[2] | 1 | import galaxy.model |
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| 2 | from galaxy.model.orm import * |
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| 3 | from galaxy.model.mapping import context as sa_session |
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| 4 | from base.twilltestcase import TwillTestCase |
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| 5 | from base.test_db_util import * |
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| 6 | |
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| 7 | class UploadData( TwillTestCase ): |
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| 8 | def test_0000_setup_upload_tests( self ): |
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| 9 | """Configuring upload tests, setting admin_user""" |
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| 10 | self.logout() |
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| 11 | self.login( email='test@bx.psu.edu' ) |
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| 12 | global admin_user |
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| 13 | admin_user = get_user( email='test@bx.psu.edu' ) |
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| 14 | def test_0005_upload_file( self ): |
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| 15 | """Test uploading 1.bed, NOT setting the file format""" |
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| 16 | history = get_latest_history_for_user( admin_user ) |
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| 17 | self.upload_file( '1.bed' ) |
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| 18 | hda = get_latest_hda() |
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| 19 | assert hda is not None, "Problem retrieving hda from database" |
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| 20 | self.verify_dataset_correctness( '1.bed', hid=str( hda.hid ) ) |
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| 21 | self.check_history_for_string( "<th>1.Chrom</th><th>2.Start</th><th>3.End</th>" ) |
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| 22 | self.delete_history( id=self.security.encode_id( history.id ) ) |
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| 23 | def test_0006_upload_file( self ): |
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| 24 | """Test uploading 1.bed.spaces, with space to tab selected, NOT setting the file format""" |
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| 25 | history = get_latest_history_for_user( admin_user ) |
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| 26 | self.upload_file( '1.bed.spaces', space_to_tab = True ) |
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| 27 | hda = get_latest_hda() |
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| 28 | assert hda is not None, "Problem retrieving hda from database" |
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| 29 | self.verify_dataset_correctness( '1.bed', hid=str( hda.hid ) ) |
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| 30 | self.check_history_for_string( "<th>1.Chrom</th><th>2.Start</th><th>3.End</th>" ) |
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| 31 | self.delete_history( id=self.security.encode_id( history.id ) ) |
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| 32 | def test_0010_upload_file( self ): |
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| 33 | """Test uploading 4.bed.gz, manually setting the file format""" |
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| 34 | self.check_history_for_string( 'Your history is empty' ) |
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| 35 | history = get_latest_history_for_user( admin_user ) |
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| 36 | self.upload_file( '4.bed.gz', dbkey='hg17', ftype='bed' ) |
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| 37 | hda = get_latest_hda() |
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| 38 | assert hda is not None, "Problem retrieving hda from database" |
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| 39 | self.verify_dataset_correctness( '4.bed', hid=str( hda.hid ) ) |
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| 40 | self.check_history_for_string( "<th>1.Chrom</th><th>2.Start</th><th>3.End</th>" ) |
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| 41 | self.delete_history( id=self.security.encode_id( history.id ) ) |
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| 42 | def test_0012_upload_file( self ): |
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| 43 | """Test uploading 4.bed.bz2, manually setting the file format""" |
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| 44 | self.check_history_for_string( 'Your history is empty' ) |
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| 45 | history = get_latest_history_for_user( admin_user ) |
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| 46 | self.upload_file( '4.bed.bz2', dbkey='hg17', ftype='bed' ) |
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| 47 | hda = get_latest_hda() |
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| 48 | assert hda is not None, "Problem retrieving hda from database" |
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| 49 | self.verify_dataset_correctness( '4.bed', hid=str( hda.hid ) ) |
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| 50 | self.check_history_for_string( "<th>1.Chrom</th><th>2.Start</th><th>3.End</th>" ) |
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| 51 | self.delete_history( id=self.security.encode_id( history.id ) ) |
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| 52 | def test_0015_upload_file( self ): |
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| 53 | """Test uploading 1.scf, manually setting the file format""" |
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| 54 | self.check_history_for_string( 'Your history is empty' ) |
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| 55 | history = get_latest_history_for_user( admin_user ) |
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| 56 | self.upload_file( '1.scf', ftype='scf' ) |
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| 57 | hda = get_latest_hda() |
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| 58 | assert hda is not None, "Problem retrieving hda from database" |
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| 59 | self.verify_dataset_correctness( '1.scf', hid=str( hda.hid ) ) |
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| 60 | self.check_history_for_string( "Binary scf sequence file</pre>" ) |
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| 61 | self.delete_history( id=self.security.encode_id( history.id ) ) |
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| 62 | def test_0020_upload_file( self ): |
