class AdminRepositoryGrid(RepositoryGrid): class DeletedColumn(grids.BooleanColumn): def get_value(self, trans, grid, repository): if repository.deleted: return 'yes' return '' columns = [ RepositoryGrid.NameColumn( "Name", key="name", link=(lambda item: dict(operation="view_or_manage_repository", id=item.id)), attach_popup=True), RepositoryGrid.HeadsColumn("Heads"), RepositoryGrid.UserColumn( "Owner", model_class=model.User, link=(lambda item: dict(operation="repositories_by_user", id=item.id)), attach_popup=False, key="User.username"), RepositoryGrid.DeprecatedColumn("Deprecated", key="deprecated", attach_popup=False), # Columns that are valid for filtering but are not visible. DeletedColumn("Deleted", key="deleted", attach_popup=False) ] columns.append( grids.MulticolFilterColumn("Search repository name", cols_to_filter=[columns[0]], key="free-text-search", visible=False, filterable="standard")) operations = [operation for operation in RepositoryGrid.operations] operations.append( grids.GridOperation("Delete", allow_multiple=False, condition=(lambda item: not item.deleted), async_compatible=False)) operations.append( grids.GridOperation("Undelete", allow_multiple=False, condition=(lambda item: item.deleted), async_compatible=False)) standard_filters = [] default_filter = {} def build_initial_query(self, trans, **kwd): return trans.sa_session.query(model.Repository) \ .join(model.User.table)
class RepositoriesReadyForReviewGrid(RepositoriesWithoutReviewsGrid): # Repositories that are ready for human review are those that either: # 1) Have no tools # 2) Have tools that have been proven to be functionally correct within Galaxy. # This grid filters out repositories that have been marked as either deprecated or deleted. title = "Repositories ready for review" columns = [ RepositoriesWithoutReviewsGrid.NameColumn( "Repository name", key="name", link=(lambda item: dict(operation="view_or_manage_repository", id=item.id)), attach_popup=True), RepositoriesWithoutReviewsGrid.DescriptionColumn("Synopsis", key="description", attach_popup=False), RepositoriesWithoutReviewsGrid.WithoutReviewsRevisionColumn( "Revisions for review"), RepositoriesWithoutReviewsGrid.UserColumn("Owner", model_class=model.User, attach_popup=False, key="User.username") ] columns.append( grids.MulticolFilterColumn("Search repository name, description", cols_to_filter=[columns[0], columns[1]], key="free-text-search", visible=False, filterable="standard")) operations = [ grids.GridOperation("Inspect repository revisions", allow_multiple=False, condition=(lambda item: not item.deleted), async_compatible=False) ] def build_initial_query(self, trans, **kwd): return trans.sa_session.query(model.Repository) \ .filter(and_(model.Repository.table.c.deleted == false(), model.Repository.table.c.deprecated == false(), model.Repository.reviews == null())) \ .join(model.RepositoryMetadata.table) \ .filter(and_(model.RepositoryMetadata.table.c.downloadable == true(), or_(model.RepositoryMetadata.table.c.includes_tools == false(), and_(model.RepositoryMetadata.table.c.includes_tools == true(), model.RepositoryMetadata.table.c.tools_functionally_correct == true())))) \ .join(model.User.table)
class RepositoriesWithoutReviewsGrid(RepositoriesWithReviewsGrid): # This grid filters out repositories that have been marked as either deprecated or deleted. title = "Repositories with no reviews" columns = [ RepositoriesWithReviewsGrid.NameColumn( "Repository name", key="name", link=(lambda item: dict(operation="view_or_manage_repository", id=item.id)), attach_popup=True), RepositoriesWithReviewsGrid.DescriptionColumn("Synopsis", key="description", attach_popup=False), RepositoriesWithReviewsGrid.WithoutReviewsRevisionColumn( "Revisions for review"), RepositoriesWithReviewsGrid.UserColumn("Owner", model_class=model.User, attach_popup=False, key="User.username") ] columns.append( grids.MulticolFilterColumn("Search repository name, description", cols_to_filter=[columns[0], columns[1]], key="free-text-search", visible=False, filterable="standard")) operations = [ grids.GridOperation("Inspect repository revisions", allow_multiple=False, condition=(lambda item: not item.deleted), async_compatible=False) ] def build_initial_query(self, trans, **kwd): return trans.sa_session.query(model.Repository) \ .filter(and_(model.Repository.table.c.deleted == false(), model.Repository.table.c.deprecated == false(), model.Repository.reviews == null())) \ .join(model.User.table)
