[galaxy-commits] commit/galaxy-central: 6 new changesets

6 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/59cd12ceafc4/ Changeset: 59cd12ceafc4 User: dannon Date: 2015-02-24 16:38:18+00:00 Summary: Cleanup of comments, doc of customtypes. Affected #: 1 file diff -r 476c79d7b00a5edde57847ca1882d7e7781030b6 -r 59cd12ceafc4628e05600be46939124d4ca59c08 lib/galaxy/model/custom_types.py --- a/lib/galaxy/model/custom_types.py +++ b/lib/galaxy/model/custom_types.py @@ -33,15 +33,6 @@ return value -# Mutable JSONType for SQLAlchemy from original gist: -# https://gist.github.com/dbarnett/1730610 -# -# Also using minor changes from this fork of the gist: -# https://gist.github.com/miracle2k/52a031cced285ba9b8cd -# -# And other minor changes to make it work for us. - - class JSONType(sqlalchemy.types.TypeDecorator): """Represents an immutable structure as a json-encoded string. @@ -69,6 +60,15 @@ class MutationObj(Mutable): + """ + Mutable JSONType for SQLAlchemy from original gist: + https://gist.github.com/dbarnett/1730610 + + Using minor changes from this fork of the gist: + https://gist.github.com/miracle2k/52a031cced285ba9b8cd + + And other minor changes to make it work for us. + """ @classmethod def coerce(cls, key, value): if isinstance(value, dict) and not isinstance(value, MutationDict): @@ -192,13 +192,6 @@ MutationObj.associate_with(JSONType) -"""A type to encode/decode JSON on the fly - -sqltype is the string type for the underlying DB column:: - - Column(JSON) -""" - metadata_pickler = AliasPickleModule( { ( "cookbook.patterns", "Bunch" ): ( "galaxy.util.bunch", "Bunch" ) } ) https://bitbucket.org/galaxy/galaxy-central/commits/834b3e714755/ Changeset: 834b3e714755 User: dan Date: 2015-02-24 16:50:58+00:00 Summary: Fix for installing .loc files from the toolshed to respect shed_tool_data_path. Mention shed_tool_data_path in galaxy.ini.sample. Affected #: 2 files diff -r 59cd12ceafc4628e05600be46939124d4ca59c08 -r 834b3e71475518902f071d4066d69e707f752730 config/galaxy.ini.sample --- a/config/galaxy.ini.sample +++ b/config/galaxy.ini.sample @@ -217,6 +217,10 @@ # https://wiki.galaxyproject.org/Admin/DataIntegration #tool_data_path = tool-data +# Directory where Tool Data Table related files will be placed +# when installed from a ToolShed. Defaults to tool_data_path +#shed_tool_data_path = tool-data + # File containing old-style genome builds #builds_file_path = tool-data/shared/ucsc/builds.txt diff -r 59cd12ceafc4628e05600be46939124d4ca59c08 -r 834b3e71475518902f071d4066d69e707f752730 lib/tool_shed/tools/data_table_manager.py --- a/lib/tool_shed/tools/data_table_manager.py +++ b/lib/tool_shed/tools/data_table_manager.py @@ -103,7 +103,7 @@ try: new_table_elems, message = self.app.tool_data_tables \ .add_new_entries_from_config_file( config_filename=filename, - tool_data_path=self.app.config.tool_data_path, + tool_data_path=self.app.config.shed_tool_data_path, shed_tool_data_table_config=self.app.config.shed_tool_data_table_config, persist=persist ) if message: https://bitbucket.org/galaxy/galaxy-central/commits/b154ff11d2ea/ Changeset: b154ff11d2ea User: jmchilton Date: 2015-02-24 17:01:35+00:00 Summary: Fix unit tests for dde2fc9572be6d909e22dda510520639db5260bf. Thanks to @ dannon for the bug report. Affected #: 1 file diff -r 834b3e71475518902f071d4066d69e707f752730 -r b154ff11d2ea00d6978da97ee60bb1013f4f7f4e test/unit/jobs/test_job_configuration.py --- a/test/unit/jobs/test_job_configuration.py +++ b/test/unit/jobs/test_job_configuration.py @@ -21,6 +21,7 @@ job_config_file=os.path.join( self.temp_directory, "job_conf.xml" ), use_tasked_jobs=False, job_resource_params_file="/tmp/fake_absent_path", + config_dict={}, ) self.