[2] | 1 | """ |
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| 2 | Details of how the data model objects are mapped onto the relational database |
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| 3 | are encapsulated here. |
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| 4 | """ |
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| 5 | import logging |
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| 6 | log = logging.getLogger( __name__ ) |
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| 7 | |
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| 8 | import sys |
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| 9 | import datetime |
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| 10 | |
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| 11 | from galaxy.model import * |
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| 12 | from galaxy.model.orm import * |
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| 13 | from galaxy.model.orm.ext.assignmapper import * |
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| 14 | from galaxy.model.custom_types import * |
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| 15 | from galaxy.util.bunch import Bunch |
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| 16 | from galaxy.security import GalaxyRBACAgent |
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| 17 | from sqlalchemy.orm.collections import attribute_mapped_collection |
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| 18 | from sqlalchemy.ext.associationproxy import association_proxy |
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| 19 | |
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| 20 | metadata = MetaData() |
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| 21 | context = Session = scoped_session( sessionmaker( autoflush=False, autocommit=True ) ) |
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| 22 | |
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| 23 | # For backward compatibility with "context.current" |
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| 24 | context.current = Session |
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| 25 | |
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| 26 | dialect_to_egg = { |
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| 27 | "sqlite" : "pysqlite>=2", |
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| 28 | "postgres" : "psycopg2", |
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| 29 | "mysql" : "MySQL_python" |
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| 30 | } |
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| 31 | |
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| 32 | # NOTE REGARDING TIMESTAMPS: |
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| 33 | # It is currently difficult to have the timestamps calculated by the |
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| 34 | # database in a portable way, so we're doing it in the client. This |
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| 35 | # also saves us from needing to postfetch on postgres. HOWEVER: it |
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| 36 | # relies on the client's clock being set correctly, so if clustering |
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| 37 | # web servers, use a time server to ensure synchronization |
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| 38 | |
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| 39 | # Return the current time in UTC without any timezone information |
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| 40 | now = datetime.datetime.utcnow |
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| 41 | |
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| 42 | User.table = Table( "galaxy_user", metadata, |
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| 43 | Column( "id", Integer, primary_key=True), |
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| 44 | Column( "create_time", DateTime, default=now ), |
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| 45 | Column( "update_time", DateTime, default=now, onupdate=now ), |
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| 46 | Column( "email", TrimmedString( 255 ), nullable=False ), |
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| 47 | Column( "username", TrimmedString( 255 ), index=True, unique=True ), |
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| 48 | Column( "password", TrimmedString( 40 ), nullable=False ), |
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| 49 | Column( "external", Boolean, default=False ), |
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| 50 | Column( "form_values_id", Integer, ForeignKey( "form_values.id" ), index=True ), |
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| 51 | Column( "deleted", Boolean, index=True, default=False ), |
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| 52 | Column( "purged", Boolean, index=True, default=False ) ) |
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| 53 | |
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| 54 | UserAddress.table = Table( "user_address", metadata, |
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| 55 | Column( "id", Integer, primary_key=True), |
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| 56 | Column( "create_time", DateTime, default=now ), |
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| 57 | Column( "update_time", DateTime, default=now, onupdate=now ), |
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| 58 | Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), |
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| 59 | Column( "desc", TrimmedString( 255 )), |
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| 60 | Column( "name", TrimmedString( 255 ), nullable=False), |
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| 61 | Column( "institution", TrimmedString( 255 )), |
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| 62 | Column( "address", TrimmedString( 255 ), nullable=False), |
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| 63 | Column( "city", TrimmedString( 255 ), nullable=False), |
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| 64 | Column( "state", TrimmedString( 255 ), nullable=False), |
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| 65 | Column( "postal_code", TrimmedString( 255 ), nullable=False), |
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| 66 | Column( "country", TrimmedString( 255 ), nullable=False), |
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| 67 | Column( "phone", TrimmedString( 255 )), |
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| 68 | Column( "deleted", Boolean, index=True, default=False ), |
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| 69 | Column( "purged", Boolean, index=True, default=False ) ) |
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| 70 | |
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| 71 | History.table = Table( "history", metadata, |
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| 72 | Column( "id", Integer, primary_key=True), |
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| 73 | Column( "create_time", DateTime, default=now ), |
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| 74 | Column( "update_time", DateTime, index=True, default=now, onupdate=now ), |
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| 75 | Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), |
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| 76 | Column( "name", TrimmedString( 255 ) ), |
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| 77 | Column( "hid_counter", Integer, default=1 ), |
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| 78 | Column( "deleted", Boolean, index=True, default=False ), |
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| 79 | Column( "purged", Boolean, index=True, default=False ), |
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| 80 | Column( "genome_build", TrimmedString( 40 ) ), |
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| 81 | Column( "importable", Boolean, default=False ), |
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| 82 | Column( "slug", TEXT, index=True ), |
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| 83 | Column( "published", Boolean, index=True, default=False ) ) |
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| 84 | |
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| 85 | HistoryUserShareAssociation.table = Table( "history_user_share_association", metadata, |
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| 86 | Column( "id", Integer, primary_key=True ), |
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| 87 | Column( "history_id", Integer, ForeignKey( "history.id" ), index=True ), |
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| 88 | Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ) |
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| 89 | ) |
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| 90 | |
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| 91 | HistoryDatasetAssociation.table = Table( "history_dataset_association", metadata, |
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| 92 | Column( "id", Integer, primary_key=True ), |
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| 93 | Column( "history_id", Integer, ForeignKey( "history.id" ), index=True ), |
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| 94 | Column( "dataset_id", Integer, ForeignKey( "dataset.id" ), index=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( "state", TrimmedString( 64 ), index=True, key="_state" ), |
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| 98 | Column( "copied_from_history_dataset_association_id", Integer, ForeignKey( "history_dataset_association.id" ), nullable=True ), |
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| 99 | Column( "copied_from_library_dataset_dataset_association_id", Integer, ForeignKey( "library_dataset_dataset_association.id" ), nullable=True ), |
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| 100 | Column( "hid", Integer ), |
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| 101 | Column( "name", TrimmedString( 255 ) ), |
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| 102 | Column( "info", TrimmedString( 255 ) ), |
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| 103 | Column( "blurb", TrimmedString( 255 ) ), |
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| 104 | Column( "peek" , TEXT ), |
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| 105 | Column( "extension", TrimmedString( 64 ) ), |
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| 106 | Column( "metadata", MetadataType(), key="_metadata" ), |
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| 107 | Column( "parent_id", Integer, ForeignKey( "history_dataset_association.id" ), nullable=True ), |
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| 108 | Column( "designation", TrimmedString( 255 ) ), |
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| 109 | Column( "deleted", Boolean, index=True, default=False ), |
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| 110 | Column( "visible", Boolean ) ) |
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| 111 | |
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| 112 | Dataset.table = Table( "dataset", metadata, |
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| 113 | Column( "id", Integer, primary_key=True ), |
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| 114 | Column( "create_time", DateTime, default=now ), |
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| 115 | Column( "update_time", DateTime, index=True, default=now, onupdate=now ), |
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| 116 | Column( "state", TrimmedString( 64 ), index=True ), |
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| 117 | Column( "deleted", Boolean, index=True, default=False ), |
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| 118 | Column( "purged", Boolean, index=True, default=False ), |
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| 119 | Column( "purgable", Boolean, default=True ), |
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| 120 | Column( "external_filename" , TEXT ), |
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| 121 | Column( "_extra_files_path", TEXT ), |
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| 122 | Column( 'file_size', Numeric( 15, 0 ) ) ) |
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| 123 | |
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| 124 | HistoryDatasetAssociationDisplayAtAuthorization.table = Table( "history_dataset_association_display_at_authorization", metadata, |
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| 125 | Column( "id", Integer, primary_key=True ), |
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| 126 | Column( "create_time", DateTime, default=now ), |
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| 127 | Column( "update_time", DateTime, index=True, default=now, onupdate=now ), |
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| 128 | Column( "history_dataset_association_id", Integer, ForeignKey( "history_dataset_association.id" ), index=True ), |
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| 129 | Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), |
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| 130 | Column( "site", TrimmedString( 255 ) ) ) |
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| 131 | |
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| 132 | ImplicitlyConvertedDatasetAssociation.table = Table( "implicitly_converted_dataset_association", metadata, |
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| 133 | Column( "id", Integer, primary_key=True ), |
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| 134 | Column( "create_time", DateTime, default=now ), |
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| 135 | Column( "update_time", DateTime, default=now, onupdate=now ), |
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| 136 | Column( "hda_id", Integer, ForeignKey( "history_dataset_association.id" ), index=True, nullable=True ), |
