1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4fa2b864adca/ Changeset: 4fa2b864adca User: davebgx Date: 2014-04-25 21:29:56 Summary: Fix library security functional tests. Affected #: 4 files diff -r 267d03b5c9cdcad228fd40e12340f01c45f12c60 -r 4fa2b864adca65df5ac73a3fa60e5a4d98b1461c test-data/library/3.bed --- /dev/null +++ b/test-data/library/3.bed @@ -0,0 +1,25 @@ +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, +chr6 108639410 108689143 NM_152827 0 - 108640045 108688818 0 3 741,125,487, 0,2984,49246, +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, +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, diff -r 267d03b5c9cdcad228fd40e12340f01c45f12c60 -r 4fa2b864adca65df5ac73a3fa60e5a4d98b1461c test-data/library/4.bed --- /dev/null +++ b/test-data/library/4.bed @@ -0,0 +1,1 @@ +chr22 30128507 31828507 uc003bnx.1_cds_2_0_chr22_29227_f 0 + diff -r 267d03b5c9cdcad228fd40e12340f01c45f12c60 -r 4fa2b864adca65df5ac73a3fa60e5a4d98b1461c test-data/library/5.bed --- /dev/null +++ b/test-data/library/5.bed @@ -0,0 +1,134 @@ +chr7 115444712 115444739 CCDS5763.1_cds_0_0_chr7_115444713_f 0 + +chr7 115468538 115468624 CCDS5763.1_cds_1_0_chr7_115468539_f 0 + +chr7 115483024 115483277 CCDS5763.1_cds_2_0_chr7_115483025_f 0 + +chr7 115484165 115484501 CCDS5763.1_cds_3_0_chr7_115484166_f 0 + +chr7 115485764 115485980 CCDS5763.1_cds_4_0_chr7_115485765_f 0 + +chr7 115486322 115486481 CCDS5763.1_cds_5_0_chr7_115486323_f 0 + +chr7 115491298 115491487 CCDS5763.1_cds_6_0_chr7_115491299_f 0 + +chr7 115468538 115468624 CCDS5764.1_cds_0_0_chr7_115468539_f 0 + +chr7 115483024 115483277 CCDS5764.1_cds_1_0_chr7_115483025_f 0 + +chr7 115484165 115484501 CCDS5764.1_cds_2_0_chr7_115484166_f 0 + +chr7 115485764 115485980 CCDS5764.1_cds_3_0_chr7_115485765_f 0 + +chr7 115486322 115486481 CCDS5764.1_cds_4_0_chr7_115486323_f 0 + +chr7 115491298 115491487 CCDS5764.1_cds_5_0_chr7_115491299_f 0 + +chr7 115733786 115733936 CCDS5766.1_cds_0_0_chr7_115733787_f 0 + +chr7 115734264 115734452 CCDS5766.1_cds_1_0_chr7_115734265_f 0 + +chr7 115739975 115740126 CCDS5766.1_cds_2_0_chr7_115739976_f 0 + +chr7 115733786 115733936 CCDS5765.1_cds_0_0_chr7_115733787_f 0 + +chr7 115739975 115740164 CCDS5765.1_cds_1_0_chr7_115739976_f 0 + +chr7 115759067 115759097 CCDS5767.1_cds_0_0_chr7_115759068_f 0 + +chr7 115760529 115760694 CCDS5767.1_cds_1_0_chr7_115760530_f 0 + +chr7 115792950 115793292 CCDS5767.1_cds_2_0_chr7_115792951_f 0 + +chr7 116096616 116096655 CCDS5768.1_cds_0_0_chr7_116096617_f 0 + +chr7 116122131 116122195 CCDS5768.1_cds_1_0_chr7_116122132_f 0 + +chr7 116126998 116127050 CCDS5768.1_cds_2_0_chr7_116126999_f 0 + +chr7 116132776 116132840 CCDS5768.1_cds_3_0_chr7_116132777_f 0 + +chr7 116138181 116138388 CCDS5768.1_cds_4_0_chr7_116138182_f 0 + +chr7 116140267 116140347 CCDS5768.1_cds_5_0_chr7_116140268_f 0 + +chr7 116144237 116144316 CCDS5768.1_cds_6_0_chr7_116144238_f 0 + +chr7 116146073 116146145 CCDS5768.1_cds_7_0_chr7_116146074_f 0 + +chr7 