/test/functional/test_library_features.py
Python | 578 lines | 557 code | 2 blank | 19 comment | 15 complexity | 9c432bbb86e14a2a7796e4330d6eed6d MD5 | raw file
1from base.twilltestcase import * 2from base.test_db_util import * 3 4 5# TODO: Functional tests start failing at 070, fix or eliminate rest of tests. 6class TestLibraryFeatures( TwillTestCase ): 7 def test_000_initiate_users( self ): 8 """Ensuring all required user accounts exist""" 9 self.logout() 10 self.login( email='test1@bx.psu.edu', username='regular-user1' ) 11 global regular_user1 12 regular_user1 = get_user( 'test1@bx.psu.edu' ) 13 assert regular_user1 is not None, 'Problem retrieving user with email "test1@bx.psu.edu" from the database' 14 global regular_user1_private_role 15 regular_user1_private_role = get_private_role( regular_user1 ) 16 self.logout() 17 self.login( email='test2@bx.psu.edu', username='regular-user2' ) 18 global regular_user2 19 regular_user2 = get_user( 'test2@bx.psu.edu' ) 20 assert regular_user2 is not None, 'Problem retrieving user with email "test2@bx.psu.edu" from the database' 21 global regular_user2_private_role 22 regular_user2_private_role = get_private_role( regular_user2 ) 23 self.logout() 24 self.login( email='test3@bx.psu.edu', username='regular-user3' ) 25 global regular_user3 26 regular_user3 = get_user( 'test3@bx.psu.edu' ) 27 assert regular_user3 is not None, 'Problem retrieving user with email "test3@bx.psu.edu" from the database' 28 global regular_user3_private_role 29 regular_user3_private_role = get_private_role( regular_user3 ) 30 self.logout() 31 self.login( email='test@bx.psu.edu', username='admin-user' ) 32 global admin_user 33 admin_user = get_user( 'test@bx.psu.edu' ) 34 assert admin_user is not None, 'Problem retrieving user with email "test@bx.psu.edu" from the database' 35 global admin_user_private_role 36 admin_user_private_role = get_private_role( admin_user ) 37 def test_005_create_libraries( self ): 38 """Testing creating libraries used in this script, then renaming one of them""" 39 # Logged in as admin_user 40 for index in range( 0, 3 ): 41 name = 'library%s' % str( index + 1 ) 42 description = '%s description' % name 43 synopsis = '%s synopsis' % name 44 self.create_library( name=name, description=description, synopsis=synopsis ) 45 self.browse_libraries_admin( strings_displayed=[ name, description ] ) 46 # Get the libraries for later use 47 global library1 48 library1 = get_library( 'library1', 'library1 description', 'library1 synopsis' ) 49 assert library1 is not None, 'Problem retrieving library (library1) from the database' 50 global library2 51 library2 = get_library( 'library2', 'library2 description', 'library2 synopsis' ) 52 assert library2 is not None, 'Problem retrieving library (library2) from the database' 53 global library3 54 library3 = get_library( 'library3', 'library3 description', 'library3 synopsis' ) 55 assert library3 is not None, 'Problem retrieving library (library3) from the database' 56 # Rename the library 57 new_name = "library1 new name" 58 new_description = "library1 new description" 59 new_synopsis = "library1 new synopsis" 60 self.library_info( 'library_admin', 61 self.security.encode_id( library1.id ), 62 library1.name, 63 new_name=new_name, 64 new_description=new_description, 65 new_synopsis=new_synopsis ) 66 self.browse_libraries_admin( strings_displayed=[ new_name, new_description ] ) 67 # Reset the library back to the original name and description 68 self.library_info( 'library_admin', 69 self.security.encode_id( library1.id ), 70 library1.name, 71 new_name=name, 72 new_description='library1 description', 73 new_synopsis='library1 synopsis' ) 74 refresh( library1 ) 75 def test_030_add_folder_to_library1( self ): 76 """Testing adding a folder to a library1""" 77 # logged in as admin_user 78 root_folder = library1.root_folder 79 name = "folder1" 80 description = "folder1 description" 81 self.add_folder( 'library_admin', 82 self.security.encode_id( library1.id ), 83 self.security.encode_id( library1.root_folder.id ), 84 name=name, 85 description=description ) 86 global folder1 87 folder1 = get_folder( root_folder.id, name, description ) 88 assert folder1 is not None, 'Problem retrieving library folder named "%s" from the database' % name 89 self.browse_library( cntrller='library_admin', 90 library_id=self.security.encode_id( library1.id ), 91 strings_displayed=[ folder1.name, folder1.description ] ) 92 def test_035_add_subfolder_to_folder( self ): 93 """Testing adding a folder to a folder""" 94 # logged in as admin_user 95 name = "Folder One's Subfolder" 96 description = "This is the Folder One's subfolder" 97 self.add_folder( 'library_admin', 98 self.security.encode_id( library1.id ), 99 self.security.encode_id( folder1.id ), 100 name=name, 101 description=description ) 102 global subfolder1 103 subfolder1 = get_folder( folder1.id, name, description ) 104 assert subfolder1 is not None, 'Problem retrieving subfolder1 from the database' 105 self.browse_library( cntrller='library_admin', 106 library_id=self.security.encode_id( library1.id ), 107 strings_displayed=[ subfolder1.name, subfolder1.description ] ) 108 def test_040_add_2nd_folder_to_library1( self ): 109 """Testing adding a 2nd folder to a library1""" 110 # logged in as admin_user 111 name = "folder2" 112 description = "folder2 description" 113 self.add_folder( 'library_admin', 114 self.security.encode_id( library1.id ), 115 self.security.encode_id( library1.root_folder.id ), 116 name=name, 117 description=description ) 118 global folder2 119 folder2 = get_folder( library1.root_folder.id, name, description ) 120 assert folder2 is not None, 'Problem retrieving library folder named "%s" from the database' % name 121 self.browse_library( cntrller='library_admin', 122 library_id=self.security.encode_id( library1.id ), 123 strings_displayed=[ folder2.name, folder2.description ] ) 124 def test_045_add_public_dataset_to_folder2( self ): 125 """Testing adding a public dataset to folder2""" 126 # Logged in as admin_user 127 filename = '2.bed' 128 ldda_message = "Testing uploading %s" % filename 129 self.upload_library_dataset( cntrller='library_admin', 130 library_id=self.security.encode_id( library1.id ), 131 folder_id=self.security.encode_id( folder2.id ), 132 filename=filename, 133 file_type='bed', 134 dbkey='hg18', 135 ldda_message=ldda_message, 136 strings_displayed=[ 'Upload files' ] ) 137 global ldda2 138 ldda2 = get_latest_ldda_by_name( filename ) 139 assert ldda2 is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda2 from the database' 140 self.browse_library( cntrller='library_admin', 141 library_id=self.security.encode_id( library1.id ), 142 strings_displayed=[ ldda2.name, ldda2.message, 'bed' ] ) 143 def test_050_add_2nd_public_dataset_to_folder2( self ): 144 """Testing adding a 2nd public dataset folder2""" 145 # Logged in as admin_user 146 filename='3.bed' 147 ldda_message = "Testing uploading %s" % filename 148 self.upload_library_dataset( cntrller='library_admin', 149 library_id=self.security.encode_id( library1.id ), 150 folder_id=self.security.encode_id( folder2.id ), 151 filename=filename, 152 file_type='bed', 153 dbkey='hg18', 154 ldda_message=ldda_message, 155 strings_displayed=[ 'Upload files' ] ) 156 global ldda3 157 ldda3 = get_latest_ldda_by_name( filename ) 158 assert ldda3 is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda3 from the database' 159 self.browse_library( cntrller='library_admin', 160 library_id=self.security.encode_id( library1.id ), 161 strings_displayed=[ ldda3.name, ldda3.message, 'bed' ] ) 162 def test_055_copy_dataset_from_history_to_subfolder( self ): 163 """Testing copying a dataset from the current history to a subfolder""" 164 # logged in as admin_user 165 self.new_history() 166 filename = '4.bed' 167 self.upload_file( filename ) 168 latest_hda = get_latest_hda() 169 self.upload_library_dataset( cntrller='library_admin', 170 