galaxy-dev October 2008

galaxy-dev@lists.galaxyproject.org

4 participants
57 discussions

[hg] galaxy 1585: Fix typo on call to set_meta.
by Greg Von Kuster 30 Oct '08

30 Oct '08

details: http://www.bx.psu.edu/hg/galaxy/rev/6259ebdd0e99 changeset: 1585:6259ebdd0e99 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Thu Oct 30 13:35:19 2008 -0400 description: Fix typo on call to set_meta. 1 file(s) affected in this change: lib/galaxy/jobs/__init__.py diffs (12 lines): diff -r 95bdb18ee62b -r 6259ebdd0e99 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py Wed Oct 29 17:32:09 2008 -0400 +++ b/lib/galaxy/jobs/__init__.py Thu Oct 30 13:35:19 2008 -0400 @@ -423,7 +423,7 @@ dataset.blurb = "error" elif dataset.has_data(): # Only set metadata values if they are missing... - dataset.set_meta( overwrite_exisiting = False ) + dataset.set_meta( overwrite = False ) dataset.set_peek() else: dataset.blurb = "empty"

1 0

[hg] galaxy 1586: Annotation profiler: Better handling of the ca...
by Greg Von Kuster 30 Oct '08

30 Oct '08

details: http://www.bx.psu.edu/hg/galaxy/rev/4e44d29377e3 changeset: 1586:4e44d29377e3 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Thu Oct 30 14:46:57 2008 -0400 description: Annotation profiler: Better handling of the case where regions extend beyond known chromosome boundaries. 1 file(s) affected in this change: tools/annotation_profiler/annotation_profiler_for_interval.py diffs (55 lines): diff -r 6259ebdd0e99 -r 4e44d29377e3 tools/annotation_profiler/annotation_profiler_for_interval.py --- a/tools/annotation_profiler/annotation_profiler_for_interval.py Thu Oct 30 13:35:19 2008 -0400 +++ b/tools/annotation_profiler/annotation_profiler_for_interval.py Thu Oct 30 14:46:57 2008 -0400 @@ -121,14 +121,27 @@ self.table_chromosome_size = {} #dict of dict of table:chrom containing total coverage of table for a chrom self.table_chromosome_count = {} #dict of dict of table:chrom containing total number of coverage ranges of table for a chrom self.table_regions_overlaped_count = {} #total number of table regions overlaping user's input intervals (non unique) - self.interval_table_overlap_count = {} #total number of user input intervals which overlap table + self.interval_table_overlap_count = {} #total number of user input intervals which overlap table + self.region_size_errors = {} #dictionary of lists of invalid ranges by chromosome def add_region( self, chrom, start, end ): - self.total_interval_size += ( end - start ) + chrom_length = self.chrom_lengths.get( chrom ) + region_start = min( start, chrom_length ) + region_end = min( end, chrom_length ) + region_length = region_end - region_start + + if region_length < 1 or region_start != start or region_end != end: + if chrom not in self.region_size_errors: + self.region_size_errors[chrom] = [] + self.region_size_errors[chrom].append( ( start, end ) ) + if region_length < 1: return + + self.total_interval_size += region_length self.total_interval_count += 1 if chrom not in self.chromosome_coverage: - self.chromosome_coverage[chrom] = bx.bitset.BitSet( self.chrom_lengths.get( chrom ) ) - self.chromosome_coverage[chrom].set_range( start, end - start ) - for table_name, coverage, regions in self.coverage_reader.iter_table_coverage_regions_by_region( chrom, start, end ): + self.chromosome_coverage[chrom] = bx.bitset.BitSet( chrom_length ) + + self.chromosome_coverage[chrom].set_range( region_start, region_length ) + for table_name, coverage, regions in self.coverage_reader.iter_table_coverage_regions_by_region( chrom, region_start, region_end ): if table_name not in self.table_coverage: self.table_coverage[table_name] = 0 self.table_chromosome_size[table_name] = {} @@ -213,7 +226,17 @@ if keep_empty or total_coverage: #only output tables that have atleast 1 base covered unless empty are requested out.write( "%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n" % ( table_name, table_chromosome_size, table_chromosome_count, table_region_coverage, table_region_count, total_interval_count, total_interval_size, total_coverage, table_regions_overlaped_count, interval_region_overlap_count, nr_interval_count, nr_interval_size, nr_coverage, nr_table_regions_overlaped_count, nr_interval_table_overlap_count ) ) - out.close() + out.close() + + #report chrom size errors as needed: + if table_coverage_summary.region_size_errors: + print "Regions provided extended beyond known chromosome lengths, and have been truncated as necessary, for the following intervals:" + for chrom, regions in table_coverage_summary.region_size_errors.items(): + if len( regions ) > 3: + extra_region_info = ", ... " + else: + extra_region_info = "" + print "%s has max length of %s, exceeded by %s%s." % ( chrom, chrom_lengths.get( chrom ), ", ".join( map( str, regions[:3] ) ), extra_region_info ) class ChromosomeLengths: def __init__( self, filename ):

1 0

[hg] galaxy 1587: Added new functional tests to all gops tools u...
by Greg Von Kuster 30 Oct '08