116150064 116150127 CCDS5768.1_cds_8_0_chr7_116150065_f 0 + +chr7 116151731 116151872 CCDS5768.1_cds_9_0_chr7_116151732_f 0 + +chr7 116187545 116187696 CCDS5770.1_cds_0_0_chr7_116187546_f 0 + +chr7 116333766 116333849 CCDS5770.1_cds_1_0_chr7_116333767_f 0 + +chr7 116353565 116353725 CCDS5770.1_cds_2_0_chr7_116353566_f 0 + +chr7 116363797 116363852 CCDS5770.1_cds_3_0_chr7_116363798_f 0 + +chr7 116364495 116364611 CCDS5770.1_cds_4_0_chr7_116364496_f 0 + +chr7 116365889 116365965 CCDS5770.1_cds_5_0_chr7_116365890_f 0 + +chr7 116368128 116368197 CCDS5770.1_cds_6_0_chr7_116368129_f 0 + +chr7 116370085 116370240 CCDS5770.1_cds_7_0_chr7_116370086_f 0 + +chr7 116372439 116372537 CCDS5770.1_cds_8_0_chr7_116372440_f 0 + +chr7 116404866 116404981 CCDS5770.1_cds_9_0_chr7_116404867_f 0 + +chr7 116423325 116423398 CCDS5770.1_cds_10_0_chr7_116423326_f 0 + +chr7 116424838 116424941 CCDS5770.1_cds_11_0_chr7_116424839_f 0 + +chr7 116443791 116443942 CCDS5770.1_cds_12_0_chr7_116443792_f 0 + +chr7 116453088 116453181 CCDS5770.1_cds_13_0_chr7_116453089_f 0 + +chr7 116455927 116456067 CCDS5770.1_cds_14_0_chr7_116455928_f 0 + +chr7 116456865 116456985 CCDS5770.1_cds_15_0_chr7_116456866_f 0 + +chr7 116187545 116187696 CCDS5769.1_cds_0_0_chr7_116187546_f 0 + +chr7 116333766 116333849 CCDS5769.1_cds_1_0_chr7_116333767_f 0 + +chr7 116353565 116353725 CCDS5769.1_cds_2_0_chr7_116353566_f 0 + +chr7 116363797 116363852 CCDS5769.1_cds_3_0_chr7_116363798_f 0 + +chr7 116364495 116364611 CCDS5769.1_cds_4_0_chr7_116364496_f 0 + +chr7 116365889 116365965 CCDS5769.1_cds_5_0_chr7_116365890_f 0 + +chr7 116370085 116370240 CCDS5769.1_cds_6_0_chr7_116370086_f 0 + +chr7 116372439 116372537 CCDS5769.1_cds_7_0_chr7_116372440_f 0 + +chr7 116404866 116404981 CCDS5769.1_cds_8_0_chr7_116404867_f 0 + +chr7 116423325 116423398 CCDS5769.1_cds_9_0_chr7_116423326_f 0 + +chr7 116424838 116424941 CCDS5769.1_cds_10_0_chr7_116424839_f 0 + +chr7 116443791 116443942 CCDS5769.1_cds_11_0_chr7_116443792_f 0 + +chr7 116453088 116453181 CCDS5769.1_cds_12_0_chr7_116453089_f 0 + +chr7 116455927 116456067 CCDS5769.1_cds_13_0_chr7_116455928_f 0 + +chr7 116463766 116463862 CCDS5769.1_cds_14_0_chr7_116463767_f 0 + +chr7 116512159 116512389 CCDS5771.1_cds_0_0_chr7_116512160_r 0 - +chr7 116531616 116531881 CCDS5771.1_cds_1_0_chr7_116531617_r 0 - +chr7 116549075 116549353 CCDS5771.1_cds_2_0_chr7_116549076_r 0 - +chr7 116554571 116554798 CCDS5771.1_cds_3_0_chr7_116554572_r 0 - +chr7 116556911 116556994 CCDS5771.1_cds_4_0_chr7_116556912_r 0 - +chr7 116597600 116597753 CCDS5772.1_cds_0_0_chr7_116597601_r 0 - +chr7 116601356 116601470 CCDS5772.1_cds_1_0_chr7_116601357_r 0 - +chr7 116602616 116602722 CCDS5772.1_cds_2_0_chr7_116602617_r 0 - +chr7 116613942 116614052 CCDS5772.1_cds_3_0_chr7_116613943_r 0 - +chr7 116615015 116615072 CCDS5772.1_cds_4_0_chr7_116615016_r 0 - +chr7 116616073 116616149 CCDS5772.1_cds_5_0_chr7_116616074_r 0 - +chr7 116616990 116617115 CCDS5772.1_cds_6_0_chr7_116616991_r 0 - +chr7 