[2] | 1 | """ |
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| 2 | This migration script adds the following new tables for supporting Galaxy forms: |
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| 3 | 1) form_definition_current |
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| 4 | 2) form_definition |
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| 5 | 3) form_values |
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| 6 | 4) request_type |
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| 7 | 5) request |
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| 8 | 6) sample |
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| 9 | 7) sample_state |
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| 10 | 8) sample_event |
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| 11 | """ |
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| 12 | from sqlalchemy import * |
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| 13 | from sqlalchemy.orm import * |
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| 14 | from sqlalchemy.exc import * |
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| 15 | from migrate import * |
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| 16 | from migrate.changeset import * |
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| 17 | |
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| 18 | import datetime |
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| 19 | now = datetime.datetime.utcnow |
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| 20 | |
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| 21 | import sys, logging |
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| 22 | log = logging.getLogger( __name__ ) |
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| 23 | log.setLevel(logging.DEBUG) |
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| 24 | handler = logging.StreamHandler( sys.stdout ) |
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| 25 | format = "%(name)s %(levelname)s %(asctime)s %(message)s" |
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| 26 | formatter = logging.Formatter( format ) |
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| 27 | handler.setFormatter( formatter ) |
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| 28 | log.addHandler( handler ) |
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| 29 | |
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| 30 | # Need our custom types, but don't import anything else from model |
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| 31 | from galaxy.model.custom_types import * |
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| 32 | |
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| 33 | metadata = MetaData( migrate_engine ) |
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| 34 | db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) |
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| 35 | |
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| 36 | def display_migration_details(): |
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| 37 | print "========================================" |
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| 38 | print "This migration script adds the following new tables for supporting Galaxy forms:" |
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| 39 | print "1) form_definition_current" |
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| 40 | print "2) form_definition" |
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| 41 | print "3) form_values" |
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| 42 | print "4) request_type" |
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| 43 | print "5) request" |
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| 44 | print "6) sample" |
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| 45 | print "7) sample_state" |
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| 46 | print "8) sample_event" |
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| 47 | print "========================================" |
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| 48 | |
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| 49 | FormDefinitionCurrent_table = Table('form_definition_current', metadata, |
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| 50 | Column( "id", Integer, primary_key=True), |
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| 51 | Column( "create_time", DateTime, default=now ), |
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| 52 | Column( "update_time", DateTime, default=now, onupdate=now ), |
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| 53 | Column( "latest_form_id", Integer, index=True ), |
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| 54 | Column( "deleted", Boolean, index=True, default=False )) |
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| 55 | |
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| 56 | FormDefinition_table = Table('form_definition', metadata, |
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| 57 | Column( "id", Integer, primary_key=True), |
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| 58 | Column( "create_time", DateTime, default=now ), |
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| 59 | Column( "update_time", DateTime, default=now, onupdate=now ), |
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| 60 | Column( "name", TrimmedString( 255 ), nullable=False ), |
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| 61 | Column( "desc", TEXT ), |
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| 62 | Column( "form_definition_current_id", Integer, ForeignKey( "form_definition_current.id" ), index=True, nullable=False ), |
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| 63 | Column( "fields", JSONType()) ) |
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| 64 | |
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| 65 | FormValues_table = Table('form_values', metadata, |
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| 66 | Column( "id", Integer, primary_key=True), |
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| 67 | Column( "create_time", DateTime, default=now ), |
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| 68 | Column( "update_time", DateTime, default=now, onupdate=now ), |
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| 69 | Column( "form_definition_id", Integer, ForeignKey( "form_definition.id" ), index=True ), |
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| 70 | Column( "content", JSONType()) ) |
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| 71 | |
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| 72 | RequestType_table = Table('request_type', metadata, |
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| 73 | Column( "id", Integer, primary_key=True), |
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| 74 | Column( "create_time", DateTime, default=now ), |
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| 75 | Column( "update_time", DateTime, default=now, onupdate=now ), |
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| 76 | Column( "name", TrimmedString( 255 ), nullable=False ), |
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| 77 | Column( "desc", TEXT ), |
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| 78 | Column( "request_form_id", Integer, ForeignKey( "form_definition.id" ), index=True ), |
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| 79 | Column( "sample_form_id", Integer, ForeignKey( "form_definition.id" ), index=True ) ) |
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| 80 | |
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| 81 | Request_table = Table('request', metadata, |
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| 82 | Column( "id", Integer, primary_key=True), |
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| 83 | Column( "create_time", DateTime, default=now ), |
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| 84 | Column( "update_time", DateTime, default=now, onupdate=now ), |
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| 85 | Column( "name", TrimmedString( 255 ), nullable=False ), |
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| 86 | Column( "desc", TEXT ), |
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| 87 | Column( "form_values_id", Integer, ForeignKey( "form_values.id" ), index=True ), |
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| 88 | Column( "request_type_id", Integer, ForeignKey( "request_type.id" ), index=True ), |
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| 89 | Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), |
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| 90 | Column( "library_id", Integer, ForeignKey( "library.id" ), index=True ), |
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| 91 | Column( "deleted", Boolean, index=True, default=False ) ) |
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| 92 | |
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| 93 | Sample_table = Table('sample', metadata, |
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| 94 | Column( "id", Integer, primary_key=True), |
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| 95 | Column( "create_time", DateTime, default=now ), |
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| 96 | Column( "update_time", DateTime, default=now, onupdate=now ), |
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| 97 | Column( "name", TrimmedString( 255 ), nullable=False ), |
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| 98 | Column( "desc", TEXT ), |
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| 99 | Column( "form_values_id", Integer, ForeignKey( "form_values.id" ), index=True ), |
