1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/db8a3bd35841/ changeset: db8a3bd35841 user: greg date: 2013-03-04 15:26:59 summary: Move the many Grid classes out of the tool shed's repository controller into the new location for tool shed grids: ~/tool_shed/grids. affected #: 8 files

diff -r 7369eda82e2cf7e10338232569ed9185bc3b526b -r db8a3bd35841ce033aff283510a0f7fe3aec3ab0 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 @@ -6,7 +6,7 @@ from galaxy.web.framework.helpers import time_ago, grids from galaxy.util import inflector import tool_shed.util.shed_util_common as suc -from repository import RepositoryGrid, CategoryGrid +from tool_shed.grids.repository_grids import RepositoryGrid, CategoryGrid

from galaxy import eggs eggs.require( 'mercurial' )

diff -r 7369eda82e2cf7e10338232569ed9185bc3b526b -r db8a3bd35841ce033aff283510a0f7fe3aec3ab0 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 @@ -1,10 +1,10 @@ -import os, logging, re, tempfile, shutil, ConfigParser, string +import os, logging, re, tempfile, ConfigParser, string from time import gmtime, strftime from datetime import date, datetime from galaxy import util, web from galaxy.util.odict import odict from galaxy.web.base.controller import BaseUIController -from galaxy.web.form_builder import CheckboxField, SelectField, build_select_field +from galaxy.web.form_builder import CheckboxField, build_select_field from galaxy.webapps.tool_shed import model from galaxy.webapps.tool_shed.model import directory_hash_id from galaxy.web.framework.helpers import grids @@ -15,12 +15,12 @@ from galaxy.webapps.tool_shed.util import workflow_util from galaxy.webapps.tool_shed.util import common_util import galaxy.tools +import tool_shed.grids.repository_grids as repository_grids +import tool_shed.grids.util as grids_util

from galaxy import eggs eggs.require('mercurial') from mercurial import hg, ui, patch, commands -eggs.require('markupsafe') -from markupsafe import escape as escape_html

log = logging.getLogger( __name__ )

@@ -29,1003 +29,25 @@ malicious_error_can_push = " Correct this changeset as soon as possible, it potentially produces malicious behavior or contains inappropriate content."

-class CategoryGrid( grids.Grid ): - - - class NameColumn( grids.TextColumn ): - - def get_value( self, trans, grid, category ): - return category.name - - - class DescriptionColumn( grids.TextColumn ): - def get_value( self, trans, grid, category ): - return category.description - - - class RepositoriesColumn( grids.TextColumn ): - - def get_value( self, trans, grid, category ): - if category.repositories: - viewable_repositories = 0 - for rca in category.repositories: - if not rca.repository.deleted and not rca.repository.deprecated: - viewable_repositories += 1 - return viewable_repositories - return 0 - - title = "Categories" - model_class = model.Category - template='/webapps/tool_shed/category/grid.mako' - default_sort_key = "name" - columns = [ - NameColumn( "Name", - key="Category.name", - link=( lambda item: dict( operation="repositories_by_category", id=item.id ) ), - attach_popup=False ), - DescriptionColumn( "Description", - key="Category.description", - attach_popup=False ), - RepositoriesColumn( "Repositories", - model_class=model.Repository, - attach_popup=False ) - ] - # Override these - default_filter = {} - global_actions = [] - operations = [] - standard_filters = [] - num_rows_per_page = 50 - preserve_state = False - use_paging = True - - -class ValidCategoryGrid( CategoryGrid ): - - - class RepositoriesColumn( grids.TextColumn ): - - def get_value( self, trans, grid, category ): - if category.repositories: - viewable_repositories = 0 - for rca in category.repositories: - repository = rca.repository - if not repository.deleted and not repository.deprecated and repository.downloadable_revisions: - viewable_repositories += 1 - return viewable_repositories - return 0 - - title = "Categories of valid repositories" - model_class = model.Category - template='/webapps/tool_shed/category/valid_grid.mako' - default_sort_key = "name" - columns = [ - CategoryGrid.NameColumn( "Name", - key="Category.name", - link=( lambda item: dict( operation="valid_repositories_by_category", id=item.id ) ), - attach_popup=False ), - CategoryGrid.DescriptionColumn( "Description", - key="Category.description", - attach_popup=False ), - # Columns that are valid for filtering but are not visible. - RepositoriesColumn( "Valid repositories", - model_class=model.Repository, - attach_popup=False ) - ] - # Override these - default_filter = {} - global_actions = [] - operations = [] - standard_filters = [] - num_rows_per_page = 50 - preserve_state = False - use_paging = True - - -class RepositoryGrid( grids.Grid ): - - - class NameColumn( grids.TextColumn ): - - def get_value( self, trans, grid, repository ): - return escape_html( repository.name ) - - - class MetadataRevisionColumn( grids.GridColumn ): - - def __init__( self, col_name ): - grids.GridColumn.