galaxy-commits May 2014

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242 discussions

commit/galaxy-central: dan: merge next-stable
by commits-noreply＠bitbucket.org 20 May '14

20 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/37509e01ee5d/ Changeset: 37509e01ee5d User: dan Date: 2014-05-20 16:32:31 Summary: merge next-stable Affected #: 2 files diff -r a968515e0a3128b39d2e5290d7d15559ae38ca44 -r 37509e01ee5db4b0552537c77f3771b9671e5dae lib/galaxy/webapps/reports/app.py --- a/lib/galaxy/webapps/reports/app.py +++ b/lib/galaxy/webapps/reports/app.py @@ -15,7 +15,7 @@ if self.config.database_connection: db_url = self.config.database_connection else: - db_url = "sqlite://%s?isolation_level=IMMEDIATE" % self.config.database + db_url = "sqlite:///%s?isolation_level=IMMEDIATE" % self.config.database # Setup the database engine and ORM self.model = galaxy.model.mapping.init( self.config.file_path, db_url, diff -r a968515e0a3128b39d2e5290d7d15559ae38ca44 -r 37509e01ee5db4b0552537c77f3771b9671e5dae lib/galaxy/webapps/reports/config.py --- a/lib/galaxy/webapps/reports/config.py +++ b/lib/galaxy/webapps/reports/config.py @@ -19,7 +19,7 @@ self.config_dict = kwargs self.root = kwargs.get( 'root_dir', '.' ) # Database related configuration - self.database = resolve_path( kwargs.get( "database_file", "database/universe.d" ), self.root ) + self.database = resolve_path( kwargs.get( "database_file", "database/universe.sqlite" ), self.root ) self.database_connection = kwargs.get( "database_connection", False ) self.database_engine_options = get_database_engine_options( kwargs ) # Where dataset files are stored 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.

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commit/galaxy-central: dan: Fix for reports app's default database/sqlite settings. Most of the reports app will still not work with sqlite however.
by commits-noreply＠bitbucket.org 20 May '14

20 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2ed7d87b4ddd/ Changeset: 2ed7d87b4ddd Branch: next-stable User: dan Date: 2014-05-20 16:32:13 Summary: Fix for reports app's default database/sqlite settings. Most of the reports app will still not work with sqlite however. Affected #: 2 files diff -r f3948f90b9002ae47f0941b0e39cb63d122415a3 -r 2ed7d87b4ddda2f32eb9d6fc8c05d74667842fef lib/galaxy/webapps/reports/app.py --- a/lib/galaxy/webapps/reports/app.py +++ b/lib/galaxy/webapps/reports/app.py @@ -15,7 +15,7 @@ if self.config.database_connection: db_url = self.config.database_connection else: - db_url = "sqlite://%s?isolation_level=IMMEDIATE" % self.config.database + db_url = "sqlite:///%s?isolation_level=IMMEDIATE" % self.config.database # Setup the database engine and ORM self.model = galaxy.model.mapping.init( self.config.file_path, db_url, diff -r f3948f90b9002ae47f0941b0e39cb63d122415a3 -r 2ed7d87b4ddda2f32eb9d6fc8c05d74667842fef lib/galaxy/webapps/reports/config.py --- a/lib/galaxy/webapps/reports/config.py +++ b/lib/galaxy/webapps/reports/config.py @@ -19,7 +19,7 @@ self.config_dict = kwargs self.root = kwargs.get( 'root_dir', '.' ) # Database related configuration - self.database = resolve_path( kwargs.get( "database_file", "database/universe.d" ), self.root ) + self.database = resolve_path( kwargs.get( "database_file", "database/universe.sqlite" ), self.root ) self.database_connection = kwargs.get( "database_connection", False ) self.database_engine_options = get_database_engine_options( kwargs ) # Where dataset files are stored 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.