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| 63 | """Test uploading 1.scf, NOT setting the file format""" |
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| 64 | self.check_history_for_string( 'Your history is empty' ) |
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| 65 | history = get_latest_history_for_user( admin_user ) |
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| 66 | self.upload_file( '1.scf' ) |
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| 67 | hda = get_latest_hda() |
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| 68 | assert hda is not None, "Problem retrieving hda from database" |
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| 69 | self.check_history_for_string( "File Format' to 'Scf' when uploading scf files" ) |
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| 70 | self.delete_history( id=self.security.encode_id( history.id ) ) |
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| 71 | def test_0025_upload_file( self ): |
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| 72 | """Test uploading 4.bed.zip, manually setting the file format""" |
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| 73 | self.check_history_for_string( 'Your history is empty' ) |
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| 74 | history = get_latest_history_for_user( admin_user ) |
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| 75 | self.upload_file( '4.bed.zip', ftype='bed' ) |
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| 76 | hda = get_latest_hda() |
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| 77 | assert hda is not None, "Problem retrieving hda from database" |
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| 78 | self.verify_dataset_correctness( '4.bed', hid=str( hda.hid ) ) |
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| 79 | self.check_history_for_string( "<th>1.Chrom</th><th>2.Start</th><th>3.End</th>" ) |
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| 80 | self.delete_history( id=self.security.encode_id( history.id ) ) |
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| 81 | def test_0030_upload_file( self ): |
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| 82 | """Test uploading 4.bed.zip, NOT setting the file format""" |
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| 83 | self.check_history_for_string( 'Your history is empty' ) |
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| 84 | history = get_latest_history_for_user( admin_user ) |
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| 85 | self.upload_file( '4.bed.zip' ) |
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| 86 | hda = get_latest_hda() |
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| 87 | assert hda is not None, "Problem retrieving hda from database" |
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| 88 | self.verify_dataset_correctness( '4.bed', hid=str( hda.hid ) ) |
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| 89 | self.check_history_for_string( "<th>1.Chrom</th><th>2.Start</th><th>3.End</th>" ) |
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| 90 | self.delete_history( id=self.security.encode_id( history.id ) ) |
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| 91 | def test_0035_upload_file( self ): |
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| 92 | """Test uploading 1.sam NOT setting the file format""" |
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| 93 | self.check_history_for_string( 'Your history is empty' ) |
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| 94 | history = get_latest_history_for_user( admin_user ) |
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| 95 | self.upload_file( '1.sam' ) |
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| 96 | hda = get_latest_hda() |
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| 97 | assert hda is not None, "Problem retrieving hda from database" |
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| 98 | self.verify_dataset_correctness( '1.sam', hid=str( hda.hid ) ) |
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| 99 | self.check_history_for_string( "<th>1.QNAME</th><th>2.FLAG</th><th>3.RNAME</th><th>4.POS</th>" ) |
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| 100 | self.delete_history( id=self.security.encode_id( history.id ) ) |
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| 101 | def test_0040_upload_file( self ): |
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| 102 | """Test uploading 1.sff, NOT setting the file format""" |
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| 103 | self.check_history_for_string( 'Your history is empty' ) |
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| 104 | history = get_latest_history_for_user( admin_user ) |
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| 105 | self.upload_file( '1.sff' ) |
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| 106 | hda = get_latest_hda() |
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| 107 | assert hda is not None, "Problem retrieving hda from database" |
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| 108 | self.verify_dataset_correctness( '1.sff', hid=str( hda.hid ) ) |
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| 109 | self.check_history_for_string( 'format: <span class="sff">sff' ) |
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| 110 | self.delete_history( id=self.security.encode_id( history.id ) ) |
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| 111 | def test_0045_upload_file( self ): |
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| 112 | """Test uploading 454Score.pdf, NOT setting the file format""" |
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| 113 | self.check_history_for_string( 'Your history is empty' ) |
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| 114 | history = get_latest_history_for_user( admin_user ) |
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| 115 | self.upload_file( '454Score.pdf' ) |
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| 116 | hda = get_latest_hda() |
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| 117 | assert hda is not None, "Problem retrieving hda from database" |
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| 118 | self.check_history_for_string( "1: 454Score.pdf</span>" ) |
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| 119 | self.delete_history( id=self.security.encode_id( history.id ) ) |
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| 120 | def test_0050_upload_file( self ): |
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| 121 | """Test uploading 454Score.png, NOT setting the file format""" |
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| 122 | self.check_history_for_string( 'Your history is empty' ) |
