9 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/a488f34b151c/ changeset: a488f34b151c user: dan date: 2012-10-15 21:27:06 summary: Fix tabs to spaces. affected #: 1 file diff -r 475a4849d6b01fc04ed67cfe960f069aea0b1a6d -r a488f34b151c36253613dc1f55bf49196c7f45d9 lib/galaxy/datatypes/assembly.py --- a/lib/galaxy/datatypes/assembly.py +++ b/lib/galaxy/datatypes/assembly.py @@ -191,7 +191,7 @@ if long_reads: gen_msg = gen_msg + ' Long Reads' if len(gen_msg) > 0: - gen_msg = 'Uses: ' + gen_msg + gen_msg = 'Uses: ' + gen_msg except: log.debug( "Velveth could not read Log file in %s" % efp) log.debug( "Velveth log info %s" % gen_msg) https://bitbucket.org/galaxy/galaxy-central/changeset/a0427bfc10b8/ changeset: a0427bfc10b8 user: dan date: 2012-10-15 21:27:06 summary: Fix tabs to spaces. affected #: 1 file diff -r a488f34b151c36253613dc1f55bf49196c7f45d9 -r a0427bfc10b8784d613bd51b14b6c87b6c5acd12 lib/galaxy/jobs/handler.py --- a/lib/galaxy/jobs/handler.py +++ b/lib/galaxy/jobs/handler.py @@ -430,7 +430,7 @@ if ( None != job.get_job_runner_name() ): runner_name = (job.get_job_runner_name().split(":",1))[0] if ( isinstance( job, model.Job ) ): - log.debug( "stopping job %d in %s runner" %( job.get_id(), runner_name ) ) + log.debug( "stopping job %d in %s runner" %( job.get_id(), runner_name ) ) elif ( isinstance( job, model.Task ) ): log.debug( "Stopping job %d, task %d in %s runner" % ( job.get_job().get_id(), job.get_id(), runner_name ) ) https://bitbucket.org/galaxy/galaxy-central/changeset/cda1965e4f45/ changeset: cda1965e4f45 user: dan date: 2012-10-15 21:27:07 summary: Fix tabs to spaces. affected #: 1 file diff -r a0427bfc10b8784d613bd51b14b6c87b6c5acd12 -r cda1965e4f458b132db3781202f9878b3645ecef lib/galaxy/model/migrate/versions/0033_published_cols_for_histories_and_workflows.py --- a/lib/galaxy/model/migrate/versions/0033_published_cols_for_histories_and_workflows.py +++ b/lib/galaxy/model/migrate/versions/0033_published_cols_for_histories_and_workflows.py @@ -15,87 +15,87 @@ db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) def upgrade(): - print __doc__ - metadata.reflect() + print __doc__ + metadata.reflect() - # Create published column in history table. - History_table = Table( "history", metadata, autoload=True ) - c = Column( "published", Boolean, index=True ) - try: - c.create( History_table ) - assert c is History_table.c.published - except Exception, e: - print "Adding published column to history table failed: %s" % str( e ) - log.debug( "Adding published column to history table failed: %s" % str( e ) ) + # Create published column in history table. + History_table = Table( "history", metadata, autoload=True ) + c = Column( "published", Boolean, index=True ) + try: + c.create( History_table ) + assert c is History_table.c.published + except Exception, e: + print "Adding published column to history table failed: %s" % str( e ) + log.debug( "Adding published column to history table failed: %s" % str( e ) ) - # Create index for published column in history table. - try: - i = Index( "ix_history_published", History_table.c.published ) - i.create() - except: - # Mysql doesn't have a named index, but alter should work - History_table.c.published.alter( unique=False ) + # Create index for published column in history table. + try: + i = Index( "ix_history_published", History_table.c.published ) + i.create() + except: + # Mysql doesn't have a named index, but alter should work + History_table.c.published.alter( unique=False ) - # Create published column in stored workflows table. - StoredWorkflow_table = Table( "stored_workflow", metadata, autoload=True ) - c = Column( "published", Boolean, index=True ) - try: - c.create( StoredWorkflow_table ) - assert c is StoredWorkflow_table.c.published - except Exception, e: - print "Adding published column to stored_workflow table failed: %s" % str( e ) - log.debug( "Adding published column to stored_workflow table failed: %s" % str( e ) ) + # Create published column in stored workflows table. + StoredWorkflow_table = Table( "stored_workflow", metadata, autoload=True ) + c = Column( "published", Boolean, index=True ) + try: + c.create( StoredWorkflow_table ) + assert c is StoredWorkflow_table.c.published + except Exception, e: + print "Adding published column to stored_workflow table failed: %s" % str( e ) + log.debug( "Adding published column to stored_workflow table failed: %s" % str( e ) ) - # Create index for published column in stored