January 2014 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: greg: Statistics fixes for the tool shed's install and test framework.
by commits-noreply＠bitbucket.org 24 Jan '14

24 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/cce4687a7ccc/ Changeset: cce4687a7ccc User: greg Date: 2014-01-24 20:14:06 Summary: Statistics fixes for the tool shed's install and test framework. Affected #: 1 file diff -r ac32a07b4eea8cee714368ecb247ce22cac01a4c -r cce4687a7ccc56a47db95498b0ae86f0f5986125 test/install_and_test_tool_shed_repositories/base/util.py --- a/test/install_and_test_tool_shed_repositories/base/util.py +++ b/test/install_and_test_tool_shed_repositories/base/util.py @@ -756,15 +756,16 @@ print 'Revision %s of repository %s owned by %s has the following installation error:' % ( changeset_revision, name, owner ) # Use log.debug here instead of print because print will throw UnicodeEncodeError exceptions. log.debug( '%s' % error_message ) + identity_tup = ( name, owner, changeset_revision ) + processed_repositories_with_installation_error = \ + install_and_test_statistics_dict.get( 'repositories_with_installation_error', [] ) + if identity_tup not in processed_repositories_with_installation_error: + install_and_test_statistics_dict[ 'repositories_with_installation_error' ].append( identity_tup ) missing_repository_dependency_info_dict = dict( tool_shed=tool_shed, name=name, owner=owner, changeset_revision=changeset_revision, error_message=error_message ) - processed_repositories_with_installation_error = \ - install_and_test_statistics_dict.get( 'repositories_with_installation_error', [] ) - if missing_repository_dependency_info_dict not in processed_repositories_with_installation_error: - install_and_test_statistics_dict[ 'repositories_with_installation_error' ].append( missing_repository_dependency_info_dict ) tool_test_results_dict[ 'installation_errors' ][ 'repository_dependencies' ].append( missing_repository_dependency_info_dict ) if repository.missing_tool_dependencies: print 'The following tool dependencies for revision %s of repository %s owned by %s have installation errors:' % \ @@ -779,14 +780,15 @@ print 'Version %s of tool dependency %s %s has the following installation error:' % ( version, type, name ) # Use log.debug here instead of print because print will throw UnicodeEncodeError exceptions. log.debug( '%s' % error_message ) + identity_tup = ( name, type, version ) + processed_tool_dependencies_with_installation_error = \ + install_and_test_statistics_dict.get( 'tool_dependencies_with_installation_error', [] ) + if identity_tup not in processed_tool_dependencies_with_installation_error: + install_and_test_statistics_dict[ 'tool_dependencies_with_installation_error' ].append( identity_tup ) missing_tool_dependency_info_dict = dict( type=type, name=name, version=version, error_message=error_message ) - processed_tool_dependencies_with_installation_error = \ - install_and_test_statistics_dict.get( 'tool_dependencies_with_installation_error', [] ) - if missing_tool_dependency_info_dict not in processed_tool_dependencies_with_installation_error: - install_and_test_statistics_dict[ 'tool_dependencies_with_installation_error' ].append( missing_tool_dependency_info_dict ) tool_test_results_dict[ 'installation_errors' ][ 'tool_dependencies' ].append( missing_tool_dependency_info_dict ) if repository.installed_repository_dependencies: print 'The following repository dependencies for revision %s of repository %s owned by %s are installed:' % \ Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: greg: Fix for discovering tools to eliminate from the toolbox for the tool shed's install and test framework.
by commits-noreply＠bitbucket.org 24 Jan '14

24 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ac32a07b4eea/ Changeset: ac32a07b4eea User: greg Date: 2014-01-24 19:56:29 Summary: Fix for discovering tools to eliminate from the toolbox for the tool shed's install and test framework. Affected #: 1 file diff -r 9fb269cab1cea862d5d5bb997c4d0fdce9607e6a -r ac32a07b4eea8cee714368ecb247ce22cac01a4c test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py @@ -578,15 +578,22 @@ # Revisit this code if at some point we notice that Twill re-runs tests that should have been deleted. # Undoubtedly the following if statement will need to be enhanced to find the tool id in question. For # example, the following or is required because Twill replaces some spaces with underscores in test names. - if app_tool_id == tool_id or app_tool_id.replace( '_', ' ' ) == tool_id.replace( '_', ' ' ): - tools_to_delete_by_id.append( tool_id ) + if app_tool_id == tool_id: + print 'Setting tool id %s for deletion from app.toolbox[ tools_by_id ].' % str( app_tool_id ) + tools_to_delete_by_id.append( app_tool_id ) + else: + reset_spaces_app_tool_id = app_tool_id.replace( '_', ' ' ) + reset_spaces_tool_id = tool_id.replace( '_', ' ' ) + if reset_spaces_app_tool_id == reset_spaces_tool_id: + print 'Setting tool id %s for deletion from app.toolbox[ tools_by_id ].' % str( app_tool_id ) + tools_to_delete_by_id.append( app_tool_id ) # Delete the discovered twill-generated tests. for key in tests_to_delete: if key in test_toolbox.__dict__: - log.debug( 'Deleting test %s from test_toolbox.' % str( key ) ) + print 'Deleting test %s from test_toolbox.' % str( key ) del test_toolbox.__dict__[ key ] for tool_id in tools_to_delete_by_id: - log.debug( 'Deleting tool id %s from app.toolbox[ tools_by_id ].' % str( tool_id ) ) + print 'Deleting tool id %s from app.toolbox[ tools_by_id ].' % str( tool_id ) del app.toolbox.tools_by_id[ tool_id ] def test_repository_tools( app, repository, repository_dict, tool_test_results_dicts, tool_test_results_dict, Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: guerler: Fix popup menus
by commits-noreply＠bitbucket.org 24 Jan '14

24 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9fb269cab1ce/ Changeset: 9fb269cab1ce User: guerler Date: 2014-01-24 18:44:52 Summary: Fix popup menus Affected #: 2 files diff -r 9414cc43797afb77190abcbda0fdf173a6a100f3 -r 9fb269cab1cea862d5d5bb997c4d0fdce9607e6a static/scripts/galaxy.base.js --- a/static/scripts/galaxy.base.js +++ b/static/scripts/galaxy.base.js @@ -179,6 +179,7 @@ // so manually do it here. if (target) { window.open(href, target); + return false; } // For all other links, do the default action. else { diff -r 9414cc43797afb77190abcbda0fdf173a6a100f3 -r 9fb269cab1cea862d5d5bb997c4d0fdce9607e6a static/scripts/packed/galaxy.base.js --- a/static/scripts/packed/galaxy.base.js +++ b/static/scripts/packed/galaxy.base.js @@ -1,1 +1,1 @@ -(function(){var b=0;var c=["ms","moz","webkit","o"];for(var 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commit/galaxy-central: greg: Add the ability for a tool shed repository owner to grant administrative privileges on a repository to other users or groups. This feature incorporates the tool shed's role based authorization framework. Each repository and repository owner are associated with a repository administrative role which can then be associated with others.
by commits-noreply＠bitbucket.org 24 Jan '14

24 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9414cc43797a/ Changeset: 9414cc43797a User: greg Date: 2014-01-24 18:31:29 Summary: Add the ability for a tool shed repository owner to grant administrative privileges on a repository to other users or groups. This feature incorporates the tool shed's role based authorization framework. Each repository and repository owner are associated with a repository administrative role which can then be associated with others. Affected #: 13 files diff -r e2eb861e6c0b0cbaf8a1a1e091d3792724495b69 -r 9414cc43797afb77190abcbda0fdf173a6a100f3 lib/galaxy/web/base/controllers/admin.py --- a/lib/galaxy/web/base/controllers/admin.py +++ b/lib/galaxy/web/base/controllers/admin.py @@ -94,6 +94,9 @@ return self.purge_role( trans, **kwargs ) if operation == "manage users and groups": return self.manage_users_and_groups_for_role( trans, **kwargs ) + if operation == "manage role associations": + # This is currently used only in the Tool Shed. + return self.manage_role_associations( trans, **kwargs ) if operation == "rename": return self.rename_role( trans, **kwargs ) # Render the list view diff -r e2eb861e6c0b0cbaf8a1a1e091d3792724495b69 -r 9414cc43797afb77190abcbda0fdf173a6a100f3 lib/galaxy/webapps/tool_shed/controllers/admin.py --- a/lib/galaxy/webapps/tool_shed/controllers/admin.py +++ b/lib/galaxy/webapps/tool_shed/controllers/admin.py @@ -1,17 +1,14 @@ +import logging from galaxy.web.base.controller import BaseUIController -from galaxy import web, util from galaxy.web.base.controllers.admin import Admin +from galaxy import util +from galaxy import web from galaxy.util import inflector import tool_shed.util.shed_util_common as suc import tool_shed.util.metadata_util as metadata_util +from tool_shed.util import repository_maintenance_util import tool_shed.grids.admin_grids as admin_grids -from galaxy import eggs -eggs.require( 'mercurial' ) -from mercurial import hg - -import logging - log = logging.getLogger( __name__ ) @@ -27,7 +24,7 @@ @web.expose @web.require_admin def browse_repositories( self, trans, **kwd ): - # We add params to the keyword dict in this method in order to rename the param + # We add parameters to the keyword dict in this method in order to rename the param # with an "f-" prefix, simulating filtering by clicking a search link. We have # to take this approach because the "-" character is illegal in HTTP requests. if 'operation' in kwd: @@ -166,6 +163,11 @@ for repository_metadata in repository.downloadable_revisions: repository_metadata.downloadable = False trans.sa_session.add( repository_metadata ) + # Mark the repository admin role as deleted. + repository_admin_role = repository.admin_role + if repository_admin_role is not None: + repository_admin_role.deleted = True + trans.sa_session.add( repository_admin_role ) repository.deleted = True trans.sa_session.add( repository ) trans.sa_session.flush() @@ -295,6 +297,33 @@ @web.expose @web.require_admin + def manage_role_associations( self, trans, **kwd ): + """Manage users, groups and repositories associated with a role.""" + role_id = kwd.get( 'id', None ) + role = repository_maintenance_util.get_role_by_id( trans, role_id ) + # We currently only have a single role associated with a repository, the repository admin role. + repository_role_association = role.repositories[ 0 ] + repository = repository_role_association.repository + associations_dict = repository_maintenance_util.handle_role_associations( trans, role, repository, **kwd ) + in_users = associations_dict.get( 'in_users', [] ) + out_users = associations_dict.get( 'out_users', [] ) + in_groups = associations_dict.get( 'in_groups', [] ) + out_groups = associations_dict.get( 'out_groups', [] ) + message = associations_dict.get( 'message', '' ) + status = associations_dict.get( 'status', 'done' ) + return trans.fill_template( '/webapps/tool_shed/role/role.mako', + in_admin_controller=True, + repository=repository, + role=role, + in_users=in_users, + out_users=out_users, + in_groups=in_groups, + out_groups=out_groups, + message=message, + status=status ) + + @web.expose + @web.require_admin def reset_metadata_on_selected_repositories_in_tool_shed( self, trans, **kwd ): if 'reset_metadata_on_selected_repositories_button' in kwd: message, status = metadata_util.reset_metadata_on_selected_repositories( trans, **kwd ) @@ -322,13 +351,19 @@ repository = suc.get_repository_in_tool_shed( trans, repository_id ) if repository: if repository.deleted: - # Inspect all repository_metadata records to determine those that are installable, and mark them accordingly. + # Inspect all repository_metadata records to determine those that are installable, and mark + # them accordingly. for repository_metadata in repository.metadata_revisions: metadata = repository_metadata.metadata if metadata: if metadata_util.is_downloadable( metadata ): repository_metadata.downloadable = True trans.sa_session.add( repository_metadata ) + # Mark the repository admin role as not deleted. + repository_admin_role = repository.admin_role + if repository_admin_role is not None: + repository_admin_role.deleted = False + trans.sa_session.add( repository_admin_role ) repository.deleted = False trans.sa_session.add( repository ) trans.sa_session.flush() diff -r e2eb861e6c0b0cbaf8a1a1e091d3792724495b69 -r 9414cc43797afb77190abcbda0fdf173a6a100f3 lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -68,6 +68,7 @@ my_writable_repositories_with_test_install_errors_grid = repository_grids.MyWritableRepositoriesWithTestInstallErrorsGrid() repositories_by_user_grid = repository_grids.RepositoriesByUserGrid() repositories_i_own_grid = repository_grids.RepositoriesIOwnGrid() + repositories_i_can_administer_grid = repository_grids.RepositoriesICanAdministerGrid() repositories_in_category_grid = repository_grids.RepositoriesInCategoryGrid() repositories_missing_tool_test_components_grid = repository_grids.RepositoriesMissingToolTestComponentsGrid() repositories_with_failing_tool_tests_grid = repository_grids.RepositoriesWithFailingToolTestsGrid() @@ -351,8 +352,9 @@ @web.expose def browse_repositories( self, trans, **kwd ): - # We add params to the keyword dict in this method in order to rename the param with an "f-" prefix, simulating filtering by clicking a search - # link. We have to take this approach because the "-" character is illegal in HTTP requests. + # We add params to the keyword dict in this method in order to rename the param with an "f-" prefix, + # simulating filtering by clicking a search link. We have to take this approach because the "-" + # character is illegal in HTTP requests. if 'operation' in kwd: operation = kwd[ 'operation' ].lower() if operation == "view_or_manage_repository": @@ -434,6 +436,32 @@ return self.repositories_by_user_grid( trans, **kwd ) @web.expose + def browse_repositories_i_can_administer( self, trans, **kwd ): + if 'operation' in kwd: + operation = kwd[ 'operation' ].lower() + if operation == "view_or_manage_repository": + return trans.response.send_redirect( web.url_for( controller='repository', + action='view_or_manage_repository', + **kwd ) ) + elif operation == "repositories_by_user": + return trans.response.send_redirect( web.url_for( controller='repository', + action='browse_repositories_by_user', + **kwd ) ) + elif operation in [ 'mark as deprecated', 'mark as not deprecated' ]: + kwd[ 'mark_deprecated' ] = operation == 'mark as deprecated' + return trans.response.send_redirect( web.url_for( controller='repository', + action='deprecate', + **kwd ) ) + selected_changeset_revision, repository = suc.get_repository_from_refresh_on_change( trans, **kwd ) + if repository: + return trans.response.send_redirect( web.url_for( controller='repository', + action='browse_repositories', + operation='view_or_manage_repository', + id=trans.security.encode_id( repository.id ), + changeset_revision=selected_changeset_revision ) ) + return self.repositories_i_can_administer_grid( trans, **kwd ) + + @web.expose def browse_repositories_i_own( self, trans, **kwd ): if 'operation' in kwd: operation = kwd[ 'operation' ].lower() @@ -921,8 +949,8 @@ status = kwd.get( 'status', 'done' ) categories = suc.get_categories( trans ) if not categories: - message = 'No categories have been configured in this instance of the Galaxy Tool Shed. ' + \ - 'An administrator needs to create some via the Administrator control panel before creating repositories.', + message = 'No categories have been configured in this instance of the Galaxy Tool Shed. ' + message += 'An administrator needs to create some via the Administrator control panel before creating repositories.', status = 'error' return trans.response.send_redirect( web.url_for( controller='repository', action='browse_repositories', @@ -1741,8 +1769,9 @@ owner = kwd.get( 'owner', None ) changeset_revision = kwd.get( 'changeset_revision', None ) repository = suc.get_repository_by_name_and_owner( trans.app, name, owner ) - # TODO: We're currently returning the tool_dependencies.xml file that is available on disk. We need to enhance this process - # to retrieve older versions of the tool-dependencies.xml file from the repository manafest. + # TODO: We're currently returning the tool_dependencies.xml file that is available on disk. We need + # to enhance this process to retrieve older versions of the tool-dependencies.xml file from the repository + #manafest. repo_dir = repository.repo_path( trans.app ) # Get the tool_dependencies.xml file from disk. tool_dependencies_config = suc.get_config_from_disk( suc.TOOL_DEPENDENCY_DEFINITION_FILENAME, repo_dir ) @@ -1951,6 +1980,9 @@ # See if there are any RepositoryMetadata records since menu items require them. repository_metadata = trans.sa_session.query( trans.model.RepositoryMetadata ).first() current_user = trans.user + # TODO: move the following to some in-memory register so these queries can be done once + # at startup. The in-memory registe can then be managed during the current session. + can_administer_repositories = False has_reviewed_repositories = False has_deprecated_repositories = False if current_user: @@ -1964,6 +1996,16 @@ if repository.deprecated: has_deprecated_repositories = True break + # See if the current user can administer any repositories, but only if not an admin user. + if not trans.user_is_admin(): + if current_user.active_repositories: + can_administer_repositories = True + else: + for repository in trans.sa_session.query( trans.model.Repository ) \ + .filter( trans.model.Repository.table.c.deleted == False ): + if trans.app.security_agent.user_can_administer_repository( current_user, repository ): + can_administer_repositories = True + break # Route in may have been from a sharable URL, in whcih case we'll have a user_id and possibly a name # The received user_id will be the id of the repository owner. user_id = kwd.get( 'user_id', None ) @@ -1971,6 +2013,7 @@ changeset_revision = kwd.get( 'changeset_revision', None ) return trans.fill_template( '/webapps/tool_shed/index.mako', repository_metadata=repository_metadata, + can_administer_repositories=can_administer_repositories, has_reviewed_repositories=has_reviewed_repositories, has_deprecated_repositories=has_deprecated_repositories, user_id=user_id, @@ -2116,9 +2159,8 @@ user = trans.user if kwd.get( 'edit_repository_button', False ): flush_needed = False - # TODO: add a can_manage in the security agent. - if not ( user.email == repository.user.email or trans.user_is_admin() ): - message = "You are not the owner of this repository, so you cannot manage it." + if not ( trans.user_is_admin() or trans.app.security_agent.user_can_administer_repository( user, repository ) ): + message = "You are not the owner of this repository, so you cannot administer it." return trans.response.send_redirect( web.url_for( controller='repository', action='view_repository', id=id, @@ -2145,6 +2187,12 @@ # Change the entry in the repository's hgrc file. hgrc_file = os.path.join( repo_dir, '.hg', 'hgrc' ) repository_maintenance_util.change_repository_name_in_hgrc_file( hgrc_file, repo_name ) + # Rename the repository's admin role to match the new repository name. + repository_admin_role = repository.admin_role + repository_admin_role.name = \ + repository_maintenance_util.get_repository_admin_role_name( str( repo_name ), + str( repository.user.username ) ) + trans.sa_session.add( repository_admin_role ) repository.name = repo_name flush_needed = True elif repository.times_downloaded != 0 and repo_name != repository.name: @@ -2345,6 +2393,55 @@ status=status ) @web.expose + @web.require_login( "manage repository administrators" ) + def manage_repository_admins( self, trans, id, **kwd ): + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) + repository = suc.get_repository_in_tool_shed( trans, id ) + changeset_revision = kwd.get( 'changeset_revision', repository.tip( trans.app ) ) + metadata = None + if changeset_revision != suc.INITIAL_CHANGELOG_HASH: + repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) + if repository_metadata: + metadata = repository_metadata.metadata + else: + # There is no repository_metadata defined for the changeset_revision, so see if it was defined + # in a previous changeset in the changelog. + repo_dir = repository.repo_path( trans.app ) + repo = hg.repository( suc.get_configured_ui(), repo_dir ) + previous_changeset_revision = \ + suc.get_previous_metadata_changeset_revision( repository, + repo, + changeset_revision, + downloadable=False ) + if previous_changeset_revision != suc.INITIAL_CHANGELOG_HASH: + repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, + id, + previous_changeset_revision ) + if repository_metadata: + metadata = repository_metadata.metadata + role = repository.admin_role + associations_dict = repository_maintenance_util.handle_role_associations( trans, role, repository, **kwd ) + in_users = associations_dict.get( 'in_users', [] ) + out_users = associations_dict.get( 'out_users', [] ) + in_groups = associations_dict.get( 'in_groups', [] ) + out_groups = associations_dict.get( 'out_groups', [] ) + message = associations_dict.get( 'message', '' ) + status = associations_dict.get( 'status', 'done' ) + return trans.fill_template( '/webapps/tool_shed/role/role.mako', + in_admin_controller=False, + repository=repository, + metadata=metadata, + changeset_revision=changeset_revision, + role=role, + in_users=in_users, + out_users=out_users, + in_groups=in_groups, + out_groups=out_groups, + message=message, + status=status ) + + @web.expose @web.require_login( "review repository revision" ) def manage_repository_reviews_of_revision( self, trans, **kwd ): return trans.response.send_redirect( web.url_for( controller='repository_review', @@ -3025,8 +3122,10 @@ repository_id = kwd.get( 'id', None ) if repository_id: repository = suc.get_repository_in_tool_shed( trans, repository_id ) + user = trans.user if repository: - if trans.user_is_admin() or repository.user == trans.user: + if user is not None and ( trans.user_is_admin() or \ + trans.app.security_agent.user_can_administer_repository( user, repository ) ): return trans.response.send_redirect( web.url_for( controller='repository', action='manage_repository', **kwd ) ) diff -r e2eb861e6c0b0cbaf8a1a1e091d3792724495b69 -r 9414cc43797afb77190abcbda0fdf173a6a100f3 lib/galaxy/webapps/tool_shed/model/__init__.py --- a/lib/galaxy/webapps/tool_shed/model/__init__.py +++ b/lib/galaxy/webapps/tool_shed/model/__init__.py @@ -40,10 +40,6 @@ roles.append( role ) return roles - def set_password_cleartext( self, cleartext ): - """Set 'self.password' to the digest of 'cleartext'.""" - self.password = new_secure_hash( text_type=cleartext ) - def check_password( self, cleartext ): """Check if 'cleartext' matches 'self.password' when hashed.""" return self.password == new_secure_hash( text_type=cleartext ) @@ -51,14 +47,18 @@ def get_disk_usage( self, nice_size=False ): return 0 + @property + def nice_total_disk_usage( self ): + return 0 + def set_disk_usage( self, bytes ): pass total_disk_usage = property( get_disk_usage, set_disk_usage ) - @property - def nice_total_disk_usage( self ): - return 0 + def set_password_cleartext( self, cleartext ): + """Set 'self.password' to the digest of 'cleartext'.""" + self.password = new_secure_hash( text_type=cleartext ) class Group( object, Dictifiable ): @@ -74,19 +74,26 @@ dict_collection_visible_keys = ( 'id', 'name' ) dict_element_visible_keys = ( 'id', 'name', 'description', 'type' ) private_id = None - types = Bunch( - PRIVATE = 'private', - SYSTEM = 'system', - USER = 'user', - ADMIN = 'admin', - SHARING = 'sharing' - ) + types = Bunch( PRIVATE = 'private', + SYSTEM = 'system', + USER = 'user', + ADMIN = 'admin', + SHARING = 'sharing' ) def __init__( self, name="", description="", type="system", deleted=False ): self.name = name self.description = description self.type = type self.deleted = deleted + + @property + def is_repository_admin_role( self ): + # A repository admin role must always be associated with a repository. The mapper returns an + # empty list for those roles that have no repositories. This method will require changes if + # new features are introduced that results in more than one role per repository. + if self.repositories: + return True + return False class UserGroupAssociation( object ): @@ -107,6 +114,12 @@ self.role = role +class RepositoryRoleAssociation( object ): + def __init__( self, repository, role ): + self.repository = repository + self.role = role + + class GalaxySession( object ): def __init__( self, @@ -131,17 +144,18 @@ class Repository( object, Dictifiable ): - dict_collection_visible_keys = ( 'id', 'name', 'type', 'description', 'user_id', 'private', 'deleted', 'times_downloaded', 'deprecated' ) - dict_element_visible_keys = ( 'id', 'name', 'type', 'description', 'long_description', 'user_id', 'private', 'deleted', 'times_downloaded', - 'deprecated' ) + dict_collection_visible_keys = ( 'id', 'name', 'type', 'description', 'user_id', 'private', 'deleted', + 'times_downloaded', 'deprecated' ) + dict_element_visible_keys = ( 'id', 'name', 'type', 'description', 'long_description', 'user_id', 'private', + 'deleted', 'times_downloaded', 'deprecated' ) file_states = Bunch( NORMAL = 'n', NEEDS_MERGING = 'm', MARKED_FOR_REMOVAL = 'r', MARKED_FOR_ADDITION = 'a', NOT_TRACKED = '?' ) - def __init__( self, id=None, name=None, type=None, description=None, long_description=None, user_id=None, private=False, deleted=None, - email_alerts=None, times_downloaded=0, deprecated=False ): + def __init__( self, id=None, name=None, type=None, description=None, long_description=None, user_id=None, private=False, + deleted=None, email_alerts=None, times_downloaded=0, deprecated=False ): self.id = id self.name = name or "Unnamed repository" self.type = type @@ -154,13 +168,23 @@ self.times_downloaded = times_downloaded self.deprecated = deprecated + @property + def admin_role( self ): + admin_role_name = '%s_%s_admin' % ( str( self.name ), str( self.user.username ) ) + for rra in self.roles: + role = rra.role + if str( role.name ) == admin_role_name: + return role + raise Exception( 'Repository %s owned by %s is not associated with a required administrative role.' % \ + ( str( self.name ), str( self.user.username ) ) ) + def allow_push( self, app ): repo = hg.repository( ui.ui(), self.repo_path( app ) ) return repo.ui.config( 'web', 'allow_push' ) def can_change_type( self, app ): - # Allow changing the type only if the repository has no contents, has never been installed, or has never been changed from - # the default type. + # Allow changing the type only if the repository has no contents, has never been installed, or has + # never been changed from the default type. if self.is_new( app ): return True if self.times_downloaded == 0: diff -r e2eb861e6c0b0cbaf8a1a1e091d3792724495b69 -r 9414cc43797afb77190abcbda0fdf173a6a100f3 lib/galaxy/webapps/tool_shed/model/mapping.py --- a/lib/galaxy/webapps/tool_shed/model/mapping.py +++ b/lib/galaxy/webapps/tool_shed/model/mapping.py @@ -74,6 +74,13 @@ Column( "create_time", DateTime, default=now ), Column( "update_time", DateTime, default=now, onupdate=now ) ) +RepositoryRoleAssociation.table = Table( "repository_role_association", metadata, + Column( "id", Integer, primary_key=True ), + Column( "repository_id", Integer, ForeignKey( "repository.id" ), index=True ), + Column( "role_id", Integer, ForeignKey( "role.id" ), index=True ), + Column( "create_time", DateTime, default=now ), + Column( "update_time", DateTime, default=now, onupdate=now ) ) + GalaxySession.table = Table( "galaxy_session", metadata, Column( "id", Integer, primary_key=True ), Column( "create_time", DateTime, default=now ), @@ -203,8 +210,17 @@ mapper( Role, Role.table, properties=dict( - users=relation( UserRoleAssociation ), - groups=relation( GroupRoleAssociation ) ) ) + repositories=relation( RepositoryRoleAssociation, + primaryjoin=( ( Role.table.c.id == RepositoryRoleAssociation.table.c.role_id ) & ( RepositoryRoleAssociation.table.c.repository_id == Repository.table.c.id ) ) ), + users=relation( UserRoleAssociation, + primaryjoin=( ( Role.table.c.id == UserRoleAssociation.table.c.role_id ) & ( UserRoleAssociation.table.c.user_id == User.table.c.id ) ) ), + groups=relation( GroupRoleAssociation, + primaryjoin=( ( Role.table.c.id == GroupRoleAssociation.table.c.role_id ) & ( GroupRoleAssociation.table.c.group_id == Group.table.c.id ) ) ) ) ) + +mapper( RepositoryRoleAssociation, RepositoryRoleAssociation.table, + properties=dict( + repository=relation( Repository ), + role=relation( Role ) ) ) mapper( UserGroupAssociation, UserGroupAssociation.table, properties=dict( user=relation( User, backref = "groups" ), @@ -245,6 +261,7 @@ order_by=desc( RepositoryMetadata.table.c.update_time ) ), metadata_revisions=relation( RepositoryMetadata, order_by=desc( RepositoryMetadata.table.c.update_time ) ), + roles=relation( RepositoryRoleAssociation ), reviews=relation( RepositoryReview, primaryjoin=( ( Repository.table.c.id == RepositoryReview.table.c.repository_id ) ) ), reviewers=relation( User, diff -r e2eb861e6c0b0cbaf8a1a1e091d3792724495b69 -r 9414cc43797afb77190abcbda0fdf173a6a100f3 lib/galaxy/webapps/tool_shed/model/migrate/versions/0022_add_repository_admin_roles.py --- /dev/null +++ b/lib/galaxy/webapps/tool_shed/model/migrate/versions/0022_add_repository_admin_roles.py @@ -0,0 +1,159 @@ +""" +Migration script to create the repository_role_association table, insert name-spaced +repository administrative roles into the role table and associate each repository and +owner with the appropriate name-spaced role. +""" +import datetime, logging, sys +from sqlalchemy import * +from sqlalchemy.orm import * +from migrate import * +from migrate.changeset import * +# Need our custom types, but don't import anything else from model +from galaxy.model.custom_types import * + +log = logging.getLogger( __name__ ) +log.setLevel(logging.DEBUG) +handler = logging.StreamHandler( sys.stdout ) +format = "%(name)s %(levelname)s %(asctime)s %(message)s" +formatter = logging.Formatter( format ) +handler.setFormatter( formatter ) +log.addHandler( handler ) + +metadata = MetaData() + +NOW = datetime.datetime.utcnow +ROLE_TYPE = 'system' + +RepositoryRoleAssociation_table = Table( "repository_role_association", metadata, + Column( "id", Integer, primary_key=True ), + Column( "repository_id", Integer, ForeignKey( "repository.id" ), index=True ), + Column( "role_id", Integer, ForeignKey( "role.id" ), index=True ), + Column( "create_time", DateTime, default=NOW ), + Column( "update_time", DateTime, default=NOW, onupdate=NOW ) ) + +def nextval( migrate_engine, table, col='id' ): + if migrate_engine.name in [ 'postgresql', 'postgres' ]: + return "nextval('%s_%s_seq')" % ( table, col ) + elif migrate_engine.name in [ 'mysql', 'sqlite' ]: + return "null" + else: + raise Exception( 'Unable to convert data for unknown database type: %s' % migrate_engine.name ) + +def localtimestamp( migrate_engine ): + if migrate_engine.name in [ 'postgresql', 'postgres', 'mysql' ]: + return "LOCALTIMESTAMP" + elif migrate_engine.name == 'sqlite': + return "current_date || ' ' || current_time" + else: + raise Exception( 'Unable to convert data for unknown database type: %s' % db ) + +def boolean_false( migrate_engine ): + if migrate_engine.name in [ 'postgresql', 'postgres', 'mysql' ]: + return False + elif migrate_engine.name == 'sqlite': + return 0 + else: + raise Exception( 'Unable to convert data for unknown database type: %s' % db ) + +def upgrade( migrate_engine ): + print __doc__ + metadata.bind = migrate_engine + metadata.reflect() + # Create