3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/748970a9369a/ Changeset: 748970a9369a User: jmchilton Date: 2014-07-29 21:46:02 Summary: Fix tool shed metadata generation code for test collection definitions. Affected #: 1 file diff -r b43506b47aadfafeb2dc06286d56de7363633599 -r 748970a9369ae8d6949d3203a7ede5a5e8c205b4 lib/tool_shed/metadata/metadata_generator.py --- a/lib/tool_shed/metadata/metadata_generator.py +++ b/lib/tool_shed/metadata/metadata_generator.py @@ -7,6 +7,7 @@ from galaxy.datatypes import checkers from galaxy.model.orm import and_ from galaxy.tools.data_manager.manager import DataManager +from galaxy.tools.test import TestCollectionDef from galaxy.web import url_for from tool_shed.repository_types import util as rt_util @@ -621,7 +622,13 @@ # </test> inputs.append( ( param_name, values ) ) else: - if len( values ) == 1: + if isinstance( values, TestCollectionDef ): + # Nested required files are being populated correctly, + # not sure we need the value here to be anything else? + collection_type = values.collection_type + metadata_display_value = "%s collection" % collection_type + inputs.append( ( param_name, metadata_display_value ) ) + elif len( values ) == 1: inputs.append( ( param_name, values[ 0 ] ) ) else: inputs.append( ( param_name, values ) ) https://bitbucket.org/galaxy/galaxy-central/commits/38ba45d6ba5b/ Changeset: 38ba45d6ba5b User: jmchilton Date: 2014-07-30 13:02:09 Summary: Configure citation manager in tool shed app. Should fix error reported by Peter Cock here http://dev.list.galaxyproject.org/Uploads-with-embedded-citations-causing-re.... Affected #: 2 files diff -r 748970a9369ae8d6949d3203a7ede5a5e8c205b4 -r 38ba45d6ba5be65b3b743fc08739e16cd6e0ac8f lib/galaxy/webapps/tool_shed/app.py --- a/lib/galaxy/webapps/tool_shed/app.py +++ b/lib/galaxy/webapps/tool_shed/app.py @@ -52,6 +52,9 @@ # because the Tool Shed should always have an empty dictionary! self.tool_data_tables = galaxy.tools.data.ToolDataTableManager( self.config.tool_data_path ) self.genome_builds = GenomeBuilds( self ) + # Citation manager needed to load tools. + from galaxy.managers.citations import CitationsManager + self.citations_manager = CitationsManager( self ) # The Tool Shed makes no use of a Galaxy toolbox, but this attribute is still required. self.toolbox = tools.ToolBox( [], self.config.tool_path, self ) # Initialize the Tool Shed security agent. diff -r 748970a9369ae8d6949d3203a7ede5a5e8c205b4 -r 38ba45d6ba5be65b3b743fc08739e16cd6e0ac8f lib/galaxy/webapps/tool_shed/config.py --- a/lib/galaxy/webapps/tool_shed/config.py +++ b/lib/galaxy/webapps/tool_shed/config.py @@ -130,6 +130,9 @@ if global_conf and "__file__" in global_conf: global_conf_parser.read(global_conf['__file__']) self.running_functional_tests = string_as_bool( kwargs.get( 'running_functional_tests', False ) ) + self.citation_cache_type = kwargs.get( "citation_cache_type", "file" ) + self.citation_cache_data_dir = resolve_path( kwargs.get( "citation_cache_data_dir", "database/tool_shed_citations/data" ), self.root ) + self.citation_cache_lock_dir = resolve_path( kwargs.get( "citation_cache_lock_dir", "database/tool_shed_citations/locks" ), self.root ) def get( self, key, default ): return self.config_dict.get( key, default ) https://bitbucket.org/galaxy/galaxy-central/commits/6b44b99b79b8/ Changeset: 6b44b99b79b8 Branch: next-stable User: jmchilton Date: 2014-07-30 13:04:48 Summary: Merge default to next-stable for tool shed fixes. Affected #: 3 files diff -r e6813f244a2ad99cec27bba6492c89008459b338 -r 6b44b99b79b8c4383e8475e409c53f9deae7f7ff lib/galaxy/webapps/tool_shed/app.py --- a/lib/galaxy/webapps/tool_shed/app.py +++ b/lib/galaxy/webapps/tool_shed/app.py @@ -52,6 +52,9 @@ # because the Tool Shed should always have an empty dictionary! self.tool_data_tables = galaxy.tools.data.ToolDataTableManager( self.config.tool_data_path ) self.genome_builds = GenomeBuilds( self ) + # Citation manager needed to load tools. + from galaxy.managers.citations import CitationsManager + self.citations_manager = CitationsManager( self ) # The Tool Shed makes no use of a Galaxy toolbox, but this attribute is still required. self.toolbox = tools.ToolBox( [], self.config.tool_path, self ) # Initialize the Tool Shed security agent. diff -r e6813f244a2ad99cec27bba6492c89008459b338 -r 6b44b99b79b8c4383e8475e409c53f9deae7f7ff lib/galaxy/webapps/tool_shed/config.py --- a/lib/galaxy/webapps/tool_shed/config.py +++ b/lib/galaxy/webapps/tool_shed/config.py @@ -130,6 +130,9 @@ if global_conf and "__file__" in global_conf: global_conf_parser.read(global_conf['__file__']) self.running_functional_tests = string_as_bool( kwargs.get( 'running_functional_tests', False ) ) + self.citation_cache_type = kwargs.get( "citation_cache_type", "file" ) + self.citation_cache_data_dir = resolve_path( kwargs.get( "citation_cache_data_dir", "database/tool_shed_citations/data" ), self.root ) + self.citation_cache_lock_dir = resolve_path( kwargs.get( "citation_cache_lock_dir", "database/tool_shed_citations/locks" ), self.root ) def get( self, key, default ): return self.config_dict.get( key, default ) diff -r e6813f244a2ad99cec27bba6492c89008459b338 -r 6b44b99b79b8c4383e8475e409c53f9deae7f7ff lib/tool_shed/metadata/metadata_generator.py --- a/lib/tool_shed/metadata/metadata_generator.py +++ b/lib/tool_shed/metadata/metadata_generator.py @@ -7,6 +7,7 @@ from galaxy.datatypes import checkers from galaxy.model.orm import and_ from galaxy.tools.data_manager.manager import DataManager +from galaxy.tools.test import TestCollectionDef from galaxy.web import url_for from tool_shed.repository_types import util as rt_util @@ -621,7 +622,13 @@ # </test> inputs.append( ( param_name, values ) ) else: - if len( values ) == 1: + if isinstance( values, TestCollectionDef ): + # Nested required files are being populated correctly, + # not sure we need the value here to be anything else? + collection_type = values.collection_type + metadata_display_value = "%s collection" % collection_type + inputs.append( ( param_name, metadata_display_value ) ) + elif len( values ) == 1: inputs.append( ( param_name, values[ 0 ] ) ) else: inputs.append( ( param_name, values ) ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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