional/test_1085_repository_dependency_handling.py --- a/test/tool_shed/functional/test_1085_repository_dependency_handling.py +++ b/test/tool_shed/functional/test_1085_repository_dependency_handling.py @@ -122,18 +122,18 @@ common.test_user_1_name ) installed_column_repository = test_db_util.get_installed_repository_by_name_owner( column_repository_name, common.test_user_1_name ) - browse_strings_displayed = [ installed_convert_repository.name, - installed_convert_repository.description, - installed_convert_repository.tool_shed, + browse_strings_displayed = [ 'convert_chars_1085', + 'Convert delimiters', + self.url.replace( 'http://', '' ), installed_convert_repository.installed_changeset_revision, - installed_column_repository.name, - installed_column_repository.description, + 'column_maker_1085', + 'Add column', installed_column_repository.installed_changeset_revision ] - strings_displayed = [ installed_convert_repository.name, - installed_convert_repository.description, - installed_convert_repository.tool_shed, + strings_displayed = [ 'convert_chars_1085', + 'Convert delimiters', + self.url.replace( 'http://', '' ), installed_convert_repository.installed_changeset_revision, - installed_column_repository.name, + 'column_maker_1085', installed_column_repository.installed_changeset_revision, 'Installed repository dependencies' ] self.display_galaxy_browse_repositories_page( strings_displayed=browse_strings_displayed ) @@ -161,9 +161,9 @@ install_repository_dependencies=False, new_tool_panel_section='new_column_maker', no_changes=False ) - strings_displayed = [ installed_column_repository.name, - installed_column_repository.description, - installed_column_repository.tool_shed, + strings_displayed = [ 'column_maker_1085', + 'Add column', + self.url.replace( 'http://', '' ), installed_column_repository.installed_changeset_revision ] self.display_installed_repository_manage_page( installed_column_repository, strings_displayed=strings_displayed ) @@ -176,9 +176,9 @@ install_repository_dependencies=False, new_tool_panel_section='new_convert_chars', no_changes=False ) - strings_displayed = [ installed_convert_repository.name, - installed_convert_repository.description, - installed_convert_repository.tool_shed, + strings_displayed = [ 'convert_chars_1085', + 'Convert delimiters', + self.url.replace( 'http://', '' ), installed_convert_repository.installed_changeset_revision ] self.display_installed_repository_manage_page( installed_convert_repository, strings_displayed=strings_displayed ) diff -r 359f6fbcde82bbf8aa1d4b932a54882f86121d71 -r d04aa3ad613211d3c88f1daa7e5a9df4d1233597 test/tool_shed/functional/test_1087_install_updated_repository_dependencies.py --- a/test/tool_shed/functional/test_1087_install_updated_repository_dependencies.py +++ b/test/tool_shed/functional/test_1087_install_updated_repository_dependencies.py @@ -103,7 +103,7 @@ '''Reinstall column_maker and verify that it now shows repository dependencies.''' installed_column_repository = test_db_util.get_installed_repository_by_name_owner( column_repository_name, common.test_user_1_name ) convert_repository = test_db_util.get_repository_by_name_and_owner( convert_repository_name, common.test_user_1_name ) - strings_displayed=[ 'Handle repository dependencies', convert_repository.name, self.get_repository_tip( convert_repository ) ] + strings_displayed=[ 'Handle repository dependencies', 'convert_chars_1087', self.get_repository_tip( convert_repository ) ] # Due to twill's limitations, only check for strings on the (redirected) reselect tool panel section page, don't actually reinstall. url = '/admin_toolshed/browse_repositories?operation=activate+or+reinstall&id=%s' % self.security.encode_id( installed_column_repository.id ) self.visit_galaxy_url( url ) diff -r 359f6fbcde82bbf8aa1d4b932a54882f86121d71 -r d04aa3ad613211d3c88f1daa7e5a9df4d1233597 test/tool_shed/functional/test_1090_install_tool_from_tool_search.py --- a/test/tool_shed/functional/test_1090_install_tool_from_tool_search.py +++ b/test/tool_shed/functional/test_1090_install_tool_from_tool_search.py @@ -270,9 +270,9 @@ bwa_color_revision = self.get_repository_tip( bwa_color_repository ) self.search_for_valid_tools( search_fields={ 'tool_id': 'bwa' }, exact_matches=False, from_galaxy=True, - strings_displayed=[ bwa_color_repository_name, bwa_base_repository_name, bwa_base_revision, bwa_color_revision ] ) - strings_displayed=[ freebayes_repository_name, emboss_repository_name, filtering_repository_name ] - strings_displayed.extend( [ bwa_color_repository_name, bwa_base_repository_name, emboss_datatypes_repository_name ] ) + strings_displayed=[ 'bwa_color_0090', 'bwa_base_0090', bwa_base_revision, bwa_color_revision ] ) + strings_displayed=[ 'freebayes_0090', 'emboss_0090', 'filtering_0090' ] + strings_displayed.extend( [ 'bwa_color_0090', 'bwa_base_0090', 'emboss_datatypes_0090' ] ) strings_displayed.extend( [ 'bwa', 'Handle', 'tool dependencies' ] ) repositories_to_install = [ bwa_color_repository, bwa_base_repository ] # BWA is a good candidate for testing the installation of tool dependencies, but it is a core requirement of functional diff -r 359f6fbcde82bbf8aa1d4b932a54882f86121d71 -r d04aa3ad613211d3c88f1daa7e5a9df4d1233597 test/tool_shed/functional/test_1100_install_repository_with_complex_dependencies.py --- a/test/tool_shed/functional/test_1100_install_repository_with_complex_dependencies.py +++ b/test/tool_shed/functional/test_1100_install_repository_with_complex_dependencies.py @@ -243,11 +243,11 @@ strings_displayed.append( self.url.replace( 'http://', '' ) ) self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed, strings_not_displayed=[] ) checks = [ ( tool_repository, - [ tool_repository.name, tool_repository.owner, tool_repository.installed_changeset_revision ], + [ 'bwa_tool_repository_0100', 'user1', tool_repository.installed_changeset_revision ], [ 'Missing tool dependencies' ] ), ( base_repository, - [ base_repository.name, base_repository.owner, base_repository.installed_changeset_revision, tool_repository.name, - tool_repository.owner, tool_repository.installed_changeset_revision ], + [ 'bwa_base_repository_0100', 'user1', base_repository.installed_changeset_revision, 'bwa_tool_repository_0100', + tool_repository.installed_changeset_revision ], [ 'Missing tool dependencies' ] ) ] for repository, strings_displayed, strings_not_displayed in checks: self.display_installed_repository_manage_page( repository, strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed ) diff -r 359f6fbcde82bbf8aa1d4b932a54882f86121d71 -r d04aa3ad613211d3c88f1daa7e5a9df4d1233597 test/tool_shed/functional/test_1110_install_repository_with_invalid_repository_dependency.py --- a/test/tool_shed/functional/test_1110_install_repository_with_invalid_repository_dependency.py +++ b/test/tool_shed/functional/test_1110_install_repository_with_invalid_repository_dependency.py @@ -174,7 +174,7 @@ self.galaxy_logout() self.galaxy_login( email=common.admin_email, username=common.admin_username ) repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) - preview_strings_displayed = [ repository.name, self.get_repository_tip( repository ), 'will be ignored' ] + preview_strings_displayed = [ 'emboss_0110', self.get_repository_tip( repository ), 'will be ignored' ] self.install_repository( emboss_repository_name, common.test_user_1_name, category_name, diff -r 359f6fbcde82bbf8aa1d4b932a54882f86121d71 -r d04aa3ad613211d3c88f1daa7e5a9df4d1233597 test/tool_shed/functional/test_1200_uninstall_and_reinstall_basic_repository.py --- a/test/tool_shed/functional/test_1200_uninstall_and_reinstall_basic_repository.py +++ b/test/tool_shed/functional/test_1200_uninstall_and_reinstall_basic_repository.py @@ -77,28 +77,28 @@ 'Test 0000 Basic Repository Features 1', new_tool_panel_section='test_1000' ) installed_repository = test_db_util.get_installed_repository_by_name_owner( 'filtering_0000', common.test_user_1_name ) - strings_displayed = [ installed_repository.name, - installed_repository.description, - installed_repository.owner, - installed_repository.tool_shed, + strings_displayed = [ 'filtering_0000', + "Galaxy's filtering tool for test 0000", + 'user1', + self.url.replace( 'http://', '' ), installed_repository.installed_changeset_revision ] self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed ) def test_0015_uninstall_filtering_repository( self ): '''Uninstall the filtering repository.''' installed_repository = test_db_util.get_installed_repository_by_name_owner( 'filtering_0000', common.test_user_1_name ) self.uninstall_repository( installed_repository, remove_from_disk=True ) - strings_not_displayed = [ installed_repository.name, - installed_repository.description, + strings_not_displayed = [ 'filtering_0000', + "Galaxy's filtering tool for test 0000", installed_repository.installed_changeset_revision ] self.display_galaxy_browse_repositories_page( strings_not_displayed=strings_not_displayed ) def test_0020_reinstall_filtering_repository( self ): '''Reinstall the filtering repository.''' installed_repository = test_db_util.get_installed_repository_by_name_owner( 'filtering_0000', common.test_user_1_name ) self.reinstall_repository( installed_repository ) - strings_displayed = [ installed_repository.name, - installed_repository.description, - installed_repository.owner, - installed_repository.tool_shed, + strings_displayed = [ 'filtering_0000', + "Galaxy's filtering tool for test 0000", + 'user1', + self.url.replace( 'http://', '' ), installed_repository.installed_changeset_revision ] self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed ) self.display_installed_repository_manage_page( installed_repository, @@ -108,18 +108,18 @@ '''Deactivate the filtering repository without removing it from disk.''' installed_repository = test_db_util.get_installed_repository_by_name_owner( 'filtering_0000', common.test_user_1_name ) self.uninstall_repository( installed_repository, remove_from_disk=False ) - strings_not_displayed = [ installed_repository.name, - installed_repository.description, + strings_not_displayed = [ 'filtering_0000', + "Galaxy's filtering tool for test 0000", installed_repository.installed_changeset_revision ] self.display_galaxy_browse_repositories_page( strings_not_displayed=strings_not_displayed ) def test_0030_reactivate_filtering_repository( self ): '''Reactivate the filtering repository and verify that it now shows up in the list of installed repositories.''' installed_repository = test_db_util.get_installed_repository_by_name_owner( 'filtering_0000', common.test_user_1_name ) self.reactivate_repository( installed_repository ) - strings_displayed = [ installed_repository.name, - installed_repository.description, - installed_repository.owner, - installed_repository.tool_shed, + strings_displayed = [ 'filtering_0000', + "Galaxy's filtering tool for test 0000", + 'user1', + self.url.replace( 'http://', '' ), installed_repository.installed_changeset_revision ] self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed ) self.display_installed_repository_manage_page( installed_repository, diff -r 359f6fbcde82bbf8aa1d4b932a54882f86121d71 -r d04aa3ad613211d3c88f1daa7e5a9df4d1233597 test/tool_shed/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py --- a/test/tool_shed/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py +++ b/test/tool_shed/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py @@ -96,10 +96,10 @@ strings_displayed=strings_displayed, new_tool_panel_section='test_1210' ) installed_repository = test_db_util.get_installed_repository_by_name_owner( 'freebayes_0010', common.test_user_1_name ) - strings_displayed = [ installed_repository.name, - installed_repository.description, - installed_repository.owner, - installed_repository.tool_shed, + strings_displayed = [ 'freebayes_0010', + "Galaxy's freebayes tool", + 'user1', + self.url.replace( 'http://', '' ), installed_repository.installed_changeset_revision ] self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed ) def test_0015_uninstall_freebayes_repository( self ): @@ -112,10 +112,10 @@ '''Reinstall the freebayes repository.''' installed_repository = test_db_util.get_installed_repository_by_name_owner( 'freebayes_0010', common.test_user_1_name ) self.reinstall_repository( installed_repository ) - strings_displayed = [ installed_repository.name, - installed_repository.description, - installed_repository.owner, - installed_repository.tool_shed, + strings_displayed = [ 'freebayes_0010', + "Galaxy's freebayes tool", + 'user1', + self.url.replace( 'http://', '' ), installed_repository.installed_changeset_revision ] self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed ) self.display_installed_repository_manage_page( installed_repository, @@ -131,10 +131,10 @@ '''Reactivate the freebayes repository and verify that it now shows up in the list of installed repositories.''' installed_repository = test_db_util.get_installed_repository_by_name_owner( 'freebayes_0010', common.test_user_1_name ) self.reactivate_repository( installed_repository ) - strings_displayed = [ installed_repository.name, - installed_repository.description, - installed_repository.owner, - installed_repository.tool_shed, + strings_displayed = [ 'freebayes_0010', + "Galaxy's freebayes tool", + 'user1', + self.url.replace( 'http://', '' ), installed_repository.installed_changeset_revision ] self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed ) self.display_installed_repository_manage_page( installed_repository, diff -r 359f6fbcde82bbf8aa1d4b932a54882f86121d71 -r d04aa3ad613211d3c88f1daa7e5a9df4d1233597 test/tool_shed/functional/test_1220_uninstall_reinstall_repository_with_repository_dependencies.py --- a/test/tool_shed/functional/test_1220_uninstall_reinstall_repository_with_repository_dependencies.py +++ b/test/tool_shed/functional/test_1220_uninstall_reinstall_repository_with_repository_dependencies.py @@ -98,10 +98,10 @@ strings_displayed=strings_displayed, new_tool_panel_section='test_1210' ) installed_repository = test_db_util.get_installed_repository_by_name_owner( emboss_repository_name, common.test_user_1_name ) - strings_displayed = [ installed_repository.name, - installed_repository.description, - installed_repository.owner, - installed_repository.tool_shed, + strings_displayed = [ 'emboss_0020', + 'Galaxy wrappers for Emboss version 5.0.0 tools', + 'user1', + self.url.replace( 'http://', '' ), installed_repository.installed_changeset_revision ] self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed ) current_datatypes = int( self.get_datatypes_count() ) @@ -122,10 +122,10 @@ '''Reinstall the emboss repository.''' installed_repository = test_db_util.get_installed_repository_by_name_owner( emboss_repository_name, common.test_user_1_name ) self.reinstall_repository( installed_repository ) - strings_displayed = [ installed_repository.name, - installed_repository.description, - installed_repository.owner, - installed_repository.tool_shed, + strings_displayed = [ 'emboss_0020', + 'Galaxy wrappers for Emboss version 5.0.0 tools', + 'user1', + self.url.replace( 'http://', '' ), installed_repository.installed_changeset_revision ] self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed ) self.display_installed_repository_manage_page( installed_repository, @@ -135,17 +135,17 @@ '''Deactivate the emboss repository without removing it from disk.''' installed_repository = test_db_util.get_installed_repository_by_name_owner( emboss_repository_name, common.test_user_1_name ) self.uninstall_repository( installed_repository, remove_from_disk=False ) - strings_not_displayed = [ installed_repository.name, + strings_not_displayed = [ 'emboss_0020', installed_repository.installed_changeset_revision ] self.display_galaxy_browse_repositories_page( strings_not_displayed=strings_not_displayed ) def test_0030_reactivate_emboss_repository( self ): '''Reactivate the emboss repository and verify that it now shows up in the list of installed repositories.''' installed_repository = test_db_util.get_installed_repository_by_name_owner( emboss_repository_name, common.test_user_1_name ) self.reactivate_repository( installed_repository ) - strings_displayed = [ installed_repository.name, - installed_repository.description, - installed_repository.owner, - installed_repository.tool_shed, + strings_displayed = [ 'emboss_0020', + 'Galaxy wrappers for Emboss version 5.0.0 tools', + 'user1', + self.url.replace( 'http://', '' ), installed_repository.installed_changeset_revision ] self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed ) self.display_installed_repository_manage_page( installed_repository, diff -r 359f6fbcde82bbf8aa1d4b932a54882f86121d71 -r d04aa3ad613211d3c88f1daa7e5a9df4d1233597 test/tool_shed/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py --- a/test/tool_shed/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py +++ b/test/tool_shed/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py @@ -158,10 +158,10 @@ strings_displayed=strings_displayed, new_tool_panel_section='test_1210' ) installed_repository = test_db_util.get_installed_repository_by_name_owner( emboss_repository_name, common.test_user_1_name ) - strings_displayed = [ installed_repository.name, - installed_repository.description, - installed_repository.owner, - installed_repository.tool_shed, + strings_displayed = [ 'emboss_0030', + 'Galaxy wrappers for Emboss version 5.0.0 tools', + 'user1', + self.url.replace( 'http://', '' ), installed_repository.installed_changeset_revision ] self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed ) current_datatypes = int( self.get_datatypes_count() ) @@ -182,10 +182,10 @@ '''Reinstall the emboss repository.''' installed_repository = test_db_util.get_installed_repository_by_name_owner( emboss_repository_name, common.test_user_1_name ) self.reinstall_repository( installed_repository ) - strings_displayed = [ installed_repository.name, - installed_repository.description, - installed_repository.owner, - installed_repository.tool_shed, + strings_displayed = [ 'emboss_0030', + 'Galaxy wrappers for Emboss version 5.0.0 tools', + 'user1', + self.url.replace( 'http://', '' ), installed_repository.installed_changeset_revision ] self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed ) self.display_installed_repository_manage_page( installed_repository, @@ -201,10 +201,10 @@ '''Reactivate the emboss repository and verify that it now shows up in the list of installed repositories.''' installed_repository = test_db_util.get_installed_repository_by_name_owner( emboss_repository_name, common.test_user_1_name ) self.reactivate_repository( installed_repository ) - strings_displayed = [ installed_repository.name, - installed_repository.description, - installed_repository.owner, - installed_repository.tool_shed, + strings_displayed = [ 'emboss_0030', + 'Galaxy wrappers for Emboss version 5.0.0 tools', + 'user1', + self.url.replace( 'http://', '' ), installed_repository.installed_changeset_revision ] self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed ) self.display_installed_repository_manage_page( installed_repository, Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: natefoo: Fix exception handling in migration script 111.
by Bitbucket 15 Feb '13

15 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/359f6fbcde82/ changeset: 359f6fbcde82 user: natefoo date: 2013-02-15 17:21:11 summary: Fix exception handling in migration script 111. affected #: 1 file diff -r 865c74ff03755f21eaaf4a557b1c2aeb1518e593 -r 359f6fbcde82bbf8aa1d4b932a54882f86121d71 lib/galaxy/model/migrate/versions/0111_add_job_destinations.py --- a/lib/galaxy/model/migrate/versions/0111_add_job_destinations.py +++ b/lib/galaxy/model/migrate/versions/0111_add_job_destinations.py @@ -26,14 +26,14 @@ try: c.create( Job_table ) assert c is Job_table.c.destination_id - except: + except Exception, e: log.error( "Adding column 'destination_id' to job table failed: %s" % str( e ) ) c = Column( "destination_params", JSONType, nullable=True ) try: c.create( Job_table ) assert c is Job_table.c.destination_params - except: + except Exception, e: log.error( "Adding column 'destination_params' to job table failed: %s" % str( e ) ) def downgrade(): 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: natefoo: Handle the Torque 'E' job state in the CLI runner.
