/lib/galaxy/model/mapping.py
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1""" 2Details of how the data model objects are mapped onto the relational database 3are encapsulated here. 4""" 5 6import logging 7import pkg_resources 8 9from sqlalchemy import and_, asc, Boolean, Column, DateTime, desc, ForeignKey, Integer, MetaData, not_, Numeric, select, String, Table, TEXT, Unicode, UniqueConstraint 10from sqlalchemy.ext.associationproxy import association_proxy 11from sqlalchemy.ext.orderinglist import ordering_list 12from sqlalchemy.types import BigInteger 13from sqlalchemy.orm import backref, object_session, relation, mapper, class_mapper 14from sqlalchemy.orm.collections import attribute_mapped_collection 15 16from galaxy import model 17from galaxy.model.orm.engine_factory import build_engine 18from galaxy.model.orm.now import now 19from galaxy.model.custom_types import JSONType, MetadataType, TrimmedString, UUIDType 20from galaxy.model.base import ModelMapping 21from galaxy.security import GalaxyRBACAgent 22 23log = logging.getLogger( __name__ ) 24 25metadata = MetaData() 26 27 28model.User.table = Table( "galaxy_user", metadata, 29 Column( "id", Integer, primary_key=True), 30 Column( "create_time", DateTime, default=now ), 31 Column( "update_time", DateTime, default=now, onupdate=now ), 32 Column( "email", TrimmedString( 255 ), index=True, nullable=False ), 33 Column( "username", TrimmedString( 255 ), index=True, unique=True ), 34 Column( "password", TrimmedString( 255 ), nullable=False ), 35 Column( "external", Boolean, default=False ), 36 Column( "form_values_id", Integer, ForeignKey( "form_values.id" ), index=True ), 37 Column( "deleted", Boolean, index=True, default=False ), 38 Column( "purged", Boolean, index=True, default=False ), 39 Column( "disk_usage", Numeric( 15, 0 ), index=True ) , 40 Column( "active", Boolean, index=True, default=True, nullable=False ), 41 Column( "activation_token", TrimmedString( 64 ), nullable=True, index=True ) ) 42 43 44model.UserAddress.table = Table( "user_address", metadata, 45 Column( "id", Integer, primary_key=True), 46 Column( "create_time", DateTime, default=now ), 47 Column( "update_time", DateTime, default=now, onupdate=now ), 48 Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), 49 Column( "desc", TrimmedString( 255 )), 50 Column( "name", TrimmedString( 255 ), nullable=False), 51 Column( "institution", TrimmedString( 255 )), 52 Column( "address", TrimmedString( 255 ), nullable=False), 53 Column( "city", TrimmedString( 255 ), nullable=False), 54 Column( "state", TrimmedString( 255 ), nullable=False), 55 Column( "postal_code", TrimmedString( 255 ), nullable=False), 56 Column( "country", TrimmedString( 255 ), nullable=False), 57 Column( "phone", TrimmedString( 255 )), 58 Column( "deleted", Boolean, index=True, default=False ), 59 Column( "purged", Boolean, index=True, default=False ) ) 60 61model.UserOpenID.table = Table( "galaxy_user_openid", metadata, 62 Column( "id", Integer, primary_key=True ), 63 Column( "create_time", DateTime, default=now ), 64 Column( "update_time", DateTime, index=True, default=now, onupdate=now ), 65 Column( "session_id", Integer, ForeignKey( "galaxy_session.id" ), index=True ), 66 Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), 67 Column( "openid", TEXT, index=True, unique=True ), 68 Column( "provider", TrimmedString( 255 ) ), 69 ) 70 71model.History.table = Table( "history", metadata, 72 Column( "id", Integer, primary_key=True), 73 Column( "create_time", DateTime, default=now ), 74 Column( "update_time", DateTime, index=True, default=now, onupdate=now ), 75 Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), 76 Column( "name", TrimmedString( 255 ) ), 77 Column( "hid_counter", Integer, default=1 ), 78 Column( "deleted", Boolean, index=True, default=False ), 79 Column( "purged", Boolean, index=True, default=False ), 80 Column( "importing", Boolean, index=True, default=False ), 81 Column( "genome_build", TrimmedString( 40 ) ), 82 Column( "importable", Boolean, default=False ), 83 Column( "slug", TEXT, index=True ), 84 Column( "published", Boolean, index=True, default=False ) ) 85 86model.HistoryUserShareAssociation.table = Table( "history_user_share_association", metadata, 87 Column( "id", Integer, primary_key=True ), 88 Column( "history_id", Integer, ForeignKey( "history.id" ), index=True ), 89 Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ) 90 ) 91 92model.HistoryDatasetAssociation.table = Table( "history_dataset_association", metadata, 93 Column( "id", Integer, primary_key=True ), 94 Column( "history_id", Integer, ForeignKey( "history.id" ), index=True ), 95 Column( "dataset_id", Integer, ForeignKey( "dataset.id" ), index=True ), 96 Column( "create_time", DateTime, default=now ), 97 Column( "update_time", DateTime, default=now, onupdate=now ), 98 Column( "state", TrimmedString( 64 ), index=True, key="_state" ), 99 Column( "copied_from_history_dataset_association_id", Integer, ForeignKey( "history_dataset_association.id" ), nullable=True ), 100 Column( "copied_from_library_dataset_dataset_association_id", Integer, ForeignKey( "library_dataset_dataset_association.id" ), nullable=True ), 101 Column( "hid", Integer ), 102 Column( "name", TrimmedString( 255 ) ), 103 Column( "info", TrimmedString( 255 ) ), 104 Column( "blurb", TrimmedString( 255 ) ), 105 Column( "peek" , TEXT ), 106 Column( "tool_version" , TEXT ), 107 Column( "extension", TrimmedString( 64 ) ), 108 Column( "metadata", MetadataType(), key="_metadata" ), 109 Column( "parent_id", Integer, ForeignKey( "history_dataset_association.id" ), nullable=True ), 110 Column( "designation", TrimmedString( 255 ) ), 111 Column( "deleted", Boolean, index=True, default=False ), 112 Column( "purged", Boolean, index=True, default=False ), 113 Column( "visible", Boolean ), 114 Column( "extended_metadata_id", Integer, 115 ForeignKey( "extended_metadata.id" ), index=True ) 116 ) 117 118model.Dataset.table = Table( "dataset", metadata, 119 Column( "id", Integer, primary_key=True ), 120 Column( "create_time", DateTime, default=now ), 121 Column( "update_time", DateTime, index=True, default=now, onupdate=now ), 122 Column( "state", TrimmedString( 64 ), index=True ), 123 Column( "deleted", Boolean, index=True, default=False ), 124 Column( "purged", Boolean, index=True, default=False ), 125 Column( "purgable", Boolean, default=True ), 126 Column( "object_store_id", TrimmedString( 255 ), index=True ), 127 Column( "external_filename" , TEXT ), 128 Column( "_extra_files_path", TEXT ), 129 Column( 'file_size', Numeric( 15, 0 ) ), 130 Column( 'total_size', Numeric( 15, 0 ) ), 131 Column( 'uuid', UUIDType() ) ) 132 133model.HistoryDatasetAssociationDisplayAtAuthorization.table = Table( "history_dataset_association_display_at_authorization", metadata, 134 Column( "id", Integer, primary_key=True ), 135 Column( "create_time", DateTime, default=now ), 136 Column( "update_time", DateTime, index=True, default=now, onupdate=now ), 137 Column( "history_dataset_association_id", Integer, ForeignKey( "history_dataset_association.id" ), index=True ), 138 Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), 139 Column( "site", TrimmedString( 255 ) ) ) 140 141model.HistoryDatasetAssociationSubset.table = Table( "history_dataset_association_subset", metadata, 142 Column( "id", Integer, primary_key=True ), 143 Column( "history_dataset_association_id", Integer, ForeignKey( "history_dataset_association.id" ), index=True ), 144 Column( "history_dataset_association_subset_id", Integer, ForeignKey( "history_dataset_association.id" ), index=True ), 145 Column( "location", Unicode(255), index=True) ) 146 147model.ImplicitlyConvertedDatasetAssociation.table = Table( "implicitly_converted_dataset_association", metadata, 148 Column( "id", Integer, primary_key=True ), 149 Column( "create_time", DateTime, default=now ), 150 Column( "update_time", DateTime, default=now, onupdate=now ), 151 Column( "hda_id", Integer, ForeignKey( "history_dataset_association.id" ), index=True, nullable=True ), 152 Column( "ldda_id", Integer, ForeignKey( "library_dataset_dataset_association.id" ), index=True, nullable=True ), 153 Column( "hda_parent_id", Integer, ForeignKey( "history_dataset_association.id" ), index=True ), 154 Column( "ldda_parent_id", Integer, ForeignKey( "library_dataset_dataset_association.id" ), index=True ), 155 Column( "deleted", Boolean, index=True, default=False ), 156 Column( "metadata_safe", Boolean, index=True, default=True ), 157 Column( "type", TrimmedString( 255 ) ) ) 158 159model.ValidationError.table = Table( "validation_error", metadata, 160 Column( "id", Integer, primary_key=True ), 161 Column( "dataset_id", Integer, ForeignKey( "history_dataset_association.id" ), index=True ), 162 Column( "message", TrimmedString( 255 ) ), 163 Column( "err_type", TrimmedString( 64 ) ), 164 Column( "attributes", TEXT ) ) 165 166model.Group.table = Table( "galaxy_group", metadata, 167 Column( "id", Integer, primary_key=True ), 168 Column( "create_time", DateTime, default=now ), 169 Column( "update_time", DateTime, default=now, onupdate=now ), 170 Column( "name", String( 255 ), index=True, unique=True ), 171 Column( "deleted", Boolean, index=True, default=False ) ) 172 173model.UserGroupAssociation.table = Table( "user_group_association", metadata, 174 Column( "id", Integer, primary_key=True ), 175 Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), 176 Column( "group_id", Integer, ForeignKey( "galaxy_group.id" ), index=True ), 177 Column( "create_time", DateTime, default=now ), 178 Column( "update_time", DateTime, default=now, onupdate=now ) ) 179 180model.UserRoleAssociation.table = Table( "user_role_association", metadata, 181 Column( "id", Integer, primary_key=True ), 182 Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), 183 Column( "role_id", Integer, ForeignKey( "role.id" ), index=True ), 184 Column( "create_time", DateTime, default=now ), 185 Column( "update_time", DateTime, default=now, onupdate=now ) ) 186 187model.GroupRoleAssociation.table = Table( "group_role_association", metadata, 188 Column( "id", Integer, primary_key=True ), 189 Column( "group_id", Integer, ForeignKey( "galaxy_group.id" ), index=True ), 190 Column( "role_id", Integer, ForeignKey( "role.id" ), index=True ), 191 Column( "create_time", DateTime, default=now ), 192 Column( "update_time", DateTime, default=now, onupdate=now ) ) 193 194model.Role.table = Table( "role", metadata, 195 Column( "id", Integer, primary_key=True ), 196 Column( "create_time", DateTime, default=now ), 197 Column( "update_time", DateTime, default=now, onupdate=now ), 198 Column( "name", String( 255 ), index=True, unique=True ), 199 Column( "description", TEXT ), 200 Column( "type", String( 40 ), index=True ), 201 Column( "deleted", Boolean, index=True, default=False ) ) 202 203model.UserQuotaAssociation.table = Table( "user_quota_association", metadata, 204 Column( "id", Integer, primary_key=True ), 205 Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), 206 Column( "quota_id", Integer, ForeignKey( "quota.id" ), index=True ), 207 Column( "create_time", DateTime, default=now ), 208 Column( "update_time", DateTime, default=now, onupdate=now ) ) 209 210model.GroupQuotaAssociation.table = Table( "group_quota_association", metadata, 211 Column( "id", Integer, primary_key=True ), 212 Column( "group_id", Integer, ForeignKey( "galaxy_group.id" ), index=True ), 213 Column( "quota_id", Integer, ForeignKey( "quota.id" ), index=True ), 214 Column( "create_time", DateTime, default=now ), 215 Column( "update_time", DateTime, default=now, onupdate=now ) ) 216 217model.Quota.table = Table( "quota", metadata, 218 Column( "id", Integer, primary_key=True ), 219 Column( "create_time", DateTime, default=now ), 220 Column( "update_time", DateTime, default=now, onupdate=now ), 221 Column( "name", String( 255 ), index=True, unique=True ), 222 Column( "description", TEXT ), 223 Column( "bytes", BigInteger ), 224 Column( "operation", String( 8 ) ), 225 Column( "deleted", Boolean, index=True, default=False ) ) 226 227model.DefaultQuotaAssociation.table = Table( "default_quota_association", metadata, 228 Column( "id", Integer, primary_key=True ), 229 Column( "create_time", DateTime, default=now ), 230 Column( "update_time", DateTime, default=now, onupdate=now ), 231 Column( "type", String( 32 ), index=True, unique=True ), 232 Column( "quota_id", Integer, ForeignKey( "quota.id" ), index=True ) ) 233 234model.DatasetPermissions.table = Table( "dataset_permissions", metadata, 235 Column( "id", Integer, primary_key=True ), 236 Column( "create_time", DateTime, default=now ), 237 Column( "update_time", DateTime, default=now, onupdate=now ), 238 Column( "action", TEXT ), 239 Column( "dataset_id", Integer, ForeignKey( "dataset.id" ), index=True ), 240 Column( "role_id", Integer, ForeignKey( "role.id" ), index=True ) ) 241 242model.LibraryPermissions.table = Table( "library_permissions", metadata, 243 Column( "id", Integer, primary_key=True ), 244 Column( "create_time", DateTime, default=now ), 245 Column( "update_time", DateTime, default=now, onupdate=now ), 246 Column( "action", TEXT ), 247 Column( "library_id", Integer, ForeignKey( "library.id" ), nullable=True, index=True ), 248 Column( "role_id", Integer, ForeignKey( "role.id" ), index=True ) ) 249 250model.LibraryFolderPermissions.table = Table( "library_folder_permissions", metadata, 251 Column( "id", Integer, primary_key=True ), 252 Column( "create_time", DateTime, default=now ), 253 Column( "update_time", DateTime, default=now, onupdate=now ), 254 Column( "action", TEXT ), 255 Column( "library_folder_id", Integer, ForeignKey( "library_folder.id" ), nullable=True, index=True ), 256 Column( "role_id", Integer, ForeignKey( "role.id" ), index=True ) ) 257 258model.LibraryDatasetPermissions.table = Table( "library_dataset_permissions", metadata, 259 Column( "id", Integer, primary_key=True ), 260 Column( "create_time", DateTime, default=now ), 261 Column( "update_time", DateTime, default=now, onupdate=now ), 262 Column( "action", TEXT ), 263 Column( "library_dataset_id", Integer, ForeignKey( "library_dataset.id" ), nullable=True, index=True ), 264 Column( "role_id", Integer, ForeignKey( "role.id" ), index=True ) ) 265 266model.LibraryDatasetDatasetAssociationPermissions.table = Table( "library_dataset_dataset_association_permissions", metadata, 267 Column( "id", Integer, primary_key=True ), 268 Column( "create_time", DateTime, default=now ), 269 Column( "update_time", DateTime, default=now, onupdate=now ), 270 Column( "action", TEXT ), 271 Column( "library_dataset_dataset_association_id", Integer, ForeignKey( "library_dataset_dataset_association.id" ), nullable=True, index=True ), 272 Column( "role_id", Integer, ForeignKey( "role.id" ), index=True ) ) 273 274model.DefaultUserPermissions.table = Table( "default_user_permissions", metadata, 275 Column( "id", Integer, primary_key=True ), 276 Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), 277 Column( "action", TEXT ), 278 Column( "role_id", Integer, ForeignKey( "role.id" ), index=True ) ) 279 280model.DefaultHistoryPermissions.table = Table( "default_history_permissions", metadata, 281 Column( "id", Integer, primary_key=True ), 282 Column( "history_id", Integer, ForeignKey( "history.id" ), index=True ), 283 Column( "action", TEXT ), 284 Column( "role_id", Integer, ForeignKey( "role.id" ), index=True ) ) 285 286model.LibraryDataset.table = Table( "library_dataset", metadata, 287 Column( "id", Integer, primary_key=True ), 288 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 289 Column( "folder_id", Integer, ForeignKey( "library_folder.id" ), index=True ), 290 Column( "order_id", Integer ), #not currently being used, but for possible future use 291 Column( "create_time", DateTime, default=now ), 292 Column( "update_time", DateTime, default=now, onupdate=now ), 293 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?) 294 Column( "info", TrimmedString( 255 ), key="_info" ), #when not None/null this will supercede display in library (but not when imported into user's history?) 295 Column( "deleted", Boolean, index=True, default=False ), 296 Column( "purged", Boolean, index=True, default=False ) ) 297 298model.LibraryDatasetDatasetAssociation.table = Table( "library_dataset_dataset_association", metadata, 299 Column( "id", Integer, primary_key=True ), 300 Column( "library_dataset_id", Integer, ForeignKey( "library_dataset.id" ), index=True ), 301 Column( "dataset_id", Integer, ForeignKey( "dataset.id" ), index=True ), 302 Column( "create_time", DateTime, default=now ), 303 Column( "update_time", DateTime, default=now, onupdate=now ), 304 Column( "state", TrimmedString( 64 ), index=True, key="_state" ), 305 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 ), 306 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 ), 307 Column( "name", TrimmedString( 255 ), index=True ), 308 Column( "info", TrimmedString( 255 ) ), 309 Column( "blurb", TrimmedString( 255 ) ), 310 Column( "peek" , TEXT ), 311 Column( "tool_version" , TEXT ), 312 Column( "extension", TrimmedString( 64 ) ), 313 Column( "metadata", MetadataType(), key="_metadata" ), 314 Column( "parent_id", Integer, ForeignKey( "library_dataset_dataset_association.id" ), nullable=True ), 315 Column( "designation", TrimmedString( 255 ) ), 316 Column( "deleted", Boolean, index=True, default=False ), 317 Column( "visible", Boolean ), 318 Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), 319 Column( "message", TrimmedString( 255 ) ), 320 Column( "extended_metadata_id", Integer, 321 ForeignKey( "extended_metadata.id" ), index=True ) 322 ) 323 324 325model.ExtendedMetadata.table = Table("extended_metadata", metadata, 326 Column( "id", Integer, primary_key=True ), 327 Column( "data", JSONType ) ) 328 329model.ExtendedMetadataIndex.table = Table("extended_metadata_index", metadata, 330 Column( "id", Integer, primary_key=True ), 331 Column( "extended_metadata_id", Integer, ForeignKey("extended_metadata.id", 332 onupdate="CASCADE", 333 ondelete="CASCADE" ), 334 index=True ), 335 Column( "path", String( 255 )), 336 Column( "value", TEXT)) 337 338model.Library.table = Table( "library", metadata, 339 Column( "id", Integer, primary_key=True ), 340 Column( "root_folder_id", Integer, ForeignKey( "library_folder.id" ), index=True ), 341 Column( "create_time", DateTime, default=now ), 342 Column( "update_time", DateTime, default=now, onupdate=now ), 343 Column( "name", String( 255 ), index=True ), 344 Column( "deleted", Boolean, index=True, default=False ), 345 Column( "purged", Boolean, index=True, default=False ), 346 Column( "description", TEXT ), 347 Column( "synopsis", TEXT ) ) 348 349model.LibraryFolder.table = Table( "library_folder", metadata, 350 Column( "id", Integer, primary_key=True ), 351 Column( "parent_id", Integer, ForeignKey( "library_folder.id" ), nullable = True, index=True ), 352 Column( "create_time", DateTime, default=now ), 353 Column( "update_time", DateTime, default=now, onupdate=now ), 354 Column( "name", TEXT, index=True ), 355 Column( "description", TEXT ), 356 Column( "order_id", Integer ), #not currently being used, but for possible future use 357 Column( "item_count", Integer ), 358 Column( "deleted", Boolean, index=True, default=False ), 359 Column( "purged", Boolean, index=True, default=False ), 360 Column( "genome_build", TrimmedString( 40 ) ) ) 361 362model.LibraryInfoAssociation.table = Table( 'library_info_association', metadata, 363 Column( "id", Integer, primary_key=True ), 364 Column( "library_id", Integer, ForeignKey( "library.id" ), index=True ), 365 Column( "form_definition_id", Integer, ForeignKey( "form_definition.id" ), index=True ), 366 Column( "form_values_id", Integer, ForeignKey( "form_values.id" ), index=True ), 367 Column( "inheritable", Boolean, index=True, default=False ), 368 Column( "deleted", Boolean, index=True, default=False ) ) 369 370model.LibraryFolderInfoAssociation.table = Table( 'library_folder_info_association', metadata, 371 Column( "id", Integer, primary_key=True ), 372 Column( "library_folder_id", Integer, ForeignKey( "library_folder.id" ), nullable=True, index=True ), 373 Column( "form_definition_id", Integer, ForeignKey( "form_definition.id" ), index=True ), 374 Column( "form_values_id", Integer, ForeignKey( "form_values.id" ), index=True ), 375 Column( "inheritable", Boolean, index=True, default=False ), 376 Column( "deleted", Boolean, index=True, default=False ) ) 377 378model.LibraryDatasetDatasetInfoAssociation.table = Table( 'library_dataset_dataset_info_association', metadata, 379 Column( "id", Integer, primary_key=True ), 380 Column( "library_dataset_dataset_association_id", Integer, ForeignKey( "library_dataset_dataset_association.id" ), nullable=True, index=True ), 381 Column( "form_definition_id", Integer, ForeignKey( "form_definition.id" ), index=True ), 382 Column( "form_values_id", Integer, ForeignKey( "form_values.id" ), index=True ), 383 Column( "deleted", Boolean, index=True, default=False ) ) 384 385model.Job.table = Table( "job", metadata, 386 Column( "id", Integer, primary_key=True ), 387 Column( "create_time", DateTime, default=now ), 388 Column( "update_time", DateTime, default=now, onupdate=now ), 389 Column( "history_id", Integer, ForeignKey( "history.id" ), index=True ), 390 Column( "library_folder_id", Integer, ForeignKey( "library_folder.id" ), index=True ), 391 Column( "tool_id", String( 255 ) ), 392 Column( "tool_version", TEXT, default="1.0.0" ), 393 Column( "state", String( 64 ), index=True ), 394 Column( "info", TrimmedString( 255 ) ), 395 Column( "command_line", TEXT ), 396 Column( "param_filename", String( 1024 ) ), 397 Column( "runner_name", String( 255 ) ), 398 Column( "stdout", TEXT ), 399 Column( "stderr", TEXT ), 400 Column( "exit_code", Integer, nullable=True ), 401 Column( "traceback", TEXT ), 402 Column( "session_id", Integer, ForeignKey( "galaxy_session.id" ), index=True, nullable=True ), 403 Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True, nullable=True ), 404 Column( "job_runner_name", String( 255 ) ), 405 Column( "job_runner_external_id", String( 255 ) ), 406 Column( "destination_id", String( 255 ), nullable=True ), 407 Column( "destination_params", JSONType, nullable=True ), 408 Column( "object_store_id", TrimmedString( 255 ), index=True ), 409 Column( "imported", Boolean, default=False, index=True ), 410 Column( "params", TrimmedString(255), index=True ), 411 Column( "handler", TrimmedString( 255 ), index=True ) ) 412 413model.JobParameter.table = Table( "job_parameter", metadata, 414 Column( "id", Integer, primary_key=True ), 415 Column( "job_id", Integer, ForeignKey( "job.id" ), index=True ), 416 Column( "name", String(255) ), 417 Column( "value", TEXT ) ) 418 419model.JobToInputDatasetAssociation.table = Table( "job_to_input_dataset", metadata, 420 Column( "id", Integer, primary_key=True ), 421 Column( "job_id", Integer, ForeignKey( "job.id" ), index=True ), 422 Column( "dataset_id", Integer, ForeignKey( "history_dataset_association.id" ), index=True ), 423 Column( "name", String(255) ) ) 424 425model.JobToOutputDatasetAssociation.table = Table( "job_to_output_dataset", metadata, 426 Column( "id", Integer, primary_key=True ), 427 Column( "job_id", Integer, ForeignKey( "job.id" ), index=True ), 428 Column( "dataset_id", Integer, ForeignKey( "history_dataset_association.id" ), index=True ), 429 Column( "name", String(255) ) ) 430 431model.JobToInputLibraryDatasetAssociation.table = Table( "job_to_input_library_dataset", metadata, 432 Column( "id", Integer, primary_key=True ), 433 Column( "job_id", Integer, ForeignKey( "job.id" ), index=True ), 434 Column( "ldda_id", Integer, ForeignKey( "library_dataset_dataset_association.id" ), index=True ), 435 Column( "name", String(255) ) ) 436 437model.JobToOutputLibraryDatasetAssociation.table = Table( "job_to_output_library_dataset", metadata, 438 Column( "id", Integer, primary_key=True ), 439 Column( "job_id", Integer, ForeignKey( "job.id" ), index=True ), 440 Column( "ldda_id", Integer, ForeignKey( "library_dataset_dataset_association.id" ), index=True ), 441 Column( "name", String(255) ) ) 442 443model.JobExternalOutputMetadata.table = Table( "job_external_output_metadata", metadata, 444 Column( "id", Integer, primary_key=True ), 445 Column( "job_id", Integer, ForeignKey( "job.id" ), index=True ), 446 Column( "history_dataset_association_id", Integer, ForeignKey( "history_dataset_association.id" ), index=True, nullable=True ), 447 Column( "library_dataset_dataset_association_id", Integer, ForeignKey( "library_dataset_dataset_association.id" ), index=True, nullable=True ), 448 Column( "filename_in", String( 255 ) ), 449 Column( "filename_out", String( 255 ) ), 450 Column( "filename_results_code", String( 255 ) ), 451 Column( "filename_kwds", String( 255 ) ), 452 Column( "filename_override_metadata", String( 255 ) ), 453 Column( "job_runner_external_pid", String( 255 ) ) ) 454 455model.JobExportHistoryArchive.table = Table( "job_export_history_archive", metadata, 456 Column( "id", Integer, primary_key=True ), 457 Column( "job_id", Integer, ForeignKey( "job.id" ), index=True ), 458 Column( "history_id", Integer, ForeignKey( "history.id" ), index=True ), 459 Column( "dataset_id", Integer, ForeignKey( "dataset.id" ), index=True ), 460 Column( "compressed", Boolean, index=True, default=False ), 461 Column( "history_attrs_filename", TEXT ), 462 Column( "datasets_attrs_filename", TEXT ), 463 Column( "jobs_attrs_filename", TEXT ) 464 ) 465 466model.JobImportHistoryArchive.table = Table( "job_import_history_archive", metadata, 467 Column( "id", Integer, primary_key=True ), 468 Column( "job_id", Integer, ForeignKey( "job.id" ), index=True ), 469 Column( "history_id", Integer, ForeignKey( "history.id" ), index=True ), 470 Column( "archive_dir", TEXT ) 471 ) 472 473model.GenomeIndexToolData.table = Table( "genome_index_tool_data", metadata, 474 Column( "id", Integer, primary_key=True ), 475 Column( "job_id", Integer, ForeignKey( "job.id" ), index=True ), 476 Column( "deferred_job_id", Integer, ForeignKey( "deferred_job.id" ), index=True ), 477 Column( "transfer_job_id", Integer, ForeignKey( "transfer_job.id" ), index=True ), 478 Column( "dataset_id", Integer, ForeignKey( "dataset.id" ), index=True ), 479 Column( "fasta_path", String( 255 ) ), 480 Column( "created_time", DateTime, default=now ), 481 Column( "modified_time", DateTime, default=now, onupdate=now ), 482 Column( "indexer", String( 64 ) ), 483 Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), 484 ) 485 486model.Task.table = Table( "task", metadata, 487 Column( "id", Integer, primary_key=True ), 488 Column( "create_time", DateTime, default=now ), 489 Column( "execution_time", DateTime ), 490 Column( "update_time", DateTime, default=now, onupdate=now ), 491 Column( "state", String( 64 ), index=True ), 492 Column( "command_line", TEXT ), 493 Column( "param_filename", String( 1024 ) ), 494 Column( "runner_name", String( 255 ) ), 495 Column( "stdout", TEXT ), 496 Column( "stderr", TEXT ), 497 Column( "exit_code", Integer, nullable=True ), 498 Column( "info", TrimmedString ( 255 ) ), 499 Column( "traceback", TEXT ), 500 Column( "job_id", Integer, ForeignKey( "job.id" ), index=True, nullable=False ), 501 Column( "working_directory", String(1024)), 502 Column( "task_runner_name", String( 255 ) ), 503 Column( "task_runner_external_id", String( 255 ) ), 504 Column( "prepare_input_files_cmd", TEXT ) ) 505 506model.PostJobAction.table = Table("post_job_action", metadata, 507 Column("id", Integer, primary_key=True), 508 Column("workflow_step_id", Integer, ForeignKey( "workflow_step.id" ), index=True, nullable=False), 509 Column("action_type", String(255), nullable=False), 510 Column("output_name", String(255), nullable=True), 511 Column("action_arguments", JSONType, nullable=True)) 512 513model.PostJobActionAssociation.table = Table("post_job_action_association", metadata, 514 Column("id", Integer, primary_key=True), 515 Column("job_id", Integer, ForeignKey( "job.id" ), index=True, nullable=False), 516 Column("post_job_action_id", Integer, ForeignKey( "post_job_action.id" ), index=True, nullable=False)) 517 518model.DeferredJob.table = Table( "deferred_job", metadata, 519 Column( "id", Integer, primary_key=True ), 520 Column( "create_time", DateTime, default=now ), 521 Column( "update_time", DateTime, default=now, onupdate=now ), 522 Column( "state", String( 64 ), index=True ), 523 Column( "plugin", String( 128 ), index=True ), 524 Column( "params", JSONType ) ) 525 526model.TransferJob.table = Table( "transfer_job", metadata, 527 Column( "id", Integer, primary_key=True ), 528 Column( "create_time", DateTime, default=now ), 529 Column( "update_time", DateTime, default=now, onupdate=now ), 530 Column( "state", String( 64 ), index=True ), 531 Column( "path", String( 1024 ) ), 532 Column( "info", TEXT ), 533 Column( "pid", Integer ), 534 Column( "socket", Integer ), 535 Column( "params", JSONType ) ) 536 537model.Event.table = Table( "event", metadata, 538 Column( "id", Integer, primary_key=True ), 539 Column( "create_time", DateTime, default=now ), 540 Column( "update_time", DateTime, default=now, onupdate=now ), 541 Column( "history_id", Integer, ForeignKey( "history.id" ), index=True, nullable=True ), 542 Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True, nullable=True ), 543 Column( "message", TrimmedString( 1024 ) ), 544 Column( "session_id", Integer, ForeignKey( "galaxy_session.id" ), index=True, nullable=True ), 545 Column( "tool_id", String( 255 ) ) ) 546 547model.GalaxySession.table = Table( "galaxy_session", metadata, 548 Column( "id", Integer, primary_key=True ), 549 Column( "create_time", DateTime, default=now ), 550 Column( "update_time", DateTime, default=now, onupdate=now ), 551 Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True, nullable=True ), 552 Column( "remote_host", String( 255 ) ), 553 Column( "remote_addr", String( 255 ) ), 554 Column( "referer", TEXT ), 555 Column( "current_history_id", Integer, ForeignKey( "history.id" ), nullable=True ), 556 Column( "session_key", TrimmedString( 255 ), index=True, unique=True ), # unique 128 bit random number coerced to a string 557 Column( "is_valid", Boolean, default=False ), 558 Column( "prev_session_id", Integer ), # saves a reference to the previous session so we have a way to chain them together 559 Column( "disk_usage", Numeric( 15, 0 ), index=True ) ) 560 561model.GalaxySessionToHistoryAssociation.table = Table( "galaxy_session_to_history", metadata, 562 Column( "id", Integer, primary_key=True ), 563 Column( "create_time", DateTime, default=now ), 564 Column( "session_id", Integer, ForeignKey( "galaxy_session.id" ), index=True ), 565 Column( "history_id", Integer, ForeignKey( "history.id" ), index=True ) ) 566 567model.StoredWorkflow.table = Table( "stored_workflow", metadata, 568 Column( "id", Integer, primary_key=True ), 569 Column( "create_time", DateTime, default=now ), 570 Column( "update_time", DateTime, default=now, onupdate=now ), 571 Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True, nullable=False ), 572 Column( "latest_workflow_id", Integer, 573 ForeignKey( "workflow.id", use_alter=True, name='stored_workflow_latest_workflow_id_fk' ), index=True ), 574 Column( "name", TEXT ), 575 Column( "deleted", Boolean, default=False ), 576 Column( "importable", Boolean, default=False ), 577 Column( "slug", TEXT, index=True ), 578 Column( "published", Boolean, index=True, default=False ) 579 ) 580 581model.Workflow.table = Table( "workflow", metadata, 582 Column( "id", Integer, primary_key=True ), 583 Column( "create_time", DateTime, default=now ), 584 Column( "update_time", DateTime, default=now, onupdate=now ), 585 Column( "stored_workflow_id", Integer, ForeignKey( "stored_workflow.id" ), index=True, nullable=False ), 586 Column( "name", TEXT ), 587 Column( "has_cycles", Boolean ), 588 Column( "has_errors", Boolean ) 589 ) 590 591model.WorkflowStep.table = Table( "workflow_step", metadata, 592 Column( "id", Integer, primary_key=True ), 593 Column( "create_time", DateTime, default=now ), 594 Column( "update_time", DateTime, default=now, onupdate=now ), 595 Column( "workflow_id", Integer, ForeignKey( "workflow.id" ), index=True, nullable=False ), 596 Column( "type", String(64) ), 597 Column( "tool_id", TEXT ), 598 Column( "tool_version", TEXT ), # Reserved for future 599 Column( "tool_inputs", JSONType ), 600 Column( "tool_errors", JSONType ), 601 Column( "position", JSONType ), 602 Column( "config", JSONType ), 603 Column( "order_index", Integer ), 604 ## Column( "input_connections", JSONType ) 605 ) 606 607model.WorkflowStepConnection.table = Table( "workflow_step_connection", metadata, 608 Column( "id", Integer, primary_key=True ), 609 Column( "output_step_id", Integer, ForeignKey( "workflow_step.id" ), index=True ), 610 Column( "input_step_id", Integer, ForeignKey( "workflow_step.id" ), index=True ), 611 Column( "output_name", TEXT ), 612 Column( "input_name", TEXT) 613 ) 614 615model.WorkflowOutput.table = Table( "workflow_output", metadata, 616 Column( "id", Integer, primary_key=True ), 617 Column( "workflow_step_id", Integer, ForeignKey("workflow_step.id"), index=True, nullable=False), 618 Column( "output_name", String(255), nullable=True) 619 ) 620 621model.WorkflowInvocation.table = Table( "workflow_invocation", metadata, 622 Column( "id", Integer, primary_key=True ), 623 Column( "create_time", DateTime, default=now ), 624 Column( "update_time", DateTime, default=now, onupdate=now ), 625 Column( "workflow_id", Integer, ForeignKey( "workflow.id" ), index=True, nullable=False ) 626 ) 627 628model.WorkflowInvocationStep.table = Table( "workflow_invocation_step", 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( "workflow_invocation_id", Integer, ForeignKey( "workflow_invocation.id" ), index=True, nullable=False ), 633 Column( "workflow_step_id", Integer, ForeignKey( "workflow_step.id" ), index=True, nullable=False ), 634 Column( "job_id", Integer, ForeignKey( "job.id" ), index=True, nullable=True ) 635 ) 636 637model.StoredWorkflowUserShareAssociation.table = Table( "stored_workflow_user_share_connection", metadata, 638 Column( "id", Integer, primary_key=True ), 639 Column( "stored_workflow_id", Integer, ForeignKey( "stored_workflow.id" ), index=True ), 640 Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ) 641 ) 642 643model.StoredWorkflowMenuEntry.table = Table( "stored_workflow_menu_entry", metadata, 644 Column( "id", Integer, primary_key=True ), 645 Column( "stored_workflow_id", Integer, ForeignKey( "stored_workflow.id" ), index=True ), 646 Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), 647 Column( "order_index", Integer ) ) 648 649model.MetadataFile.table = Table( "metadata_file", metadata, 650 Column( "id", Integer, primary_key=True ), 651 Column( "name", TEXT ), 652 Column( "hda_id", Integer, ForeignKey( "history_dataset_association.id" ), index=True, nullable=True ), 653 Column( "lda_id", Integer, ForeignKey( "library_dataset_dataset_association.id" ), index=True, nullable=True ), 654 Column( "create_time", DateTime, default=now ), 655 Column( "update_time", DateTime, index=True, default=now, onupdate=now ), 656 Column( "object_store_id", TrimmedString( 255 ), index=True ), 657 Column( "deleted", Boolean, index=True, default=False ), 658 Column( "purged", Boolean, index=True, default=False ) ) 659 660model.FormDefinitionCurrent.table = Table('form_definition_current', metadata, 661 Column( "id", Integer, primary_key=True), 662 Column( "create_time", DateTime, default=now ), 663 Column( "update_time", DateTime, default=now, onupdate=now ), 664 Column( "latest_form_id", Integer, ForeignKey( "form_definition.id" ), index=True ), 665 Column( "deleted", Boolean, index=True, default=False )) 666 667model.FormDefinition.table = Table('form_definition', metadata, 668 Column( "id", Integer, primary_key=True), 669 Column( "create_time", DateTime, default=now ), 670 Column( "update_time", DateTime, default=now, onupdate=now ), 671 Column( "name", TrimmedString( 255 ), nullable=False ), 672 Column( "desc", TEXT ), 673 Column( "form_definition_current_id", 674 Integer, 675 ForeignKey( "form_definition_current.id", name='for_def_form_def_current_id_fk', use_alter=True ), 676 index=True ), 677 Column( "fields", JSONType() ), 678 Column( "type", TrimmedString( 255 ), index=True ), 679 Column( "layout", JSONType() ), ) 680 681model.ExternalService.table = Table( 'external_service', metadata, 682 Column( "id", Integer, primary_key=True ), 683 Column( "create_time", DateTime, default=now ), 684 Column( "update_time", DateTime, default=now, onupdate=now ), 685 Column( "name", TrimmedString( 255 ), nullable=False ), 686 Column( "description", TEXT ), 687 Column( "external_service_type_id", TrimmedString( 255 ), nullable=False ), 688 