30 Oct '08

details: http://www.bx.psu.edu/hg/galaxy/rev/0da612f8a78e changeset: 1587:0da612f8a78e user: guru date: Thu Oct 30 16:03:11 2008 -0400 description: Added new functional tests to all gops tools using BitsetSafeReaderWrapper. These tests check cases where datasets have the chr,start and end values in non-standard columns. 12 file(s) affected in this change: test-data/2_mod.bed test-data/gops_complement_out_diffCols.dat test-data/gops_coverage_out_diffCols.interval test-data/gops_intersect_diffCols.bed test-data/gops_intersect_p_diffCols.bed test-data/gops_merge_diffCols.dat test-data/gops_subtract_diffCols.dat tools/new_operations/complement.xml tools/new_operations/coverage.xml tools/new_operations/intersect.xml tools/new_operations/merge.xml tools/new_operations/subtract.xml diffs (530 lines): diff -r 4e44d29377e3 -r 0da612f8a78e test-data/2_mod.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/2_mod.bed Thu Oct 30 16:03:11 2008 -0400 @@ -0,0 +1,69 @@ +#chr name score strand start end +chr1 NM_005997_cds_0_0_chr1_147962193_r 0 - 147962192 147962580 +chr1 BC007833_cds_0_0_chr1_147984546_f 0 + 147984545 147984630 +chr1 AJ011123_cds_0_0_chr1_148078401_r 0 - 148078400 148078582 +chr1 NM_002796_cds_0_0_chr1_148185137_f 0 + 148185136 148185276 +chr10 AY029205_cds_0_0_chr10_55251624_r 0 - 55251623 55253124 +chr11 AK057832_cds_0_0_chr11_116124408_r 0 - 116124407 116124501 +chr11 NM_000040_cds_1_0_chr11_116206509_f 0 + 116206508 116206563 +chr11 BC005380_cds_0_0_chr11_116211734_r 0 - 116211733 116212337 +chr11 AY358331_cds_0_0_chr11_130745912_f 0 + 130745911 130745993 +chr12 NM_052885_cds_0_0_chr12_38440095_r 0 - 38440094 38440321 +chr12 AY792511_cds_0_0_chr12_38905201_f 0 + 38905200 38905351 +chr13 NM_207440_cds_1_0_chr13_112381695_f 0 + 112381694 112381953 +chr13 NM_032116_cds_0_0_chr13_29680677_r 0 - 29680676 29680875 +chr14 U88895_cds_0_0_chr14_98521865_f 0 + 98521864 98521922 +chr14 NM_022898_cds_0_0_chr14_98710241_r 0 - 98710240 98712285 +chr15 BX537418_cds_0_0_chr15_41486873_r 0 - 41486872 41487060 +chr15 AK223365_cds_0_0_chr15_41673709_f 0 + 41673708 41673857 +chr15 NM_153700_cds_0_0_chr15_41679162_r 0 - 41679161 41679250 +chr15 AK223365_cds_0_0_chr15_41773541_f 0 + 41773540 41773689 +chr16 NM_005332_cds_0_0_chr16_142909_f 0 + 142908 143003 +chr16 BC065198_cds_0_0_chr16_179198_r 0 - 179197 179339 +chr16 AK057165_cds_2_0_chr16_244414_f 0 + 244413 244681 +chr16 AB016929_cds_0_0_chr16_259269_r 0 - 259268 259383 +chr18 NM_001792_cds_0_0_chr18_23786115_r 0 - 23786114 23786321 +chr18 NM_012397_cds_1_0_chr18_59406882_f 0 + 59406881 59407046 +chr18 AB046400_cds_0_0_chr18_59455933_r 0 - 59455932 59456337 +chr18 AY792326_cds_0_0_chr18_59528408_f 0 + 59528407 59528575 +chr19 BC013995_cds_1_0_chr19_59068596_f 0 + 59068595 59069564 +chr19 NM_198481_cds_0_0_chr19_59236027_r 0 - 59236026 59236146 +chr19 NM_004542_cds_0_0_chr19_59297999_f 0 + 59297998 59298008 +chr19 AK128544_cds_3_0_chr19_59318206_r 0 - 59318205 59318718 +chr2 NM_006773_cds_0_0_chr2_118288584_f 0 + 118288583 118288668 +chr2 BC005078_cds_0_0_chr2_118390396_r 0 - 118390395 118390500 +chr2 AY125465_cds_0_0_chr2_220108690_f 0 + 220108689 220109267 +chr2 NM_024536_cds_0_0_chr2_220229610_r 0 - 220229609 220230869 +chr20 NM_181466_cds_0_0_chr20_33330414_r 0 - 33330413 33330423 +chr20 BC085019_cds_1_0_chr20_33485371_f 0 + 33485370 33486123 +chr20 NM_000557_cds_1_0_chr20_33488492_r 0 - 33488491 33489122 +chr20 AF022655_cds_1_0_chr20_33513607_f 0 + 33513606 33513792 +chr21 NM_032910_cds_0_0_chr21_32687403_f 0 + 32687402 32687588 +chr21 NM_018277_cds_3_0_chr21_32869642_r 0 - 32869641 32870022 +chr21 NM_005806_cds_1_0_chr21_33321041_f 0 + 33321040 33322012 +chr21 AK129657_cds_0_0_chr21_33728359_r 0 - 33728358 33728724 +chr22 NM_004147_cds_0_0_chr22_30120224_f 0 + 30120223 30120265 +chr22 BC032941_cds_0_0_chr22_30160420_r 0 - 30160419 30160661 +chr22 NM_001007467_cds_1_0_chr22_30228825_f 0 + 30228824 30228916 +chr22 CR456540_cds_0_0_chr22_30340152_r 0 - 30340151 30340376 +chr5 AF099740_cds_11_0_chr5_131311207_r 0 - 131311206 131311254 +chr5 NM_000588_cds_0_0_chr5_131424299_f 0 + 131424298 131424460 +chr5 BC035813_cds_0_0_chr5_131556602_r 0 - 131556601 131556672 +chr5 BC003096_cds_0_0_chr5_131621327_f 0 + 131621326 131621419 +chr6 NM_007214_cds_0_0_chr6_108299601_r 0 - 108299600 108299744 +chr6 NM_003269_cds_0_0_chr6_108594663_f 0 + 108594662 108594687 +chr6 NM_003795_cds_0_0_chr6_108640046_r 0 - 108640045 108640151 +chr6 NM_145315_cds_0_0_chr6_108722977_f 0 + 108722976 108723115 +chr7 AF467257_cds_1_0_chr7_113660518_f 0 + 113660517 113660685 +chr7 NM_003391_cds_0_0_chr7_116512160_r 0 - 116512159 116512389 +chr7 NM_000492_cds_0_0_chr7_116714100_f 0 + 116714099 116714152 +chr7 AF377960_cds_0_0_chr7_116945542_r 0 - 116945541 116945787 +chr8 NM_000127_cds_0_0_chr8_118881132_r 0 - 118881131 118881317 +chr9 BC051300_cds_0_0_chr9_128764157_f 0 + 128764156 128764189 +chr9 NM_014908_cds_0_0_chr9_128787520_r 0 - 128787519 128789136 +chr9 NM_015354_cds_0_0_chr9_128789553_f 0 + 128789552 128789584 +chr9 AB058751_cds_0_0_chr9_128850517_r 0 - 128850516 128850624 +chrX NM_001167_cds_1_0_chrX_122745048_f 0 + 122745047 122745924 +chrX NM_000425_cds_0_0_chrX_152648965_r 0 - 152648964 152649196 +chrX AF101728_cds_0_0_chrX_152691447_f 0 + 152691446 152691471 +chrX BC052303_cds_0_0_chrX_152694030_r 0 - 152694029 152694263 diff -r 4e44d29377e3 -r 0da612f8a78e test-data/gops_complement_out_diffCols.dat --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gops_complement_out_diffCols.dat Thu Oct 30 16:03:11 2008 -0400 @@ -0,0 +1,88 @@ +chr7 . . + 0 113660517 +chr7 . . + 113660685 116512159 +chr7 . . + 116512389 116714099 +chr7 . . + 116714152 116945541 +chr7 . . + 116945787 536870912 +chr6 . . + 0 108299600 +chr6 . . + 108299744 108594662 +chr6 . . + 108594687 108640045 +chr6 . . + 108640151 108722976 +chr6 . . + 108723115 536870912 +chr5 . . + 0 131311206 +chr5 . . + 131311254 131424298 +chr5 . . + 131424460 131556601 +chr5 . . + 131556672 131621326 +chr5 . . + 131621419 536870912 +chrX . . + 0 122745047 +chrX . . + 122745924 152648964 +chrX . . + 152649196 152691446 +chrX . . + 152691471 152694029 +chrX . . + 152694263 536870912 +chr2 . . + 0 118288583 +chr2 . . + 118288668 118390395 +chr2 . . + 118390500 220108689 +chr2 . . + 220109267 220229609 +chr2 . . + 220230869 536870912 +chr1 . . + 0 147962192 +chr1 . . + 147962580 147984545 +chr1 . . + 147984630 148078400 +chr1 . . + 148078582 148185136 +chr1 . . + 148185276 536870912 +chr21 . . + 0 32687402 +chr21 . . + 32687588 32869641 +chr21 . . + 32870022 33321040 +chr21 . . + 33322012 33728358 +chr21 . . + 33728724 536870912 +chr9 . . + 0 128764156 +chr9 . . + 128764189 128787519 +chr9 . . + 128789136 128789552 +chr9 . . + 128789584 128850516 +chr9 . . + 128850624 536870912 +chr8 . . + 0 118881131 +chr8 . . + 118881317 536870912 +chr13 . . + 0 29680676 +chr13 . . + 29680875 112381694 +chr13 . . + 112381953 536870912 +chr12 . . + 0 38440094 +chr12 . . + 38440321 38905200 +chr12 . . + 38905351 536870912 +chr11 . . + 0 116124407 +chr11 . . + 116124501 116206508 +chr11 . . + 116206563 116211733 +chr11 . . + 116212337 130745911 +chr11 . . + 130745993 536870912 +chr10 . . + 0 55251623 +chr10 . . + 55253124 536870912 +chr22 . . + 0 30120223 +chr22 . . + 30120265 30160419 +chr22 . . + 30160661 30228824 +chr22 . . + 30228916 30340151 +chr22 . . + 30340376 536870912 +chr16 . . + 0 142908 +chr16 . . + 143003 179197 +chr16 . . + 179339 244413 +chr16 . . + 244681 259268 +chr16 . . + 259383 536870912 +chr15 . . + 0 41486872 +chr15 . . + 41487060 41673708 +chr15 . . + 41673857 41679161 +chr15 . . + 41679250 41773540 +chr15 . . + 41773689 536870912 +chr14 . . + 0 98521864 +chr14 . . + 98521922 98710240 +chr14 . . + 98712285 536870912 +chr20 . . + 0 33330413 +chr20 . . + 33330423 33485370 +chr20 . . + 33486123 33488491 +chr20 . . + 33489122 33513606 +chr20 . . + 33513792 536870912 +chr19 . . + 0 59068595 +chr19 . . + 59069564 59236026 +chr19 . . + 59236146 59297998 +chr19 . . + 59298008 59318205 +chr19 . . + 59318718 536870912 +chr18 . . + 0 23786114 +chr18 . . + 23786321 59406881 +chr18 . . + 59407046 59455932 +chr18 . . + 59456337 59528407 +chr18 . . + 59528575 536870912 diff -r 4e44d29377e3 -r 0da612f8a78e test-data/gops_coverage_out_diffCols.interval --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gops_coverage_out_diffCols.interval Thu Oct 30 16:03:11 2008 -0400 @@ -0,0 +1,65 @@ +chr1 147962192 147962580 CCDS989.1_cds_0_0_chr1_147962193_r 0 - 388 1.0 +chr1 147984545 147984630 CCDS990.1_cds_0_0_chr1_147984546_f 0 + 85 1.0 +chr1 148078400 148078582 CCDS993.1_cds_0_0_chr1_148078401_r 0 - 182 1.0 +chr1 148185136 148185276 CCDS996.1_cds_0_0_chr1_148185137_f 0 + 140 1.0 +chr10 55251623 55253124 CCDS7248.1_cds_0_0_chr10_55251624_r 0 - 1501 1.0 +chr11 116124407 116124501 CCDS8374.1_cds_0_0_chr11_116124408_r 0 - 94 1.0 +chr11 116206508 116206563 CCDS8377.1_cds_0_0_chr11_116206509_f 0 + 55 1.0 +chr11 116211733 116212337 CCDS8378.1_cds_0_0_chr11_116211734_r 0 - 604 1.0 +chr11 1812377 1812407 CCDS7726.1_cds_0_0_chr11_1812378_f 0 + 0 0.0 +chr12 38440094 38440321 CCDS8736.1_cds_0_0_chr12_38440095_r 0 - 227 1.0 +chr13 112381694 112381953 CCDS9526.1_cds_0_0_chr13_112381695_f 0 + 259 1.0 +chr14 98710240 98712285 CCDS9949.1_cds_0_0_chr14_98710241_r 0 - 2045 1.0 +chr15 41486872 41487060 CCDS10096.1_cds_0_0_chr15_41486873_r 0 - 188 1.0 +chr15 41673708 41673857 CCDS10097.1_cds_0_0_chr15_41673709_f 0 + 149 1.0 +chr15 41679161 41679250 CCDS10098.1_cds_0_0_chr15_41679162_r 0 - 89 1.0 +chr15 41826029 41826196 CCDS10101.1_cds_0_0_chr15_41826030_f 0 + 0 0.0 +chr16 142908 143003 CCDS10397.1_cds_0_0_chr16_142909_f 0 + 95 1.0 +chr16 179963 180135 CCDS10401.1_cds_0_0_chr16_179964_r 0 - 0 0.0 +chr16 244413 244681 CCDS10402.1_cds_0_0_chr16_244414_f 0 + 268 1.0 +chr16 259268 259383 CCDS10403.1_cds_0_0_chr16_259269_r 0 - 115 1.0 +chr18 23786114 23786321 CCDS11891.1_cds_0_0_chr18_23786115_r 0 - 207 1.0 +chr18 59406881 59407046 CCDS11985.1_cds_0_0_chr18_59406882_f 0 + 165 1.0 +chr18 59455932 59456337 CCDS11986.1_cds_0_0_chr18_59455933_r 0 - 405 1.0 +chr18 59600586 59600754 CCDS11988.1_cds_0_0_chr18_59600587_f 0 + 0 0.0 +chr19 59068595 59069564 CCDS12866.1_cds_0_0_chr19_59068596_f 0 + 969 1.0 +chr19 59236026 59236146 CCDS12872.1_cds_0_0_chr19_59236027_r 0 - 120 1.0 +chr19 59297998 59298008 CCDS12877.1_cds_0_0_chr19_59297999_f 0 + 10 1.0 +chr19 59302168 59302288 CCDS12878.1_cds_0_0_chr19_59302169_r 0 - 0 0.0 +chr2 118288583 118288668 CCDS2120.1_cds_0_0_chr2_118288584_f 0 + 85 1.0 +chr2 118394148 118394202 CCDS2121.1_cds_0_0_chr2_118394149_r 0 - 0 0.0 +chr2 220190202 220190242 CCDS2441.1_cds_0_0_chr2_220190203_f 0 + 0 0.0 +chr2 220229609 220230869 CCDS2443.1_cds_0_0_chr2_220229610_r 0 - 1260 1.0 +chr20 33330413 33330423 CCDS13249.1_cds_0_0_chr20_33330414_r 0 - 10 1.0 +chr20 33513606 33513792 CCDS13255.1_cds_0_0_chr20_33513607_f 0 + 186 1.0 +chr20 33579500 33579527 CCDS13256.1_cds_0_0_chr20_33579501_r 0 - 0 0.0 +chr20 33593260 33593348 CCDS13257.1_cds_0_0_chr20_33593261_f 0 + 0 0.0 +chr21 32707032 32707192 CCDS13614.1_cds_0_0_chr21_32707033_f 0 + 0 0.0 +chr21 32869641 32870022 CCDS13615.1_cds_0_0_chr21_32869642_r 0 - 381 1.0 +chr21 33321040 33322012 CCDS13620.1_cds_0_0_chr21_33321041_f 0 + 972 1.0 +chr21 33744994 33745040 CCDS13625.1_cds_0_0_chr21_33744995_r 0 - 0 0.0 +chr22 30120223 30120265 CCDS13897.1_cds_0_0_chr22_30120224_f 0 + 42 1.0 +chr22 30160419 30160661 CCDS13898.1_cds_0_0_chr22_30160420_r 0 - 242 1.0 +chr22 30665273 30665360 CCDS13901.1_cds_0_0_chr22_30665274_f 0 + 0 0.0 +chr22 30939054 30939266 CCDS13903.1_cds_0_0_chr22_30939055_r 0 - 0 0.0 +chr5 131424298 131424460 CCDS4149.1_cds_0_0_chr5_131424299_f 0 + 162 1.0 +chr5 131556601 131556672 CCDS4151.1_cds_0_0_chr5_131556602_r 0 - 71 1.0 +chr5 131621326 131621419 CCDS4152.1_cds_0_0_chr5_131621327_f 0 + 93 1.0 +chr5 131847541 131847666 CCDS4155.1_cds_0_0_chr5_131847542_r 0 - 0 0.0 +chr6 108299600 108299744 CCDS5061.1_cds_0_0_chr6_108299601_r 0 - 144 1.0 +chr6 108594662 108594687 CCDS5063.1_cds_0_0_chr6_108594663_f 0 + 25 1.0 +chr6 108640045 108640151 CCDS5064.1_cds_0_0_chr6_108640046_r 0 - 106 1.0 +chr6 108722976 108723115 CCDS5067.1_cds_0_0_chr6_108722977_f 0 + 139 1.0 +chr7 113660517 113660685 CCDS5760.1_cds_0_0_chr7_113660518_f 0 + 168 1.0 +chr7 116512159 116512389 CCDS5771.1_cds_0_0_chr7_116512160_r 0 - 230 1.0 +chr7 116714099 116714152 CCDS5773.1_cds_0_0_chr7_116714100_f 0 + 53 1.0 +chr7 116945541 116945787 CCDS5774.1_cds_0_0_chr7_116945542_r 0 - 246 1.0 +chr8 118881131 118881317 CCDS6324.1_cds_0_0_chr8_118881132_r 0 - 186 1.0 +chr9 128764156 128764189 CCDS6914.1_cds_0_0_chr9_128764157_f 0 + 33 1.0 +chr9 128787519 128789136 CCDS6915.1_cds_0_0_chr9_128787520_r 0 - 1617 1.0 +chr9 128882427 128882523 CCDS6917.1_cds_0_0_chr9_128882428_f 0 + 0 0.0 +chr9 128937229 128937445 CCDS6919.1_cds_0_0_chr9_128937230_r 0 - 0 0.0 +chrX 122745047 122745924 CCDS14606.1_cds_0_0_chrX_122745048_f 0 + 877 1.0 +chrX 152648964 152649196 CCDS14733.1_cds_0_0_chrX_152648965_r 0 - 232 1.0 +chrX 152691446 152691471 CCDS14735.1_cds_0_0_chrX_152691447_f 0 + 25 1.0 +chrX 152694029 152694263 CCDS14736.1_cds_0_0_chrX_152694030_r 0 - 234 1.0 diff -r 4e44d29377e3 -r 0da612f8a78e test-data/gops_intersect_diffCols.