by Bitbucket 15 Feb '13

15 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8cd0793b0fc6/ changeset: 8cd0793b0fc6 branch: stable user: natefoo date: 2013-02-15 16:53:20 summary: Handle the Torque 'E' job state in the CLI runner. affected #: 1 file diff -r 1f1072317efd5cf82cb791d75ba968c4bacffaf4 -r 8cd0793b0fc65b57f8fd93cfffc19ba105d190cf lib/galaxy/jobs/runners/cli_job/torque.py --- a/lib/galaxy/jobs/runners/cli_job/torque.py +++ b/lib/galaxy/jobs/runners/cli_job/torque.py @@ -128,5 +128,6 @@ return job_states.OK def __get_job_state(self, state): - return { 'R' : job_states.RUNNING, + return { 'E' : job_states.RUNNING, + 'R' : job_states.RUNNING, 'Q' : job_states.QUEUED }.get(state, state) 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: 4 new changesets
by Bitbucket 14 Feb '13

14 Feb '13

4 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c3d93fe36b28/ changeset: c3d93fe36b28 user: jgoecks date: 2013-02-15 00:14:18 summary: Add new config files to hgignore. affected #: 1 file diff -r c58f82badc26168885507312b71ac2351046bee8 -r c3d93fe36b28898f741c06e316d7184a993dfb9a .hgignore --- a/.hgignore +++ b/.hgignore @@ -46,6 +46,8 @@ openid_conf.xml shed_tool_data_table_conf.xml job_conf.xml +data_manager_conf.xml +shed_data_manager_conf.xml static/welcome.html.* static/welcome.html https://bitbucket.org/galaxy/galaxy-central/commits/4150920c8075/ changeset: 4150920c8075 user: jgoecks date: 2013-02-15 00:15:34 summary: Standardize on BED format for genome data providers and fix off-by-one issues. affected #: 2 files diff -r c3d93fe36b28898f741c06e316d7184a993dfb9a -r 4150920c807513bc321619c0d59784a30020b07a lib/galaxy/visualization/data_providers/genome.py --- a/lib/galaxy/visualization/data_providers/genome.py +++ b/lib/galaxy/visualization/data_providers/genome.py @@ -111,7 +111,10 @@ return result class GenomeDataProvider( BaseDataProvider ): - """ Base class for genome data providers. """ + """ + Base class for genome data providers. All genome providers should + produce data with BED interval format: 0-based, half-open coordinates. + """ dataset_type = None @@ -819,8 +822,8 @@ class BamDataProvider( GenomeDataProvider, FilterableMixin ): """ - Provides access to intervals from a sorted indexed BAM file. Position data - is reported in 1-based, closed format, i.e. SAM/BAM format. + Provides access to intervals from a sorted indexed BAM file. Coordinate + data is reported in BED format: 0-based, half-open. """ dataset_type = 'bai' diff -r c3d93fe36b28898f741c06e316d7184a993dfb9a -r 4150920c807513bc321619c0d59784a30020b07a static/scripts/viz/trackster/painters.js --- a/static/scripts/viz/trackster/painters.js +++ b/static/scripts/viz/trackster/painters.js @@ -493,8 +493,7 @@ var feature_uid = feature[0], feature_start = feature[1], - // -1 because end is not included in feature; see FeaturePainter documentation for details. - feature_end = feature[2] - 1, + feature_end = feature[2], feature_name = feature[3], feature_strand = feature[4], f_start = Math.floor( Math.max(0, (feature_start - tile_low) * w_scale) ), @@ -613,8 +612,7 @@ for (var k = 0, k_len = feature_blocks.length; k < k_len; k++) { var block = feature_blocks[k], block_start = Math.floor( Math.max(0, (block[0] - tile_low) * w_scale) ), - // -1 because end is not included in feature; see FeaturePainter documentation for details. - block_end = Math.ceil( Math.min(width, Math.max((block[1] - 1 - tile_low) * w_scale)) ), + block_end = Math.ceil( Math.min(width, Math.max((block[1] - tile_low) * w_scale)) ), last_block_start, last_block_end; // Skip drawing if block not on tile. @@ -759,8 +757,7 @@ // Go left if it clips base_offset -= cig_len; } - // -1 for feature start because data is using 1-based offset but display is 0-based. - var seq_start = (feature_start - 1) + base_offset, + var seq_start = feature_start + base_offset, s_start = Math.floor( Math.max(0, (seq_start - tile_low) * w_scale) ), s_end = Math.floor( Math.max(0, (seq_start + cig_len - tile_low) * w_scale) ); https://bitbucket.org/galaxy/galaxy-central/commits/04aaf661f80a/ changeset: 04aaf661f80a user: jgoecks date: 2013-02-15 00:31:21 summary: More Trackster fixes to standardize on 0-based coordinate system. affected #: 1 file diff -r 4150920c807513bc321619c0d59784a30020b07a -r 04aaf661f80a92cfd8c804baccac348e3cc98355 static/scripts/viz/trackster/painters.js --- a/static/scripts/viz/trackster/painters.js +++ b/static/scripts/viz/trackster/painters.js @@ -779,8 +779,7 @@ case "=": // Equals. if (is_overlap([seq_start, seq_start + cig_len], tile_region)) { // Draw. - // -1 b/c sequence data is 1-based but painter is 0-based. - var seq = ref_seq.slice(seq_offset - 1, seq_offset + cig_len); + var seq = ref_seq.slice(seq_offset, seq_offset + cig_len); if (gap > 0) { ctx.fillStyle = block_color; ctx.fillRect(s_start - gap, y_center + 1, s_end - s_start, 9); @@ -836,8 +835,7 @@ var insert_x_coord = s_start - gap; if (is_overlap([seq_start, seq_start + cig_len], tile_region)) { - // -1 b/c sequence data is 1-based but painter is 0-based. - var seq = ref_seq.slice(seq_offset - 1, seq_offset + cig_len); + var seq = ref_seq.slice(seq_offset, seq_offset + cig_len); // Insertion point is between the sequence start and the previous base: (-gap) moves // back from sequence start to insertion point. if (this.prefs.show_insertions) { https://bitbucket.org/galaxy/galaxy-central/commits/865c74ff0375/ changeset: 865c74ff0375 user: jgoecks date: 2013-02-15 00:56:27 summary: Use 0-based coordinates for BBI data and display. affected #: 3 files diff -r 04aaf661f80a92cfd8c804baccac348e3cc98355 -r 865c74ff03755f21eaaf4a557b1c2aeb1518e593 lib/galaxy/visualization/data_providers/genome.py --- a/lib/galaxy/visualization/data_providers/genome.py +++ b/lib/galaxy/visualization/data_providers/genome.py @@ -112,8 +112,8 @@ class GenomeDataProvider( BaseDataProvider ): """ - Base class for genome data providers. All genome providers should - produce data with BED interval format: 0-based, half-open coordinates. + Base class for genome data providers. All genome providers use BED coordinate + format (0-based, half-open coordinates) for both queries and returned data. """ dataset_type = None @@ -1044,7 +1044,9 @@ return all_dat is not None def get_data( self, chrom, start, end, start_val=0, max_vals=None, num_samples=1000, **kwargs ): - start = int( start ) + # Subtract 1 because start/end are in 0-based coordinate system but BBI + # provider uses 1-based coordinate system. + start = int( start ) - 1 end = int( end ) # Helper function for getting summary data regardless of chromosome diff -r 04aaf661f80a92cfd8c804baccac348e3cc98355 -r 865c74ff03755f21eaaf4a557b1c2aeb1518e593 static/scripts/packed/viz/trackster/painters.js --- a/static/scripts/packed/viz/trackster/painters.js +++ b/static/scripts/packed/viz/trackster/painters.js @@ -1,1 +1,1 @@ -define(["libs/underscore"],function(_){var extend=_.extend;var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(first_region,second_region){var first_start=first_region[0],first_end=first_region[1],second_start=second_region[0],second_end=second_region[1],overlap;if(first_start<second_start){if(first_end<second_start){overlap=BEFORE}else{if(first_end<=second_end){overlap=OVERLAP_START}else{overlap=CONTAINS}}}else{if(first_start>second_end){overlap=AFTER}else{if(first_end<=second_end){overlap=CONTAINED_BY}else{overlap=OVERLAP_END}}}return overlap};var is_overlap=function(first_region,second_region){var overlap=compute_overlap(first_region,second_region);return(overlap!==BEFORE&&overlap!==AFTER)};var dashedLine=function(ctx,x1,y1,x2,y2,dashLen){if(dashLen===undefined){dashLen=4}var dX=x2-x1;var dY=y2-y1;var dashes=Math.floor(Math.sqrt(dX*dX+dY*dY)/dashLen);var dashX=dX/dashes;var dashY=dY/dashes;var q;for(q=0;q<dashes;q++,x1+=dashX,y1+=dashY){if(q%2!==0){continue}ctx.fillRect(x1,y1,dashLen,1)}};var drawDownwardEquilateralTriangle=function(ctx,down_vertex_x,down_vertex_y,side_len){var x1=down_vertex_x-side_len/2,x2=down_vertex_x+side_len/2,y=down_vertex_y-Math.sqrt(side_len*3/2);ctx.beginPath();ctx.moveTo(x1,y);ctx.lineTo(x2,y);ctx.lineTo(down_vertex_x,down_vertex_y);ctx.lineTo(x1,y);ctx.strokeStyle=this.fillStyle;ctx.fill();ctx.stroke();ctx.closePath()};var Scaler=function(default_val){this.default_val=(default_val?default_val:1)};Scaler.prototype.gen_val=function(input){return this.default_val};var Painter=function(data,view_start,view_end,prefs,mode){this.data=data;this.view_start=view_start;this.view_end=view_end;this.prefs=extend({},this.default_prefs,prefs);this.mode=mode};Painter.prototype.default_prefs={};Painter.prototype.draw=function(ctx,width,height,w_scale){};var SummaryTreePainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode)};SummaryTreePainter.prototype.default_prefs={show_counts:false};SummaryTreePainter.prototype.draw=function(ctx,width,height,w_scale){var view_start=this.view_start,points=this.data.data,max=(this.prefs.histogram_max?this.prefs.histogram_max:this.data.max),base_y=height;delta_x_px=Math.ceil(this.data.delta*w_scale);ctx.save();for(var i=0,len=points.length;i<len;i++){var x=Math.floor((points[i][0]-view_start)*w_scale);var y=points[i][1];if(!y){continue}var y_px=y/max*height;if(y!