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| 123 | history = get_latest_history_for_user( admin_user ) |
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| 124 | self.upload_file( '454Score.png' ) |
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| 125 | hda = get_latest_hda() |
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| 126 | assert hda is not None, "Problem retrieving hda from database" |
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| 127 | self.check_history_for_string( "The uploaded file contains inappropriate content" ) |
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| 128 | def test_0055_upload_file( self ): |
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| 129 | """Test uploading lped composite datatype file, manually setting the file format""" |
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| 130 | # Logged in as admin_user |
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| 131 | self.check_history_for_string( 'Your history is empty' ) |
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| 132 | history = get_latest_history_for_user( admin_user ) |
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| 133 | # lped data types include a ped_file and a map_file ( which is binary ) |
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| 134 | 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'} ] ) |
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| 135 | # Get the latest hid for testing |
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| 136 | hda = get_latest_hda() |
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| 137 | assert hda is not None, "Problem retrieving hda from database" |
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| 138 | # We'll test against the resulting ped file and map file for correctness |
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| 139 | self.verify_composite_datatype_file_content( 'tinywga.ped', str( hda.id ), base_name = 'rgenetics.ped' ) |
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| 140 | self.verify_composite_datatype_file_content( 'tinywga.map', str( hda.id ), base_name = 'rgenetics.map' ) |
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| 141 | self.check_history_for_string( "rgenetics" ) |
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| 142 | self.delete_history( id=self.security.encode_id( history.id ) ) |
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| 143 | def test_0056_upload_file( self ): |
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| 144 | """Test uploading lped composite datatype file, manually setting the file format, and using space to tab on one file (tinywga.ped)""" |
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| 145 | # Logged in as admin_user |
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| 146 | self.check_history_for_string( 'Your history is empty' ) |
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| 147 | history = get_latest_history_for_user( admin_user ) |
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| 148 | # lped data types include a ped_file and a map_file ( which is binary ) |
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| 149 | 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'} ] ) |
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| 150 | # Get the latest hid for testing |
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| 151 | hda = get_latest_hda() |
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| 152 | assert hda is not None, "Problem retrieving hda from database" |
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| 153 | # We'll test against the resulting ped file and map file for correctness |
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| 154 | self.verify_composite_datatype_file_content( 'tinywga.ped.space_to_tab', str( hda.id ), base_name = 'rgenetics.ped' ) |
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| 155 | self.verify_composite_datatype_file_content( 'tinywga.map', str( hda.id ), base_name = 'rgenetics.map' ) |
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| 156 | self.check_history_for_string( "rgenetics" ) |
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| 157 | self.delete_history( id=self.security.encode_id( history.id ) ) |
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| 158 | def test_0060_upload_file( self ): |
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| 159 | """Test uploading pbed composite datatype file, manually setting the file format""" |
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| 160 | # Logged in as admin_user |
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| 161 | self.check_history_for_string( 'Your history is empty' ) |
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| 162 | history = get_latest_history_for_user( admin_user ) |
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| 163 | # pbed data types include a bim_file, a bed_file and a fam_file |
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| 164 | self.upload_file( None, ftype='pbed', metadata = [ { 'name':'base_name', 'value':'rgenetics' } ], composite_data = [ { 'name':'bim_file', 'value':'tinywga.bim' }, { 'name':'bed_file', 'value':'tinywga.bed'}, { 'name':'fam_file', 'value':'tinywga.fam' } ] ) |
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| 165 | # Get the latest hid for testing |
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| 166 | hda = get_latest_hda() |
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| 167 | assert hda is not None, "Problem retrieving hda from database" |
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| 168 | # We'll test against the resulting ped file and map file for correctness |
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| 169 | self.verify_composite_datatype_file_content( 'tinywga.bim', str( hda.id ), base_name = 'rgenetics.bim' ) |
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| 170 | self.verify_composite_datatype_file_content( 'tinywga.bed', str( hda.id ), base_name = 'rgenetics.bed' ) |
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| 171 | self.verify_composite_datatype_file_content( 'tinywga.fam', str( hda.id ), base_name = 'rgenetics.fam' ) |
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| 172 | self.check_history_for_string( "rgenetics" ) |
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| 173 | self.delete_history( id=self.security.encode_id( history.id ) ) |
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| 174 | def test_0065_upload_file( self ): |
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| 175 | """Test uploading asian_chars_1.txt, NOT setting the file format""" |
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| 176 | # Logged in as admin_user |