workflows table. - try: - i = Index( "ix_stored_workflow_published", StoredWorkflow_table.c.published ) - i.create() - except: - # Mysql doesn't have a named index, but alter should work - StoredWorkflow_table.c.published.alter( unique=False ) + # Create index for published column in stored workflows table. + try: + i = Index( "ix_stored_workflow_published", StoredWorkflow_table.c.published ) + i.create() + except: + # Mysql doesn't have a named index, but alter should work + StoredWorkflow_table.c.published.alter( unique=False ) - # Create importable column in page table. - Page_table = Table( "page", metadata, autoload=True ) - c = Column( "importable", Boolean, index=True ) - try: - c.create( Page_table ) - assert c is Page_table.c.importable - except Exception, e: - print "Adding importable column to page table failed: %s" % str( e ) - log.debug( "Adding importable column to page table failed: %s" % str( e ) ) - - # Create index for importable column in page table. - try: - i = Index( "ix_page_importable", Page_table.c.importable ) - i.create() - except: - # Mysql doesn't have a named index, but alter should work - Page_table.c.importable.alter( unique=False ) + # Create importable column in page table. + Page_table = Table( "page", metadata, autoload=True ) + c = Column( "importable", Boolean, index=True ) + try: + c.create( Page_table ) + assert c is Page_table.c.importable + except Exception, e: + print "Adding importable column to page table failed: %s" % str( e ) + log.debug( "Adding importable column to page table failed: %s" % str( e ) ) + + # Create index for importable column in page table. + try: + i = Index( "ix_page_importable", Page_table.c.importable ) + i.create() + except: + # Mysql doesn't have a named index, but alter should work + Page_table.c.importable.alter( unique=False ) def downgrade(): - metadata.reflect() + metadata.reflect() - # Drop published column from history table. - History_table = Table( "history", metadata, autoload=True ) - try: - History_table.c.published.drop() - except Exception, e: - print "Dropping column published from history table failed: %s" % str( e ) - log.debug( "Dropping column published from history table failed: %s" % str( e ) ) + # Drop published column from history table. + History_table = Table( "history", metadata, autoload=True ) + try: + History_table.c.published.drop() + except Exception, e: + print "Dropping column published from history table failed: %s" % str( e ) + log.debug( "Dropping column published from history table failed: %s" % str( e ) ) - # Drop published column from stored_workflow table. - StoredWorkflow_table = Table( "stored_workflow", metadata, autoload=True ) - try: - StoredWorkflow_table.c.published.drop() - except Exception, e: - print "Dropping column published from stored_workflow table failed: %s" % str( e ) - log.debug( "Dropping column published from stored_workflow table failed: %s" % str( e ) ) - + # Drop published column from stored_workflow table. + StoredWorkflow_table = Table( "stored_workflow", metadata, autoload=True ) + try: + StoredWorkflow_table.c.published.drop() + except Exception, e: + print "Dropping column published from stored_workflow table failed: %s" % str( e ) + log.debug( "Dropping column published from stored_workflow table failed: %s" % str( e ) ) + # Drop importable column from page table. - Page_table = Table( "page", metadata, autoload=True ) - try: - Page_table.c.importable.drop() - except Exception, e: - print "Dropping column importable from page table failed: %s" % str( e ) - log.debug( "Dropping column importable from page table failed: %s" % str( e ) ) \ No newline at end of file + Page_table = Table( "page", metadata, autoload=True ) + try: + Page_table.c.importable.drop() + except Exception, e: + print "Dropping column importable from page table failed: %s" % str( e ) + log.debug( "Dropping column importable from page table failed: %s" % str( e ) ) \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/changeset/43e492778950/ changeset: 43e492778950 user: dan date: 2012-10-15 21:27:07 summary: Fix tabs to spaces. affected #: 1 file diff -r cda1965e4f458b132db3781202f9878b3645ecef -r 43e49277895060d7a85efb9a65df4b74178d1de5 lib/galaxy/model/migrate/versions/0043_visualization_sharing_tagging_annotating.py --- a/lib/galaxy/model/migrate/versions/0043_visualization_sharing_tagging_annotating.py +++ b/lib/galaxy/model/migrate/versions/0043_visualization_sharing_tagging_annotating.py @@ -69,7 +69,7 @@ # Add column. deleted_column.create( Visualiation_table ) assert deleted_column is Visualiation_table.c.deleted - + # Fill column with default value. cmd = "UPDATE visualization SET deleted = %s" % default_false db_session.execute( cmd ) @@ -83,7 +83,7 @@ except Exception, e: print "Adding index 'ix_visualization_deleted' failed: %s" % str( e ) log.debug( "Adding index 'ix_visualization_deleted' failed: %s" % str( e ) ) - + try: # Add column. importable_column.create( Visualiation_table ) @@ -102,10 +102,10 @@ except Exception, e: print "Adding index 'ix_visualization_importable' failed: %s" % str( e ) log.debug( "Adding index 'ix_visualization_importable' failed: %s" % str( e ) ) - + try: - slug_column.create( Visualiation_table ) - assert slug_column is Visualiation_table.c.slug + slug_column.create( Visualiation_table ) + assert slug_column is Visualiation_table.c.slug except Exception, e: print "Adding slug column to visualization table failed: %s" % str( e ) log.debug( "Adding slug column to visualization table failed: %s" % str( e ) ) @@ -121,7 +121,7 @@ except Exception, e: print "Adding index 'ix_visualization_slug' failed: %s" % str( e ) log.debug( "Adding index 'ix_visualization_slug' failed: %s" % str( e ) ) - + try: # Add column. published_column.create( Visualiation_table ) @@ -180,25 +180,25 @@ # Drop columns for supporting sharing from visualization table. try: - Visualiation_table.c.deleted.drop() + Visualiation_table.c.deleted.drop() except Exception, e: print "Dropping deleted column from visualization table failed: %s" % str( e ) log.debug( "Dropping deleted column from visualization table failed: %s" % str( e ) ) try: - Visualiation_table.c.importable.drop() + Visualiation_table.c.importable.drop() except Exception, e: print "Dropping importable column from visualization table failed: %s" % str( e ) log.debug( "Dropping importable column from visualization table failed: %s" % str( e ) ) try: - Visualiation_table.c.slug.drop() + Visualiation_table.c.slug.drop() except Exception, e: print "Dropping slug column from visualization table failed: %s" % str( e ) log.debug( "Dropping slug column from visualization table failed: %s" % str( e ) ) try: - Visualiation_table.c.published.drop() + Visualiation_table.c.published.drop() except Exception, e: print "Dropping published column from visualization table failed: %s" % str( e ) log.debug( "Dropping published column from visualization table failed: %s" % str( e ) ) https://bitbucket.org/galaxy/galaxy-central/changeset/110787b1dc72/ changeset: 110787b1dc72 user: dan date: 2012-10-15 21:27:08 summary: Fix tabs to spaces. affected #: 1 file diff -r 43e49277895060d7a85efb9a65df4b74178d1de5 -r 110787b1dc72947098adfa878a13161856879ae3 lib/galaxy/model/migrate/versions/0051_imported_col_for_jobs_table.py --- a/lib/galaxy/model/migrate/versions/0051_imported_col_for_jobs_table.py +++ b/lib/galaxy/model/migrate/versions/0051_imported_col_for_jobs_table.py @@ -14,35 +14,35 @@ db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) def upgrade(): - print __doc__ - metadata.reflect() + print __doc__ + metadata.reflect() - # Create and initialize imported column in job table. - Jobs_table = Table( "job", metadata, autoload=True ) - c = Column( "imported", Boolean, default=False, index=True ) - try: - # Create - c.create( Jobs_table ) - assert c is Jobs_table.c.imported - - # Initialize. - if migrate_engine.name == 'mysql' or migrate_engine.name == 'sqlite': - default_false = "0" - elif migrate_engine.name == 'postgres': - default_false = "false" - db_session.execute( "UPDATE job SET imported=%s" % default_false ) - - except Exception, e: - print "Adding imported column to job table failed: %s" % str( e ) - log.debug( "Adding imported column to job table failed: %s" % str( e ) ) + # Create and initialize imported column in job table. + Jobs_table = Table( "job", metadata, autoload=True ) + c = Column( "imported", Boolean, default=False, index=True ) + try: + # Create + c.create( Jobs_table ) + assert c is Jobs_table.c.imported + + # Initialize. + if migrate_engine.name == 'mysql' or migrate_engine.name == 'sqlite': + default_false = "0" + elif migrate_engine.name == 'postgres': + default_false = "false" + db_session.execute( "UPDATE job SET imported=%s" % default_false ) + + except Exception, e: + print "Adding imported column to job table failed: %s" % str( e ) + log.debug( "Adding imported column to job table failed: %s" % str( e ) ) def downgrade(): - metadata.reflect() + metadata.reflect() - # Drop imported column from job table. - Jobs_table = Table( "job", metadata, autoload=True ) - try: - Jobs_table.c.imported.drop() - except Exception, e: - print "Dropping column imported from job table failed: %s" % str( e ) - log.debug( "Dropping column imported from job table failed: %s" % str( e ) ) \ No newline at end of file + # Drop imported column from job table. + Jobs_table = Table( "job", metadata, autoload=True ) + try: + Jobs_table.c.imported.drop() + except Exception, e: + print "Dropping column imported from job table failed: %s" % str( e ) + log.debug( "Dropping column imported from job table failed: %s" % str( e ) ) \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/changeset/cc660ea7e2f0/ changeset: cc660ea7e2f0 user: dan date: 2012-10-15 21:27:08 summary: Fix tabs to spaces. affected #: 1 file diff -r 110787b1dc72947098adfa878a13161856879ae3 -r cc660ea7e2f01a945cf11f37e8f21ae9c1cfb1ad lib/galaxy/tools/actions/index_genome.py --- a/lib/galaxy/tools/actions/index_genome.py +++ b/lib/galaxy/tools/actions/index_genome.py @@ -22,8 +22,8 @@ job.user_id = incoming['user'] start_job_state = job.state # should be job.states.NEW job.state = job.states.WAITING # we need to set job state to something other than NEW, - # or else when tracking jobs in db it will be picked up - # before we have added input / output parameters + # or else when tracking jobs in db it will be picked up + # before we have added input / output parameters trans.sa_session.add( job ) # Create dataset that will serve as archive. https://bitbucket.org/galaxy/galaxy-central/changeset/2c5adff61087/ changeset: 2c5adff61087 user: dan date: 2012-10-15 21:27:08 summary: Fix tabs to spaces. affected #: 1 file diff -r cc660ea7e2f01a945cf11f37e8f21ae9c1cfb1ad -r 2c5adff6108775882f0b8e13e5efeadb4adb4267 lib/galaxy/webapps/galaxy/controllers/data_admin.py --- a/lib/galaxy/webapps/galaxy/controllers/data_admin.py +++ b/lib/galaxy/webapps/galaxy/controllers/data_admin.py @@ -102,15 +102,15 @@ @web.expose @web.require_admin def index_build( self, trans, **kwd ): - """Index a previously downloaded genome.""" + """Index a previously downloaded genome.""" params = util.Params( kwd ) path = os.path.abspath( params.get( 'path', None ) ) indexes = [ params.get( 'indexes', None ) ] dbkey = params.get( 'dbkey', None ) intname = params.get( 'longname', None ) - indexjob = trans.app.job_manager.deferred_job_queue.plugins['GenomeIndexPlugin'].create_job( trans, path, indexes, dbkey, intname ) - return indexjob - + indexjob = trans.app.job_manager.deferred_job_queue.plugins['GenomeIndexPlugin'].create_job( trans, path, indexes, dbkey, intname ) + return indexjob + @web.expose @web.require_admin def download_build( self, trans, **kwd ): https://bitbucket.org/galaxy/galaxy-central/changeset/841271fd0b39/ changeset: 841271fd0b39 user: dan date: 2012-10-15 21:27:08 summary: Fix tabs to spaces. affected #: 1 file diff -r 2c5adff6108775882f0b8e13e5efeadb4adb4267 -r 841271fd0b3933f665146a987ac671a3c12d0983 lib/galaxy/webapps/galaxy/controllers/forms.py --- a/lib/galaxy/webapps/galaxy/controllers/forms.py +++ b/lib/galaxy/webapps/galaxy/controllers/forms.py @@ -596,7 +596,7 @@ index = 1 for row in reader: if len(row) < 7: # ignore bogus rows - continue + continue options = row[5].split(',') if len(row) >= 8: fields.append( { 'name': '%i_field_name' % index, https://bitbucket.org/galaxy/galaxy-central/changeset/d79a4e48653d/ changeset: d79a4e48653d user: dan date: 2012-10-15 21:27:09 summary: Fix tabs to spaces. affected #: 1 file diff -r 841271fd0b3933f665146a987ac671a3c12d0983 -r d79a4e48653d678a7f07e3ef6f5bf1169567b48e lib/galaxy/webapps/galaxy/controllers/ucsc_proxy.py --- a/lib/galaxy/webapps/galaxy/controllers/ucsc_proxy.py +++ b/lib/galaxy/webapps/galaxy/controllers/ucsc_proxy.py @@ -156,4 +156,4 @@ '<INPUT TYPE=RADIO NAME="hgta_regionType" VALUE="range" onClick="regionType=\'range\';">' : '<INPUT TYPE=RADIO NAME="hgta_regionType" VALUE="range" onClick="regionType=\'range\';" CHECKED>', "<OPTION VALUE=bed>" : "<OPTION VALUE=bed SELECTED>" , '<INPUT TYPE=SUBMIT NAME="hgta_doSchema" VALUE="describe table schema">' : '<INPUT TYPE=SUBMIT NAME="hgta_doSchema" VALUE="describe table schema" onClick="changeTarget(\'_blank\')" onMouseOut="changeTarget(\'_self\')">' - } + } Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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