the new repository_role_association table. + try: + RepositoryRoleAssociation_table.create() + except Exception, e: + print str(e) + log.debug( "Creating repository_role_association table failed: %s" % str( e ) ) + # Select the list of repositories and associated public user names for their owners. + user_ids = [] + repository_ids = [] + role_names = [] + cmd = 'SELECT repository.id, repository.name, repository.user_id, galaxy_user.username FROM repository, galaxy_user WHERE repository.user_id = galaxy_user.id;' + for row in migrate_engine.execute( cmd ): + repository_id = row[ 0 ] + name = row[ 1 ] + user_id = row[ 2 ] + username = row[ 3 ] + repository_ids.append( int( repository_id ) ) + role_names.append( '%s_%s_admin' % ( str( name ), str( username ) ) ) + user_ids.append( int( user_id ) ) + # Insert a new record into the role table for each new role. + for tup in zip( repository_ids, user_ids, role_names ): + repository_id, user_id, role_name = tup + cmd = "INSERT INTO role VALUES (" + cmd += "%s, " % nextval( migrate_engine, 'role' ) + cmd += "%s, " % localtimestamp( migrate_engine ) + cmd += "%s, " % localtimestamp( migrate_engine ) + cmd += "'%s', " % role_name + cmd += "'A user or group member with this role can administer this repository.', " + cmd += "'%s', " % ROLE_TYPE + cmd += "%s" % boolean_false( migrate_engine ) + cmd += ");" + migrate_engine.execute( cmd ) + # Get the id of the new role. + cmd = "SELECT id FROM role WHERE name = '%s' and type = '%s';" % ( role_name, ROLE_TYPE ) + row = migrate_engine.execute( cmd ).fetchone() + if row: + role_id = row[ 0 ] + else: + role_id = None + if role_id: + # Create a repository_role_association record to associate the repository with the new role. + cmd = "INSERT INTO repository_role_association VALUES (" + cmd += "%s, " % nextval( migrate_engine, 'repository_role_association' ) + cmd += "%d, " % int( repository_id ) + cmd += "%d, " % int( role_id ) + cmd += "%s, " % localtimestamp( migrate_engine ) + cmd += "%s " % localtimestamp( migrate_engine ) + cmd += ");" + migrate_engine.execute( cmd ) + # Create a user_role_association record to associate the repository owner with the new role. + cmd = "INSERT INTO user_role_association VALUES (" + cmd += "%s, " % nextval( migrate_engine, 'user_role_association' ) + cmd += "%d, " % int( user_id ) + cmd += "%d, " % int( role_id ) + cmd += "%s, " % localtimestamp( migrate_engine ) + cmd += "%s " % localtimestamp( migrate_engine ) + cmd += ");" + migrate_engine.execute( cmd ) + +def downgrade( migrate_engine ): + metadata.bind = migrate_engine + metadata.reflect() + # Determine the list of roles to delete by first selecting the list of repositories and associated + # public user names for their owners. + role_names = [] + cmd = 'SELECT name, username FROM repository, galaxy_user WHERE repository.user_id = galaxy_user.id;' + for row in migrate_engine.execute( cmd ): + name = row[ 0 ] + username = row[ 1 ] + role_names.append( '%s_%s_admin' % ( str( name ), str( username ) ) ) + # Delete each role as well as all users associated with each role. + for role_name in role_names: + # Select the id of the record associated with the current role_name from the role table. + cmd = "SELECT id, name FROM role WHERE name = '%s';" % role_name + row = migrate_engine.execute( cmd ).fetchone() + if row: + role_id = row[ 0 ] + else: + role_id = None + if role_id: + # Delete all user_role_association records for the current role. + cmd = "DELETE FROM user_role_association WHERE role_id = %d;" % int( role_id ) + migrate_engine.execute( cmd ) + # Delete all repository_role_association records for the current role. + cmd = "DELETE FROM repository_role_association WHERE role_id = %d;" % int( role_id ) + migrate_engine.execute( cmd ) + # Delete the role from the role table. + cmd = "DELETE FROM role WHERE id = %d;" % int( role_id ) + migrate_engine.execute( cmd ) + # Drop the repository_role_association table. + try: + RepositoryRoleAssociation_table = Table( "repository_role_association", metadata, autoload=True ) + except NoSuchTableError: + log.debug( "Failed loading table repository_role_association" ) + try: + RepositoryRoleAssociation_table.drop() + except Exception, e: + log.debug( "Dropping repository_role_association table failed: %s" % str( e ) ) diff -r e2eb861e6c0b0cbaf8a1a1e091d3792724495b69 -r 9414cc43797afb77190abcbda0fdf173a6a100f3 lib/galaxy/webapps/tool_shed/security/__init__.py --- a/lib/galaxy/webapps/tool_shed/security/__init__.py +++ b/lib/galaxy/webapps/tool_shed/security/__init__.py @@ -152,7 +152,13 @@ self.model.Role.table.c.type == self.model.Role.types.SYSTEM ) ) \ .first() - def set_entity_group_associations( self, groups=[], users=[], roles=[], delete_existing_assocs=True ): + def set_entity_group_associations( self, groups=None, users=None, roles=None, delete_existing_assocs=True ): + if groups is None: + groups = [] + if users is None: + users = [] + if roles is None: + roles = [] for group in groups: if delete_existing_assocs: for a in group.roles + group.users: @@ -163,7 +169,15 @@ for user in users: self.associate_components( group=group, user=user ) - def set_entity_role_associations( self, roles=[], users=[], groups=[], delete_existing_assocs=True ): + def set_entity_role_associations( self, roles=None, users=None, groups=None, repositories=None, delete_existing_assocs=True ): + if roles is None: + roles = [] + if users is None: + users = [] + if groups is None: + groups = [] + if repositories is None: + repositories = [] for role in roles: if delete_existing_assocs: for a in role.users + role.groups: @@ -174,7 +188,13 @@ for group in groups: self.associate_components( group=group, role=role ) - def set_entity_user_associations( self, users=[], roles=[], groups=[], delete_existing_assocs=True ): + def set_entity_user_associations( self, users=None, roles=None, groups=None, delete_existing_assocs=True ): + if users is None: + users = [] + if roles is None: + roles = [] + if groups is None: + groups = [] for user in users: if delete_existing_assocs: for a in user.non_private_roles + user.groups: @@ -193,6 +213,29 @@ return user.username in listify( repository.allow_push( app ) ) return False + def user_can_administer_repository( self, user, repository ): + """Return True if the received user can administer the received repository.""" + if user: + if repository: + repository_admin_role = repository.admin_role + for rra in repository.roles: + role = rra.role + if role.id == repository_admin_role.id: + # We have the repository's admin role, so see if the user is associated with it. + for ura in role.users: + role_member = ura.user + if role_member.id == user.id: + return True + # The user is not directly associated with the role, so see if they are a member + # of a group that is associated with the role. + for gra in role.groups: + group = gra.group + for uga in group.members: + member = uga.user + if member.id == user.id: + return True + return False + def user_can_import_repository_archive( self, user, archive_owner ): # This method should be called only if the current user is not an admin. if user.username == archive_owner: diff -r e2eb861e6c0b0cbaf8a1a1e091d3792724495b69 -r 9414cc43797afb77190abcbda0fdf173a6a100f3 lib/tool_shed/grids/admin_grids.py --- a/lib/tool_shed/grids/admin_grids.py +++ b/lib/tool_shed/grids/admin_grids.py @@ -149,20 +149,20 @@ class NameColumn( grids.TextColumn ): def get_value( self, trans, grid, role ): - return role.name + return str( role.name ) class DescriptionColumn( grids.TextColumn ): def get_value( self, trans, grid, role ): if role.description: - return role.description + return str( role.description ) return '' class TypeColumn( grids.TextColumn ): def get_value( self, trans, grid, role ): - return role.type + return str( role.type ) class StatusColumn( grids.GridColumn ): @@ -181,6 +181,14 @@ return 0 + class RepositoriesColumn( grids.GridColumn ): + + def get_value( self, trans, grid, role ): + if role.repositories: + return len( role.repositories ) + return 0 + + class UsersColumn( grids.GridColumn ): def get_value( self, trans, grid, role ): @@ -195,20 +203,16 @@ columns = [ NameColumn( "Name", key="name", - link=( lambda item: dict( operation="Manage users and groups", id=item.id ) ), + link=( lambda item: dict( operation="Manage role associations", id=item.id ) ), attach_popup=True, filterable="advanced" ), DescriptionColumn( "Description", key='description', attach_popup=False, filterable="advanced" ), - TypeColumn( "Type", - key='type', - attach_popup=False, - filterable="advanced" ), GroupsColumn( "Groups", attach_popup=False ), + RepositoriesColumn( "Repositories", attach_popup=False ), UsersColumn( "Users", attach_popup=False ), - StatusColumn( "Status", attach_popup=False ), # Columns that are valid for filtering but are not visible. grids.DeletedColumn( "Deleted", key="deleted", @@ -224,20 +228,23 @@ grids.GridAction( "Add new role", dict( controller='admin', action='roles', operation='create' ) ) ] + # Repository admin roles currently do not have any operations since they are managed automatically based + # on other events. For example, if a repository is renamed, its associated admin role is automatically + # renamed accordingly and if a repository is deleted its associated admin role is automatically deleted. operations = [ grids.GridOperation( "Rename", - condition=( lambda item: not item.deleted ), + condition=( lambda item: not item.deleted and not item.is_repository_admin_role ), allow_multiple=False, url_args=dict( action="rename_role" ) ), grids.GridOperation( "Delete", - condition=( lambda item: not item.deleted ), + condition=( lambda item: not item.deleted and not item.is_repository_admin_role ), allow_multiple=True, url_args=dict( action="mark_role_deleted" ) ), grids.GridOperation( "Undelete", - condition=( lambda item: item.deleted ), + condition=( lambda item: item.deleted and not item.is_repository_admin_role ), allow_multiple=True, url_args=dict( action="undelete_role" ) ), grids.GridOperation( "Purge", - condition=( lambda item: item.deleted ), + condition=( lambda item: item.deleted and not item.is_repository_admin_role ), allow_multiple=True, url_args=dict( action="purge_role" ) ) ] standard_filters = [ diff -r e2eb861e6c0b0cbaf8a1a1e091d3792724495b69 -r 9414cc43797afb77190abcbda0fdf173a6a100f3 lib/tool_shed/grids/repository_grids.py --- a/lib/tool_shed/grids/repository_grids.py +++ b/lib/tool_shed/grids/repository_grids.py @@ -555,6 +555,52 @@ .outerjoin( model.RepositoryCategoryAssociation.table ) \ .outerjoin( model.Category.table ) +class RepositoriesICanAdministerGrid( RepositoryGrid ): + title = "Repositories I can administer" + columns = [ + RepositoryGrid.NameColumn( "Name", + key="name", + link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), + attach_popup=False ), + RepositoryGrid.UserColumn( "Owner" ), + RepositoryGrid.MetadataRevisionColumn( "Metadata<br/>Revisions" ), + RepositoryGrid.ToolsFunctionallyCorrectColumn( "Tools<br/>Verified" ), + RepositoryGrid.DeprecatedColumn( "Deprecated" ) + ] + columns.append( grids.MulticolFilterColumn( "Search repository name", + cols_to_filter=[ columns[0] ], + key="free-text-search", + visible=False, + filterable="standard" ) ) + operations = [] + use_paging = False + + def build_initial_query( self, trans, **kwd ): + """ + Retrieve all repositories for which the current user has been granted administrative privileges. + """ + current_user = trans.user + # Build up an or-based clause list containing role table records. + clause_list = [] + # Include each of the user's roles. + for ura in current_user.roles: + clause_list.append( model.Role.table.c.id == ura.role_id ) + # Include each role associated with each group of which the user is a member. + for uga in current_user.groups: + group = uga.group + for gra in group.roles: + clause_list.append( model.Role.table.c.id == gra.role_id ) + # Filter out repositories for which the user does not have the administrative role either directly + # via a role association or indirectly via a group -> role association. + return trans.sa_session.query( model.Repository ) \ + .filter( model.Repository.table.c.deleted == False ) \ + .outerjoin( model.RepositoryRoleAssociation.table ) \ + .outerjoin( model.Role.table ) \ + .filter( or_( *clause_list ) ) \ + .join( model.User.table ) \ + .outerjoin( model.RepositoryCategoryAssociation.table ) \ + .outerjoin( model.Category.table ) + class RepositoriesMissingToolTestComponentsGrid( RepositoryGrid ): # This grid displays only the latest installable revision of each repository. diff -r e2eb861e6c0b0cbaf8a1a1e091d3792724495b69 -r 9414cc43797afb77190abcbda0fdf173a6a100f3 lib/tool_shed/util/repository_maintenance_util.py --- a/lib/tool_shed/util/repository_maintenance_util.py +++ b/lib/tool_shed/util/repository_maintenance_util.py @@ -4,6 +4,7 @@ import re import tool_shed.util.shed_util_common as suc from tool_shed.util import import_util +from galaxy import util from galaxy.web.form_builder import build_select_field from galaxy.webapps.tool_shed.model import directory_hash_id @@ -69,6 +70,8 @@ # Flush to get the id. trans.sa_session.add( repository ) trans.sa_session.flush() + # Create an admin role for the repository. + repository_admin_role = create_repository_admin_role( trans, repository ) # Determine the repository's repo_path on disk. dir = os.path.join( trans.app.config.file_path, *directory_hash_id( repository.id ) ) # Create directory if it does not exist. @@ -100,10 +103,28 @@ message = "Repository <b>%s</b> has been created." % str( repository.name ) return repository, message +def create_repository_admin_role( trans, repository ): + """ + Create a new role with name-spaced name based on the repository name and its owner's public user + name. This will ensure that the tole name is unique. + """ + name = get_repository_admin_role_name( str( repository.name ), str( repository.user.username ) ) + description = 'A user or group member with this role can administer this repository.' + role = trans.app.model.Role( name=name, description=description, type=trans.app.model.Role.types.SYSTEM ) + trans.sa_session.add( role ) + trans.sa_session.flush() + # Associate the role with the repository owner. + ura = trans.model.UserRoleAssociation( repository.user, role ) + # Associate the role with the repository. + rra = trans.model.RepositoryRoleAssociation( repository, role ) + trans.sa_session.add( rra ) + trans.sa_session.flush() + return role + def create_repository_and_import_archive( trans, repository_archive_dict, import_results_tups ): """ - Create a new repository in the tool shed and populate it with the contents of a gzip compressed tar archive - that was exported as part or all of the contents of a capsule. + Create a new repository in the tool shed and populate it with the contents of a gzip compressed + tar archive that was exported as part or all of the contents of a capsule. """ results_message = '' name = repository_archive_dict.get( 'name', None ) @@ -166,6 +187,66 @@ import_results_tups.append( ( ok, ( str( name ), str( username ) ), results_message ) ) return import_results_tups +def get_repository_admin_role_name( repository_name, repository_owner ): + return '%s_%s_admin' % ( str( repository_name ), str( repository_owner ) ) + +def get_role_by_id( trans, role_id ): + """Get a Role from the database by id.""" + return trans.sa_session.query( trans.model.Role ).get( trans.security.decode_id( role_id ) ) + +def handle_role_associations( trans, role, repository, **kwd ): + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) + repository_owner = repository.user + if kwd.get( 'manage_role_associations_button', False ): + in_users_list = util.listify( kwd.get( 'in_users', [] ) ) + in_users = [ trans.sa_session.query( trans.app.model.User ).get( x ) for x in in_users_list ] + # Make sure the repository owner is always associated with the repostory's admin role. + owner_associated = False + for user in in_users: + if user.id == repository_owner.id: + owner_associated = True + break + if not owner_associated: + in_users.append( repository_owner ) + message += "The repository owner must always be associated with the repository's administrator role. " + status = 'error' + in_groups_list = util.listify( kwd.get( 'in_groups', [] ) ) + in_groups = [ trans.sa_session.query( trans.app.model.Group ).get( x ) for x in in_groups_list ] + in_repositories = [ repository ] + trans.app.security_agent.set_entity_role_associations( roles=[ role ], + users=in_users, + groups=in_groups, + repositories=in_repositories ) + trans.sa_session.refresh( role ) + message += "Role <b>%s</b> has been associated with %d users, %d groups and %d repositories. " % \ + ( str( role.name ), len( in_users ), len( in_groups ), len( in_repositories ) ) + in_users = [] + out_users = [] + in_groups = [] + out_groups = [] + for user in trans.sa_session.query( trans.app.model.User ) \ + .filter( trans.app.model.User.table.c.deleted==False ) \ + .order_by( trans.app.model.User.table.c.email ): + if user in [ x.user for x in role.users ]: + in_users.append( ( user.id, user.email ) ) + else: + out_users.append( ( user.id, user.email ) ) + for group in trans.sa_session.query( trans.app.model.Group ) \ + .filter( trans.app.model.Group.table.c.deleted==False ) \ + .order_by( trans.app.model.Group.table.c.name ): + if group in [ x.group for x in role.groups ]: + in_groups.append( ( group.id, group.name ) ) + else: + out_groups.append( ( group.id, group.name ) ) + associations_dict = dict( in_users=in_users, + out_users=out_users, + in_groups=in_groups, + out_groups=out_groups, + message=message, + status=status ) + return associations_dict + def validate_repository_name( app, name, user ): # Repository names must be unique for each user, must be at least four characters # in length and must contain only lower-case letters, numbers, and the '_' character. diff -r e2eb861e6c0b0cbaf8a1a1e091d3792724495b69 -r 9414cc43797afb77190abcbda0fdf173a6a100f3 templates/webapps/tool_shed/common/repository_actions_menu.mako --- a/templates/webapps/tool_shed/common/repository_actions_menu.mako +++ b/templates/webapps/tool_shed/common/repository_actions_menu.mako @@ -12,6 +12,11 @@ is_admin = trans.user_is_admin() + if is_admin or trans.app.security_agent.user_can_administer_repository( trans.user, repository ): + can_administer = True + else: + can_administer = False + if repository.deprecated: is_deprecated = True else: @@ -54,7 +59,7 @@ else: can_download = False - if ( is_admin or can_push ) and not repository.deleted and not repository.deprecated and not is_new: + if ( can_administer or can_push ) and not repository.deleted and not repository.deprecated and not is_new: can_reset_all_metadata = True else: can_reset_all_metadata = False @@ -109,11 +114,6 @@ else: can_undeprecate = False - if is_admin or repository.user == trans.user: - can_manage = True - else: - can_manage = False - can_view_change_log = not is_new if can_push: @@ -147,7 +147,7 @@ %if can_upload: <a class="action-button" target="galaxy_main" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a> %endif - %if can_manage: + %if can_administer: <a class="action-button" target="galaxy_main" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ) )}">Manage repository</a> %else: <a class="action-button" target="galaxy_main" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ) )}">View repository</a> @@ -173,6 +173,9 @@ %if can_undeprecate: <a class="action-button" target="galaxy_main" href="${h.url_for( controller='repository', action='deprecate', id=trans.security.encode_id( repository.id ), mark_deprecated=False )}">Mark repository as not deprecated</a> %endif + %if can_administer: + <a class="action-button" target="galaxy_main" href="${h.url_for( controller='repository', action='manage_repository_admins', id=trans.security.encode_id( repository.id ) )}">Manage repository administrators</a> + %endif %if can_download: %if changeset_revision is not None: <a class="action-button" href="${h.url_for( controller='repository', action='export', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision )}">Export this revision</a> diff -r e2eb861e6c0b0cbaf8a1a1e091d3792724495b69 -r 9414cc43797afb77190abcbda0fdf173a6a100f3 templates/webapps/tool_shed/index.mako --- a/templates/webapps/tool_shed/index.mako +++ b/templates/webapps/tool_shed/index.mako @@ -97,7 +97,7 @@ <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_categories' )}">Browse by category</a></div> %if trans.user: - %if trans.user.active_repositories: + %if trans.user.active_repositories or can_administer_repositories: <div class="toolSectionPad"></div><div class="toolSectionTitle"> Repositories I Can Change @@ -105,6 +105,11 @@ <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_repositories_i_own' )}">Repositories I own</a></div> + %if can_administer_repositories: + <div class="toolTitle"> + <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_repositories_i_can_administer' )}">Repositories I can administer</a> + </div> + %endif %if has_reviewed_repositories: <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_repositories', operation='reviewed_repositories_i_own' )}">Reviewed repositories I own</a> diff -r e2eb861e6c0b0cbaf8a1a1e091d3792724495b69 -r 9414cc43797afb77190abcbda0fdf173a6a100f3 templates/webapps/tool_shed/role/role.mako --- /dev/null +++ b/templates/webapps/tool_shed/role/role.mako @@ -0,0 +1,136 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> +<%namespace file="/webapps/tool_shed/common/repository_actions_menu.mako" import="render_tool_shed_repository_actions" /> + +<%def name="javascripts()"> + ${parent.javascripts()} + <script type="text/javascript"> + $(function(){ + $("input:text:first").focus(); + }) + </script> +</%def> + +<%def name="render_select( name, options )"> + <select name="${name}" id="${name}" style="min-width: 250px; height: 150px;" multiple> + %for option in options: + <option value="${option[0]}">${option[1]}</option> + %endfor + </select> +</%def> + +<script type="text/javascript"> +$().ready(function() { + $('#repositories_add_button').click(function() { + return !$('#out_repositories option:selected').remove().appendTo('#in_repositories'); + }); + $('#repositories_remove_button').click(function() { + return !$('#in_repositories option:selected').remove().appendTo('#out_repositories'); + }); + $('#users_add_button').click(function() { + return !$('#out_users option:selected').remove().appendTo('#in_users'); + }); + $('#users_remove_button').click(function() { + return !$('#in_users option:selected').remove().appendTo('#out_users'); + }); + $('#groups_add_button').click(function() { + return !$('#out_groups option:selected').remove().appendTo('#in_groups'); + }); + $('#groups_remove_button').click(function() { + return !$('#in_groups option:selected').remove().appendTo('#out_groups'); + }); + $('form#manage_role_associations').submit(function() { + $('#in_repositories option').each(function(i) { + $(this).attr("selected", "selected"); + }); + $('#in_users option').each(function(i) { + $(this).attr("selected", "selected"); + }); + $('#in_groups option').each(function(i) { + $(this).attr("selected", "selected"); + }); + }); +}); +</script> + +<% + if trans.user_is_admin() and in_admin_controller: + render_for_admin = True + else: + render_for_admin = False +%> + +%if not render_for_admin: + ${render_tool_shed_repository_actions( repository, metadata=metadata, changeset_revision=changeset_revision )} +%endif + +%if message: + ${render_msg( message, status )} +%endif + +<div class="warningmessage"> + <b>${role.name}</b> is the administrator role for the repository <b>${repository.name}</b> owned by + <b>${repository.user.username}</b>. ${role.description} +</div> + +<div class="toolForm"> + <div class="toolFormTitle">Manage users and groups associated with role <b>${role.name}</b></div> + <div class="toolFormBody"> + % if not render_for_admin: + <div class="form-row"> + <label>Repository name:</label> + ${repository.name} + <div style="clear: both"></div> + </div> + <div class="form-row"> + <label>Repository owner:</label> + ${repository.user.username} + <div style="clear: both"></div> + </div> + %endif + <% + if render_for_admin: + controller_module = 'admin' + controller_method = 'manage_role_associations' + id_param = trans.security.encode_id( role.id ) + else: + controller_module = 'repository' + controller_method = 'manage_repository_admins' + id_param = trans.security.encode_id( repository.id ) + %> + <form name="manage_role_associations" id="manage_role_associations" action="${h.url_for( controller=controller_module, action=controller_method, id=id_param )}" method="post" > + <div class="form-row"> + <div style="float: left; margin-right: 10px;"> + <label>Users associated with '${role.name}'</label> + ${render_select( "in_users", in_users )}<br/> + <input type="submit" id="users_remove_button" value=">>"/> + <div style="clear: both"></div> + </div> + <div> + <label>Users not associated with '${role.name}'</label> + ${render_select( "out_users", out_users )}<br/> + <input type="submit" id="users_add_button" value="<<"/> + <div style="clear: both"></div> + </div> + </div> + <div class="form-row"> + <div style="float: left; margin-right: 10px;"> + <label>Groups associated with '${role.name}'</label> + ${render_select( "in_groups", in_groups )}<br/> + <input type="submit" id="groups_remove_button" value=">>"/> + <div style="clear: both"></div> + </div> + <div> + <label>Groups not associated with '${role.name}'</label> + ${render_select( "out_groups", out_groups )}<br/> + <input type="submit" id="groups_add_button" value="<<"/> + <div style="clear: both"></div> + </div> + </div> + <div style="clear: both"></div> + <div class="form-row"> + <input type="submit" name="manage_role_associations_button" value="Save"/> + </div> + </form> + </div> +</div> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: guerler: Packscripts
by commits-noreply＠bitbucket.org 24 Jan '14

24 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e2eb861e6c0b/ Changeset: e2eb861e6c0b User: guerler Date: 2014-01-24 18:19:57 Summary: Packscripts Affected #: 2 files diff -r 96d7f3af0b618c195ba4a00e47be26102e59a368 -r e2eb861e6c0b0cbaf8a1a1e091d3792724495b69 static/scripts/galaxy.base.js --- a/static/scripts/galaxy.base.js +++ b/static/scripts/galaxy.base.js @@ -185,7 +185,6 @@ link.click(); } } - //return false; } }; } diff -r 96d7f3af0b618c195ba4a00e47be26102e59a368 -r e2eb861e6c0b0cbaf8a1a1e091d3792724495b69 static/scripts/packed/galaxy.base.js --- a/static/scripts/packed/galaxy.base.js +++ b/static/scripts/packed/galaxy.base.js @@ -1,1 +1,1 @@ -(function(){var b=0;var c=["ms","moz","webkit","o"];for(var 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true});make_popupmenu(c,b);c.addClass("popup");d.remove()})}function naturalSort(j,h){var p=/(-?[0-9\.]+)/g,k=j.toString().toLowerCase()||"",g=h.toString().toLowerCase()||"",l=String.fromCharCode(0),n=k.replace(p,l+"$1"+l).split(l),e=g.replace(p,l+"$1"+l).split(l),d=(new Date(k)).getTime(),o=d?(new Date(g)).getTime():null;if(o){if(d<o){return -1}else{if(d>o){return 1}}}var m,f;for(var i=0,c=Math.max(n.length,e.length);i<c;i++){m=parseFloat(n[i])||n[i];f=parseFloat(e[i])||e[i];if(m<f){return -1}else{if(m>f){return 1}}}return 0}$.fn.refresh_select2=function(){var b=$(this);var a={width:"resolve",closeOnSelect:!b.is("[MULTIPLE]")};return b.select2(a)};function replace_big_select_inputs(a,c,b){if(!jQuery.fn.select2){return}if(a===undefined){a=20}if(c===undefined){c=3000}b=b||$("select");b.each(function(){var e=$(this);var d=e.find("option").length;if((d<a)||(d>c)){return}if(e.hasClass("no-autocomplete")){return}e.refresh_select2()})}$.fn.make_text_editable=function(g){var d=("num_cols" in g?g.num_cols:30),c=("num_rows" in g?g.num_rows:4),e=("use_textarea" in g?g.use_textarea:false),b=("on_finish" in g?g.on_finish:null),f=("help_text" in g?g.help_text:null);var a=$(this);a.addClass("editable-text").click(function(l){if($(this).children(":input").length>0){return}a.removeClass("editable-text");var i=function(m){a.find(":input").remove();if(m!==""){a.text(m)}else{a.html("<br>")}a.addClass("editable-text");if(b){b(m)}};var h=("cur_text" in g?g.cur_text:a.text()),k,j;if(e){k=$("<textarea/>").attr({rows:c,cols:d}).text($.trim(h)).keyup(function(m){if(m.keyCode===27){i(h)}});j=$("<button/>").text("Done").click(function(){i(k.val());return false})}else{k=$("<input type='text'/>").attr({value:$.trim(h),size:d}).blur(function(){i(h)}).keyup(function(m){if(m.keyCode===27){$(this).trigger("blur")}else{if(m.keyCode===13){i($(this).val())}}})}a.text("");a.append(k);if(j){a.append(j)}k.focus();k.select();l.stopPropagation()});if(f){a.attr("title",f).tooltip()}return a};function 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h=$.jStorage.get("history_expand_state");if(!h){h={}}$("div.historyItemBody:visible").each(function(){if($.browser.mozilla){$(this).find("pre.peek").css("overflow","hidden")}$(this).slideUp("fast");if(h){delete h[$(this).parent().attr("id")]}});$.jStorage.set("history_expand_state",h)}).show()};b()}function commatize(b){b+="";var a=/(\d+)(\d{3})/;while(a.test(b)){b=b.replace(a,"$1,$2")}return b}function reset_tool_search(a){var c=$("#galaxy_tools").contents();if(c.length===0){c=$(document)}$(this).removeClass("search_active");c.find(".toolTitle").removeClass("search_match");c.find(".toolSectionBody").hide();c.find(".toolTitle").show();c.find(".toolPanelLabel").show();c.find(".toolSectionWrapper").each(function(){if($(this).attr("id")!=="recently_used_wrapper"){$(this).show()}else{if($(this).hasClass("user_pref_visible")){$(this).show()}}});c.find("#search-no-results").hide();c.find("#search-spinner").hide();if(a){var b=c.find("#tool-search-query");b.val("search tools")}}var 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b=a.attr("last_selected_value");if($.inArray(e,c)===-1&&$.inArray(b,c)===-1){return}}$(window).trigger("refresh_on_change");$(document).trigger("convert_to_values");a.get(0).form.submit()});$(":checkbox[refresh_on_change='true']").off("click").click(function(){var a=$(this),e=a.val(),d=false,c=a.attr("refresh_on_change_values");if(c){c=c.split(",");var b=a.attr("last_selected_value");if($.inArray(e,c)===-1&&$.inArray(b,c)===-1){return}}$(window).trigger("refresh_on_change");a.get(0).form.submit()});$("a[confirm]").off("click").click(function(){return confirm($(this).attr("confirm"))})}$(document).ready(function(){init_refresh_on_change();if($.fn.tooltip){$(".unified-panel-header [title]").tooltip({placement:"bottom"});$("[title]").tooltip({placement:"top"})}make_popup_menus();replace_big_select_inputs(20,1500);$("a").click(function(){var b=$(this);var c=(parent.frames&&parent.frames.galaxy_main);if((b.attr("target")=="galaxy_main")&&(!c)){var a=b.attr("href");if(a.indexOf("?")==-1){a+="?"}else{a+="&"}a+="use_panels=True";b.attr("href",a);b.attr("target","_self")}return b})}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: guerler: Undo fix for popup menus
by commits-noreply＠bitbucket.org 24 Jan '14

24 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/96d7f3af0b61/ Changeset: 96d7f3af0b61 User: guerler Date: 2014-01-24 18:07:44 Summary: Undo fix for popup menus Affected #: 1 file diff -r ef31ebe84aaef0998f2c2d828c8b10352d33de85 -r 96d7f3af0b618c195ba4a00e47be26102e59a368 static/scripts/galaxy.base.js --- a/static/scripts/galaxy.base.js +++ b/static/scripts/galaxy.base.js @@ -185,7 +185,7 @@ link.click(); } } - return false; + //return false; } }; } 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: dan: Fix for automatic population of history name when running a workflow and sending results to a new history.