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commit/galaxy-central: dan: merge next-stable
by commits-noreply＠bitbucket.org 20 May '14

20 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a968515e0a31/ Changeset: a968515e0a31 User: dan Date: 2014-05-20 16:18:49 Summary: merge next-stable Affected #: 1 file diff -r 9fee549c5ef78f80e35fa5ca37c1861267bc12f8 -r a968515e0a3128b39d2e5290d7d15559ae38ca44 lib/galaxy/util/dbkeys.py --- a/lib/galaxy/util/dbkeys.py +++ b/lib/galaxy/util/dbkeys.py @@ -22,17 +22,16 @@ self._static_dbkeys[ key ] = value def get_genome_build_names( self, trans=None ): - #FIXME: how to deal with key duplicates? - #Load old builds.txt static keys - rval = ( self._static_dbkeys.items() ) - #load dbkeys from dbkey data table - dbkey_table = self._app.tool_data_tables.get( self._data_table_name, None ) - if dbkey_table is not None: - for field_dict in dbkey_table.get_named_fields_list(): - rval.append( ( field_dict[ 'value' ], field_dict[ 'name' ] ) ) - #load user custom genome builds + # FIXME: how to deal with key duplicates? + rval = [] + # load user custom genome builds if trans is not None: if trans.history: + # This is a little bit Odd. We are adding every .len file in the current history to dbkey list, + # but this is previous behavior from trans.db_names, so we'll continue to do it. + # It does allow one-off, history specific dbkeys to be created by a user. But we are not filtering, + # so a len file will be listed twice (as the build name and again as dataset name), + # if custom dbkey creation/conversion occurred within the current history. datasets = trans.sa_session.query( self._app.model.HistoryDatasetAssociation ) \ .filter_by( deleted=False, history_id=trans.history.id, extension="len" ) for dataset in datasets: @@ -42,10 +41,17 @@ user_keys = from_json_string( user.preferences['dbkeys'] ) for key, chrom_dict in user_keys.iteritems(): rval.append( ( key, "%s (%s) [Custom]" % ( chrom_dict['name'], key ) ) ) + # Load old builds.txt static keys + rval.extend( self._static_dbkeys.items() ) + #load dbkeys from dbkey data table + dbkey_table = self._app.tool_data_tables.get( self._data_table_name, None ) + if dbkey_table is not None: + for field_dict in dbkey_table.get_named_fields_list(): + rval.append( ( field_dict[ 'value' ], field_dict[ 'name' ] ) ) return rval def get_chrom_info( self, dbkey, trans=None, custom_build_hack_get_len_from_fasta_conversion=True ): - #FIXME: flag to turn off custom_build_hack_get_len_from_fasta_conversion should not be required + # FIXME: flag to turn off custom_build_hack_get_len_from_fasta_conversion should not be required chrom_info = None db_dataset = None # Collect chromInfo from custom builds @@ -75,7 +81,7 @@ dbkey_table = self._app.tool_data_tables.get( self._data_table_name, None ) if dbkey_table is not None: chrom_info = dbkey_table.get_entry( 'value', dbkey, 'len_path', default=None ) - #use configured len path + # use configured server len path if not chrom_info: # Default to built-in build. chrom_info = os.path.join( self._static_chrom_info_path, "%s.len" % dbkey ) 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.

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commit/galaxy-central: dan: To maintain previous behavior, list custom genome build names first.
by commits-noreply＠bitbucket.org 20 May '14

