[2] | 1 | """ |
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| 2 | Migration script to (a) create tables for annotating objects and (b) create tags for workflow steps. |
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| 3 | """ |
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| 4 | |
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| 5 | from sqlalchemy import * |
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| 6 | from sqlalchemy.orm import * |
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| 7 | from migrate import * |
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| 8 | from migrate.changeset import * |
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| 9 | |
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| 10 | import logging |
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| 11 | log = logging.getLogger( __name__ ) |
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| 12 | |
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| 13 | metadata = MetaData( migrate_engine ) |
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| 14 | db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) |
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| 15 | |
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| 16 | # Annotation tables. |
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| 17 | |
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| 18 | HistoryAnnotationAssociation_table = Table( "history_annotation_association", metadata, |
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| 19 | Column( "id", Integer, primary_key=True ), |
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| 20 | Column( "history_id", Integer, ForeignKey( "history.id" ), index=True ), |
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| 21 | Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), |
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| 22 | Column( "annotation", TEXT, index=True) ) |
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| 23 | |
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| 24 | HistoryDatasetAssociationAnnotationAssociation_table = Table( "history_dataset_association_annotation_association", metadata, |
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| 25 | Column( "id", Integer, primary_key=True ), |
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| 26 | Column( "history_dataset_association_id", Integer, ForeignKey( "history_dataset_association.id" ), index=True ), |
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| 27 | Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), |
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| 28 | Column( "annotation", TEXT, index=True) ) |
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| 29 | |
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| 30 | StoredWorkflowAnnotationAssociation_table = Table( "stored_workflow_annotation_association", metadata, |
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| 31 | Column( "id", Integer, primary_key=True ), |
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| 32 | Column( "stored_workflow_id", Integer, ForeignKey( "stored_workflow.id" ), index=True ), |
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| 33 | Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), |
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| 34 | Column( "annotation", TEXT, index=True) ) |
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| 35 | |
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| 36 | WorkflowStepAnnotationAssociation_table = Table( "workflow_step_annotation_association", metadata, |
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| 37 | Column( "id", Integer, primary_key=True ), |
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| 38 | Column( "workflow_step_id", Integer, ForeignKey( "workflow_step.id" ), index=True ), |
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| 39 | Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), |
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| 40 | Column( "annotation", TEXT, index=True) ) |
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| 41 | |
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| 42 | # Tagging tables. |
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| 43 | |
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| 44 | WorkflowStepTagAssociation_table = Table( "workflow_step_tag_association", metadata, |
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| 45 | Column( "id", Integer, primary_key=True ), |
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| 46 | Column( "workflow_step_id", Integer, ForeignKey( "workflow_step.id" ), index=True ), |
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| 47 | Column( "tag_id", Integer, ForeignKey( "tag.id" ), index=True ), |
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| 48 | Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), |
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| 49 | Column( "user_tname", Unicode(255), index=True), |
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| 50 | Column( "value", Unicode(255), index=True), |
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| 51 | Column( "user_value", Unicode(255), index=True) ) |
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| 52 | |
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| 53 | def upgrade(): |
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| 54 | print __doc__ |
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| 55 | metadata.reflect() |
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| 56 | |
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| 57 | # Create history_annotation_association table. |
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| 58 | try: |
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| 59 | HistoryAnnotationAssociation_table.create() |
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| 60 | except Exception, e: |
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| 61 | print str(e) |
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| 62 | log.debug( "Creating history_annotation_association table failed: %s" % str( e ) ) |
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| 63 | |
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| 64 | # Create history_dataset_association_annotation_association table. |
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| 65 | try: |
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| 66 | HistoryDatasetAssociationAnnotationAssociation_table.create() |
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| 67 | except Exception, e: |
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| 68 | print str(e) |
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| 69 | log.debug( "Creating history_dataset_association_annotation_association table failed: %s" % str( e ) ) |
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| 70 | |
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| 71 | # Create stored_workflow_annotation_association table. |
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| 72 | try: |
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| 73 | StoredWorkflowAnnotationAssociation_table.create() |
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| 74 | except Exception, e: |
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| 75 | print str(e) |
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| 76 | log.debug( "Creating stored_workflow_annotation_association table failed: %s" % str( e ) ) |
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| 77 | |
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| 78 | # Create workflow_step_annotation_association table. |
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| 79 | try: |
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| 80 | WorkflowStepAnnotationAssociation_table.create() |
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| 81 | except Exception, e: |
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| 82 | print str(e) |
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| 83 | log.debug( "Creating workflow_step_annotation_association table failed: %s" % str( e ) ) |
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| 84 | |
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| 85 | # Create workflow_step_tag_association table. |
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| 86 | try: |
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| 87 | WorkflowStepTagAssociation_table.create() |
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| 88 | except Exception, e: |
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| 89 | print str(e) |
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| 90 | log.debug( "Creating workflow_step_tag_association table failed: %s" % str( e ) ) |
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| 91 | |
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| 92 | def downgrade(): |
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| 93 | metadata.reflect() |
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| 94 | |
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| 95 | # Drop history_annotation_association table. |
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| 96 | try: |
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| 97 | HistoryAnnotationAssociation_table.drop() |
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| 98 | except Exception, e: |
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| 99 | print str(e) |
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| 100 | log.debug( "Dropping history_annotation_association table failed: %s" % str( e ) ) |
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| 101 | |
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| 102 | # Drop history_dataset_association_annotation_association table. |
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| 103 | try: |
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| 104 | HistoryDatasetAssociationAnnotationAssociation_table.drop() |
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| 105 | except Exception, e: |
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| 106 | print str(e) |
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| 107 | log.debug( "Dropping history_dataset_association_annotation_association table failed: %s" % str( e ) ) |
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| 108 | |
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| 109 | # Drop stored_workflow_annotation_association table. |
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| 110 | try: |
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| 111 | StoredWorkflowAnnotationAssociation_table.drop() |
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| 112 | except Exception, e: |
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| 113 | print str(e) |
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| 114 | log.debug( "Dropping stored_workflow_annotation_association table failed: %s" % str( e ) ) |
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| 115 | |
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| 116 | # Drop workflow_step_annotation_association table. |
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| 117 | try: |
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| 118 | WorkflowStepAnnotationAssociation_table.drop() |
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| 119 | except Exception, e: |
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| 120 | print str(e) |
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| 121 | log.debug( "Dropping workflow_step_annotation_association table failed: %s" % str( e ) ) |
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| 122 | |
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| 123 | # Drop workflow_step_tag_association table. |
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| 124 | try: |
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| 125 | WorkflowStepTagAssociation_table.drop() |
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| 126 | except Exception, e: |
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| 127 | print str(e) |
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| 128 | log.debug( "Dropping workflow_step_tag_association table failed: %s" % str( e ) ) |
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| 129 | |
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