__write_config_from( SIMPLE_JOB_CONF ) self.app = bunch.Bunch( config=self.config, job_metrics=MockJobMetrics() ) https://bitbucket.org/galaxy/galaxy-central/commits/64b4a5b00522/ Changeset: 64b4a5b00522 User: dannon Date: 2015-02-24 18:47:29+00:00 Summary: Fix for JSONType getstate/setstate with pickle (exhibited error during uploading of a file). Affected #: 1 file diff -r b154ff11d2ea00d6978da97ee60bb1013f4f7f4e -r 64b4a5b005224c5639482de4eda52adcfa25df10 lib/galaxy/model/custom_types.py --- a/lib/galaxy/model/custom_types.py +++ b/lib/galaxy/model/custom_types.py @@ -143,6 +143,12 @@ dict.__delitem__(self, key) self.changed() + def __getstate__(self): + return dict(self) + + def __setstate__(self, state): + self.update(state) + class MutationList(MutationObj, list): @classmethod https://bitbucket.org/galaxy/galaxy-central/commits/9f3d45b2e032/ Changeset: 9f3d45b2e032 User: dannon Date: 2015-02-24 18:56:19+00:00 Summary: Add getstate/setstate for pickling to the MutationList as well, though I'm not sure we use this anywhere. Future-proofing. Affected #: 1 file diff -r 64b4a5b005224c5639482de4eda52adcfa25df10 -r 9f3d45b2e032b7d208c1e7e021ab3460795272fe lib/galaxy/model/custom_types.py --- a/lib/galaxy/model/custom_types.py +++ b/lib/galaxy/model/custom_types.py @@ -195,6 +195,12 @@ list.remove(self, value) self.changed() + def __getstate__(self): + return list(self) + + def __setstate__(self, state): + self.update(state) + MutationObj.associate_with(JSONType) https://bitbucket.org/galaxy/galaxy-central/commits/a12fc23ff137/ Changeset: a12fc23ff137 User: dannon Date: 2015-02-24 19:18:24+00:00 Summary: Commentary in custom_types w/ a TODO. Remove irrelevant comments about OrderedDict, since we're not relying on that. Affected #: 1 file diff -r 9f3d45b2e032b7d208c1e7e021ab3460795272fe -r a12fc23ff13785d2c2ef7d223dca100ef334ea87 lib/galaxy/model/custom_types.py --- a/lib/galaxy/model/custom_types.py +++ b/lib/galaxy/model/custom_types.py @@ -34,12 +34,16 @@ class JSONType(sqlalchemy.types.TypeDecorator): - """Represents an immutable structure as a json-encoded string. + """ + Represents an immutable structure as a json-encoded string. If default is, for example, a dict, then a NULL value in the database will be exposed as an empty dict. """ + # TODO: Figure out why this is a large binary, and provide a migratino to + # something like sqlalchemy.String, or even better, when applicable, native + # sqlalchemy.dialects.postgresql.JSON impl = LargeBinary def process_bind_param(self, value, dialect): @@ -131,9 +135,6 @@ return self def __setitem__(self, key, value): - # Due to the way OrderedDict works, this is called during __init__. - # At this time we don't have a key set, but what is more, the value - # being set has already been coerced. So special case this and skip. if hasattr(self, '_key'): value = MutationObj.coerce(self._key, value) dict.__setitem__(self, key, value) 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.