==0&&y_px<1){y_px=1}ctx.fillStyle=this.prefs.block_color;ctx.fillRect(x,base_y-y_px,delta_x_px,y_px);var text_padding_req_x=4;if(this.prefs.show_counts&&(ctx.measureText(y).width+text_padding_req_x)<delta_x_px){ctx.fillStyle=this.prefs.label_color;ctx.textAlign="center";ctx.fillText(y,x+(delta_x_px/2),10)}}ctx.restore()};var LinePainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);var i,len;if(this.prefs.min_value===undefined){var min_value=Infinity;for(i=0,len=this.data.length;i<len;i++){min_value=Math.min(min_value,this.data[i][1])}this.prefs.min_value=min_value}if(this.prefs.max_value===undefined){var max_value=-Infinity;for(i=0,len=this.data.length;i<len;i++){max_value=Math.max(max_value,this.data[i][1])}this.prefs.max_value=max_value}};LinePainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};LinePainter.prototype.draw=function(ctx,width,height,w_scale){var in_path=false,min_value=this.prefs.min_value,max_value=this.prefs.max_value,vertical_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data;ctx.save();var y_zero=Math.round(height+min_value/vertical_range*height);if(mode!=="Intensity"){ctx.fillStyle="#aaa";ctx.fillRect(0,y_zero,width,1)}ctx.beginPath();var x_scaled,y,delta_x_px;if(data.length>1){delta_x_px=Math.ceil((data[1][0]-data[0][0])*w_scale)}else{delta_x_px=10}var pref_color=parseInt(this.prefs.color.slice(1),16),pref_r=(pref_color&16711680)>>16,pref_g=(pref_color&65280)>>8,pref_b=pref_color&255;for(var i=0,len=data.length;i<len;i++){ctx.fillStyle=ctx.strokeStyle=this.prefs.color;x_scaled=Math.round((data[i][0]-view_start-1)*w_scale);y=data[i][1];var top_overflow=false,bot_overflow=false;if(y===null){if(in_path&&mode==="Filled"){ctx.lineTo(x_scaled,height_px)}in_path=false;continue}if(y<min_value){bot_overflow=true;y=min_value}else{if(y>max_value){top_overflow=true;y=max_value}}if(mode==="Histogram"){y=Math.round(y/vertical_range*height_px);ctx.fillRect(x_scaled,y_zero,delta_x_px,-y)}else{if(mode==="Intensity"){var saturation=(y-min_value)/vertical_range,new_r=Math.round(pref_r+(255-pref_r)*(1-saturation)),new_g=Math.round(pref_g+(255-pref_g)*(1-saturation)),new_b=Math.round(pref_b+(255-pref_b)*(1-saturation));ctx.fillStyle="rgb("+new_r+","+new_g+","+new_b+")";ctx.fillRect(x_scaled,0,delta_x_px,height_px)}else{y=Math.round(height_px-(y-min_value)/vertical_range*height_px);if(in_path){ctx.lineTo(x_scaled,y)}else{in_path=true;if(mode==="Filled"){ctx.moveTo(x_scaled,height_px);ctx.lineTo(x_scaled,y)}else{ctx.moveTo(x_scaled,y)}}}}ctx.fillStyle=this.prefs.overflow_color;if(top_overflow||bot_overflow){var overflow_x;if(mode==="Histogram"||mode==="Intensity"){overflow_x=delta_x_px}else{x_scaled-=2;overflow_x=4}if(top_overflow){ctx.fillRect(x_scaled,0,overflow_x,3)}if(bot_overflow){ctx.fillRect(x_scaled,height_px-3,overflow_x,3)}}ctx.fillStyle=this.prefs.color}if(mode==="Filled"){if(in_path){ctx.lineTo(x_scaled,y_zero);ctx.lineTo(0,y_zero)}ctx.fill()}else{ctx.stroke()}ctx.restore()};var FeaturePositionMapper=function(slot_height){this.feature_positions={};this.slot_height=slot_height;this.translation=0;this.y_translation=0};FeaturePositionMapper.prototype.map_feature_data=function(feature_data,slot,x_start,x_end){if(!this.feature_positions[slot]){this.feature_positions[slot]=[]}this.feature_positions[slot].push({data:feature_data,x_start:x_start,x_end:x_end})};FeaturePositionMapper.prototype.get_feature_data=function(x,y){var slot=Math.floor((y-this.y_translation)/this.slot_height),feature_dict;if(!this.feature_positions[slot]){return null}x+=this.translation;for(var i=0;i<this.feature_positions[slot].length;i++){feature_dict=this.feature_positions[slot][i];if(x>=feature_dict.x_start&&x<=feature_dict.x_end){return feature_dict.data}}};var FeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){Painter.call(this,data,view_start,view_end,prefs,mode);this.alpha_scaler=(alpha_scaler?alpha_scaler:new Scaler());this.height_scaler=(height_scaler?height_scaler:new Scaler())};FeaturePainter.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};extend(FeaturePainter.prototype,{get_required_height:function(rows_required,width){var required_height=this.get_row_height(),y_scale=required_height,mode=this.mode;if(mode==="no_detail"||mode==="Squish"||mode==="Pack"){required_height=rows_required*y_scale}return required_height+this.get_top_padding(width)+this.get_bottom_padding(width)},get_top_padding:function(width){return 0},get_bottom_padding:function(width){return Math.max(Math.round(this.get_row_height()/2),5)},draw:function(ctx,width,height,w_scale,slots){var data=this.data,view_start=this.view_start,view_end=this.view_end;ctx.save();ctx.fillStyle=this.prefs.block_color;ctx.textAlign="right";var y_scale=this.get_row_height(),feature_mapper=new FeaturePositionMapper(y_scale),x_draw_coords;for(var i=0,len=data.length;i<len;i++){var feature=data[i],feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],slot=(slots&&slots[feature_uid]!==undefined?slots[feature_uid]:null);if((feature_start<view_end&&feature_end>view_start)&&(this.mode==="Dense"||slot!==null)){x_draw_coords=this.draw_element(ctx,this.mode,feature,slot,view_start,view_end,w_scale,y_scale,width);feature_mapper.map_feature_data(feature,slot,x_draw_coords[0],x_draw_coords[1])}}ctx.restore();feature_mapper.y_translation=this.get_top_padding(width);return feature_mapper},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){console.log("WARNING: Unimplemented function.");return[0,0]}});var DENSE_TRACK_HEIGHT=10,NO_DETAIL_TRACK_HEIGHT=3,SQUISH_TRACK_HEIGHT=5,PACK_TRACK_HEIGHT=10,NO_DETAIL_FEATURE_HEIGHT=1,DENSE_FEATURE_HEIGHT=9,SQUISH_FEATURE_HEIGHT=3,PACK_FEATURE_HEIGHT=9,LABEL_SPACING=2,CONNECTOR_COLOR="#ccc";var LinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.draw_background_connector=true;this.draw_individual_connectors=false};extend(LinkedFeaturePainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var mode=this.mode,height;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="no_detail"){height=NO_DETAIL_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT}}}return height},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2]-1,feature_name=feature[3],feature_strand=feature[4],f_start=Math.floor(Math.max(0,(feature_start-tile_low)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low)*w_scale))),draw_start=f_start,draw_end=f_end,y_center=(mode==="Dense"?0:(0+slot))*y_scale+this.get_top_padding(width),thickness,y_start,thick_start=null,thick_end=null,block_color=(!feature_strand||feature_strand==="+"||feature_strand==="."?this.prefs.block_color:this.prefs.reverse_strand_color);label_color=this.prefs.label_color;ctx.globalAlpha=this.alpha_scaler.gen_val(feature);if(mode==="Dense"){slot=1}if(mode==="no_detail"){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_center+5,f_end-f_start,NO_DETAIL_FEATURE_HEIGHT)}else{var feature_ts=feature[5],feature_te=feature[6],feature_blocks=feature[7],full_height=true;if(feature_ts&&feature_te){thick_start=Math.floor(Math.max(0,(feature_ts-tile_low)*w_scale));thick_end=Math.ceil(Math.min(width,Math.max(0,(feature_te-tile_low)*w_scale)))}var thin_height,thick_height;if(mode==="Squish"){thin_height=1;thick_height=SQUISH_FEATURE_HEIGHT;full_height=false}else{if(mode==="Dense"){thin_height=5;thick_height=DENSE_FEATURE_HEIGHT}else{thin_height=5;thick_height=PACK_FEATURE_HEIGHT}}if(!feature_blocks){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_center+1,f_end-f_start,thick_height);if(feature_strand&&full_height){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}ctx.fillRect(f_start,y_center+1,f_end-f_start,thick_height)}}else{var cur_y_center,cur_height;if(mode==="Squish"||mode==="Dense"){cur_y_center=y_center+Math.floor(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}else{if(feature_strand){cur_y_center=y_center;cur_height=thick_height}else{cur_y_center+=(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}}if(this.draw_background_connector){if(mode==="Squish"||mode==="Dense"){ctx.fillStyle=CONNECTOR_COLOR}else{if(feature_strand){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand")}}}else{ctx.fillStyle=CONNECTOR_COLOR}}ctx.fillRect(f_start,cur_y_center,f_end-f_start,cur_height)}var start_and_height;for(var k=0,k_len=feature_blocks.length;k<k_len;k++){var block=feature_blocks[k],block_start=Math.floor(Math.max(0,(block[0]-tile_low)*w_scale)),block_end=Math.ceil(Math.min(width,Math.max((block[1]-1-tile_low)*w_scale))),last_block_start,last_block_end;if(block_start>block_end){continue}ctx.fillStyle=block_color;ctx.fillRect(block_start,y_center+(thick_height-thin_height)/2+1,block_end-block_start,thin_height);if(thick_start!==undefined&&feature_te>feature_ts&&!