class ReviewedRepositoriesIOwnGrid(RepositoriesWithReviewsGrid): title = "Reviewed repositories I own" columns = [ RepositoriesWithReviewsGrid.NameColumn( "Repository name", key="name", link=(lambda item: dict(operation="view_or_manage_repository", id=item.id)), attach_popup=True), RepositoriesWithReviewsGrid.WithReviewsRevisionColumn( "Reviewed revisions"), RepositoriesWithReviewsGrid.WithoutReviewsRevisionColumn( "Revisions for review"), RepositoriesWithReviewsGrid.ReviewersColumn("Reviewers", attach_popup=False), RepositoryGrid.DeprecatedColumn("Deprecated") ] columns.append( grids.MulticolFilterColumn("Search repository name", cols_to_filter=[columns[0]], key="free-text-search", visible=False, filterable="standard")) operations = [ grids.GridOperation("Inspect repository revisions", allow_multiple=False, condition=(lambda item: not item.deleted), async_compatible=False) ] def build_initial_query(self, trans, **kwd): return trans.sa_session.query(model.Repository) \ .join((model.RepositoryReview.table, model.RepositoryReview.table.c.repository_id == model.Repository.table.c.id)) \ .filter(model.Repository.table.c.user_id == trans.user.id) \ .join((model.User.table, model.User.table.c.id == model.RepositoryReview.table.c.user_id)) \ .outerjoin((model.ComponentReview.table, model.ComponentReview.table.c.repository_review_id == model.RepositoryReview.table.c.id)) \ .outerjoin((model.Component.table, model.Component.table.c.id == model.ComponentReview.table.c.component_id))
class RepositoriesWithReviewsGrid(RepositoryGrid): # This grid filters out repositories that have been marked as either deprecated or deleted. class WithReviewsRevisionColumn(grids.GridColumn): def get_value(self, trans, grid, repository): # Restrict to revisions that have been reviewed. if repository.reviews: rval = '' repo = hg_util.get_repo_for_repository(trans.app, repository=repository, repo_path=None, create=False) for review in repository.reviews: changeset_revision = review.changeset_revision rev, label = hg_util.get_rev_label_from_changeset_revision( repo, changeset_revision) rval += '<a href="manage_repository_reviews_of_revision?id=%s&changeset_revision=%s">%s</a><br/>' % \ (trans.security.encode_id(repository.id), changeset_revision, label) return rval return '' class WithoutReviewsRevisionColumn(grids.GridColumn): def get_value(self, trans, grid, repository): # Restrict the options to revisions that have not yet been reviewed. repository_metadata_revisions = metadata_util.get_repository_metadata_revisions_for_review( repository, reviewed=False) if repository_metadata_revisions: rval = '' for repository_metadata in repository_metadata_revisions: rev, label, changeset_revision = \ hg_util.get_rev_label_changeset_revision_from_repository_metadata(trans.app, repository_metadata, repository=repository, include_date=True, include_hash=False) rval += '<a href="manage_repository_reviews_of_revision?id=%s&changeset_revision=%s">%s</a><br/>' % \ (trans.security.encode_id(repository.id), changeset_revision, label) return rval return '' class ReviewersColumn(grids.TextColumn): def get_value(self, trans, grid, repository): rval = '' if repository.reviewers: for user in repository.reviewers: rval += '<a class="view-info" href="repository_reviews_by_user?id=%s">' % trans.security.encode_id( user.id) rval += '%s</a> | ' % user.username rval = rval.rstrip(' | ') return rval class RatingColumn(grids.TextColumn): def get_value(self, trans, grid, repository): rval = '' for review in repository.reviews: if review.rating: for index in range(1, 6): rval += '<input ' rval += 'name="star1-%s" ' % trans.security.encode_id( review.id) rval += 'type="radio" ' rval += 'class="community_rating_star star" ' rval += 'disabled="disabled" ' rval += 'value="%s" ' % str(review.rating) if review.rating > (index - 0.5) and review.rating < ( index + 0.5): rval += 'checked="checked" ' rval += '/>' rval += '<br/>' return rval class ApprovedColumn(grids.TextColumn): def get_value(self, trans, grid, repository): rval = '' for review in repository.reviews: if review.approved: rval += '%s<br/>' % review.approved return rval title = "All reviewed repositories" model_class = model.Repository template = '/webapps/tool_shed/repository_review/grid.mako' default_sort_key = "Repository.name" columns = [ RepositoryGrid.NameColumn( "Repository name", key="name", link=(lambda item: dict(operation="view_or_manage_repository", id=item.id)), attach_popup=True), RepositoryGrid.UserColumn("Owner", model_class=model.User, attach_popup=False, key="User.username"), WithReviewsRevisionColumn("Reviewed revisions"), ReviewersColumn("Reviewers", attach_popup=False), RatingColumn("Rating", attach_popup=False), ApprovedColumn("Approved", attach_popup=False) ] columns.append( grids.MulticolFilterColumn("Search repository name", cols_to_filter=[columns[0]], key="free-text-search", visible=False, filterable="standard")) operations = [ grids.GridOperation("Inspect repository revisions", allow_multiple=False, condition=(lambda item: not item.deleted), async_compatible=False) ] def build_initial_query(self, trans, **kwd): return trans.sa_session.query(model.Repository) \ .filter(and_(model.Repository.table.c.deleted == false(), model.Repository.table.c.deprecated == false())) \ .join((model.RepositoryReview.table, model.RepositoryReview.table.c.repository_id == model.Repository.table.c.id)) \ .join((model.User.table, model.User.table.c.id == model.Repository.table.c.user_id)) \ .outerjoin((model.ComponentReview.table, model.ComponentReview.table.c.repository_review_id == model.RepositoryReview.table.c.id)) \ .outerjoin((model.Component.table, model.Component.table.c.id == model.ComponentReview.table.c.component_id))
class RepositoryReviewsByUserGrid(grids.Grid): # This grid filters out repositories that have been marked as deprecated. class RepositoryNameColumn(grids.TextColumn): def get_value(self, trans, grid, review): return escape(review.repository.name) class RepositoryDescriptionColumn(grids.TextColumn): def get_value(self, trans, grid, review): return escape(review.repository.description) class RevisionColumn(grids.TextColumn): def get_value(self, trans, grid, review): encoded_review_id = trans.security.encode_id(review.id) rval = '<a class="action-button" href="' if review.user == trans.user: rval += 'edit_review' else: rval += 'browse_review' revision_label = hg_util.get_revision_label( trans.app, review.repository, review.changeset_revision, include_date=True, include_hash=False) rval += '?id=%s">%s</a>' % (encoded_review_id, revision_label) return rval class RatingColumn(grids.TextColumn): def get_value(self, trans, grid, review): if review.rating: for index in range(1, 6): rval = '<input ' rval += 'name="star1-%s" ' % trans.security.encode_id( review.id) rval += 'type="radio" ' rval += 'class="community_rating_star star" ' rval += 'disabled="disabled" ' rval += 'value="%s" ' % str(review.rating) if review.rating > (index - 0.5) and review.rating < (index + 0.5): rval += 'checked="checked" ' rval += '/>' return rval return '' title = "Reviews by user" model_class = model.RepositoryReview template = '/webapps/tool_shed/repository_review/grid.mako' default_sort_key = 'repository_id' use_hide_message = False columns = [ RepositoryNameColumn( "Repository Name", model_class=model.Repository, key="Repository.name", link=(lambda item: dict(operation="view_or_manage_repository", id=item.id)), attach_popup=True), RepositoryDescriptionColumn("Description", model_class=model.Repository, key="Repository.description", attach_popup=False), RevisionColumn("Revision", attach_popup=False), RatingColumn("Rating", attach_popup=False), ] # Override