mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-01 15:37:32 +08:00
More functional test cleanup, eliminated redundant tests, unused test data, and renamed some test data files.
This commit is contained in:
Greg Von Kuster
@@ -1,29 +0,0 @@
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AF099740 ENST00000296869
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AF377960 ENST00000160373
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AK131266 ENST00000350908
|
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BC005078 ENST00000319432
|
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BC007833 ENST00000349792
|
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NM_000054 ENST00000337474
|
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NM_000127 ENST00000333324
|
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NM_000425 ENST00000361699
|
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NM_000492 ENST00000003084
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NM_000588 ENST00000296870
|
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NM_001167 ENST00000245836
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NM_001666 ENST00000350060
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NM_001927 ENST00000273074
|
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NM_002651 ENST00000271657
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NM_002796 ENST00000290541
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NM_003269 ENST00000230083
|
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NM_003391 ENST00000265441
|
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NM_003687 ENST00000253754
|
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NM_004199 ENST00000166534
|
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NM_005997 ENST00000295315
|
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NM_006773 ENST00000263239
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NM_007214 ENST00000027474
|
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NM_014908 ENST00000308871
|
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NM_015354 ENST00000259310
|
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NM_020145 ENST00000291931
|
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NM_024536 ENST00000243776
|
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NM_145315 ENST00000258002
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NM_152827 ENST00000230085
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NM_174933 ENST00000308941
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@@ -1,29 +0,0 @@
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chr1 147962006 147975713 NM_005997 0 - 147962192 147975670 0 6 574,145,177,115,153,160, 0,1543,7859,9048,9340,13547,
|
||||
chr1 147984101 148035079 BC007833 0 + 147984545 148033414 0 14 529,32,81,131,118,153,300,206,84,49,85,130,46,1668, 0,25695,28767,33118,33695,33998,35644,38005,39629,40577,41402,43885,48367,49310,
|
||||
chr1 148077485 148111797 NM_002651 0 - 148078400 148111728 0 12 1097,121,133,266,124,105,110,228,228,45,937,77, 0,2081,2472,6871,9907,10257,11604,14199,15637,18274,23636,34235,
|
||||
chr1 148185113 148187485 NM_002796 0 + 148185136 148187378 0 7 163,207,147,82,117,89,120, 0,416,877,1199,1674,1977,2252,
|
||||
chr2 118288484 118306183 NM_006773 0 + 118288583 118304530 0 14 184,285,144,136,101,200,115,140,162,153,114,57,178,1796, 0,2765,4970,6482,6971,7183,7468,9890,10261,10768,11590,14270,14610,15903,
|
||||
chr2 118389378 118390700 BC005078 0 - 118390395 118390500 0 1 1322, 0,
|
||||
chr2 220108603 220116964 NM_001927 0 + 220108689 220116217 0 9 664,61,96,162,126,221,44,83,789, 0,1718,1874,2118,2451,2963,5400,7286,7572,
|
||||
chr2 220229182 220233943 NM_024536 0 - 220229609 220233765 0 4 1687,180,574,492, 0,1990,2660,4269,
|
||||
chr5 131170738 131357870 AF099740 0 - 131311206 131357817 0 31 112,124,120,81,65,40,120,129,61,88,94,79,72,102,144,117,89,73,96,135,135,78,74,52,33,179,100,102,65,115,248, 0,11593,44117,47607,104668,109739,114675,126366,135488,137518,138009,140437,152389,153373,155388,159269,160793,162981,164403,165577,166119,167611,169501,178260,179675,180901,181658,182260,182953,183706,186884,
|
||||
chr5 131424245 131426795 NM_000588 0 + 131424298 131426383 0 5 215,42,90,42,535, 0,313,1658,1872,2015,
|
||||
chr5 131556201 131590458 NM_004199 0 - 131556601 131582218 0 15 471,97,69,66,54,100,71,177,194,240,138,152,97,100,170, 0,2316,2802,5596,6269,11138,11472,15098,16528,17674,21306,24587,25142,25935,34087,
|
||||
chr5 131621285 131637046 NM_003687 0 + 131621326 131635821 0 7 134,152,82,179,164,118,1430, 0,4915,8770,13221,13609,14097,14331,
|
||||
chr6 108298214 108386086 NM_007214 0 - 108299600 108385906 0 21 1530,105,99,102,159,174,60,83,148,155,93,133,95,109,51,59,62,113,115,100,304, 0,2490,6246,10831,12670,23164,23520,27331,31052,32526,34311,36130,36365,38609,41028,42398,43048,51479,54500,59097,87568,
|
||||
chr6 108593954 108616704 NM_003269 0 + 108594662 108615360 0 9 733,146,88,236,147,97,150,106,1507, 0,5400,8778,10445,12037,14265,14749,15488,21243,
|
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chr6 108639410 108689143 NM_152827 0 - 108640045 108688818 0 3 741,125,487, 0,2984,49246,
