[2] | 1 | """ |
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| 2 | Migration script to (a) add and populate necessary columns for doing community tagging of histories, datasets, and pages and \ |
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| 3 | (b) add table for doing individual and community tagging of workflows. |
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| 4 | |
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| 5 | SQLite does not support 'ALTER TABLE ADD FOREIGN KEY', so this script will generate error messages when run against \ |
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| 6 | SQLite; however, script does execute successfully against SQLite. |
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| 7 | """ |
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| 8 | |
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| 9 | from sqlalchemy import * |
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| 10 | from sqlalchemy.orm import * |
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| 11 | from migrate import * |
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| 12 | from migrate.changeset import * |
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| 13 | |
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| 14 | import logging |
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| 15 | log = logging.getLogger( __name__ ) |
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| 16 | |
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| 17 | metadata = MetaData( migrate_engine ) |
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| 18 | db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) |
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| 19 | |
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| 20 | StoredWorkflowTagAssociation_table = Table( "stored_workflow_tag_association", metadata, |
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| 21 | Column( "id", Integer, primary_key=True ), |
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| 22 | Column( "stored_workflow_id", Integer, ForeignKey( "stored_workflow.id" ), index=True ), |
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| 23 | Column( "tag_id", Integer, ForeignKey( "tag.id" ), index=True ), |
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| 24 | Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), |
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| 25 | Column( "user_tname", Unicode(255), index=True), |
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| 26 | Column( "value", Unicode(255), index=True), |
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| 27 | Column( "user_value", Unicode(255), index=True) ) |
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| 28 | |
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| 29 | WorkflowTagAssociation_table = Table( "workflow_tag_association", metadata, |
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| 30 | Column( "id", Integer, primary_key=True ), |
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| 31 | Column( "workflow_id", Integer, ForeignKey( "workflow.id" ), index=True ), |
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| 32 | Column( "tag_id", Integer, ForeignKey( "tag.id" ), index=True ), |
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| 33 | Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), |
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| 34 | Column( "user_tname", Unicode(255), index=True), |
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| 35 | Column( "value", Unicode(255), index=True), |
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| 36 | Column( "user_value", Unicode(255), index=True) ) |
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| 37 | |
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| 38 | def upgrade(): |
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| 39 | print __doc__ |
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| 40 | metadata.reflect() |
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| 41 | |
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| 42 | # Create user_id column in history_tag_association table. |
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| 43 | HistoryTagAssociation_table = Table( "history_tag_association", metadata, autoload=True ) |
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| 44 | c = Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ) |
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| 45 | try: |
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| 46 | c.create( HistoryTagAssociation_table ) |
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| 47 | assert c is HistoryTagAssociation_table.c.user_id |
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| 48 | except Exception, e: |
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| 49 | # SQLite does not support 'ALTER TABLE ADD FOREIGN KEY', so catch exception if it arises. |
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| 50 | print str(e) |
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| 51 | log.debug( "Adding user_id column to history_tag_association table failed: %s" % str( e ) ) |
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| 52 | |
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| 53 | # Create user_id index for history_tag_association table. |
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| 54 | try: |
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| 55 | i = Index( "ix_history_tag_association_user_id", HistoryTagAssociation_table.c.user_id ) |
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| 56 | i.create() |
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| 57 | except: |
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| 58 | # Mysql doesn't have a named index, but alter should work |
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| 59 | HistoryTagAssociation_table.c.user_id.alter( unique=False ) |
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| 60 | |
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| 61 | # Populate column so that user_id is the id of the user who owns the history (and, up to now, was the only person able to tag the history). |
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| 62 | if c is HistoryTagAssociation_table.c.user_id: |
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| 63 | db_session.execute( |
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| 64 | "UPDATE history_tag_association SET user_id=( SELECT user_id FROM history WHERE history_tag_association.history_id = history.id )" |
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| 65 | ) |
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| 66 | |
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| 67 | # Create user_id column in history_dataset_association_tag_association table. |
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| 68 | HistoryDatasetAssociationTagAssociation_table = Table( "history_dataset_association_tag_association", metadata, autoload=True ) |
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| 69 | c = Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ) |
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| 70 | try: |
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| 71 | c.create( HistoryDatasetAssociationTagAssociation_table ) |
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| 72 | assert c is HistoryDatasetAssociationTagAssociation_table.c.user_id |
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| 73 | except Exception, e: |
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| 74 | # SQLite does not support 'ALTER TABLE ADD FOREIGN KEY', so catch exception if it arises. |
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| 75 | print str(e) |
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| 76 | log.debug( "Adding user_id column to history_dataset_association_tag_association table failed: %s" % str( e ) ) |
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| 77 | |
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| 78 | # Create user_id index for history_dataset_association_tag_association table. |
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| 79 | try: |
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| 80 | i = Index( "ix_history_dataset_association_tag_association_user_id", HistoryDatasetAssociationTagAssociation_table.c.user_id ) |
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| 81 | i.create() |
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| 82 | except: |
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| 83 | # Mysql doesn't have a named index, but alter should work |
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| 84 | HistoryDatasetAssociationTagAssociation_table.c.user_id.alter( unique=False ) |
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| 85 | |