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| 137 | Column( "hda_parent_id", Integer, ForeignKey( "history_dataset_association.id" ), index=True ), |
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| 138 | Column( "deleted", Boolean, index=True, default=False ), |
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| 139 | Column( "metadata_safe", Boolean, index=True, default=True ), |
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| 140 | Column( "type", TrimmedString( 255 ) ) ) |
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| 141 | |
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| 142 | ValidationError.table = Table( "validation_error", metadata, |
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| 143 | Column( "id", Integer, primary_key=True ), |
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| 144 | Column( "dataset_id", Integer, ForeignKey( "history_dataset_association.id" ), index=True ), |
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| 145 | Column( "message", TrimmedString( 255 ) ), |
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| 146 | Column( "err_type", TrimmedString( 64 ) ), |
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| 147 | Column( "attributes", TEXT ) ) |
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| 148 | |
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| 149 | Group.table = Table( "galaxy_group", metadata, |
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| 150 | Column( "id", Integer, primary_key=True ), |
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| 151 | Column( "create_time", DateTime, default=now ), |
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| 152 | Column( "update_time", DateTime, default=now, onupdate=now ), |
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| 153 | Column( "name", String( 255 ), index=True, unique=True ), |
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| 154 | Column( "deleted", Boolean, index=True, default=False ) ) |
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| 155 | |
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| 156 | UserGroupAssociation.table = Table( "user_group_association", metadata, |
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| 157 | Column( "id", Integer, primary_key=True ), |
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| 158 | Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), |
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| 159 | Column( "group_id", Integer, ForeignKey( "galaxy_group.id" ), index=True ), |
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| 160 | Column( "create_time", DateTime, default=now ), |
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| 161 | Column( "update_time", DateTime, default=now, onupdate=now ) ) |
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| 162 | |
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| 163 | UserRoleAssociation.table = Table( "user_role_association", metadata, |
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| 164 | Column( "id", Integer, primary_key=True ), |
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| 165 | Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), |
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| 166 | Column( "role_id", Integer, ForeignKey( "role.id" ), index=True ), |
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| 167 | Column( "create_time", DateTime, default=now ), |
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| 168 | Column( "update_time", DateTime, default=now, onupdate=now ) ) |
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| 169 | |
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| 170 | GroupRoleAssociation.table = Table( "group_role_association", metadata, |
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| 171 | Column( "id", Integer, primary_key=True ), |
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| 172 | Column( "group_id", Integer, ForeignKey( "galaxy_group.id" ), index=True ), |
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| 173 | Column( "role_id", Integer, ForeignKey( "role.id" ), index=True ), |
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| 174 | Column( "create_time", DateTime, default=now ), |
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| 175 | Column( "update_time", DateTime, default=now, onupdate=now ) ) |
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| 176 | |
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| 177 | Role.table = Table( "role", metadata, |
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| 178 | Column( "id", Integer, primary_key=True ), |
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| 179 | Column( "create_time", DateTime, default=now ), |
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| 180 | Column( "update_time", DateTime, default=now, onupdate=now ), |
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| 181 | Column( "name", String( 255 ), index=True, unique=True ), |
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| 182 | Column( "description", TEXT ), |
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| 183 | Column( "type", String( 40 ), index=True ), |
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| 184 | Column( "deleted", Boolean, index=True, default=False ) ) |
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| 185 | |
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| 186 | DatasetPermissions.table = Table( "dataset_permissions", metadata, |
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| 187 | Column( "id", Integer, primary_key=True ), |
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| 188 | Column( "create_time", DateTime, default=now ), |
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| 189 | Column( "update_time", DateTime, default=now, onupdate=now ), |
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| 190 | Column( "action", TEXT ), |
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| 191 | Column( "dataset_id", Integer, ForeignKey( "dataset.id" ), index=True ), |
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| 192 | Column( "role_id", Integer, ForeignKey( "role.id" ), index=True ) ) |
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| 193 | |
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| 194 | LibraryPermissions.table = Table( "library_permissions", metadata, |
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| 195 | Column( "id", Integer, primary_key=True ), |
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| 196 | Column( "create_time", DateTime, default=now ), |
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| 197 | Column( "update_time", DateTime, default=now, onupdate=now ), |
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| 198 | Column( "action", TEXT ), |
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| 199 | Column( "library_id", Integer, ForeignKey( "library.id" ), nullable=True, index=True ), |
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| 200 | Column( "role_id", Integer, ForeignKey( "role.id" ), index=True ) ) |
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| 201 | |
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| 202 | LibraryFolderPermissions.table = Table( "library_folder_permissions", metadata, |
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| 203 | Column( "id", Integer, primary_key=True ), |
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| 204 | Column( "create_time", DateTime, default=now ), |
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| 205 | Column( "update_time", DateTime, default=now, onupdate=now ), |
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| 206 | Column( "action", TEXT ), |
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| 207 | Column( "library_folder_id", Integer, ForeignKey( "library_folder.id" ), nullable=True, index=True ), |
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| 208 | Column( "role_id", Integer, ForeignKey( "role.id" ), index=True ) ) |
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| 209 | |
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| 210 | LibraryDatasetPermissions.table = Table( "library_dataset_permissions", metadata, |
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| 211 | Column( "id", Integer, primary_key=True ), |
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| 212 | Column( "create_time", DateTime, default=now ), |
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| 213 | Column( "update_time", DateTime, default=now, onupdate=now ), |
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| 214 | Column( "action", TEXT ), |
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| 215 | Column( "library_dataset_id", Integer, ForeignKey( "library_dataset.id" ), nullable=True, index=True ), |
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| 216 | Column( "role_id", Integer, ForeignKey( "role.id" ), index=True ) ) |
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| 217 | |
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| 218 | LibraryDatasetDatasetAssociationPermissions.table = Table( "library_dataset_dataset_association_permissions", metadata, |
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| 219 | Column( "id", Integer, primary_key=True ), |
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| 220 | Column( "create_time", DateTime, default=now ), |
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| 221 | Column( "update_time", DateTime, default=now, onupdate=now ), |
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| 222 | Column( "action", TEXT ), |
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| 223 | Column( "library_dataset_dataset_association_id", Integer, ForeignKey( "library_dataset_dataset_association.id" ), nullable=True, index=True ), |
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| 224 | Column( "role_id", Integer, ForeignKey( "role.id" ), index=True ) ) |
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| 225 | |
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| 226 | DefaultUserPermissions.table = Table( "default_user_permissions", metadata, |
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| 227 | Column( "id", Integer, primary_key=True ), |
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| 228 | Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), |
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| 229 | Column( "action", TEXT ), |
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| 230 | Column( "role_id", Integer, ForeignKey( "role.id" ), index=True ) ) |
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| 231 | |
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| 232 | DefaultHistoryPermissions.table = Table( "default_history_permissions", metadata, |
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| 233 | Column( "id", Integer, primary_key=True ), |
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| 234 | Column( "history_id", Integer, ForeignKey( "history.id" ), index=True ), |
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| 235 | Column( "action", TEXT ), |
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| 236 | Column( "role_id", Integer, ForeignKey( "role.id" ), index=True ) ) |
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| 237 | |
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| 238 | LibraryDataset.table = Table( "library_dataset", metadata, |
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| 239 | Column( "id", Integer, primary_key=True ), |
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| 240 | Column( "library_dataset_dataset_association_id", Integer, ForeignKey( "library_dataset_dataset_association.id", use_alter=True, name="library_dataset_dataset_association_id_fk" ), nullable=True, index=True ),#current version of dataset, if null, there is not a current version selected |
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| 241 | Column( "folder_id", Integer, ForeignKey( "library_folder.id" ), index=True ), |
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| 242 | Column( "order_id", Integer ), #not currently being used, but for possible future use |
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| 243 | Column( "create_time", DateTime, default=now ), |
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| 244 | Column( "update_time", DateTime, default=now, onupdate=now ), |
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| 245 | Column( "name", TrimmedString( 255 ), key="_name", index=True ), #when not None/null this will supercede display in library (but not when imported into user's history?) |
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| 246 | Column( "info", TrimmedString( 255 ), key="_info" ), #when not None/null this will supercede display in library (but not when imported into user's history?) |
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| 247 | Column( "deleted", Boolean, index=True, default=False ) ) |
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| 248 | |
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| 249 | LibraryDatasetDatasetAssociation.table = Table( "library_dataset_dataset_association", metadata, |
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| 250 | Column( "id", Integer, primary_key=True ), |
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| 251 | Column( "library_dataset_id", Integer, ForeignKey( "library_dataset.id" ), index=True ), |
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| 252 | Column( "dataset_id", Integer, ForeignKey( "dataset.id" ), index=True ), |
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| 253 | Column( "create_time", DateTime, default=now ), |
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| 254 | Column( "update_time", DateTime, default=now, onupdate=now ), |
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| 255 | Column( "state", TrimmedString( 64 ), index=True, key="_state" ), |
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| 256 | Column( "copied_from_history_dataset_association_id", Integer, ForeignKey( "history_dataset_association.id", use_alter=True, name='history_dataset_association_dataset_id_fkey' ), nullable=True ), |
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| 257 | Column( "copied_from_library_dataset_dataset_association_id", Integer, ForeignKey( "library_dataset_dataset_association.id", use_alter=True, name='library_dataset_dataset_association_id_fkey' ), nullable=True ), |