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gops_intersect_diffCols.bed Thu Oct 30 16:03:11 2008 -0400 @@ -0,0 +1,49 @@ +chr1 147962192 147962580 CCDS989.1_cds_0_0_chr1_147962193_r 0 - +chr1 147984545 147984630 CCDS990.1_cds_0_0_chr1_147984546_f 0 + +chr1 148078400 148078582 CCDS993.1_cds_0_0_chr1_148078401_r 0 - +chr1 148185136 148185276 CCDS996.1_cds_0_0_chr1_148185137_f 0 + +chr10 55251623 55253124 CCDS7248.1_cds_0_0_chr10_55251624_r 0 - +chr11 116124407 116124501 CCDS8374.1_cds_0_0_chr11_116124408_r 0 - +chr11 116206508 116206563 CCDS8377.1_cds_0_0_chr11_116206509_f 0 + +chr11 116211733 116212337 CCDS8378.1_cds_0_0_chr11_116211734_r 0 - +chr12 38440094 38440321 CCDS8736.1_cds_0_0_chr12_38440095_r 0 - +chr13 112381694 112381953 CCDS9526.1_cds_0_0_chr13_112381695_f 0 + +chr14 98710240 98712285 CCDS9949.1_cds_0_0_chr14_98710241_r 0 - +chr15 41486872 41487060 CCDS10096.1_cds_0_0_chr15_41486873_r 0 - +chr15 41673708 41673857 CCDS10097.1_cds_0_0_chr15_41673709_f 0 + +chr15 41679161 41679250 CCDS10098.1_cds_0_0_chr15_41679162_r 0 - +chr16 142908 143003 CCDS10397.1_cds_0_0_chr16_142909_f 0 + +chr16 244413 244681 CCDS10402.1_cds_0_0_chr16_244414_f 0 + +chr16 259268 259383 CCDS10403.1_cds_0_0_chr16_259269_r 0 - +chr18 23786114 23786321 CCDS11891.1_cds_0_0_chr18_23786115_r 0 - +chr18 59406881 59407046 CCDS11985.1_cds_0_0_chr18_59406882_f 0 + +chr18 59455932 59456337 CCDS11986.1_cds_0_0_chr18_59455933_r 0 - +chr19 59068595 59069564 CCDS12866.1_cds_0_0_chr19_59068596_f 0 + +chr19 59236026 59236146 CCDS12872.1_cds_0_0_chr19_59236027_r 0 - +chr19 59297998 59298008 CCDS12877.1_cds_0_0_chr19_59297999_f 0 + +chr2 118288583 118288668 CCDS2120.1_cds_0_0_chr2_118288584_f 0 + +chr2 220229609 220230869 CCDS2443.1_cds_0_0_chr2_220229610_r 0 - +chr20 33330413 33330423 CCDS13249.1_cds_0_0_chr20_33330414_r 0 - +chr20 33513606 33513792 CCDS13255.1_cds_0_0_chr20_33513607_f 0 + +chr21 32869641 32870022 CCDS13615.1_cds_0_0_chr21_32869642_r 0 - +chr21 33321040 33322012 CCDS13620.1_cds_0_0_chr21_33321041_f 0 + +chr22 30120223 30120265 CCDS13897.1_cds_0_0_chr22_30120224_f 0 + +chr22 30160419 30160661 CCDS13898.1_cds_0_0_chr22_30160420_r 0 - +chr5 131424298 131424460 CCDS4149.1_cds_0_0_chr5_131424299_f 0 + +chr5 131556601 131556672 CCDS4151.1_cds_0_0_chr5_131556602_r 0 - +chr5 131621326 131621419 CCDS4152.1_cds_0_0_chr5_131621327_f 0 + +chr6 108299600 108299744 CCDS5061.1_cds_0_0_chr6_108299601_r 0 - +chr6 108594662 108594687 CCDS5063.1_cds_0_0_chr6_108594663_f 0 + +chr6 108640045 108640151 CCDS5064.1_cds_0_0_chr6_108640046_r 0 - +chr6 108722976 108723115 CCDS5067.1_cds_0_0_chr6_108722977_f 0 + +chr7 113660517 113660685 CCDS5760.1_cds_0_0_chr7_113660518_f 0 + +chr7 116512159 116512389 CCDS5771.1_cds_0_0_chr7_116512160_r 0 - +chr7 116714099 116714152 CCDS5773.1_cds_0_0_chr7_116714100_f 0 + +chr7 116945541 116945787 CCDS5774.1_cds_0_0_chr7_116945542_r 0 - +chr8 118881131 118881317 CCDS6324.1_cds_0_0_chr8_118881132_r 0 - +chr9 128764156 128764189 CCDS6914.1_cds_0_0_chr9_128764157_f 0 + +chr9 128787519 128789136 CCDS6915.1_cds_0_0_chr9_128787520_r 0 - +chrX 122745047 122745924 CCDS14606.1_cds_0_0_chrX_122745048_f 0 + +chrX 152648964 152649196 CCDS14733.1_cds_0_0_chrX_152648965_r 0 - +chrX 152691446 152691471 CCDS14735.1_cds_0_0_chrX_152691447_f 0 + +chrX 152694029 152694263 CCDS14736.1_cds_0_0_chrX_152694030_r 0 - diff -r 4e44d29377e3 -r 0da612f8a78e test-data/gops_intersect_p_diffCols.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gops_intersect_p_diffCols.bed Thu Oct 30 16:03:11 2008 -0400 @@ -0,0 +1,49 @@ +chr1 147962192 147962580 CCDS989.1_cds_0_0_chr1_147962193_r 0 - +chr1 147984545 147984630 CCDS990.1_cds_0_0_chr1_147984546_f 0 + +chr1 148078400 148078582 CCDS993.1_cds_0_0_chr1_148078401_r 0 - +chr1 148185136 148185276 CCDS996.1_cds_0_0_chr1_148185137_f 0 + +chr10 55251623 55253124 CCDS7248.1_cds_0_0_chr10_55251624_r 0 - +chr11 116124407 116124501 CCDS8374.1_cds_0_0_chr11_116124408_r 0 - +chr11 116206508 116206563 CCDS8377.1_cds_0_0_chr11_116206509_f 0 + +chr11 116211733 116212337 CCDS8378.1_cds_0_0_chr11_116211734_r 0 - +chr12 38440094 38440321 CCDS8736.1_cds_0_0_chr12_38440095_r 0 - +chr13 112381694 112381953 CCDS9526.1_cds_0_0_chr13_112381695_f 0 + +chr14 98710240 98712285 CCDS9949.1_cds_0_0_chr14_98710241_r 0 - +chr15 41486872 41487060 CCDS10096.1_cds_0_0_chr15_41486873_r 0 - +chr15 41673708 41673857 CCDS10097.1_cds_0_0_chr15_41673709_f 0 + +chr15 41679161 41679250 CCDS10098.1_cds_0_0_chr15_41679162_r 0 - +chr16 142908 143003 CCDS10397.1_cds_0_0_chr16_142909_f 0 + +chr16 244413 244681 CCDS10402.1_cds_0_0_chr16_244414_f 0 + +chr16 259268 259383 CCDS10403.1_cds_0_0_chr16_259269_r 0 - +chr18 23786114 23786321 CCDS11891.1_cds_0_0_chr18_23786115_r 0 - +chr18 59406881 59407046 CCDS11985.1_cds_0_0_chr18_59406882_f 0 + +chr18 59455932 59456337 CCDS11986.1_cds_0_0_chr18_59455933_r 0 - +chr19 59068595 59069564 CCDS12866.1_cds_0_0_chr19_59068596_f 0 + +chr19 59236026 59236146 CCDS12872.1_cds_0_0_chr19_59236027_r 0 - +chr19 59297998 59298008 CCDS12877.1_cds_0_0_chr19_59297999_f 0 + +chr2 118288583 118288668 CCDS2120.1_cds_0_0_chr2_118288584_f 0 + +chr2 220229609 220230869 CCDS2443.1_cds_0_0_chr2_220229610_r 0 - +chr20 33330413 33330423 CCDS13249.1_cds_0_0_chr20_33330414_r 0 - +chr20 33513606 33513792 CCDS13255.1_cds_0_0_chr20_33513607_f 0 + +chr21 32869641 32870022 CCDS13615.1_cds_0_0_chr21_32869642_r 0 - +chr21 33321040 33322012 CCDS13620.1_cds_0_0_chr21_33321041_f 0 + +chr22 30120223 30120265 CCDS13897.1_cds_0_0_chr22_30120224_f 0 + +chr22 30160419 30160661 CCDS13898.1_cds_0_0_chr22_30160420_r 0 - +chr5 131424298 131424460 CCDS4149.1_cds_0_0_chr5_131424299_f 0 + +chr5 131556601 131556672 CCDS4151.1_cds_0_0_chr5_131556602_r 0 - +chr5 131621326 131621419 CCDS4152.1_cds_0_0_chr5_131621327_f 0 + +chr6 108299600 108299744 CCDS5061.1_cds_0_0_chr6_108299601_r 0 - +chr6 108594662 108594687 CCDS5063.1_cds_0_0_chr6_108594663_f 0 + +chr6 108640045 108640151 CCDS5064.1_cds_0_0_chr6_108640046_r 0 - +chr6 108722976 108723115 CCDS5067.1_cds_0_0_chr6_108722977_f 0 + +chr7 113660517 113660685 CCDS5760.1_cds_0_0_chr7_113660518_f 0 + +chr7 116512159 116512389 CCDS5771.1_cds_0_0_chr7_116512160_r 0 - +chr7 116714099 116714152 CCDS5773.1_cds_0_0_chr7_116714100_f 0 + +chr7 116945541 116945787 CCDS5774.1_cds_0_0_chr7_116945542_r 0 - +chr8 118881131 118881317 CCDS6324.1_cds_0_0_chr8_118881132_r 0 - +chr9 128764156 128764189 CCDS6914.1_cds_0_0_chr9_128764157_f 0 + +chr9 128787519 128789136 CCDS6915.1_cds_0_0_chr9_128787520_r 0 - +chrX 122745047 122745924 CCDS14606.1_cds_0_0_chrX_122745048_f 0 + +chrX 152648964 152649196 CCDS14733.1_cds_0_0_chrX_152648965_r 0 - +chrX 152691446 152691471 CCDS14735.1_cds_0_0_chrX_152691447_f 0 + +chrX 152694029 152694263 CCDS14736.1_cds_0_0_chrX_152694030_r 0 - diff -r 4e44d29377e3 -r 0da612f8a78e test-data/gops_merge_diffCols.dat --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gops_merge_diffCols.dat Thu Oct 30 16:03:11 2008 -0400 @@ -0,0 +1,69 @@ +#chr name score strand start end +chr7 113660517 113660685 +chr7 116512159 116512389 +chr7 116714099 116714152 +chr7 116945541 116945787 +chr6 108299600 108299744 +chr6 108594662 108594687 +chr6 108640045 108640151 +chr6 108722976 108723115 +chr5 131311206 131311254 +chr5 131424298 131424460 +chr5 131556601 131556672 +chr5 131621326 131621419 +chrX 122745047 122745924 +chrX 152648964 152649196 +chrX 152691446 152691471 +chrX 152694029 152694263 +chr2 118288583 118288668 +chr2 118390395 118390500 +chr2 220108689 220109267 +chr2 220229609 220230869 +chr1 147962192 147962580 +chr1 147984545 147984630 +chr1 148078400 148078582 +chr1 148185136 148185276 +chr21 32687402 32687588 +chr21 32869641 32870022 +chr21 33321040 33322012 +chr21 33728358 33728724 +chr9 128764156 128764189 +chr9 128787519 128789136 +chr9 128789552 128789584 +chr9 128850516 128850624 +chr8 118881131 118881317 +chr13 29680676 29680875 +chr13 112381694 112381953 +chr12 38440094 38440321 +chr12 38905200 38905351 +chr11 116124407 116124501 +chr11 116206508 116206563 +chr11 116211733 116212337 +chr11 130745911 130745993 +chr10 55251623 55253124 +chr22 30120223 30120265 +chr22 30160419 30160661 +chr22 30228824 30228916 +chr22 30340151 30340376 +chr16 142908 143003 +chr16 179197 179339 +chr16 244413 244681 +chr16 259268 259383 +chr15 41486872 41487060 +chr15 41673708 41673857 +chr15 41679161 41679250 +chr15 41773540 41773689 +chr14 98521864 98521922 +chr14 98710240 98712285 +chr20 33330413 33330423 +chr20 33485370 33486123 +chr20 33488491 33489122 +chr20 33513606 33513792 +chr19 59068595 59069564 +chr19 59236026 59236146 +chr19 59297998 59298008 +chr19 59318205 59318718 +chr18 23786114 23786321 +chr18 59406881 59407046 +chr18 59455932 59456337 +chr18 59528407 59528575 diff -r 4e44d29377e3 -r 0da612f8a78e test-data/gops_subtract_diffCols.dat --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gops_subtract_diffCols.dat Thu Oct 30 16:03:11 2008 -0400 @@ -0,0 +1,16 @@ +chr11 1812377 1812407 CCDS7726.1_cds_0_0_chr11_1812378_f 0 + +chr15 41826029 41826196 CCDS10101.1_cds_0_0_chr15_41826030_f 0 + +chr16 179963 180135 CCDS10401.1_cds_0_0_chr16_179964_r 0 - +chr18 59600586 59600754 CCDS11988.1_cds_0_0_chr18_59600587_f 0 + +chr19 59302168 59302288 CCDS12878.1_cds_0_0_chr19_59302169_r 0 - +chr2 118394148 118394202 CCDS2121.1_cds_0_0_chr2_118394149_r 0 - +chr2 220190202 220190242 CCDS2441.1_cds_0_0_chr2_220190203_f 0 + +chr20 33579500 33579527 CCDS13256.1_cds_0_0_chr20_33579501_r 0 - +chr20 33593260 33593348 CCDS13257.1_cds_0_0_chr20_33593261_f 0 + +chr21 32707032 32707192 CCDS13614.1_cds_0_0_chr21_32707033_f 0 + +chr21 33744994 33745040 CCDS13625.1_cds_0_0_chr21_33744995_r 0 - +chr22 30665273 30665360 CCDS13901.1_cds_0_0_chr22_30665274_f 0 + +chr22 30939054 30939266 CCDS13903.1_cds_0_0_chr22_30939055_r 0 - +chr5 131847541 131847666 CCDS4155.1_cds_0_0_chr5_131847542_r 0 - +chr9 128882427 128882523 CCDS6917.1_cds_0_0_chr9_128882428_f 0 + +chr9 128937229 128937445 CCDS6919.1_cds_0_0_chr9_128937230_r 0 - diff -r 4e44d29377e3 -r 0da612f8a78e tools/new_operations/complement.xml --- a/tools/new_operations/complement.xml Thu Oct 30 14:46:57 2008 -0400 +++ b/tools/new_operations/complement.xml Thu Oct 30 16:03:11 2008 -0400 @@ -17,6 +17,11 @@ <param name="input1" value="1.bed" /> <param name="allchroms" value="true" /> <output name="output" file="gops_complement_out.bed" /> + </test> + <test> + <param name="input1" value="2_mod.bed" ftype="interval"/> + <param name="allchroms" value="true" /> + <output name="output" file="gops_complement_out_diffCols.dat" /> </test> <test> <param name="input1" value="gops_bigint.interval" /> diff -r 4e44d29377e3 -r 0da612f8a78e tools/new_operations/coverage.xml --- a/tools/new_operations/coverage.xml Thu Oct 30 14:46:57 2008 -0400 +++ b/tools/new_operations/coverage.xml Thu Oct 30 16:03:11 2008 -0400 @@ -18,6 +18,11 @@ <param name="input1" value="1.bed" /> <param name="input2" value="2.bed" /> <output name="output" file="gops_coverage_out.interval" /> + </test> + <test> + <param name="input1" value="1.bed" /> + <param name="input2" value="2_mod.bed" ftype="interval"/> + <output name="output" file="gops_coverage_out_diffCols.interval" /> </test> <test> <param name="input1" value="gops_bigint.interval" /> diff -r 4e44d29377e3 -r 0da612f8a78e tools/new_operations/intersect.xml --- a/tools/new_operations/intersect.xml Thu Oct 30 14:46:57 2008 -0400 +++ b/tools/new_operations/intersect.xml Thu Oct 30 16:03:11 2008 -0400 @@ -21,13 +21,27 @@ <data format="input" name="output" metadata_source="input1" /> </outputs> <code file="operation_filter.py"/> - <tests> + <tests> + <test> + <param name="input1" value="1.bed" /> + <param name="input2" value="2.bed" /> + <param name="min" value="1" /> + <param name="returntype" value="" /> + <output name="output" file="gops_intersect_out.bed" /> + </test> <test> <param name="input1" value="1.bed" /> - <param name="input2" value="2.bed" /> + <param name="input2" value="2_mod.bed" ftype="interval"/> <param name="min" value="1" /> - <param name="returntype" value="" /> - <output name="output" file="gops_intersect_out.bed" /> + <param name="returntype" value="" /> + <output name="output" file="gops_intersect_diffCols.bed" /> + </test> + <test> + <param name="input1" value="1.bed" /> + <param name="input2" value="2_mod.bed" ftype="interval"/> + <param name="min" value="1" /> + <param name="returntype" value="Overlapping pieces of Intervals" /> + <output name="output" file="gops_intersect_p_diffCols.bed" /> </test> <test> <param name="input1" value="1.bed" /> diff -r 4e44d29377e3 -r 0da612f8a78e tools/new_operations/merge.xml --- a/tools/new_operations/merge.xml Thu Oct 30 14:46:57 2008 -0400 +++ b/tools/new_operations/merge.xml Thu Oct 30 16:03:11 2008 -0400 @@ -19,6 +19,11 @@ <test> <param name="input1" value="1.bed" /> <output name="output" file="gops-merge.dat" /> + <param name="returntype" value="true" /> + </test> + <test> + <param name="input1" value="2_mod.bed" ftype="interval"/> + <output name="output" file="gops_merge_diffCols.dat" /> <param name="returntype" value="true" /> </test> <test> diff -r 4e44d29377e3 -r 0da612f8a78e tools/new_operations/subtract.xml --- a/tools/new_operations/subtract.xml Thu Oct 30 14:46:57 2008 -0400 +++ b/tools/new_operations/subtract.xml Thu Oct 30 16:03:11 2008 -0400 @@ -31,6 +31,13 @@ <param name="min" value="1" /> <param name="returntype" value="" /> <output name="output" file="gops-subtract.dat" /> + </test> + <test> + <param name="input1" value="1.bed" /> + <param name="input2" value="2_mod.bed" ftype="interval"/> + <param name="min" value="1" /> + <param name="returntype" value="" /> + <output name="output" file="gops_subtract_diffCols.dat" /> </test> <test> <param name="input1" value="gops_subtract_bigint.bed" />