20 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f3948f90b900/ Changeset: f3948f90b900 Branch: next-stable User: dan Date: 2014-05-20 16:18:28 Summary: To maintain previous behavior, list custom genome build names first. Affected #: 1 file diff -r b3342bc20de522e5b98f9b97de69737b069d6d64 -r f3948f90b9002ae47f0941b0e39cb63d122415a3 lib/galaxy/util/dbkeys.py --- a/lib/galaxy/util/dbkeys.py +++ b/lib/galaxy/util/dbkeys.py @@ -22,17 +22,16 @@ self._static_dbkeys[ key ] = value def get_genome_build_names( self, trans=None ): - #FIXME: how to deal with key duplicates? - #Load old builds.txt static keys - rval = ( self._static_dbkeys.items() ) - #load dbkeys from dbkey data table - dbkey_table = self._app.tool_data_tables.get( self._data_table_name, None ) - if dbkey_table is not None: - for field_dict in dbkey_table.get_named_fields_list(): - rval.append( ( field_dict[ 'value' ], field_dict[ 'name' ] ) ) - #load user custom genome builds + # FIXME: how to deal with key duplicates? + rval = [] + # load user custom genome builds if trans is not None: if trans.history: + # This is a little bit Odd. We are adding every .len file in the current history to dbkey list, + # but this is previous behavior from trans.db_names, so we'll continue to do it. + # It does allow one-off, history specific dbkeys to be created by a user. But we are not filtering, + # so a len file will be listed twice (as the build name and again as dataset name), + # if custom dbkey creation/conversion occurred within the current history. datasets = trans.sa_session.query( self._app.model.HistoryDatasetAssociation ) \ .filter_by( deleted=False, history_id=trans.history.id, extension="len" ) for dataset in datasets: @@ -42,10 +41,17 @@ user_keys = from_json_string( user.preferences['dbkeys'] ) for key, chrom_dict in user_keys.iteritems(): rval.append( ( key, "%s (%s) [Custom]" % ( chrom_dict['name'], key ) ) ) + # Load old builds.txt static keys + rval.extend( self._static_dbkeys.items() ) + #load dbkeys from dbkey data table + dbkey_table = self._app.tool_data_tables.get( self._data_table_name, None ) + if dbkey_table is not None: + for field_dict in dbkey_table.get_named_fields_list(): + rval.append( ( field_dict[ 'value' ], field_dict[ 'name' ] ) ) return rval def get_chrom_info( self, dbkey, trans=None, custom_build_hack_get_len_from_fasta_conversion=True ): - #FIXME: flag to turn off custom_build_hack_get_len_from_fasta_conversion should not be required + # FIXME: flag to turn off custom_build_hack_get_len_from_fasta_conversion should not be required chrom_info = None db_dataset = None # Collect chromInfo from custom builds @@ -75,7 +81,7 @@ dbkey_table = self._app.tool_data_tables.get( self._data_table_name, None ) if dbkey_table is not None: chrom_info = dbkey_table.get_entry( 'value', dbkey, 'len_path', default=None ) - #use configured len path + # use configured server len path if not chrom_info: # Default to built-in build. chrom_info = os.path.join( self._static_chrom_info_path, "%s.len" % dbkey ) 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.

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commit/galaxy-central: dan: merge next-stable
by commits-noreply＠bitbucket.org 20 May '14

20 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9fee549c5ef7/ Changeset: 9fee549c5ef7 User: dan Date: 2014-05-20 16:01:53 Summary: merge next-stable Affected #: 2 files diff -r 11403745e7ceb0a6946af648dcd3ca24a638ca7e -r 9fee549c5ef78f80e35fa5ca37c1861267bc12f8 lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py +++ b/lib/galaxy/tools/actions/__init__.py @@ -193,7 +193,7 @@ # Collect chromInfo dataset and add as parameters to incoming db_datasets = {} - ( chrom_info, db_dataset ) = trans.app.genome_builds.get_chrom_info( input_dbkey, tool, trans=trans ) + ( chrom_info, db_dataset ) = trans.app.genome_builds.get_chrom_info( input_dbkey, trans=trans, custom_build_hack_get_len_from_fasta_conversion=tool.id!='CONVERTER_fasta_to_len' ) if db_dataset: inp_data.update( { "chromInfo": db_dataset } ) incoming[ "chromInfo" ] = chrom_info diff -r 11403745e7ceb0a6946af648dcd3ca24a638ca7e -r 9fee549c5ef78f80e35fa5ca37c1861267bc12f8 lib/galaxy/util/dbkeys.py --- a/lib/galaxy/util/dbkeys.py +++ b/lib/galaxy/util/dbkeys.py @@ -44,19 +44,18 @@ rval.append( ( key, "%s (%s) [Custom]" % ( chrom_dict['name'], key ) ) ) return rval - def get_chrom_info( self, dbkey, tool, trans=None ): + def get_chrom_info( self, dbkey, trans=None, custom_build_hack_get_len_from_fasta_conversion=True ): + #FIXME: flag to turn off custom_build_hack_get_len_from_fasta_conversion should not be required chrom_info = None db_dataset = None # Collect chromInfo from custom builds if trans: db_dataset = trans.db_dataset_for( dbkey ) if db_dataset: - #incoming[ "chromInfo" ] = db_dataset.file_name chrom_info = db_dataset.file_name else: - # -- Get chrom_info (len file) from either a custom or built-in build. -- + # Do Custom Build handling if trans.user and ( 'dbkeys' in trans.user.preferences ) and ( dbkey in from_json_string( trans.user.preferences[ 'dbkeys' ] ) ): - # Custom build. custom_build_dict = from_json_string( trans.user.preferences[ 'dbkeys' ] )[ dbkey ] # HACK: the attempt to get chrom_info below will trigger the # fasta-to-len converter if the dataset is not available or, @@ -64,17 +63,19 @@ # running the fasta-to-len tool. So, use a hack in the second # condition below to avoid getting chrom_info when running the # fasta-to-len converter. - if 'fasta' in custom_build_dict and tool.id != 'CONVERTER_fasta_to_len': + if 'fasta' in custom_build_dict and custom_build_hack_get_len_from_fasta_conversion: # Build is defined by fasta; get len file, which is obtained from converting fasta. build_fasta_dataset = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( custom_build_dict[ 'fasta' ] ) chrom_info = build_fasta_dataset.get_converted_dataset( trans, 'len' ).file_name elif 'len' in custom_build_dict: # Build is defined by len file, so use it. chrom_info = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( custom_build_dict[ 'len' ] ).file_name + # Check Data table if not chrom_info: dbkey_table = self._app.tool_data_tables.get( self._data_table_name, None ) if dbkey_table is not None: chrom_info = dbkey_table.get_entry( 'value', dbkey, 'len_path', default=None ) + #use configured len path if not chrom_info: # Default to built-in build. chrom_info = os.path.join( self._static_chrom_info_path, "%s.len" % dbkey ) 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.