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| 258 | Column( "name", TrimmedString( 255 ), index=True ), |
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| 259 | Column( "info", TrimmedString( 255 ) ), |
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| 260 | Column( "blurb", TrimmedString( 255 ) ), |
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| 261 | Column( "peek" , TEXT ), |
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| 262 | Column( "extension", TrimmedString( 64 ) ), |
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| 263 | Column( "metadata", MetadataType(), key="_metadata" ), |
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| 264 | Column( "parent_id", Integer, ForeignKey( "library_dataset_dataset_association.id" ), nullable=True ), |
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| 265 | Column( "designation", TrimmedString( 255 ) ), |
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| 266 | Column( "deleted", Boolean, index=True, default=False ), |
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| 267 | Column( "visible", Boolean ), |
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| 268 | Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), |
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| 269 | Column( "message", TrimmedString( 255 ) ) ) |
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| 270 | |
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| 271 | Library.table = Table( "library", metadata, |
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| 272 | Column( "id", Integer, primary_key=True ), |
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| 273 | Column( "root_folder_id", Integer, ForeignKey( "library_folder.id" ), index=True ), |
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| 274 | Column( "create_time", DateTime, default=now ), |
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| 275 | Column( "update_time", DateTime, default=now, onupdate=now ), |
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| 276 | Column( "name", String( 255 ), index=True ), |
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| 277 | Column( "deleted", Boolean, index=True, default=False ), |
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| 278 | Column( "purged", Boolean, index=True, default=False ), |
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| 279 | Column( "description", TEXT ), |
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| 280 | Column( "synopsis", TEXT ) ) |
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| 281 | |
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| 282 | LibraryFolder.table = Table( "library_folder", metadata, |
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| 283 | Column( "id", Integer, primary_key=True ), |
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| 284 | Column( "parent_id", Integer, ForeignKey( "library_folder.id" ), nullable = True, index=True ), |
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| 285 | Column( "create_time", DateTime, default=now ), |
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| 286 | Column( "update_time", DateTime, default=now, onupdate=now ), |
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| 287 | Column( "name", TEXT, index=True ), |
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| 288 | Column( "description", TEXT ), |
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| 289 | Column( "order_id", Integer ), #not currently being used, but for possible future use |
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| 290 | Column( "item_count", Integer ), |
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| 291 | Column( "deleted", Boolean, index=True, default=False ), |
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| 292 | Column( "purged", Boolean, index=True, default=False ), |
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| 293 | Column( "genome_build", TrimmedString( 40 ) ) ) |
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| 294 | |
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| 295 | LibraryInfoAssociation.table = Table( 'library_info_association', metadata, |
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| 296 | Column( "id", Integer, primary_key=True ), |
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| 297 | Column( "library_id", Integer, ForeignKey( "library.id" ), index=True ), |
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| 298 | Column( "form_definition_id", Integer, ForeignKey( "form_definition.id" ), index=True ), |
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| 299 | Column( "form_values_id", Integer, ForeignKey( "form_values.id" ), index=True ), |
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| 300 | Column( "inheritable", Boolean, index=True, default=False ), |
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| 301 | Column( "deleted", Boolean, index=True, default=False ) ) |
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| 302 | |
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| 303 | LibraryFolderInfoAssociation.table = Table( 'library_folder_info_association', metadata, |
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| 304 | Column( "id", Integer, primary_key=True ), |
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| 305 | Column( "library_folder_id", Integer, ForeignKey( "library_folder.id" ), nullable=True, index=True ), |
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| 306 | Column( "form_definition_id", Integer, ForeignKey( "form_definition.id" ), index=True ), |
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| 307 | Column( "form_values_id", Integer, ForeignKey( "form_values.id" ), index=True ), |
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| 308 | Column( "inheritable", Boolean, index=True, default=False ), |
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| 309 | Column( "deleted", Boolean, index=True, default=False ) ) |
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| 310 | |
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| 311 | LibraryDatasetDatasetInfoAssociation.table = Table( 'library_dataset_dataset_info_association', metadata, |
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| 312 | Column( "id", Integer, primary_key=True ), |
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| 313 | Column( "library_dataset_dataset_association_id", Integer, ForeignKey( "library_dataset_dataset_association.id" ), nullable=True, index=True ), |
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| 314 | Column( "form_definition_id", Integer, ForeignKey( "form_definition.id" ), index=True ), |
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| 315 | Column( "form_values_id", Integer, ForeignKey( "form_values.id" ), index=True ), |
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| 316 | Column( "deleted", Boolean, index=True, default=False ) ) |
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| 317 | |
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| 318 | Job.table = Table( "job", metadata, |
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| 319 | Column( "id", Integer, primary_key=True ), |
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| 320 | Column( "create_time", DateTime, default=now ), |
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| 321 | Column( "update_time", DateTime, default=now, onupdate=now ), |
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| 322 | Column( "history_id", Integer, ForeignKey( "history.id" ), index=True ), |
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| 323 | Column( "library_folder_id", Integer, ForeignKey( "library_folder.id" ), index=True ), |
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| 324 | Column( "tool_id", String( 255 ) ), |
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| 325 | Column( "tool_version", TEXT, default="1.0.0" ), |
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| 326 | Column( "state", String( 64 ), index=True ), |
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| 327 | Column( "info", TrimmedString( 255 ) ), |
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| 328 | Column( "command_line", TEXT ), |
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| 329 | Column( "param_filename", String( 1024 ) ), |
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| 330 | Column( "runner_name", String( 255 ) ), |
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| 331 | Column( "stdout", TEXT ), |
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| 332 | Column( "stderr", TEXT ), |
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| 333 | Column( "traceback", TEXT ), |
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| 334 | Column( "session_id", Integer, ForeignKey( "galaxy_session.id" ), index=True, nullable=True ), |
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| 335 | Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True, nullable=True ), |
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| 336 | Column( "job_runner_name", String( 255 ) ), |
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| 337 | Column( "job_runner_external_id", String( 255 ) ), |
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| 338 | Column( "imported", Boolean, default=False, index=True ) ) |
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| 339 | |
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| 340 | JobParameter.table = Table( "job_parameter", metadata, |
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| 341 | Column( "id", Integer, primary_key=True ), |
---|
| 342 | Column( "job_id", Integer, ForeignKey( "job.id" ), index=True ), |
---|
| 343 | Column( "name", String(255) ), |
---|
| 344 | Column( "value", TEXT ) ) |
---|
| 345 | |
---|
| 346 | JobToInputDatasetAssociation.table = Table( "job_to_input_dataset", metadata, |
---|
| 347 | Column( "id", Integer, primary_key=True ), |
---|
| 348 | Column( "job_id", Integer, ForeignKey( "job.id" ), index=True ), |
---|
| 349 | Column( "dataset_id", Integer, ForeignKey( "history_dataset_association.id" ), index=True ), |
---|
| 350 | Column( "name", String(255) ) ) |
---|
| 351 | |
---|
| 352 | JobToOutputDatasetAssociation.table = Table( "job_to_output_dataset", metadata, |
---|
| 353 | Column( "id", Integer, primary_key=True ), |
---|
| 354 | Column( "job_id", Integer, ForeignKey( "job.id" ), index=True ), |
---|
| 355 | Column( "dataset_id", Integer, ForeignKey( "history_dataset_association.id" ), index=True ), |
---|
| 356 | Column( "name", String(255) ) ) |
---|
| 357 | |
---|
| 358 | JobToOutputLibraryDatasetAssociation.table = Table( "job_to_output_library_dataset", metadata, |
---|
| 359 | Column( "id", Integer, primary_key=True ), |
---|
| 360 | Column( "job_id", Integer, ForeignKey( "job.id" ), index=True ), |
---|
| 361 | Column( "ldda_id", Integer, ForeignKey( "library_dataset_dataset_association.id" ), index=True ), |
---|
| 362 | Column( "name", String(255) ) ) |
---|
| 363 | |
---|
| 364 | JobExternalOutputMetadata.table = Table( "job_external_output_metadata", metadata, |
---|
| 365 | Column( "id", Integer, primary_key=True ), |
---|
| 366 | Column( "job_id", Integer, ForeignKey( "job.id" ), index=True ), |
---|
| 367 | Column( "history_dataset_association_id", Integer, ForeignKey( "history_dataset_association.id" ), index=True, nullable=True ), |
---|
| 368 | Column( "library_dataset_dataset_association_id", Integer, ForeignKey( "library_dataset_dataset_association.id" ), index=True, nullable=True ), |
---|
| 369 | Column( "filename_in", String( 255 ) ), |
---|
| 370 | Column( "filename_out", String( 255 ) ), |
---|
| 371 | Column( "filename_results_code", String( 255 ) ), |
---|
| 372 | Column( "filename_kwds", String( 255 ) ), |
---|
| 373 | Column( "filename_override_metadata", String( 255 ) ), |
---|
| 374 | Column( "job_runner_external_pid", String( 255 ) ) ) |
---|
| 375 | |
---|
| 376 | JobExportHistoryArchive.table = Table( "job_export_history_archive", metadata, |
---|
| 377 | Column( "id", Integer, primary_key=True ), |
---|
| 378 | Column( "job_id", Integer, ForeignKey( "job.id" ), index=True ), |
---|
| 379 | Column( "history_id", Integer, ForeignKey( "history.id" ), index=True ), |
---|
| 380 | Column( "dataset_id", Integer, ForeignKey( "dataset.id" ), index=True ), |
---|
| 381 | Column( "compressed", Boolean, index=True, default=False ), |
---|
| 382 | Column( "history_attrs_filename", TEXT ), |
---|
| 383 | Column( "datasets_attrs_filename", TEXT ), |
---|
| 384 | Column( "jobs_attrs_filename", TEXT ) |
---|
| 385 | ) |
---|
| 386 | |
---|
| 387 | PostJobAction.table = Table("post_job_action", metadata, |
---|
| 388 | Column("id", Integer, primary_key=True), |
---|
| 389 | Column("workflow_step_id", Integer, ForeignKey( "workflow_step.id" ), index=True, nullable=False), |
---|
| 390 | Column("action_type", String(255), nullable=False), |
---|
| 391 | Column("output_name", String(255), nullable=True), |
---|
| 392 | Column("action_arguments", JSONType, nullable=True)) |
---|
| 393 | |
---|
| 394 | PostJobActionAssociation.table = Table("post_job_action_association", metadata, |
---|
| 395 | Column("id", Integer, primary_key=True), |
---|
| 396 | Column("job_id", Integer, ForeignKey( "job.id" ), index=True, nullable=False), |
---|
| 397 | Column("post_job_action_id", Integer, ForeignKey( "post_job_action.id" ), index=True, nullable=False)) |
---|
| 398 | |
---|
| 399 | Event.table = Table( "event", metadata, |
---|
| 400 | Column( "id", Integer, primary_key=True ), |
---|
| 401 | Column( "create_time", DateTime, default=now ), |
---|
| 402 | Column( "update_time", DateTime, default=now, onupdate=now ), |
---|
| 403 | Column( "history_id", Integer, ForeignKey( "history.id" ), index=True, nullable=True ), |
---|
| 404 | Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True, nullable=True ), |
---|
| 405 | Column( "message", TrimmedString( 1024 ) ), |
---|
| 406 | Column( "session_id", Integer, ForeignKey( "galaxy_session.id" ), index=True, nullable=True ), |
---|
| 407 | Column( "tool_id", String( 255 ) ) ) |
---|
| 408 | |
---|
| 409 | GalaxySession.table = Table( "galaxy_session", metadata, |
---|
| 410 | Column( "id", Integer, primary_key=True ), |
---|
| 411 | Column( "create_time", DateTime, default=now ), |
---|