1 0

[hg] galaxy 1588: Use LD_RUN_PATH when building pbs_python
by Greg Von Kuster 30 Oct '08

30 Oct '08

details: http://www.bx.psu.edu/hg/galaxy/rev/ea92290c4e10 changeset: 1588:ea92290c4e10 user: Nate Coraor <nate(a)bx.psu.edu> date: Thu Oct 30 16:11:44 2008 -0400 description: Use LD_RUN_PATH when building pbs_python 1 file(s) affected in this change: scripts/scramble/scripts/pbs_python.py diffs (13 lines): diff -r 0da612f8a78e -r ea92290c4e10 scripts/scramble/scripts/pbs_python.py --- a/scripts/scramble/scripts/pbs_python.py Thu Oct 30 16:03:11 2008 -0400 +++ b/scripts/scramble/scripts/pbs_python.py Thu Oct 30 16:11:44 2008 -0400 @@ -27,6 +27,9 @@ print "scramble(): removing dir:", dir shutil.rmtree( dir ) +# the build process doesn't set an rpath for libtorque +os.environ['LD_RUN_PATH'] = os.environ['LIBTORQUE_DIR'] + print "scramble(): Running pbs_python configure script" p = subprocess.Popen( args = "sh configure --with-pbsdir=%s" % os.environ['LIBTORQUE_DIR'], shell = True ) r = p.wait()

1 0

[hg] galaxy 1589: Migrate central repo to alchemy 4.
by Greg Von Kuster 30 Oct '08