these default_filter = {} global_actions = [] operations = [ grids.GridOperation("Inspect repository revisions", allow_multiple=False, condition=(lambda item: not item.deleted), async_compatible=False) ] standard_filters = [] num_rows_per_page = 50 use_paging = False def build_initial_query(self, trans, **kwd): user_id = trans.security.decode_id(kwd['id']) return trans.sa_session.query(model.RepositoryReview) \ .filter(and_(model.RepositoryReview.table.c.deleted == false(), model.RepositoryReview.table.c.user_id == user_id)) \ .join((model.Repository.table, model.RepositoryReview.table.c.repository_id == model.Repository.table.c.id)) \ .filter(model.Repository.table.c.deprecated == false())
class RepositoryMetadataGrid(grids.Grid): class IdColumn(grids.IntegerColumn): def get_value(self, trans, grid, repository_metadata): return repository_metadata.id class NameColumn(grids.TextColumn): def get_value(self, trans, grid, repository_metadata): return escape(repository_metadata.repository.name) class OwnerColumn(grids.TextColumn): def get_value(self, trans, grid, repository_metadata): return escape(repository_metadata.repository.user.username) class RevisionColumn(grids.TextColumn): def get_value(self, trans, grid, repository_metadata): repository = repository_metadata.repository return hg_util.get_revision_label( trans.app, repository, repository_metadata.changeset_revision, include_date=True, include_hash=True) class ToolsColumn(grids.TextColumn): def get_value(self, trans, grid, repository_metadata): tools_str = '0' if repository_metadata: metadata = repository_metadata.metadata if metadata: if 'tools' in metadata: # We used to display the following, but grid was too cluttered. # for tool_metadata_dict in metadata[ 'tools' ]: # tools_str += '%s <b>%s</b><br/>' % ( tool_metadata_dict[ 'id' ], tool_metadata_dict[ 'version' ] ) return '%d' % len(metadata['tools']) return tools_str class DatatypesColumn(grids.TextColumn): def get_value(self, trans, grid, repository_metadata): datatypes_str = '0' if repository_metadata: metadata = repository_metadata.metadata if metadata: if 'datatypes' in metadata: # We used to display the following, but grid was too cluttered. # for datatype_metadata_dict in metadata[ 'datatypes' ]: # datatypes_str += '%s<br/>' % datatype_metadata_dict[ 'extension' ] return '%d' % len(metadata['datatypes']) return datatypes_str class WorkflowsColumn(grids.TextColumn): def get_value(self, trans, grid, repository_metadata): workflows_str = '0' if repository_metadata: metadata = repository_metadata.metadata if metadata: if 'workflows' in metadata: # We used to display the following, but grid was too cluttered. # workflows_str += '<b>Workflows:</b><br/>' # metadata[ 'workflows' ] is a list of tuples where each contained tuple is # [ <relative path to the .ga file in the repository>, <exported workflow dict> ] # workflow_tups = metadata[ 'workflows' ] # workflow_metadata_dicts = [ workflow_tup[1] for workflow_tup in workflow_tups ] # for workflow_metadata_dict in workflow_metadata_dicts: # workflows_str += '%s<br/>' % workflow_metadata_dict[ 'name' ] return '%d' % len(metadata['workflows']) return workflows_str class DeletedColumn(grids.BooleanColumn): def get_value(self, trans, grid, repository_metadata): if repository_metadata.repository.deleted: return 'yes' return '' class DeprecatedColumn(grids.BooleanColumn): def get_value(self, trans, grid, repository_metadata): if repository_metadata.repository.deprecated: return 'yes' return '' class MaliciousColumn(grids.BooleanColumn): def get_value(self, trans, grid, repository_metadata): if repository_metadata.malicious: return 'yes' return '' # Grid definition title = "Repository Metadata" model_class = model.RepositoryMetadata default_sort_key = "name" use_hide_message = False columns = [ IdColumn("Id", visible=False, attach_popup=False), NameColumn( "Name", key="name", model_class=model.Repository, link=(lambda