| 412 | Column( "update_time", DateTime, default=now, onupdate=now ), |
---|
| 413 | Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True, nullable=True ), |
---|
| 414 | Column( "remote_host", String( 255 ) ), |
---|
| 415 | Column( "remote_addr", String( 255 ) ), |
---|
| 416 | Column( "referer", TEXT ), |
---|
| 417 | Column( "current_history_id", Integer, ForeignKey( "history.id" ), nullable=True ), |
---|
| 418 | Column( "session_key", TrimmedString( 255 ), index=True, unique=True ), # unique 128 bit random number coerced to a string |
---|
| 419 | Column( "is_valid", Boolean, default=False ), |
---|
| 420 | Column( "prev_session_id", Integer ) # saves a reference to the previous session so we have a way to chain them together |
---|
| 421 | ) |
---|
| 422 | |
---|
| 423 | GalaxySessionToHistoryAssociation.table = Table( "galaxy_session_to_history", metadata, |
---|
| 424 | Column( "id", Integer, primary_key=True ), |
---|
| 425 | Column( "create_time", DateTime, default=now ), |
---|
| 426 | Column( "session_id", Integer, ForeignKey( "galaxy_session.id" ), index=True ), |
---|
| 427 | Column( "history_id", Integer, ForeignKey( "history.id" ), index=True ) ) |
---|
| 428 | |
---|
| 429 | StoredWorkflow.table = Table( "stored_workflow", metadata, |
---|
| 430 | Column( "id", Integer, primary_key=True ), |
---|
| 431 | Column( "create_time", DateTime, default=now ), |
---|
| 432 | Column( "update_time", DateTime, default=now, onupdate=now ), |
---|
| 433 | Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True, nullable=False ), |
---|
| 434 | Column( "latest_workflow_id", Integer, |
---|
| 435 | ForeignKey( "workflow.id", use_alter=True, name='stored_workflow_latest_workflow_id_fk' ), index=True ), |
---|
| 436 | Column( "name", TEXT ), |
---|
| 437 | Column( "deleted", Boolean, default=False ), |
---|
| 438 | Column( "importable", Boolean, default=False ), |
---|
| 439 | Column( "slug", TEXT, index=True ), |
---|
| 440 | Column( "published", Boolean, index=True, default=False ) |
---|
| 441 | ) |
---|
| 442 | |
---|
| 443 | Workflow.table = Table( "workflow", metadata, |
---|
| 444 | Column( "id", Integer, primary_key=True ), |
---|
| 445 | Column( "create_time", DateTime, default=now ), |
---|
| 446 | Column( "update_time", DateTime, default=now, onupdate=now ), |
---|
| 447 | Column( "stored_workflow_id", Integer, ForeignKey( "stored_workflow.id" ), index=True, nullable=False ), |
---|
| 448 | Column( "name", TEXT ), |
---|
| 449 | Column( "has_cycles", Boolean ), |
---|
| 450 | Column( "has_errors", Boolean ) |
---|
| 451 | ) |
---|
| 452 | |
---|
| 453 | WorkflowStep.table = Table( "workflow_step", metadata, |
---|
| 454 | Column( "id", Integer, primary_key=True ), |
---|
| 455 | Column( "create_time", DateTime, default=now ), |
---|
| 456 | Column( "update_time", DateTime, default=now, onupdate=now ), |
---|
| 457 | Column( "workflow_id", Integer, ForeignKey( "workflow.id" ), index=True, nullable=False ), |
---|
| 458 | Column( "type", String(64) ), |
---|
| 459 | Column( "tool_id", TEXT ), |
---|
| 460 | Column( "tool_version", TEXT ), # Reserved for future |
---|
| 461 | Column( "tool_inputs", JSONType ), |
---|
| 462 | Column( "tool_errors", JSONType ), |
---|
| 463 | Column( "position", JSONType ), |
---|
| 464 | Column( "config", JSONType ), |
---|
| 465 | Column( "order_index", Integer ), |
---|
| 466 | ## Column( "input_connections", JSONType ) |
---|
| 467 | ) |
---|
| 468 | |
---|
| 469 | WorkflowStepConnection.table = Table( "workflow_step_connection", metadata, |
---|
| 470 | Column( "id", Integer, primary_key=True ), |
---|
| 471 | Column( "output_step_id", Integer, ForeignKey( "workflow_step.id" ), index=True ), |
---|
| 472 | Column( "input_step_id", Integer, ForeignKey( "workflow_step.id" ), index=True ), |
---|
| 473 | Column( "output_name", TEXT ), |
---|
| 474 | Column( "input_name", TEXT) |
---|
| 475 | ) |
---|
| 476 | |
---|
| 477 | WorkflowOutput.table = Table( "workflow_output", metadata, |
---|
| 478 | Column( "id", Integer, primary_key=True ), |
---|
| 479 | Column( "workflow_step_id", Integer, ForeignKey("workflow_step.id"), index=True, nullable=False), |
---|
| 480 | Column( "output_name", String(255), nullable=True) |
---|
| 481 | ) |
---|
| 482 | |
---|
| 483 | WorkflowInvocation.table = Table( "workflow_invocation", metadata, |
---|
| 484 | Column( "id", Integer, primary_key=True ), |
---|
| 485 | Column( "create_time", DateTime, default=now ), |
---|
| 486 | Column( "update_time", DateTime, default=now, onupdate=now ), |
---|
| 487 | Column( "workflow_id", Integer, ForeignKey( "workflow.id" ), index=True, nullable=False ) |
---|
| 488 | ) |
---|
| 489 | |
---|
| 490 | WorkflowInvocationStep.table = Table( "workflow_invocation_step", metadata, |
---|
| 491 | Column( "id", Integer, primary_key=True ), |
---|
| 492 | Column( "create_time", DateTime, default=now ), |
---|
| 493 | Column( "update_time", DateTime, default=now, onupdate=now ), |
---|
| 494 | Column( "workflow_invocation_id", Integer, ForeignKey( "workflow_invocation.id" ), index=True, nullable=False ), |
---|
| 495 | Column( "workflow_step_id", Integer, ForeignKey( "workflow_step.id" ), index=True, nullable=False ), |
---|
| 496 | Column( "job_id", Integer, ForeignKey( "job.id" ), index=True, nullable=True ) |
---|
| 497 | ) |
---|
| 498 | |
---|
| 499 | StoredWorkflowUserShareAssociation.table = Table( "stored_workflow_user_share_connection", metadata, |
---|
| 500 | Column( "id", Integer, primary_key=True ), |
---|
| 501 | Column( "stored_workflow_id", Integer, ForeignKey( "stored_workflow.id" ), index=True ), |
---|
| 502 | Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ) |
---|
| 503 | ) |
---|
| 504 | |
---|
| 505 | StoredWorkflowMenuEntry.table = Table( "stored_workflow_menu_entry", metadata, |
---|
| 506 | Column( "id", Integer, primary_key=True ), |
---|
| 507 | Column( "stored_workflow_id", Integer, ForeignKey( "stored_workflow.id" ), index=True ), |
---|
| 508 | Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), |
---|
| 509 | Column( "order_index", Integer ) ) |
---|
| 510 | |
---|
| 511 | MetadataFile.table = Table( "metadata_file", metadata, |
---|
| 512 | Column( "id", Integer, primary_key=True ), |
---|
| 513 | Column( "name", TEXT ), |
---|
| 514 | Column( "hda_id", Integer, ForeignKey( "history_dataset_association.id" ), index=True, nullable=True ), |
---|
| 515 | Column( "lda_id", Integer, ForeignKey( "library_dataset_dataset_association.id" ), index=True, nullable=True ), |
---|
| 516 | Column( "create_time", DateTime, default=now ), |
---|
| 517 | Column( "update_time", DateTime, index=True, default=now, onupdate=now ), |
---|
| 518 | Column( "deleted", Boolean, index=True, default=False ), |
---|
| 519 | Column( "purged", Boolean, index=True, default=False ) ) |
---|
| 520 | |
---|
| 521 | FormDefinitionCurrent.table = Table('form_definition_current', metadata, |
---|
| 522 | Column( "id", Integer, primary_key=True), |
---|
| 523 | Column( "create_time", DateTime, default=now ), |
---|
| 524 | Column( "update_time", DateTime, default=now, onupdate=now ), |
---|
| 525 | Column( "latest_form_id", Integer, ForeignKey( "form_definition.id" ), index=True ), |
---|
| 526 | Column( "deleted", Boolean, index=True, default=False )) |
---|
| 527 | |
---|
| 528 | FormDefinition.table = Table('form_definition', metadata, |
---|
| 529 | Column( "id", Integer, primary_key=True), |
---|
| 530 | Column( "create_time", DateTime, default=now ), |
---|
| 531 | Column( "update_time", DateTime, default=now, onupdate=now ), |
---|
| 532 | Column( "name", TrimmedString( 255 ), nullable=False ), |
---|
| 533 | Column( "desc", TEXT ), |
---|
| 534 | Column( "form_definition_current_id", |
---|
| 535 | Integer, |
---|
| 536 | ForeignKey( "form_definition_current.id", name='for_def_form_def_current_id_fk', use_alter=True ), |
---|
| 537 | index=True ), |
---|
| 538 | Column( "fields", JSONType() ), |
---|
| 539 | Column( "type", TrimmedString( 255 ), index=True ), |
---|
| 540 | Column( "layout", JSONType() ), ) |
---|
| 541 | |
---|
| 542 | RequestType.table = Table('request_type', metadata, |
---|
| 543 | Column( "id", Integer, primary_key=True), |
---|
| 544 | Column( "create_time", DateTime, default=now ), |
---|
| 545 | Column( "update_time", DateTime, default=now, onupdate=now ), |
---|
| 546 | Column( "name", TrimmedString( 255 ), nullable=False ), |
---|
| 547 | Column( "desc", TEXT ), |
---|
| 548 | Column( "request_form_id", Integer, ForeignKey( "form_definition.id" ), index=True ), |
---|
| 549 | Column( "sample_form_id", Integer, ForeignKey( "form_definition.id" ), index=True ), |
---|
| 550 | Column( "datatx_info", JSONType() ), |
---|
| 551 | Column( "deleted", Boolean, index=True, default=False ) ) |
---|
| 552 | |
---|
| 553 | RequestTypePermissions.table = Table( "request_type_permissions", metadata, |
---|
| 554 | Column( "id", Integer, primary_key=True ), |
---|
| 555 | Column( "create_time", DateTime, default=now ), |
---|
| 556 | Column( "update_time", DateTime, default=now, onupdate=now ), |
---|
| 557 | Column( "action", TEXT ), |
---|
| 558 | Column( "request_type_id", Integer, ForeignKey( "request_type.id" ), nullable=True, index=True ), |
---|
| 559 | Column( "role_id", Integer, ForeignKey( "role.id" ), index=True ) ) |
---|
| 560 | |
---|
| 561 | FormValues.table = Table('form_values', metadata, |
---|
| 562 | Column( "id", Integer, primary_key=True), |
---|
| 563 | Column( "create_time", DateTime, default=now ), |
---|
| 564 | Column( "update_time", DateTime, default=now, onupdate=now ), |
---|
| 565 | Column( "form_definition_id", Integer, ForeignKey( "form_definition.id" ), index=True ), |
---|
| 566 | Column( "content", JSONType()) ) |
---|
| 567 | |
---|
| 568 | Request.table = Table('request', metadata, |
---|
| 569 | Column( "id", Integer, primary_key=True), |
---|
| 570 | Column( "create_time", DateTime, default=now ), |
---|
| 571 | Column( "update_time", DateTime, default=now, onupdate=now ), |
---|
| 572 | Column( "name", TrimmedString( 255 ), nullable=False ), |
---|
| 573 | Column( "desc", TEXT ), |
---|
| 574 | Column( "notification", JSONType() ), |
---|
| 575 | Column( "form_values_id", Integer, ForeignKey( "form_values.id" ), index=True ), |
---|
| 576 | Column( "request_type_id", Integer, ForeignKey( "request_type.id" ), index=True ), |
---|
| 577 | Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), |
---|
| 578 | Column( "deleted", Boolean, index=True, default=False ) ) |
---|
| 579 | |
---|
| 580 | RequestEvent.table = Table('request_event', metadata, |
---|
| 581 | Column( "id", Integer, primary_key=True), |
---|
| 582 | Column( "create_time", DateTime, default=now ), |
---|
| 583 | Column( "update_time", DateTime, default=now, onupdate=now ), |
---|
| 584 | Column( "request_id", Integer, ForeignKey( "request.id" ), index=True ), |
---|
| 585 | Column( "state", TrimmedString( 255 ), index=True ), |
---|
| 586 | Column( "comment", TEXT ) ) |
---|
| 587 | |
---|
| 588 | Sample.table = Table('sample', metadata, |
---|
| 589 | Column( "id", Integer, primary_key=True ), |
---|
| 590 | Column( "create_time", DateTime, default=now ), |
---|
| 591 | Column( "update_time", DateTime, default=now, onupdate=now ), |
---|
| 592 | Column( "name", TrimmedString( 255 ), nullable=False ), |
---|
| 593 | Column( "desc", TEXT ), |
---|
| 594 | Column( "form_values_id", Integer, ForeignKey( "form_values.id" ), index=True ), |
---|
| 595 | Column( "request_id", Integer, ForeignKey( "request.id" ), index=True ), |
---|
| 596 | Column( "bar_code", TrimmedString( 255 ), index=True ), |
---|
| 597 | Column( "library_id", Integer, ForeignKey( "library.id" ), index=True ), |
---|
| 598 | Column( "folder_id", Integer, ForeignKey( "library_folder.id" ), index=True ), |
---|
| 599 | Column( "deleted", Boolean, index=True, default=False ) ) |
---|
| 600 | |
---|
| 601 | SampleState.table = Table('sample_state', metadata, |
---|
| 602 | Column( "id", Integer, primary_key=True ), |
---|
| 603 | Column( "create_time", DateTime, default=now ), |
---|
| 604 | Column( "update_time", DateTime, default=now, onupdate=now ), |
---|
| 605 | Column( "name", TrimmedString( 255 ), nullable=False ), |
---|
| 606 | Column( "desc", TEXT ), |
---|
| 607 | Column( "request_type_id", Integer, ForeignKey( "request_type.id" ), index=True ) ) |
---|
| 608 | |
---|
| 609 | SampleEvent.table = Table('sample_event', metadata, |
---|
| 610 | Column( "id", Integer, primary_key=True ), |
---|
| 611 | Column( "create_time", DateTime, default=now ), |
---|
| 612 | Column( "update_time", DateTime, default=now, onupdate=now ), |
---|
| 613 | Column( "sample_id", Integer, ForeignKey( "sample.id" ), index=True ), |
---|
| 614 | Column( "sample_state_id", Integer, ForeignKey( "sample_state.id" ), index=True ), |
---|
| 615 | Column( "comment", TEXT ) ) |
---|
| 616 | |
---|
| 617 | SampleDataset.table = Table('sample_dataset', metadata, |
---|
| 618 | Column( "id", Integer, primary_key=True ), |
---|
| 619 | Column( "create_time", DateTime, default=now ), |
---|
| 620 | Column( "update_time", DateTime, default=now, onupdate=now ), |
---|
| 621 | Column( "sample_id", Integer, ForeignKey( "sample.id" ), index=True ), |
---|
| 622 | Column( "name", TrimmedString( 255 ), nullable=False ), |
---|
| 623 | Column( "file_path", TEXT ), |
---|
| 624 | Column( "status", TrimmedString( 255 ), nullable=False ), |
---|
| 625 | Column( "error_msg", TEXT ), |
---|
| 626 | Column( "size", TrimmedString( 255 ) ) ) |
---|
| 627 | |
---|
| 628 | Page.table = Table( "page", metadata, |
---|
| 629 | Column( "id", Integer, primary_key=True ), |
---|
| 630 | Column( "create_time", DateTime, default=now ), |
---|
| 631 | Column( "update_time", DateTime, default=now, onupdate=now ), |
---|
| 632 | Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True, nullable=False ), |
---|
| 633 | Column( "latest_revision_id", Integer, |
---|
| 634 | ForeignKey( "page_revision.id", use_alter=True, name='page_latest_revision_id_fk' ), index=True ), |
---|
| 635 | Column( "title", TEXT ), |
---|
| 636 | Column( "slug", TEXT, unique=True, index=True ), |
---|
| 637 | Column( "importable", Boolean, index=True, default=False ), |
---|
| 638 | Column( "published", Boolean, index=True, default=False ), |
---|
| 639 | Column( "deleted", Boolean, index=True, default=False ), |
---|
| 640 | ) |
---|
| 641 | |
---|
| 642 | PageRevision.table = Table( "page_revision", metadata, |