30 Oct '08

details: http://www.bx.psu.edu/hg/galaxy/rev/1d113c5386da changeset: 1589:1d113c5386da user: Greg Von Kuster <greg(a)bx.psu.edu> date: Thu Oct 30 16:17:46 2008 -0400 description: Migrate central repo to alchemy 4. 18 file(s) affected in this change: eggs.ini lib/galaxy/app.py lib/galaxy/jobs/__init__.py lib/galaxy/model/custom_types.py lib/galaxy/model/mapping.py lib/galaxy/model/mapping_tests.py lib/galaxy/model/orm/__init__.py lib/galaxy/model/orm/ext/__init__.py lib/galaxy/model/orm/ext/assignmapper.py lib/galaxy/web/controllers/root.py lib/galaxy/web/controllers/user.py lib/galaxy/web/controllers/workflow.py lib/galaxy/web/framework/__init__.py lib/galaxy/webapps/reports/controllers/jobs.py lib/galaxy/webapps/reports/controllers/system.py lib/galaxy/webapps/reports/controllers/users.py scripts/cleanup_datasets/cleanup_datasets.py tools/stats/grouping.py diffs (623 lines): diff -r ea92290c4e10 -r 1d113c5386da eggs.ini --- a/eggs.ini Thu Oct 30 16:11:44 2008 -0400 +++ b/eggs.ini Thu Oct 30 16:17:46 2008 -0400 @@ -40,7 +40,7 @@ PasteScript = 1.3.6 Routes = 1.6.3 simplejson = 1.5 -SQLAlchemy = 0.3.11 +SQLAlchemy = 0.4.7p1 Tempita = 0.1 twill = 0.9 WebError = 0.8a @@ -85,7 +85,7 @@ PasteScript = http://cheeseshop.python.org/packages/source/P/PasteScript/PasteScript-1.3.… Routes = http://pypi.python.org/packages/source/R/Routes/Routes-1.6.3.tar.gz simplejson = http://cheeseshop.python.org/packages/source/s/simplejson/simplejson-1.5.ta… -SQLAlchemy = http://pypi.python.org/packages/source/S/SQLAlchemy/SQLAlchemy-0.3.11.tar.gz +SQLAlchemy = http://pypi.python.org/packages/source/S/SQLAlchemy/SQLAlchemy-0.4.7p1.tar.… Tempita = http://pypi.python.org/packages/source/T/Tempita/Tempita-0.1.tar.gz twill = http://darcs.idyll.org/~t/projects/twill-0.9.tar.gz WebError = http://pypi.python.org/packages/source/W/WebError/WebError-0.8a.tar.gz diff -r ea92290c4e10 -r 1d113c5386da lib/galaxy/app.py --- a/lib/galaxy/app.py Thu Oct 30 16:11:44 2008 -0400 +++ b/lib/galaxy/app.py Thu Oct 30 16:17:46 2008 -0400 @@ -20,7 +20,7 @@ if self.config.database_connection: db_url = self.config.database_connection else: - db_url = "sqlite://%s?isolation_level=IMMEDIATE" % self.config.database + db_url = "sqlite:///%s?isolation_level=IMMEDIATE" % self.config.database # Setup the database engine and ORM self.model = galaxy.model.mapping.init( self.config.file_path, db_url, diff -r ea92290c4e10 -r 1d113c5386da lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py Thu Oct 30 16:11:44 2008 -0400 +++ b/lib/galaxy/jobs/__init__.py Thu Oct 30 16:17:46 2008 -0400 @@ -97,11 +97,10 @@ model = self.app.model # Jobs in the NEW state won't be requeued unless we're tracking in the database if not self.track_jobs_in_database: - for job in model.Job.select( model.Job.c.state == model.Job.states.NEW ): + for job in model.Job.filter( model.Job.c.state==model.Job.states.NEW ).all(): log.debug( "no runner: %s is still in new state, adding to the jobs queue" %job.id ) self.queue.put( ( job.id, job.tool_id ) ) - for job in model.Job.select( (model.Job.c.state == model.Job.states.RUNNING) - | (model.Job.c.state == model.Job.states.QUEUED) ): + for job in model.Job.filter( (model.Job.c.state == model.Job.states.RUNNING) | (model.Job.c.state == model.Job.states.QUEUED) ).all(): if job.job_runner_name is not None: # why are we passing the queue to the wrapper? job_wrapper = JobWrapper( job.id, self.app.toolbox.tools_by_id[ job.tool_id ], self ) @@ -136,7 +135,7 @@ new_jobs = [] if self.track_jobs_in_database: model = self.app.model - for j in model.Job.select( model.Job.c.state == model.Job.states.NEW ): + for j in model.Job.filter( model.Job.c.state==model.Job.states.NEW ).all(): job = JobWrapper( j.id, self.app.toolbox.tools_by_id[ j.tool_id ], self ) new_jobs.append( job ) else: diff -r ea92290c4e10 -r 1d113c5386da lib/galaxy/model/custom_types.py --- a/lib/galaxy/model/custom_types.py Thu Oct 30 16:11:44 2008 -0400 +++ b/lib/galaxy/model/custom_types.py Thu Oct 30 16:17:46 2008 -0400 @@ -18,16 +18,15 @@ self.mutable = mutable super( JSONType, self).__init__() - def convert_result_value( self, value, dialect ): + def process_bind_param( self, value, dialect ): if value is None: return None - buf = self.impl.convert_result_value( value, dialect ) - return self.jsonifyer.loads( str(buf) ) - - def convert_bind_param( self, value, dialect ): + return self.jsonifyer.dumps( value ) + + def process_result_value( self, value, dialect ): if value is None: return None - return self.impl.convert_bind_param( self.jsonifyer.dumps(value), dialect ) + return self.jsonifyer.loads( str( value ) ) def copy_value( self, value ): if self.mutable: @@ -60,10 +59,10 @@ self.mutable = mutable super( MetadataType, self).__init__() - def convert_result_value( self, value, dialect ): + def process_result_value( self, value, dialect ): if value is None: return None - buf = self.impl.convert_result_value( value, dialect ) + buf = value ret = None try: ret = self.pickler.loads( str(buf) ) @@ -77,7 +76,7 @@ class TrimmedString( TypeDecorator ): impl = String - def convert_bind_param( self, value, dialect ): + def process_bind_param( self, value, dialect ): """Automatically truncate string values""" if self.impl.length and value is not None: value = value[0:self.impl.length] diff -r ea92290c4e10 -r 1d113c5386da lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py Thu Oct 30 16:11:44 2008 -0400 +++ b/lib/galaxy/model/mapping.py Thu Oct 30 16:17:46 2008 -0400 @@ -5,23 +5,20 @@ import logging log = logging.getLogger( __name__ ) -import pkg_resources -pkg_resources.require( "sqlalchemy>=0.3" ) - import sys import datetime -from sqlalchemy.ext.sessioncontext import SessionContext -from sqlalchemy.ext.assignmapper import assign_mapper -from sqlalchemy.ext.orderinglist import ordering_list - -from sqlalchemy import * from galaxy.model import * +from galaxy.model.orm import * +from galaxy.model.orm.ext.assignmapper import * from galaxy.model.custom_types import * from galaxy.util.bunch import Bunch -metadata = DynamicMetaData( threadlocal=False ) -context = SessionContext( create_session ) +metadata = MetaData() +context = Session = scoped_session( sessionmaker( autoflush=False, transactional=False ) ) + +# For backward compatibility with "context.current" +context.current = Session dialect_to_egg = { "sqlite" : "pysqlite>=2", @@ -120,15 +117,15 @@ Column( "update_time", DateTime, default=now, onupdate=now ), Column( "history_id", Integer, ForeignKey( "history.id" ), index=True ), Column( "tool_id", String( 255 ) ), - Column( "tool_version", String, default="1.0.0" ), + Column( "tool_version", TEXT, default="1.0.0" ), Column( "state", String( 64 ) ), Column( "info", TrimmedString( 255 ) ), - Column( "command_line", String() ), + Column( "command_line", TEXT ), Column( "param_filename", String( 1024 ) ), Column( "runner_name", String( 255 ) ), - Column( "stdout", String() ), - Column( "stderr", String() ), - Column( "traceback", String() ), + Column( "stdout", TEXT ), + Column( "stderr", TEXT ), + Column( "traceback", TEXT ), Column( "session_id", Integer, ForeignKey( "galaxy_session.id" ), index=True, nullable=True ), Column( "job_runner_name", String( 255 ) ), Column( "job_runner_external_id", String( 255 ) ) ) @@ -188,7 +185,7 @@ Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True, nullable=False ), Column( "latest_workflow_id", Integer, ForeignKey( "workflow.id", use_alter=True, name='stored_workflow_latest_workflow_id_fk' ), index=True ), - Column( "name", String ), + Column( "name", TEXT ), Column( "deleted", Boolean, default=False ), ) @@ -197,7 +194,7 @@ Column( "create_time", DateTime, default=now ), Column( "update_time", DateTime, default=now, onupdate=now ), Column( "stored_workflow_id", Integer, ForeignKey( "stored_workflow.id" ), index=True, nullable=False ), - Column( "name", String ), + Column( "name", TEXT ), Column( "has_cycles", Boolean ), Column( "has_errors", Boolean ) ) @@ -208,8 +205,8 @@ Column( "update_time", DateTime, default=now, onupdate=now ), Column( "workflow_id", Integer, ForeignKey( "workflow.id" ), index=True, nullable=False ), Column( "type", String(64) ), - Column( "tool_id", String ), - Column( "tool_version", String ), # Reserved for future + Column( "tool_id", TEXT ), + Column( "tool_version", TEXT ), # Reserved for future Column( "tool_inputs", JSONType ), Column( "tool_errors", JSONType ), Column( "position", JSONType ), @@ -222,8 +219,8 @@ Column( "id", Integer, primary_key=True ), Column( "output_step_id", Integer, ForeignKey( "workflow_step.id" ), index=True ), Column( "input_step_id", Integer, ForeignKey( "workflow_step.id" ), index=True ), - Column( "output_name", String ), - Column( "input_name", String) + Column( "output_name", TEXT ), + Column( "input_name", TEXT) ) StoredWorkflowUserShareAssociation.table = Table( "stored_workflow_user_share_connection", metadata, @@ -240,7 +237,7 @@ MetadataFile.table = Table( "metadata_file", metadata, Column( "id", Integer, primary_key=True ), - Column( "name", String ), + Column( "name", TEXT ), Column( "hda_id", Integer, ForeignKey( "history_dataset_association.id" ), index=True, nullable=True ), Column( "create_time", DateTime, default=now ), Column( "update_time", DateTime, index=True, default=now, onupdate=now ), @@ -257,9 +254,7 @@ dataset=relation( Dataset, primaryjoin=( Dataset.table.c.id == HistoryDatasetAssociation.table.c.dataset_id ), lazy=False ), - history=relation( - History, - primaryjoin=( History.table.c.id == HistoryDatasetAssociation.table.c.history_id ) ), + # .history defined in History mapper copied_to_history_dataset_associations=relation( HistoryDatasetAssociation, primaryjoin=( HistoryDatasetAssociation.table.c.copied_from_history_dataset_association_id == HistoryDatasetAssociation.table.c.id ), @@ -380,11 +375,12 @@ Override __next_hid to generate from the database in a concurrency safe way. """ - conn = self.table.engine.contextual_connect() + conn = object_session( self ).connection() + table = self.table trans = conn.begin() try: - next_hid = select( [self.c.hid_counter], self.c.id == self.id, for_update=True ).scalar() - self.table.update( self.c.id == self.id ).execute( hid_counter = ( next_hid + 1 ) ) + next_hid = select( [table.c.hid_counter], table.c.id == self.id, for_update=True ).scalar() + table.update( table.c.id == self.id ).execute( hid_counter = ( next_hid + 1 ) ) trans.commit() return next_hid except: @@ -413,17 +409,21 @@ # Create the database engine engine = create_engine( url, **engine_options ) # Connect the metadata to the database. - metadata.connect( engine ) - ## metadata.engine.echo = True + metadata.bind = engine + # Clear any existing contextual sessions and reconfigure + Session.remove() + Session.configure( bind=engine ) # Create tables if needed if create_tables: metadata.create_all() # metadata.engine.commit() # Pack everything into a bunch result = Bunch( **globals() ) - result.engine = metadata.engine - result.flush = lambda *args, **kwargs: context.current.flush( *args, **kwargs ) - result.context = context + result.engine = engine + result.flush = lambda *args, **kwargs: Session.flush( *args, **kwargs ) + result.session = Session + # For backward compatibility with "model.context.current" + result.context = Session result.create_tables = create_tables return result diff -r ea92290c4e10 -r 1d113c5386da lib/galaxy/model/mapping_tests.py --- a/lib/galaxy/model/mapping_tests.py Thu Oct 30 16:11:44 2008 -0400 +++ b/lib/galaxy/model/mapping_tests.py Thu Oct 30 16:17:46 2008 -0400 @@ -22,13 +22,13 @@ model.context.current.flush() model.context.current.clear() # Check - users = model.User.select() + users = model.User.query().all() assert len( users ) == 1 assert users[0].email == "james(a)foo.bar.baz" assert users[0].password == "password" assert len( users[0].histories ) == 1 assert users[0].histories[0].name == "History 1" - hists = model.History.select() + hists = model.History.query().all() assert hists[0].name == "History 1" assert hists[1].name == ( "H" * 255 ) assert hists[0].user == users[0] @@ -40,7 +40,7 @@ hists[1].name = "History 2b" model.context.current.flush() model.context.current.clear() - hists = model.History.select() + hists = model.History.query().all() assert hists[0].name == "History 1" assert hists[1].name == "History 2b" # gvk TODO need to ad test for GalaxySessions, but not yet sure what they should look like. diff -r ea92290c4e10 -r 1d113c5386da lib/galaxy/model/orm/__init__.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/model/orm/__init__.py Thu Oct 30 16:17:46 2008 -0400 @@ -0,0 +1,7 @@ +import pkg_resources +pkg_resources.require( "SQLAlchemy >= 0.4" ) + +from sqlalchemy import * +from sqlalchemy.orm import * + +from sqlalchemy.ext.orderinglist import ordering_list diff -r ea92290c4e10 -r 1d113c5386da lib/galaxy/model/orm/ext/__init__.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/model/orm/ext/__init__.py Thu Oct 30 16:17:46 2008 -0400 @@ -0,0 +1,3 @@ +""" +Galaxy specific SQLAlchemy extensions. +""" \ No newline at end of file diff -r ea92290c4e10 -r 1d113c5386da lib/galaxy/model/orm/ext/assignmapper.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/model/orm/ext/assignmapper.py Thu Oct 30 16:17:46 2008 -0400 @@ -0,0 +1,62 @@ +""" +This is similar to the assignmapper extensions in SQLAclhemy 0.3 and 0.4 but +with some compatibility fixes. It assumes that the session is a ScopedSession, +and thus has the "mapper" method to attach contextual mappers to a class. It +adds additional query and session methods to the class to support the +SQLAlchemy 0.3 style of access. The following methods which would normally be +accessed through "Object.query().method()" are available directly through the +object: + + 'get', 'filter', 'filter_by', 'select', 'select_by', + 'selectfirst', 'selectfirst_by', 'selectone', 'selectone_by', + 'get_by', 'join_to', 'join_via', 'count', 'count_by', + 'options', 'instances' + +Additionally, the following Session methods, which normally accept an instance +or list of instances, are available directly through the objects, e.g. +"Session.flush( [instance] )" can be performed as "instance.flush()": + + 'refresh', 'expire', 'delete', 'expunge', 'update' +""" + +__all__ = [ 'assign_mapper' ] + +from sqlalchemy import util, exceptions +import types +from sqlalchemy.orm import mapper, Query + +def _monkeypatch_query_method( name, session, class_ ): + def do(self, *args, **kwargs): + ## util.warn_deprecated('Query methods on the class are deprecated; use %s.query.%s instead' % (class_.__name__, name)) + return getattr( class_.query, name)(*args, **kwargs) + try: + do.__name__ = name + except: + pass + if not hasattr(class_, name): + setattr(class_, name, classmethod(do)) + +def _monkeypatch_session_method(name, session, class_, make_list=False): + def do(self, *args, **kwargs): + if make_list: + self = [ self ] + return getattr(session, name)( self, *args, **kwargs ) + try: + do.__name__ = name + except: + pass + if not hasattr(class_, name): + setattr(class_, name, do) + +def assign_mapper( session, class_, *args, **kwargs ): + m = class_.mapper = session.mapper( class_, *args, **kwargs ) + for name in ('get', 'filter', 'filter_by', 'select', 'select_by', + 'selectfirst', 'selectfirst_by', 'selectone', 'selectone_by', + 'get_by', 'join_to', 'join_via', 'count', 'count_by', + 'options', 'instances'): + _monkeypatch_query_method(name, session, class_) + for name in ('refresh', 'expire', 'delete', 'expunge', 'update'): + _monkeypatch_session_method(name, session, class_) + for name in ( 'flush', ): + _monkeypatch_session_method( name, session, class_, make_list=True ) + return m diff -r ea92290c4e10 -r 1d113c5386da lib/galaxy/web/controllers/root.py --- a/lib/galaxy/web/controllers/root.py Thu Oct 30 16:11:44 2008 -0400 +++ b/lib/galaxy/web/controllers/root.py Thu Oct 30 16:17:46 2008 -0400 @@ -429,7 +429,7 @@ if not email: return trans.fill_template("/history/share.mako", histories=histories, email=email, send_to_err=send_to_err) user = trans.get_user() - send_to_user = trans.app.model.User.get_by( email = email ) + send_to_user = trans.app.model.User.filter_by( email=email ).first() if not send_to_user: send_to_err = "No such user" elif user.email == email: @@ -488,7 +488,7 @@ new_history.user_id = user.id galaxy_session = trans.get_galaxy_session() try: - association = trans.app.model.GalaxySessionToHistoryAssociation.selectone_by( session_id=galaxy_session.id, history_id=new_history.id ) + association = trans.app.model.GalaxySessionToHistoryAssociation.filter_by( session_id=galaxy_session.id, history_id=new_history.id ).first() except: association = None new_history.add_galaxy_session( galaxy_session, association=association ) @@ -505,7 +505,7 @@ new_history.user_id = None galaxy_session = trans.get_galaxy_session() try: - association = trans.app.model.GalaxySessionToHistoryAssociation.selectone_by( session_id=galaxy_session.id, history_id=new_history.id ) + association = trans.app.model.GalaxySessionToHistoryAssociation.filter_by( session_id=galaxy_session.id, history_id=new_history.id ).first() except: association = None new_history.add_galaxy_session( galaxy_session, association=association ) @@ -530,7 +530,7 @@ if new_history: galaxy_session = trans.get_galaxy_session() try: - association = trans.app.model.GalaxySessionToHistoryAssociation.selectone_by( session_id=galaxy_session.id, history_id=new_history.id ) + association = trans.app.model.GalaxySessionToHistoryAssociation.filter_by( session_id=galaxy_session.id, history_id=new_history.id ).first() except: association = None new_history.add_galaxy_session( galaxy_session, association=association ) diff -r ea92290c4e10 -r 1d113c5386da lib/galaxy/web/controllers/user.py --- a/lib/galaxy/web/controllers/user.py Thu Oct 30 16:11:44 2008 -0400 +++ b/lib/galaxy/web/controllers/user.py Thu Oct 30 16:17:46 2008 -0400 @@ -53,7 +53,7 @@ email_err = "Please enter a real email address" elif len( email) > 255: email_err = "Email address exceeds maximum allowable length" - elif len( trans.app.model.User.select_by( email=email ) ) > 0: + elif trans.app.model.User.filter_by( email=email ).first(): email_err = "User with that email already exists" elif email != conf_email: conf_email_err = "Email addresses do not match." @@ -73,7 +73,7 @@ email_error = password_error = None # Attempt login if email or password: - user = trans.app.model.User.get_by( email = email ) + user = trans.app.model.User.filter_by( email=email ).first() if not user: email_error = "No such user" elif user.external: @@ -108,7 +108,7 @@ email_error = "Please enter a real email address" elif len( email) > 255: email_error = "Email address exceeds maximum allowable length" - elif len( trans.app.model.User.select_by( email=email ) ) > 0: + elif trans.app.model.User.filter_by( email=email ).first(): email_error = "User with that email already exists" elif len( password ) < 6: password_error = "Please use a password of at least 6 characters" @@ -143,7 +143,7 @@ @web.expose def reset_password(self, trans, email=None, **kwd): error = '' - reset_user = trans.app.model.User.get_by( email = email ) + reset_user = trans.app.model.User.filter_by( email=email ).first() user = trans.get_user() if reset_user: if user and user.id != reset_user.id: diff -r ea92290c4e10 -r 1d113c5386da lib/galaxy/web/controllers/workflow.py --- a/lib/galaxy/web/controllers/workflow.py Thu Oct 30 16:11:44 2008 -0400 +++ b/lib/galaxy/web/controllers/workflow.py Thu Oct 30 16:17:46 2008 -0400 @@ -44,7 +44,7 @@ # Load workflow from database stored = get_stored_workflow( trans, id ) if email: - other = model.User.get_by( email=email ) + other = model.User.filter_by( email=email ).first() if not other: mtype = "error" msg = ( "User '%s' does not exist" % email ) diff -r ea92290c4e10 -r 1d113c5386da lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py Thu Oct 30 16:11:44 2008 -0400 +++ b/lib/galaxy/web/framework/__init__.py Thu Oct 30 16:17:46 2008 -0400 @@ -24,7 +24,7 @@ import mako.template import mako.lookup -pkg_resources.require( "sqlalchemy>=0.3" ) +pkg_resources.require( "SQLAlchemy >= 0.4" ) from sqlalchemy import desc import logging @@ -172,7 +172,7 @@ if secure_id: session_key = self.security.decode_session_key( secure_id ) try: - galaxy_session = self.app.model.GalaxySession.selectone_by( session_key=session_key ) + galaxy_session = self.app.model.GalaxySession.filter_by( session_key=session_key ).first() if galaxy_session and galaxy_session.is_valid and galaxy_session.current_history_id: history = self.app.model.History.get( galaxy_session.current_history_id ) if history and not history.deleted: @@ -216,7 +216,7 @@ galaxy_session.user_id = self.user.id try: # See if we have already associated the history with the session - association = self.app.model.GalaxySessionToHistoryAssociation.select_by( session_id=galaxy_session.id, history_id=history.id )[0] + association = self.app.model.GalaxySessionToHistoryAssociation.filter_by( session_id=galaxy_session.id, history_id=history.id ).first() except: association = None history.add_galaxy_session( galaxy_session, association=association ) @@ -265,7 +265,7 @@ """Return the user in $HTTP_REMOTE_USER and create if necessary""" # remote_user middleware ensures HTTP_REMOTE_USER exists try: - user = self.app.model.User.selectone_by( email=self.environ[ 'HTTP_REMOTE_USER' ] ) + user = self.app.model.User.filter_by( email=self.environ[ 'HTTP_REMOTE_USER' ] ).first() except: user = self.app.model.User( email=self.environ[ 'HTTP_REMOTE_USER' ] ) user.set_password_cleartext( 'external' ) @@ -281,7 +281,7 @@ if secure_id: session_key = self.security.decode_session_key( secure_id ) try: - galaxy_session = self.app.model.GalaxySession.selectone_by( session_key=session_key ) + galaxy_session = self.app.model.GalaxySession.filter_by( session_key=session_key ).first() if galaxy_session and galaxy_session.is_valid and galaxy_session.user_id: user = self.app.model.User.get( galaxy_session.user_id ) if user: @@ -321,7 +321,7 @@ session_key = self.security.decode_session_key( secure_id ) try: # Retrive the galaxy_session id via the unique session_key - galaxy_session = self.app.model.GalaxySession.selectone_by( session_key=session_key ) + galaxy_session = self.app.model.GalaxySession.filter_by( session_key=session_key ).first() if galaxy_session and galaxy_session.is_valid: self.__galaxy_session = galaxy_session except: @@ -382,7 +382,7 @@ if self.history is not None: # See if we have already associated the session with the history try: - association = self.app.model.GalaxySessionToHistoryAssociation.select_by( session_id=galaxy_session.id, history_id=self.history.id )[0] + association = self.app.model.GalaxySessionToHistoryAssociation.filter_by( session_id=galaxy_session.id, history_id=self.history.id ).first() except: association = None galaxy_session.add_history( self.history, association=association ) diff -r ea92290c4e10 -r 1d113c5386da lib/galaxy/webapps/reports/controllers/jobs.py --- a/lib/galaxy/webapps/reports/controllers/jobs.py Thu Oct 30 16:11:44 2008 -0400 +++ b/lib/galaxy/webapps/reports/controllers/jobs.py Thu Oct 30 16:17:46 2008 -0400 @@ -5,7 +5,7 @@ from galaxy.webapps.reports.base.controller import * import galaxy.model import pkg_resources -pkg_resources.require( "sqlalchemy>=0.3" ) +pkg_resources.require( "SQLAlchemy >= 0.4" ) import sqlalchemy as sa import logging log = logging.getLogger( __name__ ) diff -r ea92290c4e10 -r 1d113c5386da lib/galaxy/webapps/reports/controllers/system.py --- a/lib/galaxy/webapps/reports/controllers/system.py Thu Oct 30 16:11:44 2008 -0400 +++ b/lib/galaxy/webapps/reports/controllers/system.py Thu Oct 30 16:17:46 2008 -0400 @@ -2,8 +2,9 @@ from datetime import datetime, timedelta from galaxy.webapps.reports.base.controller import * import pkg_resources -pkg_resources.require( "sqlalchemy>=0.3" ) -from sqlalchemy import eagerload, desc +pkg_resources.require( "SQLAlchemy >= 0.4" ) +from sqlalchemy.orm import eagerload +from sqlalchemy import desc import logging log = logging.getLogger( __name__ ) diff -r ea92290c4e10 -r 1d113c5386da lib/galaxy/webapps/reports/controllers/users.py --- a/lib/galaxy/webapps/reports/controllers/users.py Thu Oct 30 16:11:44 2008 -0400 +++ b/lib/galaxy/webapps/reports/controllers/users.py Thu Oct 30 16:17:46 2008 -0400 @@ -3,7 +3,7 @@ from galaxy.webapps.reports.base.controller import * import galaxy.model import pkg_resources -pkg_resources.require( "sqlalchemy>=0.3" ) +pkg_resources.require( "SQLAlchemy >= 0.4" ) import sqlalchemy as sa import logging log = logging.getLogger( __name__ ) diff -r ea92290c4e10 -r 1d113c5386da scripts/cleanup_datasets/cleanup_datasets.py --- a/scripts/cleanup_datasets/cleanup_datasets.py Thu Oct 30 16:11:44 2008 -0400 +++ b/scripts/cleanup_datasets/cleanup_datasets.py Thu Oct 30 16:17:46 2008 -0400 @@ -13,8 +13,8 @@ import galaxy.model.mapping import pkg_resources -pkg_resources.require( "sqlalchemy>=0.3" ) -from sqlalchemy import eagerload +pkg_resources.require( "SQLAlchemy >= 0.4" ) +from sqlalchemy.orm import eagerload assert sys.version_info[:2] >= ( 2, 4 ) @@ -191,8 +191,6 @@ if errmsg: errors = True print errmsg - else: - print "%s" % dataset.file_name else: dataset.purged = True dataset.flush() @@ -258,7 +256,6 @@ print errmsg else: dataset_count += 1 - print "%s" % dataset.file_name else: dataset.purged = True dataset.file_size = 0 @@ -302,6 +299,7 @@ else: # Remove dataset file from disk os.unlink( dataset.file_name ) + print "%s" % dataset.file_name # Mark all associated MetadataFiles as deleted and purged and remove them from disk print "The following metadata files associated with dataset '%s' have been purged" % dataset.file_name for hda in dataset.history_associations: diff -r ea92290c4e10 -r 1d113c5386da tools/stats/grouping.py --- a/tools/stats/grouping.py Thu Oct 30 16:11:44 2008 -0400 +++ b/tools/stats/grouping.py Thu Oct 30 16:17:46 2008 -0400 @@ -90,7 +90,7 @@ for ii, line in enumerate( file( tmpfile.name )): if line and not line.startswith( '#' ): - line = line.strip() + line = line.rstrip( '\r\n' ) try: fields = line.split("\t") item = fields[group_col]