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commit/galaxy-central: dan: Cleanup for dbkey handling.
by commits-noreply＠bitbucket.org 20 May '14

20 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b3342bc20de5/ Changeset: b3342bc20de5 Branch: next-stable User: dan Date: 2014-05-20 16:01:28 Summary: Cleanup for dbkey handling. Affected #: 2 files diff -r b29ac7cfd60ed2aaec658f520f3e47f1af4d1ab2 -r b3342bc20de522e5b98f9b97de69737b069d6d64 lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py +++ b/lib/galaxy/tools/actions/__init__.py @@ -193,7 +193,7 @@ # Collect chromInfo dataset and add as parameters to incoming db_datasets = {} - ( chrom_info, db_dataset ) = trans.app.genome_builds.get_chrom_info( input_dbkey, tool, trans=trans ) + ( chrom_info, db_dataset ) = trans.app.genome_builds.get_chrom_info( input_dbkey, trans=trans, custom_build_hack_get_len_from_fasta_conversion=tool.id!='CONVERTER_fasta_to_len' ) if db_dataset: inp_data.update( { "chromInfo": db_dataset } ) incoming[ "chromInfo" ] = chrom_info diff -r b29ac7cfd60ed2aaec658f520f3e47f1af4d1ab2 -r b3342bc20de522e5b98f9b97de69737b069d6d64 lib/galaxy/util/dbkeys.py --- a/lib/galaxy/util/dbkeys.py +++ b/lib/galaxy/util/dbkeys.py @@ -44,19 +44,18 @@ rval.append( ( key, "%s (%s) [Custom]" % ( chrom_dict['name'], key ) ) ) return rval - def get_chrom_info( self, dbkey, tool, trans=None ): + def get_chrom_info( self, dbkey, trans=None, custom_build_hack_get_len_from_fasta_conversion=True ): + #FIXME: flag to turn off custom_build_hack_get_len_from_fasta_conversion should not be required chrom_info = None db_dataset = None # Collect chromInfo from custom builds if trans: db_dataset = trans.db_dataset_for( dbkey ) if db_dataset: - #incoming[ "chromInfo" ] = db_dataset.file_name chrom_info = db_dataset.file_name else: - # -- Get chrom_info (len file) from either a custom or built-in build. -- + # Do Custom Build handling if trans.user and ( 'dbkeys' in trans.user.preferences ) and ( dbkey in from_json_string( trans.user.preferences[ 'dbkeys' ] ) ): - # Custom build. custom_build_dict = from_json_string( trans.user.preferences[ 'dbkeys' ] )[ dbkey ] # HACK: the attempt to get chrom_info below will trigger the # fasta-to-len converter if the dataset is not available or, @@ -64,17 +63,19 @@ # running the fasta-to-len tool. So, use a hack in the second # condition below to avoid getting chrom_info when running the # fasta-to-len converter. - if 'fasta' in custom_build_dict and tool.id != 'CONVERTER_fasta_to_len': + if 'fasta' in custom_build_dict and custom_build_hack_get_len_from_fasta_conversion: # Build is defined by fasta; get len file, which is obtained from converting fasta. build_fasta_dataset = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( custom_build_dict[ 'fasta' ] ) chrom_info = build_fasta_dataset.get_converted_dataset( trans, 'len' ).file_name elif 'len' in custom_build_dict: # Build is defined by len file, so use it. chrom_info = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( custom_build_dict[ 'len' ] ).file_name + # Check Data table if not chrom_info: dbkey_table = self._app.tool_data_tables.get( self._data_table_name, None ) if dbkey_table is not None: chrom_info = dbkey_table.get_entry( 'value', dbkey, 'len_path', default=None ) + #use configured len path if not chrom_info: # Default to built-in build. chrom_info = os.path.join( self._static_chrom_info_path, "%s.len" % dbkey ) 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.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 20 May '14