---|
| 643 | Column( "id", Integer, primary_key=True ), |
---|
| 644 | Column( "create_time", DateTime, default=now ), |
---|
| 645 | Column( "update_time", DateTime, default=now, onupdate=now ), |
---|
| 646 | Column( "page_id", Integer, ForeignKey( "page.id" ), index=True, nullable=False ), |
---|
| 647 | Column( "title", TEXT ), |
---|
| 648 | Column( "content", TEXT ) |
---|
| 649 | ) |
---|
| 650 | |
---|
| 651 | PageUserShareAssociation.table = Table( "page_user_share_association", metadata, |
---|
| 652 | Column( "id", Integer, primary_key=True ), |
---|
| 653 | Column( "page_id", Integer, ForeignKey( "page.id" ), index=True ), |
---|
| 654 | Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ) |
---|
| 655 | ) |
---|
| 656 | |
---|
| 657 | Visualization.table = Table( "visualization", metadata, |
---|
| 658 | Column( "id", Integer, primary_key=True ), |
---|
| 659 | Column( "create_time", DateTime, default=now ), |
---|
| 660 | Column( "update_time", DateTime, default=now, onupdate=now ), |
---|
| 661 | Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True, nullable=False ), |
---|
| 662 | Column( "latest_revision_id", Integer, |
---|
| 663 | ForeignKey( "visualization_revision.id", use_alter=True, name='visualization_latest_revision_id_fk' ), index=True ), |
---|
| 664 | Column( "title", TEXT ), |
---|
| 665 | Column( "type", TEXT ), |
---|
| 666 | Column( "dbkey", TEXT, index=True ), |
---|
| 667 | Column( "deleted", Boolean, default=False, index=True ), |
---|
| 668 | Column( "importable", Boolean, default=False, index=True ), |
---|
| 669 | Column( "slug", TEXT, index=True ), |
---|
| 670 | Column( "published", Boolean, default=False, index=True ) |
---|
| 671 | ) |
---|
| 672 | |
---|
| 673 | VisualizationRevision.table = Table( "visualization_revision", metadata, |
---|
| 674 | Column( "id", Integer, primary_key=True ), |
---|
| 675 | Column( "create_time", DateTime, default=now ), |
---|
| 676 | Column( "update_time", DateTime, default=now, onupdate=now ), |
---|
| 677 | Column( "visualization_id", Integer, ForeignKey( "visualization.id" ), index=True, nullable=False ), |
---|
| 678 | Column( "title", TEXT ), |
---|
| 679 | Column( "dbkey", TEXT, index=True ), |
---|
| 680 | Column( "config", JSONType ) |
---|
| 681 | ) |
---|
| 682 | |
---|
| 683 | VisualizationUserShareAssociation.table = Table( "visualization_user_share_association", metadata, |
---|
| 684 | Column( "id", Integer, primary_key=True ), |
---|
| 685 | Column( "visualization_id", Integer, ForeignKey( "visualization.id" ), index=True ), |
---|
| 686 | Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ) |
---|
| 687 | ) |
---|
| 688 | |
---|
| 689 | # Tagging tables. |
---|
| 690 | |
---|
| 691 | Tag.table = Table( "tag", metadata, |
---|
| 692 | Column( "id", Integer, primary_key=True ), |
---|
| 693 | Column( "type", Integer ), |
---|
| 694 | Column( "parent_id", Integer, ForeignKey( "tag.id" ) ), |
---|
| 695 | Column( "name", TrimmedString(255) ), |
---|
| 696 | UniqueConstraint( "name" ) ) |
---|
| 697 | |
---|
| 698 | HistoryTagAssociation.table = Table( "history_tag_association", metadata, |
---|
| 699 | Column( "id", Integer, primary_key=True ), |
---|
| 700 | Column( "history_id", Integer, ForeignKey( "history.id" ), index=True ), |
---|
| 701 | Column( "tag_id", Integer, ForeignKey( "tag.id" ), index=True ), |
---|
| 702 | Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), |
---|
| 703 | Column( "user_tname", TrimmedString(255), index=True), |
---|
| 704 | Column( "value", TrimmedString(255), index=True), |
---|
| 705 | Column( "user_value", TrimmedString(255), index=True) ) |
---|
| 706 | |
---|
| 707 | DatasetTagAssociation.table = Table( "dataset_tag_association", metadata, |
---|
| 708 | Column( "id", Integer, primary_key=True ), |
---|
| 709 | Column( "dataset_id", Integer, ForeignKey( "dataset.id" ), index=True ), |
---|
| 710 | Column( "tag_id", Integer, ForeignKey( "tag.id" ), index=True ), |
---|
| 711 | Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), |
---|
| 712 | Column( "user_tname", TrimmedString(255), index=True), |
---|
| 713 | Column( "value", TrimmedString(255), index=True), |
---|
| 714 | Column( "user_value", TrimmedString(255), index=True) ) |
---|
| 715 | |
---|
| 716 | HistoryDatasetAssociationTagAssociation.table = Table( "history_dataset_association_tag_association", metadata, |
---|
| 717 | Column( "id", Integer, primary_key=True ), |
---|
| 718 | Column( "history_dataset_association_id", Integer, ForeignKey( "history_dataset_association.id" ), index=True ), |
---|
| 719 | Column( "tag_id", Integer, ForeignKey( "tag.id" ), index=True ), |
---|
| 720 | Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), |
---|
| 721 | Column( "user_tname", TrimmedString(255), index=True), |
---|
| 722 | Column( "value", TrimmedString(255), index=True), |
---|
| 723 | Column( "user_value", TrimmedString(255), index=True) ) |
---|
| 724 | |
---|
| 725 | StoredWorkflowTagAssociation.table = Table( "stored_workflow_tag_association", metadata, |
---|
| 726 | Column( "id", Integer, primary_key=True ), |
---|
| 727 | Column( "stored_workflow_id", Integer, ForeignKey( "stored_workflow.id" ), index=True ), |
---|
| 728 | Column( "tag_id", Integer, ForeignKey( "tag.id" ), index=True ), |
---|
| 729 | Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), |
---|
| 730 | Column( "user_tname", Unicode(255), index=True), |
---|
| 731 | Column( "value", Unicode(255), index=True), |
---|
| 732 | Column( "user_value", Unicode(255), index=True) ) |
---|
| 733 | |
---|
| 734 | PageTagAssociation.table = Table( "page_tag_association", metadata, |
---|
| 735 | Column( "id", Integer, primary_key=True ), |
---|
| 736 | Column( "page_id", Integer, ForeignKey( "page.id" ), index=True ), |
---|
| 737 | Column( "tag_id", Integer, ForeignKey( "tag.id" ), index=True ), |
---|
| 738 | Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), |
---|
| 739 | Column( "user_tname", TrimmedString(255), index=True), |
---|
| 740 | Column( "value", TrimmedString(255), index=True), |
---|
| 741 | Column( "user_value", TrimmedString(255), index=True) ) |
---|
| 742 | |
---|
| 743 | WorkflowStepTagAssociation.table = Table( "workflow_step_tag_association", metadata, |
---|
| 744 | Column( "id", Integer, primary_key=True ), |
---|
| 745 | Column( "workflow_step_id", Integer, ForeignKey( "workflow_step.id" ), index=True ), |
---|
| 746 | Column( "tag_id", Integer, ForeignKey( "tag.id" ), index=True ), |
---|
| 747 | Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), |
---|
| 748 | Column( "user_tname", Unicode(255), index=True), |
---|
| 749 | Column( "value", Unicode(255), index=True), |
---|
| 750 | Column( "user_value", Unicode(255), index=True) ) |
---|
| 751 | |
---|
| 752 | VisualizationTagAssociation.table = Table( "visualization_tag_association", metadata, |
---|
| 753 | Column( "id", Integer, primary_key=True ), |
---|
| 754 | Column( "visualization_id", Integer, ForeignKey( "visualization.id" ), index=True ), |
---|
| 755 | Column( "tag_id", Integer, ForeignKey( "tag.id" ), index=True ), |
---|
| 756 | Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), |
---|
| 757 | Column( "user_tname", TrimmedString(255), index=True), |
---|
| 758 | Column( "value", TrimmedString(255), index=True), |
---|
| 759 | Column( "user_value", TrimmedString(255), index=True) ) |
---|
| 760 | |
---|
| 761 | # Annotation tables. |
---|
| 762 | |
---|
| 763 | HistoryAnnotationAssociation.table = Table( "history_annotation_association", metadata, |
---|
| 764 | Column( "id", Integer, primary_key=True ), |
---|
| 765 | Column( "history_id", Integer, ForeignKey( "history.id" ), index=True ), |
---|
| 766 | Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), |
---|
| 767 | Column( "annotation", TEXT, index=True) ) |
---|
| 768 | |
---|
| 769 | HistoryDatasetAssociationAnnotationAssociation.table = Table( "history_dataset_association_annotation_association", metadata, |
---|
| 770 | Column( "id", Integer, primary_key=True ), |
---|
| 771 | Column( "history_dataset_association_id", Integer, ForeignKey( "history_dataset_association.id" ), index=True ), |
---|
| 772 | Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), |
---|
| 773 | Column( "annotation", TEXT, index=True) ) |
---|
| 774 | |
---|
| 775 | StoredWorkflowAnnotationAssociation.table = Table( "stored_workflow_annotation_association", metadata, |
---|
| 776 | Column( "id", Integer, primary_key=True ), |
---|
| 777 | Column( "stored_workflow_id", Integer, ForeignKey( "stored_workflow.id" ), index=True ), |
---|
| 778 | Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), |
---|
| 779 | Column( "annotation", TEXT, index=True) ) |
---|
| 780 | |
---|
| 781 | WorkflowStepAnnotationAssociation.table = Table( "workflow_step_annotation_association", metadata, |
---|
| 782 | Column( "id", Integer, primary_key=True ), |
---|
| 783 | Column( "workflow_step_id", Integer, ForeignKey( "workflow_step.id" ), index=True ), |
---|
| 784 | Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), |
---|
| 785 | Column( "annotation", TEXT, index=True) ) |
---|
| 786 | |
---|
| 787 | PageAnnotationAssociation.table = Table( "page_annotation_association", metadata, |
---|
| 788 | Column( "id", Integer, primary_key=True ), |
---|
| 789 | Column( "page_id", Integer, ForeignKey( "page.id" ), index=True ), |
---|
| 790 | Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), |
---|
| 791 | Column( "annotation", TEXT, index=True) ) |
---|
| 792 | |
---|
| 793 | VisualizationAnnotationAssociation.table = Table( "visualization_annotation_association", metadata, |
---|
| 794 | Column( "id", Integer, primary_key=True ), |
---|
| 795 | Column( "visualization_id", Integer, ForeignKey( "visualization.id" ), index=True ), |
---|
| 796 | Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), |
---|
| 797 | Column( "annotation", TEXT, index=True) ) |
---|
| 798 | |
---|
| 799 | # Ratings tables. |
---|
| 800 | HistoryRatingAssociation.table = Table( "history_rating_association", metadata, |
---|
| 801 | Column( "id", Integer, primary_key=True ), |
---|
| 802 | Column( "history_id", Integer, ForeignKey( "history.id" ), index=True ), |
---|
| 803 | Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), |
---|
| 804 | Column( "rating", Integer, index=True) ) |
---|
| 805 | |
---|
| 806 | HistoryDatasetAssociationRatingAssociation.table = Table( "history_dataset_association_rating_association", metadata, |
---|
| 807 | Column( "id", Integer, primary_key=True ), |
---|
| 808 | Column( "history_dataset_association_id", Integer, ForeignKey( "history_dataset_association.id" ), index=True ), |
---|
| 809 | Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), |
---|
| 810 | Column( "rating", Integer, index=True) ) |
---|
| 811 | |
---|
| 812 | StoredWorkflowRatingAssociation.table = Table( "stored_workflow_rating_association", metadata, |
---|
| 813 | Column( "id", Integer, primary_key=True ), |
---|
| 814 | Column( "stored_workflow_id", Integer, ForeignKey( "stored_workflow.id" ), index=True ), |
---|
| 815 | Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), |
---|
| 816 | Column( "rating", Integer, index=True) ) |
---|
| 817 | |
---|
| 818 | PageRatingAssociation.table = Table( "page_rating_association", metadata, |
---|
| 819 | Column( "id", Integer, primary_key=True ), |
---|
| 820 | Column( "page_id", Integer, ForeignKey( "page.id" ), index=True ), |
---|
| 821 | Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), |
---|
| 822 | Column( "rating", Integer, index=True) ) |
---|
| 823 | |
---|
| 824 | VisualizationRatingAssociation.table = Table( "visualization_rating_association", metadata, |
---|
| 825 | Column( "id", Integer, primary_key=True ), |
---|
| 826 | Column( "visualization_id", Integer, ForeignKey( "visualization.id" ), index=True ), |
---|
| 827 | Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), |
---|
| 828 | Column( "rating", Integer, index=True) ) |
---|
| 829 | |
---|
| 830 | # User tables. |
---|
| 831 | |
---|
| 832 | UserPreference.table = Table( "user_preference", metadata, |
---|
| 833 | Column( "id", Integer, primary_key=True ), |
---|
| 834 | Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), |
---|
| 835 | Column( "name", Unicode( 255 ), index=True), |
---|
| 836 | Column( "value", Unicode( 1024 ) ) ) |
---|
| 837 | |
---|
| 838 | UserAction.table = Table( "user_action", metadata, |
---|
| 839 | Column( "id", Integer, primary_key=True ), |
---|
| 840 | Column( "create_time", DateTime, default=now ), |
---|
| 841 | Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), |
---|
| 842 | Column( "session_id", Integer, ForeignKey( "galaxy_session.id" ), index=True ), |
---|
| 843 | Column( "action", Unicode( 255 ) ), |
---|
| 844 | Column( "context", Unicode( 512 ) ), |
---|
| 845 | Column( "params", Unicode( 1024 ) ) ) |
---|
| 846 | |
---|
| 847 | APIKeys.table = Table( "api_keys", metadata, |
---|
| 848 | Column( "id", Integer, primary_key=True ), |
---|
| 849 | Column( "create_time", DateTime, default=now ), |
---|
| 850 | Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), |
---|
| 851 | Column( "key", TrimmedString( 32 ), index=True, unique=True ) ) |
---|
| 852 | |
---|
| 853 | # With the tables defined we can define the mappers and setup the |
---|
| 854 | # relationships between the model objects. |
---|
| 855 | |
---|
| 856 | assign_mapper( context, Sample, Sample.table, |
---|
| 857 | properties=dict( |
---|
| 858 | events=relation( SampleEvent, backref="sample", |
---|
| 859 | order_by=desc( SampleEvent.table.c.update_time ) ), |
---|
| 860 | datasets=relation( SampleDataset, backref="sample", |
---|
| 861 | order_by=desc( SampleDataset.table.c.update_time ) ), |
---|
| 862 | values=relation( FormValues, |
---|
| 863 | primaryjoin=( Sample.table.c.form_values_id == FormValues.table.c.id ) ), |
---|
| 864 | request=relation( Request, |
---|
| 865 | primaryjoin=( Sample.table.c.request_id == Request.table.c.id ) ), |
---|
| 866 | folder=relation( LibraryFolder, |
---|
| 867 | primaryjoin=( Sample.table.c.folder_id == LibraryFolder.table.c.id ) ), |
---|
| 868 | library=relation( Library, |
---|
| 869 | primaryjoin=( Sample.table.c.library_id == Library.table.c.id ) ), |
---|
| 870 | ) ) |
---|
| 871 | |
---|
| 872 | assign_mapper( context, FormValues, FormValues.table, |
---|
| 873 | properties=dict( form_definition=relation( FormDefinition, |
---|