1 0

[hg] galaxy 1584: Update bx-python to r456.
by Nate Coraor 29 Oct '08

29 Oct '08

details: http://www.bx.psu.edu/hg/galaxy/rev/95bdb18ee62b changeset: 1584:95bdb18ee62b user: Nate Coraor <nate(a)bx.psu.edu> date: Wed Oct 29 17:32:09 2008 -0400 description: Update bx-python to r456. 1 file(s) affected in this change: eggs.ini diffs (18 lines): diff -r bfb4189733db -r 95bdb18ee62b eggs.ini --- a/eggs.ini Wed Oct 29 17:20:54 2008 -0400 +++ b/eggs.ini Wed Oct 29 17:32:09 2008 -0400 @@ -55,12 +55,12 @@ MySQL_python = _5.0.51a_static python_lzo = _static flup = .dev_r2311 -bx_python = _dev_r449 +bx_python = _dev_r456 nose = .dev_r101 ; source location, necessary for scrambling [source] -bx_python = http://dist.g2.bx.psu.edu/bx-python_dist-r449.tar.bz2 +bx_python = http://dist.g2.bx.psu.edu/bx-python_dist-r456.tar.bz2 Cheetah = http://umn.dl.sourceforge.net/sourceforge/cheetahtemplate/Cheetah-1.0.tar.gz DRMAA_python = http://gridengine.sunsource.net/files/documents/7/36/DRMAA-python-0.2.tar.gz MySQL_python = http://superb-west.dl.sourceforge.net/sourceforge/mysql-python/MySQL-python… http://mysql.mirrors.pair.com/Downloads/MySQL-5.0/mysql-5.0.51a.tar.gz

1 0

[hg] galaxy 1583: Fix pbs_python to just use existing torque.
by Nate Coraor 29 Oct '08

