1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/40a7ef4efb22/ changeset: 40a7ef4efb22 user: greg date: 2013-02-17 18:46:13 summary: Fix tool shed functional test that was broken in commit 8852:d04aa3ad6132. affected #: 2 files

diff -r 64b4ef5e2cc8e18a2872eaeb64fa46f50ae7f814 -r 40a7ef4efb22afdc6bde4bce4e75d691e4ac7a7f test/tool_shed/base/twilltestcase.py --- a/test/tool_shed/base/twilltestcase.py +++ b/test/tool_shed/base/twilltestcase.py @@ -903,28 +903,58 @@ 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 <Galaxy root>/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: # <tables> - # <!-- Locations of all fasta files under genome directory --> - # <table name="all_fasta" comment_char="#"> - # <columns>value, dbkey, name, path</columns> - # <file path="tool-data/all_fasta.loc" /> + # <table comment_char="#" name="sam_fa_indexes"> + # <columns>line_type, value, path</columns> + # <file path="tool-data/sam_fa_indices.loc" /> # </table> # </tables> - 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: + for table_elem in data_tables.findall( 'table' ): + # The value of table_elem will be something like: <table comment_char="#" name="sam_fa_indexes"> + 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: <file path="tool-data/sam_fa_indices.loc" /> + # 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 ) - full_path = os.path.join( self.tool_data_path, file_path ) - assert file_path is not None, 'No file path configured for this data table.' - assert os.path.exists( full_path ), 'Tool data table file %s not found.' % full_path - found = True + # 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: <table comment_char="#" name="sam_fa_indexes"> 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 -r 64b4ef5e2cc8e18a2872eaeb64fa46f50ae7f814 -r 40a7ef4efb22afdc6bde4bce4e75d691e4ac7a7f test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py --- a/test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py +++ b/test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py @@ -127,5 +127,5 @@ 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' ] )

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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