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[hg] galaxy 3465: Fix comment and indentation.
by Greg Von Kuster 03 Mar '10

03 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/0967cea77985 changeset: 3465:0967cea77985 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Tue Mar 02 12:32:44 2010 -0500 description: Fix comment and indentation. diffstat: templates/workflow/display.mako | 6 +++--- 1 files changed, 3 insertions(+), 3 deletions(-) diffs (16 lines): diff -r 69db124587e3 -r 0967cea77985 templates/workflow/display.mako --- a/templates/workflow/display.mako Tue Mar 02 12:10:43 2010 -0500 +++ b/templates/workflow/display.mako Tue Mar 02 12:32:44 2010 -0500 @@ -86,9 +86,9 @@ <%def name="render_item( workflow, steps )"> <% - # HACK: Rendering workflow steps requires that trans have a history; however, if a user's first visit to Galaxy is here, he won't have a history - # and an error will occur. To prevent this error, make sure user has a history. - trans.get_history( create=True ) + # HACK: Rendering workflow steps requires that trans have a history; however, if it's user's first visit to Galaxy is here, he won't have a history + # and an error will occur. To prevent this error, make sure user has a history. + trans.get_history( create=True ) %> <table class="annotated-item"> <tr><th>Step</th><th class="annotation">Description/Notes</th></tr>

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[hg] galaxy 3464: I am having a bad day
by Greg Von Kuster 03 Mar '10

03 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/69db124587e3 changeset: 3464:69db124587e3 user: Nate Coraor <nate(a)bx.psu.edu> date: Tue Mar 02 12:10:43 2010 -0500 description: I am having a bad day diffstat: scripts/scramble/scripts/pbs_python.py | 4 ++-- 1 files changed, 2 insertions(+), 2 deletions(-) diffs (14 lines): diff -r 5f6b53b08623 -r 69db124587e3 scripts/scramble/scripts/pbs_python.py --- a/scripts/scramble/scripts/pbs_python.py Tue Mar 02 12:08:01 2010 -0500 +++ b/scripts/scramble/scripts/pbs_python.py Tue Mar 02 12:10:43 2010 -0500 @@ -29,8 +29,8 @@ i = open( 'setup.py.orig', 'r' ) o = open( 'setup.py', 'w' ) for line in i.readlines(): - if line == " version = '2.9.0',\n": - line = " version = '2.9.4',\n" + if line == " version = '2.9.0',\n": + line = " version = '2.9.4',\n" print >>o, line, i.close() o.close()

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[hg] galaxy 3463: pbs_python 2.9.8 doesn't work
by Greg Von Kuster 03 Mar '10

03 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/5f6b53b08623 changeset: 3463:5f6b53b08623 user: Nate Coraor <nate(a)bx.psu.edu> date: Tue Mar 02 12:08:01 2010 -0500 description: pbs_python 2.9.8 doesn't work diffstat: eggs.ini | 2 +- scripts/scramble/scripts/pbs_python.py | 13 +++++++++++++ 2 files changed, 14 insertions(+), 1 deletions(-) diffs (35 lines): diff -r db7ee1dc19c4 -r 5f6b53b08623 eggs.ini --- a/eggs.ini Tue Mar 02 11:52:16 2010 -0500 +++ b/eggs.ini Tue Mar 02 12:08:01 2010 -0500 @@ -16,7 +16,7 @@ Cheetah = 2.2.2 DRMAA_python = 0.2 MySQL_python = 1.2.3c1 -pbs_python = 2.9.8 +pbs_python = 2.9.4 psycopg2 = 2.0.6 pycrypto = 2.0.1 pysam = 0.1.1 diff -r db7ee1dc19c4 -r 5f6b53b08623 scripts/scramble/scripts/pbs_python.py --- a/scripts/scramble/scripts/pbs_python.py Tue Mar 02 11:52:16 2010 -0500 +++ b/scripts/scramble/scripts/pbs_python.py Tue Mar 02 12:08:01 2010 -0500 @@ -22,6 +22,19 @@ # run the config script run( 'sh configure --with-pbsdir=%s' % os.environ['LIBTORQUE_DIR'], os.getcwd(), 'Running pbs_python configure script' ) +# version string in 2.9.4 setup.py is wrong +print "scramble(): Patching setup.py" +if not os.path.exists( 'setup.py.orig' ): + shutil.copyfile( 'setup.py', 'setup.py.orig' ) + i = open( 'setup.py.orig', 'r' ) + o = open( 'setup.py', '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() + # reset args for distutils me = sys.argv[0] sys.argv = [ me ]

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[hg] galaxy 3462: Scratch that, just upgrade pbs_python instead
by Greg Von Kuster 03 Mar '10

