root/galaxy-central/test/functional/test_get_data.py

リビジョン 2, 29.3 KB (コミッタ: hatakeyama, 14 年 前)

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