library_id=self.security.encode_id( library1.id ), 171 folder_id=self.security.encode_id( subfolder1.id ), 172 upload_option='import_from_history', 173 hda_ids=self.security.encode_id( latest_hda.id ), 174 ldda_message='Imported from history', 175 strings_displayed=[ 'Active datasets in your current history' ] ) 176 global ldda4 177 ldda4 = get_latest_ldda_by_name( filename ) 178 assert ldda4 is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda4 from the database' 179 self.browse_library( cntrller='library_admin', 180 library_id=self.security.encode_id( library1.id ), 181 strings_displayed=[ ldda4.name, ldda4.message, 'bed' ] ) 182 def test_060_editing_dataset_attribute_info( self ): 183 """Testing editing a library dataset's attribute information""" 184 # logged in as admin_user 185 new_ldda_name = '4.bed ( version 1 )' 186 self.ldda_edit_info( 'library_admin', 187 self.security.encode_id( library1.id ), 188 self.security.encode_id( subfolder1.id ), 189 self.security.encode_id( ldda4.id ), 190 ldda4.name, 191 new_ldda_name=new_ldda_name ) 192 refresh( ldda4 ) 193 self.browse_library( cntrller='library_admin', 194 library_id=self.security.encode_id( library1.id ), 195 strings_displayed=[ new_ldda_name, ldda4.message ] ) 196 def test_065_uploading_new_dataset_version( self ): 197 """Testing uploading a new version of a library dataset""" 198 # logged in as admin_user 199 filename = '4.bed' 200 ldda_message = 'Testing uploading a new version of a dataset' 201 self.upload_library_dataset( cntrller='library_admin', 202 library_id=self.security.encode_id( library1.id ), 203 folder_id=self.security.encode_id( subfolder1.id ), 204 replace_id=self.security.encode_id( ldda4.library_dataset.id ), 205 filename=filename, 206 file_type='auto', 207 dbkey='hg18', 208 ldda_message=ldda_message, 209 strings_displayed=[ 'Upload files', 'You are currently selecting a new file to replace' ] ) 210 global ldda4_version2 211 ldda4_version2 = get_latest_ldda_by_name( filename ) 212 assert ldda4_version2 is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda4_version2 from the database' 213 self.ldda_edit_info( 'library_admin', 214 self.security.encode_id( library1.id ), 215 self.security.encode_id( subfolder1.id ), 216 self.security.encode_id( ldda4_version2.id ), 217 ldda4_version2.name, 218 strings_displayed=[ 'This is the latest version of this library dataset' ] ) 219 # Check the previous version 220 self.ldda_edit_info( 'library_admin', 221 self.security.encode_id( library1.id ), 222 self.security.encode_id( subfolder1.id ), 223 self.security.encode_id( ldda4.id ), 224 ldda4.name, 225 strings_displayed=[ 'This is an expired version of this library dataset' ] ) 226 # Make sure ldda4 is no longer displayed in the library 227 self.browse_library( cntrller='library_admin', 228 library_id=self.security.encode_id( library1.id ), 229 strings_not_displayed=[ ldda4.name, ldda4.message ] ) 230 def test_070_upload_directory_of_files_from_libraries_view( self ): 231 """Testing uploading a directory of files to a root folder from the Data Libraries view""" 232 # logged in as admin_user 233 # admin_user will not have the option to upload a directory of files from the 234 # Libraries view since a sub-directory named the same as their email is not contained 235 # in the configured user_library_import_dir ( in the test_data directory, only regular_user1 236 # and regular_user3 have directories ). We'll need to give these 2 user LIBRARY_ADD permission 237 # on library1 to test this feature. 238 permissions_in = [ 'LIBRARY_ADD' ] 239 permissions_out = [ 'LIBRARY_ACCESS', 'LIBRARY_MODIFY', 'LIBRARY_MANAGE' ] 240 role_ids = '%s,%s' % ( str( regular_user1_private_role.id ), str( regular_user3_private_role.id ) ) 241 self.library_permissions( self.security.encode_id( library1.id ), 242 library1.name, 243 role_ids, 244 permissions_in, 245 permissions_out ) 246 self.logout() 247 # Now that we have permissions set on the library, we can proceed to test uploading files 248 self.login( email=regular_user1.email ) 249 ldda_message = 'Uploaded all files in test-data/users/test1...' 