/test/functional/test_get_data.py
Python | 639 lines | 367 code | 118 blank | 154 comment | 38 complexity | dc27a6774ab8ce31c04b2474425282fb MD5 | raw file
1from base.twilltestcase import TwillTestCase 2from base.test_db_util import ( 3 get_user, 4 get_latest_history_for_user, 5 get_latest_hda, 6) 7 8admin_user = None 9 10 11class UploadData( TwillTestCase ): 12 13 def test_0000_setup_upload_tests( self ): 14 """ 15 Configuring upload tests, setting admin_user 16 """ 17 self.logout() 18 self.login( email='test@bx.psu.edu' ) 19 global admin_user 20 admin_user = get_user( email='test@bx.psu.edu' ) 21 22 def create_fresh_history( self, user ): 23 """ 24 Deletes latest history for the given user, checks for an empty history, 25 and returns that new, empty history 26 """ 27 # in order to remove a lot of boiler plate - and not have cascading errors 28 history = get_latest_history_for_user( user ) 29 self.delete_history( id=self.security.encode_id( history.id ) ) 30 self.is_history_empty() 31 return get_latest_history_for_user( user ) 32 33 def test_0005_upload_file( self ): 34 """ 35 Test uploading 1.bed, NOT setting the file format 36 """ 37 history = self.create_fresh_history( admin_user ) 38 39 self.upload_file( '1.bed' ) 40 hda = get_latest_hda() 41 assert hda is not None, "Problem retrieving hda from database" 42 self.verify_dataset_correctness( '1.bed', hid=str( hda.hid ) ) 43 self.check_history_for_string( "<th>1.Chrom</th><th>2.Start</th><th>3.End</th>" ) 44 45 self.delete_history( id=self.security.encode_id( history.id ) ) 46 47 def test_0006_upload_file( self ): 48 """ 49 Test uploading 1.bed.spaces, with space to tab selected, NOT setting the file format 50 """ 51 history = self.create_fresh_history( admin_user ) 52 53 self.upload_file( '1.bed.spaces', space_to_tab=True ) 54 hda = get_latest_hda() 55 assert hda is not None, "Problem retrieving hda from database" 56 self.verify_dataset_correctness( '1.bed', hid=str( hda.hid ) ) 57 self.check_history_for_string( "<th>1.Chrom</th><th>2.Start</th><th>3.End</th>" ) 58 59 self.delete_history( id=self.security.encode_id( history.id ) ) 60 61 def test_0010_upload_file( self ): 62 """ 63 Test uploading 4.bed.gz, manually setting the file format 64 """ 65 history = self.create_fresh_history( admin_user ) 66 67 self.upload_file( '4.bed.gz', dbkey='hg17', ftype='bed' ) 68 hda = get_latest_hda() 69 assert hda is not None, "Problem retrieving hda from database" 70 self.verify_dataset_correctness( '4.bed', hid=str( hda.hid ) ) 71 self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), 72 "peek", "<th>1.Chrom</th><th>2.Start</th><th>3.End</th>", use_string_contains=True ) 73 74 self.delete_history( id=self.security.encode_id( history.id ) ) 75 76 def test_0012_upload_file( self ): 77 """ 78 Test uploading 4.bed.bz2, manually setting the file format 79 """ 80 history = self.create_fresh_history( admin_user ) 81 82 self.upload_file( '4.bed.bz2', dbkey='hg17', ftype='bed' ) 83 hda = get_latest_hda() 84 assert hda is not None, "Problem retrieving hda from database" 85 86 self.verify_dataset_correctness( '4.bed', hid=str( hda.hid ) ) 87 self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), 88 "peek", "<th>1.Chrom</th><th>2.Start</th><th>3.End</th>", use_string_contains=True ) 89 90 self.delete_history( id=self.security.encode_id( history.id ) ) 91 92 def test_0015_upload_file( self ): 93 """ 94 Test uploading 1.scf, manually setting the file format 95 """ 96 history = self.create_fresh_history( admin_user ) 97 98 self.upload_file( '1.scf', ftype='scf' ) 99 hda = get_latest_hda() 100 assert hda is not None, "Problem retrieving hda from database" 101 self.verify_dataset_correctness( '1.scf', hid=str( hda.hid ) ) 102 self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), 103 "peek", "Binary scf sequence file", use_string_contains=True ) 104 105 self.delete_history( id=self.security.encode_id( history.id ) ) 106 107 def test_0020_upload_file( self ): 108 """ 109 Test uploading 1.scf, NOT setting the file format 110 """ 111 history = self.create_fresh_history( admin_user ) 112 113 self.upload_file( '1.scf' ) 114 hda = get_latest_hda() 115 assert hda is not None, "Problem retrieving hda from database" 116 self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), 117 "misc_info", "File Format' to 'Scf' when uploading scf files", use_string_contains=True ) 118 119 self.delete_history( id=self.security.encode_id( history.id ) ) 120 121 def test_0025_upload_file( self ): 122 """ 123 Test uploading 4.bed.zip, manually setting the file format 124 """ 125 history = self.create_fresh_history( admin_user ) 126 127 self.upload_file( '4.bed.zip', ftype='bed' ) 128 hda = get_latest_hda() 129 assert hda is not None, "Problem retrieving hda from database" 130 self.verify_dataset_correctness( '4.bed', hid=str( hda.hid ) ) 131 self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), 132 "peek", "<th>1.Chrom</th><th>2.Start</th><th>3.End</th>", use_string_contains=True ) 133 134 self.delete_history( id=self.security.encode_id( history.id ) ) 135 136 def test_0030_upload_file( self ): 137 """ 138 Test uploading 4.bed.zip, NOT setting the file format 139 """ 140 history = self.create_fresh_history( admin_user ) 141 142 self.upload_file( '4.bed.zip' ) 143 hda = get_latest_hda() 144 assert hda is not None, "Problem retrieving hda from database" 145 self.verify_dataset_correctness( '4.bed', hid=str( hda.hid ) ) 146 self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), 147 "peek", "<th>1.Chrom</th><th>2.Start</th><th>3.End</th>", use_string_contains=True ) 148 149 self.delete_history( id=self.security.encode_id( history.id ) ) 150 151 def test_0035_upload_file( self ): 152 """ 153 Test uploading 1.sam NOT setting the file format 154 """ 155 history = self.create_fresh_history( admin_user ) 156 157 self.upload_file( '1.sam' ) 158 hda = get_latest_hda() 159 assert hda is not None, "Problem retrieving hda from database" 160 self.verify_dataset_correctness( '1.sam', hid=str( hda.hid ) ) 161 self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), 162 "peek", "<th>1.QNAME</th><th>2.FLAG</th><th>3.RNAME</th><th>4.POS</th>", use_string_contains=True ) 163 164 self.delete_history( id=self.security.encode_id( history.id ) ) 165 166 def test_0040_upload_file( self ): 167 """ 168 Test uploading 1.sff, NOT setting the file format 169 """ 170 history = self.create_fresh_history( admin_user ) 171 172 self.upload_file( '1.sff' ) 173 hda = get_latest_hda() 174 assert hda is not None, "Problem retrieving hda from database" 175 self.verify_dataset_correctness( '1.sff', hid=str( hda.hid ) ) 176 self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), 177 "misc_info", "sff", use_string_contains=True ) 178 179 self.delete_history( id=self.security.encode_id( history.id ) ) 180 181 def test_0045_upload_file( self ): 182 """ 183 Test uploading 454Score.pdf, NOT setting the file format 184 """ 185 history = self.create_fresh_history( admin_user ) 186 187 self.upload_file( '454Score.pdf' ) 188 hda = get_latest_hda() 189 assert hda is not None, "Problem retrieving hda from database" 190 self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), 191 "name", "454Score.pdf" ) 192 193 self.delete_history( id=self.security.encode_id( history.id ) ) 194 195 def test_0050_upload_file( self ): 196 """ 197 Test uploading 454Score.png, NOT setting the file format 198 """ 199 history = self.create_fresh_history( admin_user ) 200 201 self.upload_file( '454Score.png' ) 202 hda = get_latest_hda() 203 assert hda is not None, "Problem retrieving hda from database" 204 self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), 205 "name", "454Score.png" ) 206 207 self.delete_history( id=self.security.encode_id( history.id ) ) 208 209 def test_0055_upload_file( self ): 210 """ 