by commits-noreply＠bitbucket.org 24 Jan '14

24 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ef31ebe84aae/ Changeset: ef31ebe84aae User: dan Date: 2014-01-24 18:05:11 Summary: Fix for automatic population of history name when running a workflow and sending results to a new history. Affected #: 1 file diff -r 5b85de149657c2d9bbb3163db6ced3bb23fbfbc0 -r ef31ebe84aaef0998f2c2d828c8b10352d33de85 templates/webapps/galaxy/workflow/run.mako --- a/templates/webapps/galaxy/workflow/run.mako +++ b/templates/webapps/galaxy/workflow/run.mako @@ -603,7 +603,7 @@ %if history_id is None: <p id='new_history_p'><input type="checkbox" name='new_history' value="true" id='new_history_cbx'/><label for='new_history_cbx'>Send results to a new history </label> - <span id="new_history_input">named: <input type='text' name='new_history_name' value='${h.to_unicode( workflow.name )}'/></span> + <span id="new_history_input">named: <input type='text' name='new_history_name' value='${ h.to_unicode( workflow.name ) | h }'/></span></p> %endif <input type="submit" class="btn btn-primary" name="run_workflow" value="Run workflow" /> 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: guerler: Fix for popup menus
by commits-noreply＠bitbucket.org 24 Jan '14

24 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5b85de149657/ Changeset: 5b85de149657 User: guerler Date: 2014-01-24 18:01:30 Summary: Fix for popup menus Affected #: 3 files diff -r 210a768c98bc394eeabd231aac1056733bec9b11 -r 5b85de149657c2d9bbb3163db6ced3bb23fbfbc0 static/scripts/galaxy.base.js --- a/static/scripts/galaxy.base.js +++ b/static/scripts/galaxy.base.js @@ -185,6 +185,7 @@ link.click(); } } + return false; } }; } @@ -625,44 +626,50 @@ // Initialize refresh events. function init_refresh_on_change () { - $("select[refresh_on_change='true']").change( function() { - var select_field = $(this), - select_val = select_field.val(), - refresh = false, - ref_on_change_vals = select_field.attr("refresh_on_change_values"); - if (ref_on_change_vals) { - ref_on_change_vals = ref_on_change_vals.split(','); - var last_selected_value = select_field.attr("last_selected_value"); - if ($.inArray(select_val, ref_on_change_vals) === -1 && $.inArray(last_selected_value, ref_on_change_vals) === -1) { - return; + $("select[refresh_on_change='true']") + .off('change') + .change(function() { + var select_field = $(this), + select_val = select_field.val(), + refresh = false, + ref_on_change_vals = select_field.attr("refresh_on_change_values"); + if (ref_on_change_vals) { + ref_on_change_vals = ref_on_change_vals.split(','); + var last_selected_value = select_field.attr("last_selected_value"); + if ($.inArray(select_val, ref_on_change_vals) === -1 && $.inArray(last_selected_value, ref_on_change_vals) === -1) { + return; + } } - } - $(window).trigger("refresh_on_change"); - $(document).trigger("convert_to_values"); // Convert autocomplete text to values - select_field.get(0).form.submit(); - }); + $(window).trigger("refresh_on_change"); + $(document).trigger("convert_to_values"); // Convert autocomplete text to values + select_field.get(0).form.submit(); + }); // checkboxes refresh on change - $(":checkbox[refresh_on_change='true']").click( function() { - var select_field = $(this), - select_val = select_field.val(), - refresh = false, - ref_on_change_vals = select_field.attr("refresh_on_change_values"); - if (ref_on_change_vals) { - ref_on_change_vals = ref_on_change_vals.split(','); - var last_selected_value = select_field.attr("last_selected_value"); - if ($.inArray(select_val, ref_on_change_vals) === -1 && $.inArray(last_selected_value, ref_on_change_vals) === -1) { - return; + $(":checkbox[refresh_on_change='true']") + .off('click') + .click( function() { + var select_field = $(this), + select_val = select_field.val(), + refresh = false, + ref_on_change_vals = select_field.attr("refresh_on_change_values"); + if (ref_on_change_vals) { + ref_on_change_vals = ref_on_change_vals.split(','); + var last_selected_value = select_field.attr("last_selected_value"); + if ($.inArray(select_val, ref_on_change_vals) === -1 && $.inArray(last_selected_value, ref_on_change_vals) === -1) { + return; + } } - } - $(window).trigger("refresh_on_change"); - select_field.get(0).form.submit(); - }); + $(window).trigger("refresh_on_change"); + select_field.get(0).form.submit(); + }); // Links with confirmation - $( "a[confirm]" ).click( function() { - return confirm( $(this).attr("confirm") ); - }); + $( "a[confirm]" ) + .off('click') + .click( function() { + return confirm( $(this).attr("confirm") ); + }); }; $(document).ready( function() { diff -r 210a768c98bc394eeabd231aac1056733bec9b11 -r 5b85de149657c2d9bbb3163db6ced3bb23fbfbc0 static/scripts/packed/galaxy.base.js --- a/static/scripts/packed/galaxy.base.js +++ b/static/scripts/packed/galaxy.base.js @@ -1,1 +1,1 @@ -(function(){var b=0;var c=["ms","moz","webkit","o"];for(var a=0;a<c.length&&!window.requestAnimationFrame;++a){window.requestAnimationFrame=window[c[a]+"RequestAnimationFrame"];window.cancelRequestAnimationFrame=window[c[a]+"CancelRequestAnimationFrame"]}if(!window.requestAnimationFrame){window.requestAnimationFrame=function(h,e){var d=new Date().getTime();var f=Math.max(0,16-(d-b));var g=window.setTimeout(function(){h(d+f)},f);b=d+f;return g}}if(!window.cancelAnimationFrame){window.cancelAnimationFrame=function(d){clearTimeout(d)}}}());if(!Array.indexOf){Array.prototype.indexOf=function(c){for(var b=0,a=this.length;b<a;b++){if(this[b]==c){return b}}return -1}}function obj_length(c){if(c.length!==undefined){return c.length}var b=0;for(var a in c){b++}return b}$.fn.makeAbsolute=function(a){return this.each(function(){var b=$(this);var c=b.position();b.css({position:"absolute",marginLeft:0,marginTop:0,top:c.top,left:c.left,right:$(window).width()-(c.left+b.width())});if(a){b.remove().appendTo("body")}})};function make_popupmenu(b,c){var 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a=b.attr("href");if(a.indexOf("?")==-1){a+="?"}else{a+="&"}a+="use_panels=True";b.attr("href",a);b.attr("target","_self")}return b})}); \ No newline at end of file +(function(){var b=0;var c=["ms","moz","webkit","o"];for(var a=0;a<c.length&&!window.requestAnimationFrame;++a){window.requestAnimationFrame=window[c[a]+"RequestAnimationFrame"];window.cancelRequestAnimationFrame=window[c[a]+"CancelRequestAnimationFrame"]}if(!window.requestAnimationFrame){window.requestAnimationFrame=function(h,e){var d=new Date().getTime();var f=Math.max(0,16-(d-b));var g=window.setTimeout(function(){h(d+f)},f);b=d+f;return g}}if(!window.cancelAnimationFrame){window.cancelAnimationFrame=function(d){clearTimeout(d)}}}());if(!Array.indexOf){Array.prototype.indexOf=function(c){for(var b=0,a=this.length;b<a;b++){if(this[b]==c){return b}}return -1}}function obj_length(c){if(c.length!==undefined){return c.length}var b=0;for(var a in c){b++}return b}$.fn.makeAbsolute=function(a){return this.each(function(){var 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true});make_popupmenu(c,b);c.addClass("popup");d.remove()})}function naturalSort(j,h){var p=/(-?[0-9\.]+)/g,k=j.toString().toLowerCase()||"",g=h.toString().toLowerCase()||"",l=String.fromCharCode(0),n=k.replace(p,l+"$1"+l).split(l),e=g.replace(p,l+"$1"+l).split(l),d=(new Date(k)).getTime(),o=d?(new Date(g)).getTime():null;if(o){if(d<o){return -1}else{if(d>o){return 1}}}var m,f;for(var i=0,c=Math.max(n.length,e.length);i<c;i++){m=parseFloat(n[i])||n[i];f=parseFloat(e[i])||e[i];if(m<f){return -1}else{if(m>f){return 1}}}return 0}$.fn.refresh_select2=function(){var b=$(this);var a={width:"resolve",closeOnSelect:!b.is("[MULTIPLE]")};return b.select2(a)};function replace_big_select_inputs(a,c,b){if(!jQuery.fn.select2){return}if(a===undefined){a=20}if(c===undefined){c=3000}b=b||$("select");b.each(function(){var e=$(this);var d=e.find("option").length;if((d<a)||(d>c)){return}if(e.hasClass("no-autocomplete")){return}e.refresh_select2()})}$.fn.make_text_editable=function(g){var d=("num_cols" in g?g.num_cols:30),c=("num_rows" in g?g.num_rows:4),e=("use_textarea" in g?g.use_textarea:false),b=("on_finish" in g?g.on_finish:null),f=("help_text" in g?g.help_text:null);var a=$(this);a.addClass("editable-text").click(function(l){if($(this).children(":input").length>0){return}a.removeClass("editable-text");var i=function(m){a.find(":input").remove();if(m!==""){a.text(m)}else{a.html("<br>")}a.addClass("editable-text");if(b){b(m)}};var h=("cur_text" in g?g.cur_text:a.text()),k,j;if(e){k=$("<textarea/>").attr({rows:c,cols:d}).text($.trim(h)).keyup(function(m){if(m.keyCode===27){i(h)}});j=$("<button/>").text("Done").click(function(){i(k.val());return false})}else{k=$("<input type='text'/>").attr({value:$.trim(h),size:d}).blur(function(){i(h)}).keyup(function(m){if(m.keyCode===27){$(this).trigger("blur")}else{if(m.keyCode===13){i($(this).val())}}})}a.text("");a.append(k);if(j){a.append(j)}k.focus();k.select();l.stopPropagation()});if(f){a.attr("title",f).tooltip()}return a};function async_save_text(d,f,e,a,c,h,i,g,b){if(c===undefined){c=30}if(i===undefined){i=4}$("#"+d).click(function(){if($("#renaming-active").length>0){return}var l=$("#"+f),k=l.text(),j;if(h){j=$("<textarea></textarea>").attr({rows:i,cols:c}).text($.trim(k))}else{j=$("<input type='text'></input>").attr({value:$.trim(k),size:c})}j.attr("id","renaming-active");j.blur(function(){$(this).remove();l.show();if(b){b(j)}});j.keyup(function(n){if(n.keyCode===27){$(this).trigger("blur")}else{if(n.keyCode===13){var m={};m[a]=$(this).val();$(this).trigger("blur");$.ajax({url:e,data:m,error:function(){alert("Text editing for elt "+f+" failed")},success:function(o){if(o!==""){l.text(o)}else{l.html("<em>None</em>")}if(b){b(j)}}})}}});if(g){g(j)}l.hide();j.insertAfter(l);j.focus();j.select();return})}function init_history_items(d,a,c){var b=function(){try{var e=$.jStorage.get("history_expand_state");if(e){for(var g in e){$("#"+g+" div.historyItemBody").show()}}}catch(f){$.jStorage.deleteKey("history_expand_state")}if($.browser.mozilla){$("div.historyItemBody").each(function(){if(!$(this).is(":visible")){$(this).find("pre.peek").css("overflow","hidden")}})}d.each(function(){var j=this.id,h=$(this).children("div.historyItemBody"),i=h.find("pre.peek");$(this).find(".historyItemTitleBar > .historyItemTitle").wrap("<a href='javascript:void(0);'></a>").click(function(){var k;if(h.is(":visible")){if($.browser.mozilla){i.css("overflow","hidden")}h.slideUp("fast");if(!c){k=$.jStorage.get("history_expand_state");if(k){delete k[j];$.jStorage.set("history_expand_state",k)}}}else{h.slideDown("fast",function(){if($.browser.mozilla){i.css("overflow","auto")}});if(!c){k=$.jStorage.get("history_expand_state");if(!k){k={}}k[j]=true;$.jStorage.set("history_expand_state",k)}}return false})});$("#top-links > a.toggle").click(function(){var h=$.jStorage.get("history_expand_state");if(!h){h={}}$("div.historyItemBody:visible").each(function(){if($.browser.mozilla){$(this).find("pre.peek").css("overflow","hidden")}$(this).slideUp("fast");if(h){delete h[$(this).parent().attr("id")]}});$.jStorage.set("history_expand_state",h)}).show()};b()}function commatize(b){b+="";var a=/(\d+)(\d{3})/;while(a.test(b)){b=b.replace(a,"$1,$2")}return b}function reset_tool_search(a){var c=$("#galaxy_tools").contents();if(c.length===0){c=$(document)}$(this).removeClass("search_active");c.find(".toolTitle").removeClass("search_match");c.find(".toolSectionBody").hide();c.find(".toolTitle").show();c.find(".toolPanelLabel").show();c.find(".toolSectionWrapper").each(function(){if($(this).attr("id")!=="recently_used_wrapper"){$(this).show()}else{if($(this).hasClass("user_pref_visible")){$(this).show()}}});c.find("#search-no-results").hide();c.find("#search-spinner").hide();if(a){var b=c.find("#tool-search-query");b.val("search tools")}}var GalaxyAsync=function(a){this.url_dict={};this.log_action=(a===undefined?false:a)};GalaxyAsync.prototype.set_func_url=function(a,b){this.url_dict[a]=b};GalaxyAsync.prototype.set_user_pref=function(a,b){var c=this.url_dict[arguments.callee];if(c===undefined){return false}$.ajax({url:c,data:{pref_name:a,pref_value:b},error:function(){return false},success:function(){return true}})};GalaxyAsync.prototype.log_user_action=function(c,b,d){if(!this.log_action){return}var a=this.url_dict[arguments.callee];if(a===undefined){return false}$.ajax({url:a,data:{action:c,context:b,params:d},error:function(){return false},success:function(){return true}})};function init_refresh_on_change(){$("select[refresh_on_change='true']").off("change").change(function(){var a=$(this),e=a.val(),d=false,c=a.attr("refresh_on_change_values");if(c){c=c.split(",");var b=a.attr("last_selected_value");if($.inArray(e,c)===-1&&$.inArray(b,c)===-1){return}}$(window).trigger("refresh_on_change");$(document).trigger("convert_to_values");a.get(0).form.submit()});$(":checkbox[refresh_on_change='true']").off("click").click(function(){var a=$(this),e=a.val(),d=false,c=a.attr("refresh_on_change_values");if(c){c=c.split(",");var b=a.attr("last_selected_value");if($.inArray(e,c)===-1&&$.inArray(b,c)===-1){return}}$(window).trigger("refresh_on_change");a.get(0).form.submit()});$("a[confirm]").off("click").click(function(){return confirm($(this).attr("confirm"))})}$(document).ready(function(){init_refresh_on_change();if($.fn.tooltip){$(".unified-panel-header [title]").tooltip({placement:"bottom"});$("[title]").tooltip({placement:"top"})}make_popup_menus();replace_big_select_inputs(20,1500);$("a").click(function(){var b=$(this);var c=(parent.frames&&parent.frames.galaxy_main);if((b.attr("target")=="galaxy_main")&&(!c)){var a=b.attr("href");if(a.indexOf("?")