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| 100 | Column( "request_id", Integer, ForeignKey( "request.id" ), index=True ), |
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| 101 | Column( "deleted", Boolean, index=True, default=False ) ) |
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| 102 | |
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| 103 | SampleState_table = Table('sample_state', metadata, |
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| 104 | Column( "id", Integer, primary_key=True), |
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| 105 | Column( "create_time", DateTime, default=now ), |
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| 106 | Column( "update_time", DateTime, default=now, onupdate=now ), |
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| 107 | Column( "name", TrimmedString( 255 ), nullable=False ), |
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| 108 | Column( "desc", TEXT ), |
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| 109 | Column( "request_type_id", Integer, ForeignKey( "request_type.id" ), index=True ) ) |
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| 110 | |
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| 111 | SampleEvent_table = Table('sample_event', metadata, |
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| 112 | Column( "id", Integer, primary_key=True), |
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| 113 | Column( "create_time", DateTime, default=now ), |
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| 114 | Column( "update_time", DateTime, default=now, onupdate=now ), |
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| 115 | Column( "sample_id", Integer, ForeignKey( "sample.id" ), index=True ), |
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| 116 | Column( "sample_state_id", Integer, ForeignKey( "sample_state.id" ), index=True ), |
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| 117 | Column( "comment", TEXT ) ) |
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| 118 | |
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| 119 | def upgrade(): |
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| 120 | display_migration_details() |
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| 121 | # Load existing tables |
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| 122 | metadata.reflect() |
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| 123 | # Add all of the new tables above |
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| 124 | # metadata.create_all() |
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| 125 | try: |
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| 126 | FormDefinitionCurrent_table.create() |
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| 127 | except Exception, e: |
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| 128 | log.debug( "Creating form_definition_current table failed: %s" % str( e ) ) |
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| 129 | try: |
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| 130 | FormDefinition_table.create() |
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| 131 | except Exception, e: |
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| 132 | log.debug( "Creating form_definition table failed: %s" % str( e ) ) |
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| 133 | # Add 1 foreign key constraint to the form_definition_current table |
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| 134 | if FormDefinitionCurrent_table and FormDefinition_table: |
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| 135 | try: |
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| 136 | cons = ForeignKeyConstraint( [FormDefinitionCurrent_table.c.latest_form_id], |
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| 137 | [FormDefinition_table.c.id], |
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| 138 | name='form_definition_current_latest_form_id_fk' ) |
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| 139 | # Create the constraint |
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| 140 | cons.create() |
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| 141 | except Exception, e: |
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| 142 | log.debug( "Adding foreign key constraint 'form_definition_current_latest_form_id_fk' to table 'form_definition_current' failed: %s" % ( str( e ) ) ) |
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| 143 | try: |
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| 144 | FormValues_table.create() |
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| 145 | except Exception, e: |
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| 146 | log.debug( "Creating form_values table failed: %s" % str( e ) ) |
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| 147 | try: |
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| 148 | RequestType_table.create() |
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| 149 | except Exception, e: |
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| 150 | log.debug( "Creating request_type table failed: %s" % str( e ) ) |
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| 151 | try: |
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| 152 | Request_table.create() |
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| 153 | except Exception, e: |
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| 154 | log.debug( "Creating request table failed: %s" % str( e ) ) |
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| 155 | try: |
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| 156 | Sample_table.create() |
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| 157 | except Exception, e: |
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| 158 | log.debug( "Creating sample table failed: %s" % str( e ) ) |
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| 159 | try: |
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| 160 | SampleState_table.create() |
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| 161 | except Exception, e: |
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| 162 | log.debug( "Creating sample_state table failed: %s" % str( e ) ) |
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| 163 | try: |
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| 164 | SampleEvent_table.create() |
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| 165 | except Exception, e: |
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| 166 | log.debug( "Creating sample_event table failed: %s" % str( e ) ) |
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| 167 | |
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| 168 | def downgrade(): |
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| 169 | # Load existing tables |
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| 170 | metadata.reflect() |
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| 171 | try: |
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| 172 | FormDefinition_table.drop() |
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| 173 | except Exception, e: |
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| 174 | log.debug( "Dropping form_definition table failed: %s" % str( e ) ) |
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| 175 | try: |
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| 176 | FormDefinitionCurrent_table.drop() |
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| 177 | except Exception, e: |
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| 178 | log.debug( "Dropping form_definition_current table failed: %s" % str( e ) ) |
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| 179 | try: |
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| 180 | FormValues_table.drop() |
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| 181 | except Exception, e: |
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| 182 | log.debug( "Dropping form_values table failed: %s" % str( e ) ) |
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| 183 | try: |
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| 184 | Request_table.drop() |
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| 185 | except Exception, e: |
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| 186 | log.debug( "Dropping request table failed: %s" % str( e ) ) |
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| 187 | try: |
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| 188 | RequestType_table.drop() |
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| 189 | except Exception, e: |
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| 190 | log.debug( "Dropping request_type table failed: %s" % str( e ) ) |
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| 191 | try: |
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| 192 | Sample_table.drop() |
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| 193 | except Exception, e: |
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| 194 | log.debug( "Dropping sample table failed: %s" % str( e ) ) |
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| 195 | try: |
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| 196 | SampleState_table.drop() |
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| 197 | except Exception, e: |
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| 198 | log.debug( "Dropping sample_state table failed: %s" % str( e ) ) |
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| 199 | try: |
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| 200 | SampleEvent_table.drop() |
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| 201 | except Exception, e: |
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| 202 | log.debug( "Dropping sample_event table failed: %s" % str( e ) ) |
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