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| 177 | self.check_history_for_string( 'Your history is empty' ) |
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| 178 | history = get_latest_history_for_user( admin_user ) |
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| 179 | self.upload_file( 'asian_chars_1.txt' ) |
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| 180 | hda = get_latest_hda() |
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| 181 | assert hda is not None, "Problem retrieving hda from database" |
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| 182 | self.verify_dataset_correctness( 'asian_chars_1.txt', hid=str( hda.hid ) ) |
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| 183 | self.check_history_for_string( 'uploaded multi-byte char file' ) |
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| 184 | self.delete_history( id=self.security.encode_id( history.id ) ) |
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| 185 | def test_0070_upload_file( self ): |
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| 186 | """Test uploading 2gen.fastq, NOT setting the file format""" |
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| 187 | # Logged in as admin_user |
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| 188 | self.check_history_for_string( 'Your history is empty' ) |
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| 189 | history = get_latest_history_for_user( admin_user ) |
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| 190 | self.upload_file( '2gen.fastq' ) |
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| 191 | hda = get_latest_hda() |
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| 192 | assert hda is not None, "Problem retrieving hda from database" |
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| 193 | self.verify_dataset_correctness( '2gen.fastq', hid=str( hda.hid ) ) |
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| 194 | self.check_history_for_string( '2gen.fastq format: <span class="fastq">fastq</span>, database: \? Info: uploaded fastq file' ) |
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| 195 | self.delete_history( id=self.security.encode_id( history.id ) ) |
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| 196 | def test_0075_upload_file( self ): |
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| 197 | """Test uploading 1.wig, NOT setting the file format""" |
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| 198 | # Logged in as admin_user |
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| 199 | self.check_history_for_string( 'Your history is empty' ) |
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| 200 | history = get_latest_history_for_user( admin_user ) |
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| 201 | self.upload_file( '1.wig' ) |
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| 202 | hda = get_latest_hda() |
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| 203 | assert hda is not None, "Problem retrieving hda from database" |
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| 204 | self.verify_dataset_correctness( '1.wig', hid=str( hda.hid ) ) |
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| 205 | self.check_history_for_string( '1.wig format: <span class="wig">wig</span>, database: \? Info: uploaded file' ) |
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| 206 | self.check_metadata_for_string( 'value="1.wig" value="\?"' ) |
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| 207 | self.check_metadata_for_string( 'Change data type selected value="wig" selected="yes"' ) |
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| 208 | self.delete_history( id=self.security.encode_id( history.id ) ) |
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| 209 | def test_0080_upload_file( self ): |
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| 210 | """Test uploading 1.tabular, NOT setting the file format""" |
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| 211 | # Logged in as admin_user |
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| 212 | self.check_history_for_string( 'Your history is empty' ) |
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| 213 | history = get_latest_history_for_user( admin_user ) |
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| 214 | self.upload_file( '1.tabular' ) |
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| 215 | hda = get_latest_hda() |
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| 216 | assert hda is not None, "Problem retrieving hda from database" |
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| 217 | self.verify_dataset_correctness( '1.tabular', hid=str( hda.hid ) ) |
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| 218 | self.check_history_for_string( '1.tabular format: <span class="tabular">tabular</span>, database: \? Info: uploaded file' ) |
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| 219 | self.check_metadata_for_string( 'value="1.tabular" value="\?"' ) |
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| 220 | self.check_metadata_for_string( 'Change data type selected value="tabular" selected="yes"' ) |
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| 221 | self.delete_history( id=self.security.encode_id( history.id ) ) |
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| 222 | def test_0085_upload_file( self ): |
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| 223 | """Test uploading qualscores.qualsolid, NOT setting the file format""" |
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| 224 | # Logged in as admin_user |
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| 225 | self.check_history_for_string( 'Your history is empty' ) |
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| 226 | history = get_latest_history_for_user( admin_user ) |
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| 227 | self.upload_file( 'qualscores.qualsolid' ) |
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| 228 | hda = get_latest_hda() |
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| 229 | assert hda is not None, "Problem retrieving hda from database" |
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| 230 | self.verify_dataset_correctness( 'qualscores.qualsolid', hid=str( hda.hid ) ) |
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| 231 | self.check_history_for_string( '48 lines, format: <span class="qualsolid">qualsolid</span>, database: \? Info: uploaded file' ) |
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| 232 | self.check_metadata_for_string( 'Change data type value="qualsolid" selected="yes">qualsolid' ) |
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| 233 | self.delete_history( id=self.security.encode_id( history.id ) ) |