| 874 | primaryjoin=( FormValues.table.c.form_definition_id == FormDefinition.table.c.id ) ) |
---|
| 875 | ) |
---|
| 876 | ) |
---|
| 877 | |
---|
| 878 | assign_mapper( context, Request, Request.table, |
---|
| 879 | properties=dict( values=relation( FormValues, |
---|
| 880 | primaryjoin=( Request.table.c.form_values_id == FormValues.table.c.id ) ), |
---|
| 881 | type=relation( RequestType, |
---|
| 882 | primaryjoin=( Request.table.c.request_type_id == RequestType.table.c.id ) ), |
---|
| 883 | user=relation( User, |
---|
| 884 | primaryjoin=( Request.table.c.user_id == User.table.c.id ), |
---|
| 885 | backref="requests" ), |
---|
| 886 | samples=relation( Sample, |
---|
| 887 | primaryjoin=( Request.table.c.id == Sample.table.c.request_id ), |
---|
| 888 | order_by=asc( Sample.table.c.id ) ), |
---|
| 889 | events=relation( RequestEvent, backref="request", |
---|
| 890 | order_by=desc( RequestEvent.table.c.update_time ) ) |
---|
| 891 | ) ) |
---|
| 892 | |
---|
| 893 | assign_mapper( context, RequestEvent, RequestEvent.table, |
---|
| 894 | properties=None ) |
---|
| 895 | |
---|
| 896 | assign_mapper( context, RequestType, RequestType.table, |
---|
| 897 | properties=dict( states=relation( SampleState, |
---|
| 898 | backref="request_type", |
---|
| 899 | primaryjoin=( RequestType.table.c.id == SampleState.table.c.request_type_id ), |
---|
| 900 | order_by=asc( SampleState.table.c.update_time ) ), |
---|
| 901 | request_form=relation( FormDefinition, |
---|
| 902 | primaryjoin=( RequestType.table.c.request_form_id == FormDefinition.table.c.id ) ), |
---|
| 903 | sample_form=relation( FormDefinition, |
---|
| 904 | primaryjoin=( RequestType.table.c.sample_form_id == FormDefinition.table.c.id ) ), |
---|
| 905 | ) ) |
---|
| 906 | |
---|
| 907 | assign_mapper( context, RequestTypePermissions, RequestTypePermissions.table, |
---|
| 908 | properties=dict( |
---|
| 909 | request_type=relation( RequestType, backref="actions" ), |
---|
| 910 | role=relation( Role, backref="request_type_actions" ) |
---|
| 911 | ) |
---|
| 912 | ) |
---|
| 913 | |
---|
| 914 | assign_mapper( context, FormDefinition, FormDefinition.table, |
---|
| 915 | properties=dict( current=relation( FormDefinitionCurrent, |
---|
| 916 | primaryjoin=( FormDefinition.table.c.form_definition_current_id == FormDefinitionCurrent.table.c.id ) ) |
---|
| 917 | ) ) |
---|
| 918 | assign_mapper( context, FormDefinitionCurrent, FormDefinitionCurrent.table, |
---|
| 919 | properties=dict( forms=relation( FormDefinition, backref='form_definition_current', |
---|
| 920 | cascade="all, delete-orphan", |
---|
| 921 | primaryjoin=( FormDefinitionCurrent.table.c.id == FormDefinition.table.c.form_definition_current_id ) ), |
---|
| 922 | latest_form=relation( FormDefinition, post_update=True, |
---|
| 923 | primaryjoin=( FormDefinitionCurrent.table.c.latest_form_id == FormDefinition.table.c.id ) ) |
---|
| 924 | ) ) |
---|
| 925 | |
---|
| 926 | assign_mapper( context, SampleEvent, SampleEvent.table, |
---|
| 927 | properties=dict( state=relation( SampleState, |
---|
| 928 | primaryjoin=( SampleEvent.table.c.sample_state_id == SampleState.table.c.id ) ), |
---|
| 929 | |
---|
| 930 | ) ) |
---|
| 931 | |
---|
| 932 | assign_mapper( context, SampleState, SampleState.table, |
---|
| 933 | properties=None ) |
---|
| 934 | |
---|
| 935 | assign_mapper( context, SampleDataset, SampleDataset.table, |
---|
| 936 | properties=None ) |
---|
| 937 | |
---|
| 938 | assign_mapper( context, UserAddress, UserAddress.table, |
---|
| 939 | properties=dict( |
---|
| 940 | user=relation( User, |
---|
| 941 | primaryjoin=( UserAddress.table.c.user_id == User.table.c.id ), |
---|
| 942 | backref='addresses', |
---|
| 943 | order_by=desc(UserAddress.table.c.update_time)), |
---|
| 944 | ) ) |
---|
| 945 | |
---|
| 946 | |
---|
| 947 | assign_mapper( context, ValidationError, ValidationError.table ) |
---|
| 948 | |
---|
| 949 | assign_mapper( context, HistoryDatasetAssociation, HistoryDatasetAssociation.table, |
---|
| 950 | properties=dict( |
---|
| 951 | dataset=relation( |
---|
| 952 | Dataset, |
---|
| 953 | primaryjoin=( Dataset.table.c.id == HistoryDatasetAssociation.table.c.dataset_id ), lazy=False ), |
---|
| 954 | # .history defined in History mapper |
---|
| 955 | copied_to_history_dataset_associations=relation( |
---|
| 956 | HistoryDatasetAssociation, |
---|
| 957 | primaryjoin=( HistoryDatasetAssociation.table.c.copied_from_history_dataset_association_id == HistoryDatasetAssociation.table.c.id ), |
---|
| 958 | backref=backref( "copied_from_history_dataset_association", primaryjoin=( HistoryDatasetAssociation.table.c.copied_from_history_dataset_association_id == HistoryDatasetAssociation.table.c.id ), remote_side=[HistoryDatasetAssociation.table.c.id], uselist=False ) ), |
---|
| 959 | copied_to_library_dataset_dataset_associations=relation( |
---|
| 960 | LibraryDatasetDatasetAssociation, |
---|
| 961 | primaryjoin=( HistoryDatasetAssociation.table.c.copied_from_library_dataset_dataset_association_id == LibraryDatasetDatasetAssociation.table.c.id ), |
---|
| 962 | backref=backref( "copied_from_history_dataset_association", primaryjoin=( HistoryDatasetAssociation.table.c.copied_from_library_dataset_dataset_association_id == LibraryDatasetDatasetAssociation.table.c.id ), remote_side=[LibraryDatasetDatasetAssociation.table.c.id], uselist=False ) ), |
---|
| 963 | implicitly_converted_datasets=relation( |
---|
| 964 | ImplicitlyConvertedDatasetAssociation, |
---|
| 965 | primaryjoin=( ImplicitlyConvertedDatasetAssociation.table.c.hda_parent_id == HistoryDatasetAssociation.table.c.id ) ), |
---|
| 966 | children=relation( |
---|
| 967 | HistoryDatasetAssociation, |
---|
| 968 | primaryjoin=( HistoryDatasetAssociation.table.c.parent_id == HistoryDatasetAssociation.table.c.id ), |
---|
| 969 | backref=backref( "parent", primaryjoin=( HistoryDatasetAssociation.table.c.parent_id == HistoryDatasetAssociation.table.c.id ), remote_side=[HistoryDatasetAssociation.table.c.id], uselist=False ) ), |
---|
| 970 | visible_children=relation( |
---|
| 971 | HistoryDatasetAssociation, |
---|
| 972 | primaryjoin=( ( HistoryDatasetAssociation.table.c.parent_id == HistoryDatasetAssociation.table.c.id ) & ( HistoryDatasetAssociation.table.c.visible == True ) ) ), |
---|
| 973 | tags=relation( HistoryDatasetAssociationTagAssociation, order_by=HistoryDatasetAssociationTagAssociation.table.c.id, backref='history_tag_associations' ), |
---|
| 974 | annotations=relation( HistoryDatasetAssociationAnnotationAssociation, order_by=HistoryDatasetAssociationAnnotationAssociation.table.c.id, backref="hdas" ), |
---|
| 975 | ratings=relation( HistoryDatasetAssociationRatingAssociation, order_by=HistoryDatasetAssociationRatingAssociation.table.c.id, backref="hdas" ) ) |
---|
| 976 | ) |
---|
| 977 | |
---|
| 978 | assign_mapper( context, Dataset, Dataset.table, |
---|
| 979 | properties=dict( |
---|
| 980 | history_associations=relation( |
---|
| 981 | HistoryDatasetAssociation, |
---|
| 982 | primaryjoin=( Dataset.table.c.id == HistoryDatasetAssociation.table.c.dataset_id ) ), |
---|
| 983 | active_history_associations=relation( |
---|
| 984 | HistoryDatasetAssociation, |
---|
| 985 | primaryjoin=( ( Dataset.table.c.id == HistoryDatasetAssociation.table.c.dataset_id ) & ( HistoryDatasetAssociation.table.c.deleted == False ) ) ), |
---|
| 986 | library_associations=relation( |
---|
| 987 | LibraryDatasetDatasetAssociation, |
---|
| 988 | primaryjoin=( Dataset.table.c.id == LibraryDatasetDatasetAssociation.table.c.dataset_id ) ), |
---|
| 989 | active_library_associations=relation( |
---|
| 990 | LibraryDatasetDatasetAssociation, |
---|
| 991 | primaryjoin=( ( Dataset.table.c.id == LibraryDatasetDatasetAssociation.table.c.dataset_id ) & ( LibraryDatasetDatasetAssociation.table.c.deleted == False ) ) ), |
---|
| 992 | tags=relation(DatasetTagAssociation, order_by=DatasetTagAssociation.table.c.id, backref='datasets') |
---|
| 993 | ) ) |
---|
| 994 | |
---|
| 995 | assign_mapper( context, HistoryDatasetAssociationDisplayAtAuthorization, HistoryDatasetAssociationDisplayAtAuthorization.table, |
---|
| 996 | properties=dict( history_dataset_association = relation( HistoryDatasetAssociation ), |
---|
| 997 | user = relation( User ) ) ) |
---|
| 998 | |
---|
| 999 | assign_mapper( context, ImplicitlyConvertedDatasetAssociation, ImplicitlyConvertedDatasetAssociation.table, |
---|
| 1000 | properties=dict( parent=relation( |
---|
| 1001 | HistoryDatasetAssociation, |
---|
| 1002 | primaryjoin=( ImplicitlyConvertedDatasetAssociation.table.c.hda_parent_id == HistoryDatasetAssociation.table.c.id ) ), |
---|
| 1003 | |
---|
| 1004 | dataset=relation( |
---|
| 1005 | HistoryDatasetAssociation, |
---|
| 1006 | primaryjoin=( ImplicitlyConvertedDatasetAssociation.table.c.hda_id == HistoryDatasetAssociation.table.c.id ) ) ) ) |
---|
| 1007 | |
---|
| 1008 | assign_mapper( context, History, History.table, |
---|
| 1009 | properties=dict( galaxy_sessions=relation( GalaxySessionToHistoryAssociation ), |
---|
| 1010 | datasets=relation( HistoryDatasetAssociation, backref="history", order_by=asc(HistoryDatasetAssociation.table.c.hid) ), |
---|
| 1011 | active_datasets=relation( HistoryDatasetAssociation, primaryjoin=( ( HistoryDatasetAssociation.table.c.history_id == History.table.c.id ) & ( not_( HistoryDatasetAssociation.table.c.deleted ) ) ), order_by=asc( HistoryDatasetAssociation.table.c.hid ), viewonly=True ), |
---|
| 1012 | tags=relation( HistoryTagAssociation, order_by=HistoryTagAssociation.table.c.id, backref="histories" ), |
---|
| 1013 | annotations=relation( HistoryAnnotationAssociation, order_by=HistoryAnnotationAssociation.table.c.id, backref="histories" ), |
---|
| 1014 | ratings=relation( HistoryRatingAssociation, order_by=HistoryRatingAssociation.table.c.id, backref="histories" ) ) |
---|
| 1015 | ) |
---|
| 1016 | |
---|
| 1017 | # Set up proxy so that |
---|
| 1018 | # History.users_shared_with |
---|
| 1019 | # returns a list of users that history is shared with. |
---|
| 1020 | History.users_shared_with_dot_users = association_proxy( 'users_shared_with', 'user' ) |
---|
| 1021 | |
---|
| 1022 | assign_mapper( context, HistoryUserShareAssociation, HistoryUserShareAssociation.table, |
---|
| 1023 | properties=dict( user=relation( User, backref='histories_shared_by_others' ), |
---|
| 1024 | history=relation( History, backref='users_shared_with' ) |
---|
| 1025 | ) ) |
---|
| 1026 | |
---|
| 1027 | assign_mapper( context, User, User.table, |
---|
| 1028 | properties=dict( histories=relation( History, backref="user", |
---|
| 1029 | order_by=desc(History.table.c.update_time) ), |
---|
| 1030 | active_histories=relation( History, primaryjoin=( ( History.table.c.user_id == User.table.c.id ) & ( not_( History.table.c.deleted ) ) ), order_by=desc( History.table.c.update_time ) ), |
---|
| 1031 | galaxy_sessions=relation( GalaxySession, order_by=desc( GalaxySession.table.c.update_time ) ), |
---|
| 1032 | stored_workflow_menu_entries=relation( StoredWorkflowMenuEntry, backref="user", |
---|
| 1033 | cascade="all, delete-orphan", |
---|
| 1034 | collection_class=ordering_list( 'order_index' ) ), |
---|
| 1035 | _preferences=relation( UserPreference, backref="user", collection_class=attribute_mapped_collection('name')), |
---|
| 1036 | # addresses=relation( UserAddress, |
---|
| 1037 | # primaryjoin=( User.table.c.id == UserAddress.table.c.user_id ) ) |
---|
| 1038 | values=relation( FormValues, |
---|
| 1039 | primaryjoin=( User.table.c.form_values_id == FormValues.table.c.id ) ), |
---|
| 1040 | api_keys=relation( APIKeys, backref="user", order_by=desc( APIKeys.table.c.create_time ) ), |
---|
| 1041 | ) ) |
---|
| 1042 | |
---|
| 1043 | # Set up proxy so that this syntax is possible: |
---|
| 1044 | # <user_obj>.preferences[pref_name] = pref_value |
---|
| 1045 | User.preferences = association_proxy('_preferences', 'value', creator=UserPreference) |
---|
| 1046 | |
---|
| 1047 | assign_mapper( context, Group, Group.table, |
---|
| 1048 | properties=dict( users=relation( UserGroupAssociation ) ) ) |
---|
| 1049 | |
---|
| 1050 | assign_mapper( context, UserGroupAssociation, UserGroupAssociation.table, |
---|
| 1051 | properties=dict( user=relation( User, backref = "groups" ), |
---|
| 1052 | group=relation( Group, backref = "members" ) ) ) |
---|
| 1053 | |
---|
| 1054 | assign_mapper( context, DefaultUserPermissions, DefaultUserPermissions.table, |
---|
| 1055 | properties=dict( user=relation( User, backref = "default_permissions" ), |
---|
| 1056 | role=relation( Role ) ) ) |
---|
| 1057 | |
---|
| 1058 | assign_mapper( context, DefaultHistoryPermissions, DefaultHistoryPermissions.table, |
---|
| 1059 | properties=dict( history=relation( History, backref = "default_permissions" ), |
---|
| 1060 | role=relation( Role ) ) ) |
---|
| 1061 | |
---|
| 1062 | assign_mapper( context, Role, Role.table, |
---|
| 1063 | properties=dict( |
---|
| 1064 | users=relation( UserRoleAssociation ), |
---|
| 1065 | groups=relation( GroupRoleAssociation ) |
---|
| 1066 | ) |
---|
| 1067 | ) |
---|
| 1068 | |
---|
| 1069 | assign_mapper( context, UserRoleAssociation, UserRoleAssociation.table, |
---|
| 1070 | properties=dict( |
---|
| 1071 | user=relation( User, backref="roles" ), |
---|
| 1072 | non_private_roles=relation( User, |
---|
| 1073 | backref="non_private_roles", |
---|
| 1074 | primaryjoin=( ( User.table.c.id == UserRoleAssociation.table.c.user_id ) & ( UserRoleAssociation.table.c.role_id == Role.table.c.id ) & not_( Role.table.c.name == User.table.c.email ) ) ), |
---|
| 1075 | role=relation( Role ) |
---|
| 1076 | ) |
---|
| 1077 | ) |
---|
| 1078 | |
---|
| 1079 | assign_mapper( context, GroupRoleAssociation, GroupRoleAssociation.table, |
---|
| 1080 | properties=dict( |
---|
| 1081 | group=relation( Group, backref="roles" ), |
---|
| 1082 | role=relation( Role ) |
---|
| 1083 | ) |
---|
| 1084 | ) |
---|
| 1085 | |
---|
| 1086 | assign_mapper( context, DatasetPermissions, DatasetPermissions.table, |
---|
| 1087 | properties=dict( |
---|
| 1088 | dataset=relation( Dataset, backref="actions" ), |
---|
| 1089 | role=relation( Role, backref="dataset_actions" ) |
---|
| 1090 | ) |
---|
| 1091 | ) |
---|
| 1092 | |
---|
| 1093 | assign_mapper( context, LibraryPermissions, LibraryPermissions.table, |
---|
| 1094 | properties=dict( |
---|
| 1095 | library=relation( Library, backref="actions" ), |
---|
| 1096 | role=relation( Role, backref="library_actions" ) |
