[2] | 1 | """ |
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| 2 | This migration script eliminates all of the tables that were used for the 1st version of the |
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| 3 | library templates where template fields and contents were each stored as a separate table row |
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| 4 | in various library item tables. All of these tables are dropped in this script, eliminating all |
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| 5 | existing template data. A total of 14 existing tables are dropped. |
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| 6 | |
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| 7 | We're now basing library templates on forms, so field contents are |
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| 8 | stored as a jsonified list in the form_values table. This script introduces the following 3 |
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| 9 | new association tables: |
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| 10 | 1) library_info_association |
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| 11 | 2) library_folder_info_association |
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| 12 | 3) library_dataset_dataset_info_association |
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| 13 | |
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| 14 | If using mysql, this script will throw an (OperationalError) exception due to a long index name on |
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| 15 | the library_dataset_dataset_info_association table, which is OK because the script creates an index |
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| 16 | with a shortened name. |
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| 17 | """ |
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| 18 | from sqlalchemy import * |
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| 19 | from sqlalchemy.orm import * |
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| 20 | from sqlalchemy.exc import * |
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| 21 | from migrate import * |
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| 22 | from migrate.changeset import * |
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| 23 | import sys, logging |
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| 24 | |
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| 25 | log = logging.getLogger( __name__ ) |
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| 26 | log.setLevel(logging.DEBUG) |
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| 27 | handler = logging.StreamHandler( sys.stdout ) |
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| 28 | format = "%(name)s %(levelname)s %(asctime)s %(message)s" |
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| 29 | formatter = logging.Formatter( format ) |
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| 30 | handler.setFormatter( formatter ) |
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| 31 | log.addHandler( handler ) |
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| 32 | |
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| 33 | metadata = MetaData( migrate_engine ) |
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| 34 | |
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| 35 | def display_migration_details(): |
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| 36 | print "========================================" |
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| 37 | print "This migration script eliminates all of the tables that were used for the 1st version of the" |
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| 38 | print "library templates where template fields and contents were each stored as a separate table row" |
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| 39 | print "in various library item tables. All of these tables are dropped in this script, eliminating all" |
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| 40 | print "existing template data. A total of 14 existing tables are dropped." |
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| 41 | print "" |
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| 42 | print "We're now basing library templates on Galaxy forms, so field contents are stored as a jsonified" |
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| 43 | print "list in the form_values table. This script introduces the following 3 new association tables:" |
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| 44 | print "1) library_info_association" |
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| 45 | print "2) library_folder_info_association" |
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| 46 | print "3) library_dataset_dataset_info_association" |
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| 47 | print "" |
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| 48 | print "If using mysql, this script will throw an (OperationalError) exception due to a long index name" |
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| 49 | print "on the library_dataset_dataset_info_association table, which is OK because the script creates" |
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| 50 | print "an index with a shortened name." |
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| 51 | print "========================================" |
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| 52 | |
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| 53 | if migrate_engine.name == 'postgres': |
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| 54 | # http://blog.pythonisito.com/2008/01/cascading-drop-table-with-sqlalchemy.html |
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| 55 | from sqlalchemy.databases import postgres |
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| 56 | class PGCascadeSchemaDropper(postgres.PGSchemaDropper): |
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| 57 | def visit_table(self, table): |
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| 58 | for column in table.columns: |
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| 59 | if column.default is not None: |
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| 60 | self.traverse_single(column.default) |
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| 61 | self.append("\nDROP TABLE " + |
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| 62 | self.preparer.format_table(table) + |
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| 63 | " CASCADE") |
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| 64 | self.execute() |