__init__( self, col_name ) - - def get_value( self, trans, grid, repository ): - """Display a SelectField whose options are the changeset_revision strings of all metadata revisions of this repository.""" - # A repository's metadata revisions may not all be installable, as some may contain only invalid tools. - select_field = build_changeset_revision_select_field( trans, repository, downloadable=False ) - if len( select_field.options ) > 1: - return select_field.get_html() - elif len( select_field.options ) == 1: - return select_field.options[ 0 ][ 0 ] - return '' - - - class TipRevisionColumn( grids.GridColumn ): - - def __init__( self, col_name ): - grids.GridColumn.__init__( self, col_name ) - - def get_value( self, trans, grid, repository ): - """Display the repository tip revision label.""" - return escape_html( repository.revision( trans.app ) ) - - - class DescriptionColumn( grids.TextColumn ): - - def get_value( self, trans, grid, repository ): - return escape_html( repository.description ) - - - class CategoryColumn( grids.TextColumn ): - - def get_value( self, trans, grid, repository ): - rval = '<ul>' - if repository.categories: - for rca in repository.categories: - rval += '<li><a href="browse_repositories?operation=repositories_by_category&id=%s">%s</a></li>' \ - % ( trans.security.encode_id( rca.category.id ), rca.category.name ) - else: - rval += '<li>not set</li>' - rval += '</ul>' - return rval - - - class RepositoryCategoryColumn( grids.GridColumn ): - - def filter( self, trans, user, query, column_filter ): - """Modify query to filter by category.""" - if column_filter == "All": - return query - return query.filter( model.Category.name == column_filter ) - - - class UserColumn( grids.TextColumn ): - - def get_value( self, trans, grid, repository ): - if repository.user: - return escape_html( repository.user.username ) - return 'no user' - - - class EmailColumn( grids.TextColumn ): - - def filter( self, trans, user, query, column_filter ): - if column_filter == 'All': - return query - return query.filter( and_( model.Repository.table.c.user_id == model.User.table.c.id, - model.User.table.c.email == column_filter ) ) - - - class EmailAlertsColumn( grids.TextColumn ): - - def get_value( self, trans, grid, repository ): - if trans.user and repository.email_alerts and trans.user.email in json.from_json_string( repository.email_alerts ): - return 'yes' - return '' - - - class DeprecatedColumn( grids.TextColumn ): - - def get_value( self, trans, grid, repository ): - if repository.deprecated: - return 'yes' - return '' - - title = "Repositories" - model_class = model.Repository - template='/webapps/tool_shed/repository/grid.mako' - default_sort_key = "name" - columns = [ - NameColumn( "Name", - key="name", - link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), - attach_popup=True ), - DescriptionColumn( "Synopsis", - key="description", - attach_popup=False ), - MetadataRevisionColumn( "Metadata Revisions" ), - TipRevisionColumn( "Tip Revision" ), - CategoryColumn( "Category", - model_class=model.Category, - key="Category.name", - attach_popup=False ), - UserColumn( "Owner", - model_class=model.User, - link=( lambda item: dict( operation="repositories_by_user", id=item.id ) ), - attach_popup=False, - key="User.username" ), - # Columns that are valid for filtering but are not visible. - EmailColumn( "Email", - model_class=model.User, - key="email", - visible=False ), - RepositoryCategoryColumn( "Category", - model_class=model.Category, - key="Category.name", - visible=False ) - ] - 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( "Receive email alerts", - allow_multiple=False, - condition=( lambda item: not item.deleted ), - async_compatible=False ) ] - standard_filters = [] - default_filter = dict( deleted="False" ) - num_rows_per_page = 50 - preserve_state = False - use_paging = True - - 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.User.table ) \ - .outerjoin( model.RepositoryCategoryAssociation.table ) \ - .outerjoin( model.Category.table ) - - -class RepositoriesByUserGrid( RepositoryGrid ): - title = "Repositories by user" - columns = [ - RepositoryGrid.NameColumn( "Name", - key="name", - link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), - attach_popup=False ), - RepositoryGrid.MetadataRevisionColumn( "Metadata Revisions" ), - RepositoryGrid.TipRevisionColumn( "Tip Revision" ), - RepositoryGrid.DescriptionColumn( "Synopsis", - key="description", - attach_popup=False ), - RepositoryGrid.CategoryColumn( "Category", - model_class=model.Category, - key="Category.name", - attach_popup=False ) - ] - operations = [] - standard_filters = [] - default_filter = dict( deleted="False" ) - num_rows_per_page = 50 - preserve_state = False - use_paging = True - - def build_initial_query( self, trans, **kwd ): - decoded_user_id = trans.security.decode_id( kwd[ 'user_id' ] ) - return trans.sa_session.query( model.Repository ) \ - .filter( and_( model.Repository.table.c.deleted == False, - model.Repository.table.c.deprecated == False, - model.Repository.table.c.user_id == decoded_user_id ) ) \ - .join( model.User.table ) \ - .outerjoin( model.RepositoryCategoryAssociation.table ) \ - .outerjoin( model.Category.table ) - - -class RepositoriesIOwnGrid( RepositoryGrid ): - title = "Repositories I own" - columns = [ - RepositoryGrid.NameColumn( "Name", - key="name", - link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), - attach_popup=True ), - RepositoryGrid.MetadataRevisionColumn( "Metadata Revisions" ), - RepositoryGrid.TipRevisionColumn( "Tip