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| 234 | def test_0090_upload_file( self ): |
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| 235 | """Test uploading qualscores.qual454, NOT setting the file format""" |
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| 236 | # Logged in as admin_user |
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| 237 | self.check_history_for_string( 'Your history is empty' ) |
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| 238 | history = get_latest_history_for_user( admin_user ) |
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| 239 | self.upload_file( 'qualscores.qual454' ) |
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| 240 | hda = get_latest_hda() |
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| 241 | assert hda is not None, "Problem retrieving hda from database" |
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| 242 | self.verify_dataset_correctness( 'qualscores.qual454', hid=str( hda.hid ) ) |
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| 243 | self.check_history_for_string( '49 lines, format: <span class="qual454">qual454</span>, database: \?' ) |
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| 244 | self.check_metadata_for_string( 'Change data type value="qual454" selected="yes">qual454' ) |
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| 245 | self.delete_history( id=self.security.encode_id( history.id ) ) |
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| 246 | def test_0095_upload_file( self ): |
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| 247 | """Test uploading 3.maf, NOT setting the file format""" |
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| 248 | # Logged in as admin_user |
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| 249 | self.check_history_for_string( 'Your history is empty' ) |
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| 250 | history = get_latest_history_for_user( admin_user ) |
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| 251 | self.upload_file( '3.maf' ) |
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| 252 | hda = get_latest_hda() |
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| 253 | assert hda is not None, "Problem retrieving hda from database" |
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| 254 | self.verify_dataset_correctness( '3.maf', hid=str( hda.hid ) ) |
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| 255 | self.check_history_for_string( '3.maf format: <span class="maf">maf</span>, database: \? Info: uploaded file' ) |
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| 256 | self.check_metadata_for_string( 'value="3.maf" value="\?"' ) |
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| 257 | self.check_metadata_for_string( 'Convert to new format <option value="interval">Convert MAF to Genomic Intervals <option value="fasta">Convert MAF to Fasta' ) |
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| 258 | self.check_metadata_for_string( 'Change data type selected value="maf" selected="yes"' ) |
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| 259 | self.delete_history( id=self.security.encode_id( history.id ) ) |
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| 260 | def test_0100_upload_file( self ): |
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| 261 | """Test uploading 1.lav, NOT setting the file format""" |
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| 262 | # Logged in as admin_user |
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| 263 | self.check_history_for_string( 'Your history is empty' ) |
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| 264 | history = get_latest_history_for_user( admin_user ) |
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| 265 | self.upload_file( '1.lav' ) |
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| 266 | hda = get_latest_hda() |
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| 267 | assert hda is not None, "Problem retrieving hda from database" |
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| 268 | self.verify_dataset_correctness( '1.lav', hid=str( hda.hid ) ) |
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| 269 | self.check_history_for_string( '1.lav format: <span class="lav">lav</span>, database: \? Info: uploaded file' ) |
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| 270 | self.check_metadata_for_string( 'value="1.lav" value="\?"' ) |
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| 271 | self.check_metadata_for_string( 'Change data type selected value="lav" selected="yes"' ) |
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| 272 | self.delete_history( id=self.security.encode_id( history.id ) ) |
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| 273 | def test_0105_upload_file( self ): |
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| 274 | """Test uploading 1.interval, NOT setting the file format""" |
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| 275 | # Logged in as admin_user |
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| 276 | self.check_history_for_string( 'Your history is empty' ) |
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| 277 | history = get_latest_history_for_user( admin_user ) |
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| 278 | self.upload_file( '1.interval' ) |
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| 279 | hda = get_latest_hda() |
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| 280 | assert hda is not None, "Problem retrieving hda from database" |
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| 281 | self.verify_dataset_correctness( '1.interval', hid=str( hda.hid ) ) |
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| 282 | self.check_history_for_string( '1.interval format: <span class="interval">interval</span>, database: \? Info: uploaded file' ) |
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| 283 | self.check_metadata_for_string( 'value="1.interval" value="\?"' ) |
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| 284 | self.check_metadata_for_string( 'Chrom column: <option value="1" selected> Start column: <option value="2" selected>' ) |
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| 285 | self.check_metadata_for_string( 'End column: <option value="3" selected> Strand column <option value="6" selected>' ) |
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| 286 | self.check_metadata_for_string( 'Convert to new format <option value="bed">Convert Genomic Intervals To BED' ) |
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| 287 | self.check_metadata_for_string( 'Change data type selected value="interval" selected="yes"' ) |
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| 288 | self.delete_history( id=self.security.encode_id( history.id ) ) |