==-1){a+="?"}else{a+="&"}a+="use_panels=True";b.attr("href",a);b.attr("target","_self")}return b})}); \ No newline at end of file diff -r 210a768c98bc394eeabd231aac1056733bec9b11 -r 5b85de149657c2d9bbb3163db6ced3bb23fbfbc0 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 LinePainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);if(this.prefs.min_value===undefined){this.prefs.min_value=_.min(_.map(this.data,function(d){return d[1]}))||0}if(this.prefs.max_value===undefined){this.prefs.max_value=_.max(_.map(this.data,function(d){return d[1]}))||0}};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 painter_color=this.prefs.block_color||this.prefs.color,pref_color=parseInt(painter_color.slice(1),16),pref_r=(pref_color&16711680)>>16,pref_g=(pref_color&65280)>>8,pref_b=pref_color&255,top_overflow=false,bot_overflow=false;for(var i=0,len=data.length;i<len;i++){ctx.fillStyle=ctx.strokeStyle=painter_color;top_overflow=bot_overflow=false;x_scaled=Math.round((data[i][0]-view_start)*w_scale);y=data[i][1];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=painter_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)},get_top_padding:function(width){return 0},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){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-0.5)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low-0.5)*w_scale))),draw_start=f_start,draw_end=f_end,y_start=(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_start+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_start+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_start+1,f_end-f_start,thick_height)}}else{var cur_y_start,cur_height;if(mode==="Squish"||mode==="Dense"){cur_y_start=y_start+Math.floor(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}else{if(feature_strand){cur_y_start=y_start;cur_height=thick_height}else{cur_y_start+=(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_start,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-0.5)*w_scale)),block_end=Math.ceil(Math.min(width,Math.max((block[1]-tile_low-0.5)*w_scale))),last_block_start,last_block_end;if(block_start>block_end){continue}ctx.fillStyle=block_color;ctx.fillRect(block_start,y_start+(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_start+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_start+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_start)}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_start+1,f_end-f_start,ws_height);ctx.fillRect(f_start,cur_y_start+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_start+8);draw_end+=ctx.measureText(feature_name).width+LABEL_SPACING}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_start+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,base_color_fn){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.ref_seq=(ref_seq?ref_seq.data:null);this.base_color_fn=base_color_fn};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},_parse_cigar:function(cigar_str){var cigar_ops="MIDNSHP=X";var blocks=[[0,0]],cur_block=blocks[0],base_pos=0,parsed_cigar=_.map(cigar_str.match(/[0-9]+[MIDNSHP=X]/g),function(op){var op_len=parseInt(op.slice(0,-1),10),op_char=op.slice(-1);if(op_char==="N"){if(cur_block[1]!==0){cur_block=[base_pos+op_len,base_pos+op_len];blocks.push(cur_block)}}else{if("ISHP".indexOf(op_char)===-1){cur_block[1]+=op_len;base_pos+=op_len}}return[cigar_ops.indexOf(op_char),op_len]});return{blocks:blocks,cigar:parsed_cigar}},draw_read:function(ctx,mode,w_scale,y_start,tile_low,tile_high,feature_start,cigar,strand,read_seq){ctx.textAlign="center";var tile_region=[tile_low,tile_high],base_offset=0,seq_offset=0,gap=Math.round(w_scale/2),char_width_px=ctx.canvas.manager.char_width_px,block_color=(strand==="+"?this.prefs.block_color:this.prefs.reverse_strand_color),pack_mode=(mode==="Pack"),paint_utils=new ReadPainterUtils(ctx,(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT),w_scale,mode);var draw_last=[];if(!cigar){cigar=[[0,read_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];var seq_start=feature_start+base_offset,s_start=Math.floor(Math.max(-0.5*w_scale,(seq_start-tile_low-0.5)*w_scale)),s_end=Math.floor(Math.max(0,(seq_start+cig_len-tile_low-0.5)*w_scale));if(!is_overlap([seq_start,seq_start+cig_len],tile_region)){continue}if(s_start===s_end){s_end+=1}switch(cig_op){case"H":break;case"S":seq_offset+=cig_len;break;case"M":case"=":case"X":ctx.fillStyle=block_color;ctx.fillRect(s_start,y_start+(pack_mode?1:4),s_end-s_start,(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT));var seq=read_seq.slice(seq_offset,seq_offset+cig_len),ref_char,read_char;for(var c=0,str_len=seq.length;c<str_len;c++){if(seq_start+c>=tile_low&&seq_start+c<=tile_high){ref_char=(this.ref_seq?this.ref_seq[seq_start-tile_low+c]:null);read_char=seq[c];if((ref_char&&(!this.prefs.show_differences||(read_char.toLowerCase!=="n"&&(ref_char.toLowerCase()!==read_char.toLowerCase()))))||(!ref_char&&!this.prefs.show_differences)){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillStyle=this.base_color_fn(seq[c]);if(pack_mode&&w_scale>char_width_px){ctx.fillText(seq[c],c_start,y_start+9)}else{if(w_scale>0.05){ctx.fillRect(c_start-gap,y_start+(pack_mode?1:4),Math.max(1,Math.round(w_scale)),(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT))}}}}}seq_offset+=cig_len;base_offset+=cig_len;break;case"N":ctx.fillStyle=CONNECTOR_COLOR;ctx.fillRect(s_start,y_start+5,s_end-s_start,1);base_offset+=cig_len;break;case"D":paint_utils.draw_deletion(s_start,y_start,1);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=read_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")&&read_seq!==undefined&&w_scale>char_width_px){ctx.fillStyle="yellow";ctx.fillRect(x_center-gap,y_start-9,s_end-s_start,9);draw_last[draw_last.length]={type:"triangle",data:[insert_x_coord,y_start+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_start)}}else{ctx.fillStyle="yellow";ctx.fillRect(x_center,y_start+(this.mode!=="Dense"?2:5),s_end-s_start,(mode!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){draw_last.push({type:"text",data:[seq.length,insert_x_coord,y_start+9]})}else{}}}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(-0.5*w_scale,(feature_start-tile_low-0.5)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low-0.5)*w_scale))),y_start=(mode==="Dense"?0:(0+slot))*y_scale,label_color=this.prefs.label_color;if(feature[5] instanceof Array){var connector=true;if(feature[4][1]>=tile_low&&feature[4][0]<=tile_high&&feature[4][2]){this.draw_read(ctx,mode,w_scale,y_start,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_start,tile_low,tile_high,feature[5][0],feature[5][2],feature[5][3],feature[5][4])}else{connector=false}var b1_end=Math.ceil(Math.min(width,Math.max(-0.5*w_scale,(feature[4][1]-tile_low-0.5)*w_scale))),b2_start=Math.floor(Math.max(-0.5*w_scale,(feature[5][0]-tile_low-0.5)*w_scale));if(connector&&b2_start>b1_end){ctx.fillStyle=CONNECTOR_COLOR;dashedLine(ctx,b1_end,y_start+5,b2_start,y_start+5)}}else{this.draw_read(ctx,mode,w_scale,y_start,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;if(tile_low===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING,y_start+8)}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_start+8)}}return[0,0]}});var RefBasedReadPainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler,ref_seq,base_color_fn){ReadPainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler,ref_seq,base_color_fn)};extend(RefBasedReadPainter.prototype,ReadPainter.prototype,FeaturePainter,{draw_read:function(ctx,mode,w_scale,y_start,tile_low,tile_high,feature_start,cigar,strand,read_seq){ctx.textAlign="center";var tile_region=[tile_low,tile_high],base_offset=0,seq_offset=0,gap=Math.round(w_scale/2),char_width_px=ctx.canvas.manager.char_width_px,block_color=(strand==="+"?this.prefs.block_color:this.prefs.reverse_strand_color),pack_mode=(mode==="Pack"),paint_utils=new ReadPainterUtils(ctx,(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT),w_scale,mode),drawing_blocks=[];var draw_last=[];var t=this._parse_cigar(cigar);cigar=t.cigar;drawing_blocks=t.blocks;for(var i=0;i<drawing_blocks.length;i++){var block=drawing_blocks[i];if(is_overlap([feature_start+block[0],feature_start+block[1]],tile_region)){var s_start=Math.floor(Math.max(-0.5*w_scale,(feature_start+block[0]-tile_low-0.5)*w_scale)),s_end=Math.floor(Math.max(0,(feature_start+block[1]-tile_low-0.5)*w_scale));if(s_start===s_end){s_end+=1}ctx.fillStyle=block_color;ctx.fillRect(s_start,y_start+(pack_mode?1:4),s_end-s_start,(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT))}}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];var seq_start=feature_start+base_offset,s_start=Math.floor(Math.max(0,-0.5*w_scale,(seq_start-tile_low-0.5)*w_scale)),s_end=Math.floor(Math.max(0,(seq_start+cig_len-tile_low-0.5)*w_scale));if(!is_overlap([seq_start,seq_start+cig_len],tile_region)){continue}if(s_start===s_end){s_end+=1}switch(cig_op){case"H":case"S":case"P":break;case"M":base_offset+=cig_len;break;case"=":case"X":var cur_seq="";if(cig_op==="X"){cur_seq=read_seq.slice(seq_offset,seq_offset+cig_len)}else{if(this.ref_seq){cur_seq=this.ref_seq.slice(Math.max(0,seq_start-tile_low),Math.min(seq_start-tile_low+cig_len,tile_high-tile_low))}}var start_pos=Math.max(seq_start,tile_low);for(var c=0;c<cur_seq.length;c++){if(cur_seq&&!this.prefs.show_differences||cig_op==="X"){var c_start=Math.floor(Math.max(0,(start_pos+c-tile_low)*w_scale));ctx.fillStyle=this.base_color_fn(cur_seq[c]);if(pack_mode&&w_scale>char_width_px){ctx.fillText(cur_seq[c],c_start,y_start+9)}else{if(w_scale>0.05){ctx.fillRect(c_start-gap,y_start+(pack_mode?1:4),Math.max(1,Math.round(w_scale)),(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT))}}}}if(cig_op==="X"){seq_offset+=cig_len}base_offset+=cig_len;break;case"N":ctx.fillStyle=CONNECTOR_COLOR;ctx.fillRect(s_start,y_start+5,s_end-s_start,1);base_offset+=cig_len;break;case"D":paint_utils.draw_deletion(s_start,y_start+(pack_mode?1:4),cig_len);base_offset+=cig_len;break;case"I":var insert_x_coord=s_start-gap;if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var seq=read_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")&&read_seq!==undefined&&w_scale>char_width_px){ctx.fillStyle="yellow";ctx.fillRect(x_center-gap,y_start-9,s_end-s_start,9);draw_last[draw_last.length]={type:"triangle",data:[insert_x_coord,y_start+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_start)}}else{ctx.fillStyle="yellow";ctx.fillRect(x_center,y_start+(this.mode!=="Dense"?2:5),s_end-s_start,(mode!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){draw_last.push({type:"text",data:[seq.length,insert_x_coord,y_start+9]})}else{}}}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])}}}}});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_start){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_start,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()};var ReadPainterUtils=function(ctx,row_height,px_per_base,mode){this.ctx=ctx;this.row_height=row_height;this.px_per_base=px_per_base;this.draw_details=(mode==="Pack"||mode==="Auto")&&(px_per_base>=ctx.canvas.manager.char_width_px);this.delete_details_thickness=0.2};extend(ReadPainterUtils.prototype,{draw_deletion:function(x,y,len){this.ctx.fillStyle="black";var thickness=(this.draw_details?this.delete_details_thickness:1)*this.row_height;y+=0.5*(this.row_height-thickness);this.ctx.fillRect(x,y,len*this.px_per_base,thickness)}});var VariantPainter=function(data,view_start,view_end,prefs,mode,base_color_fn){Painter.call(this,data,view_start,view_end,prefs,mode);this.base_color_fn=base_color_fn;this.divider_height=1};extend(VariantPainter.prototype,Painter.prototype,{get_row_height:function(){var mode=this.mode,height;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT}}return height},get_required_height:function(num_samples){var height=this.prefs.summary_height;if(num_samples>1&&this.prefs.show_sample_data){height+=this.divider_height+num_samples*this.get_row_height()}return height},draw:function(ctx,width,height,w_scale){ctx.save();var get_deletion_info=function(ref,alt){var ref_len=ref.length,alt_len=alt.length,start=0,len=1,is_delete=false;if(alt==="-"){is_delete=true;len=ref.length}else{if(ref.indexOf(alt)===0&&ref_len>alt_len){is_delete=true;len=ref_len=alt_len;start+=alt_len}}return(is_delete?{start:start,len:len}:null)};var locus_data,pos,id,ref,alt,qual,filter,sample_gts,allele_counts,variant,draw_x_start,char_x_start,draw_y_start,genotype,base_px=Math.max(1,Math.floor(w_scale)),num_samples=(this.data.length?this.data[0][7].split(",").length:0),row_height=(this.mode==="Squish"?SQUISH_TRACK_HEIGHT:PACK_TRACK_HEIGHT),feature_height=(w_scale<0.1?row_height:(this.mode==="Squish"?SQUISH_FEATURE_HEIGHT:PACK_FEATURE_HEIGHT)),draw_summary=true,paint_utils=new ReadPainterUtils(ctx,row_height,w_scale,this.mode),j;if(num_samples===1){row_height=feature_height=(w_scale<ctx.canvas.manager.char_width_px?this.prefs.summary_height:row_height);draw_summary=false}if(this.prefs.show_sample_data&&draw_summary){ctx.fillStyle="#F3F3F3";ctx.globalAlpha=1;ctx.fillRect(0,this.prefs.summary_height-this.divider_height,width,this.divider_height)}ctx.textAlign="center";for(var i=0;i<this.data.length;i++){locus_data=this.data[i];pos=locus_data[1];ref=locus_data[3];alt=[locus_data[4].split(",")];sample_gts=locus_data[7].split(",");allele_counts=locus_data.slice(8);alt=_.map(_.flatten(alt),function(a){var type,alt_info={},delete_info=get_deletion_info(ref,a);if(delete_info){type="deletion";_.extend(alt_info,delete_info)}else{type="snp"}return _.extend(alt_info,{type:type,value:a,})});if(pos<this.view_start||pos>this.view_end){continue}draw_x_start=Math.floor(Math.max(-0.5*w_scale,(pos-this.view_start-0.5)*w_scale));char_x_start=Math.floor(Math.max(0,(pos-this.view_start)*w_scale));if(draw_summary){ctx.fillStyle="#999999";ctx.globalAlpha=1;ctx.fillRect(draw_x_start,0,base_px,this.prefs.summary_height);draw_y_start=this.prefs.summary_height;for(j=0;j<alt.length;j++){ctx.fillStyle=(alt[j].type==="deletion"?"black":this.base_color_fn(alt[j].value));allele_frac=allele_counts/sample_gts.length;draw_height=Math.ceil(this.prefs.summary_height*allele_frac);ctx.fillRect(draw_x_start,draw_y_start-draw_height,base_px,draw_height);draw_y_start-=draw_height}}if(!this.prefs.show_sample_data){continue}draw_y_start=(draw_summary?this.prefs.summary_height+this.divider_height:0);for(j=0;j<sample_gts.length;j++,draw_y_start+=row_height){genotype=(sample_gts[j]?sample_gts[j].split(/\/|\|/):["0","0"]);variant=null;if(genotype[0]===genotype[1]){if(genotype[0]==="."){}else{if(genotype[0]!