116618730 116618865 CCDS5772.1_cds_7_0_chr7_116618731_r 0 - +chr7 116619702 116619814 CCDS5772.1_cds_8_0_chr7_116619703_r 0 - +chr7 116654167 116654279 CCDS5772.1_cds_9_0_chr7_116654168_r 0 - +chr7 116656241 116656364 CCDS5772.1_cds_10_0_chr7_116656242_r 0 - +chr7 116660840 116660940 CCDS5772.1_cds_11_0_chr7_116660841_r 0 - +chr7 116661360 116661465 CCDS5772.1_cds_12_0_chr7_116661361_r 0 - +chr7 116714099 116714152 CCDS5773.1_cds_0_0_chr7_116714100_f 0 + +chr7 116738257 116738368 CCDS5773.1_cds_1_0_chr7_116738258_f 0 + +chr7 116743038 116743147 CCDS5773.1_cds_2_0_chr7_116743039_f 0 + +chr7 116764903 116765119 CCDS5773.1_cds_3_0_chr7_116764904_f 0 + +chr7 116768280 116768370 CCDS5773.1_cds_4_0_chr7_116768281_f 0 + +chr7 116769252 116769416 CCDS5773.1_cds_5_0_chr7_116769253_f 0 + +chr7 116770552 116770678 CCDS5773.1_cds_6_0_chr7_116770553_f 0 + +chr7 116774104 116774351 CCDS5773.1_cds_7_0_chr7_116774105_f 0 + +chr7 116776020 116776113 CCDS5773.1_cds_8_0_chr7_116776021_f 0 + +chr7 116782645 116782828 CCDS5773.1_cds_9_0_chr7_116782646_f 0 + +chr7 116793468 116793660 CCDS5773.1_cds_10_0_chr7_116793469_f 0 + +chr7 116821743 116821838 CCDS5773.1_cds_11_0_chr7_116821744_f 0 + +chr7 116824357 116824444 CCDS5773.1_cds_12_0_chr7_116824358_f 0 + +chr7 116825938 116826662 CCDS5773.1_cds_13_0_chr7_116825939_f 0 + +chr7 116828934 116829063 CCDS5773.1_cds_14_0_chr7_116828935_f 0 + +chr7 116836830 116836868 CCDS5773.1_cds_15_0_chr7_116836831_f 0 + +chr7 116837536 116837787 CCDS5773.1_cds_16_0_chr7_116837537_f 0 + +chr7 116840678 116840758 CCDS5773.1_cds_17_0_chr7_116840679_f 0 + +chr7 116844523 116844674 CCDS5773.1_cds_18_0_chr7_116844524_f 0 + +chr7 116845585 116845813 CCDS5773.1_cds_19_0_chr7_116845586_f 0 + +chr7 116848617 116848718 CCDS5773.1_cds_20_0_chr7_116848618_f 0 + +chr7 116861526 116861775 CCDS5773.1_cds_21_0_chr7_116861527_f 0 + +chr7 116876442 116876598 CCDS5773.1_cds_22_0_chr7_116876443_f 0 + +chr7 116886846 116886936 CCDS5773.1_cds_23_0_chr7_116886847_f 0 + +chr7 116898692 116898865 CCDS5773.1_cds_24_0_chr7_116898693_f 0 + +chr7 116899463 116899569 CCDS5773.1_cds_25_0_chr7_116899464_f 0 + +chr7 116900912 116901113 CCDS5773.1_cds_26_0_chr7_116900913_f 0 + +chr7 116945541 116945787 CCDS5774.1_cds_0_0_chr7_116945542_r 0 - +chr7 116952022 116952124 CCDS5774.1_cds_1_0_chr7_116952023_r 0 - +chr7 116953508 116953641 CCDS5774.1_cds_2_0_chr7_116953509_r 0 - +chr7 116955071 116955135 CCDS5774.1_cds_3_0_chr7_116955072_r 0 - +chr7 116958551 116958737 CCDS5774.1_cds_4_0_chr7_116958552_r 0 - +chr7 116959056 116959262 CCDS5774.1_cds_5_0_chr7_116959057_r 0 - +chr7 116962093 116962272 CCDS5774.1_cds_6_0_chr7_116962094_r 0 - +chr7 116968917 116969105 CCDS5774.1_cds_7_0_chr7_116968918_r 0 - +chr7 116969273 116969426 CCDS5774.1_cds_8_0_chr7_116969274_r 0 - +chr7 116979835 116979935 CCDS5774.1_cds_9_0_chr7_116979836_r 0 - +chr7 116980017 116980104 CCDS5774.1_cds_10_0_chr7_116980018_r 0 - +chr7 116990559 116990639 CCDS5774.1_cds_11_0_chr7_116990560_r 