250 # Since regular_user1 does not have any sub-directories contained within her configured 251 # user_library_import_dir, the only option in her server_dir select list will be the 252 # directory named the same as her email 253 self.upload_library_dataset( cntrller='library', 254 library_id=self.security.encode_id( library1.id ), 255 folder_id=self.security.encode_id( library1.root_folder.id ), 256 upload_option='upload_directory', 257 server_dir=regular_user1.email, 258 ldda_message=ldda_message, 259 strings_displayed = [ "Upload a directory of files" ] ) 260 self.logout() 261 self.login( regular_user3.email ) 262 ldda_message = 'Uploaded all files in test-data/users/test3.../run1' 263 # Since regular_user2 has a subdirectory contained within her configured user_library_import_dir, 264 # she will have a "None" option in her server_dir select list 265 self.upload_library_dataset( cntrller='library', 266 library_id=self.security.encode_id( library1.id ), 267 folder_id=self.security.encode_id( library1.root_folder.id ), 268 upload_option='upload_directory', 269 server_dir='run1', 270 ldda_message=ldda_message, 271 strings_displayed=[ 'Upload a directory of files', '<option>None</option>' ] ) 272 def test_075_download_archive_of_library_files( self ): 273 """Testing downloading an archive of files from library1""" 274 # logged in as regular_user3 275 self.logout() 276 self.login( email=admin_user.email ) 277 filename = '1.bed' 278 self.upload_library_dataset( cntrller='library_admin', 279 library_id=self.security.encode_id( library1.id ), 280 folder_id=self.security.encode_id( library1.root_folder.id ), 281 filename=filename, 282 file_type='bed', 283 dbkey='hg18', 284 strings_displayed=[ 'Upload files' ] ) 285 global ldda1 286 ldda1 = get_latest_ldda_by_name( filename ) 287 assert ldda1 is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda1 from the database' 288 for format in ( 'tbz', 'tgz', 'zip' ): 289 archive = self.download_archive_of_library_files( cntrller='library', 290 library_id=self.security.encode_id( library1.id ), 291 ldda_ids=[ self.security.encode_id( ldda1.id ), self.security.encode_id( ldda2.id ) ], 292 format=format ) 293 self.check_archive_contents( archive, ( ldda1, ldda2 ) ) 294 os.remove( archive ) 295 def test_080_check_libraries_for_uploaded_directories_of_files( self ): 296 """Testing the results of uploading directories of files to library1""" 297 # We'll make sure the directories of files were uploaded in test_070... above. 298 # We do this here because the check would generally fail if we did it in the 299 # test_070... method since the files would not finish uploading before the check 300 # was done. Hopefully doing the check here will allow for enough time... 301 ldda_message = 'Uploaded all files in test-data/users/test1...' 302 self.browse_library( 'library', 303 self.security.encode_id( library1.id ), 304 strings_displayed=[ 'fasta', ldda_message, '1.fasta' ] ) 305 ldda_message = 'Uploaded all files in test-data/users/test3.../run1' 306 self.browse_library( 'library', 307 self.security.encode_id( library1.id ), 308 strings_displayed=[ 'fasta', ldda_message, '2.fasta' ] ) 309 def test_085_mark_ldda2_deleted( self ): 310 """Testing marking ldda2 as deleted""" 311 # Logged in as admin_user 312 self.delete_library_item( 'library_admin', 313 self.security.encode_id( library1.id ), 314 self.security.encode_id( ldda2.library_dataset.id ), 315 ldda2.name, 316 item_type='library_dataset' ) 317 self.browse_library( cntrller='library_admin', 318 library_id=self.security.encode_id( library1.id ), 319 strings_not_displayed=[ ldda2.name, ldda2.message ] ) 320 def test_090_display_and_hide_deleted_ldda2( self ): 321 """Testing displaying and hiding a deleted ldda2""" 322 # Logged in as admin_user 323 self.browse_library( cntrller='library_admin', 324 