Revision" ), - RepositoryGrid.CategoryColumn( "Category", - model_class=model.Category, - key="Category.name", - 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( "Mark as deprecated", - allow_multiple=False, - condition=( lambda item: not item.deleted and not item.deprecated ), - async_compatible=False, - confirm="Are you sure that you want to deprecate this repository?" ), - grids.GridOperation( "Mark as not deprecated", - allow_multiple=False, - condition=( lambda item: not item.deleted and item.deprecated ), - 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.user_id == trans.user.id ) ) \ - .join( model.User.table ) \ - .outerjoin( model.RepositoryCategoryAssociation.table ) \ - .outerjoin( model.Category.table ) - - -class DeprecatedRepositoriesIOwnGrid( RepositoriesIOwnGrid ): - title = "Deprecated repositories I own" - columns = [ - RepositoriesIOwnGrid.NameColumn( "Name", - key="name", - link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), - attach_popup=True ), - RepositoriesIOwnGrid.MetadataRevisionColumn( "Metadata Revisions" ), - RepositoriesIOwnGrid.TipRevisionColumn( "Tip Revision" ), - RepositoriesIOwnGrid.CategoryColumn( "Category", - model_class=model.Category, - key="Category.name", - attach_popup=False ), - ] - columns.append( grids.MulticolFilterColumn( "Search repository name", - cols_to_filter=[ columns[0] ], - key="free-text-search", - visible=False, - filterable="standard" ) ) - - 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.user_id == trans.user.id, - model.Repository.table.c.deprecated == True ) ) \ - .join( model.User.table ) \ - .outerjoin( model.RepositoryCategoryAssociation.table ) \ - .outerjoin( model.Category.table ) - - -class EmailAlertsRepositoryGrid( RepositoryGrid ): - columns = [ - RepositoryGrid.NameColumn( "Name", - key="name", - link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), - attach_popup=False ), - RepositoryGrid.DescriptionColumn( "Synopsis", - key="description", - attach_popup=False ), - 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.EmailAlertsColumn( "Alert", attach_popup=False ), - # Columns that are valid for filtering but are not visible. - grids.DeletedColumn( "Deleted", - key="deleted", - visible=False, - filterable="advanced" ) - ] - operations = [ grids.GridOperation( "Receive email alerts", - allow_multiple=True, - condition=( lambda item: not item.deleted ), - async_compatible=False ) ] - global_actions = [ - grids.GridAction( "User preferences", dict( controller='user', action='index', cntrller='repository' ) ) - ] - - -class MyWritableRepositoriesGrid( RepositoryGrid ): - # This grid filters out repositories that have been marked as either deprecated or deleted. - columns = [ - RepositoryGrid.NameColumn( "Name", - key="name", - link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), - attach_popup=True ), - RepositoryGrid.MetadataRevisionColumn( "Metadata Revisions" ), - RepositoryGrid.TipRevisionColumn( "Tip Revision" ), - 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.EmailAlertsColumn( "Alert", attach_popup=False ), - # Columns that are valid for filtering but are not visible. - RepositoryGrid.EmailColumn( "Email", - model_class=model.User, - key="email", - visible=False ), - RepositoryGrid.RepositoryCategoryColumn( "Category", - model_class=model.Category, - key="Category.name", - visible=False ) - ] - columns.append( grids.MulticolFilterColumn( "Search repository name", - cols_to_filter=[ columns[0] ], - key="free-text-search", - visible=False, - filterable="standard" ) ) - operations = [ grids.GridOperation( "Receive email alerts", - allow_multiple=False, - condition=( lambda item: not item.deleted ), - async_compatible=False ) ] - - def build_initial_query( self, trans, **kwd ): - # TODO: improve performance by adding a db table associating users with repositories for which they have write access. - username = trans.user.username - clause_list = [] - for repository in trans.sa_session.query( model.Repository ) \ - .filter( and_( model.Repository.table.c.deprecated == False, - model.Repository.table.c.deleted == False ) ): - allow_push = repository.allow_push( trans.app ) - if allow_push: - allow_push_usernames = allow_push.split( ',' ) - if username in allow_push_usernames: - clause_list.append( model.Repository.table.c.id == repository.id ) - if clause_list: - return trans.sa_session.query( model.Repository ) \ - .filter( or_( *clause_list ) ) \ - .join( model.User.table ) \ - .outerjoin( model.RepositoryCategoryAssociation.table ) \ - .outerjoin( model.Category.table ) - # Return an empty query. - return trans.sa_session.query( model.Repository ) \ - .filter( model.Repository.table.c.id < 0 ) - - -class ValidRepositoryGrid( RepositoryGrid ): - # This grid filters out repositories that have been marked as either deleted or deprecated. - - - class CategoryColumn( grids.TextColumn ): - - def get_value( self, trans, grid, repository ): - rval = '<ul>' - if repository.categories: - for rca in repository.categories: - rval += '<li><a href="browse_repositories?operation=valid_repositories_by_category&id=%s">%s</a></li>' \ - % ( trans.security.encode_id( rca.category.id ), rca.category.name ) - else: - rval += '<li>not set</li>' - rval += '</ul>' - return rval - - - class RepositoryCategoryColumn( grids.GridColumn ): - - def filter( self, trans, user, query, column_filter ): - """Modify query to filter by category.""" - if column_filter == "All": - return query - return query.filter( model.Category.name == column_filter ) - - - class RevisionColumn( grids.GridColumn ): - - def __init__( self, col_name ): - grids.GridColumn.