Column( "version", TrimmedString( 255 ) ), 689 Column( "form_definition_id", Integer, ForeignKey( "form_definition.id" ), index=True ), 690 Column( "form_values_id", Integer, ForeignKey( "form_values.id" ), index=True ), 691 Column( "deleted", Boolean, index=True, default=False ) ) 692 693model.RequestType.table = Table('request_type', metadata, 694 Column( "id", Integer, primary_key=True), 695 Column( "create_time", DateTime, default=now ), 696 Column( "update_time", DateTime, default=now, onupdate=now ), 697 Column( "name", TrimmedString( 255 ), nullable=False ), 698 Column( "desc", TEXT ), 699 Column( "request_form_id", Integer, ForeignKey( "form_definition.id" ), index=True ), 700 Column( "sample_form_id", Integer, ForeignKey( "form_definition.id" ), index=True ), 701 Column( "deleted", Boolean, index=True, default=False ) ) 702 703model.RequestTypeExternalServiceAssociation.table = Table( "request_type_external_service_association", metadata, 704 Column( "id", Integer, primary_key=True ), 705 Column( "request_type_id", Integer, ForeignKey( "request_type.id" ), index=True ), 706 Column( "external_service_id", Integer, ForeignKey( "external_service.id" ), index=True ) ) 707 708model.RequestTypePermissions.table = Table( "request_type_permissions", metadata, 709 Column( "id", Integer, primary_key=True ), 710 Column( "create_time", DateTime, default=now ), 711 Column( "update_time", DateTime, default=now, onupdate=now ), 712 Column( "action", TEXT ), 713 Column( "request_type_id", Integer, ForeignKey( "request_type.id" ), nullable=True, index=True ), 714 Column( "role_id", Integer, ForeignKey( "role.id" ), index=True ) ) 715 716model.FormValues.table = Table('form_values', metadata, 717 Column( "id", Integer, primary_key=True), 718 Column( "create_time", DateTime, default=now ), 719 Column( "update_time", DateTime, default=now, onupdate=now ), 720 Column( "form_definition_id", Integer, ForeignKey( "form_definition.id" ), index=True ), 721 Column( "content", JSONType()) ) 722 723model.Request.table = Table('request', metadata, 724 Column( "id", Integer, primary_key=True), 725 Column( "create_time", DateTime, default=now ), 726 Column( "update_time", DateTime, default=now, onupdate=now ), 727 Column( "name", TrimmedString( 255 ), nullable=False ), 728 Column( "desc", TEXT ), 729 Column( "notification", JSONType() ), 730 Column( "form_values_id", Integer, ForeignKey( "form_values.id" ), index=True ), 731 Column( "request_type_id", Integer, ForeignKey( "request_type.id" ), index=True ), 732 Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), 733 Column( "deleted", Boolean, index=True, default=False ) ) 734 735model.RequestEvent.table = Table('request_event', metadata, 736 Column( "id", Integer, primary_key=True), 737 Column( "create_time", DateTime, default=now ), 738 Column( "update_time", DateTime, default=now, onupdate=now ), 739 Column( "request_id", Integer, ForeignKey( "request.id" ), index=True ), 740 Column( "state", TrimmedString( 255 ), index=True ), 741 Column( "comment", TEXT ) ) 742 743model.Sample.table = Table('sample', metadata, 744 Column( "id", Integer, primary_key=True ), 745 Column( "create_time", DateTime, default=now ), 746 Column( "update_time", DateTime, default=now, onupdate=now ), 747 Column( "name", TrimmedString( 255 ), nullable=False ), 748 Column( "desc", TEXT ), 749 Column( "form_values_id", Integer, ForeignKey( "form_values.id" ), index=True ), 750 Column( "request_id", Integer, ForeignKey( "request.id" ), index=True ), 751 Column( "bar_code", TrimmedString( 255 ), index=True ), 752 Column( "library_id", Integer, ForeignKey( "library.id" ), index=True ), 753 Column( "folder_id", Integer, ForeignKey( "library_folder.id" ), index=True ), 754 Column( "deleted", Boolean, index=True, default=False ), 755 Column( "workflow", JSONType, nullable=True ), 756 Column( "history_id", Integer, ForeignKey( "history.id" ), nullable=True) ) 757 758model.SampleState.table = Table('sample_state', metadata, 759 Column( "id", Integer, primary_key=True ), 760 Column( "create_time", DateTime, default=now ), 761 Column( "update_time", DateTime, default=now, onupdate=now ), 762 Column( "name", TrimmedString( 255 ), nullable=False ), 763 Column( "desc", TEXT ), 764 Column( "request_type_id", Integer, ForeignKey( "request_type.id" ), index=True ) ) 765 766model.SampleEvent.table = Table('sample_event', metadata, 767 Column( "id", Integer, primary_key=True ), 768 Column( "create_time", DateTime, default=now ), 769 Column( "update_time", DateTime, default=now, onupdate=now ), 770 Column( "sample_id", Integer, ForeignKey( "sample.id" ), index=True ), 771 Column( "sample_state_id", Integer, ForeignKey( "sample_state.id" ), index=True ), 772 Column( "comment", TEXT ) ) 773 774model.SampleDataset.table = Table('sample_dataset', metadata, 775 Column( "id", Integer, primary_key=True ), 776 Column( "create_time", DateTime, default=now ), 777 Column( "update_time", DateTime, default=now, onupdate=now ), 778 Column( "sample_id", Integer, ForeignKey( "sample.id" ), index=True ), 779 Column( "name", TrimmedString( 255 ), nullable=False ), 780 Column( "file_path", TEXT ), 781 Column( "status", TrimmedString( 255 ), nullable=False ), 782 Column( "error_msg", TEXT ), 783 Column( "size", TrimmedString( 255 ) ), 784 Column( "external_service_id", Integer, ForeignKey( "external_service.id" ), index=True ) ) 785 786model.Run.table = Table( 'run', metadata, 787 Column( "id", Integer, primary_key=True ), 788 Column( "create_time", DateTime, default=now ), 789 Column( "update_time", DateTime, default=now, onupdate=now ), 790 Column( "form_definition_id", Integer, ForeignKey( "form_definition.id" ), index=True ), 791 Column( "form_values_id", Integer, ForeignKey( "form_values.id" ), index=True ), 792 Column( "deleted", Boolean, index=True, default=False ), 793 Column( "subindex", TrimmedString( 255 ), index=True ) ) 794 795model.RequestTypeRunAssociation.table = Table( "request_type_run_association", metadata, 796 Column( "id", Integer, primary_key=True ), 797 Column( "request_type_id", Integer, ForeignKey( "request_type.id" ), index=True, nullable=False ), 798 