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| 289 | def test_0110_upload_file( self ): |
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| 290 | """Test uploading 5.gff3, NOT setting the file format""" |
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| 291 | # Logged in as admin_user |
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| 292 | self.check_history_for_string( 'Your history is empty' ) |
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| 293 | history = get_latest_history_for_user( admin_user ) |
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| 294 | self.upload_file( '5.gff3' ) |
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| 295 | hda = get_latest_hda() |
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| 296 | assert hda is not None, "Problem retrieving hda from database" |
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| 297 | self.verify_dataset_correctness( '5.gff3', hid=str( hda.hid ) ) |
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| 298 | self.check_history_for_string( '5.gff3 format: <span class="gff3">gff3</span>, database: \? Info: uploaded file' ) |
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| 299 | self.check_metadata_for_string( 'value="5.gff3" value="\?"' ) |
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| 300 | self.check_metadata_for_string( 'Convert to new format <option value="bed">Convert GFF to BED' ) |
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| 301 | self.check_metadata_for_string( 'Change data type selected value="gff3" selected="yes"' ) |
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| 302 | self.delete_history( id=self.security.encode_id( history.id ) ) |
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| 303 | def test_0115_upload_file( self ): |
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| 304 | """Test uploading html_file.txt, NOT setting the file format""" |
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| 305 | # Logged in as admin_user |
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| 306 | self.check_history_for_string( 'Your history is empty' ) |
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| 307 | history = get_latest_history_for_user( admin_user ) |
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| 308 | self.upload_file( 'html_file.txt' ) |
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| 309 | hda = get_latest_hda() |
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| 310 | assert hda is not None, "Problem retrieving hda from database" |
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| 311 | self.check_history_for_string( 'The uploaded file contains inappropriate content' ) |
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| 312 | self.delete_history( id=self.security.encode_id( history.id ) ) |
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| 313 | def test_0120_upload_file( self ): |
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| 314 | """Test uploading 5.gff, NOT setting the file format""" |
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| 315 | # Logged in as admin_user |
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| 316 | self.check_history_for_string( 'Your history is empty' ) |
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| 317 | history = get_latest_history_for_user( admin_user ) |
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| 318 | self.upload_file( '5.gff' ) |
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| 319 | hda = get_latest_hda() |
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| 320 | assert hda is not None, "Problem retrieving hda from database" |
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| 321 | self.verify_dataset_correctness( '5.gff', hid=str( hda.hid ) ) |
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| 322 | self.check_history_for_string( '5.gff format: <span class="gff">gff</span>, database: \? Info: uploaded file' ) |
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| 323 | self.check_metadata_for_string( 'value="5.gff" value="\?"' ) |
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| 324 | self.check_metadata_for_string( 'Convert to new format <option value="bed">Convert GFF to BED' ) |
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| 325 | self.check_metadata_for_string( 'Change data type selected value="gff" selected="yes"' ) |
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| 326 | self.delete_history( id=self.security.encode_id( history.id ) ) |
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| 327 | def test_0125_upload_file( self ): |
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| 328 | """Test uploading 1.fasta, NOT setting the file format""" |
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| 329 | # Logged in as admin_user |
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| 330 | self.check_history_for_string( 'Your history is empty' ) |
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| 331 | history = get_latest_history_for_user( admin_user ) |
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| 332 | self.upload_file( '1.fasta' ) |
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| 333 | hda = get_latest_hda() |
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| 334 | assert hda is not None, "Problem retrieving hda from database" |
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| 335 | self.verify_dataset_correctness( '1.fasta', hid=str( hda.hid ) ) |
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| 336 | self.check_history_for_string( '1.fasta format: <span class="fasta">fasta</span>, database: \? Info: uploaded file' ) |
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| 337 | self.check_metadata_for_string( 'value="1.fasta" value="\?" Change data type selected value="fasta" selected="yes"' ) |
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| 338 | self.delete_history( id=self.security.encode_id( history.id ) ) |
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| 339 | def test_0130_upload_file( self ): |
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| 340 | """Test uploading 1.customtrack, NOT setting the file format""" |
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| 341 | # Logged in as admin_user |
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| 342 | self.check_history_for_string( 'Your history is empty' ) |
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| 343 | history = get_latest_history_for_user( admin_user ) |
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| 344 | self.upload_file( '1.customtrack' ) |
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| 345 | hda = get_latest_hda() |
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| 346 | assert hda is not None, "Problem retrieving hda from database" |