(block_start>thick_end||block_end<thick_start)){var block_thick_start=Math.max(block_start,thick_start),block_thick_end=Math.min(block_end,thick_end);ctx.fillRect(block_thick_start,y_center+1,block_thick_end-block_thick_start,thick_height);if(feature_blocks.length===1&&mode==="Pack"){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}if(block_thick_start+14<block_thick_end){block_thick_start+=2;block_thick_end-=2}ctx.fillRect(block_thick_start,y_center+1,block_thick_end-block_thick_start,thick_height)}}if(this.draw_individual_connectors&&last_block_start){this.draw_connector(ctx,last_block_start,last_block_end,block_start,block_end,y_center)}last_block_start=block_start;last_block_end=block_end}if(mode==="Pack"){ctx.globalAlpha=1;ctx.fillStyle="white";var hscale_factor=this.height_scaler.gen_val(feature),new_height=Math.ceil(thick_height*hscale_factor),ws_height=Math.round((thick_height-new_height)/2);if(hscale_factor!==1){ctx.fillRect(f_start,cur_y_center+1,f_end-f_start,ws_height);ctx.fillRect(f_start,cur_y_center+thick_height-ws_height+1,f_end-f_start,ws_height)}}}ctx.globalAlpha=1;if(feature_name&&mode==="Pack"&&feature_start>tile_low){ctx.fillStyle=label_color;if(tile_low===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING,y_center+8);draw_end+=ctx.measureText(feature_name).width+LABEL_SPACING}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_center+8);draw_start-=ctx.measureText(feature_name).width+LABEL_SPACING}}}ctx.globalAlpha=1;return[draw_start,draw_end]}});var ReadPainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler,ref_seq){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.ref_seq=(ref_seq?ref_seq.data:null)};extend(ReadPainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var height,mode=this.mode;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT;if(this.prefs.show_insertions){height*=2}}}return height},draw_read:function(ctx,mode,w_scale,y_center,tile_low,tile_high,feature_start,cigar,strand,ref_seq){ctx.textAlign="center";var tile_region=[tile_low,tile_high],base_offset=0,seq_offset=0,gap=0,char_width_px=ctx.canvas.manager.char_width_px,block_color=(strand==="+"?this.prefs.block_color:this.prefs.reverse_strand_color);var draw_last=[];if((mode==="Pack"||this.mode==="Auto")&&ref_seq!==undefined&&w_scale>char_width_px){gap=Math.round(w_scale/2)}if(!cigar){cigar=[[0,ref_seq.length]]}for(var cig_id=0,len=cigar.length;cig_id<len;cig_id++){var cig=cigar[cig_id],cig_op="MIDNSHP=X"[cig[0]],cig_len=cig[1];if(cig_op==="H"||cig_op==="S"){base_offset-=cig_len}var seq_start=(feature_start-1)+base_offset,s_start=Math.floor(Math.max(0,(seq_start-tile_low)*w_scale)),s_end=Math.floor(Math.max(0,(seq_start+cig_len-tile_low)*w_scale));if(s_start===s_end){s_end+=1}switch(cig_op){case"H":break;case"S":case"M":case"=":if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var seq=ref_seq.slice(seq_offset-1,seq_offset+cig_len);if(gap>0){ctx.fillStyle=block_color;ctx.fillRect(s_start-gap,y_center+1,s_end-s_start,9);ctx.fillStyle=CONNECTOR_COLOR;for(var c=0,str_len=seq.length;c<str_len;c++){if(this.prefs.show_differences){if(this.ref_seq){var ref_char=this.ref_seq[seq_start-tile_low+c];if(!ref_char||ref_char.toLowerCase()===seq[c].toLowerCase()){continue}}else{continue}}if(seq_start+c>=tile_low&&seq_start+c<=tile_high){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillText(seq[c],c_start,y_center+9)}}}else{ctx.fillStyle=block_color;ctx.fillRect(s_start,y_center+4,s_end-s_start,SQUISH_FEATURE_HEIGHT)}}seq_offset+=cig_len;base_offset+=cig_len;break;case"N":ctx.fillStyle=CONNECTOR_COLOR;ctx.fillRect(s_start-gap,y_center+5,s_end-s_start,1);base_offset+=cig_len;break;case"D":ctx.fillStyle="red";ctx.fillRect(s_start-gap,y_center+4,s_end-s_start,3);base_offset+=cig_len;break;case"P":break;case"I":var insert_x_coord=s_start-gap;if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var seq=ref_seq.slice(seq_offset-1,seq_offset+cig_len);if(this.prefs.show_insertions){var x_center=s_start-(s_end-s_start)/2;if((mode==="Pack"||this.mode==="Auto")&&ref_seq!==undefined&&w_scale>char_width_px){ctx.fillStyle="yellow";ctx.fillRect(x_center-gap,y_center-9,s_end-s_start,9);draw_last[draw_last.length]={type:"triangle",data:[insert_x_coord,y_center+4,5]};ctx.fillStyle=CONNECTOR_COLOR;switch(compute_overlap([seq_start,seq_start+cig_len],tile_region)){case (OVERLAP_START):seq=seq.slice(tile_low-seq_start);break;case (OVERLAP_END):seq=seq.slice(0,seq_start-tile_high);break;case (CONTAINED_BY):break;case (CONTAINS):seq=seq.slice(tile_low-seq_start,seq_start-tile_high);break}for(var c=0,str_len=seq.length;c<str_len;c++){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillText(seq[c],c_start-(s_end-s_start)/2,y_center)}}else{ctx.fillStyle="yellow";ctx.fillRect(x_center,y_center+(this.mode!=="Dense"?2:5),s_end-s_start,(mode!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((mode==="Pack"||this.mode==="Auto")&&ref_seq!==undefined&&w_scale>char_width_px){draw_last.push({type:"text",data:[seq.length,insert_x_coord,y_center+9]})}else{}}}seq_offset+=cig_len;break;case"X":seq_offset+=cig_len;break}}ctx.fillStyle="yellow";var item,type,data;for(var i=0;i<draw_last.length;i++){item=draw_last[i];type=item.type;data=item.data;if(type==="text"){ctx.save();ctx.font="bold "+ctx.font;ctx.fillText(data[0],data[1],data[2]);ctx.restore()}else{if(type==="triangle"){drawDownwardEquilateralTriangle(ctx,data[0],data[1],data[2])}}}},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],feature_name=feature[3],f_start=Math.floor(Math.max(0,(feature_start-tile_low)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low)*w_scale))),y_center=(mode==="Dense"?0:(0+slot))*y_scale,label_color=this.prefs.label_color,gap=0;if((mode==="Pack"||this.mode==="Auto")&&w_scale>ctx.canvas.manager.char_width_px){var gap=Math.round(w_scale/2)}if(feature[5] instanceof Array){var b1_start=Math.floor(Math.max(0,(feature[4][0]-tile_low)*w_scale)),b1_end=Math.ceil(Math.min(width,Math.max(0,(feature[4][1]-tile_low)*w_scale))),b2_start=Math.floor(Math.max(0,(feature[5][0]-tile_low)*w_scale)),b2_end=Math.ceil(Math.min(width,Math.max(0,(feature[5][1]-tile_low)*w_scale))),connector=true;if(feature[4][1]>=tile_low&&feature[4][0]<=tile_high&&feature[4][2]){this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature[4][0],feature[4][2],feature[4][3],feature[4][4])}else{connector=false}if(feature[5][1]>=tile_low&&feature[5][0]<=tile_high&&feature[5][2]){this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature[5][0],feature[5][2],feature[5][3],feature[5][4])}else{connector=false}if(connector&&b2_start>b1_end){ctx.fillStyle=CONNECTOR_COLOR;dashedLine(ctx,b1_end-gap,y_center+5,b2_start-gap,y_center+5)}}else{this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature_start,feature[4],feature[5],feature[6])}if(mode==="Pack"&&feature_start>tile_low&&feature_name!=="."){ctx.fillStyle=this.prefs.label_color;var tile_index=1;if(tile_index===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING-gap,y_center+8)}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING-gap,y_center+8)}}return[0,0]}});var ArcLinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){LinkedFeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.longest_feature_length=this.calculate_longest_feature_length();this.draw_background_connector=false;this.draw_individual_connectors=true};extend(ArcLinkedFeaturePainter.prototype,FeaturePainter.prototype,LinkedFeaturePainter.prototype,{calculate_longest_feature_length:function(){var longest_feature_length=0;for(var i=0,len=this.data.length;i<len;i++){var feature=this.data[i],feature_start=feature[1],feature_end=feature[2];longest_feature_length=Math.max(longest_feature_length,feature_end-feature_start)}return longest_feature_length},get_top_padding:function(width){var view_range=this.view_end-this.view_start,w_scale=width/view_range;return Math.min(128,Math.ceil((this.longest_feature_length/2)*w_scale))},draw_connector:function(ctx,block1_start,block1_end,block2_start,block2_end,y_center){var x_center=(block1_end+block2_start)/2,radius=block2_start-x_center;var angle1=Math.PI,angle2=0;if(radius>0){ctx.beginPath();ctx.arc(x_center,y_center,block2_start-x_center,Math.PI,0);ctx.stroke()}}});var Color=function(rgb,a){if(Array.isArray(rgb)){this.rgb=rgb}else{if(rgb.length==6){this.rgb=rgb.match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{if(rgb.length==7){this.rgb=rgb.substring(1,7).match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{this.rgb=rgb.split("").map(function(c){return parseInt(c+c,16)})}}}this.alpha=typeof(a)==="number"?a:1};Color.prototype={eval:function(){return this},toCSS:function(){if(this.alpha<1){return"rgba("+this.rgb.map(function(c){return Math.round(c)}).concat(this.alpha).join(", ")+")"}else{return"#"+this.rgb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")}},toHSL:function(){var r=this.rgb[0]/255,g=this.rgb[1]/255,b=this.rgb[2]/255,a=this.alpha;var max=Math.max(r,g,b),min=Math.min(r,g,b);var