__init__( self, col_name ) - - def get_value( self, trans, grid, repository ): - """Display a SelectField whose options are the changeset_revision strings of all download-able revisions of this repository.""" - select_field = build_changeset_revision_select_field( trans, repository, downloadable=True ) - if len( select_field.options ) > 1: - return select_field.get_html() - elif len( select_field.options ) == 1: - return select_field.options[ 0 ][ 0 ] - return '' - - title = "Valid repositories" - columns = [ - RepositoryGrid.NameColumn( "Name", - key="name", - attach_popup=True ), - RepositoryGrid.DescriptionColumn( "Synopsis", - key="description", - attach_popup=False ), - RevisionColumn( "Installable Revisions" ), - RepositoryGrid.UserColumn( "Owner", - model_class=model.User, - attach_popup=False ), - # Columns that are valid for filtering but are not visible. - RepositoryCategoryColumn( "Category", - model_class=model.Category, - key="Category.name", - visible=False ) - ] - columns.append( grids.MulticolFilterColumn( "Search repository name, description", - cols_to_filter=[ columns[0], columns[1] ], - key="free-text-search", - visible=False, - filterable="standard" ) ) - operations = [] - - def build_initial_query( self, trans, **kwd ): - if 'id' in kwd: - # The user is browsing categories of valid repositories, so filter the request by the received id, which is a category id. - return trans.sa_session.query( model.Repository ) \ - .filter( and_( model.Repository.table.c.deleted == False, - model.Repository.table.c.deprecated == False ) ) \ - .join( model.RepositoryMetadata.table ) \ - .join( model.User.table ) \ - .join( model.RepositoryCategoryAssociation.table ) \ - .join( model.Category.table ) \ - .filter( and_( model.Category.table.c.id == trans.security.decode_id( kwd[ 'id' ] ), - model.RepositoryMetadata.table.c.downloadable == True ) ) - # The user performed a free text search on the ValidCategoryGrid. - return trans.sa_session.query( model.Repository ) \ - .filter( and_( model.Repository.table.c.deleted == False, - model.Repository.table.c.deprecated == False ) ) \ - .join( model.RepositoryMetadata.table ) \ - .join( model.User.table ) \ - .outerjoin( model.RepositoryCategoryAssociation.table ) \ - .outerjoin( model.Category.table ) \ - .filter( model.RepositoryMetadata.table.c.downloadable == True ) - - -class MatchedRepositoryGrid( grids.Grid ): - # This grid filters out repositories that have been marked as deprecated. - - - class NameColumn( grids.TextColumn ): - - def get_value( self, trans, grid, repository_metadata ): - return repository_metadata.repository.name - - - class DescriptionColumn( grids.TextColumn ): - - def get_value( self, trans, grid, repository_metadata ): - return repository_metadata.repository.description - - - class RevisionColumn( grids.TextColumn ): - - def get_value( self, trans, grid, repository_metadata ): - return repository_metadata.changeset_revision - - - class UserColumn( grids.TextColumn ): - - def get_value( self, trans, grid, repository_metadata ): - if repository_metadata.repository.user: - return repository_metadata.repository.user.username - return 'no user' - - # Grid definition - title = "Matching repositories" - model_class = model.RepositoryMetadata - template='/webapps/tool_shed/repository/grid.mako' - default_sort_key = "Repository.name" - columns = [ - NameColumn( "Repository name", - link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), - attach_popup=True ), - DescriptionColumn( "Synopsis", - attach_popup=False ), - RevisionColumn( "Revision" ), - UserColumn( "Owner", - model_class=model.User, - attach_popup=False ) - ] - operations = [ - grids.GridOperation( "Install to Galaxy", allow_multiple=True ) - ] - standard_filters = [] - default_filter = {} - num_rows_per_page = 50 - preserve_state = False - use_paging = True - - def build_initial_query( self, trans, **kwd ): - match_tuples = kwd.get( 'match_tuples', [] ) - clause_list = [] - if match_tuples: - for match_tuple in match_tuples: - repository_id, changeset_revision = match_tuple - clause_list.append( "%s=%d and %s='%s'" % ( model.RepositoryMetadata.table.c.repository_id, - int( repository_id ), - model.RepositoryMetadata.table.c.changeset_revision, - changeset_revision ) ) - return trans.sa_session.query( model.RepositoryMetadata ) \ - .join( model.Repository ) \ - .filter( and_( model.Repository.table.c.deleted == False, - model.Repository.table.c.deprecated == False ) ) \ - .join( model.User.table ) \ - .filter( or_( *clause_list ) ) \ - .order_by( model.Repository.name ) - # Return an empty query - return trans.sa_session.query( model.RepositoryMetadata ) \ - .filter( model.RepositoryMetadata.id < 0 ) - - -class InstallMatchedRepositoryGrid( MatchedRepositoryGrid ): - columns = [ col for col in MatchedRepositoryGrid.columns ] - # Override the NameColumn - columns[ 0 ] = MatchedRepositoryGrid.NameColumn( "Name", - link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), - attach_popup=False ) - - -class RepositoryMetadataGrid( grids.Grid ): - - - class RepositoryNameColumn( grids.TextColumn ): - - def get_value( self, trans, grid, repository_metadata ): - repository = repository_metadata.repository - return escape_html( repository.name ) - - - class RepositoryOwnerColumn( grids.TextColumn ): - - def get_value( self, trans, grid, repository_metadata ): - repository = repository_metadata.repository - return escape_html( repository.user.username ) - - - class ChangesetRevisionColumn( grids.TextColumn ): - - def get_value( self, trans, grid, repository_metadata ): - return escape_html( repository_metadata.changeset_revision ) - - - class MaliciousColumn( grids.BooleanColumn ): - def get_value( self, trans, grid, repository_metadata ): - if repository_metadata.malicious: - return 'yes' - return '' - - - class DownloadableColumn( grids.BooleanColumn ): - def get_value( self, trans, grid, repository_metadata ): - if repository_metadata.downloadable: - return 'yes' - return '' - - - class ToolsFunctionallyCorrectColumn( grids.BooleanColumn ): - def get_value( self, trans, grid, repository_metadata ): - if repository_metadata.tools_functionally_correct: - return 'yes' - return '' - - - class DoNotTestColumn( grids.BooleanColumn ): - def get_value( self, trans, grid, repository_metadata ): - if repository_metadata.do_not_test: - return 'yes' - return '' - - - class TimeLastTestedColumn( grids.DateTimeColumn ): - def get_value( self, trans, grid, repository_metadata ): - return repository_metadata.time_last_tested - - - class HasRepositoryDependenciesColumn( grids.BooleanColumn ): - def get_value( self, trans, grid, repository_metadata ): - if repository_metadata.has_repository_dependencies: - return 'yes' - return '' - - - class IncludesDatatypesColumn( grids.BooleanColumn ): - def get_value( self, trans, grid, repository_metadata ): - if repository_metadata.includes_datatypes: - return 'yes' - return '' - - - class IncludesToolsColumn( grids.BooleanColumn ): - def get_value( self, trans, grid, repository_metadata ): - if repository_metadata.includes_tools: - return 'yes' - return '' - - - class IncludesToolDependenciesColumn( grids.BooleanColumn ): - def get_value( self, trans, grid, repository_metadata ): - if repository_metadata.includes_tool_dependencies: - return 'yes' - return '' - - - class IncludesWorkflowsColumn( grids.BooleanColumn ): - def get_value( self, trans, grid, repository_metadata ): - if repository_metadata.includes_workflows: - return 'yes' - return '' - - title = "Repository metadata" - model_class = model.RepositoryMetadata - template='/webapps/tool_shed/repository/grid.mako' - default_sort_key = "Repository.name" - columns = [ - RepositoryNameColumn( "Repository name", - link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), - attach_popup=False ), - RepositoryOwnerColumn( "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 = [] - standard_filters = [] - default_filter = dict( malicious="False" ) - num_rows_per_page = 50 - preserve_state = False - use_paging = True - - def build_initial_query( self, trans, **kwd ): - return trans.sa_session.query( model.RepositoryMetadata ) \ - .join( model.Repository ) \ - .filter( and_( model.Repository.table.c.deleted == False, - model.Repository.table.c.deprecated == False ) ) \ - .join( model.User.table ) \ - .order_by( model.Repository.name ) - - -class RepositoryDependenciesGrid( RepositoryMetadataGrid ): - - - class RequiredRepositoryColumn( grids.TextColumn ): - - def get_value( self, trans, grid, repository_metadata ): - rd_str = '' - if repository_metadata: - metadata = repository_metadata.metadata - if metadata: - rd_dict = metadata.get( 'repository_dependencies', {} ) - if rd_dict: - rd_tups = rd_dict[ 'repository_dependencies' ] - # "repository_dependencies": [["http://localhost:9009", "bwa059", "test", "a07baa797d53"]] - # Sort rd_tups by by required repository name. - sorted_rd_tups = sorted( rd_tups, key=lambda rd_tup: rd_tup[ 1 ] ) - num_tups = len( sorted_rd_tups ) - for index, rd_tup in enumerate( sorted_rd_tups ): - name = rd_tup[ 1 ] - owner = rd_tup[ 2 ] - required_repository = suc.get_repository_by_name_and_owner( trans.app, name, owner ) - if required_repository: - required_repository_id = trans.security.encode_id( required_repository.id ) - rd_str += '<a href="browse_repository_dependencies?operation=browse_repository&id=%s">' % required_repository_id - rd_str += '<b>name:</b> %s | <b>owner:</b> %s | <b>revision:</b> %s' % ( escape_html( rd_tup[ 1 ] ), escape_html( rd_tup[ 2 ] ), escape_html( rd_tup[ 3 ] ) ) - if required_repository: - rd_str += '</a>' - if index < num_tups - 1: - rd_str += '<br/>' - return rd_str - - title = "Repository dependency definitions in this tool shed" - columns = [ - RepositoryMetadataGrid.RepositoryNameColumn( "Repository name", - model_class=model.Repository, - link=( lambda item: dict( operation="browse_repository", id=item.repository.id ) ), - attach_popup=False, - key="Repository.name" ), - RepositoryMetadataGrid.RepositoryOwnerColumn( "Owner", - model_class=model.User, - attach_popup=False, - key="User.username" ), - RepositoryMetadataGrid.ChangesetRevisionColumn( "Revision", - attach_popup=False ), - RequiredRepositoryColumn( "Repository dependency", - attach_popup=False ) - ] - columns.append( grids.MulticolFilterColumn( "Search repository name, owner", - cols_to_filter=[ columns[0], columns[1] ], - key="free-text-search", - visible=False, - filterable="standard" ) ) - - def build_initial_query( self, trans, **kwd ): - return trans.sa_session.query( model.RepositoryMetadata ) \ - .join( model.Repository ) \ - .filter( and_( model.RepositoryMetadata.table.c.has_repository_dependencies == True, - model.Repository.table.c.deleted == False, - model.Repository.table.c.deprecated == False ) ) \ - .join( model.User.table ) \ - .order_by( model.Repository.name ) - - -class ToolDependenciesGrid( RepositoryMetadataGrid ): - - - class ToolDependencyColumn( grids.TextColumn ): - - def get_value( self, trans, grid, repository_metadata ): - td_str = '' - if repository_metadata: - metadata = repository_metadata.metadata - if metadata: - tds_dict = metadata.get( 'tool_dependencies', {} ) - if tds_dict: - # Example: {"bwa/0.5.9": {"name": "bwa", "type": "package", "version": "0.5.9"}} - sorted_keys = sorted( [ k for k in tds_dict.keys() ] ) - num_keys = len( sorted_keys ) - # Handle environment settings first. - if 'set_environment' in sorted_keys: - # Example: "set_environment": [{"name": "JAVA_JAR_FILE", "type": "set_environment"}] - env_dicts = tds_dict[ 'set_environment' ] - num_env_dicts = len( env_dicts ) - td_str += '<b>environment:</b> ' - for index, env_dict in enumerate( env_dicts ): - td_str += '%s' % escape_html( env_dict[ 'name' ] ) - if index < num_env_dicts - 1: - td_str += ', ' - td_str += '<br/>' - for index, key in enumerate( sorted_keys ): - if key == 'set_environment': - continue - td_dict = tds_dict[ key ] - # Example: {"name": "bwa", "type": "package", "version": "0.5.9"} - name = td_dict[ 'name' ] - type = td_dict[ 'type' ] - version = td_dict[ 'version' ] - td_str += '<b>%s</b> version <b>%s</b>' % ( escape_html( name ), escape_html( version ) ) - if index < num_keys - 1: - td_str += '<br/>' - return td_str - - title = "Tool dependency definitions in this tool shed" - columns = [ - RepositoryMetadataGrid.RepositoryNameColumn( "Repository name", - model_class=model.Repository, - link=( lambda item: dict( operation="browse_repository", id=item.repository.id ) ), - attach_popup=False, - key="Repository.name" ), - RepositoryMetadataGrid.RepositoryOwnerColumn( "Owner", - model_class=model.User, - attach_popup=False, - key="User.username" ), - RepositoryMetadataGrid.ChangesetRevisionColumn( "Revision", - attach_popup=False ), - ToolDependencyColumn( "Tool dependency", - attach_popup=False ) - ] - columns.append( grids.MulticolFilterColumn( "Search repository name, owner", - cols_to_filter=[ columns[0], columns[1] ], - key="free-text-search", - visible=False, - filterable="standard" ) ) - - def build_initial_query( self, trans, **kwd ): - return trans.sa_session.query( model.RepositoryMetadata ) \ - .join( model.Repository ) \ - .filter( and_( model.RepositoryMetadata.table.c.includes_tool_dependencies == True, - model.Repository.table.c.deleted == False, - model.Repository.table.c.deprecated == False ) ) \ - .join( model.User.table ) \ - .order_by( model.Repository.name ) - - -class ToolsGrid( RepositoryMetadataGrid ): - - - class ToolsColumn( grids.TextColumn ): - - def get_value( self, trans, grid, repository_metadata ): - tool_str = '' - if repository_metadata: - metadata = repository_metadata.metadata - if metadata: - tool_dicts = metadata.get( 'tools', [] ) - if tool_dicts: - num_tool_dicts = len( tool_dicts ) - for index, tool_dict in enumerate( tool_dicts ): - tool_id = tool_dict[ 'id' ] - name = tool_dict[ 'name' ] - version = tool_dict[ 'version' ] - tool_str += '<b>%s</b> | %s | %s' % ( escape_html( tool_id ), escape_html( name ), escape_html( version ) ) - if index < num_tool_dicts - 1: - tool_str += '<br/>' - return tool_str - - title = "Valid tools in this tool shed" - columns = [ - RepositoryMetadataGrid.RepositoryNameColumn( "Repository name", - model_class=model.Repository, - link=( lambda item: dict( operation="view_or_manage_repository", id=item.repository.id ) ), - attach_popup=False, - key="Repository.name" ), - RepositoryMetadataGrid.RepositoryOwnerColumn( "Owner", - model_class=model.User, - attach_popup=False, - key="User.username" ), - RepositoryMetadataGrid.ChangesetRevisionColumn( "Revision", - attach_popup=False ), - ToolsColumn( "Tool id | name | version", - attach_popup=False ) - ] - columns.append( grids.MulticolFilterColumn( "Search repository name, owner", - cols_to_filter=[ columns[0], columns[1] ], - key="free-text-search", - visible=False, - filterable="standard" ) ) - - def build_initial_query( self, trans, **kwd ): - return trans.sa_session.query( model.RepositoryMetadata ) \ - .join( model.Repository ) \ - .filter( and_( model.RepositoryMetadata.table.c.includes_tools == True, - model.Repository.table.c.deleted == False, - model.Repository.table.c.deprecated == False ) ) \ - .join( model.User.table ) \ - .order_by( model.Repository.name ) - - -class DatatypesGrid( RepositoryMetadataGrid ): - - - class DatatypesColumn( grids.TextColumn ): - - def get_value( self, trans, grid, repository_metadata ): - datatype_str = '' - if repository_metadata: - metadata = repository_metadata.metadata - if metadata: - datatype_dicts = metadata.get( 