|
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chr6 108722790 108950942 NM_145315 0 + 108722976 108950321 0 13 325,224,52,102,131,100,59,83,71,101,141,114,750, 0,28931,52094,60760,61796,71339,107102,152319,181970,182297,215317,224802,227402,
|
||||
chr7 113320332 113924911 AK131266 0 + 113862563 113893433 0 20 285,91,178,90,58,75,138,51,201,178,214,105,88,84,77,102,122,70,164,1124, 0,201692,340175,448290,451999,484480,542213,543265,543478,545201,556083,558358,565876,567599,573029,573245,575738,577123,577946,603455,
|
||||
chr7 116511232 116557294 NM_003391 0 - 116512159 116556994 0 5 1157,265,278,227,383, 0,20384,37843,43339,45679,
|
||||
chr7 116713967 116902666 NM_000492 0 + 116714099 116901113 0 27 185,111,109,216,90,164,126,247,93,183,192,95,87,724,129,38,251,80,151,228,101,249,156,90,173,106,1754, 0,24290,29071,50936,54313,55285,56585,60137,62053,68678,79501,107776,110390,111971,114967,122863,123569,126711,130556,131618,134650,147559,162475,172879,184725,185496,186945,
|
||||
chr7 116944658 117107512 AF377960 0 - 116945541 116979926 0 23 1129,102,133,64,186,206,179,188,153,100,87,80,96,276,118,255,151,100,204,1654,225,108,173, 0,7364,8850,10413,13893,14398,17435,24259,24615,35177,35359,45901,47221,49781,56405,66857,69787,72208,73597,80474,100111,150555,162681,
|
||||
chr8 118880786 119193239 NM_000127 0 - 118881131 119192466 0 11 531,172,161,90,96,119,133,120,108,94,1735, 0,5355,7850,13505,19068,20309,23098,30863,36077,37741,310718,
|
||||
chr9 128763240 128783870 NM_174933 0 + 128764156 128783586 0 12 261,118,74,159,76,48,56,63,129,117,127,370, 0,522,875,5630,12374,12603,15040,15175,18961,19191,20037,20260,
|
||||
chr9 128787362 128789566 NM_014908 0 - 128787519 128789136 0 1 2204, 0,
|
||||
chr9 128789530 128848928 NM_015354 0 + 128789552 128848511 0 44 54,55,74,85,81,45,93,120,212,115,201,90,66,120,127,153,127,88,77,115,121,67,129,140,107,207,170,70,68,196,78,86,146,182,201,93,159,138,75,228,132,74,130,594, 0,1491,5075,8652,9254,10312,11104,11317,20808,21702,23060,25462,31564,32908,33566,34851,35204,35595,35776,37202,38860,39111,39891,40349,42422,45499,45827,46675,47158,47621,50453,50840,51474,51926,53831,54186,55119,55619,57449,57605,57947,58352,58541,58804,
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chr9 128849867 128870133 NM_020145 0 - 128850516 128869987 0 11 757,241,101,90,24,63,93,134,129,142,209, 0,1071,1736,2085,2635,4201,6376,6736,13056,14247,20057,
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chrX 122719582 122773357 NM_001167 0 + 122745047 122766566 0 7 96,909,100,79,43,201,6985, 0,25433,28421,31040,32533,40295,46790,
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chrX 152648233 152662158 NM_000425 0 - 152648964 152662138 0 28 963,12,73,135,156,120,174,123,202,116,223,71,198,111,125,157,167,112,144,132,185,112,171,123,203,106,11,100, 0,1436,1545,1951,2390,2653,2889,3156,3367,3772,4717,5122,5424,5868,6066,6370,6629,6909,7588,7871,8124,8456,8858,9125,10220,10660,11296,13825,
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chrX 152691216 152693487 NM_000054 0 + 152691446 152693029 0 3 255,885,664, 0,616,1607,
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chrX 152693677 152712545 NM_001666 0 - 152694029 152712503 0 22 586,100,93,184,74,234,106,135,78,61,103,28,85,192,102,222,129,183,63,163,205,109, 0,1693,2066,2364,2635,2794,3129,3323,3545,3752,5323,5647,5841,6032,6401,11455,11778,13249,13719,13987,14227,18759,
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+27
-37
@@ -146,14 +146,13 @@ class TwillTestCase(unittest.TestCase):
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def switch_history(self, hid=None):
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"""Switches to a history in the current list of histories"""
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data_list = self.get_datasets_in_all_histories()
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data_list = self.get_datasets_in_histories()
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self.assertTrue( data_list )
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if hid is None: # take last hid
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elem = data_list[-1]
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hid = elem.get('hid')
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if hid < 0:
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hid = len(data_list) + hid + 1
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print hid
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hid = str(hid)
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elems = [ elem for elem in data_list if elem.get('hid') == hid ]
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self.assertEqual(len(elems), 1)
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@@ -165,17 +164,17 @@ class TwillTestCase(unittest.TestCase):
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assert elem.get( 'state' ) == state, \
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"Expecting dataset state '%s' but is '%s'. Dataset blurb: %s" % ( state, elem.get('state'), elem.text.strip() )