20 May '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b29ac7cfd60e/ Changeset: b29ac7cfd60e Branch: next-stable User: dannon Date: 2014-05-20 01:54:05 Summary: Additional anyjson requires (appeared to cause Toolshed issues for Greg) Affected #: 2 files diff -r faf07312a7daf640f5ecdddd531e90268404a4fd -r b29ac7cfd60ed2aaec658f520f3e47f1af4d1ab2 lib/galaxy/queue_worker.py --- a/lib/galaxy/queue_worker.py +++ b/lib/galaxy/queue_worker.py @@ -9,6 +9,7 @@ import galaxy.queues from galaxy import eggs, util +eggs.require('anyjson') if sys.version_info < (2, 7, 0): # Kombu requires importlib and ordereddict to function under Python 2.6. eggs.require('importlib') diff -r faf07312a7daf640f5ecdddd531e90268404a4fd -r b29ac7cfd60ed2aaec658f520f3e47f1af4d1ab2 lib/galaxy/queues.py --- a/lib/galaxy/queues.py +++ b/lib/galaxy/queues.py @@ -8,6 +8,7 @@ from galaxy import eggs +eggs.require('anyjson') if sys.version_info < (2, 7, 0): # Kombu requires importlib and ordereddict to function in Python 2.6. eggs.require('importlib') https://bitbucket.org/galaxy/galaxy-central/commits/11403745e7ce/ Changeset: 11403745e7ce User: dannon Date: 2014-05-20 01:54:25 Summary: Merge next-stable Affected #: 2 files diff -r 4b3cfc947e1d151d61351d75397863760f1443f1 -r 11403745e7ceb0a6946af648dcd3ca24a638ca7e lib/galaxy/queue_worker.py --- a/lib/galaxy/queue_worker.py +++ b/lib/galaxy/queue_worker.py @@ -9,6 +9,7 @@ import galaxy.queues from galaxy import eggs, util +eggs.require('anyjson') if sys.version_info < (2, 7, 0): # Kombu requires importlib and ordereddict to function under Python 2.6. eggs.require('importlib') diff -r 4b3cfc947e1d151d61351d75397863760f1443f1 -r 11403745e7ceb0a6946af648dcd3ca24a638ca7e lib/galaxy/queues.py --- a/lib/galaxy/queues.py +++ b/lib/galaxy/queues.py @@ -8,6 +8,7 @@ from galaxy import eggs +eggs.require('anyjson') if sys.version_info < (2, 7, 0): # Kombu requires importlib and ordereddict to function in Python 2.6. eggs.require('importlib') 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.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 20 May '14