Column( "run_id", Integer, ForeignKey( "run.id" ), index=True, nullable=False ) ) 799 800model.SampleRunAssociation.table = Table( "sample_run_association", metadata, 801 Column( "id", Integer, primary_key=True ), 802 Column( "sample_id", Integer, ForeignKey( "sample.id" ), index=True, nullable=False ), 803 Column( "run_id", Integer, ForeignKey( "run.id" ), index=True, nullable=False ) ) 804 805model.Page.table = Table( "page", metadata, 806 Column( "id", Integer, primary_key=True ), 807 Column( "create_time", DateTime, default=now ), 808 Column( "update_time", DateTime, default=now, onupdate=now ), 809 Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True, nullable=False ), 810 Column( "latest_revision_id", Integer, 811 ForeignKey( "page_revision.id", use_alter=True, name='page_latest_revision_id_fk' ), index=True ), 812 Column( "title", TEXT ), 813 Column( "slug", TEXT, unique=True, index=True ), 814 Column( "importable", Boolean, index=True, default=False ), 815 Column( "published", Boolean, index=True, default=False ), 816 Column( "deleted", Boolean, index=True, default=False ), 817 ) 818 819model.PageRevision.table = Table( "page_revision", metadata, 820 Column( "id", Integer, primary_key=True ), 821 Column( "create_time", DateTime, default=now ), 822 Column( "update_time", DateTime, default=now, onupdate=now ), 823 Column( "page_id", Integer, ForeignKey( "page.id" ), index=True, nullable=False ), 824 Column( "title", TEXT ), 825 Column( "content", TEXT ) 826 ) 827 828model.PageUserShareAssociation.table = Table( "page_user_share_association", metadata, 829 Column( "id", Integer, primary_key=True ), 830 Column( "page_id", Integer, ForeignKey( "page.id" ), index=True ), 831 Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ) 832 ) 833 834model.Visualization.table = Table( "visualization", metadata, 835 Column( "id", Integer, primary_key=True ), 836 Column( "create_time", DateTime, default=now ), 837 Column( "update_time", DateTime, default=now, onupdate=now ), 838 Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True, nullable=False ), 839 Column( "latest_revision_id", Integer, 840 ForeignKey( "visualization_revision.id", use_alter=True, name='visualization_latest_revision_id_fk' ), index=True ), 841 Column( "title", TEXT ), 842 Column( "type", TEXT ), 843 Column( "dbkey", TEXT, index=True ), 844 Column( "deleted", Boolean, default=False, index=True ), 845 Column( "importable", Boolean, default=False, index=True ), 846 Column( "slug", TEXT, index=True ), 847 Column( "published", Boolean, default=False, index=True ) 848 ) 849 850model.VisualizationRevision.table = Table( "visualization_revision", metadata, 851 Column( "id", Integer, primary_key=True ), 852 Column( "create_time", DateTime, default=now ), 853 Column( "update_time", DateTime, default=now, onupdate=now ), 854 Column( "visualization_id", Integer, ForeignKey( "visualization.id" ), index=True, nullable=False ), 855 Column( "title", TEXT ), 856 Column( "dbkey", TEXT, index=True ), 857 Column( "config", JSONType ) 858 ) 859 860model.VisualizationUserShareAssociation.table = Table( "visualization_user_share_association", metadata, 861 Column( "id", Integer, primary_key=True ), 862 Column( "visualization_id", Integer, ForeignKey( "visualization.id" ), index=True ), 863 Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ) 864 ) 865 866#Data Manager tables 867model.DataManagerHistoryAssociation.table = Table( "data_manager_history_association", metadata, 868 Column( "id", Integer, primary_key=True), 869 Column( "create_time", DateTime, default=now ), 870 Column( "update_time", DateTime, index=True, default=now, onupdate=now ), 871 Column( "history_id", Integer, ForeignKey( "history.id" ), index=True ), 872 Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ) 873 ) 874 875model.DataManagerJobAssociation.table = Table( "data_manager_job_association", metadata, 876 Column( "id", Integer, primary_key=True), 877 Column( "create_time", DateTime, default=now ), 878 Column( "update_time", DateTime, index=True, default=now, onupdate=now ), 879 Column( "job_id", Integer, ForeignKey( "job.id" ), index=True ), 880 Column( "data_manager_id", TEXT, index=True ) 881 ) 882 883# Tagging tables. 884 885model.Tag.table = Table( "tag", metadata, 886 Column( "id", Integer, primary_key=True ), 887 Column( "type", Integer ), 888 Column( "parent_id", Integer, ForeignKey( "tag.id" ) ), 889 Column( "name", TrimmedString(255) ), 890 UniqueConstraint( "name" ) ) 891 892model.HistoryTagAssociation.table = Table( "history_tag_association", metadata, 893 Column( "id", Integer, primary_key=True ), 894 Column( "history_id", Integer, ForeignKey( "history.id" ), index=True ), 895 Column( "tag_id", Integer, ForeignKey( "tag.id" ), index=True ), 896 Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), 897 Column( "user_tname", TrimmedString(255), index=True), 898 Column( "value", TrimmedString(255), index=True), 899 Column( "user_value", TrimmedString(255), index=True) ) 900 901model.DatasetTagAssociation.table = Table( "dataset_tag_association", metadata, 902 Column( "id", Integer, primary_key=True ), 903 Column( "dataset_id", Integer, ForeignKey( "dataset.id" ), index=True ), 904 Column( "tag_id", Integer, ForeignKey( "tag.id" ), index=True ), 905 Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), 906 Column( "user_tname", TrimmedString(255), index=True), 907 Column( "value", TrimmedString(255), index=True), 908 Column( "user_value", TrimmedString(255), index=True) ) 909 910model.HistoryDatasetAssociationTagAssociation.table = Table( "history_dataset_association_tag_association", metadata, 911 Column( "id", Integer, primary_key=True ), 912 Column( "history_dataset_association_id", Integer, ForeignKey( "history_dataset_association.id" ), index=True ), 913 Column( "tag_id", Integer, ForeignKey( "tag.id" ), index=True ), 914 Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), 915 Column( "user_tname", TrimmedString(255), index=True), 916 Column( "value", TrimmedString(255), index=True), 917 Column( "user_value", TrimmedString(255), index=True) ) 918 919…
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