211 Test uploading lped composite datatype file, manually setting the file format 212 """ 213 # Logged in as admin_user 214 history = self.create_fresh_history( admin_user ) 215 216 # lped data types include a ped_file and a map_file ( which is binary ) 217 self.upload_file( None, ftype='lped', metadata=[ { 'name':'base_name', 'value':'rgenetics' } ], composite_data=[ { 'name':'ped_file', 'value':'tinywga.ped' }, { 'name':'map_file', 'value':'tinywga.map'} ] ) 218 # Get the latest hid for testing 219 hda = get_latest_hda() 220 assert hda is not None, "Problem retrieving hda from database" 221 # We'll test against the resulting ped file and map file for correctness 222 self.verify_composite_datatype_file_content( 'tinywga.ped', str( hda.id ), base_name='rgenetics.ped' ) 223 self.verify_composite_datatype_file_content( 'tinywga.map', str( hda.id ), base_name='rgenetics.map' ) 224 self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), 225 "metadata_base_name", "rgenetics", use_string_contains=True ) 226 227 self.delete_history( id=self.security.encode_id( history.id ) ) 228 229 def test_0056_upload_file( self ): 230 """ 231 Test uploading lped composite datatype file, manually setting the file format, and using space to tab on one file (tinywga.ped) 232 """ 233 # Logged in as admin_user 234 history = self.create_fresh_history( admin_user ) 235 236 # lped data types include a ped_file and a map_file ( which is binary ) 237 self.upload_file( None, ftype='lped', metadata=[ { 'name':'base_name', 'value':'rgenetics' } ], composite_data=[ { 'name':'ped_file', 'value':'tinywga.ped', 'space_to_tab':True }, { 'name':'map_file', 'value':'tinywga.map'} ] ) 238 # Get the latest hid for testing 239 hda = get_latest_hda() 240 assert hda is not None, "Problem retrieving hda from database" 241 # We'll test against the resulting ped file and map file for correctness 242 self.verify_composite_datatype_file_content( 'tinywga.ped.space_to_tab', str( hda.id ), base_name='rgenetics.ped' ) 243 self.verify_composite_datatype_file_content( 'tinywga.map', str( hda.id ), base_name='rgenetics.map' ) 244 self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), 245 "metadata_base_name", "rgenetics", use_string_contains=True ) 246 247 self.delete_history( id=self.security.encode_id( history.id ) ) 248 249 def test_0060_upload_file( self ): 250 """ 251 Test uploading pbed composite datatype file, manually setting the file format 252 """ 253 # Logged in as admin_user 254 history = self.create_fresh_history( admin_user ) 255 256 # pbed data types include a bim_file, a bed_file and a fam_file 257 self.upload_file( None, ftype='pbed', 258 metadata=[ { 'name':'base_name', 'value':'rgenetics' } ], 259 composite_data=[ 260 { 'name':'bim_file', 'value':'tinywga.bim' }, 261 { 'name':'bed_file', 'value':'tinywga.bed' }, 262 { 'name':'fam_file', 'value':'tinywga.fam' } ]) 263 # Get the latest hid for testing 264 hda = get_latest_hda() 265 assert hda is not None, "Problem retrieving hda from database" 266 # We'll test against the resulting ped file and map file for correctness 267 self.verify_composite_datatype_file_content( 'tinywga.bim', str( hda.id ), base_name='rgenetics.bim' ) 268 self.verify_composite_datatype_file_content( 'tinywga.bed', str( hda.id ), base_name='rgenetics.bed' ) 269 self.verify_composite_datatype_file_content( 'tinywga.fam', str( hda.id ), base_name='rgenetics.fam' ) 270 self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), 271 "metadata_base_name", "rgenetics", use_string_contains=True ) 272 273 self.delete_history( id=self.security.encode_id( history.id ) ) 274 275 def test_0065_upload_file( self ): 276 """ 277 Test uploading asian_chars_1.txt, NOT setting the file format 278 """ 279 # Logged in as admin_user 280 history = self.create_fresh_history( admin_user ) 281 282 self.upload_file( 'asian_chars_1.txt' ) 283 hda = get_latest_hda() 284 assert