20 May '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/faf07312a7da/ Changeset: faf07312a7da Branch: next-stable User: dannon Date: 2014-05-20 00:58:13 Summary: Kombu also requires ordereddict backport to support python2.6, more eggs. Affected #: 3 files diff -r 1ec7fa5ac5e379d308843d633d0bff3d83b34806 -r faf07312a7daf640f5ecdddd531e90268404a4fd eggs.ini --- a/eggs.ini +++ b/eggs.ini @@ -51,6 +51,7 @@ nose = 0.11.1 NoseHTML = 0.4.1 NoseTestDiff = 0.1 +ordereddict = 1.1 paramiko = 1.11.1 Parsley = 1.1 Paste = 1.7.5.1 diff -r 1ec7fa5ac5e379d308843d633d0bff3d83b34806 -r faf07312a7daf640f5ecdddd531e90268404a4fd lib/galaxy/queue_worker.py --- a/lib/galaxy/queue_worker.py +++ b/lib/galaxy/queue_worker.py @@ -10,8 +10,9 @@ import galaxy.queues from galaxy import eggs, util if sys.version_info < (2, 7, 0): - # Kombu requires importlib to function under Python 2.6. + # Kombu requires importlib and ordereddict to function under Python 2.6. eggs.require('importlib') + eggs.require('ordereddict') eggs.require('kombu') from kombu import Connection diff -r 1ec7fa5ac5e379d308843d633d0bff3d83b34806 -r faf07312a7daf640f5ecdddd531e90268404a4fd lib/galaxy/queues.py --- a/lib/galaxy/queues.py +++ b/lib/galaxy/queues.py @@ -9,8 +9,9 @@ from galaxy import eggs if sys.version_info < (2, 7, 0): - # Kombu requires importlib to function in Python 2.6. + # Kombu requires importlib and ordereddict to function in Python 2.6. eggs.require('importlib') + eggs.require('ordereddict') eggs.require('kombu') from kombu import Exchange, Queue https://bitbucket.org/galaxy/galaxy-central/commits/4b3cfc947e1d/ Changeset: 4b3cfc947e1d User: dannon Date: 2014-05-20 00:58:28 Summary: Merge from next-stable. Affected #: 3 files diff -r e170406ece79b72e991dd94345f5f1da9efd88a6 -r 4b3cfc947e1d151d61351d75397863760f1443f1 eggs.ini --- a/eggs.ini +++ b/eggs.ini @@ -51,6 +51,7 @@ nose = 0.11.1 NoseHTML = 0.4.1 NoseTestDiff = 0.1 +ordereddict = 1.1 paramiko = 1.11.1 Parsley = 1.1 Paste = 1.7.5.1 diff -r e170406ece79b72e991dd94345f5f1da9efd88a6 -r 4b3cfc947e1d151d61351d75397863760f1443f1 lib/galaxy/queue_worker.py --- a/lib/galaxy/queue_worker.py +++ b/lib/galaxy/queue_worker.py @@ -10,8 +10,9 @@ import galaxy.queues from galaxy import eggs, util if sys.version_info < (2, 7, 0): - # Kombu requires importlib to function under Python 2.6. + # Kombu requires importlib and ordereddict to function under Python 2.6. eggs.require('importlib') + eggs.require('ordereddict') eggs.require('kombu') from kombu import Connection diff -r e170406ece79b72e991dd94345f5f1da9efd88a6 -r 4b3cfc947e1d151d61351d75397863760f1443f1 lib/galaxy/queues.py --- a/lib/galaxy/queues.py +++ b/lib/galaxy/queues.py @@ -9,8 +9,9 @@ from galaxy import eggs if sys.version_info < (2, 7, 0): - # Kombu requires importlib to function in Python 2.6. + # Kombu requires importlib and ordereddict to function in Python 2.6. eggs.require('importlib') + eggs.require('ordereddict') eggs.require('kombu') from kombu import Exchange, Queue 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.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 20 May '14