=="0"){variant=alt[parseInt(genotype[0],10)-1];ctx.globalAlpha=1}}}else{variant=(genotype[0]!=="0"?genotype[0]:genotype[1]);variant=alt[parseInt(variant,10)-1];ctx.globalAlpha=0.5}if(variant){if(variant.type==="snp"){var snp=variant.value;ctx.fillStyle=this.base_color_fn(snp);if(paint_utils.draw_details){ctx.fillText(snp,char_x_start,draw_y_start+row_height)}else{ctx.fillRect(draw_x_start,draw_y_start+1,base_px,feature_height)}}else{if(variant.type==="deletion"){paint_utils.draw_deletion(draw_x_start+base_px*variant.start,draw_y_start+1,variant.len)}else{}}}}}ctx.restore()}});return{Scaler:Scaler,LinePainter:LinePainter,LinkedFeaturePainter:LinkedFeaturePainter,ReadPainter:ReadPainter,RefBasedReadPainter:RefBasedReadPainter,ArcLinkedFeaturePainter:ArcLinkedFeaturePainter,DiagonalHeatmapPainter:DiagonalHeatmapPainter,VariantPainter:VariantPainter}}); \ 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 LinePainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);if(this.prefs.min_value===undefined){this.prefs.min_value=_.min(_.map(this.data,function(d){return d[1]}))||0}if(this.prefs.max_value===undefined){this.prefs.max_value=_.max(_.map(this.data,function(d){return d[1]}))||0}};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 painter_color=this.prefs.block_color||this.prefs.color,pref_color=parseInt(painter_color.slice(1),16),pref_r=(pref_color&16711680)>>16,pref_g=(pref_color&65280)>>8,pref_b=pref_color&255,top_overflow=false,bot_overflow=false;for(var i=0,len=data.length;i<len;i++){ctx.fillStyle=ctx.strokeStyle=painter_color;top_overflow=bot_overflow=false;x_scaled=Math.round((data[i][0]-view_start)*w_scale);y=data[i][1];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=painter_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)},get_top_padding:function(width){return 0},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){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-0.5)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low-0.5)*w_scale))),draw_start=f_start,draw_end=f_end,y_start=(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_start+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_start+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_start+1,f_end-f_start,thick_height)}}else{var cur_y_start,cur_height;if(mode==="Squish"||mode==="Dense"){cur_y_start=y_start+Math.floor(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}else{if(feature_strand){cur_y_start=y_start;cur_height=thick_height}else{cur_y_start+=(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_start,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-0.5)*w_scale)),block_end=Math.ceil(Math.min(width,Math.max((block[1]-tile_low-0.5)*w_scale))),last_block_start,last_block_end;if(block_start>block_end){continue}ctx.fillStyle=block_color;ctx.fillRect(block_start,y_start+(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_start+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_start+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_start)}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_start+1,f_end-f_start,ws_height);ctx.fillRect(f_start,cur_y_start+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_start+8);draw_end+=ctx.measureText(feature_name).width+LABEL_SPACING}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_start+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,base_color_fn){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.ref_seq=(ref_seq?ref_seq.data:null);this.base_color_fn=base_color_fn};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},_parse_cigar:function(cigar_str){var cigar_ops="MIDNSHP=X";var blocks=[[0,0]],cur_block=blocks[0],base_pos=0,parsed_cigar=_.map(cigar_str.match(/[0-9]+[MIDNSHP=X]/g),function(op){var op_len=parseInt(op.slice(0,-1),10),op_char=op.slice(-1);if(op_char==="N"){if(cur_block[1]!==0){cur_block=[base_pos+op_len,base_pos+op_len];blocks.push(cur_block)}}else{if("ISHP".indexOf(op_char)===-1){cur_block[1]+=op_len;base_pos+=op_len}}return[cigar_ops.indexOf(op_char),op_len]});return{blocks:blocks,cigar:parsed_cigar}},draw_read:function(ctx,mode,w_scale,y_start,tile_low,tile_high,feature_start,cigar,strand,read_seq){ctx.textAlign="center";var tile_region=[tile_low,tile_high],base_offset=0,seq_offset=0,gap=Math.round(w_scale/2),char_width_px=ctx.canvas.manager.char_width_px,block_color=(strand==="+"?this.prefs.block_color:this.prefs.reverse_strand_color),pack_mode=(mode==="Pack"),paint_utils=new ReadPainterUtils(ctx,(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT),w_scale,mode);var draw_last=[];if(!cigar){cigar=[[0,read_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];var seq_start=feature_start+base_offset,s_start=Math.floor(Math.max(-0.5*w_scale,(seq_start-tile_low-0.5)*w_scale)),s_end=Math.floor(Math.max(0,(seq_start+cig_len-tile_low-0.5)*w_scale));if(!is_overlap([seq_start,seq_start+cig_len],tile_region)){if("MDN=X".indexOf(cig_op)!==-1){base_offset+=cig_len}continue}if(s_start===s_end){s_end+=1}switch(cig_op){case"H":break;case"S":seq_offset+=cig_len;break;case"M":case"=":case"X":ctx.fillStyle=block_color;ctx.fillRect(s_start,y_start+(pack_mode?1:4),s_end-s_start,(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT));var seq=read_seq.slice(seq_offset,seq_offset+cig_len),ref_char,read_char;for(var c=0,str_len=seq.length;c<str_len;c++){if(seq_start+c>=tile_low&&seq_start+c<=tile_high){ref_char=(this.ref_seq?this.ref_seq[seq_start-tile_low+c]:null);read_char=seq[c];if((ref_char&&(!this.prefs.show_differences||(read_char.toLowerCase!=="n"&&(ref_char.toLowerCase()!==read_char.toLowerCase()))))||(!ref_char&&!this.prefs.show_differences)){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillStyle=this.base_color_fn(seq[c]);if(pack_mode&&w_scale>char_width_px){ctx.fillText(seq[c],c_start,y_start+9)}else{if(w_scale>0.05){ctx.fillRect(c_start-gap,y_start+(pack_mode?1:4),Math.max(1,Math.round(w_scale)),(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT))}}}}}seq_offset+=cig_len;base_offset+=cig_len;break;case"N":ctx.fillStyle=CONNECTOR_COLOR;ctx.fillRect(s_start,y_start+5,s_end-s_start,1);base_offset+=cig_len;break;case"D":paint_utils.draw_deletion(s_start,y_start,1);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=read_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")&&read_seq!==undefined&&w_scale>char_width_px){ctx.fillStyle="yellow";ctx.fillRect(x_center-gap,y_start-9,s_end-s_start,9);draw_last[draw_last.length]={type:"triangle",data:[insert_x_coord,y_start+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_start)}}else{ctx.fillStyle="yellow";ctx.fillRect(x_center,y_start+(this.mode!=="Dense"?2:5),s_end-s_start,(mode!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){draw_last.push({type:"text",data:[seq.length,insert_x_coord,y_start+9]})}else{}}}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(-0.5*w_scale,(feature_start-tile_low-0.5)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low-0.5)*w_scale))),y_start=(mode==="Dense"?0:(0+slot))*y_scale,label_color=this.prefs.label_color;if(feature[5] instanceof Array){var connector=true;if(feature[4][1]>=tile_low&&feature[4][0]<=tile_high&&feature[4][2]){this.draw_read(ctx,mode,w_scale,y_start,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_start,tile_low,tile_high,feature[5][0],feature[5][2],feature[5][3],feature[5][4])}else{connector=false}var b1_end=Math.ceil(Math.min(width,Math.max(-0.5*w_scale,(feature[4][1]-tile_low-0.5)*w_scale))),b2_start=Math.floor(Math.max(-0.5*w_scale,(feature[5][0]-tile_low-0.5)*w_scale));if(connector&&b2_start>b1_end){ctx.fillStyle=CONNECTOR_COLOR;dashedLine(ctx,b1_end,y_start+5,b2_start,y_start+5)}}else{this.draw_read(ctx,mode,w_scale,y_start,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;if(tile_low===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING,y_start+8)}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_start+8)}}return[0,0]}});var RefBasedReadPainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler,ref_seq,base_color_fn){ReadPainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler,ref_seq,base_color_fn)};extend(RefBasedReadPainter.prototype,ReadPainter.prototype,FeaturePainter,{draw_read:function(ctx,mode,w_scale,y_start,tile_low,tile_high,feature_start,cigar,strand,read_seq){ctx.textAlign="center";var tile_region=[tile_low,tile_high],base_offset=0,seq_offset=0,gap=Math.round(w_scale/2),char_width_px=ctx.canvas.manager.char_width_px,block_color=(strand==="+"?this.prefs.block_color:this.prefs.reverse_strand_color),pack_mode=(mode==="Pack"),paint_utils=new ReadPainterUtils(ctx,(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT),w_scale,mode),drawing_blocks=[];var draw_last=[];var t=this._parse_cigar(cigar);cigar=t.cigar;drawing_blocks=t.blocks;for(var i=0;i<drawing_blocks.length;i++){var block=drawing_blocks[i];if(is_overlap([feature_start+block[0],feature_start+block[1]],tile_region)){var s_start=Math.floor(Math.max(-0.5*w_scale,(feature_start+block[0]-tile_low-0.5)*w_scale)),s_end=Math.floor(Math.max(0,(feature_start+block[1]-tile_low-0.5)*w_scale));if(s_start===s_end){s_end+=1}ctx.fillStyle=block_color;ctx.fillRect(s_start,y_start+(pack_mode?1:4),s_end-s_start,(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT))}}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];var seq_start=feature_start+base_offset,s_start=Math.floor(Math.max(0,-0.5*w_scale,(seq_start-tile_low-0.5)*w_scale)),s_end=Math.floor(Math.max(0,(seq_start+cig_len-tile_low-0.5)*w_scale));if(!is_overlap([seq_start,seq_start+cig_len],tile_region)){continue}if(s_start===s_end){s_end+=1}switch(cig_op){case"H":case"S":case"P":break;case"M":base_offset+=cig_len;break;case"=":case"X":var cur_seq="";if(cig_op==="X"){cur_seq=read_seq.slice(seq_offset,seq_offset+cig_len)}else{if(this.ref_seq){cur_seq=this.ref_seq.slice(Math.max(0,seq_start-tile_low),Math.min(seq_start-tile_low+cig_len,tile_high-tile_low))}}var start_pos=Math.max(seq_start,tile_low);for(var c=0;c<cur_seq.length;c++){if(cur_seq&&!this.prefs.show_differences||cig_op==="X"){var c_start=Math.floor(Math.max(0,(start_pos+c-tile_low)*w_scale));ctx.fillStyle=this.base_color_fn(cur_seq[c]);if(pack_mode&&w_scale>char_width_px){ctx.fillText(cur_seq[c],c_start,y_start+9)}else{if(w_scale>0.05){ctx.fillRect(c_start-gap,y_start+(pack_mode?1:4),Math.max(1,Math.round(w_scale)),(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT))}}}}if(cig_op==="X"){seq_offset+=cig_len}base_offset+=cig_len;break;case"N":ctx.fillStyle=CONNECTOR_COLOR;ctx.fillRect(s_start,y_start+5,s_end-s_start,1);base_offset+=cig_len;break;case"D":paint_utils.draw_deletion(s_start,y_start+(pack_mode?1:4),cig_len);base_offset+=cig_len;break;case"I":var insert_x_coord=s_start-gap;if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var seq=read_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")&&read_seq!==undefined&&w_scale>char_width_px){ctx.fillStyle="yellow";ctx.fillRect(x_center-gap,y_start-9,s_end-s_start,9);draw_last[draw_last.length]={type:"triangle",data:[insert_x_coord,y_start+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_start)}}else{ctx.fillStyle="yellow";ctx.fillRect(x_center,y_start+(this.mode!=="Dense"?2:5),s_end-s_start,(mode!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){draw_last.push({type:"text",data:[seq.length,insert_x_coord,y_start+9]})}else{}}}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])}}}}});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_start){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_start,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()};var ReadPainterUtils=function(ctx,row_height,px_per_base,mode){this.ctx=ctx;this.row_height=row_height;this.px_per_base=px_per_base;this.draw_details=(mode==="Pack"||mode==="Auto")&&(px_per_base>=ctx.canvas.manager.char_width_px);this.delete_details_thickness=0.2};extend(ReadPainterUtils.prototype,{draw_deletion:function(x,y,len){this.ctx.fillStyle="black";var thickness=(this.draw_details?this.delete_details_thickness:1)*this.row_height;y+=0.5*(this.row_height-thickness);this.ctx.fillRect(x,y,len*this.px_per_base,thickness)}});var VariantPainter=function(data,view_start,view_end,prefs,mode,base_color_fn){Painter.call(this,data,view_start,view_end,prefs,mode);this.base_color_fn=base_color_fn;this.divider_height=1};extend(VariantPainter.prototype,Painter.prototype,{get_row_height:function(){var mode=this.mode,height;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT}}return height},get_required_height:function(num_samples){var height=this.prefs.summary_height;if(num_samples>1&&this.prefs.show_sample_data){height+=this.divider_height+num_samples*this.get_row_height()}return height},draw:function(ctx,width,height,w_scale){ctx.save();var get_deletion_info=function(ref,alt){var ref_len=ref.length,alt_len=alt.length,start=0,len=1,is_delete=false;if(alt==="-"){is_delete=true;len=ref.length}else{if(ref.indexOf(alt)===0&&ref_len>alt_len){is_delete=true;len=ref_len=alt_len;start+=alt_len}}return(is_delete?