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| 65 | postgres.dialect.schemadropper = PGCascadeSchemaDropper |
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| 66 | |
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| 67 | LibraryInfoAssociation_table = Table( 'library_info_association', metadata, |
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| 68 | Column( "id", Integer, primary_key=True), |
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| 69 | Column( "library_id", Integer, ForeignKey( "library.id" ), index=True ), |
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| 70 | Column( "form_definition_id", Integer, ForeignKey( "form_definition.id" ), index=True ), |
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| 71 | Column( "form_values_id", Integer, ForeignKey( "form_values.id" ), index=True ) ) |
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| 72 | |
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| 73 | LibraryFolderInfoAssociation_table = Table( 'library_folder_info_association', metadata, |
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| 74 | Column( "id", Integer, primary_key=True), |
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| 75 | Column( "library_folder_id", Integer, ForeignKey( "library_folder.id" ), nullable=True, index=True ), |
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| 76 | Column( "form_definition_id", Integer, ForeignKey( "form_definition.id" ), index=True ), |
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| 77 | Column( "form_values_id", Integer, ForeignKey( "form_values.id" ), index=True ) ) |
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| 78 | |
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| 79 | LibraryDatasetDatasetInfoAssociation_table = Table( 'library_dataset_dataset_info_association', metadata, |
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| 80 | Column( "id", Integer, primary_key=True), |
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| 81 | Column( "library_dataset_dataset_association_id", Integer, ForeignKey( "library_dataset_dataset_association.id" ), nullable=True, index=True ), |
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| 82 | Column( "form_definition_id", Integer, ForeignKey( "form_definition.id" ), index=True ), |
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| 83 | Column( "form_values_id", Integer, ForeignKey( "form_values.id" ), index=True ) ) |
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| 84 | |
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| 85 | def upgrade(): |
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| 86 | display_migration_details() |
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| 87 | # Load existing tables |
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| 88 | metadata.reflect() |
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| 89 | # Drop all of the original library_item_info tables |
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| 90 | # NOTE: all existing library item into template data is eliminated here via table drops |
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| 91 | try: |
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| 92 | LibraryItemInfoPermissions_table = Table( "library_item_info_permissions", metadata, autoload=True ) |
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| 93 | except NoSuchTableError: |
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| 94 | LibraryItemInfoPermissions_table = None |
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| 95 | log.debug( "Failed loading table library_item_info_permissions" ) |
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| 96 | try: |
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| 97 | LibraryItemInfoPermissions_table.drop() |
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| 98 | except Exception, e: |
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| 99 | log.debug( "Dropping library_item_info_permissions table failed: %s" % str( e ) ) |
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| 100 | |
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| 101 | try: |
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| 102 | LibraryItemInfoTemplatePermissions_table = Table( "library_item_info_template_permissions", metadata, autoload=True ) |
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| 103 | except NoSuchTableError: |
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| 104 | LibraryItemInfoTemplatePermissions_table = None |
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| 105 | log.debug( "Failed loading table library_item_info_template_permissions" ) |
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| 106 | try: |
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| 107 | LibraryItemInfoTemplatePermissions_table.drop() |
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| 108 | except Exception, e: |
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| 109 | log.debug( "Dropping library_item_info_template_permissions table failed: %s" % str( e ) ) |
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| 110 | |
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| 111 | try: |
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| 112 | LibraryItemInfoElement_table = Table( "library_item_info_element", metadata, autoload=True ) |
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| 113 | except NoSuchTableError: |
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| 114 | LibraryItemInfoElement_table = None |
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| 115 | log.debug( "Failed loading table library_item_info_element" ) |
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| 116 | try: |
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| 117 | LibraryItemInfoElement_table.drop() |
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| 118 | except Exception, e: |
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| 119 | log.debug( "Dropping library_item_info_element table failed: %s" % str( e ) ) |
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| 120 | |
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| 121 | try: |
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| 122 | LibraryItemInfoTemplateElement_table = Table( "library_item_info_template_element", metadata, autoload=True ) |
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| 123 | except NoSuchTableError: |
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| 124 | LibraryItemInfoTemplateElement_table = None |
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| 125 | log.debug( "Failed loading table library_item_info_template_element" ) |