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| 347 | self.verify_dataset_correctness( '1.customtrack', hid=str( hda.hid ) ) |
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| 348 | self.check_history_for_string( '1.customtrack format: <span class="customtrack">customtrack</span>, database: \? Info: uploaded file' ) |
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| 349 | self.check_metadata_for_string( 'value="1.customtrack" value="\?" Change data type selected value="customtrack" selected="yes"' ) |
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| 350 | self.delete_history( id=self.security.encode_id( history.id ) ) |
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| 351 | def test_0135_upload_file( self ): |
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| 352 | """Test uploading shrimp_cs_test1.csfasta, NOT setting the file format""" |
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| 353 | # Logged in as admin_user |
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| 354 | self.check_history_for_string( 'Your history is empty' ) |
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| 355 | history = get_latest_history_for_user( admin_user ) |
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| 356 | self.upload_file( 'shrimp_cs_test1.csfasta' ) |
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| 357 | hda = get_latest_hda() |
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| 358 | assert hda is not None, "Problem retrieving hda from database" |
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| 359 | self.verify_dataset_correctness( 'shrimp_cs_test1.csfasta', hid=str( hda.hid ) ) |
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| 360 | self.check_history_for_string( '2,500 sequences, format: <span class="csfasta">csfasta</span>, <td>>2_14_26_F3,-1282216.0</td>' ) |
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| 361 | self.check_metadata_for_string( 'value="shrimp_cs_test1.csfasta" value="\?" Change data type value="csfasta" selected="yes"' ) |
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| 362 | self.delete_history( id=self.security.encode_id( history.id ) ) |
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| 363 | def test_0140_upload_file( self ): |
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| 364 | """Test uploading megablast_xml_parser_test1.gz, NOT setting the file format""" |
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| 365 | # Logged in as admin_user |
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| 366 | self.check_history_for_string( 'Your history is empty' ) |
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| 367 | history = get_latest_history_for_user( admin_user ) |
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| 368 | self.upload_file( 'megablast_xml_parser_test1.gz' ) |
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| 369 | hda = get_latest_hda() |
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| 370 | assert hda is not None, "Problem retrieving hda from database" |
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| 371 | self.check_history_for_string( 'NCBI Blast XML data format: <span class="blastxml">blastxml</span>' ) |
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| 372 | self.delete_history( id=self.security.encode_id( history.id ) ) |
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| 373 | def test_0145_upload_file( self ): |
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| 374 | """Test uploading 1.axt, NOT setting the file format""" |
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| 375 | # Logged in as admin_user |
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| 376 | self.check_history_for_string( 'Your history is empty' ) |
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| 377 | history = get_latest_history_for_user( admin_user ) |
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| 378 | self.upload_file( '1.axt' ) |
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| 379 | hda = get_latest_hda() |
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| 380 | assert hda is not None, "Problem retrieving hda from database" |
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| 381 | self.verify_dataset_correctness( '1.axt', hid=str( hda.hid ) ) |
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| 382 | self.check_history_for_string( '1.axt format: <span class="axt">axt</span>, database: \? Info: uploaded file' ) |
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| 383 | self.check_metadata_for_string( 'value="1.axt" value="\?" Change data type selected value="axt" selected="yes"' ) |
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| 384 | self.delete_history( id=self.security.encode_id( history.id ) ) |
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| 385 | def test_0150_upload_file( self ): |
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| 386 | """Test uploading 1.bam, which is a sorted Bam file creaed by the Galaxy sam_to_bam tool, NOT setting the file format""" |
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| 387 | self.check_history_for_string( 'Your history is empty' ) |
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| 388 | history = get_latest_history_for_user( admin_user ) |
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| 389 | self.upload_file( '1.bam' ) |
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| 390 | hda = get_latest_hda() |
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| 391 | assert hda is not None, "Problem retrieving hda from database" |
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| 392 | self.verify_dataset_correctness( '1.bam', hid=str( hda.hid ) ) |
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| 393 | self.check_history_for_string( '<span class="bam">bam</span>' ) |
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| 394 | # Make sure the Bam index was created |
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| 395 | assert hda.metadata.bam_index is not None, "Bam index was not correctly created for 1.bam" |
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| 396 | self.delete_history( id=self.security.encode_id( history.id ) ) |
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| 397 | def test_0155_upload_file( self ): |
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| 398 | """Test uploading 3.bam, which is an unsorted Bam file, NOT setting the file format""" |
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| 399 | self.check_history_for_string( 'Your history is empty' ) |
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| 400 | history = get_latest_history_for_user( admin_user ) |
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| 401 | self.upload_file( '3.bam' ) |