h,s,l=(max+min)/2,d=max-min;if(max===min){h=s=0}else{s=l>0.5?d/(2-max-min):d/(max+min);switch(max){case r:h=(g-b)/d+(g<b?6:0);break;case g:h=(b-r)/d+2;break;case b:h=(r-g)/d+4;break}h/=6}return{h:h*360,s:s,l:l,a:a}},toARGB:function(){var argb=[Math.round(this.alpha*255)].concat(this.rgb);return"#"+argb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")},mix:function(color2,weight){color1=this;var p=weight;var w=p*2-1;var a=color1.toHSL().a-color2.toHSL().a;var w1=(((w*a==-1)?w:(w+a)/(1+w*a))+1)/2;var w2=1-w1;var rgb=[color1.rgb[0]*w1+color2.rgb[0]*w2,color1.rgb[1]*w1+color2.rgb[1]*w2,color1.rgb[2]*w1+color2.rgb[2]*w2];var alpha=color1.alpha*p+color2.alpha*(1-p);return new Color(rgb,alpha)}};var LinearRamp=function(start_color,end_color,start_value,end_value){this.start_color=new Color(start_color);this.end_color=new Color(end_color);this.start_value=start_value;this.end_value=end_value;this.value_range=end_value-start_value};LinearRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);value=(value-this.start_value)/this.value_range;return this.start_color.mix(this.end_color,1-value).toCSS()};var SplitRamp=function(start_color,middle_color,end_color,start_value,end_value){this.positive_ramp=new LinearRamp(middle_color,end_color,0,end_value);this.negative_ramp=new LinearRamp(middle_color,start_color,0,-start_value);this.start_value=start_value;this.end_value=end_value};SplitRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);if(value>=0){return this.positive_ramp.map_value(value)}else{return this.negative_ramp.map_value(-value)}};var DiagonalHeatmapPainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);var i,len;if(this.prefs.min_value===undefined){var min_value=Infinity;for(i=0,len=this.data.length;i<len;i++){min_value=Math.min(min_value,this.data[i][5])}this.prefs.min_value=min_value}if(this.prefs.max_value===undefined){var max_value=-Infinity;for(i=0,len=this.data.length;i<len;i++){max_value=Math.max(max_value,this.data[i][5])}this.prefs.max_value=max_value}};DiagonalHeatmapPainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Heatmap",pos_color:"#FF8C00",neg_color:"#4169E1"};DiagonalHeatmapPainter.prototype.draw=function(ctx,width,height,w_scale){var min_value=this.prefs.min_value,max_value=this.prefs.max_value,value_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data,invsqrt2=1/Math.sqrt(2);var ramp=(new SplitRamp(this.prefs.neg_color,"#FFFFFF",this.prefs.pos_color,min_value,max_value));var d,s1,e1,s2,e2,value;var scale=function(p){return(p-view_start)*w_scale};ctx.save();ctx.rotate(-45*Math.PI/180);ctx.scale(invsqrt2,invsqrt2);for(var i=0,len=data.length;i<len;i++){d=data[i];s1=scale(d[1]);e1=scale(d[2]);s2=scale(d[4]);e2=scale(d[5]);value=d[6];ctx.fillStyle=(ramp.map_value(value));ctx.fillRect(s1,s2,(e1-s1),(e2-s2))}ctx.restore()};return{Scaler:Scaler,SummaryTreePainter:SummaryTreePainter,LinePainter:LinePainter,LinkedFeaturePainter:LinkedFeaturePainter,ReadPainter:ReadPainter,ArcLinkedFeaturePainter:ArcLinkedFeaturePainter,DiagonalHeatmapPainter:DiagonalHeatmapPainter}}); \ No newline at end of file +define(["libs/underscore"],function(_){var extend=_.extend;var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(first_region,second_region){var first_start=first_region[0],first_end=first_region[1],second_start=second_region[0],second_end=second_region[1],overlap;if(first_start<second_start){if(first_end<second_start){overlap=BEFORE}else{if(first_end<=second_end){overlap=OVERLAP_START}else{overlap=CONTAINS}}}else{if(first_start>second_end){overlap=AFTER}else{if(first_end<=second_end){overlap=CONTAINED_BY}else{overlap=OVERLAP_END}}}return overlap};var is_overlap=function(first_region,second_region){var overlap=compute_overlap(first_region,second_region);return(overlap!==BEFORE&&overlap!==AFTER)};var dashedLine=function(ctx,x1,y1,x2,y2,dashLen){if(dashLen===undefined){dashLen=4}var dX=x2-x1;var dY=y2-y1;var dashes=Math.floor(Math.sqrt(dX*dX+dY*dY)/dashLen);var dashX=dX/dashes;var dashY=dY/dashes;var q;for(q=0;q<dashes;q++,x1+=dashX,y1+=dashY){if(q%2!==0){continue}ctx.fillRect(x1,y1,dashLen,1)}};var drawDownwardEquilateralTriangle=function(ctx,down_vertex_x,down_vertex_y,side_len){var x1=down_vertex_x-side_len/2,x2=down_vertex_x+side_len/2,y=down_vertex_y-Math.sqrt(side_len*3/2);ctx.beginPath();ctx.moveTo(x1,y);ctx.lineTo(x2,y);ctx.lineTo(down_vertex_x,down_vertex_y);ctx.lineTo(x1,y);ctx.strokeStyle=this.fillStyle;ctx.fill();ctx.stroke();ctx.closePath()};var Scaler=function(default_val){this.default_val=(default_val?default_val:1)};Scaler.prototype.gen_val=function(input){return this.default_val};var Painter=function(data,view_start,view_end,prefs,mode){this.data=data;this.view_start=view_start;this.view_end=view_end;this.prefs=extend({},this.default_prefs,prefs);this.mode=mode};Painter.prototype.default_prefs={};Painter.prototype.draw=function(ctx,width,height,w_scale){};var SummaryTreePainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode)};SummaryTreePainter.prototype.default_prefs={show_counts:false};SummaryTreePainter.prototype.draw=function(ctx,width,height,w_scale){var view_start=this.view_start,points=this.data.data,max=(this.prefs.histogram_max?this.prefs.histogram_max:this.data.max),base_y=height;delta_x_px=Math.ceil(this.data.delta*w_scale);ctx.save();for(var i=0,len=points.length;i<len;i++){var x=Math.floor((points[i][0]-view_start)*w_scale);var y=points[i][1];if(!y){continue}var y_px=y/max*height;if(y!==0&&y_px<1){y_px=1}ctx.fillStyle=this.prefs.block_color;ctx.fillRect(x,base_y-y_px,delta_x_px,y_px);var text_padding_req_x=4;if(this.prefs.show_counts&&(ctx.measureText(y).width+text_padding_req_x)<delta_x_px){ctx.fillStyle=this.prefs.label_color;ctx.textAlign="center";ctx.fillText(y,x+(delta_x_px/2),10)}}ctx.restore()};var LinePainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);var i,len;if(this.prefs.min_value===undefined){var min_value=Infinity;for(i=0,len=this.data.length;i<len;i++){min_value=Math.min(min_value,this.data[i][1])}this.prefs.min_value=min_value}if(this.prefs.max_value===undefined){var max_value=-Infinity;for(i=0,len=this.data.length;i<len;i++){max_value=Math.max(max_value,this.data[i][1])}this.prefs.max_value=max_value}};LinePainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};LinePainter.prototype.draw=function(ctx,width,height,w_scale){var in_path=false,min_value=this.prefs.min_value,max_value=this.prefs.max_value,vertical_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data;ctx.save();var y_zero=Math.round(height+min_value/vertical_range*height);if(mode!=="Intensity"){ctx.fillStyle="#aaa";ctx.fillRect(0,y_zero,width,1)}ctx.beginPath();var x_scaled,y,delta_x_px;if(data.length>1){delta_x_px=Math.ceil((data[1][0]-data[0][0])*w_scale)}else{delta_x_px=10}var pref_color=parseInt(this.prefs.color.slice(1),16),pref_r=(pref_color&16711680)>>16,pref_g=(pref_color&65280)>>8,pref_b=pref_color&255;for(var i=0,len=data.length;i<len;i++){ctx.fillStyle=ctx.strokeStyle=this.prefs.color;x_scaled=Math.round((data[i][0]-view_start)*w_scale);y=data[i][1];var top_overflow=false,bot_overflow=false;if(y===null){if(in_path&&mode==="Filled"){ctx.lineTo(x_scaled,height_px)}in_path=false;continue}if(y<min_value){bot_overflow=true;y=min_value}else{if(y>max_value){top_overflow=true;y=max_value}}if(mode==="Histogram"){y=Math.round(y/vertical_range*height_px);ctx.fillRect(x_scaled,y_zero,delta_x_px,-y)}else{if(mode==="Intensity"){var saturation=(y-min_value)/vertical_range,new_r=Math.round(pref_r+(255-pref_r)*(1-saturation)),new_g=Math.round(pref_g+(255-pref_g)*(1-saturation)),new_b=Math.round(pref_b+(255-pref_b)*(1-saturation));ctx.fillStyle="rgb("+new_r+","+new_g+","+new_b+")";ctx.fillRect(x_scaled,0,delta_x_px,height_px)}else{y=Math.round(height_px-(y-min_value)/vertical_range*height_px);if(in_path){ctx.lineTo(x_scaled,y)}else{in_path=true;if(mode==="Filled"){ctx.moveTo(x_scaled,height_px);ctx.lineTo(x_scaled,y)}else{ctx.moveTo(x_scaled,y)}}}}ctx.fillStyle=this.prefs.overflow_color;if(top_overflow||bot_overflow){var overflow_x;if(mode==="Histogram"||mode==="Intensity"){overflow_x=delta_x_px}else{x_scaled-=2;overflow_x=4}if(top_overflow){ctx.fillRect(x_scaled,0,overflow_x,3)}if(bot_overflow){ctx.fillRect(x_scaled,height_px-3,overflow_x,3)}}ctx.fillStyle=this.prefs.color}if(mode==="Filled"){if(in_path){ctx.lineTo(x_scaled,y_zero);ctx.lineTo(0,y_zero)}ctx.fill()}else{ctx.stroke()}ctx.restore()};var FeaturePositionMapper=function(slot_height){this.feature_positions={};this.slot_height=slot_height;this.translation=0;this.y_translation=0};FeaturePositionMapper.prototype.map_feature_data=function(feature_data,slot,x_start,x_end){if(!this.feature_positions[slot]){this.feature_positions[slot]=[]}this.feature_positions[slot].push({data:feature_data,x_start:x_start,x_end:x_end})};FeaturePositionMapper.prototype.get_feature_data=function(x,y){var slot=Math.floor((y-this.y_translation)/this.slot_height),feature_dict;if(!this.feature_positions[slot]){return null}x+=this.translation;for(var i=0;i<this.feature_positions[slot].length;i++){feature_dict=this.feature_positions[slot][i];if(x>=feature_dict.x_start&&x<=feature_dict.x_end){return feature_dict.data}}};var FeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){Painter.call(this,data,view_start,view_end,prefs,mode);this.alpha_scaler=(alpha_scaler?alpha_scaler:new Scaler());this.height_scaler=(height_scaler?height_scaler:new Scaler())};FeaturePainter.