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| 126 | try: |
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| 127 | LibraryItemInfoTemplateElement_table.drop() |
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| 128 | except Exception, e: |
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| 129 | log.debug( "Dropping library_item_info_template_element table failed: %s" % str( e ) ) |
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| 130 | |
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| 131 | try: |
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| 132 | LibraryInfoTemplateAssociation_table = Table( "library_info_template_association", metadata, autoload=True ) |
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| 133 | except NoSuchTableError: |
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| 134 | LibraryInfoTemplateAssociation_table = None |
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| 135 | log.debug( "Failed loading table library_info_template_association" ) |
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| 136 | try: |
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| 137 | LibraryInfoTemplateAssociation_table.drop() |
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| 138 | except Exception, e: |
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| 139 | log.debug( "Dropping library_info_template_association table failed: %s" % str( e ) ) |
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| 140 | |
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| 141 | try: |
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| 142 | LibraryFolderInfoTemplateAssociation_table = Table( "library_folder_info_template_association", metadata, autoload=True ) |
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| 143 | except NoSuchTableError: |
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| 144 | LibraryFolderInfoTemplateAssociation_table = None |
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| 145 | log.debug( "Failed loading table library_folder_info_template_association" ) |
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| 146 | try: |
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| 147 | LibraryFolderInfoTemplateAssociation_table.drop() |
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| 148 | except Exception, e: |
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| 149 | log.debug( "Dropping library_folder_info_template_association table failed: %s" % str( e ) ) |
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| 150 | |
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| 151 | try: |
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| 152 | LibraryDatasetInfoTemplateAssociation_table = Table( "library_dataset_info_template_association", metadata, autoload=True ) |
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| 153 | except NoSuchTableError: |
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| 154 | LibraryDatasetInfoTemplateAssociation_table = None |
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| 155 | log.debug( "Failed loading table library_dataset_info_template_association" ) |
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| 156 | try: |
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| 157 | LibraryDatasetInfoTemplateAssociation_table.drop() |
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| 158 | except Exception, e: |
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| 159 | log.debug( "Dropping library_dataset_info_template_association table failed: %s" % str( e ) ) |
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| 160 | |
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| 161 | try: |
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| 162 | LibraryDatasetDatasetInfoTemplateAssociation_table = Table( "library_dataset_dataset_info_template_association", metadata, autoload=True ) |
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| 163 | except NoSuchTableError: |
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| 164 | LibraryDatasetDatasetInfoTemplateAssociation_table = None |
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| 165 | log.debug( "Failed loading table library_dataset_dataset_info_template_association" ) |
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| 166 | try: |
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| 167 | LibraryDatasetDatasetInfoTemplateAssociation_table.drop() |
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| 168 | except Exception, e: |
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| 169 | log.debug( "Dropping library_dataset_dataset_info_template_association table failed: %s" % str( e ) ) |
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| 170 | |
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| 171 | try: |
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| 172 | LibraryInfoAssociation_table = Table( "library_info_association", metadata, autoload=True ) |
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| 173 | except NoSuchTableError: |
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| 174 | LibraryInfoAssociation_table = None |
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| 175 | log.debug( "Failed loading table library_info_association" ) |
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| 176 | try: |
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| 177 | LibraryInfoAssociation_table.drop() |
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| 178 | except Exception, e: |
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| 179 | log.debug( "Dropping library_info_association table failed: %s" % str( e ) ) |
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| 180 | |
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| 181 | try: |
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| 182 | LibraryFolderInfoAssociation_table = Table( "library_folder_info_association", metadata, autoload=True ) |
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| 183 | except NoSuchTableError: |
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| 184 | LibraryFolderInfoAssociation_table = None |
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| 185 | log.debug( "Failed loading table library_folder_info_association" ) |
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| 186 | try: |
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| 187 | LibraryFolderInfoAssociation_table.drop() |
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| 188 | except Exception, e: |
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| 189 | log.debug( "Dropping library_folder_info_association table failed: %s" % str( e ) ) |
