[galaxy-commits] commit/galaxy-central: 4 new changesets

4 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c8a799823eb9/ Changeset: c8a799823eb9 User: dannon Date: 2013-06-20 16:14:31 Summary: Handle dialect strings with either postgres or postgresql Affected #: 1 file diff -r 2a6a9157ff83744e8526538042f65ebe891d5526 -r c8a799823eb9a248e2d444d1bbc5fa4f117e6a0e lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py +++ b/lib/galaxy/model/mapping.py @@ -32,6 +32,7 @@ dialect_to_egg = { "sqlite" : "pysqlite>=2", "postgres" : "psycopg2", + "postgresql" : "psycopg2", "mysql" : "MySQL_python" } https://bitbucket.org/galaxy/galaxy-central/commits/f90ebd0f10ff/ Changeset: f90ebd0f10ff User: dannon Date: 2013-06-20 16:50:31 Summary: Consolidate dialect_to_egg to a single location. Affected #: 7 files diff -r c8a799823eb9a248e2d444d1bbc5fa4f117e6a0e -r f90ebd0f10ffda2657b06d53400e2f01cecb959b lib/galaxy/model/migrate/check.py --- a/lib/galaxy/model/migrate/check.py +++ b/lib/galaxy/model/migrate/check.py @@ -12,16 +12,13 @@ from sqlalchemy.exc import NoSuchTableError from migrate.versioning import repository, schema +from galaxy.model.mapping import dialect_to_egg + log = logging.getLogger( __name__ ) # path relative to galaxy migrate_repository_directory = os.path.dirname( __file__ ).replace( os.getcwd() + os.path.sep, '', 1 ) migrate_repository = repository.Repository( migrate_repository_directory ) -dialect_to_egg = { - "sqlite" : "pysqlite>=2", - "postgres" : "psycopg2", - "mysql" : "MySQL_python" -} def create_or_verify_database( url, galaxy_config_file, engine_options={}, app=None ): """ diff -r c8a799823eb9a248e2d444d1bbc5fa4f117e6a0e -r f90ebd0f10ffda2657b06d53400e2f01cecb959b lib/galaxy/webapps/tool_shed/model/mapping.py --- a/lib/galaxy/webapps/tool_shed/model/mapping.py +++ b/lib/galaxy/webapps/tool_shed/model/mapping.py @@ -12,6 +12,7 @@ from galaxy.model.orm import * from galaxy.model.custom_types import * from galaxy.util.bunch import Bunch +from galaxy.model.mapping import dialect_to_egg import galaxy.webapps.tool_shed.util.shed_statistics as shed_statistics import galaxy.webapps.tool_shed.util.hgweb_config from galaxy.webapps.tool_shed.security import CommunityRBACAgent @@ -22,12 +23,6 @@ # For backward compatibility with "context.current" context.current = Session -dialect_to_egg = { - "sqlite" : "pysqlite>=2", - "postgres" : "psycopg2", - "mysql" : "MySQL_python" -} - # NOTE REGARDING TIMESTAMPS: # It is currently difficult to have the timestamps calculated by the # database in a portable way, so we're doing it in the client. This diff -r c8a799823eb9a248e2d444d1bbc5fa4f117e6a0e -r f90ebd0f10ffda2657b06d53400e2f01cecb959b lib/galaxy/webapps/tool_shed/model/migrate/check.py --- a/lib/galaxy/webapps/tool_shed/model/migrate/check.py +++ b/lib/galaxy/webapps/tool_shed/model/migrate/check.py @@ -8,20 +8,18 @@ pkg_resources.require( "sqlalchemy-migrate" ) pkg_resources.require( "Tempita" ) + from migrate.versioning import repository, schema from sqlalchemy import * from sqlalchemy.exc import NoSuchTableError +from galaxy.model.mapping import dialect_to_egg + log = logging.getLogger( __name__ ) # path relative to galaxy migrate_repository_directory = os.path.dirname( __file__ ).replace( os.getcwd() + os.path.sep, '', 1 ) migrate_repository = repository.Repository( migrate_repository_directory ) -dialect_to_egg = { - "sqlite" : "pysqlite>=2", - "postgres" : "psycopg2", - "mysql" : "MySQL_python" -} def create_or_verify_database( url, engine_options={} ): """ diff -r c8a799823eb9a248e2d444d1bbc5fa4f117e6a0e -r f90ebd0f10ffda2657b06d53400e2f01cecb959b lib/tool_shed/galaxy_install/migrate/check.py --- a/lib/tool_shed/galaxy_install/migrate/check.py +++ b/lib/tool_shed/galaxy_install/migrate/check.py @@ -9,6 +9,7 @@ from migrate.versioning import repository, schema from sqlalchemy import * from galaxy.util.odict import odict +from galaxy.model.mapping import dialect_to_egg from tool_shed.util import common_util log = logging.getLogger( __name__ ) @@ -16,11 +17,6 @@ # Path