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};extend(FeaturePainter.prototype,{get_required_height:function(rows_required,width){var required_height=this.get_row_height(),y_scale=required_height,mode=this.mode;if(mode==="no_detail"||mode==="Squish"||mode==="Pack"){required_height=rows_required*y_scale}return required_height+this.get_top_padding(width)+this.get_bottom_padding(width)},get_top_padding:function(width){return 0},get_bottom_padding:function(width){return Math.max(Math.round(this.get_row_height()/2),5)},draw:function(ctx,width,height,w_scale,slots){var data=this.data,view_start=this.view_start,view_end=this.view_end;ctx.save();ctx.fillStyle=this.prefs.block_color;ctx.textAlign="right";var y_scale=this.get_row_height(),feature_mapper=new FeaturePositionMapper(y_scale),x_draw_coords;for(var i=0,len=data.length;i<len;i++){var feature=data[i],feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],slot=(slots&&slots[feature_uid]!==undefined?slots[feature_uid]:null);if((feature_start<view_end&&feature_end>view_start)&&(this.mode==="Dense"||slot!==null)){x_draw_coords=this.draw_element(ctx,this.mode,feature,slot,view_start,view_end,w_scale,y_scale,width);feature_mapper.map_feature_data(feature,slot,x_draw_coords[0],x_draw_coords[1])}}ctx.restore();feature_mapper.y_translation=this.get_top_padding(width);return feature_mapper},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){console.log("WARNING: Unimplemented function.");return[0,0]}});var DENSE_TRACK_HEIGHT=10,NO_DETAIL_TRACK_HEIGHT=3,SQUISH_TRACK_HEIGHT=5,PACK_TRACK_HEIGHT=10,NO_DETAIL_FEATURE_HEIGHT=1,DENSE_FEATURE_HEIGHT=9,SQUISH_FEATURE_HEIGHT=3,PACK_FEATURE_HEIGHT=9,LABEL_SPACING=2,CONNECTOR_COLOR="#ccc";var LinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.draw_background_connector=true;this.draw_individual_connectors=false};extend(LinkedFeaturePainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var mode=this.mode,height;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="no_detail"){height=NO_DETAIL_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT}}}return height},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],feature_name=feature[3],feature_strand=feature[4],f_start=Math.floor(Math.max(0,(feature_start-tile_low)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low)*w_scale))),draw_start=f_start,draw_end=f_end,y_center=(mode==="Dense"?0:(0+slot))*y_scale+this.get_top_padding(width),thickness,y_start,thick_start=null,thick_end=null,block_color=(!feature_strand||feature_strand==="+"||feature_strand==="."?this.prefs.block_color:this.prefs.reverse_strand_color);label_color=this.prefs.label_color;ctx.globalAlpha=this.alpha_scaler.gen_val(feature);if(mode==="Dense"){slot=1}if(mode==="no_detail"){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_center+5,f_end-f_start,NO_DETAIL_FEATURE_HEIGHT)}else{var feature_ts=feature[5],feature_te=feature[6],feature_blocks=feature[7],full_height=true;if(feature_ts&&feature_te){thick_start=Math.floor(Math.max(0,(feature_ts-tile_low)*w_scale));thick_end=Math.ceil(Math.min(width,Math.max(0,(feature_te-tile_low)*w_scale)))}var thin_height,thick_height;if(mode==="Squish"){thin_height=1;thick_height=SQUISH_FEATURE_HEIGHT;full_height=false}else{if(mode==="Dense"){thin_height=5;thick_height=DENSE_FEATURE_HEIGHT}else{thin_height=5;thick_height=PACK_FEATURE_HEIGHT}}if(!feature_blocks){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_center+1,f_end-f_start,thick_height);if(feature_strand&&full_height){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}ctx.fillRect(f_start,y_center+1,f_end-f_start,thick_height)}}else{var cur_y_center,cur_height;if(mode==="Squish"||mode==="Dense"){cur_y_center=y_center+Math.floor(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}else{if(feature_strand){cur_y_center=y_center;cur_height=thick_height}else{cur_y_center+=(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}}if(this.draw_background_connector){if(mode==="Squish"||mode==="Dense"){ctx.fillStyle=CONNECTOR_COLOR}else{if(feature_strand){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand")}}}else{ctx.fillStyle=CONNECTOR_COLOR}}ctx.fillRect(f_start,cur_y_center,f_end-f_start,cur_height)}var start_and_height;for(var k=0,k_len=feature_blocks.length;k<k_len;k++){var block=feature_blocks[k],block_start=Math.floor(Math.max(0,(block[0]-tile_low)*w_scale)),block_end=Math.ceil(Math.min(width,Math.max((block[1]-tile_low)*w_scale))),last_block_start,last_block_end;if(block_start>block_end){continue}ctx.fillStyle=block_color;ctx.fillRect(block_start,y_center+(thick_height-thin_height)/2+1,block_end-block_start,thin_height);if(thick_start!==undefined&&feature_te>feature_ts&&!(block_start>thick_end||block_end<thick_start)){var block_thick_start=Math.max(block_start,thick_start),block_thick_end=Math.min(block_end,thick_end);ctx.fillRect(block_thick_start,y_center+1,block_thick_end-block_thick_start,thick_height);if(feature_blocks.length===1&&mode==="Pack"){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}if(block_thick_start+14<block_thick_end){block_thick_start+=2;block_thick_end-=2}ctx.fillRect(block_thick_start,y_center+1,block_thick_end-block_thick_start,thick_height)}}if(this.draw_individual_connectors&&last_block_start){this.draw_connector(ctx,last_block_start,last_block_end,block_start,block_end,y_center)}last_block_start=block_start;last_block_end=block_end}if(mode==="Pack"){ctx.globalAlpha=1;ctx.fillStyle="white";var hscale_factor=this.height_scaler.gen_val(feature),new_height=Math.ceil(thick_height*hscale_factor),ws_height=Math.round((thick_height-new_height)/2);if(hscale_factor!==1){ctx.fillRect(f_start,cur_y_center+1,f_end-f_start,ws_height);ctx.fillRect(f_start,cur_y_center+thick_height-ws_height+1,f_end-f_start,ws_height)}}}ctx.globalAlpha=1;if(feature_name&&mode==="Pack"&&feature_start>tile_low){ctx.fillStyle=label_color;if(tile_low===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING,y_center+8);draw_end+=ctx.measureText(feature_name).width+LABEL_SPACING}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_center+8);draw_start-=ctx.measureText(feature_name).width+LABEL_SPACING}}}ctx.globalAlpha=1;return[draw_start,draw_end]}});var ReadPainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler,ref_seq){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.ref_seq=(ref_seq?ref_seq.data:null)};extend(ReadPainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var height,mode=this.mode;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT;if(this.prefs.show_insertions){height*=2}}}return height},draw_read:function(ctx,mode,w_scale,y_center,tile_low,tile_high,feature_start,cigar,strand,ref_seq){ctx.textAlign="center";var tile_region=[tile_low,tile_high],base_offset=0,seq_offset=0,gap=0,char_width_px=ctx.canvas.manager.char_width_px,block_color=(strand==="+"?this.prefs.block_color:this.prefs.reverse_strand_color);var draw_last=[];if((mode==="Pack"||this.mode==="Auto")&&ref_seq!==undefined&&w_scale>char_width_px){gap=Math.round(w_scale/2)}if(!cigar){cigar=[[0,ref_seq.length]]}for(var cig_id=0,len=cigar.length;cig_id<len;cig_id++){var cig=cigar[cig_id],cig_op="MIDNSHP=X"[cig[0]],cig_len=cig[1];if(cig_op==="H"||cig_op==="S"){base_offset-=cig_len}var seq_start=feature_start+base_offset,s_start=Math.floor(Math.max(0,(seq_start-tile_low)*w_scale)),s_end=Math.floor(Math.max(0,(seq_start+cig_len-tile_low)*w_scale));if(s_start===s_end){s_end+=1}switch(cig_op){case"H":break;case"S":case"M":case"=":if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var seq=ref_seq.slice(seq_offset,seq_offset+cig_len);if(gap>0){ctx.fillStyle=block_color;ctx.fillRect(s_start-gap,y_center+1,s_end-s_start,9);ctx.fillStyle=CONNECTOR_COLOR;for(var c=0,str_len=seq.length;c<str_len;c++){if(this.prefs.show_differences){if(this.ref_seq){var ref_char=this.ref_seq[seq_start-tile_low+c];if(!ref_char||ref_char.toLowerCase()===seq[c].toLowerCase()){continue}}else{continue}}if(seq_start+c>=tile_low&&seq_start+c<=tile_high){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillText(seq[c],c_start,y_center+9)}}}else{ctx.fillStyle=block_color;ctx.fillRect(s_start,y_center+4,s_end-s_start,SQUISH_FEATURE_HEIGHT)}}seq_offset+=cig_len;base_offset+=cig_len;break;case"N":ctx.fillStyle=CONNECTOR_COLOR;ctx.fillRect(s_start-gap,y_center+5,s_end-s_start,1);base_offset+=cig_len;break;case"D":ctx.fillStyle="red";ctx.fillRect(s_start-gap,y_center+4,s_end-s_start,3);base_offset+=cig_len;break;case"P":break;case"I":var insert_x_coord=s_start-gap;if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var seq=ref_seq.slice(seq_offset,seq_offset+cig_len);if(this.prefs.show_insertions){var x_center=s_start-(s_end-s_start)/2;if((mode==="Pack"||this.mode==="Auto")&&ref_seq!