From fc387566ca1f63fdeaeb51becb65b40a4df93162 Mon Sep 17 00:00:00 2001 From: Greg Von Kuster Date: Sun, 17 Feb 2013 12:46:13 -0500 Subject: [PATCH] Fix tool shed functional test that was broken in commit 8852:d04aa3ad6132. --- test/tool_shed/base/twilltestcase.py | 60 ++++++++++++++----- ...stall_repository_with_tool_dependencies.py | 2 +- 2 files changed, 46 insertions(+), 16 deletions(-) diff --git a/test/tool_shed/base/twilltestcase.py b/test/tool_shed/base/twilltestcase.py index d6c373048eb..56258021698 100644 --- a/test/tool_shed/base/twilltestcase.py +++ b/test/tool_shed/base/twilltestcase.py @@ -903,28 +903,58 @@ class ShedTwillTestCase( TwillTestCase ): self.reset_installed_repository_metadata( installed_repository ) new_metadata = installed_repository.metadata assert metadata == new_metadata, 'Metadata for installed repository %s differs after metadata reset.' % name - def verify_installed_repository_data_table_entries( self, data_tables=[] ): - data_table = util.parse_xml( self.shed_tool_data_table_conf ) + def verify_installed_repository_data_table_entries( self, required_data_table_entries ): + # The value of the received required_data_table_entries will be something like: [ 'sam_fa_indexes' ] + data_tables = util.parse_xml( self.shed_tool_data_table_conf ) found = False + # With the tool shed, the "path" attribute that is hard-coded into the tool_data_tble_conf.xml + # file is ignored. This is because the tool shed requires the directory location to which this + # path points to be empty except when a specific tool is loaded. The default location for this + # directory configured for the tool shed is /shed-tool-data. When a tool is loaded + # in the tool shed, all contained .loc.sample files are copied to this directory and the + # ToolDataTableManager parses and loads the files in the same way that Galaxy does with a very + # important exception. When the tool shed loads a tool and parses and loads the copied ,loc.sample + # files, the ToolDataTableManager is already instantiated, and so it's add_new_entries_from_config_file() + # method is called and the tool_data_path parameter is used to over-ride the hard-coded "tool-data" + # directory that Galaxy always uses. + # # Tool data table xml structure: # - # - # - # value, dbkey, name, path - # + #
+ # line_type, value, path + # #
# - for table_elem in data_table.findall( 'table' ): - for data_table in data_tables: - if 'name' in table_elem.attrib and table_elem.attrib[ 'name' ] == data_table: - file_elem = table_elem.find( 'file' ) - file_path = file_elem.get( 'path', None ) - full_path = os.path.join( self.tool_data_path, file_path ) - assert file_path is not None, 'No file path configured for this data table.' - assert os.path.exists( full_path ), 'Tool data table file %s not found.' % full_path + for table_elem in data_tables.findall( 'table' ): + # The value of table_elem will be something like: + for required_data_table_entry in required_data_table_entries: + # The value of required_data_table_entry will be something like: 'sam_fa_indexes' + if 'name' in table_elem.attrib and table_elem.attrib[ 'name' ] == required_data_table_entry: found = True + # We're processing something like: sam_fa_indexes + file_elem = table_elem.find( 'file' ) + # We have something like: + # The "path" attribute of the "file" tag is the location that Galaxy always uses because the + # Galaxy ToolDataTableManager was implemented in such a way that the hard-coded path is used + # rather than allowing the location to be a configurable setting like the tool shed requires. + file_path = file_elem.get( 'path', None ) + # The value of file_path will be something like: "tool-data/all_fasta.loc" + assert file_path is not None, 'The "path" attribute is missing for the %s entry.' % name + # The following test is probably not necesary, but the tool-data directory should exist! + galaxy_tool_data_dir, loc_file_name = os.path.split( file_path ) + assert galaxy_tool_data_dir is not None, 'The hard-coded Galaxy tool-data directory is missing for the %s entry.' % name + assert os.path.exists( galaxy_tool_data_dir ), 'The Galaxy tool-data directory does not exist.' + # Make sure the loc_file_name was correctly copied into the configured directory location. + configured_file_location = os.path.join( self.tool_data_path, loc_file_name ) + assert os.path.isfile( configured_file_location ), 'The expected copied file "%s" is missing.' % configured_file_location + # We've found the value of the required_data_table_entry in data_tables, which is the parsed + # shed_tool_data_table_conf.xml, so all is well! break - assert found, 'No entry for %s in %s.' % ( data_table, self.shed_tool_data_table_conf ) + if found: + break + # We better have an entry like:
in our parsed data_tables + # or we know that the repository was not correctly installed! + assert found, 'No entry for %s in %s.' % ( required_data_table_entry, self.shed_tool_data_table_conf ) def verify_repository_reviews( self, repository, reviewer=None, strings_displayed=[], strings_not_displayed=[] ): changeset_revision = self.get_repository_tip( repository ) # Verify that the currently logged in user has a repository review for the specified repository, reviewer, and changeset revision. diff --git a/test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py b/test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py index c8c03b2d0c6..49be3d0166b 100644 --- a/test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py +++ b/test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py @@ -127,5 +127,5 @@ class ToolWithToolDependencies( ShedTwillTestCase ): self.verify_installed_repository_metadata_unchanged( repository_name, common.test_user_1_name ) def test_0025_verify_sample_files( self ): '''Verify that the installed repository populated shed_tool_data_table.xml and the sample files.''' - self.verify_installed_repository_data_table_entries( data_tables=[ 'sam_fa_indexes' ] ) + self.verify_installed_repository_data_table_entries( required_data_table_entries=[ 'sam_fa_indexes' ] )