relative to galaxy migrate_repository_directory = os.path.dirname( __file__ ).replace( os.getcwd() + os.path.sep, '', 1 ) migrate_repository = repository.Repository( migrate_repository_directory ) -dialect_to_egg = { - "sqlite" : "pysqlite>=2", - "postgres" : "psycopg2", - "mysql" : "MySQL_python" -} def verify_tools( app, url, galaxy_config_file, engine_options={} ): # Check the value in the migrate_tools.version database table column to verify that the number is in diff -r c8a799823eb9a248e2d444d1bbc5fa4f117e6a0e -r f90ebd0f10ffda2657b06d53400e2f01cecb959b scripts/db_shell.py --- a/scripts/db_shell.py +++ b/scripts/db_shell.py @@ -26,6 +26,8 @@ from ConfigParser import SafeConfigParser +from galaxy.model.mapping import dialect_to_egg + log = logging.getLogger( __name__ ) if sys.argv[-1] in [ 'tool_shed' ]: @@ -56,11 +58,6 @@ else: db_url = "sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE" -dialect_to_egg = { - "sqlite" : "pysqlite>=2", - "postgres" : "psycopg2", - "mysql" : "MySQL_python" -} dialect = ( db_url.split( ':', 1 ) )[0] try: egg = dialect_to_egg[dialect] diff -r c8a799823eb9a248e2d444d1bbc5fa4f117e6a0e -r f90ebd0f10ffda2657b06d53400e2f01cecb959b scripts/manage_db.py --- a/scripts/manage_db.py +++ b/scripts/manage_db.py @@ -14,6 +14,8 @@ from migrate.versioning.shell import main from ConfigParser import SafeConfigParser +from galaxy.model.mapping import dialect_to_egg + log = logging.getLogger( __name__ ) if sys.argv[-1] in [ 'tool_shed' ]: @@ -44,11 +46,6 @@ else: db_url = "sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE" -dialect_to_egg = { - "sqlite" : "pysqlite>=2", - "postgres" : "psycopg2", - "mysql" : "MySQL_python" -} dialect = ( db_url.split( ':', 1 ) )[0] try: egg = dialect_to_egg[dialect] diff -r c8a799823eb9a248e2d444d1bbc5fa4f117e6a0e -r f90ebd0f10ffda2657b06d53400e2f01cecb959b scripts/manage_tools.py --- a/scripts/manage_tools.py +++ b/scripts/manage_tools.py @@ -15,6 +15,8 @@ from migrate.versioning.shell import main from ConfigParser import SafeConfigParser +from galaxy.model.mapping import dialect_to_egg + log = logging.getLogger( __name__ ) config_file = 'universe_wsgi.ini' @@ -40,11 +42,6 @@ else: db_url = "sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE" -dialect_to_egg = { - "sqlite" : "pysqlite>=2", - "postgres" : "psycopg2", - "mysql" : "MySQL_python" -} dialect = ( db_url.split( ':', 1 ) )[0] try: egg = dialect_to_egg[dialect] https://bitbucket.org/galaxy/galaxy-central/commits/8ca89d2f055f/ Changeset: 8ca89d2f055f User: dannon Date: 2013-06-20 16:58:52 Summary: galaxy.model.orm is a more sensible location than mapping for dialect_to_egg Affected #: 9 files diff -r f90ebd0f10ffda2657b06d53400e2f01cecb959b -r 8ca89d2f055f04ffbf069b773deeb26fa60c9d72 lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py +++ b/lib/galaxy/model/mapping.py @@ -16,6 +16,7 @@ from sqlalchemy.orm.collections import attribute_mapped_collection from galaxy import model +from galaxy.model.orm import dialect_to_egg from galaxy.model.custom_types import JSONType, MetadataType, TrimmedString, UUIDType from galaxy.security import GalaxyRBACAgent from galaxy.util.bunch import Bunch @@ -29,12 +30,6 @@ # For backward compatibility with "context.current" context.current = Session -dialect_to_egg = { - "sqlite" : "pysqlite>=2", - "postgres" : "psycopg2", - "postgresql" : "psycopg2", - "mysql" : "MySQL_python" -} # NOTE REGARDING TIMESTAMPS: # It is currently difficult to have the timestamps calculated by the diff -r f90ebd0f10ffda2657b06d53400e2f01cecb959b -r 8ca89d2f055f04ffbf069b773deeb26fa60c9d72 lib/galaxy/model/migrate/check.py --- a/lib/galaxy/model/migrate/check.py +++ b/lib/galaxy/model/migrate/check.py @@ -12,7 +12,7 @@ from sqlalchemy.exc import NoSuchTableError from migrate.versioning import repository, schema -from galaxy.model.mapping import dialect_to_egg +from galaxy.model.orm import dialect_to_egg log = logging.getLogger( __name__ ) diff -r f90ebd0f10ffda2657b06d53400e2f01cecb959b -r 8ca89d2f055f04ffbf069b773deeb26fa60c9d72 lib/galaxy/model/orm/__init__.py --- a/lib/galaxy/model/orm/__init__.py +++ b/lib/galaxy/model/orm/__init__.py @@ -7,3 +7,10 @@ import sqlalchemy.exc from sqlalchemy.ext.orderinglist import ordering_list + +dialect_to_egg = { + "sqlite" : "pysqlite>=2", + "postgres" : "psycopg2", + "postgresql" : "psycopg2", + "mysql" : "MySQL_python" +} diff -r f90ebd0f10ffda2657b06d53400e2f01cecb959b -r 8ca89d2f055f04ffbf069b773deeb26fa60c9d72 lib/galaxy/webapps/tool_shed/model/mapping.py --- a/lib/galaxy/webapps/tool_shed/model/mapping.py +++ b/lib/galaxy/webapps/tool_shed/model/mapping.py @@ -12,7 +12,7 @@ from galaxy.model.orm import * from galaxy.model.custom_types import * from galaxy.util.bunch import Bunch -from galaxy.model.mapping import dialect_to_egg +from galaxy.model.orm import dialect_to_egg import galaxy.webapps.tool_shed.util.shed_statistics as shed_statistics import galaxy.webapps.tool_shed.util.hgweb_config from galaxy.webapps.tool_shed.security import CommunityRBACAgent diff -r f90ebd0f10ffda2657b06d53400e2f01cecb959b -r 8ca89d2f055f04ffbf069b773deeb26fa60c9d72 lib/galaxy/webapps/tool_shed/model/migrate/check.py --- a/lib/galaxy/webapps/tool_shed/model/migrate/check.py +++ b/lib/galaxy/webapps/tool_shed/model/migrate/check.py @@ -13,7 +13,7 @@ from sqlalchemy import * from sqlalchemy.exc import NoSuchTableError -from galaxy.model.mapping import dialect_to_egg +from galaxy.model.orm import dialect_to_egg log = logging.getLogger( __name__ ) diff -r f90ebd0f10ffda2657b06d53400e2f01cecb959b -r 8ca89d2f055f04ffbf069b773deeb26fa60c9d72 lib/tool_shed/galaxy_install/migrate/check.py --- a/lib/tool_shed/galaxy_install/migrate/check.py +++ b/lib/tool_shed/galaxy_install/migrate/check.py @@ -9,7 +9,7 @@ from migrate.versioning import repository, schema from sqlalchemy import * from galaxy.util.odict import odict -from galaxy.model.mapping import dialect_to_egg +from galaxy.model.orm import dialect_to_egg from tool_shed.util import common_util log = logging.getLogger( __name__ ) diff -r f90ebd0f10ffda2657b06d53400e2f01cecb959b -r 8ca89d2f055f04ffbf069b773deeb26fa60c9d72 scripts/db_shell.py --- a/scripts/db_shell.py +++ b/scripts/db_shell.py @@ -26,7 +26,7 @@ from ConfigParser import SafeConfigParser -from galaxy.model.mapping import dialect_to_egg +from galaxy.model.orm import dialect_to_egg log = logging.getLogger( __name__ ) diff -r f90ebd0f10ffda2657b06d53400e2f01cecb959b -r 8ca89d2f055f04ffbf069b773deeb26fa60c9d72 scripts/manage_db.py --- a/scripts/manage_db.py +++ b/scripts/manage_db.py @@ -14,7 +14,7 @@ from migrate.versioning.shell import main from ConfigParser import SafeConfigParser -from galaxy.model.mapping import dialect_to_egg +from galaxy.model.orm import dialect_to_egg log = logging.getLogger( __name__ ) diff -r f90ebd0f10ffda2657b06d53400e2f01cecb959b -r 8ca89d2f055f04ffbf069b773deeb26fa60c9d72 scripts/manage_tools.py --- a/scripts/manage_tools.py +++ b/scripts/manage_tools.py @@ -15,7 +15,7 @@ from migrate.versioning.shell import main from ConfigParser import SafeConfigParser -from galaxy.model.mapping import dialect_to_egg +from galaxy.model.orm import dialect_to_egg log = logging.getLogger( __name__ ) https://bitbucket.org/galaxy/galaxy-central/commits/7362302b2c63/ Changeset: 7362302b2c63 User: dannon Date: 2013-06-20 16:59:07 Summary: Merge. Affected #: 1 file diff -r 8ca89d2f055f04ffbf069b773deeb26fa60c9d72 -r 7362302b2c638d377931fa710d40ba2f86f25dba lib/galaxy/webapps/galaxy/api/provenance.py --- a/lib/galaxy/webapps/galaxy/api/provenance.py +++ b/lib/galaxy/webapps/galaxy/api/provenance.py @@ -3,13 +3,13 @@ """ import logging from galaxy import web -from galaxy.web.base.controller import BaseAPIController +from galaxy.web.base.controller import BaseAPIController, UsesHistoryMixin from paste.httpexceptions import HTTPNotImplemented, HTTPBadRequest log = logging.getLogger( __name__ ) -class BaseProvenanceController( BaseAPIController ): +class BaseProvenanceController( BaseAPIController, UsesHistoryMixin ): """ """ @web.expose_api 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.