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| 402 | hda = get_latest_hda() |
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| 403 | assert hda is not None, "Problem retrieving hda from database" |
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| 404 | # Since 3.bam is not sorted, we cannot verify dataset correctness since the uploaded |
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| 405 | # dataset will be sorted. However, the check below to see if the index was created is |
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| 406 | # sufficient. |
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| 407 | self.check_history_for_string( '<span class="bam">bam</span>' ) |
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| 408 | # Make sure the Bam index was created |
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| 409 | assert hda.metadata.bam_index is not None, "Bam index was not correctly created for 3.bam" |
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| 410 | self.delete_history( id=self.security.encode_id( history.id ) ) |
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| 411 | def test_0160_url_paste( self ): |
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| 412 | """Test url paste behavior""" |
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| 413 | # Logged in as admin_user |
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| 414 | # Deleting the current history should have created a new history |
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| 415 | self.check_history_for_string( 'Your history is empty' ) |
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| 416 | history = get_latest_history_for_user( admin_user ) |
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| 417 | self.upload_url_paste( 'hello world' ) |
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| 418 | self.check_history_for_string( 'Pasted Entry' ) |
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| 419 | self.check_history_for_string( 'hello world' ) |
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| 420 | self.upload_url_paste( u'hello world' ) |
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| 421 | self.check_history_for_string( 'Pasted Entry' ) |
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| 422 | self.check_history_for_string( 'hello world' ) |
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| 423 | self.delete_history( id=self.security.encode_id( history.id ) ) |
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| 424 | def test_0165_upload_file( self ): |
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| 425 | """Test uploading 1.pileup, NOT setting the file format""" |
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| 426 | self.check_history_for_string( 'Your history is empty' ) |
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| 427 | history = get_latest_history_for_user( admin_user ) |
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| 428 | self.upload_file( '1.pileup' ) |
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| 429 | hda = get_latest_hda() |
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| 430 | assert hda is not None, "Problem retrieving hda from database" |
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| 431 | self.verify_dataset_correctness( '1.pileup', hid=str( hda.hid ) ) |
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| 432 | self.check_history_for_string( '1.pileup format: <span class="pileup">pileup</span>, database: \? Info: uploaded file' ) |
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| 433 | self.check_metadata_for_string( 'value="1.pileup" value="\?" Change data type selected value="pileup" selected="yes"' ) |
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| 434 | self.delete_history( id=self.security.encode_id( history.id ) ) |
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| 435 | def test_0170_upload_file( self ): |
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| 436 | """Test uploading 1.bigbed, NOT setting the file format""" |
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| 437 | self.check_history_for_string( 'Your history is empty' ) |
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| 438 | history = get_latest_history_for_user( admin_user ) |
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| 439 | self.upload_file( '1.bigbed' ) |
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| 440 | hda = get_latest_hda() |
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| 441 | assert hda is not None, "Problem retrieving hda from database" |
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| 442 | self.verify_dataset_correctness( '1.bigbed', hid=str( hda.hid ) ) |
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| 443 | self.check_history_for_string( '1.bigbed</span> database: \? Info: uploaded bigbed file' ) |
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| 444 | self.check_metadata_for_string( 'value="1.bigbed" value="\?" Change data type selected value="bigbed" selected="yes"' ) |
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| 445 | self.delete_history( id=self.security.encode_id( history.id ) ) |
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| 446 | def test_0175_upload_file( self ): |
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| 447 | """Test uploading 1.bigwig, NOT setting the file format""" |
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| 448 | self.check_history_for_string( 'Your history is empty' ) |
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| 449 | history = get_latest_history_for_user( admin_user ) |
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| 450 | self.upload_file( '1.bigwig' ) |
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| 451 | hda = get_latest_hda() |
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| 452 | assert hda is not None, "Problem retrieving hda from database" |
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| 453 | self.verify_dataset_correctness( '1.bigwig', hid=str( hda.hid ) ) |
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| 454 | self.check_history_for_string( '1.bigwig</span> database: \? Info: uploaded bigwig file' ) |
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| 455 | self.check_metadata_for_string( 'value="1.bigwig" value="\?" Change data type selected value="bigwig" selected="yes"' ) |
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| 456 | self.delete_history( id=self.security.encode_id( history.id ) ) |
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| 457 | def test_9999_clean_up( self ): |
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| 458 | self.logout() |
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