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def check_data(self, filename, hid=None, wait=True):
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"""Verifies that the contents of a history item are indentical to the contents of a file"""
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def verify_dataset_correctness(self, filename, hid=None, wait=True):
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"""Verifies that the attributes and contents of a history item meet expectations"""
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if wait: # wait for tools to finish
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self.wait()
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if wait: self.wait() #wait for job to finish
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data_list = self.get_datasets_in_history()
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self.assertTrue( data_list )
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if hid is None: # take last hid
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elem = data_list[-1]
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hid = str( elem.get('hid') )
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else:
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hid = str(hid)
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elems = [ elem for elem in data_list if elem.get('hid') == hid ]
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@@ -185,15 +184,13 @@ class TwillTestCase(unittest.TestCase):
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if elem.get('state') != 'ok':
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tc.go("./history")
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tc.code(200)
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# print tc.show()
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hid = elem.get('hid')
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self.assertTrue( hid )
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self._assert_dataset_state( elem, 'ok' )
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local_name = self.get_filename(filename)
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temp_name = self.get_filename('temp_%s' % filename)
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tc.go("./display?hid=" + str(hid) )
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temp_name = self.get_filename('temp_%s' % filename)
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tc.go("./display?hid=" + hid )
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data = self.last_page()
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file(temp_name, 'wb').write(data)
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@@ -204,14 +201,13 @@ class TwillTestCase(unittest.TestCase):
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errmsg = 'History item %s different than expected, difference:' % hid
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errmsg += str( err )
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raise AssertionError( errmsg )
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os.remove(temp_name)
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def check_genome_build(self, dbkey='hg17' ):
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"""Returns the last used genome_build at history id 'hid'"""
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tree = self.history_as_xml_tree()
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elems = [ elem for elem in tree.findall("data") ]
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self.assertTrue(len(elems)>0)
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def verify_genome_build(self, dbkey='hg17' ):
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"""Verifies that the last used genome_build at history id 'hid' is as expected"""
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data_list = self.get_datasets_in_history()
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self.assertTrue( data_list )
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elems = [ elem for elem in data_list ]
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elem = elems[-1]
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genome_build = elem.get('dbkey')
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self.assertTrue( genome_build == dbkey )
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@@ -223,7 +219,7 @@ class TwillTestCase(unittest.TestCase):
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tc.find(subpatt)
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def edit_metadata(self, hid, check_patt=None, **kwd):
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"""Edits the metadata sssociated with a history item"""
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"""Edits the metadata associated with a history item"""
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tc.go('./edit?hid=%d' % hid )
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if check_patt:
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tc.find(check_patt)
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@@ -245,7 +241,7 @@ class TwillTestCase(unittest.TestCase):