29 Oct '08

details: http://www.bx.psu.edu/hg/galaxy/rev/bfb4189733db changeset: 1583:bfb4189733db user: Nate Coraor <nate(a)bx.psu.edu> date: Wed Oct 29 17:20:54 2008 -0400 description: Fix pbs_python to just use existing torque. 3 file(s) affected in this change: eggs.ini scripts/scramble/scripts/pbs_python-macosx.py scripts/scramble/scripts/pbs_python.py diffs (290 lines): diff -r c9f19b8b21ba -r bfb4189733db eggs.ini --- a/eggs.ini Wed Oct 29 12:35:50 2008 -0400 +++ b/eggs.ini Wed Oct 29 17:20:54 2008 -0400 @@ -52,7 +52,6 @@ [tags] psycopg2 = _8.2.6_static pysqlite = _3.5.4_static -pbs_python = _2.1.8 MySQL_python = _5.0.51a_static python_lzo = _static flup = .dev_r2311 @@ -65,7 +64,7 @@ Cheetah = http://umn.dl.sourceforge.net/sourceforge/cheetahtemplate/Cheetah-1.0.tar.gz DRMAA_python = http://gridengine.sunsource.net/files/documents/7/36/DRMAA-python-0.2.tar.gz MySQL_python = http://superb-west.dl.sourceforge.net/sourceforge/mysql-python/MySQL-python… http://mysql.mirrors.pair.com/Downloads/MySQL-5.0/mysql-5.0.51a.tar.gz -pbs_python = http://ftp.sara.nl/pub/outgoing/pbs_python-2.9.4.tar.gz http://www.clusterresources.com/downloads/torque/torque-%s.tar.gz +pbs_python = http://ftp.sara.nl/pub/outgoing/pbs_python-2.9.4.tar.gz psycopg2 = http://initd.org/pub/software/psycopg/PSYCOPG-2-0/psycopg2-2.0.6.tar.gz http://ftp8.us.postgresql.org/postgresql/source/v8.2.6/postgresql-8.2.6.tar… pycrypto = http://www.amk.ca/files/python/crypto/pycrypto-2.0.1.tar.gz pysqlite = http://initd.org/pub/software/pysqlite/releases/2.3/2.3.5/pysqlite-2.3.5.ta… http://www.sqlite.org/sqlite-source-3_5_4.zip diff -r c9f19b8b21ba -r bfb4189733db scripts/scramble/scripts/pbs_python-macosx.py --- a/scripts/scramble/scripts/pbs_python-macosx.py Wed Oct 29 12:35:50 2008 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,138 +0,0 @@ -import os, sys, subprocess, tarfile, shutil - -def unpack_prebuilt_torque(): - if not os.access( TORQUE_BINARY_ARCHIVE, os.F_OK ): - print "unpack_prebuilt_torque(): No binary archive of Torque available for this platform - will build it now" - build_torque() - else: - print "unpack_prebuilt_torque(): Found a previously built Torque binary archive for this platform." - print "unpack_prebuilt_torque(): To force Torque to be rebuilt, remove the archive:" - print " ", TORQUE_BINARY_ARCHIVE - t = tarfile.open( TORQUE_BINARY_ARCHIVE, "r" ) - for fn in t.getnames(): - t.extract( fn ) - t.close() - -def build_torque(): - # untar - print "build_torque(): Unpacking Torque source archive from:" - print " ", TORQUE_ARCHIVE - t = tarfile.open( TORQUE_ARCHIVE, "r" ) - for fn in t.getnames(): - t.extract( fn ) - t.close() - # patch - file = os.path.join( "torque-%s" %TORQUE_VERSION, "src", "include", "libpbs.h" ) - print "build_torque(): Patching", file - if not os.access( "%s.orig" %file, os.F_OK ): - shutil.copyfile( file, "%s.orig" %file ) - i = open( "%s.orig" %file, "r" ) - o = open( file, "w" ) - for line in i.readlines(): - if line == "#define NCONNECTS 5\n": - line = "#define NCONNECTS 50\n" - print >>o, line, - i.close() - o.close() - # configure - print "build_torque(): Running Torque configure script" - p = subprocess.Popen( args = CONFIGURE, shell = True, cwd = os.path.join( os.getcwd(), "torque-%s" %TORQUE_VERSION) ) - r = p.wait() - if r != 0: - print "build_torque(): Torque configure script failed" - sys.exit( 1 ) - # compile - print "build_torque(): Building Torque (make)" - p = subprocess.Popen( args = "make", shell = True, cwd = os.path.join( os.getcwd(), "torque-%s" %TORQUE_VERSION) ) - r = p.wait() - # libtool won't pass -arch to the linker, maybe it's an old libtool? whatever, this works - p = subprocess.Popen( args = "gcc -dynamiclib -undefined dynamic_lookup -o .libs/libtorque.0.0.0.dylib .libs/dis.o .libs/discui_.o .libs/discul_.o .libs/disi10d_.o .libs/disi10l_.o .libs/disiui_.o .libs/disp10d_.o .libs/disp10l_.o .libs/disrcs.o .libs/disrd.o .libs/disrf.o .libs/disrfcs.o .libs/disrfst.o .libs/disrl_.o .libs/disrl.o .libs/disrsc.o .libs/disrsi_.o .libs/disrsi.o .libs/disrsl_.o .libs/disrsl.o .libs/disrss.o .libs/disrst.o .libs/disruc.o .libs/disrui.o .libs/disrul.o .libs/disrus.o .libs/diswcs.o .libs/diswf.o .libs/diswl_.o .libs/diswsi.o .libs/diswsl.o .libs/diswui_.o .libs/diswui.o .libs/diswul.o .libs/advise.o .libs/dec_attrl.o .libs/dec_attropl.o .libs/dec_Authen.o .libs/dec_CpyFil.o .libs/dec_JobCred.o .libs/dec_JobFile.o .libs/dec_JobId.o .libs/dec_JobObit.o .libs/dec_Manage.o .libs/dec_MoveJob.o .libs/dec_MsgJob.o .libs/dec_QueueJob.o .libs/dec_Reg.o .libs/dec_ReqExt.o .libs/dec_ReqHdr.o .libs/dec_Resc.o .libs/dec_rpyc.o .libs/dec_rpys.o .libs/dec _RunJob.o .libs/dec_Shut.o .libs/dec_Sig.o .libs/dec_Status.o .libs/dec_svrattrl.o .libs/dec_Track.o .libs/enc_attrl.o .libs/enc_attropl.o .libs/enc_CpyFil.o .libs/enc_JobCred.o .libs/enc_JobFile.o .libs/enc_JobId.o .libs/enc_JobObit.o .libs/enc_Manage.o .libs/enc_MoveJob.o .libs/enc_MsgJob.o .libs/enc_QueueJob.o .libs/enc_Reg.o .libs/enc_reply.o .libs/enc_ReqExt.o .libs/enc_ReqHdr.o .libs/enc_RunJob.o .libs/enc_Shut.o .libs/enc_Sig.o .libs/enc_Status.o .libs/enc_svrattrl.o .libs/enc_Track.o .libs/get_svrport.o .libs/nonblock.o .libs/PBS_attr.o .libs/pbsD_alterjo.o .libs/pbsD_asyrun.o .libs/PBS_data.o .libs/pbsD_connect.o .libs/pbsD_deljob.o .libs/pbsD_holdjob.o .libs/pbsD_locjob.o .libs/PBSD_manage2.o .libs/pbsD_manager.o .libs/pbsD_movejob.o .libs/PBSD_manager_caps.o .libs/PBSD_msg2.o .libs/pbsD_msgjob.o .libs/pbsD_orderjo.o .libs/PBSD_rdrpy.o .libs/pbsD_rerunjo.o .libs/pbsD_resc.o .libs/pbsD_rlsjob.o .libs/pbsD_runjob.o .libs/pbsD_selectj.o .libs/PBSD_sig2.o .libs/pbsD_si gjob.o .libs/pbsD_stagein.o .libs/pbsD_statjob.o .libs/pbsD_statnode.o .libs/pbsD_statque.o .libs/pbsD_statsrv.o .libs/PBSD_status2.o .libs/PBSD_status.o .libs/pbsD_submit.o .libs/PBSD_submit_caps.o .libs/pbsD_termin.o .libs/pbs_geterrmg.o .libs/pbs_statfree.o .libs/rpp.o .libs/tcp_dis.o .libs/tm.o .libs/list_link.o .libs/ck_job_name.o .libs/cnt2server.o .libs/cvtdate.o .libs/get_server.o .libs/locate_job.o .libs/parse_at.o .libs/parse_depend.o .libs/parse_destid.o .libs/parse_equal.o .libs/parse_jobid.o .libs/parse_stage.o .libs/prepare_path.o .libs/prt_job_err.o .libs/set_attr.o .libs/set_resource.o .libs/chk_file_sec.o .libs/log_event.o .libs/pbs_log.o .libs/pbs_messages.o .libs/setup_env.o .libs/get_hostaddr.o .libs/get_hostname.o .libs/md5.o .libs/net_client.o .libs/net_server.o .libs/net_set_clse.o .libs/rm.o .libs/port_forwarding.o -lkvm -Wl,-syslibroot -Wl,/Developer/SDKs/MacOSX10.4u.sdk -install_name /usr/local/lib/libtorque.0.dylib -compatibility_version 1 -curre nt_version 1.0 -arch i386 -arch ppc", shell = True, cwd = os.getcwd()+"/torque-%s/src/lib/Libpbs" %TORQUE_VERSION ) - r = p.wait() - p = subprocess.Popen( args = "make", shell = True, cwd = os.path.join( os.getcwd(), "torque-%s" %TORQUE_VERSION) ) - r = p.wait() - if r != 0: - print "build_torque(): Building Torque (make) failed" - sys.exit( 1 ) - # install - print "build_torque(): Installing Torque (make install_lib)" - p = subprocess.Popen( args = "make DESTDIR=%s/torque install_lib" %os.getcwd(), shell = True, cwd = os.path.join( os.getcwd(), "torque-%s" %TORQUE_VERSION) ) - r = p.wait() - if r != 0: - print "build_torque(): Installing Torque (make install_lib) failed" - sys.exit( 1 ) - # pack - print "build_torque(): Creating binary Torque archive for future builds of pbs_python" - t = tarfile.open( TORQUE_BINARY_ARCHIVE, "w:bz2" ) - t.add( "torque" ) - t.close() - -# change back to the build dir -if os.path.dirname( sys.argv[0] ) != "": - os.chdir( os.path.dirname( sys.argv[0] ) ) - -# find setuptools -scramble_lib = os.path.join( "..", "..", "..", "lib" ) -sys.path.append( scramble_lib ) -try: - from setuptools import * - import pkg_resources -except: - from ez_setup import use_setuptools - use_setuptools( download_delay=8, to_dir=scramble_lib ) - from setuptools import * - import pkg_resources - -# get the tag -if os.access( ".galaxy_tag", os.F_OK ): - tagfile = open( ".galaxy_tag", "r" ) - tag = tagfile.readline().strip() -else: - tag = None - -TORQUE_VERSION = ( tag.split( "_" ) )[1] -TORQUE_ARCHIVE = os.path.abspath( os.path.join( "..", "..", "..", "archives", "torque-%s.tar.gz" %TORQUE_VERSION ) ) -TORQUE_BINARY_ARCHIVE = os.path.abspath( os.path.join( "..", "..", "..", "archives", "torque-%s-%s.tar.bz2" %( TORQUE_VERSION, pkg_resources.get_platform() ) ) ) -CONFIGURE = "CFLAGS='-O -g -isysroot /Developer/SDKs/MacOSX10.4u.sdk -arch i386 -arch ppc' " -CONFIGURE += "LDFLAGS='-Wl,-syslibroot,/Developer/SDKs/MacOSX10.4u.sdk -arch i386 -arch ppc' " -CONFIGURE += "./configure --prefix=/usr/local --disable-dependency-tracking --without-tcl --without-tk" - -# clean, in case you're running this by hand from a dirty module source dir -for dir in [ "build", "dist", "torque-%s" %TORQUE_VERSION ]: - if os.access( dir, os.F_OK ): - print "scramble_it.py: removing dir:", dir - shutil.rmtree( dir ) - -# build/unpack Torque -unpack_prebuilt_torque() - -print "scramble_it(): Running pbs_python configure script" -p = subprocess.Popen( args = "sh configure --with-pbsdir=torque/usr/local/lib", shell = True ) -r = p.wait() -if r != 0: - print "scramble_it(): pbs_python configure script failed" - sys.exit( 1 ) - -# version string in 2.9.4 setup.py is wrong -file = "setup.py" -print "scramble_it(): Patching", file -if not os.access( "%s.orig" %file, os.F_OK ): - shutil.copyfile( file, "%s.orig" %file ) -i = open( "%s.orig" %file, "r" ) -o = open( file, "w" ) -for line in i.readlines(): - if line == " version = '2.9.0',\n": - line = " version = '2.9.4',\n" - print >>o, line, -i.close() -o.close() - -# tag -me = sys.argv[0] -sys.argv = [ me ] -if tag is not None: - sys.argv.append( "egg_info" ) - sys.argv.append( "--tag-build=%s" %tag ) -sys.argv.append( "bdist_egg" ) - -# go -execfile( "setup.py", globals(), locals() ) diff -r c9f19b8b21ba -r bfb4189733db scripts/scramble/scripts/pbs_python.py --- a/scripts/scramble/scripts/pbs_python.py Wed Oct 29 12:35:50 2008 -0400 +++ b/scripts/scramble/scripts/pbs_python.py Wed Oct 29 17:20:54 2008 -0400 @@ -1,65 +1,9 @@ -import os, sys, subprocess, tarfile, shutil +import os, sys, shutil, subprocess -def unpack_prebuilt_torque(): - if not os.access( TORQUE_BINARY_ARCHIVE, os.F_OK ): - print "unpack_prebuilt_torque(): No binary archive of Torque available for this platform - will build it now" - build_torque() - else: - print "unpack_prebuilt_torque(): Found a previously built Torque binary archive for this platform." - print "unpack_prebuilt_torque(): To force Torque to be rebuilt, remove the archive:" - print " ", TORQUE_BINARY_ARCHIVE - t = tarfile.open( TORQUE_BINARY_ARCHIVE, "r" ) - for fn in t.getnames(): - t.extract( fn ) - t.close() - -def build_torque(): - # untar - print "build_torque(): Unpacking Torque source archive from:" - print " ", TORQUE_ARCHIVE - t = tarfile.open( TORQUE_ARCHIVE, "r" ) - for fn in t.getnames(): - t.extract( fn ) - t.close() - # patch - file = os.path.join( "torque-%s" %TORQUE_VERSION, "src", "include", "libpbs.h" ) - print "build_torque(): Patching", file - if not os.access( "%s.orig" %file, os.F_OK ): - shutil.copyfile( file, "%s.orig" %file ) - i = open( "%s.orig" %file, "r" ) - o = open( file, "w" ) - for line in i.readlines(): - if line == "#define NCONNECTS 5\n": - line = "#define NCONNECTS 50\n" - print >>o, line, - i.close() - o.close() - # configure - print "build_torque(): Running Torque configure script" - p = subprocess.Popen( args = CONFIGURE, shell = True, cwd = os.path.join( os.getcwd(), "torque-%s" %TORQUE_VERSION) ) - r = p.wait() - if r != 0: - print "build_torque(): Torque configure script failed" - sys.exit( 1 ) - # compile - print "build_torque(): Building Torque (make)" - p = subprocess.Popen( args = "make", shell = True, cwd = os.path.join( os.getcwd(), "torque-%s" %TORQUE_VERSION) ) - r = p.wait() - if r != 0: - print "build_torque(): Building Torque (make) failed" - sys.exit( 1 ) - # install - print "build_torque(): Installing Torque (make install_lib)" - p = subprocess.Popen( args = "make DESTDIR=%s/torque install_lib" %os.getcwd(), shell = True, cwd = os.path.join( os.getcwd(), "torque-%s" %TORQUE_VERSION) ) - r = p.wait() - if r != 0: - print "build_torque(): Installing Torque (make install_lib) failed" - sys.exit( 1 ) - # pack - print "build_torque(): Creating binary Torque archive for future builds of pbs_python" - t = tarfile.open( TORQUE_BINARY_ARCHIVE, "w:bz2" ) - t.add( "torque" ) - t.close() +if "LIBTORQUE_DIR" not in os.environ: + print "scramble(): Please set LIBTORQUE_DIR to the path of the" + print "scramble(): directory containing libtorque.so" + sys.exit(1) # change back to the build dir if os.path.dirname( sys.argv[0] ) != "": @@ -77,37 +21,22 @@ from setuptools import * import pkg_resources -# get the tag -if os.access( ".galaxy_tag", os.F_OK ): - tagfile = open( ".galaxy_tag", "r" ) - tag = tagfile.readline().strip() -else: - tag = None - -TORQUE_VERSION = ( tag.split( "_" ) )[1] -TORQUE_ARCHIVE = os.path.abspath( os.path.join( "..", "..", "..", "archives", "torque-%s.tar.gz" %TORQUE_VERSION ) ) -TORQUE_BINARY_ARCHIVE = os.path.abspath( os.path.join( "..", "..", "..", "archives", "torque-%s-%s.tar.bz2" %( TORQUE_VERSION, pkg_resources.get_platform() ) ) ) -CONFIGURE = "CFLAGS='-fPIC' ./configure --prefix=/usr/local --without-tcl --without-tk" - # clean, in case you're running this by hand from a dirty module source dir -for dir in [ "build", "dist", "torque-%s" %TORQUE_VERSION ]: +for dir in [ "build", "dist" ]: if os.access( dir, os.F_OK ): - print "scramble_it.py: removing dir:", dir + print "scramble(): removing dir:", dir shutil.rmtree( dir ) -# build/unpack Torque -unpack_prebuilt_torque() - -print "scramble_it(): Running pbs_python configure script" -p = subprocess.Popen( args = "sh configure --with-pbsdir=torque/usr/local/lib", shell = True ) +print "scramble(): Running pbs_python configure script" +p = subprocess.Popen( args = "sh configure --with-pbsdir=%s" % os.environ['LIBTORQUE_DIR'], shell = True ) r = p.wait() if r != 0: - print "scramble_it(): pbs_python configure script failed" + print "scramble(): pbs_python configure script failed" sys.exit( 1 ) # version string in 2.9.4 setup.py is wrong file = "setup.py" -print "scramble_it(): Patching", file +print "scramble(): Patching", file if not os.access( "%s.orig" %file, os.F_OK ): shutil.copyfile( file, "%s.orig" %file ) i = open( "%s.orig" %file, "r" ) @@ -122,9 +51,6 @@ # tag me = sys.argv[0] sys.argv = [ me ] -if tag is not None: - sys.argv.append( "egg_info" ) - sys.argv.append( "--tag-build=%s" %tag ) sys.argv.append( "bdist_egg" ) # go

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[hg] galaxy 1582: Re-add JOB_ERROR since some finish hooks use i...
by Nate Coraor 29 Oct '08

29 Oct '08

details: http://www.bx.psu.edu/hg/galaxy/rev/c9f19b8b21ba changeset: 1582:c9f19b8b21ba user: Nate Coraor <nate(a)bx.psu.edu> date: Wed Oct 29 12:35:50 2008 -0400 description: Re-add JOB_ERROR since some finish hooks use it (albeit improperly). 2 file(s) affected in this change: lib/galaxy/jobs/__init__.py lib/galaxy/jobs/runners/pbs.py diffs (33 lines): diff -r 4841a9e393c7 -r c9f19b8b21ba lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py Tue Oct 28 14:31:02 2008 -0400 +++ b/lib/galaxy/jobs/__init__.py Wed Oct 29 12:35:50 2008 -0400 @@ -15,7 +15,7 @@ log = logging.getLogger( __name__ ) # States for running a job. These are NOT the same as data states -JOB_WAIT, JOB_INPUT_ERROR, JOB_INPUT_DELETED, JOB_OK, JOB_READY, JOB_DELETED = 'wait', 'input_error', 'input_deleted', 'ok', 'ready', 'deleted' +JOB_WAIT, JOB_ERROR, JOB_INPUT_ERROR, JOB_INPUT_DELETED, JOB_OK, JOB_READY, JOB_DELETED = 'wait', 'error', 'input_error', 'input_deleted', 'ok', 'ready', 'deleted' class Sleeper( object ): """ @@ -163,6 +163,8 @@ if job_state == JOB_WAIT: if not self.track_jobs_in_database: new_waiting.append( job ) + elif job_state == JOB_ERROR: + log.info( "job %d ended with an error" % job.job_id ) elif job_state == JOB_INPUT_ERROR: log.info( "job %d unable to run: one or more inputs in error state" % job.job_id ) elif job_state == JOB_INPUT_DELETED: diff -r 4841a9e393c7 -r c9f19b8b21ba lib/galaxy/jobs/runners/pbs.py --- a/lib/galaxy/jobs/runners/pbs.py Tue Oct 28 14:31:02 2008 -0400 +++ b/lib/galaxy/jobs/runners/pbs.py Wed Oct 29 12:35:50 2008 -0400 @@ -358,7 +358,7 @@ pbs_job_state.job_wrapper.finish( stdout, stderr ) except: log.exception("Job wrapper finish method failed") - job_wrapper.fail("Unable to finish job", exception=True) + pbs_job_state.job_wrapper.fail("Unable to finish job", exception=True) # clean up the pbs files self.cleanup( ( ofile, efile, job_file ) )