hda is not None, "Problem retrieving hda from database" 285 self.verify_dataset_correctness( 'asian_chars_1.txt', hid=str( hda.hid ) ) 286 self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), 287 "misc_info", "uploaded multi-byte char file", use_string_contains=True ) 288 289 self.delete_history( id=self.security.encode_id( history.id ) ) 290 291 def test_0070_upload_file( self ): 292 """ 293 Test uploading 2gen.fastq, NOT setting the file format 294 """ 295 # Logged in as admin_user 296 history = self.create_fresh_history( admin_user ) 297 298 self.upload_file( '2gen.fastq' ) 299 hda = get_latest_hda() 300 assert hda is not None, "Problem retrieving hda from database" 301 self.verify_dataset_correctness( '2gen.fastq', hid=str( hda.hid ) ) 302 self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), "data_type", "fastq" ) 303 304 self.delete_history( id=self.security.encode_id( history.id ) ) 305 306 def test_0075_upload_file( self ): 307 """ 308 Test uploading 1.wig, NOT setting the file format 309 """ 310 # Logged in as admin_user 311 history = self.create_fresh_history( admin_user ) 312 313 self.upload_file( '1.wig' ) 314 hda = get_latest_hda() 315 assert hda is not None, "Problem retrieving hda from database" 316 self.verify_dataset_correctness( '1.wig', hid=str( hda.hid ) ) 317 self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), "data_type", "wig" ) 318 self.check_metadata_for_string( 'value="1.wig" value="\?"' ) 319 self.check_metadata_for_string( 'Change data type selected value="wig" selected="yes"' ) 320 321 self.delete_history( id=self.security.encode_id( history.id ) ) 322 323 def test_0080_upload_file( self ): 324 """ 325 Test uploading 1.tabular, NOT setting the file format 326 """ 327 # Logged in as admin_user 328 history = self.create_fresh_history( admin_user ) 329 330 self.upload_file( '1.tabular' ) 331 hda = get_latest_hda() 332 assert hda is not None, "Problem retrieving hda from database" 333 self.verify_dataset_correctness( '1.tabular', hid=str( hda.hid ) ) 334 self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), "data_type", "tabular" ) 335 self.check_metadata_for_string( 'value="1.tabular" value="\?"' ) 336 self.check_metadata_for_string( 'Change data type selected value="tabular" selected="yes"' ) 337 338 self.delete_history( id=self.security.encode_id( history.id ) ) 339 340 def test_0085_upload_file( self ): 341 """ 342 Test uploading qualscores.qualsolid, NOT setting the file format 343 """ 344 # Logged in as admin_user 345 history = self.create_fresh_history( admin_user ) 346 347 self.upload_file( 'qualscores.qualsolid' ) 348 hda = get_latest_hda() 349 assert hda is not None, "Problem retrieving hda from database" 350 self.verify_dataset_correctness( 'qualscores.qualsolid', hid=str( hda.hid ) ) 351 self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), "data_type", "qualsolid" ) 352 self.check_metadata_for_string( 'Change data type value="qualsolid" selected="yes">qualsolid' ) 353 354 self.delete_history( id=self.security.encode_id( history.id ) ) 355 356 def test_0090_upload_file( self ): 357 """ 358 Test uploading qualscores.qual454, NOT setting the file format 359 """ 360 # Logged in as admin_user 361 history = self.create_fresh_history( admin_user ) 362 363 self.upload_file( 'qualscores.qual454' ) 364 hda = get_latest_hda() 365 assert hda is not None, "Problem retrieving hda from database" 366 self.verify_dataset_correctness( 'qualscores.qual454', hid=str( hda.hid ) ) 367 self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), "data_type", "qual454" ) 368 self.check_metadata_for_string( 'Change data type value="qual454" selected="yes">qual454' ) 369 370 self.delete_history( id=self.security.encode_id( history.id ) ) 371 372 def test_0095_upload_file( self ): 373 """ 374 Test uploading 3.maf, NOT setting the file format 375 """ 376 # Logged in as admin_user 377 history = self.create_fresh_history( admin_user ) 378 379 self.upload_file( '3.maf' ) 380 hda = get_latest_hda() 381 assert hda is not None, "Problem retrieving hda from database" 382 self.verify_dataset_correctness( '3.maf', hid=str( hda.hid ) ) 383 self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), "data_type", "maf" ) 384 self.check_metadata_for_string( 'value="3.maf" value="\?"' ) 385 self.check_metadata_for_string( 'Convert to new format <option value="interval">Convert MAF to Genomic Intervals <option value="fasta">Convert MAF to Fasta' ) 386 self.check_metadata_for_string( 'Change data type selected value="maf" selected="yes"' ) 387 388 self.delete_history( id=self.security.encode_id( history.id ) ) 389 390 def test_0100_upload_file( self ): 391 """ 392 Test uploading 1.lav, NOT setting the file format 393 """ 394 # Logged in as admin_user 395 history = self.create_fresh_history( admin_user ) 396 397 self.upload_file( '1.lav' ) 398 hda = get_latest_hda() 399 assert hda is not None, "Problem retrieving hda from database" 400 self.verify_dataset_correctness( '1.lav', hid=str( hda.hid ) ) 401 self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), "data_type", "lav" ) 402 self.check_metadata_for_string( 'value="1.lav" value="\?"' ) 403 self.check_metadata_for_string( 'Change data type selected value="lav" selected="yes"' ) 404 405 self.delete_history( id=self.security.encode_id( history.id ) ) 406 407 def test_0105_upload_file( self ): 408 """ 409 Test uploading 1.interval, NOT setting the file format 410 """ 411 # Logged in as admin_user 412 history = self.create_fresh_history( admin_user ) 413 414 self.upload_file( '1.interval' ) 415 hda = get_latest_hda() 416 assert hda is not None, "Problem retrieving hda from database" 417 self.verify_dataset_correctness( '1.interval', hid=str( hda.hid ) ) 418 self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), "data_type", "interval" ) 419 self.check_metadata_for_string( 'value="1.interval" value="\?"' ) 420 self.check_metadata_for_string( 'Chrom column: <option value="1" selected> Start column: <option value="2" selected>' ) 421 self.check_metadata_for_string( 'End column: <option value="3" selected> Strand column <option value="6" selected>' ) 422 self.check_metadata_for_string( 'Convert to new format <option value="bed">Convert Genomic Intervals To BED' ) 423 self.check_metadata_for_string( 'Change data type selected value="interval" selected="yes"' ) 424 425 self.delete_history( id=self.security.encode_id( history.id ) ) 426 427 def test_0110_upload_file( self ): 428 """ 429 Test uploading 5.gff3, NOT setting the file format 430 """ 431 # Logged in as admin_user 432 history = self.create_fresh_history( admin_user ) 433 434 self.upload_file( '5.gff3' ) 435 hda = get_latest_hda() 436 assert hda is not None, "Problem retrieving hda from database" 437 self.verify_dataset_correctness( '5.gff3', hid=str( hda.hid ) ) 438 self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), "data_type", "gff3" ) 439 self.check_metadata_for_string( 'value="5.gff3" value="\?"' ) 440 self.check_metadata_for_string( 'Convert to new format <option value="bed">Convert GFF to BED' ) 441 self.check_metadata_for_string( 'Change data type selected value="gff3" selected="yes"' ) 442 443 self.delete_history( id=self.security.encode_id( history.id ) ) 444 445 def test_0115_upload_file( self ): 446 """ 447 Test uploading html_file.txt, NOT setting the file format 448 """ 449 # Logged in as admin_user 450 history = self.create_fresh_history( admin_user ) 451 452 self.upload_file( 'html_file.txt' ) 453 hda = get_latest_hda() 454 assert hda is not None, "Problem retrieving hda from database" 455 self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), 456 "misc_info", "The uploaded file contains inappropriate HTML content", use_string_contains=True ) 457 458 self.delete_history( id=self.security.encode_id( history.id ) ) 459 460 def test_0120_upload_file( self ): 461 """ 462 Test uploading 5.gff, NOT setting the file format 463 464 Test sniffer for gff. 465 """ 466 history = self.create_fresh_history( admin_user ) 467 468 self.upload_file( '5.gff' ) 469 hda = get_latest_hda() 470 assert hda is not None, "Problem retrieving hda from database" 471 self.verify_dataset_correctness( '5.gff', hid=str( hda.hid ) ) 472 self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), "data_type", "gff" ) 473 self.check_metadata_for_string( 'value="5.gff" value="\?"' ) 474 self.check_metadata_for_string( 'Convert to new format <option value="bed">Convert GFF to BED' ) 475 self.check_metadata_for_string( 'Change data type selected value="gff" selected="yes"' ) 476 477 self.delete_history( id=self.security.encode_id( history.id ) ) 478 479 def test_0125_upload_file( self ): 480 """ 481 Test uploading 1.fasta, NOT setting the file format 482 """ 483 # Logged in as admin_user 484 history = self.create_fresh_history( admin_user ) 485 486 self.upload_file( '1.fasta' ) 487 hda = get_latest_hda() 488 assert hda is not None, "Problem retrieving hda from database" 489 self.verify_dataset_correctness( '1.fasta', hid=str( hda.hid ) ) 490 self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), "data_type", "fasta" ) 491 self.check_metadata_for_string( 'value="1.fasta" value="\?" Change data type selected value="fasta" selected="yes"' ) 492 493 self.delete_history( id=self.security.encode_id( history.id ) ) 494 495 def test_0130_upload_file( self ): 496 """ 497 Test uploading 1.customtrack, NOT setting the file format 498 """ 499 # Logged in as admin_user 500 history = self.create_fresh_history( admin_user ) 501 502 self.upload_file( '1.customtrack' ) 503 hda = get_latest_hda() 504 assert hda is not None, "Problem retrieving hda from database" 505 self.verify_dataset_correctness( '1.customtrack', hid=str( hda.hid ) ) 506 self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), "data_type", "customtrack" ) 507 self.check_metadata_for_string( 'value="1.customtrack" value="\?" Change data type selected value="customtrack" selected="yes"' ) 508 509 self.delete_history( id=self.security.encode_id( history.id ) ) 510 511 def test_0135_upload_file( self ): 512 """ 513 Test uploading shrimp_cs_test1.csfasta, NOT setting the file format 514 """ 515 # Logged in as admin_user 516 history = self.create_fresh_history( admin_user ) 517 518 self.upload_file( 'shrimp_cs_test1.csfasta' ) 519 hda = get_latest_hda() 520 assert hda is not None, "Problem retrieving hda from database" 521 self.verify_dataset_correctness( 'shrimp_cs_test1.csfasta', hid=str( hda.hid ) ) 522 self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), "data_type", "csfasta" ) 523 self.check_metadata_for_string( 'value="shrimp_cs_test1.csfasta" value="\?" Change data type value="csfasta" selected="yes"' ) 524 525 self.delete_history( id=self.security.encode_id( history.id ) ) 526 527 def test_0145_upload_file( self ): 528 """ 529 Test uploading 1.axt, NOT setting the file format 530 """ 531 # Logged in as admin_user 532 history = self.create_fresh_history( admin_user ) 533 534 self.upload_file( '1.axt' ) 535 hda = get_latest_hda() 536 assert hda is not None, "Problem retrieving hda from database" 537 self.verify_dataset_correctness( '1.axt', hid=str( hda.hid ) ) 538 self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), "data_type", "axt" ) 539 self.check_metadata_for_string( 'value="1.axt" value="\?" Change data type selected value="axt" selected="yes"' ) 540 541 self.delete_history( id=self.security.encode_id( history.id ) ) 542 543 def test_0150_upload_file( self ): 544 """ 545 Test uploading 1.bam, which is a sorted Bam file creaed by the Galaxy sam_to_bam tool, NOT setting the file format 546 """ 547 history = self.create_fresh_history( admin_user ) 548 549 self.upload_file( '1.bam' ) 550 hda = get_latest_hda() 551 assert hda is not None, "Problem retrieving hda from database" 552 self.verify_dataset_correctness( '1.bam', hid=str( hda.hid ), attributes={ 'ftype' : 'bam' } ) 553 self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), "data_type", "bam" ) 554 # Make sure the Bam index was created 555 assert hda.metadata.bam_index is not None, "Bam index was not correctly created for 1.bam" 556 557 self.delete_history( id=self.security.encode_id( history.id ) ) 558 559 def test_0155_upload_file( self ): 560 """ 561 Test uploading 3unsorted.bam, which is an unsorted Bam file, NOT setting the file format 562 """ 563 history = self.create_fresh_history( admin_user ) 564 565 self.upload_file( '3unsorted.bam' ) 566 hda = get_latest_hda() 567 assert hda is not None, "Problem retrieving hda from database" 568 # Since 3unsorted.bam is not sorted, we cannot verify dataset correctness since the uploaded 569 # dataset will be sorted. However, the check below to see if the index was created is 570 # sufficient. 571 self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), "data_type", "bam" ) 572 # Make sure the Bam index was created 573 assert hda.metadata.bam_index is not None, "Bam index was not correctly created for 3unsorted.bam" 574 575 self.delete_history( id=self.security.encode_id( history.id ) ) 576 577 def test_0160_url_paste( self ): 578 """ 579 Test url paste behavior 580 """ 581 # Logged in as admin_user 582 history = self.create_fresh_history( admin_user ) 583 584 self.upload_url_paste( 'hello world' ) 585 self.check_history_for_exact_string( 'Pasted Entry' ) 586 self.check_history_for_exact_string( 'hello world' ) 587 self.upload_url_paste( u'hello world' ) 588 self.check_history_for_exact_string( 'Pasted Entry' ) 589 self.check_history_for_exact_string( 'hello world' ) 590 591 self.delete_history( id=self.security.encode_id( history.id ) ) 592 593 def test_0165_upload_file( self ): 594 """ 595 Test uploading 1.pileup, NOT setting the file format 596 """ 597 history = self.create_fresh_history( admin_user ) 598 599 self.upload_file( '1.pileup' ) 600 hda = get_latest_hda() 601 assert hda is not None, "Problem retrieving hda from database" 602 self.verify_dataset_correctness( '1.pileup', hid=str( hda.hid ) ) 603 self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), "data_type", "pileup" ) 604 self.check_metadata_for_string( 'value="1.pileup" value="\?" Change data type selected value="pileup" selected="yes"' ) 605 606 self.delete_history( id=self.security.encode_id( history.id ) ) 607 608 def test_0170_upload_file( self ): 609 """ 610 Test uploading 1.bigbed, NOT setting the file format 611 """ 612 history = self.create_fresh_history( admin_user ) 613 614 self.upload_file( '1.bigbed' ) 615 hda = get_latest_hda() 616 assert hda is not None, "Problem retrieving hda from database" 617 self.verify_dataset_correctness( '1.bigbed', hid=str( hda.hid ) ) 618 self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), "data_type", "bigbed" ) 619 self.check_metadata_for_string( 'value="1.bigbed" value="\?" Change data type selected value="bigbed" selected="yes"' ) 620 621 self.delete_history( id=self.security.encode_id( history.id ) ) 622 623 def test_0175_upload_file( self ): 624 """ 625 Test uploading 1.bigwig, NOT setting the file format 626 """ 627 history = self.create_fresh_history( admin_user ) 628 629 self.upload_file( '1.bigwig' ) 630 hda = get_latest_hda() 631 assert hda is not None, "Problem retrieving hda from database" 632 self.verify_dataset_correctness( '1.bigwig', hid=str( hda.hid ) ) 633 self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), "data_type", "bigwig" ) 634 self.check_metadata_for_string( 'value="1.bigwig" value="\?" Change data type selected value="bigwig" selected="yes"' ) 635 636 self.delete_history( id=self.security.encode_id( history.id ) ) 637 638 def test_9999_clean_up( self ): 639 self.logout()