20 May '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1ec7fa5ac5e3/ Changeset: 1ec7fa5ac5e3 Branch: next-stable User: dannon Date: 2014-05-20 00:11:52 Summary: Add conditional requirement of importlib for python 2.6/kombu. Affected #: 3 files diff -r 5c2c82003b8fe415f16182bd90398c4b0cbdecae -r 1ec7fa5ac5e379d308843d633d0bff3d83b34806 eggs.ini --- a/eggs.ini +++ b/eggs.ini @@ -43,6 +43,7 @@ elementtree = 1.2.6_20050316 Fabric = 1.7.0 GeneTrack = 2.0.0_beta_1 +importlib = 1.0.3 kombu = 3.0.12 lrucache = 0.2 Mako = 0.4.1 diff -r 5c2c82003b8fe415f16182bd90398c4b0cbdecae -r 1ec7fa5ac5e379d308843d633d0bff3d83b34806 lib/galaxy/queue_worker.py --- a/lib/galaxy/queue_worker.py +++ b/lib/galaxy/queue_worker.py @@ -5,8 +5,13 @@ import logging import threading +import sys + import galaxy.queues from galaxy import eggs, util +if sys.version_info < (2, 7, 0): + # Kombu requires importlib to function under Python 2.6. + eggs.require('importlib') eggs.require('kombu') from kombu import Connection diff -r 5c2c82003b8fe415f16182bd90398c4b0cbdecae -r 1ec7fa5ac5e379d308843d633d0bff3d83b34806 lib/galaxy/queues.py --- a/lib/galaxy/queues.py +++ b/lib/galaxy/queues.py @@ -4,9 +4,14 @@ """ +import sys + from galaxy import eggs -eggs.require("kombu") +if sys.version_info < (2, 7, 0): + # Kombu requires importlib to function in Python 2.6. + eggs.require('importlib') +eggs.require('kombu') from kombu import Exchange, Queue ALL_CONTROL = "control.*" https://bitbucket.org/galaxy/galaxy-central/commits/e170406ece79/ Changeset: e170406ece79 User: dannon Date: 2014-05-20 00:12:05 Summary: Merge next-stable Affected #: 3 files diff -r 3100a0f55b14c4193e2621009bb5e3f9d1c2e634 -r e170406ece79b72e991dd94345f5f1da9efd88a6 eggs.ini --- a/eggs.ini +++ b/eggs.ini @@ -43,6 +43,7 @@ elementtree = 1.2.6_20050316 Fabric = 1.7.0 GeneTrack = 2.0.0_beta_1 +importlib = 1.0.3 kombu = 3.0.12 lrucache = 0.2 Mako = 0.4.1 diff -r 3100a0f55b14c4193e2621009bb5e3f9d1c2e634 -r e170406ece79b72e991dd94345f5f1da9efd88a6 lib/galaxy/queue_worker.py --- a/lib/galaxy/queue_worker.py +++ b/lib/galaxy/queue_worker.py @@ -5,8 +5,13 @@ import logging import threading +import sys + import galaxy.queues from galaxy import eggs, util +if sys.version_info < (2, 7, 0): + # Kombu requires importlib to function under Python 2.6. + eggs.require('importlib') eggs.require('kombu') from kombu import Connection diff -r 3100a0f55b14c4193e2621009bb5e3f9d1c2e634 -r e170406ece79b72e991dd94345f5f1da9efd88a6 lib/galaxy/queues.py --- a/lib/galaxy/queues.py +++ b/lib/galaxy/queues.py @@ -4,9 +4,14 @@ """ +import sys + from galaxy import eggs -eggs.require("kombu") +if sys.version_info < (2, 7, 0): + # Kombu requires importlib to function in Python 2.6. + eggs.require('importlib') +eggs.require('kombu') from kombu import Exchange, Queue ALL_CONTROL = "control.*" 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.

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commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 19 May '14