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| 86 | # Populate column so that user_id is the id of the user who owns the history_dataset_association (and, up to now, was the only person able to tag the page). |
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| 87 | if c is HistoryDatasetAssociationTagAssociation_table.c.user_id: |
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| 88 | db_session.execute( |
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| 89 | "UPDATE history_dataset_association_tag_association SET user_id=( SELECT history.user_id FROM history, history_dataset_association WHERE history_dataset_association.history_id = history.id AND history_dataset_association.id = history_dataset_association_tag_association.history_dataset_association_id)" |
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| 90 | ) |
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| 91 | |
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| 92 | # Create user_id column in page_tag_association table. |
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| 93 | PageTagAssociation_table = Table( "page_tag_association", metadata, autoload=True ) |
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| 94 | c = Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ) |
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| 95 | try: |
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| 96 | c.create( PageTagAssociation_table ) |
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| 97 | assert c is PageTagAssociation_table.c.user_id |
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| 98 | except Exception, e: |
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| 99 | # SQLite does not support 'ALTER TABLE ADD FOREIGN KEY', so catch exception if it arises. |
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| 100 | print str(e) |
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| 101 | log.debug( "Adding user_id column to history_tag_association table failed: %s" % str( e ) ) |
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| 102 | |
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| 103 | # Create user_id index for page_tag_association table. |
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| 104 | try: |
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| 105 | i = Index( "ix_page_tag_association_user_id", PageTagAssociation_table.c.user_id ) |
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| 106 | i.create() |
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| 107 | except: |
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| 108 | # Mysql doesn't have a named index, but alter should work |
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| 109 | PageTagAssociation_table.c.user_id.alter( unique=False ) |
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| 110 | |
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| 111 | # Populate column so that user_id is the id of the user who owns the page (and, up to now, was the only person able to tag the page). |
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| 112 | if c is PageTagAssociation_table.c.user_id: |
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| 113 | db_session.execute( |
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| 114 | "UPDATE page_tag_association SET user_id=( SELECT user_id FROM page WHERE page_tag_association.page_id = page.id )" |
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| 115 | ) |
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| 116 | |
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| 117 | # Create stored_workflow_tag_association table. |
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| 118 | try: |
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| 119 | StoredWorkflowTagAssociation_table.create() |
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| 120 | except Exception, e: |
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| 121 | print str(e) |
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| 122 | log.debug( "Creating stored_workflow_tag_association table failed: %s" % str( e ) ) |
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| 123 | |
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| 124 | # Create workflow_tag_association table. |
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| 125 | try: |
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| 126 | WorkflowTagAssociation_table.create() |
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| 127 | except Exception, e: |
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| 128 | print str(e) |
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| 129 | log.debug( "Creating workflow_tag_association table failed: %s" % str( e ) ) |
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| 130 | |
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| 131 | def downgrade(): |
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| 132 | metadata.reflect() |
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| 133 | |
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| 134 | # Drop user_id column from history_tag_association table. |
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| 135 | HistoryTagAssociation_table = Table( "history_tag_association", metadata, autoload=True ) |
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| 136 | try: |
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| 137 | HistoryTagAssociation_table.c.user_id.drop() |
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| 138 | except Exception, e: |
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| 139 | print str(e) |
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| 140 | log.debug( "Dropping column user_id from history_tag_association table failed: %s" % str( e ) ) |
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| 141 | |
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| 142 | |
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| 143 | # Drop user_id column from history_dataset_association_tag_association table. |
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| 144 | HistoryDatasetAssociationTagAssociation_table = Table( "history_dataset_association_tag_association", metadata, autoload=True ) |
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| 145 | try: |
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| 146 | HistoryDatasetAssociationTagAssociation_table.c.user_id.drop() |
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| 147 | except Exception, e: |
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| 148 | print str(e) |
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| 149 | log.debug( "Dropping column user_id from history_dataset_association_tag_association table failed: %s" % str( e ) ) |
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| 150 | |
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| 151 | # Drop user_id column from page_tag_association table. |
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| 152 | PageTagAssociation_table = Table( "page_tag_association", metadata, autoload=True ) |
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| 153 | try: |
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| 154 | PageTagAssociation_table.c.user_id.drop() |
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| 155 | except Exception, e: |
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| 156 | print str(e) |
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| 157 | log.debug( "Dropping column user_id from page_tag_association table failed: %s" % str( e ) ) |
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| 158 | |
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| 159 | # Drop stored_workflow_tag_association table. |
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| 160 | try: |
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| 161 | StoredWorkflowTagAssociation_table.drop() |
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| 162 | except Exception, e: |
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| 163 | print str(e) |
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| 164 | log.debug( "Dropping stored_workflow_tag_association table failed: %s" % str( e ) ) |
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| 165 | |
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| 166 | # Drop workflow_tag_association table. |
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| 167 | try: |
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| 168 | WorkflowTagAssociation_table.drop() |
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| 169 | except Exception, e: |
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| 170 | print str(e) |
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| 171 | log.debug( "Dropping workflow_tag_association table failed: %s" % str( e ) ) |
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