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hids.append(hid)
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return hids
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def get_datasets_in_all_histories(self):
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def get_datasets_in_histories(self):
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"""Returns all datasets in all histories"""
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tree = self.histories_as_xml_tree()
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data_list = [ elem for elem in tree.findall("data") ]
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@@ -260,13 +256,6 @@ class TwillTestCase(unittest.TestCase):
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"""Clears a form"""
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tc.formclear(str(form))
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def go2myurl(self, myurl):
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tc.go("%s" % myurl)
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print "+++++++++++++++++++++++++++++"
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print tc.show()
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print "-----------------------------"
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tc.code(200)
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def home(self):
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tc.go("%s" % self.url)
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tc.code(200)
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@@ -297,11 +286,11 @@ class TwillTestCase(unittest.TestCase):
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if 'onchange' in control.attrs.keys():
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changed = False
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for elem in kwd[control.name]:
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#----------------------------------------------
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#---for file parameter, control.value is the index of the file list, but elem is the filename
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#---the following is to get the filename of that index
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"""
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For file parameter, control.value is the index of the file list, but elem is the filename.
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The following loop gets the filename of that index.
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"""
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param_text = ''
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for param in tc.show().split('<select') :
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param = ('<select' + param.split('select>')[0] + 'select>').replace('selected', 'selected="yes"')
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if param.find('onchang') != -1 and param.find('name="%s"' % control.name) != -1:
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@@ -311,8 +300,8 @@ class TwillTestCase(unittest.TestCase):
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param_text = option.text.strip()
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break
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break
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#----------------------------------------------
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if elem not in control.value and param_text.find(elem)==-1 :
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if elem not in control.value and param_text.find(elem) == -1 :
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changed = True
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break
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if changed:
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@@ -345,6 +334,13 @@ class TwillTestCase(unittest.TestCase):
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break
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tc.submit(button)
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def visit_url(self, myurl):
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tc.go("%s" % myurl)
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print "+++++++++++++++++++++++++++++"
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print tc.show()
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print "-----------------------------"
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tc.code(200)
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#Functions associated with Galaxy tools
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def run_tool(self, tool_id, **kwd):
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tool_id = tool_id.replace(" ", "+")
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@@ -370,9 +366,3 @@ class TwillTestCase(unittest.TestCase):
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else:
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break
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self.assertNotEqual(count, maxiter)