library_id=self.security.encode_id( library1.id ), 325 show_deleted=True, 326 strings_displayed=[ ldda2.name, ldda2.message ] ) 327 self.browse_library( 'library_admin', 328 self.security.encode_id( library1.id ), 329 strings_not_displayed=[ ldda2.name, ldda2.message ] ) 330 def test_095_mark_folder2_deleted( self ): 331 """Testing marking folder2 as deleted""" 332 # Logged in as admin_user 333 self.delete_library_item( 'library_admin', 334 self.security.encode_id( library1.id ), 335 self.security.encode_id( folder2.id ), 336 folder2.name, 337 item_type='folder' ) 338 self.browse_library( cntrller='library_admin', 339 library_id=self.security.encode_id( library1.id ), 340 strings_not_displayed=[ folder2.name ] ) 341 def test_100_mark_folder_undeleted( self ): 342 """Testing marking a library folder as undeleted""" 343 # Logged in as admin_user 344 self.undelete_library_item( 'library_admin', 345 self.security.encode_id( library1.id ), 346 self.security.encode_id( folder2.id ), 347 folder2.name, 348 item_type='folder' ) 349 # 2.bed was deleted before the folder was deleted, so state should have been saved. In order 350 # for 2.bed to be displayed, it would itself have to be marked undeleted. 351 self.browse_library( cntrller='library_admin', 352 library_id=self.security.encode_id( library1.id ), 353 strings_displayed=[ folder2.name ], 354 strings_not_displayed=[ ldda2.name ] ) 355 def test_105_mark_library_deleted( self ): 356 """Testing marking a library as deleted""" 357 # Logged in as admin_user 358 # First mark folder2 as deleted to further test state saving when we undelete the library 359 self.delete_library_item( 'library_admin', 360 self.security.encode_id( library1.id ), 361 self.security.encode_id( folder2.id ), 362 folder2.name, 363 item_type='folder' ) 364 self.delete_library_item( 'library_admin', 365 self.security.encode_id( library1.id ), 366 self.security.encode_id( library1.id ), 367 library1.name, 368 item_type='library' ) 369 self.browse_libraries_admin( strings_not_displayed=[ library1.name ] ) 370 self.browse_libraries_admin( deleted=True, strings_displayed=[ library1.name ] ) 371 def test_110_mark_library_undeleted( self ): 372 """Testing marking a library as undeleted""" 373 # Logged in as admin_user 374 self.undelete_library_item( 'library_admin', 375 self.security.encode_id( library1.id ), 376 self.security.encode_id( library1.id ), 377 library1.name, 378 item_type='library' ) 379 self.browse_libraries_admin( strings_displayed=[ library1.name ] ) 380 self.browse_library( cntrller='library_admin', 381 library_id=self.security.encode_id( library1.id ), 382 strings_displayed=[ library1.name ], 383 strings_not_displayed=[ folder2.name ] ) 384 def test_115_purge_library( self ): 385 """Testing purging a library""" 386 # Logged in as admin_user 387 self.delete_library_item( 'library_admin', 388 self.security.encode_id( library1.id ), 389 self.security.encode_id( library1.id ), 390 library1.name, 391 item_type='library' ) 392 self.purge_library( self.security.encode_id( library1.id ), library1.name ) 393 # Make sure the library was purged 394 refresh( library1 ) 395 if not ( library1.deleted and library1.purged ): 396 raise AssertionError( 'The library id %s named "%s" has not been marked as deleted and purged.' % ( str( library1.id ), library1.name ) ) 397 def check_folder( library_folder ): 398 for folder in library_folder.folders: 399 refresh( folder ) 400 # Make sure all of the library_folders are purged 401 if not folder.purged: 402 raise AssertionError( 'The library_folder id %s named "%s" has not been marked purged.' % ( str( folder.id ), folder.name ) ) 403 check_folder( folder ) 404 # Make sure all of the LibraryDatasets and associated objects are deleted 405 refresh( library_folder ) 406 for library_dataset in library_folder.datasets: 407 refresh( library_dataset ) 408 ldda = library_dataset.library_dataset_dataset_association 409 if ldda: 410 refresh( ldda ) 411 if not ldda.deleted: 412 