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| 190 | |
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| 191 | try: |
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| 192 | LibraryDatasetInfoAssociation_table = Table( "library_dataset_info_association", metadata, autoload=True ) |
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| 193 | except NoSuchTableError: |
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| 194 | LibraryDatasetInfoAssociation_table = None |
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| 195 | log.debug( "Failed loading table library_dataset_info_association" ) |
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| 196 | try: |
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| 197 | LibraryDatasetInfoAssociation_table.drop() |
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| 198 | except Exception, e: |
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| 199 | log.debug( "Dropping library_dataset_info_association table failed: %s" % str( e ) ) |
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| 200 | |
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| 201 | try: |
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| 202 | LibraryDatasetDatasetInfoAssociation_table = Table( "library_dataset_dataset_info_association", metadata, autoload=True ) |
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| 203 | except NoSuchTableError: |
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| 204 | LibraryDatasetDatasetInfoAssociation_table = None |
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| 205 | log.debug( "Failed loading table library_dataset_dataset_info_association" ) |
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| 206 | try: |
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| 207 | LibraryDatasetDatasetInfoAssociation_table.drop() |
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| 208 | except Exception, e: |
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| 209 | log.debug( "Dropping library_dataset_dataset_info_association table failed: %s" % str( e ) ) |
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| 210 | |
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| 211 | try: |
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| 212 | LibraryItemInfo_table = Table( "library_item_info", metadata, autoload=True ) |
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| 213 | except NoSuchTableError: |
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| 214 | LibraryItemInfo_table = None |
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| 215 | log.debug( "Failed loading table library_item_info" ) |
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| 216 | try: |
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| 217 | LibraryItemInfo_table.drop() |
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| 218 | except Exception, e: |
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| 219 | log.debug( "Dropping library_item_info table failed: %s" % str( e ) ) |
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| 220 | |
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| 221 | try: |
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| 222 | LibraryItemInfoTemplate_table = Table( "library_item_info_template", metadata, autoload=True ) |
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| 223 | except NoSuchTableError: |
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| 224 | LibraryItemInfoTemplate_table = None |
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| 225 | log.debug( "Failed loading table library_item_info_template" ) |
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| 226 | try: |
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| 227 | LibraryItemInfoTemplate_table.drop() |
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| 228 | except Exception, e: |
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| 229 | log.debug( "Dropping library_item_info_template table failed: %s" % str( e ) ) |
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| 230 | |
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| 231 | # Create all new tables above |
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| 232 | try: |
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| 233 | LibraryInfoAssociation_table.create() |
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| 234 | except Exception, e: |
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| 235 | log.debug( "Creating library_info_association table failed: %s" % str( e ) ) |
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| 236 | try: |
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| 237 | LibraryFolderInfoAssociation_table.create() |
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| 238 | except Exception, e: |
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| 239 | log.debug( "Creating library_folder_info_association table failed: %s" % str( e ) ) |
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| 240 | try: |
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| 241 | LibraryDatasetDatasetInfoAssociation_table.create() |
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| 242 | except Exception, e: |
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| 243 | log.debug( "Creating library_dataset_dataset_info_association table failed: %s" % str( e ) ) |
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| 244 | # Fix index on LibraryDatasetDatasetInfoAssociation_table for mysql |
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| 245 | if migrate_engine.name == 'mysql': |
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| 246 | # Load existing tables |
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| 247 | metadata.reflect() |
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| 248 | i = Index( "ix_lddaia_ldda_id", LibraryDatasetDatasetInfoAssociation_table.c.library_dataset_dataset_association_id ) |
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| 249 | try: |
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| 250 | i.create() |
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| 251 | except Exception, e: |
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| 252 | log.debug( "Adding index 'ix_lddaia_ldda_id' to table 'library_dataset_dataset_info_association' table failed: %s" % str( e ) ) |
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| 253 | |
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| 254 | def downgrade(): |
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| 255 | log.debug( "Downgrade is not possible." ) |
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