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@@ -1,30 +1,30 @@
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from base.twilltestcase import TwillTestCase
|
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""" The numbering of the tests is essential as they will be executed in order, sorted by name"""
|
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""" Tests are executed in order, sorted by name"""
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class UploadData( TwillTestCase ):
|
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def test_upload( self ):
|
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"""test_get_data.test_upload: Testing single upload"""
|
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self.new_history()
|
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self.upload_file('MyData.bed')
|
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self.check_data('MyData.bed', hid=1)
|
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self.check_genome_build('hg17')
|
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self.upload_file('MyData.bed',ftype='auto', dbkey='hg18')
|
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self.verify_dataset_correctness('MyData.bed', hid=1)
|
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self.verify_genome_build(dbkey='hg18')
|
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self.new_history()
|
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self.upload_file('7.bed')
|
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self.check_data('sc_3E_Genes.bed', hid=1)
|
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self.verify_dataset_correctness('7.bed', hid=1)
|
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self.new_history()
|
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self.upload_file('8.bed', ftype='bed')
|
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self.check_data('sc_3E_knownToEnsembl.bed', hid=1)
|
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def test_30_multi_upload(self):
|
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self.upload_file('8.tabular', ftype='bed')
|
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self.verify_dataset_correctness('8.tabular', hid=1)
|
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def test_multi_upload(self):
|
||||
"""test_get_data.test_multi_upload: Testing multiple uploads"""
|
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self.new_history()
|
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self.upload_file('1.bed')
|
||||
self.check_data('1.bed', hid=1)
|
||||
self.verify_dataset_correctness('1.bed', hid=1)
|
||||
self.upload_file('2.bed', dbkey='hg17')
|
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self.check_data('2.bed', hid=2)
|
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self.verify_dataset_correctness('2.bed', hid=2)
|
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self.upload_file('3.bed', dbkey='hg17', ftype='bed')
|
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self.check_data('3.bed', hid=3)
|
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self.verify_dataset_correctness('3.bed', hid=3)
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class GetEncodeData( TwillTestCase ):
|
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@@ -34,15 +34,15 @@ class GetEncodeData( TwillTestCase ):
|
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self.run_tool('encode_import_chromatin_and_chromosomes1', hg17=['cc.EarlyRepSeg.20051216.bed'] )
|
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#hg17=[ "cc.EarlyRepSeg.20051216.bed", "cc.EarlyRepSeg.20051216.gencode_partitioned.bed", "cc.LateRepSeg.20051216.bed", "cc.LateRepSeg.20051216.gencode_partitioned.bed", "cc.MidRepSeg.20051216.bed", "cc.MidRepSeg.20051216.gencode_partitioned.bed" ] )
|
||||
self.wait()
|
||||
self.check_data('cc.EarlyRepSeg.20051216.bed', hid=1)
|
||||
#self.check_data('cc.EarlyRepSeg.20051216.gencode_partitioned.bed', hid=2)
|
||||
#self.check_data('cc.LateRepSeg.20051216.bed', hid=3)
|
||||
#self.check_data('cc.LateRepSeg.20051216.gencode_partitioned.bed', hid=4)
|
||||
#self.check_data('cc.MidRepSeg.20051216.bed', hid=5)
|
||||
#self.check_data('cc.MidRepSeg.20051216.gencode_partitioned.bed', hid=6)
|
||||
self.verify_dataset_correctness('cc.EarlyRepSeg.20051216.bed', hid=1)
|
||||
#self.verify_dataset_correctness('cc.EarlyRepSeg.20051216.gencode_partitioned.bed', hid=2)
|
||||
#self.verify_dataset_correctness('cc.LateRepSeg.20051216.bed', hid=3)
|
||||
#self.verify_dataset_correctness('cc.LateRepSeg.20051216.gencode_partitioned.bed', hid=4)
|
||||
#self.verify_dataset_correctness('cc.MidRepSeg.20051216.bed', hid=5)
|
||||
#self.verify_dataset_correctness('cc.MidRepSeg.20051216.gencode_partitioned.bed', hid=6)
|
||||
self.run_tool('encode_import_gencode1', hg17=['gencode.CDS.20051206.bed'])
|
||||
self.wait()
|
||||
self.check_data('sc_3D_cds.bed', hid=2)
|
||||
self.verify_dataset_correctness('sc_3D_cds.bed', hid=2)
|
||||
|
||||
class DataSources( TwillTestCase ):
|
||||
|
||||
@@ -68,5 +68,5 @@ class DataSources( TwillTestCase ):