---|
| 1097 | ) |
---|
| 1098 | ) |
---|
| 1099 | |
---|
| 1100 | assign_mapper( context, LibraryFolderPermissions, LibraryFolderPermissions.table, |
---|
| 1101 | properties=dict( |
---|
| 1102 | folder=relation( LibraryFolder, backref="actions" ), |
---|
| 1103 | role=relation( Role, backref="library_folder_actions" ) |
---|
| 1104 | ) |
---|
| 1105 | ) |
---|
| 1106 | |
---|
| 1107 | assign_mapper( context, LibraryDatasetPermissions, LibraryDatasetPermissions.table, |
---|
| 1108 | properties=dict( |
---|
| 1109 | library_dataset=relation( LibraryDataset, backref="actions" ), |
---|
| 1110 | role=relation( Role, backref="library_dataset_actions" ) |
---|
| 1111 | ) |
---|
| 1112 | ) |
---|
| 1113 | |
---|
| 1114 | assign_mapper( context, LibraryDatasetDatasetAssociationPermissions, LibraryDatasetDatasetAssociationPermissions.table, |
---|
| 1115 | properties=dict( |
---|
| 1116 | library_dataset_dataset_association = relation( LibraryDatasetDatasetAssociation, backref="actions" ), |
---|
| 1117 | role=relation( Role, backref="library_dataset_dataset_actions" ) |
---|
| 1118 | ) |
---|
| 1119 | ) |
---|
| 1120 | |
---|
| 1121 | assign_mapper( context, Library, Library.table, |
---|
| 1122 | properties=dict( |
---|
| 1123 | root_folder=relation( LibraryFolder, backref=backref( "library_root" ) ) |
---|
| 1124 | ) |
---|
| 1125 | ) |
---|
| 1126 | |
---|
| 1127 | assign_mapper( context, LibraryInfoAssociation, LibraryInfoAssociation.table, |
---|
| 1128 | properties=dict( library=relation( Library, |
---|
| 1129 | primaryjoin=( ( LibraryInfoAssociation.table.c.library_id == Library.table.c.id ) & ( not_( LibraryInfoAssociation.table.c.deleted ) ) ), backref="info_association" ), |
---|
| 1130 | template=relation( FormDefinition, |
---|
| 1131 | primaryjoin=( LibraryInfoAssociation.table.c.form_definition_id == FormDefinition.table.c.id ) ), |
---|
| 1132 | info=relation( FormValues, |
---|
| 1133 | primaryjoin=( LibraryInfoAssociation.table.c.form_values_id == FormValues.table.c.id ) ) |
---|
| 1134 | ) ) |
---|
| 1135 | |
---|
| 1136 | assign_mapper( context, LibraryFolder, LibraryFolder.table, |
---|
| 1137 | properties=dict( |
---|
| 1138 | folders=relation( |
---|
| 1139 | LibraryFolder, |
---|
| 1140 | primaryjoin=( LibraryFolder.table.c.parent_id == LibraryFolder.table.c.id ), |
---|
| 1141 | order_by=asc( LibraryFolder.table.c.name ), |
---|
| 1142 | backref=backref( "parent", primaryjoin=( LibraryFolder.table.c.parent_id == LibraryFolder.table.c.id ), remote_side=[LibraryFolder.table.c.id] ) ), |
---|
| 1143 | active_folders=relation( LibraryFolder, |
---|
| 1144 | primaryjoin=( ( LibraryFolder.table.c.parent_id == LibraryFolder.table.c.id ) & ( not_( LibraryFolder.table.c.deleted ) ) ), |
---|
| 1145 | order_by=asc( LibraryFolder.table.c.name ), |
---|
| 1146 | lazy=True, #"""sqlalchemy.exceptions.ArgumentError: Error creating eager relationship 'active_folders' on parent class '<class 'galaxy.model.LibraryFolder'>' to child class '<class 'galaxy.model.LibraryFolder'>': Cant use eager loading on a self referential relationship.""" |
---|
| 1147 | viewonly=True ), |
---|
| 1148 | datasets=relation( LibraryDataset, |
---|
| 1149 | primaryjoin=( ( LibraryDataset.table.c.folder_id == LibraryFolder.table.c.id ) ), |
---|
| 1150 | order_by=asc( LibraryDataset.table.c._name ), |
---|
| 1151 | lazy=False, |
---|
| 1152 | viewonly=True ) |
---|
| 1153 | ) ) |
---|
| 1154 | |
---|
| 1155 | assign_mapper( context, LibraryFolderInfoAssociation, LibraryFolderInfoAssociation.table, |
---|
| 1156 | properties=dict( folder=relation( LibraryFolder, |
---|
| 1157 | primaryjoin=( ( LibraryFolderInfoAssociation.table.c.library_folder_id == LibraryFolder.table.c.id ) & ( not_( LibraryFolderInfoAssociation.table.c.deleted ) ) ), backref="info_association" ), |
---|
| 1158 | template=relation( FormDefinition, |
---|
| 1159 | primaryjoin=( LibraryFolderInfoAssociation.table.c.form_definition_id == FormDefinition.table.c.id ) ), |
---|
| 1160 | info=relation( FormValues, |
---|
| 1161 | primaryjoin=( LibraryFolderInfoAssociation.table.c.form_values_id == FormValues.table.c.id ) ) |
---|
| 1162 | ) ) |
---|
| 1163 | |
---|
| 1164 | assign_mapper( context, LibraryDataset, LibraryDataset.table, |
---|
| 1165 | properties=dict( |
---|
| 1166 | folder=relation( LibraryFolder ), |
---|
| 1167 | library_dataset_dataset_association=relation( LibraryDatasetDatasetAssociation, primaryjoin=( LibraryDataset.table.c.library_dataset_dataset_association_id == LibraryDatasetDatasetAssociation.table.c.id ) ), |
---|
| 1168 | expired_datasets = relation( LibraryDatasetDatasetAssociation, foreign_keys=[LibraryDataset.table.c.id,LibraryDataset.table.c.library_dataset_dataset_association_id ], primaryjoin=( ( LibraryDataset.table.c.id == LibraryDatasetDatasetAssociation.table.c.library_dataset_id ) & ( not_( LibraryDataset.table.c.library_dataset_dataset_association_id == LibraryDatasetDatasetAssociation.table.c.id ) ) ), viewonly=True, uselist=True ) |
---|
| 1169 | ) ) |
---|
| 1170 | |
---|
| 1171 | assign_mapper( context, LibraryDatasetDatasetAssociation, LibraryDatasetDatasetAssociation.table, |
---|
| 1172 | properties=dict( |
---|
| 1173 | dataset=relation( Dataset ), |
---|
| 1174 | library_dataset = relation( LibraryDataset, |
---|
| 1175 | primaryjoin=( LibraryDatasetDatasetAssociation.table.c.library_dataset_id == LibraryDataset.table.c.id ) ), |
---|
| 1176 | user=relation( User.mapper ), |
---|
| 1177 | copied_to_library_dataset_dataset_associations=relation( |
---|
| 1178 | LibraryDatasetDatasetAssociation, |
---|
| 1179 | primaryjoin=( LibraryDatasetDatasetAssociation.table.c.copied_from_library_dataset_dataset_association_id == LibraryDatasetDatasetAssociation.table.c.id ), |
---|
| 1180 | backref=backref( "copied_from_library_dataset_dataset_association", primaryjoin=( LibraryDatasetDatasetAssociation.table.c.copied_from_library_dataset_dataset_association_id == LibraryDatasetDatasetAssociation.table.c.id ), remote_side=[LibraryDatasetDatasetAssociation.table.c.id] ) ), |
---|
| 1181 | copied_to_history_dataset_associations=relation( |
---|
| 1182 | HistoryDatasetAssociation, |
---|
| 1183 | primaryjoin=( HistoryDatasetAssociation.table.c.copied_from_library_dataset_dataset_association_id == LibraryDatasetDatasetAssociation.table.c.id ), |
---|
| 1184 | backref=backref( "copied_from_library_dataset_dataset_association", primaryjoin=( HistoryDatasetAssociation.table.c.copied_from_library_dataset_dataset_association_id == LibraryDatasetDatasetAssociation.table.c.id ), remote_side=[LibraryDatasetDatasetAssociation.table.c.id], uselist=False ) ), |
---|
| 1185 | children=relation( |
---|
| 1186 | LibraryDatasetDatasetAssociation, |
---|
| 1187 | primaryjoin=( LibraryDatasetDatasetAssociation.table.c.parent_id == LibraryDatasetDatasetAssociation.table.c.id ), |
---|
| 1188 | backref=backref( "parent", primaryjoin=( LibraryDatasetDatasetAssociation.table.c.parent_id == LibraryDatasetDatasetAssociation.table.c.id ), remote_side=[LibraryDatasetDatasetAssociation.table.c.id] ) ), |
---|
| 1189 | visible_children=relation( |
---|
| 1190 | LibraryDatasetDatasetAssociation, |
---|
| 1191 | primaryjoin=( ( LibraryDatasetDatasetAssociation.table.c.parent_id == LibraryDatasetDatasetAssociation.table.c.id ) & ( LibraryDatasetDatasetAssociation.table.c.visible == True ) ) ) |
---|
| 1192 | ) ) |
---|
| 1193 | |
---|
| 1194 | assign_mapper( context, LibraryDatasetDatasetInfoAssociation, LibraryDatasetDatasetInfoAssociation.table, |
---|
| 1195 | properties=dict( library_dataset_dataset_association=relation( LibraryDatasetDatasetAssociation, |
---|
| 1196 | primaryjoin=( ( LibraryDatasetDatasetInfoAssociation.table.c.library_dataset_dataset_association_id == LibraryDatasetDatasetAssociation.table.c.id ) & ( not_( LibraryDatasetDatasetInfoAssociation.table.c.deleted ) ) ), backref="info_association" ), |
---|
| 1197 | template=relation( FormDefinition, |
---|
| 1198 | primaryjoin=( LibraryDatasetDatasetInfoAssociation.table.c.form_definition_id == FormDefinition.table.c.id ) ), |
---|
| 1199 | info=relation( FormValues, |
---|
| 1200 | primaryjoin=( LibraryDatasetDatasetInfoAssociation.table.c.form_values_id == FormValues.table.c.id ) ) |
---|
| 1201 | ) ) |
---|
| 1202 | |
---|
| 1203 | assign_mapper( context, JobToInputDatasetAssociation, JobToInputDatasetAssociation.table, |
---|
| 1204 | properties=dict( job=relation( Job ), dataset=relation( HistoryDatasetAssociation, lazy=False ) ) ) |
---|
| 1205 | |
---|
| 1206 | assign_mapper( context, JobToOutputDatasetAssociation, JobToOutputDatasetAssociation.table, |
---|
| 1207 | properties=dict( job=relation( Job ), dataset=relation( HistoryDatasetAssociation, lazy=False ) ) ) |
---|
| 1208 | |
---|
| 1209 | assign_mapper( context, JobToOutputLibraryDatasetAssociation, JobToOutputLibraryDatasetAssociation.table, |
---|
| 1210 | properties=dict( job=relation( Job ), dataset=relation( LibraryDatasetDatasetAssociation, lazy=False ) ) ) |
---|
| 1211 | |
---|
| 1212 | assign_mapper( context, JobParameter, JobParameter.table ) |
---|
| 1213 | |
---|
| 1214 | assign_mapper( context, JobExternalOutputMetadata, JobExternalOutputMetadata.table, |
---|
| 1215 | properties=dict( job = relation( Job ), |
---|
| 1216 | history_dataset_association = relation( HistoryDatasetAssociation, lazy = False ), |
---|
| 1217 | library_dataset_dataset_association = relation( LibraryDatasetDatasetAssociation, lazy = False ) ) ) |
---|
| 1218 | |
---|
| 1219 | assign_mapper( context, JobExportHistoryArchive, JobExportHistoryArchive.table, |
---|
| 1220 | properties=dict( job = relation( Job ), |
---|
| 1221 | history = relation( History ), |
---|
| 1222 | dataset = relation( Dataset ) ) ) |
---|
| 1223 | |
---|
| 1224 | assign_mapper( context, PostJobAction, PostJobAction.table, |
---|
| 1225 | properties=dict(workflow_step = relation( WorkflowStep, backref='post_job_actions', primaryjoin=(WorkflowStep.table.c.id == PostJobAction.table.c.workflow_step_id)))) |
---|
| 1226 | |
---|
| 1227 | assign_mapper( context, PostJobActionAssociation, PostJobActionAssociation.table, |
---|
| 1228 | properties=dict( job = relation( Job ), |
---|
| 1229 | post_job_action = relation( PostJobAction) ) ) |
---|
| 1230 | |
---|
| 1231 | assign_mapper( context, Job, Job.table, |
---|
| 1232 | properties=dict( user=relation( User.mapper ), |
---|
| 1233 | galaxy_session=relation( GalaxySession ), |
---|
| 1234 | history=relation( History ), |
---|
| 1235 | library_folder=relation( LibraryFolder ), |
---|
| 1236 | parameters=relation( JobParameter, lazy=False ), |
---|
| 1237 | input_datasets=relation( JobToInputDatasetAssociation, lazy=False ), |
---|
| 1238 | output_datasets=relation( JobToOutputDatasetAssociation, lazy=False ), |
---|
| 1239 | post_job_actions=relation( PostJobActionAssociation, lazy=False ), |
---|
| 1240 | output_library_datasets=relation( JobToOutputLibraryDatasetAssociation, lazy=False ), |
---|
| 1241 | external_output_metadata = relation( JobExternalOutputMetadata, lazy = False ) ) ) |
---|
| 1242 | |
---|
| 1243 | assign_mapper( context, Event, Event.table, |
---|
| 1244 | properties=dict( history=relation( History ), |
---|
| 1245 | galaxy_session=relation( GalaxySession ), |
---|
| 1246 | user=relation( User.mapper ) ) ) |
---|
| 1247 | |
---|
| 1248 | assign_mapper( context, GalaxySession, GalaxySession.table, |
---|
| 1249 | properties=dict( histories=relation( GalaxySessionToHistoryAssociation ), |
---|
| 1250 | current_history=relation( History ), |
---|
| 1251 | user=relation( User.mapper ) ) ) |
---|
| 1252 | |
---|
| 1253 | assign_mapper( context, GalaxySessionToHistoryAssociation, GalaxySessionToHistoryAssociation.table, |
---|
| 1254 | properties=dict( galaxy_session=relation( GalaxySession ), |
---|
| 1255 | history=relation( History ) ) ) |
---|
| 1256 | |
---|
| 1257 | HistoryDatasetAssociation.mapper.add_property( "creating_job_associations", relation( JobToOutputDatasetAssociation ) ) |
---|
| 1258 | |
---|
| 1259 | assign_mapper( context, Workflow, Workflow.table, |
---|
| 1260 | properties=dict( steps=relation( WorkflowStep, backref='workflow', |
---|
| 1261 | order_by=asc(WorkflowStep.table.c.order_index), |
---|
| 1262 | cascade="all, delete-orphan", |
---|
| 1263 | lazy=False ), |
---|
| 1264 | # outputs = relation( WorkflowOutput, backref='workflow', |
---|
| 1265 | # primaryjoin=(Workflow.table.c.id == WorkflowStep.table.c.workflow_id), |
---|
| 1266 | # secondaryjoin=(WorkflowStep.table.c.id == WorkflowOutput.table.c.workflow_step_id)) |
---|
| 1267 | ) ) |
---|
| 1268 | |
---|
| 1269 | assign_mapper( context, WorkflowStep, WorkflowStep.table, |
---|
| 1270 | properties=dict( |
---|
| 1271 | tags=relation(WorkflowStepTagAssociation, order_by=WorkflowStepTagAssociation.table.c.id, backref="workflow_steps"), |
---|
| 1272 | annotations=relation( WorkflowStepAnnotationAssociation, order_by=WorkflowStepAnnotationAssociation.table.c.id, backref="workflow_steps" ) ) |
---|
| 1273 | ) |
---|
| 1274 | |
---|
| 1275 | assign_mapper( context, WorkflowOutput, WorkflowOutput.table, |
---|
| 1276 | properties=dict(workflow_step = relation( WorkflowStep, backref='workflow_outputs', primaryjoin=(WorkflowStep.table.c.id == WorkflowOutput.table.c.workflow_step_id)))) |
---|
| 1277 | |
---|
| 1278 | assign_mapper( context, WorkflowStepConnection, WorkflowStepConnection.table, |
---|
| 1279 | properties=dict( input_step=relation( WorkflowStep, backref="input_connections", cascade="all", |
---|
| 1280 | primaryjoin=( WorkflowStepConnection.table.c.input_step_id == WorkflowStep.table.c.id ) ), |
---|
| 1281 | output_step=relation( WorkflowStep, backref="output_connections", cascade="all", |
---|
| 1282 | primaryjoin=( WorkflowStepConnection.table.c.output_step_id == WorkflowStep.table.c.id ) ) ) ) |
---|
| 1283 | |
---|
| 1284 | |
---|
| 1285 | assign_mapper( context, StoredWorkflow, StoredWorkflow.table, |
---|
| 1286 | properties=dict( user=relation( User, |
---|
| 1287 | primaryjoin=( User.table.c.id == StoredWorkflow.table.c.user_id ), |
---|
| 1288 | backref='stored_workflows' ), |
---|
| 1289 | workflows=relation( Workflow, backref='stored_workflow', |
---|
| 1290 | cascade="all, delete-orphan", |
---|
| 1291 | primaryjoin=( StoredWorkflow.table.c.id == Workflow.table.c.stored_workflow_id ) ), |
---|
| 1292 | latest_workflow=relation( Workflow, post_update=True, |
---|
| 1293 | primaryjoin=( StoredWorkflow.table.c.latest_workflow_id == Workflow.table.c.id ), |