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[hg] galaxy 1580: Use a weakref in metadata to prevent a circula...
by Greg Von Kuster 28 Oct '08

28 Oct '08

details: http://www.bx.psu.edu/hg/galaxy/rev/91f6455e19e4 changeset: 1580:91f6455e19e4 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Tue Oct 28 12:57:39 2008 -0400 description: Use a weakref in metadata to prevent a circular reference possibly interfering with garbage collection: hda/lda (parent) <--> MetadataCollection (self) 1 file(s) affected in this change: lib/galaxy/datatypes/metadata.py diffs (32 lines): diff -r 778fcc385ab7 -r 91f6455e19e4 lib/galaxy/datatypes/metadata.py --- a/lib/galaxy/datatypes/metadata.py Tue Oct 28 11:27:42 2008 -0400 +++ b/lib/galaxy/datatypes/metadata.py Tue Oct 28 12:57:39 2008 -0400 @@ -1,4 +1,4 @@ -import sys, logging, copy, shutil +import sys, logging, copy, shutil, weakref from galaxy.util import string_as_bool from galaxy.util.odict import odict @@ -40,6 +40,13 @@ #initialize dict if needed if self.parent._metadata is None: self.parent._metadata = {} + def get_parent( self ): + if "_parent" in self.__dict__: + return self.__dict__["_parent"]() + return None + def set_parent( self, parent ): + self.__dict__["_parent"] = weakref.ref( parent ) # use weakref to prevent a circular reference interfering with garbage collection: hda/lda (parent) <--> MetadataCollection (self) ; needs to be hashable, so cannot use proxy. + parent = property( get_parent, set_parent ) @property def spec( self ): return self.parent.datatype.metadata_spec @@ -65,7 +72,7 @@ return self.parent._metadata[name] def __setattr__( self, name, value ): if name == "parent": - self.__dict__[name] = value + return self.set_parent( value ) else: if name in self.spec: self.parent._metadata[name] = self.spec[name].unwrap( value )

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[hg] galaxy 1581: Purge metadata files associated with a dataset...
by Greg Von Kuster 28 Oct '08

28 Oct '08

details: http://www.bx.psu.edu/hg/galaxy/rev/4841a9e393c7 changeset: 1581:4841a9e393c7 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Tue Oct 28 14:31:02 2008 -0400 description: Purge metadata files associated with a dataset when the dataset is purged. Also remembered log.exception logs the exception, so corrected a few things in jobs.__init__. 2 file(s) affected in this change: lib/galaxy/jobs/__init__.py scripts/cleanup_datasets/cleanup_datasets.py diffs (279 lines): diff -r 91f6455e19e4 -r 4841a9e393c7 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py Tue Oct 28 12:57:39 2008 -0400 +++ b/lib/galaxy/jobs/__init__.py Tue Oct 28 14:31:02 2008 -0400 @@ -62,7 +62,7 @@ else : self.use_policy = False log.info("Scheduler policy not defined as expected, defaulting to FIFO") - except AttributeError, detail : # try may throw AttributeError + except AttributeError, detail: # try may throw AttributeError self.use_policy = False log.exception("Error while loading scheduler policy class, defaulting to FIFO") else : @@ -117,8 +117,8 @@ while self.running: try: self.monitor_step() - except Exception, e: - log.exception( "Exception in monitor_step: %s" % str( e ) ) + except: + log.exception( "Exception in monitor_step" ) # Sleep self.sleeper.sleep( 1 ) @@ -184,9 +184,8 @@ job.info = msg log.error( msg ) except Exception, e: - msg = "failure running job %d: %s" % ( job.job_id, str( e ) ) - job.info = msg - log.exception( msg ) + job.info = "failure running job %d: %s" % ( job.job_id, str( e ) ) + log.exception( "failure running job %d" % job.job_id ) # Update the waiting list self.waiting = new_waiting # If special (e.g. fair) scheduling is enabled, dispatch all jobs @@ -201,9 +200,8 @@ # squeue is empty, so stop dispatching break except Exception, e: # if something else breaks while dispatching - msg = "failure running job %d: %s" % ( sjob.job_id, str( e ) ) - job.fail( msg ) - log.exception( msg ) + job.fail( "failure running job %d: %s" % ( sjob.job_id, str( e ) ) ) + log.exception( "failure running job %d" % sjob.job_id ) def put( self, job_id, tool ): """Add a job to the queue (by job identifier)""" @@ -473,8 +471,8 @@ os.remove( fname ) if self.working_directory is not None: os.rmdir( self.working_directory ) - except Exception, e: - log.exception( "Unable to cleanup job %s, exception: %s" % ( str( self.job_id ), str( e ) ) ) + except: + log.exception( "Unable to cleanup job %d" % self.job_id ) def get_command_line( self ): return self.command_line @@ -573,8 +571,8 @@ while self.running: try: self.monitor_step() - except Exception, e: - log.exception( "Exception in monitor_step: %s" % str( e ) ) + except: + log.exception( "Exception in monitor_step" ) # Sleep self.sleeper.sleep( 1 ) diff -r 91f6455e19e4 -r 4841a9e393c7 scripts/cleanup_datasets/cleanup_datasets.py --- a/scripts/cleanup_datasets/cleanup_datasets.py Tue Oct 28 12:57:39 2008 -0400 +++ b/scripts/cleanup_datasets/cleanup_datasets.py Tue Oct 28 14:31:02 2008 -0400 @@ -47,6 +47,7 @@ app = CleanupDatasetsApplication( database_connection=database_connection, file_path=file_path ) h = app.model.History d = app.model.Dataset + m = app.model.MetadataFile cutoff_time = datetime.utcnow() - timedelta( days=options.days ) now = strftime( "%Y-%m-%d %H:%M:%S" ) @@ -63,7 +64,7 @@ print "# Datasets will be removed from disk...\n" else: print "# Datasets will NOT be removed from disk...\n" - purge_histories( h, d, cutoff_time, options.remove_from_disk ) + purge_histories( h, d, m, cutoff_time, options.remove_from_disk ) elif options.info_purge_datasets: info_purge_datasets( d, cutoff_time ) elif options.purge_datasets: @@ -71,7 +72,7 @@ print "# Datasets will be removed from disk...\n" else: print "# Datasets will NOT be removed from disk...\n" - purge_datasets( d, cutoff_time, options.remove_from_disk ) + purge_datasets( d, m, cutoff_time, options.remove_from_disk ) sys.exit(0) def info_delete_userless_histories( h, cutoff_time ): @@ -79,7 +80,7 @@ history_count = 0 dataset_count = 0 where = ( h.table.c.user_id==None ) & ( h.table.c.deleted=='f' ) & ( h.table.c.update_time < cutoff_time ) - histories = h.query().filter( where ).options( eagerload( 'active_datasets' ) ) + histories = h.query().filter( where ).options( eagerload( 'active_datasets' ) ).all() print '# The following datasets and associated userless histories will be deleted' start = time.clock() @@ -105,13 +106,13 @@ print '# The following datasets and associated userless histories have been deleted' start = time.clock() - histories = h.query().filter( h_where ).options( eagerload( 'active_datasets' ) ) + histories = h.query().filter( h_where ).options( eagerload( 'active_datasets' ) ).all() for history in histories: for dataset_assoc in history.active_datasets: if not dataset_assoc.deleted: # Mark all datasets as deleted d_where = ( d.table.c.id==dataset_assoc.dataset_id ) - datasets = d.query().filter( d_where ) + datasets = d.query().filter( d_where ).all() for dataset in datasets: if not dataset.deleted: dataset.deleted = True @@ -139,13 +140,13 @@ print '# The following datasets and associated deleted histories will be purged' start = time.clock() - histories = h.query().filter( h_where ).options( eagerload( 'datasets' ) ) + histories = h.query().filter( h_where ).options( eagerload( 'datasets' ) ).all() for history in histories: for dataset_assoc in history.datasets: # Datasets can only be purged if their HistoryDatasetAssociation has been deleted. if dataset_assoc.deleted: d_where = ( d.table.c.id==dataset_assoc.dataset_id ) - datasets = d.query().filter( d_where ) + datasets = d.query().filter( d_where ).all() for dataset in datasets: if dataset.purgable and not dataset.purged: print "%s" % dataset.file_name @@ -160,7 +161,7 @@ print '# %d histories ( including a total of %d datasets ) will be purged. Freed disk space: ' %( history_count, dataset_count ), disk_space, '\n' print "Elapsed time: ", stop - start, "\n" -def purge_histories( h, d, cutoff_time, remove_from_disk ): +def purge_histories( h, d, m, cutoff_time, remove_from_disk ): # Purges deleted histories whose update_time is older than the cutoff_time. # The datasets associated with each history are also purged. history_count = 0 @@ -172,13 +173,13 @@ print '# The following datasets and associated deleted histories have been purged' start = time.clock() - histories = h.query().filter( h_where ).options( eagerload( 'datasets' ) ) + histories = h.query().filter( h_where ).options( eagerload( 'datasets' ) ).all() for history in histories: errors = False for dataset_assoc in history.datasets: if dataset_assoc.deleted: d_where = ( d.table.c.id==dataset_assoc.dataset_id ) - datasets = d.query().filter( d_where ) + datasets = d.query().filter( d_where ).all() for dataset in datasets: if dataset.purgable and not dataset.purged: file_size = dataset.file_size @@ -186,7 +187,7 @@ dataset.file_size = 0 if remove_from_disk: dataset.flush() - errmsg = purge_dataset( dataset ) + errmsg = purge_dataset( dataset, m ) if errmsg: errors = True print errmsg @@ -196,6 +197,14 @@ dataset.purged = True dataset.flush() print "%s" % dataset.file_name + # Mark all associated MetadataFiles as deleted and purged + print "The following metadata files associated with dataset '%s' have been marked purged" % dataset.file_name + for hda in dataset.history_associations: + for metadata_file in m.filter( m.table.c.hda_id==hda.id ).all(): + metadata_file.deleted = True + metadata_file.purged = True + metadata_file.flush() + print "%s" % metadata_file.file_name() dataset_count += 1 try: disk_space += file_size @@ -218,7 +227,7 @@ print '# The following deleted datasets will be purged' start = time.clock() - datasets = d.query().filter( where ) + datasets = d.query().filter( where ).all() for dataset in datasets: print "%s" % dataset.file_name dataset_count += 1 @@ -230,7 +239,7 @@ print '# %d datasets will be purged. Freed disk space: ' %dataset_count, disk_space, '\n' print "Elapsed time: ", stop - start, "\n" -def purge_datasets( d, cutoff_time, remove_from_disk ): +def purge_datasets( d, m, cutoff_time, remove_from_disk ): # Purges deleted datasets whose update_time is older than cutoff_time. Files may or may # not be removed from disk. dataset_count = 0 @@ -240,11 +249,11 @@ print '# The following deleted datasets have been purged' start = time.clock() - datasets = d.query().filter( where ) + datasets = d.query().filter( where ).all() for dataset in datasets: file_size = dataset.file_size if remove_from_disk: - errmsg = purge_dataset( dataset ) + errmsg = purge_dataset( dataset, m ) if errmsg: print errmsg else: @@ -255,6 +264,14 @@ dataset.file_size = 0 dataset.flush() print "%s" % dataset.file_name + # Mark all associated MetadataFiles as deleted and purged + print "The following metadata files associated with dataset '%s' have been marked purged" % dataset.file_name + for hda in dataset.history_associations: + for metadata_file in m.filter( m.table.c.hda_id==hda.id ).all(): + metadata_file.deleted = True + metadata_file.purged = True + metadata_file.flush() + print "%s" % metadata_file.file_name() dataset_count += 1 try: disk_space += file_size @@ -266,11 +283,10 @@ print '# Freed disk space: ', disk_space, '\n' print "Elapsed time: ", stop - start, "\n" -def purge_dataset( dataset ): +def purge_dataset( dataset, m ): # Removes the file from disk and updates the database accordingly. if dataset.deleted: # Remove files from disk and update the database - purgable = False try: dataset.purged = True dataset.file_size = 0 @@ -284,15 +300,24 @@ if not shared_data.deleted: break #only purge when not shared else: + # Remove dataset file from disk os.unlink( dataset.file_name ) - purgable = True + # Mark all associated MetadataFiles as deleted and purged and remove them from disk + print "The following metadata files associated with dataset '%s' have been purged" % dataset.file_name + for hda in dataset.history_associations: + for metadata_file in m.filter( m.table.c.hda_id==hda.id ).all(): + os.unlink( metadata_file.file_name() ) + metadata_file.deleted = True + metadata_file.purged = True + metadata_file.flush() + print "%s" % metadata_file.file_name() + try: + # Remove associated extra files from disk if they exist + os.unlink( dataset.extra_files_path ) + except: + pass except Exception, exc: return "# Error, exception: %s caught attempting to purge %s\n" %( str( exc ), dataset.file_name ) - try: - if purgable: - os.unlink( dataset.extra_files_path ) - except: - pass else: return "# Error: '%s' has not previously been deleted, so it cannot be purged\n" %dataset.file_name return ""

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galaxy-dev October 2008