'datatypes', [] ) - if datatype_dicts: - num_datatype_dicts = len( datatype_dicts ) - for index, datatype_dict in enumerate( datatype_dicts ): - # Example: {"display_in_upload": "true", "dtype": "galaxy.datatypes.blast:BlastXml", "extension": "blastxml", "mimetype": "application/xml"} - extension = datatype_dict.get( 'extension', '' ) - dtype = datatype_dict.get( 'dtype', '' ) - mimetype = datatype_dict.get( 'mimetype', '' ) - display_in_upload = datatype_dict.get( 'display_in_upload', False ) - datatype_str += '<b>%s</b> | %s | %s' % ( escape_html( extension ), escape_html( dtype ), escape_html( mimetype ) ) - if index < num_datatype_dicts - 1: - datatype_str += '<br/>' - return datatype_str - - title = "Custom datatypes in this tool shed" - columns = [ - RepositoryMetadataGrid.RepositoryNameColumn( "Repository name", - model_class=model.Repository, - link=( lambda item: dict( operation="view_or_manage_repository", id=item.repository.id ) ), - attach_popup=False, - key="Repository.name" ), - RepositoryMetadataGrid.RepositoryOwnerColumn( "Owner", - model_class=model.User, - attach_popup=False, - key="User.username" ), - RepositoryMetadataGrid.ChangesetRevisionColumn( "Revision", - attach_popup=False ), - DatatypesColumn( "Datatype extension | Type | Mimetype", - attach_popup=False ) - ] - columns.append( grids.MulticolFilterColumn( "Search repository name, owner", - cols_to_filter=[ columns[0], columns[1] ], - key="free-text-search", - visible=False, - filterable="standard" ) ) - - def build_initial_query( self, trans, **kwd ): - return trans.sa_session.query( model.RepositoryMetadata ) \ - .join( model.Repository ) \ - .filter( and_( model.RepositoryMetadata.table.c.includes_datatypes == True, - model.Repository.table.c.deleted == False, - model.Repository.table.c.deprecated == False ) ) \ - .join( model.User.table ) \ - .order_by( model.Repository.name ) - class RepositoryController( BaseUIController, common_util.ItemRatings ):

- category_grid = CategoryGrid() - datatypes_grid = DatatypesGrid() - deprecated_repositories_i_own_grid = DeprecatedRepositoriesIOwnGrid() - email_alerts_repository_grid = EmailAlertsRepositoryGrid() - install_matched_repository_grid = InstallMatchedRepositoryGrid() - matched_repository_grid = MatchedRepositoryGrid() - my_writable_repositories_grid = MyWritableRepositoriesGrid() - repositories_by_user_grid = RepositoriesByUserGrid() - repositories_i_own_grid = RepositoriesIOwnGrid() - repository_dependencies_grid = RepositoryDependenciesGrid() - repository_grid = RepositoryGrid() + category_grid = repository_grids.CategoryGrid() + datatypes_grid = repository_grids.DatatypesGrid() + deprecated_repositories_i_own_grid = repository_grids.DeprecatedRepositoriesIOwnGrid() + email_alerts_repository_grid = repository_grids.EmailAlertsRepositoryGrid() + install_matched_repository_grid = repository_grids.InstallMatchedRepositoryGrid() + matched_repository_grid = repository_grids.MatchedRepositoryGrid() + my_writable_repositories_grid = repository_grids.MyWritableRepositoriesGrid() + repositories_by_user_grid = repository_grids.RepositoriesByUserGrid() + repositories_i_own_grid = repository_grids.RepositoriesIOwnGrid() + repository_dependencies_grid = repository_grids.RepositoryDependenciesGrid() + repository_grid = repository_grids.RepositoryGrid() # The repository_metadata_grid is not currently displayed, but is sub-classed by several grids. - repository_metadata_grid = RepositoryMetadataGrid() - tool_dependencies_grid = ToolDependenciesGrid() - tools_grid = ToolsGrid() - valid_category_grid = ValidCategoryGrid() - valid_repository_grid = ValidRepositoryGrid() + repository_metadata_grid = repository_grids.RepositoryMetadataGrid() + tool_dependencies_grid = repository_grids.ToolDependenciesGrid() + tools_grid = repository_grids.ToolsGrid() + valid_category_grid = repository_grids.ValidCategoryGrid() + valid_repository_grid = repository_grids.ValidRepositoryGrid()

@web.expose def browse_categories( self, trans, **kwd ): @@ -2579,11 +1601,11 @@ allow_push_select_field = self.__build_allow_push_select_field( trans, current_allow_push_list ) checked = alerts_checked or user.email in email_alerts alerts_check_box = CheckboxField( 'alerts', checked=checked ) - changeset_revision_select_field = build_changeset_revision_select_field( trans, - repository, - selected_value=changeset_revision, - add_id_to_name=False, - downloadable=False ) + changeset_revision_select_field = grids_util.build_changeset_revision_select_field( trans, + repository, + selected_value=changeset_revision, + add_id_to_name=False, + downloadable=False ) revision_label = suc.get_revision_label( trans, repository, repository.tip( trans.app ) ) repository_metadata = None repository_metadata_id = None @@ -2749,11 +1771,11 @@ metadata = None repository_dependencies = None revision_label = suc.get_revision_label( trans, repository, changeset_revision ) - changeset_revision_select_field = build_changeset_revision_select_field( trans, - repository, - selected_value=changeset_revision, - add_id_to_name=False, - downloadable=False ) + changeset_revision_select_field = grids_util.build_changeset_revision_select_field( trans, + repository, + selected_value=changeset_revision, + add_id_to_name=False, + downloadable=False ) containers_dict = suc.build_repository_containers_for_tool_shed( trans, repository, changeset_revision, repository_dependencies, repository_metadata ) return trans.fill_template( '/webapps/tool_shed/repository/preview_tools_in_changeset.mako', repository=repository, @@ -3378,11 +2400,11 @@ trans.sa_session.flush() checked = alerts_checked or ( user and user.email in email_alerts ) alerts_check_box = CheckboxField( 'alerts', checked=checked ) - changeset_revision_select_field = build_changeset_revision_select_field( trans, - repository, - selected_value=changeset_revision, - add_id_to_name=False, - downloadable=False ) + changeset_revision_select_field = grids_util.build_changeset_revision_select_field( trans, + repository, + selected_value=changeset_revision, + add_id_to_name=False, + downloadable=False ) revision_label = suc.get_revision_label( trans, repository, changeset_revision ) repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) if repository_metadata: @@ -3500,11 +2522,11 @@ metadata = None #tool_test_errors = None is_malicious = suc.changeset_is_malicious( trans, repository_id, repository.tip( trans.app ) ) - changeset_revision_select_field = build_changeset_revision_select_field( trans, - repository, - selected_value=changeset_revision, - add_id_to_name=False, - downloadable=False ) + changeset_revision_select_field = grids_util.build_changeset_revision_select_field( trans, + repository, + selected_value=changeset_revision, + add_id_to_name=False, + downloadable=False ) trans.app.config.tool_data_path = original_tool_data_path reviewed_by_user = suc.changeset_revision_reviewed_by_user( trans, trans.user, repository, changeset_revision ) if reviewed_by_user: @@ -3552,56 +2574,3 @@ metadata=metadata, message=message, status=status ) - -# ----- Utility methods ----- - -def build_changeset_revision_select_field( trans, repository, selected_value=None, add_id_to_name=True, - downloadable=False, reviewed=False, not_reviewed=False ): - """Build a SelectField whose options are the changeset_rev strings of certain revisions of the received repository.""" - options = [] - changeset_tups = [] - refresh_on_change_values = [] - if downloadable: - # Restrict the options to downloadable revisions. - repository_metadata_revisions = repository.downloadable_revisions - elif reviewed: - # Restrict the options to revisions that have been reviewed. - repository_metadata_revisions = [] - metadata_changeset_revision_hashes = [] - for metadata_revision in repository.metadata_revisions: - metadata_changeset_revision_hashes.append( metadata_revision.changeset_revision ) - for review in repository.reviews: - if review.changeset_revision in metadata_changeset_revision_hashes: - repository_metadata_revisions.append( review.repository_metadata ) - elif not_reviewed: - # Restrict the options to revisions that have not yet been reviewed. - repository_metadata_revisions = [] - reviewed_metadata_changeset_revision_hashes = [] - for review in repository.reviews: - reviewed_metadata_changeset_revision_hashes.append( review.changeset_revision ) - for metadata_revision in repository.metadata_revisions: - if metadata_revision.changeset_revision not in reviewed_metadata_changeset_revision_hashes: - repository_metadata_revisions.append( metadata_revision ) - else: - # Restrict the options to all revisions that have associated metadata. - repository_metadata_revisions = repository.metadata_revisions - for repository_metadata in repository_metadata_revisions: - rev, label, changeset_revision = suc.get_rev_label_changeset_revision_from_repository_metadata( trans, repository_metadata, repository=repository ) - changeset_tups.append( ( rev, label, changeset_revision ) ) - refresh_on_change_values.append( changeset_revision ) - # Sort options by the revision label. Even though the downloadable_revisions query sorts by update_time, - # the changeset revisions may not be sorted correctly because setting metadata over time will reset update_time. - for changeset_tup in sorted( changeset_tups ): - # Display the latest revision first. - options.insert( 0, ( changeset_tup[1], changeset_tup[2] ) ) - if add_id_to_name: - name = 'changeset_revision_%d' % repository.id - else: - name = 'changeset_revision' - select_field = SelectField( name=name, - refresh_on_change=True, - refresh_on_change_values=refresh_on_change_values ) - for option_tup in options: - selected = selected_value and option_tup[1] == selected_value - select_field.add_option( option_tup[0], option_tup[1], selected=selected ) - return select_field

diff -r 7369eda82e2cf7e10338232569ed9185bc3b526b -r db8a3bd35841ce033aff283510a0f7fe3aec3ab0 lib/galaxy/webapps/tool_shed/controllers/repository_review.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository_review.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository_review.py @@ -8,7 +8,7 @@ from sqlalchemy.sql.expression import func from galaxy.webapps.tool_shed.util import common_util from galaxy.webapps.tool_shed.util.container_util import STRSEP -from repository import RepositoryGrid +from tool_shed.grids.repository_grids import RepositoryGrid import tool_shed.util.shed_util_common as suc from galaxy.util.odict import odict

This diff is so big that we needed to truncate the remainder.

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.