19 May '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/70f062a9e200/ Changeset: 70f062a9e200 User: dannon Date: 2014-05-19 23:44:25 Summary: Merge from next-stable. Affected #: 1 file diff -r 05302ebc73772d383ef55781e7c59d7365258e5b -r 70f062a9e200c1b8d6ef5dc43a6c99f41ea70083 lib/galaxy/util/dbkeys.py --- a/lib/galaxy/util/dbkeys.py +++ b/lib/galaxy/util/dbkeys.py @@ -55,9 +55,9 @@ chrom_info = db_dataset.file_name else: # -- Get chrom_info (len file) from either a custom or built-in build. -- - if trans.user and ( 'dbkeys' in trans.user.preferences ) and ( input_dbkey in from_json_string( trans.user.preferences[ 'dbkeys' ] ) ): + if trans.user and ( 'dbkeys' in trans.user.preferences ) and ( dbkey in from_json_string( trans.user.preferences[ 'dbkeys' ] ) ): # Custom build. - custom_build_dict = from_json_string( trans.user.preferences[ 'dbkeys' ] )[ input_dbkey ] + custom_build_dict = from_json_string( trans.user.preferences[ 'dbkeys' ] )[ dbkey ] # HACK: the attempt to get chrom_info below will trigger the # fasta-to-len converter if the dataset is not available or, # which will in turn create a recursive loop when https://bitbucket.org/galaxy/galaxy-central/commits/5c2c82003b8f/ Changeset: 5c2c82003b8f Branch: next-stable User: dannon Date: 2014-05-19 23:47:20 Summary: Fix get_chrom_info to take (and use) the tool in question. Affected #: 2 files diff -r d62fd7469c626064d8fe9792ea4584c57b5ed431 -r 5c2c82003b8fe415f16182bd90398c4b0cbdecae lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py +++ b/lib/galaxy/tools/actions/__init__.py @@ -193,7 +193,7 @@ # Collect chromInfo dataset and add as parameters to incoming db_datasets = {} - ( chrom_info, db_dataset ) = trans.app.genome_builds.get_chrom_info( input_dbkey, trans=trans ) + ( chrom_info, db_dataset ) = trans.app.genome_builds.get_chrom_info( input_dbkey, tool, trans=trans ) if db_dataset: inp_data.update( { "chromInfo": db_dataset } ) incoming[ "chromInfo" ] = chrom_info diff -r d62fd7469c626064d8fe9792ea4584c57b5ed431 -r 5c2c82003b8fe415f16182bd90398c4b0cbdecae lib/galaxy/util/dbkeys.py --- a/lib/galaxy/util/dbkeys.py +++ b/lib/galaxy/util/dbkeys.py @@ -2,7 +2,7 @@ Functionality for dealing with dbkeys. """ #dbkeys read from disk using builds.txt -from galaxy.util import dbnames, galaxy_directory +from galaxy.util import dbnames from galaxy.util.json import from_json_string from galaxy.util.odict import odict import os.path @@ -44,7 +44,7 @@ rval.append( ( key, "%s (%s) [Custom]" % ( chrom_dict['name'], key ) ) ) return rval - def get_chrom_info( self, dbkey, trans=None ): + def get_chrom_info( self, dbkey, tool, trans=None ): chrom_info = None db_dataset = None # Collect chromInfo from custom builds https://bitbucket.org/galaxy/galaxy-central/commits/3100a0f55b14/ Changeset: 3100a0f55b14 User: dannon Date: 2014-05-19 23:47:36 Summary: Merge next-stable. Affected #: 2 files diff -r 70f062a9e200c1b8d6ef5dc43a6c99f41ea70083 -r 3100a0f55b14c4193e2621009bb5e3f9d1c2e634 lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py +++ b/lib/galaxy/tools/actions/__init__.py @@ -193,7 +193,7 @@ # Collect chromInfo dataset and add as parameters to incoming db_datasets = {} - ( chrom_info, db_dataset ) = trans.app.genome_builds.get_chrom_info( input_dbkey, trans=trans ) + ( chrom_info, db_dataset ) = trans.app.genome_builds.get_chrom_info( input_dbkey, tool, trans=trans ) if db_dataset: inp_data.update( { "chromInfo": db_dataset } ) incoming[ "chromInfo" ] = chrom_info diff -r 70f062a9e200c1b8d6ef5dc43a6c99f41ea70083 -r 3100a0f55b14c4193e2621009bb5e3f9d1c2e634 lib/galaxy/util/dbkeys.py --- a/lib/galaxy/util/dbkeys.py +++ b/lib/galaxy/util/dbkeys.py @@ -2,7 +2,7 @@ Functionality for dealing with dbkeys. """ #dbkeys read from disk using builds.txt -from galaxy.util import dbnames, galaxy_directory +from galaxy.util import dbnames from galaxy.util.json import from_json_string from galaxy.util.odict import odict import os.path @@ -44,7 +44,7 @@ rval.append( ( key, "%s (%s) [Custom]" % ( chrom_dict['name'], key ) ) ) return rval - def get_chrom_info( self, dbkey, trans=None ): + def get_chrom_info( self, dbkey, tool, trans=None ): chrom_info = None db_dataset = None # Collect chromInfo from custom builds 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.

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galaxy-commits May 2014