---|
| 1294 | lazy=False ), |
---|
| 1295 | tags=relation( StoredWorkflowTagAssociation, order_by=StoredWorkflowTagAssociation.table.c.id, backref="stored_workflows" ), |
---|
| 1296 | annotations=relation( StoredWorkflowAnnotationAssociation, order_by=StoredWorkflowAnnotationAssociation.table.c.id, backref="stored_workflows" ), |
---|
| 1297 | ratings=relation( StoredWorkflowRatingAssociation, order_by=StoredWorkflowRatingAssociation.table.c.id, backref="stored_workflows" ) ) |
---|
| 1298 | ) |
---|
| 1299 | |
---|
| 1300 | # Set up proxy so that |
---|
| 1301 | # StoredWorkflow.users_shared_with |
---|
| 1302 | # returns a list of users that workflow is shared with. |
---|
| 1303 | StoredWorkflow.users_shared_with_dot_users = association_proxy( 'users_shared_with', 'user' ) |
---|
| 1304 | |
---|
| 1305 | assign_mapper( context, StoredWorkflowUserShareAssociation, StoredWorkflowUserShareAssociation.table, |
---|
| 1306 | properties=dict( user=relation( User, backref='workflows_shared_by_others' ), |
---|
| 1307 | stored_workflow=relation( StoredWorkflow, backref='users_shared_with' ) |
---|
| 1308 | ) ) |
---|
| 1309 | |
---|
| 1310 | assign_mapper( context, StoredWorkflowMenuEntry, StoredWorkflowMenuEntry.table, |
---|
| 1311 | properties=dict( stored_workflow=relation( StoredWorkflow ) ) ) |
---|
| 1312 | |
---|
| 1313 | assign_mapper( context, WorkflowInvocation, WorkflowInvocation.table, |
---|
| 1314 | properties=dict( |
---|
| 1315 | steps=relation( WorkflowInvocationStep, backref='workflow_invocation', lazy=False ), |
---|
| 1316 | workflow=relation( Workflow ) ) ) |
---|
| 1317 | |
---|
| 1318 | assign_mapper( context, WorkflowInvocationStep, WorkflowInvocationStep.table, |
---|
| 1319 | properties=dict( |
---|
| 1320 | workflow_step = relation( WorkflowStep ), |
---|
| 1321 | job = relation( Job, backref=backref( 'workflow_invocation_step', uselist=False ) ) ) ) |
---|
| 1322 | |
---|
| 1323 | assign_mapper( context, MetadataFile, MetadataFile.table, |
---|
| 1324 | properties=dict( history_dataset=relation( HistoryDatasetAssociation ), library_dataset=relation( LibraryDatasetDatasetAssociation ) ) ) |
---|
| 1325 | |
---|
| 1326 | assign_mapper( context, PageRevision, PageRevision.table ) |
---|
| 1327 | |
---|
| 1328 | assign_mapper( context, Page, Page.table, |
---|
| 1329 | properties=dict( user=relation( User ), |
---|
| 1330 | revisions=relation( PageRevision, backref='page', |
---|
| 1331 | cascade="all, delete-orphan", |
---|
| 1332 | primaryjoin=( Page.table.c.id == PageRevision.table.c.page_id ) ), |
---|
| 1333 | latest_revision=relation( PageRevision, post_update=True, |
---|
| 1334 | primaryjoin=( Page.table.c.latest_revision_id == PageRevision.table.c.id ), |
---|
| 1335 | lazy=False ), |
---|
| 1336 | tags=relation(PageTagAssociation, order_by=PageTagAssociation.table.c.id, backref="pages"), |
---|
| 1337 | annotations=relation( PageAnnotationAssociation, order_by=PageAnnotationAssociation.table.c.id, backref="pages" ), |
---|
| 1338 | ratings=relation( PageRatingAssociation, order_by=PageRatingAssociation.table.c.id, backref="pages" ) |
---|
| 1339 | ) ) |
---|
| 1340 | |
---|
| 1341 | # Set up proxy so that |
---|
| 1342 | # Page.users_shared_with |
---|
| 1343 | # returns a list of users that page is shared with. |
---|
| 1344 | Page.users_shared_with_dot_users = association_proxy( 'users_shared_with', 'user' ) |
---|
| 1345 | |
---|
| 1346 | assign_mapper( context, PageUserShareAssociation, PageUserShareAssociation.table, |
---|
| 1347 | properties=dict( user=relation( User, backref='pages_shared_by_others' ), |
---|
| 1348 | page=relation( Page, backref='users_shared_with' ) |
---|
| 1349 | ) ) |
---|
| 1350 | |
---|
| 1351 | assign_mapper( context, VisualizationRevision, VisualizationRevision.table ) |
---|
| 1352 | |
---|
| 1353 | assign_mapper( context, Visualization, Visualization.table, |
---|
| 1354 | properties=dict( user=relation( User ), |
---|
| 1355 | revisions=relation( VisualizationRevision, backref='visualization', |
---|
| 1356 | cascade="all, delete-orphan", |
---|
| 1357 | primaryjoin=( Visualization.table.c.id == VisualizationRevision.table.c.visualization_id ) ), |
---|
| 1358 | latest_revision=relation( VisualizationRevision, post_update=True, |
---|
| 1359 | primaryjoin=( Visualization.table.c.latest_revision_id == VisualizationRevision.table.c.id ), |
---|
| 1360 | lazy=False ), |
---|
| 1361 | tags=relation( VisualizationTagAssociation, order_by=VisualizationTagAssociation.table.c.id, backref="visualizations" ), |
---|
| 1362 | annotations=relation( VisualizationAnnotationAssociation, order_by=VisualizationAnnotationAssociation.table.c.id, backref="visualizations" ), |
---|
| 1363 | ratings=relation( VisualizationRatingAssociation, order_by=VisualizationRatingAssociation.table.c.id, backref="visualizations" ) |
---|
| 1364 | ) ) |
---|
| 1365 | |
---|
| 1366 | # Set up proxy so that |
---|
| 1367 | # Visualization.users_shared_with |
---|
| 1368 | # returns a list of users that visualization is shared with. |
---|
| 1369 | Visualization.users_shared_with_dot_users = association_proxy( 'users_shared_with', 'user' ) |
---|
| 1370 | |
---|
| 1371 | assign_mapper( context, VisualizationUserShareAssociation, VisualizationUserShareAssociation.table, |
---|
| 1372 | properties=dict( user=relation( User, backref='visualizations_shared_by_others' ), |
---|
| 1373 | visualization=relation( Visualization, backref='users_shared_with' ) |
---|
| 1374 | ) ) |
---|
| 1375 | |
---|
| 1376 | # Tag tables. |
---|
| 1377 | |
---|
| 1378 | assign_mapper( context, Tag, Tag.table, |
---|
| 1379 | properties=dict( children=relation(Tag, backref=backref( 'parent', remote_side=[Tag.table.c.id] ) ) |
---|
| 1380 | ) ) |
---|
| 1381 | |
---|
| 1382 | assign_mapper( context, HistoryTagAssociation, HistoryTagAssociation.table, |
---|
| 1383 | properties=dict( tag=relation(Tag, backref="tagged_histories"), user=relation( User ) ) |
---|
| 1384 | ) |
---|
| 1385 | |
---|
| 1386 | assign_mapper( context, DatasetTagAssociation, DatasetTagAssociation.table, |
---|
| 1387 | properties=dict( tag=relation(Tag, backref="tagged_datasets"), user=relation( User ) ) |
---|
| 1388 | ) |
---|
| 1389 | |
---|
| 1390 | assign_mapper( context, HistoryDatasetAssociationTagAssociation, HistoryDatasetAssociationTagAssociation.table, |
---|
| 1391 | properties=dict( tag=relation(Tag, backref="tagged_history_dataset_associations"), user=relation( User ) ) |
---|
| 1392 | ) |
---|
| 1393 | |
---|
| 1394 | assign_mapper( context, PageTagAssociation, PageTagAssociation.table, |
---|
| 1395 | properties=dict( tag=relation(Tag, backref="tagged_pages"), user=relation( User ) ) |
---|
| 1396 | ) |
---|
| 1397 | |
---|
| 1398 | assign_mapper( context, StoredWorkflowTagAssociation, StoredWorkflowTagAssociation.table, |
---|
| 1399 | properties=dict( tag=relation(Tag, backref="tagged_workflows"), user=relation( User ) ) |
---|
| 1400 | ) |
---|
| 1401 | |
---|
| 1402 | assign_mapper( context, WorkflowStepTagAssociation, WorkflowStepTagAssociation.table, |
---|
| 1403 | properties=dict( tag=relation(Tag, backref="tagged_workflow_steps"), user=relation( User ) ) |
---|
| 1404 | ) |
---|
| 1405 | |
---|
| 1406 | assign_mapper( context, VisualizationTagAssociation, VisualizationTagAssociation.table, |
---|
| 1407 | properties=dict( tag=relation(Tag, backref="tagged_visualizations"), user=relation( User ) ) |
---|
| 1408 | ) |
---|
| 1409 | |
---|
| 1410 | # Annotation tables. |
---|
| 1411 | |
---|
| 1412 | assign_mapper( context, HistoryAnnotationAssociation, HistoryAnnotationAssociation.table, |
---|
| 1413 | properties=dict( history=relation( History ), user=relation( User ) ) |
---|
| 1414 | ) |
---|
| 1415 | |
---|
| 1416 | assign_mapper( context, HistoryDatasetAssociationAnnotationAssociation, HistoryDatasetAssociationAnnotationAssociation.table, |
---|
| 1417 | properties=dict( hda=relation( HistoryDatasetAssociation ), user=relation( User ) ) |
---|
| 1418 | ) |
---|
| 1419 | |
---|
| 1420 | assign_mapper( context, StoredWorkflowAnnotationAssociation, StoredWorkflowAnnotationAssociation.table, |
---|
| 1421 | properties=dict( stored_workflow=relation( StoredWorkflow ), user=relation( User ) ) |
---|
| 1422 | ) |
---|
| 1423 | |
---|
| 1424 | assign_mapper( context, WorkflowStepAnnotationAssociation, WorkflowStepAnnotationAssociation.table, |
---|
| 1425 | properties=dict( workflow_step=relation( WorkflowStep ), user=relation( User ) ) |
---|
| 1426 | ) |
---|
| 1427 | |
---|
| 1428 | assign_mapper( context, PageAnnotationAssociation, PageAnnotationAssociation.table, |
---|
| 1429 | properties=dict( page=relation( Page ), user=relation( User ) ) |
---|
| 1430 | ) |
---|
| 1431 | |
---|
| 1432 | assign_mapper( context, VisualizationAnnotationAssociation, VisualizationAnnotationAssociation.table, |
---|
| 1433 | properties=dict( visualization=relation( Visualization ), user=relation( User ) ) |
---|
| 1434 | ) |
---|
| 1435 | |
---|
| 1436 | # Rating tables. |
---|
| 1437 | |
---|
| 1438 | assign_mapper( context, HistoryRatingAssociation, HistoryRatingAssociation.table, |
---|
| 1439 | properties=dict( history=relation( History ), user=relation( User ) ) |
---|
| 1440 | ) |
---|
| 1441 | |
---|
| 1442 | assign_mapper( context, HistoryDatasetAssociationRatingAssociation, HistoryDatasetAssociationRatingAssociation.table, |
---|
| 1443 | properties=dict( hda=relation( HistoryDatasetAssociation ), user=relation( User ) ) |
---|
| 1444 | ) |
---|
| 1445 | |
---|
| 1446 | assign_mapper( context, StoredWorkflowRatingAssociation, StoredWorkflowRatingAssociation.table, |
---|
| 1447 | properties=dict( stored_workflow=relation( StoredWorkflow ), user=relation( User ) ) |
---|
| 1448 | ) |
---|
| 1449 | |
---|
| 1450 | assign_mapper( context, PageRatingAssociation, PageRatingAssociation.table, |
---|
| 1451 | properties=dict( page=relation( Page ), user=relation( User ) ) |
---|
| 1452 | ) |
---|
| 1453 | |
---|
| 1454 | assign_mapper( context, VisualizationRatingAssociation, VisualizationRatingAssociation.table, |
---|
| 1455 | properties=dict( visualization=relation( Visualization ), user=relation( User ) ) |
---|
| 1456 | ) |
---|
| 1457 | |
---|
| 1458 | # User tables. |
---|
| 1459 | |
---|
| 1460 | assign_mapper( context, UserPreference, UserPreference.table, |
---|
| 1461 | properties = {} |
---|
| 1462 | ) |
---|
| 1463 | |
---|
| 1464 | assign_mapper( context, UserAction, UserAction.table, |
---|
| 1465 | properties = dict( user=relation( User.mapper ) ) |
---|
| 1466 | ) |
---|
| 1467 | |
---|
| 1468 | assign_mapper( context, APIKeys, APIKeys.table, |
---|
| 1469 | properties = {} ) |
---|
| 1470 | |
---|
| 1471 | # Helper methods. |
---|
| 1472 | |
---|
| 1473 | def db_next_hid( self ): |
---|
| 1474 | """ |
---|
| 1475 | Override __next_hid to generate from the database in a concurrency |
---|
| 1476 | safe way. |
---|
| 1477 | """ |
---|
| 1478 | conn = object_session( self ).connection() |
---|
| 1479 | table = self.table |
---|
| 1480 | trans = conn.begin() |
---|
| 1481 | try: |
---|
| 1482 | next_hid = select( [table.c.hid_counter], table.c.id == self.id, for_update=True ).scalar() |
---|
| 1483 | table.update( table.c.id == self.id ).execute( hid_counter = ( next_hid + 1 ) ) |
---|
| 1484 | trans.commit() |
---|
| 1485 | return next_hid |
---|
| 1486 | except: |
---|
| 1487 | trans.rollback() |
---|
| 1488 | raise |
---|
| 1489 | |
---|
| 1490 | History._next_hid = db_next_hid |
---|
| 1491 | |
---|
| 1492 | def guess_dialect_for_url( url ): |
---|
| 1493 | return (url.split(':', 1))[0] |
---|
| 1494 | |
---|
| 1495 | def load_egg_for_url( url ): |
---|
| 1496 | # Load the appropriate db module |
---|
| 1497 | dialect = guess_dialect_for_url( url ) |
---|
| 1498 | try: |
---|
| 1499 | egg = dialect_to_egg[dialect] |
---|
| 1500 | try: |
---|
| 1501 | pkg_resources.require( egg ) |
---|
| 1502 | log.debug( "%s egg successfully loaded for %s dialect" % ( egg, dialect ) ) |
---|
| 1503 | except: |
---|
| 1504 | # If the module's in the path elsewhere (i.e. non-egg), it'll still load. |
---|
| 1505 | log.warning( "%s egg not found, but an attempt will be made to use %s anyway" % ( egg, dialect ) ) |
---|
| 1506 | except KeyError: |
---|
| 1507 | # Let this go, it could possibly work with db's we don't support |
---|
| 1508 | log.error( "database_connection contains an unknown SQLAlchemy database dialect: %s" % dialect ) |
---|
| 1509 | |
---|
| 1510 | def init( file_path, url, engine_options={}, create_tables=False, database_query_profiling_proxy=False ): |
---|
| 1511 | """Connect mappings to the database""" |
---|
| 1512 | # Connect dataset to the file path |
---|
| 1513 | Dataset.file_path = file_path |
---|
| 1514 | # Load the appropriate db module |
---|
| 1515 | load_egg_for_url( url ) |
---|
| 1516 | # Should we use the logging proxy? |
---|
| 1517 | if database_query_profiling_proxy: |
---|
| 1518 | import galaxy.model.orm.logging_connection_proxy as logging_connection_proxy |
---|
| 1519 | proxy = logging_connection_proxy.LoggingProxy() |
---|
| 1520 | else: |
---|
| 1521 | proxy = None |
---|
| 1522 | # Create the database engine |
---|
| 1523 | engine = create_engine( url, proxy=proxy, **engine_options ) |
---|
| 1524 | # Connect the metadata to the database. |
---|
| 1525 | metadata.bind = engine |
---|
| 1526 | # Clear any existing contextual sessions and reconfigure |
---|
| 1527 | Session.remove() |
---|
| 1528 | Session.configure( bind=engine ) |
---|
| 1529 | # Create tables if needed |
---|
| 1530 | if create_tables: |
---|
| 1531 | metadata.create_all() |
---|
| 1532 | # metadata.engine.commit() |
---|
| 1533 | # Pack everything into a bunch |
---|
| 1534 | result = Bunch( **globals() ) |
---|
| 1535 | result.engine = engine |
---|
| 1536 | # model.flush() has been removed. |
---|
| 1537 | result.session = Session |
---|
| 1538 | # For backward compatibility with "model.context.current" |
---|
| 1539 | result.context = Session |
---|
| 1540 | result.create_tables = create_tables |
---|
| 1541 | #load local galaxy security policy |
---|
| 1542 | result.security_agent = GalaxyRBACAgent( result ) |
---|
| 1543 | return result |
---|
| 1544 | |
---|
| 1545 | def get_suite(): |
---|
| 1546 | """Get unittest suite for this module""" |
---|
| 1547 | import unittest, mapping_tests |
---|
| 1548 | return unittest.makeSuite( mapping_tests.MappingTests ) |
---|
| 1549 | |
---|