raise AssertionError( 'The library_dataset_dataset_association id %s named "%s" has not been marked as deleted.' % \ 413 ( str( ldda.id ), ldda.name ) ) 414 # Make sure all of the datasets have been deleted 415 dataset = ldda.dataset 416 refresh( dataset ) 417 if not dataset.deleted: 418 raise AssertionError( 'The dataset with id "%s" has not been marked as deleted when it should have been.' % \ 419 str( ldda.dataset.id ) ) 420 if not library_dataset.deleted: 421 raise AssertionError( 'The library_dataset id %s named "%s" has not been marked as deleted.' % \ 422 ( str( library_dataset.id ), library_dataset.name ) ) 423 check_folder( library1.root_folder ) 424 def test_120_populate_public_library2( self ): 425 """Testing library datasets within a library""" 426 # Logged in as admin_user 427 # Add a folder named Three to library2 root 428 root_folder = library2.root_folder 429 name = "One" 430 description = "One description" 431 self.add_folder( 'library_admin', 432 self.security.encode_id( library2.id ), 433 self.security.encode_id( root_folder.id ), 434 name=name, 435 description=description ) 436 global folder3 437 folder3 = get_folder( root_folder.id, name, description ) 438 assert folder3 is not None, 'Problem retrieving library folder named "%s" from the database' % name 439 # Upload dataset 1.bed to folder One 440 filename = '1.bed' 441 ldda_message = "Testing uploading %s" % filename 442 self.upload_library_dataset( cntrller='library_admin', 443 library_id=self.security.encode_id( library2.id ), 444 folder_id=self.security.encode_id( folder3.id ), 445 filename=filename, 446 file_type='bed', 447 dbkey='hg18', 448 ldda_message=ldda_message, 449 strings_displayed=[ 'Upload files' ] ) 450 global ldda5 451 ldda5 = get_latest_ldda_by_name( filename ) 452 assert ldda5 is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda5 from the database' 453 # Add a sub-folder named Two to folder One 454 name = "Two" 455 description = "Two description" 456 self.add_folder( 'library_admin', 457 self.security.encode_id( library2.id ), 458 self.security.encode_id( folder3.id ), 459 name=name, 460 description=description ) 461 global folder4 462 folder4 = get_folder( folder3.id, name, description ) 463 assert folder4 is not None, 'Problem retrieving library folder named "%s" from the database' % name 464 # Upload dataset 2.bed to folder Two 465 filename = '2.bed' 466 ldda_message = "Testing uploading %s" % filename 467 self.upload_library_dataset( cntrller='library_admin', 468 library_id=self.security.encode_id( library2.id ), 469 folder_id=self.security.encode_id( folder4.id ), 470 filename=filename, 471 file_type='bed', 472 dbkey='hg18', 473 ldda_message=ldda_message, 474 strings_displayed=[ 'Upload files' ] ) 475 global ldda6 476 ldda6 = get_latest_ldda_by_name( filename ) 477 assert ldda6 is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda6 from the database' 478 # Add a folder named Three to library2 root 479 name = "Three" 480 description = "Three description" 481 self.add_folder( 'library_admin', 482 self.security.encode_id( library2.id ), 483 self.security.encode_id( root_folder.id ), 484 name=name, 485 description=description ) 486 global folder5 487 folder5 = get_folder( root_folder.id, name, description ) 488 assert folder5 is not None, 'Problem retrieving library folder named "%s" from the database' % name 489 # Upload dataset 3.bed to library2 root folder 490 filename = '3.bed' 491 ldda_message = "Testing uploading %s" % filename 492 self.upload_library_dataset( cntrller='library_admin', 493 library_id=self.security.encode_id( library2.id ), 494 folder_id=self.security.encode_id( root_folder.id ), 495 filename=filename, 496 file_type='bed', 497 dbkey='hg18', 498 ldda_message=ldda_message, 499 strings_displayed=[ 'Upload files' ] ) 500 global ldda7 501 ldda7 = get_latest_ldda_by_name( filename ) 502 assert ldda7 is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda7 from the database' 503 def