item: dict( operation="view_or_manage_repository_revision", id=item.id)), attach_popup=True), OwnerColumn("Owner", attach_popup=False), RevisionColumn("Revision", attach_popup=False), ToolsColumn("Tools", attach_popup=False), DatatypesColumn("Datatypes", attach_popup=False), WorkflowsColumn("Workflows", attach_popup=False), DeletedColumn("Deleted", attach_popup=False), DeprecatedColumn("Deprecated", attach_popup=False), MaliciousColumn("Malicious", attach_popup=False) ] columns.append( grids.MulticolFilterColumn("Search repository name", cols_to_filter=[columns[1]], key="free-text-search", visible=False, filterable="standard")) operations = [ grids.GridOperation( "Delete", allow_multiple=False, allow_popup=True, async_compatible=False, confirm= "Repository metadata records cannot be recovered after they are deleted. Click OK to delete the selected items." ) ] standard_filters = [] default_filter = {} use_paging = False def build_initial_query(self, trans, **kwd): return trans.sa_session.query(model.RepositoryMetadata) \ .join(model.Repository.table)
class GroupGrid(grids.Grid): class NameColumn(grids.TextColumn): def get_value(self, trans, grid, group): return str(group.name) class StatusColumn(grids.GridColumn): def get_value(self, trans, grid, group): if group.deleted: return "deleted" return "" class RolesColumn(grids.GridColumn): def get_value(self, trans, grid, group): if group.roles: return len(group.roles) return 0 class UsersColumn(grids.GridColumn): def get_value(self, trans, grid, group): if group.members: return len(group.members) return 0 title = "Groups" model_class = model.Group default_sort_key = "name" columns = [ NameColumn("Name", key="name", link=(lambda item: dict(operation="Manage users and roles", id=item.id)), attach_popup=True), UsersColumn("Users", attach_popup=False), RolesColumn("Roles", attach_popup=False), StatusColumn("Status", attach_popup=False), # Columns that are valid for filtering but are not visible. grids.DeletedColumn("Deleted", key="deleted", visible=False, filterable="advanced") ] columns.append( grids.MulticolFilterColumn("Search", cols_to_filter=[columns[0]], key="free-text-search", visible=False, filterable="standard")) global_actions = [ grids.GridAction( "Add new group", dict(controller='admin', action='groups', operation='create')) ] operations = [ grids.GridOperation("Rename", condition=(lambda item: not item.deleted), allow_multiple=False, url_args=dict(action="rename_group")), grids.GridOperation("Delete", condition=(lambda item: not item.deleted), allow_multiple=True, url_args=dict(action="mark_group_deleted")), grids.GridOperation("Undelete", condition=(lambda item: item.deleted), allow_multiple=True, url_args=dict(action="undelete_group")), grids.GridOperation("Purge", condition=(lambda item: item.deleted), allow_multiple=True, url_args=dict(action="purge_group")) ] standard_filters = [ grids.GridColumnFilter("Active", args=dict(deleted=False)), grids.GridColumnFilter("Deleted", args=dict(deleted=True)), grids.GridColumnFilter("All", args=dict(deleted='All')) ] use_paging = False
class UserGrid(grids.Grid): class UserLoginColumn(grids.TextColumn): def get_value(self, trans, grid, user): return escape(user.email) class UserNameColumn(grids.TextColumn): def get_value(self, trans, grid, user): if user.username: return escape(user.username) return 'not set' class GroupsColumn(grids.GridColumn): def get_value(self, trans, grid, user): if user.groups: return len(user.groups) return 0 class RolesColumn(grids.GridColumn): def get_value(self, trans, grid, user): if user.roles: return len(user.roles) return 0 class ExternalColumn(grids.GridColumn): def get_value(self, trans, grid, user): if user.external: return 'yes' return 'no' class LastLoginColumn(grids.GridColumn): def get_value(self, trans, grid, user): if user.galaxy_sessions: return self.format(user.galaxy_sessions[0].update_time) return 'never' class StatusColumn(grids.GridColumn): def get_value(self, trans, grid, user): if user.purged: return "purged" elif