==undefined&&w_scale>char_width_px){ctx.fillStyle="yellow";ctx.fillRect(x_center-gap,y_center-9,s_end-s_start,9);draw_last[draw_last.length]={type:"triangle",data:[insert_x_coord,y_center+4,5]};ctx.fillStyle=CONNECTOR_COLOR;switch(compute_overlap([seq_start,seq_start+cig_len],tile_region)){case (OVERLAP_START):seq=seq.slice(tile_low-seq_start);break;case (OVERLAP_END):seq=seq.slice(0,seq_start-tile_high);break;case (CONTAINED_BY):break;case (CONTAINS):seq=seq.slice(tile_low-seq_start,seq_start-tile_high);break}for(var c=0,str_len=seq.length;c<str_len;c++){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillText(seq[c],c_start-(s_end-s_start)/2,y_center)}}else{ctx.fillStyle="yellow";ctx.fillRect(x_center,y_center+(this.mode!=="Dense"?2:5),s_end-s_start,(mode!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((mode==="Pack"||this.mode==="Auto")&&ref_seq!==undefined&&w_scale>char_width_px){draw_last.push({type:"text",data:[seq.length,insert_x_coord,y_center+9]})}else{}}}seq_offset+=cig_len;break;case"X":seq_offset+=cig_len;break}}ctx.fillStyle="yellow";var item,type,data;for(var i=0;i<draw_last.length;i++){item=draw_last[i];type=item.type;data=item.data;if(type==="text"){ctx.save();ctx.font="bold "+ctx.font;ctx.fillText(data[0],data[1],data[2]);ctx.restore()}else{if(type==="triangle"){drawDownwardEquilateralTriangle(ctx,data[0],data[1],data[2])}}}},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],feature_name=feature[3],f_start=Math.floor(Math.max(0,(feature_start-tile_low)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low)*w_scale))),y_center=(mode==="Dense"?0:(0+slot))*y_scale,label_color=this.prefs.label_color,gap=0;if((mode==="Pack"||this.mode==="Auto")&&w_scale>ctx.canvas.manager.char_width_px){var gap=Math.round(w_scale/2)}if(feature[5] instanceof Array){var b1_start=Math.floor(Math.max(0,(feature[4][0]-tile_low)*w_scale)),b1_end=Math.ceil(Math.min(width,Math.max(0,(feature[4][1]-tile_low)*w_scale))),b2_start=Math.floor(Math.max(0,(feature[5][0]-tile_low)*w_scale)),b2_end=Math.ceil(Math.min(width,Math.max(0,(feature[5][1]-tile_low)*w_scale))),connector=true;if(feature[4][1]>=tile_low&&feature[4][0]<=tile_high&&feature[4][2]){this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature[4][0],feature[4][2],feature[4][3],feature[4][4])}else{connector=false}if(feature[5][1]>=tile_low&&feature[5][0]<=tile_high&&feature[5][2]){this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature[5][0],feature[5][2],feature[5][3],feature[5][4])}else{connector=false}if(connector&&b2_start>b1_end){ctx.fillStyle=CONNECTOR_COLOR;dashedLine(ctx,b1_end-gap,y_center+5,b2_start-gap,y_center+5)}}else{this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature_start,feature[4],feature[5],feature[6])}if(mode==="Pack"&&feature_start>tile_low&&feature_name!=="."){ctx.fillStyle=this.prefs.label_color;var tile_index=1;if(tile_index===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING-gap,y_center+8)}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING-gap,y_center+8)}}return[0,0]}});var ArcLinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){LinkedFeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.longest_feature_length=this.calculate_longest_feature_length();this.draw_background_connector=false;this.draw_individual_connectors=true};extend(ArcLinkedFeaturePainter.prototype,FeaturePainter.prototype,LinkedFeaturePainter.prototype,{calculate_longest_feature_length:function(){var longest_feature_length=0;for(var i=0,len=this.data.length;i<len;i++){var feature=this.data[i],feature_start=feature[1],feature_end=feature[2];longest_feature_length=Math.max(longest_feature_length,feature_end-feature_start)}return longest_feature_length},get_top_padding:function(width){var view_range=this.view_end-this.view_start,w_scale=width/view_range;return Math.min(128,Math.ceil((this.longest_feature_length/2)*w_scale))},draw_connector:function(ctx,block1_start,block1_end,block2_start,block2_end,y_center){var x_center=(block1_end+block2_start)/2,radius=block2_start-x_center;var angle1=Math.PI,angle2=0;if(radius>0){ctx.beginPath();ctx.arc(x_center,y_center,block2_start-x_center,Math.PI,0);ctx.stroke()}}});var Color=function(rgb,a){if(Array.isArray(rgb)){this.rgb=rgb}else{if(rgb.length==6){this.rgb=rgb.match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{if(rgb.length==7){this.rgb=rgb.substring(1,7).match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{this.rgb=rgb.split("").map(function(c){return parseInt(c+c,16)})}}}this.alpha=typeof(a)==="number"?a:1};Color.prototype={eval:function(){return this},toCSS:function(){if(this.alpha<1){return"rgba("+this.rgb.map(function(c){return Math.round(c)}).concat(this.alpha).join(", ")+")"}else{return"#"+this.rgb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")}},toHSL:function(){var r=this.rgb[0]/255,g=this.rgb[1]/255,b=this.rgb[2]/255,a=this.alpha;var max=Math.max(r,g,b),min=Math.min(r,g,b);var h,s,l=(max+min)/2,d=max-min;if(max===min){h=s=0}else{s=l>0.5?d/(2-max-min):d/(max+min);switch(max){case r:h=(g-b)/d+(g<b?6:0);break;case g:h=(b-r)/d+2;break;case b:h=(r-g)/d+4;break}h/=6}return{h:h*360,s:s,l:l,a:a}},toARGB:function(){var argb=[Math.round(this.alpha*255)].concat(this.rgb);return"#"+argb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")},mix:function(color2,weight){color1=this;var p=weight;var w=p*2-1;var a=color1.toHSL().a-color2.toHSL().a;var w1=(((w*a==-1)?w:(w+a)/(1+w*a))+1)/2;var w2=1-w1;var rgb=[color1.rgb[0]*w1+color2.rgb[0]*w2,color1.rgb[1]*w1+color2.rgb[1]*w2,color1.rgb[2]*w1+color2.rgb[2]*w2];var alpha=color1.alpha*p+color2.alpha*(1-p);return new Color(rgb,alpha)}};var LinearRamp=function(start_color,end_color,start_value,end_value){this.start_color=new Color(start_color);this.end_color=new Color(end_color);this.start_value=start_value;this.end_value=end_value;this.value_range=end_value-start_value};LinearRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);value=(value-this.start_value)/this.value_range;return this.start_color.mix(this.end_color,1-value).toCSS()};var SplitRamp=function(start_color,middle_color,end_color,start_value,end_value){this.positive_ramp=new LinearRamp(middle_color,end_color,0,end_value);this.negative_ramp=new LinearRamp(middle_color,start_color,0,-start_value);this.start_value=start_value;this.end_value=end_value};SplitRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);if(value>=0){return this.positive_ramp.map_value(value)}else{return this.negative_ramp.map_value(-value)}};var DiagonalHeatmapPainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);var i,len;if(this.prefs.min_value===undefined){var min_value=Infinity;for(i=0,len=this.data.length;i<len;i++){min_value=Math.min(min_value,this.data[i][5])}this.prefs.min_value=min_value}if(this.prefs.max_value===undefined){var max_value=-Infinity;for(i=0,len=this.data.length;i<len;i++){max_value=Math.max(max_value,this.data[i][5])}this.prefs.max_value=max_value}};DiagonalHeatmapPainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Heatmap",pos_color:"#FF8C00",neg_color:"#4169E1"};DiagonalHeatmapPainter.prototype.draw=function(ctx,width,height,w_scale){var min_value=this.prefs.min_value,max_value=this.prefs.max_value,value_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data,invsqrt2=1/Math.sqrt(2);var ramp=(new SplitRamp(this.prefs.neg_color,"#FFFFFF",this.prefs.pos_color,min_value,max_value));var d,s1,e1,s2,e2,value;var scale=function(p){return(p-view_start)*w_scale};ctx.save();ctx.rotate(-45*Math.PI/180);ctx.scale(invsqrt2,invsqrt2);for(var i=0,len=data.length;i<len;i++){d=data[i];s1=scale(d[1]);e1=scale(d[2]);s2=scale(d[4]);e2=scale(d[5]);value=d[6];ctx.fillStyle=(ramp.map_value(value));ctx.fillRect(s1,s2,(e1-s1),(e2-s2))}ctx.restore()};return{Scaler:Scaler,SummaryTreePainter:SummaryTreePainter,LinePainter:LinePainter,LinkedFeaturePainter:LinkedFeaturePainter,ReadPainter:ReadPainter,ArcLinkedFeaturePainter:ArcLinkedFeaturePainter,DiagonalHeatmapPainter:DiagonalHeatmapPainter}}); \ No newline at end of file diff -r 04aaf661f80a92cfd8c804baccac348e3cc98355 -r 865c74ff03755f21eaaf4a557b1c2aeb1518e593 static/scripts/viz/trackster/painters.js --- a/static/scripts/viz/trackster/painters.js +++ b/static/scripts/viz/trackster/painters.js @@ -236,9 +236,7 @@ // Paint track. for (var i = 0, len = data.length; i < len; i++) { ctx.fillStyle = ctx.strokeStyle = this.prefs.color; - // -1 because LineTrack data uses 1-based coordinate system but painter - // uses 0-based system. - x_scaled = Math.round((data[i][0] - view_start - 1) * w_scale); + x_scaled = Math.round((data[i][0] - view_start) * w_scale); y = data[i][1]; var top_overflow = false, bot_overflow = false; if (y === null) { Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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