test_125_move_dataset_within_library2( self ): 504 """Testing moving a dataset within library2""" 505 # Logged in as admin_user 506 # Move 3.bed to folder Three 507 self.move_library_item( cntrller='library_admin', 508 item_type='ldda', 509 item_id=self.security.encode_id( ldda7.id ), 510 source_library_id=self.security.encode_id( library2.id ), 511 make_target_current=True, 512 target_folder_id=self.security.encode_id( folder5.id ), 513 strings_displayed=[ 'Move data library items', 514 '3.bed' ], 515 strings_displayed_after_submit=[ '1 dataset moved to folder (Three) within data library (library2)' ] ) 516 def test_130_move_folder_to_another_library( self ): 517 """Testing moving a folder to another library""" 518 # Logged in as admin_user 519 # Move folder Three which now includes 3.bed to library3 520 self.move_library_item( cntrller='library_admin', 521 item_type='folder', 522 item_id=self.security.encode_id( folder5.id ), 523 source_library_id=self.security.encode_id( library2.id ), 524 make_target_current=False, 525 target_library_id=self.security.encode_id( library3.id ), 526 target_folder_id=self.security.encode_id( library3.root_folder.id ), 527 strings_displayed=[ 'Move data library items', 528 'Three' ], 529 strings_displayed_after_submit=[ 'Moved folder (Three) to folder (library3) within data library (library3)' ] ) 530 # Make sure folder Three is not longer in library2 531 self.browse_library( cntrller='library_admin', 532 library_id=self.security.encode_id( library2.id ), 533 strings_displayed=[ folder4.name, folder4.description ], 534 strings_not_displayed=[ folder5.name, folder5.description ] ) 535 # Make sure folder Three was moved to library3 536 self.browse_library( cntrller='library_admin', 537 library_id=self.security.encode_id( library3.id ), 538 strings_displayed=[ folder5.name, folder5.description, ldda7.name ] ) 539 def test_135_upload_unsorted_bam_to_library_using_file_path_with_link_to_file( self ): 540 """Test uploading 3unsorted.bam, using filesystem_paths option in combination with link_to_files""" 541 filename = '3unsorted.bam' 542 self.upload_library_dataset( cntrller='library_admin', 543 library_id=self.security.encode_id( library2.id ), 544 folder_id=self.security.encode_id( library2.root_folder.id ), 545 upload_option='upload_paths', 546 link_data_only='link_to_files', 547 filesystem_paths='test-data/3unsorted.bam' ) 548 global ldda8 549 ldda8 = get_latest_ldda_by_name( filename ) 550 assert ldda8 is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda8 from the database' 551 # The upload above should produce an error condition in the uploaded library dataset since 552 # the uploaded bam file is not sorted, and we are linking to the file. 553 self.ldda_info( cntrller='library_admin', 554 library_id=self.security.encode_id( library2.id ), 555 folder_id=self.security.encode_id( library2.root_folder.id ), 556 ldda_id=self.security.encode_id( ldda8.id ), 557 strings_displayed=[ 'The uploaded files need grooming, so change your <b>Copy data into Galaxy?</b> selection to be' ] ) 558 def test_999_reset_data_for_later_test_runs( self ): 559 """Reseting data to enable later test runs to pass""" 560 # Logged in as admin_user 561 ################## 562 # Purge all libraries 563 ################## 564 for library in [ library1, library2, library3 ]: 565 self.delete_library_item( 'library_admin', 566 self.security.encode_id( library.id ), 567 self.security.encode_id( library.id ), 568 library.name, 569 item_type='library' ) 570 self.purge_library( self.security.encode_id( library.id ), library.name ) 571 ################## 572 # Make sure all users are associated only with their private roles 573 ################## 574 for user in [ admin_user, regular_user1, regular_user2, regular_user3 ]: 575 refresh( user ) 576 if len( user.roles) != 1: 577 raise AssertionError( '%d UserRoleAssociations are associated with %s ( should be 1 )' % ( len( user.roles ), user.email ) ) 578 self.logout()