0 - +chr7 116991879 116991975 CCDS5774.1_cds_12_0_chr7_116991880_r 0 - +chr7 116994439 116994715 CCDS5774.1_cds_13_0_chr7_116994440_r 0 - +chr7 117001063 117001181 CCDS5774.1_cds_14_0_chr7_117001064_r 0 - +chr7 117011515 117011770 CCDS5774.1_cds_15_0_chr7_117011516_r 0 - +chr7 117014445 117014596 CCDS5774.1_cds_16_0_chr7_117014446_r 0 - +chr7 117016866 117016966 CCDS5774.1_cds_17_0_chr7_117016867_r 0 - +chr7 117018255 117018459 CCDS5774.1_cds_18_0_chr7_117018256_r 0 - +chr7 117025132 117026786 CCDS5774.1_cds_19_0_chr7_117025133_r 0 - +chr7 117044769 117044994 CCDS5774.1_cds_20_0_chr7_117044770_r 0 - +chr7 117095213 117095321 CCDS5774.1_cds_21_0_chr7_117095214_r 0 - +chr7 117107339 117107420 CCDS5774.1_cds_22_0_chr7_117107340_r 0 - +chr5 131424298 131424460 CCDS4149.1_cds_0_0_chr5_131424299_f 0 + +chr5 131424558 131424600 CCDS4149.1_cds_1_0_chr5_131424559_f 0 + +chr5 131425903 131425993 CCDS4149.1_cds_2_0_chr5_131425904_f 0 + +chr5 131426117 131426159 CCDS4149.1_cds_3_0_chr5_131426118_f 0 + diff -r 267d03b5c9cdcad228fd40e12340f01c45f12c60 -r 4fa2b864adca65df5ac73a3fa60e5a4d98b1461c test/base/twilltestcase.py --- a/test/base/twilltestcase.py +++ b/test/base/twilltestcase.py @@ -2254,7 +2254,7 @@ # NOTE: due to the library_wait() method call at the end of this method, no tests should be done # for strings_displayed_after_submit. params = dict( cntrller=cntrller, library_id=library_id, folder_id=folder_id ) - url = "%s/library_common/upload_library_dataset" % self.url + url = "/library_common/upload_library_dataset" if replace_id: # If we're uploading a new version of a library dataset, we have to include the replace_id param in the # request because the form field named replace_id will not be displayed on the upload form if we dont. @@ -2309,17 +2309,15 @@ def ldda_permissions( self, cntrller, library_id, folder_id, id, role_ids_str, permissions_in=[], permissions_out=[], strings_displayed=[], ldda_name='' ): # role_ids_str must be a comma-separated string of role ids - url = "%s/library_common/ldda_permissions?cntrller=%s&library_id=%s&folder_id=%s&id=%s" % \ - ( self.url, cntrller, library_id, folder_id, id ) + params = dict( cntrller=cntrller, library_id=library_id, folder_id=folder_id, id=id ) + url = "/library_common/ldda_permissions" for po in permissions_out: - key = '%s_out' % po - url = "%s&%s=%s" % ( url, key, role_ids_str ) + params[ '%s_out' % po ] = role_ids_str for pi in permissions_in: - key = '%s_in' % pi - url = "%s&%s=%s" % ( url, key, role_ids_str ) + params[ '%s_in' % pi ] = role_ids_str if permissions_in or permissions_out: - url += "&update_roles_button=Save" - self.visit_url( url ) + params[ 'update_roles_button' ] = 'Save' + self.visit_url( url, params ) if not strings_displayed: strings_displayed = [ "Permissions updated for dataset '%s'." % ldda_name ] for check_str in strings_displayed: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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