|
||||
# using Postgres. Upgrading our version of sqlite may fix this, but
|
||||
# confirmation is required.
|
||||
# """
|
||||
# self.check_data('hbvar_hybrid_genes.dat')
|
||||
# self.verify_dataset_correctness('hbvar_hybrid_genes.dat')
|
||||
pass
|
||||
|
||||
@@ -33,7 +33,7 @@ class ToolTestCase( TwillTestCase ):
|
||||
# Check the result
|
||||
assert len( self.testdef.outputs ) == 1, "ToolTestCase does not deal with multiple outputs properly yet."
|
||||
for name, file in self.testdef.outputs:
|
||||
self.check_data( file )
|
||||
self.verify_dataset_correctness( file )
|
||||
def shortDescription( self ):
|
||||
return self.name
|
||||
|
||||
|
||||
@@ -19,12 +19,6 @@
|
||||
<param name="pattern" value="^chr[0-9]*"/>
|
||||
<output name="out_file1" file="fs-grep.dat"/>
|
||||
</test>
|
||||
<test>
|
||||
<param name="input" value="7.bed"/>
|
||||
<param name="invert" value="false"/>
|
||||
<param name="pattern" value="AY143171"/>
|
||||
<output name="out_file1" file="sc_3E_select.bed"/>
|
||||
</test>
|
||||
</tests>
|
||||
<help>
|
||||
|
||||
|
||||
@@ -23,13 +23,6 @@
|
||||
<param name="field2" value="2"/>
|
||||
<output name="out_file1" file="fs-joiner.dat"/>
|
||||
</test>
|
||||
<test>
|
||||
<param name="input1" value="7.bed"/>
|
||||
<param name="input2" value="8.bed"/>
|
||||
<param name="field1" value="4"/>
|
||||
<param name="field2" value="1"/>
|
||||
<output name="out_file1" file="sc_3E_join.bed"/>
|
||||
</test>
|
||||
</tests>
|
||||
<help>
|
||||
|
||||
|
||||
@@ -22,14 +22,14 @@
|
||||
<param name="column" value="1"/>
|
||||
<param name="order" value="ASC"/>
|
||||
<param name="style" value="num"/>
|
||||
<output name="out_file1" file="fs-sort.dat"/>
|
||||
<output name="out_file1" file="sort1_num.bed"/>
|
||||
</test>
|
||||
<test>
|
||||
<param name="input" value="7.bed"/>
|
||||
<param name="column" value="1"/>
|
||||
<param name="order" value="ASC"/>
|
||||
<param name="style" value="alpha"/>
|
||||
<output name="out_file1" file="sc_3E_sort.bed"/>
|
||||
<output name="out_file1" file="sort1_alpha.bed"/>
|
||||
</test>
|
||||
</tests>
|
||||
<help>
|
||||
|
||||
@@ -14,12 +14,12 @@
|
||||
<test>
|
||||
<param name="input" value="1.bed"/>
|
||||
<param name="cond" value="c1=='chr22'"/>
|
||||
<output name="out_file1" file="fs-filter.dat"/>
|
||||
<output name="out_file1" file="filter1_test1.bed"/>
|
||||
</test>
|
||||
<test>
|
||||
<param name="input" value="7.bed"/>
|
||||
<param name="cond" value="c1=='chr1' and c3-c2>=2000 and c6=='+'"/>
|
||||
<output name="out_file1" file="sc_3E_filter.bed"/>
|
||||
<output name="out_file1" file="filter1_test2.bed"/>
|
||||
</test>
|
||||
</tests>
|
||||
<help>
|
||||
|
||||
Reference in New Issue
Block a user