user.deleted: return "deleted" return "" class EmailColumn(grids.GridColumn): def filter(self, trans, user, query, column_filter): if column_filter == 'All': return query return query.filter( and_(model.Tool.table.c.user_id == model.User.table.c.id, model.User.table.c.email == column_filter)) title = "Users" model_class = model.User default_sort_key = "email" columns = [ UserLoginColumn( "Email", key="email", link=(lambda item: dict(operation="information", id=item.id)), attach_popup=True, filterable="advanced"), UserNameColumn("User Name", key="username", attach_popup=False, filterable="advanced"), GroupsColumn("Groups", attach_popup=False), RolesColumn("Roles", attach_popup=False), ExternalColumn("External", attach_popup=False), LastLoginColumn("Last Login", format=time_ago), StatusColumn("Status", attach_popup=False), # Columns that are valid for filtering but are not visible. EmailColumn("Email", key="email", visible=False) ] columns.append( grids.MulticolFilterColumn("Search", cols_to_filter=[columns[0], columns[1]], key="free-text-search", visible=False, filterable="standard")) global_actions = [ grids.GridAction( "Create new user", dict(controller='admin', action='users', operation='create')) ] operations = [ grids.GridOperation( "Manage Roles and Groups", condition=(lambda item: not item.deleted), allow_multiple=False, url_args=dict(action="manage_roles_and_groups_for_user")), grids.GridOperation("Reset Password", condition=(lambda item: not item.deleted), allow_multiple=True, allow_popup=False, url_args=dict(action="reset_user_password")) ] standard_filters = [ grids.GridColumnFilter("Active", args=dict(deleted=False)), grids.GridColumnFilter("Deleted", args=dict(deleted=True, purged=False)), grids.GridColumnFilter("Purged", args=dict(purged=True)), grids.GridColumnFilter("All", args=dict(deleted='All')) ] use_paging = False def get_current_item(self, trans, **kwargs): return trans.user
class RoleGrid(grids.Grid): class NameColumn(grids.TextColumn): def get_value(self, trans, grid, role): return escape(str(role.name)) class DescriptionColumn(grids.TextColumn): def get_value(self, trans, grid, role): if role.description: return str(role.description) return '' class TypeColumn(grids.TextColumn): def get_value(self, trans, grid, role): return str(role.type) class StatusColumn(grids.GridColumn): def get_value(self, trans, grid, role): if role.deleted: return "deleted" return "" class GroupsColumn(grids.GridColumn): def get_value(self, trans, grid, role): if role.groups: return len(role.groups) 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): if role.users: return len(role.users) return 0 title = "Roles" model_class = model.Role default_sort_key = "name" columns = [ NameColumn("Name", key="name", 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"), GroupsColumn("Groups", attach_popup=False), RepositoriesColumn("Repositories", attach_popup=False), UsersColumn("Users", attach_popup=False), # Columns that are valid for filtering but are not visible. grids.DeletedColumn("Deleted", key="deleted", visible=False, filterable="advanced") ] columns.append( grids.MulticolFilterColumn("Search", cols_to_filter=[columns[0]], key="free-text-search", visible=False, filterable="standard")) global_actions = [ 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 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 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 and not item. is_repository_admin_role), allow_multiple=True, url_args=dict(action="undelete_role")), grids.GridOperation("Purge", condition=(lambda item: item.deleted and not item. is_repository_admin_role), allow_multiple=True, url_args=dict(action="purge_role")) ] standard_filters = [ grids.GridColumnFilter("Active", args=dict(deleted=False)), grids.GridColumnFilter("Deleted", args=dict(deleted=True)), grids.GridColumnFilter("All", args=dict(deleted='All')) ] use_paging = False def apply_query_filter(self, trans, query, **kwd): return query.filter(model.Role.type != model.Role.types.PRIVATE)