{start:start,len:len}:null)};var locus_data,pos,id,ref,alt,qual,filter,sample_gts,allele_counts,variant,draw_x_start,char_x_start,draw_y_start,genotype,base_px=Math.max(1,Math.floor(w_scale)),num_samples=(this.data.length?this.data[0][7].split(",").length:0),row_height=(this.mode==="Squish"?SQUISH_TRACK_HEIGHT:PACK_TRACK_HEIGHT),feature_height=(w_scale<0.1?row_height:(this.mode==="Squish"?SQUISH_FEATURE_HEIGHT:PACK_FEATURE_HEIGHT)),draw_summary=true,paint_utils=new ReadPainterUtils(ctx,row_height,w_scale,this.mode),j;if(num_samples===1){row_height=feature_height=(w_scale<ctx.canvas.manager.char_width_px?this.prefs.summary_height:row_height);draw_summary=false}if(this.prefs.show_sample_data&&draw_summary){ctx.fillStyle="#F3F3F3";ctx.globalAlpha=1;ctx.fillRect(0,this.prefs.summary_height-this.divider_height,width,this.divider_height)}ctx.textAlign="center";for(var i=0;i<this.data.length;i++){locus_data=this.data[i];pos=locus_data[1];ref=locus_data[3];alt=[locus_data[4].split(",")];sample_gts=locus_data[7].split(",");allele_counts=locus_data.slice(8);alt=_.map(_.flatten(alt),function(a){var type,alt_info={},delete_info=get_deletion_info(ref,a);if(delete_info){type="deletion";_.extend(alt_info,delete_info)}else{type="snp"}return _.extend(alt_info,{type:type,value:a,})});if(pos<this.view_start||pos>this.view_end){continue}draw_x_start=Math.floor(Math.max(-0.5*w_scale,(pos-this.view_start-0.5)*w_scale));char_x_start=Math.floor(Math.max(0,(pos-this.view_start)*w_scale));if(draw_summary){ctx.fillStyle="#999999";ctx.globalAlpha=1;ctx.fillRect(draw_x_start,0,base_px,this.prefs.summary_height);draw_y_start=this.prefs.summary_height;for(j=0;j<alt.length;j++){ctx.fillStyle=(alt[j].type==="deletion"?"black":this.base_color_fn(alt[j].value));allele_frac=allele_counts/sample_gts.length;draw_height=Math.ceil(this.prefs.summary_height*allele_frac);ctx.fillRect(draw_x_start,draw_y_start-draw_height,base_px,draw_height);draw_y_start-=draw_height}}if(!this.prefs.show_sample_data){continue}draw_y_start=(draw_summary?this.prefs.summary_height+this.divider_height:0);for(j=0;j<sample_gts.length;j++,draw_y_start+=row_height){genotype=(sample_gts[j]?sample_gts[j].split(/\/|\|/):["0","0"]);variant=null;if(genotype[0]===genotype[1]){if(genotype[0]==="."){}else{if(genotype[0]!=="0"){variant=alt[parseInt(genotype[0],10)-1];ctx.globalAlpha=1}}}else{variant=(genotype[0]!=="0"?genotype[0]:genotype[1]);variant=alt[parseInt(variant,10)-1];ctx.globalAlpha=0.5}if(variant){if(variant.type==="snp"){var snp=variant.value;ctx.fillStyle=this.base_color_fn(snp);if(paint_utils.draw_details){ctx.fillText(snp,char_x_start,draw_y_start+row_height)}else{ctx.fillRect(draw_x_start,draw_y_start+1,base_px,feature_height)}}else{if(variant.type==="deletion"){paint_utils.draw_deletion(draw_x_start+base_px*variant.start,draw_y_start+1,variant.len)}else{}}}}}ctx.restore()}});return{Scaler:Scaler,LinePainter:LinePainter,LinkedFeaturePainter:LinkedFeaturePainter,ReadPainter:ReadPainter,RefBasedReadPainter:RefBasedReadPainter,ArcLinkedFeaturePainter:ArcLinkedFeaturePainter,DiagonalHeatmapPainter:DiagonalHeatmapPainter,VariantPainter:VariantPainter}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 23 Jan '14

23 Jan '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/fcf498d29780/ Changeset: fcf498d29780 User: guerler Date: 2014-01-24 05:40:40 Summary: Frame: Add widget option to frames Affected #: 2 files diff -r ce250b678c13cabd72f13e3ed118976b7fcb4fe8 -r fcf498d297805f3ba634582de24991b99e510d6e lib/galaxy/datatypes/tabular.py --- a/lib/galaxy/datatypes/tabular.py +++ b/lib/galaxy/datatypes/tabular.py @@ -275,7 +275,7 @@ cursor = f.read(1) return to_json_string( { 'ck_data': util.unicodify( ck_data ), 'ck_index': ck_index + 1 } ) - def display_data(self, trans, dataset, preview=False, filename=None, to_ext=None, chunk=None): + def display_data(self, trans, dataset, preview=False, filename=None, to_ext=None, chunk=None, **kwd): preview = util.string_as_bool( preview ) if chunk: return self.get_chunk(trans, dataset, chunk) diff -r ce250b678c13cabd72f13e3ed118976b7fcb4fe8 -r fcf498d297805f3ba634582de24991b99e510d6e static/scripts/galaxy.frame.js --- a/static/scripts/galaxy.frame.js +++ b/static/scripts/galaxy.frame.js @@ -1096,6 +1096,11 @@ // identify content type if (type == 'url') { + if (content.indexOf('?') == -1) + content += '?'; + else + content += '&'; + content += 'widget=True'; content = '<iframe scrolling="auto" class="f-iframe" src="' + content + '"></iframe>'; } https://bitbucket.org/galaxy/galaxy-central/commits/210a768c98bc/ Changeset: 210a768c98bc User: guerler Date: 2014-01-24 05:41:17 Summary: merge Affected #: 2 files diff -r fcf498d297805f3ba634582de24991b99e510d6e -r 210a768c98bc394eeabd231aac1056733bec9b11 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -35,7 +35,9 @@ PasswordField, SelectField, TextArea, TextField, WorkflowField, WorkflowMappingField) from sqlalchemy.orm import object_session +from sqlalchemy.orm import joinedload from sqlalchemy.sql.expression import func +from sqlalchemy import not_ log = logging.getLogger( __name__ ) @@ -897,6 +899,22 @@ rval = galaxy.datatypes.data.nice_size( rval ) return rval + @property + def active_datasets_children_and_roles( self ): + if not hasattr(self, '_active_datasets_children_and_roles'): + db_session = object_session( self ) + query = db_session.query( HistoryDatasetAssociation ).filter( HistoryDatasetAssociation.table.c.history_id == self.id ). \ + filter( not_( HistoryDatasetAssociation.deleted ) ). \ + order_by( HistoryDatasetAssociation.table.c.hid.asc() ). \ + options( + joinedload("children"), + joinedload("dataset"), + joinedload("dataset.actions"), + joinedload("dataset.actions.role"), + ) + self._active_datasets_children_and_roles = query.all() + return self._active_datasets_children_and_roles + def contents_iter( self, **kwds ): """ Fetch filtered list of contents of history. diff -r fcf498d297805f3ba634582de24991b99e510d6e -r 210a768c98bc394eeabd231aac1056733bec9b11 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -1653,7 +1653,7 @@ field.add_option( "%s: (as %s) %s" % ( hid, target_ext, hda_name ), hda.id, selected ) # Also collect children via association object dataset_collector( hda.children, hid ) - dataset_collector( history.active_datasets, None ) + dataset_collector( history.active_datasets_children_and_roles, None ) some_data = bool( field.options ) if some_data: if value is None or len( field.options ) == 1: @@ -1709,7 +1709,7 @@ most_recent_dataset.append(data) # Also collect children via association object dataset_collector( data.children ) - dataset_collector( history.datasets ) + dataset_collector( history.active_datasets_children_and_roles ) most_recent_dataset.reverse() if already_used is not None: for val in most_recent_dataset: 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: 3 new changesets
by commits-noreply＠bitbucket.org 23 Jan '14

23 Jan '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e950fc8b720a/ Changeset: e950fc8b720a User: jmchilton Date: 2014-01-15 21:42:24 Summary: Bug fix related to tool dataset collection of HDA children. If the parent dataset is deleted don't allow it child to be selected as the initial value for a param when generating state - it won't work anyway because these don't appear in the final selection box. Affected #: 1 file diff -r 9fe1a6fc375b3fad14dac271ed8f85e02fc6ef6d -r e950fc8b720ad9db8b27c4599ab947ebfb0bcb7e lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -1719,7 +1719,7 @@ most_recent_dataset.append(data) # Also collect children via association object dataset_collector( data.children ) - dataset_collector( history.datasets ) + dataset_collector( history.active_datasets ) most_recent_dataset.reverse() if already_used is not None: for val in most_recent_dataset: https://bitbucket.org/galaxy/galaxy-central/commits/0951e07b7486/ Changeset: 0951e07b7486 User: jmchilton Date: 2014-01-15 21:42:24 Summary: Optimize database access during tool rendering. Prefetch all children, permission, and role data that will be needed for calculation in first database call. Number of database calls no longer proporational to size of history. 17x speed up on my laptop with ~400 history items - typical tool form update times drop from over 5 seconds to under a third of a second. That is with sqlite database on local SSD, I imagine with remote databases and/or larger histories this speed improvement could be even more significant. Affected #: 2 files diff -r e950fc8b720ad9db8b27c4599ab947ebfb0bcb7e -r 0951e07b74866c1539a7df46b051bb431f67acf4 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -35,7 +35,9 @@ PasswordField, SelectField, TextArea, TextField, WorkflowField, WorkflowMappingField) from sqlalchemy.orm import object_session +from sqlalchemy.orm import joinedload from sqlalchemy.sql.expression import func +from sqlalchemy import not_ log = logging.getLogger( __name__ ) @@ -898,6 +900,22 @@ rval = galaxy.datatypes.data.nice_size( rval ) return rval + @property + def active_datasets_children_and_roles( self ): + if not hasattr(self, '_active_datasets_children_and_roles'): + db_session = object_session( self ) + query = db_session.query( HistoryDatasetAssociation ).filter( HistoryDatasetAssociation.table.c.history_id == self.id ). \ + filter( not_( HistoryDatasetAssociation.deleted ) ). \ + order_by( HistoryDatasetAssociation.table.c.hid.asc() ). \ + options( + joinedload("children"), + joinedload("dataset"), + joinedload("dataset.actions"), + joinedload("dataset.actions.role"), + ) + self._active_datasets_children_and_roles = query.all() + return self._active_datasets_children_and_roles + def contents_iter( self, **kwds ): """ Fetch filtered list of contents of history. diff -r e950fc8b720ad9db8b27c4599ab947ebfb0bcb7e -r 0951e07b74866c1539a7df46b051bb431f67acf4 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -1655,7 +1655,7 @@ field.add_option( "%s: (as %s) %s" % ( hid, target_ext, hda_name ), hda.id, selected ) # Also collect children via association object dataset_collector( hda.children, hid ) - dataset_collector( history.active_datasets, None ) + dataset_collector( history.active_datasets_children_and_roles, None ) some_data = bool( field.options ) if some_data: if value is None or len( field.options ) == 1: @@ -1719,7 +1719,7 @@ most_recent_dataset.append(data) # Also collect children via association object dataset_collector( data.children ) - dataset_collector( history.active_datasets ) + dataset_collector( history.active_datasets_children_and_roles ) most_recent_dataset.reverse() if already_used is not None: for val in most_recent_dataset: https://bitbucket.org/galaxy/galaxy-central/commits/581b149358aa/ Changeset: 581b149358aa User: jmchilton Date: 2014-01-24 05:40:41 Summary: Merged in jmchilton/galaxy-central-fork-1 (pull request #297) Optimize database access during tool rendering. Affected #: 2 files diff -r ce250b678c13cabd72f13e3ed118976b7fcb4fe8 -r 581b149358aa655dd7c25a460f1ec48093268e93 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -35,7 +35,9 @@ PasswordField, SelectField, TextArea, TextField, WorkflowField, WorkflowMappingField) from sqlalchemy.orm import object_session +from sqlalchemy.orm import joinedload from sqlalchemy.sql.expression import func +from sqlalchemy import not_ log = logging.getLogger( __name__ ) @@ -897,6 +899,22 @@ rval = galaxy.datatypes.data.nice_size( rval ) return rval + @property + def active_datasets_children_and_roles( self ): + if not hasattr(self, '_active_datasets_children_and_roles'): + db_session = object_session( self ) + query = db_session.query( HistoryDatasetAssociation ).filter( HistoryDatasetAssociation.table.c.history_id == self.id ). \ + filter( not_( HistoryDatasetAssociation.deleted ) ). \ + order_by( HistoryDatasetAssociation.table.c.hid.asc() ). \ + options( + joinedload("children"), + joinedload("dataset"), + joinedload("dataset.actions"), + joinedload("dataset.actions.role"), + ) + self._active_datasets_children_and_roles = query.all() + return self._active_datasets_children_and_roles + def contents_iter( self, **kwds ): """ Fetch filtered list of contents of history. diff -r ce250b678c13cabd72f13e3ed118976b7fcb4fe8 -r 581b149358aa655dd7c25a460f1ec48093268e93 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -1653,7 +1653,7 @@ field.add_option( "%s: (as %s) %s" % ( hid, target_ext, hda_name ), hda.id, selected ) # Also collect children via association object dataset_collector( hda.children, hid ) - dataset_collector( history.active_datasets, None ) + dataset_collector( history.active_datasets_children_and_roles, None ) some_data = bool( field.options ) if some_data: if value is None or len( field.options ) == 1: @@ -1709,7 +1709,7 @@ most_recent_dataset.append(data) # Also collect children via association object dataset_collector( data.children ) - dataset_collector( history.datasets ) + dataset_collector( history.active_datasets_children_and_roles ) most_recent_dataset.reverse() if already_used is not None: for val in most_recent_dataset: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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