03 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/db7ee1dc19c4 changeset: 3462:db7ee1dc19c4 user: Nate Coraor <nate(a)bx.psu.edu> date: Tue Mar 02 11:52:16 2010 -0500 description: Scratch that, just upgrade pbs_python instead diffstat: eggs.ini | 2 +- lib/galaxy/eggs/scramble.py | 2 +- scripts/scramble/patches/pbs_python/setup.py | 64 ---------------------------- scripts/scramble/scripts/pbs_python.py | 3 - 4 files changed, 2 insertions(+), 69 deletions(-) diffs (105 lines): diff -r cb10a08016eb -r db7ee1dc19c4 eggs.ini --- a/eggs.ini Tue Mar 02 11:37:55 2010 -0500 +++ b/eggs.ini Tue Mar 02 11:52:16 2010 -0500 @@ -16,7 +16,7 @@ Cheetah = 2.2.2 DRMAA_python = 0.2 MySQL_python = 1.2.3c1 -pbs_python = 2.9.4 +pbs_python = 2.9.8 psycopg2 = 2.0.6 pycrypto = 2.0.1 pysam = 0.1.1 diff -r cb10a08016eb -r db7ee1dc19c4 lib/galaxy/eggs/scramble.py --- a/lib/galaxy/eggs/scramble.py Tue Mar 02 11:37:55 2010 -0500 +++ b/lib/galaxy/eggs/scramble.py Tue Mar 02 11:52:16 2010 -0500 @@ -56,7 +56,7 @@ self.run_scramble_script() new_egg = os.path.join( self.buildpath, 'dist', os.path.basename( self.distribution.location ) ) if not os.path.exists( new_egg ): - raise ScrambleFailure( self, "%s(): Egg build for %s did not appear to fail, but no egg found to copy from expected path:\n %s" % ( sys._getframe().f_code.co_name, self.name, egg_name ) ) + raise ScrambleFailure( self, "%s(): Egg build for %s did not appear to fail, but no egg found to copy from expected path:\n %s" % ( sys._getframe().f_code.co_name, self.name, new_egg ) ) shutil.copyfile( new_egg, self.distribution.location ) log.warning( "%s(): Copied egg to:" % sys._getframe().f_code.co_name ) log.warning( " %s" % self.distribution.location ) diff -r cb10a08016eb -r db7ee1dc19c4 scripts/scramble/patches/pbs_python/setup.py --- a/scripts/scramble/patches/pbs_python/setup.py Tue Mar 02 11:37:55 2010 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,64 +0,0 @@ -#!/usr/bin/env python -# -# $Id: setup.py 434 2005-11-04 15:02:07Z bas $ -# -# set ts=4 -# - -import sys -import os - -from distutils.core import setup, Extension - -# Try some usefule defaults if not set -# -PBS_LIB_DIR='/opt/local/lib' -NEW_BUILD_SYSTEM=1 - -if not PBS_LIB_DIR: - for dir in ['/usr/lib', '/usr/local/lib', '/opt/pbs/usr/lib', '/usr/lib/torque', '/opt/pbs/lib', '/opt/torque/lib' ]: - dummy_new = os.path.join(dir, 'libtorque.so') - dummy_old = os.path.join(dir, 'libpbs.a') - if os.path.exists(dummy_new): - PBS_LIB_DIR=dir - break - elif os.path.exists(dummy_old): - PBS_LIB_DIR=dir - NEW_BUILD_SYSTEM=0 - break - -if not PBS_LIB_DIR: - print 'Please specify where the PBS libraries are!!' - print 'edit setup.py and fill in the PBS_LIB_DIR variable' - sys.exit(1) - -# Test if we have all the libs: -# -if NEW_BUILD_SYSTEM: - LIBS = ['torque'] -else: - LIBS = ['log', 'net', 'pbs'] - for lib in LIBS: - library = 'lib%s.a' %(lib) - dummy = os.path.join(PBS_LIB_DIR, library) - if not os.path.exists(dummy): - print 'You need to install "%s" in %s' %(library, PBS_LIB_DIR) - sys.exit(1) - -setup ( name = 'pbs_python', - version = '2.9.4', - description = 'openpbs/torque python interface', - author = 'Bas van der Vlies', - author_email = 'basv(a)sara.nl', - url = 'http://www.sara.nl/index_eng.html', - - extra_path = 'pbs', - package_dir = { '' : 'src' }, - py_modules = [ 'pbs', 'PBSQuery' ], - - ext_modules = [ - Extension( '_pbs', ['src/pbs_wrap.c'], - library_dirs = [ PBS_LIB_DIR ], - libraries = LIBS) - ] -) diff -r cb10a08016eb -r db7ee1dc19c4 scripts/scramble/scripts/pbs_python.py --- a/scripts/scramble/scripts/pbs_python.py Tue Mar 02 11:37:55 2010 -0500 +++ b/scripts/scramble/scripts/pbs_python.py Tue Mar 02 11:52:16 2010 -0500 @@ -19,9 +19,6 @@ # the build process doesn't set an rpath for libtorque os.environ['LD_RUN_PATH'] = os.environ['LIBTORQUE_DIR'] -# patch setup.py -shutil.copy( os.path.join( patches, 'pbs_python', 'setup.py' ), 'setup.py' ) - # run the config script run( 'sh configure --with-pbsdir=%s' % os.environ['LIBTORQUE_DIR'], os.getcwd(), 'Running pbs_python configure script' )

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[hg] galaxy 3461: Use the old method for fixing pbs_python's ver...
by Greg Von Kuster 03 Mar '10

03 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/cb10a08016eb changeset: 3461:cb10a08016eb user: Nate Coraor <nate(a)bx.psu.edu> date: Tue Mar 02 11:37:55 2010 -0500 description: Use the old method for fixing pbs_python's version diffstat: scripts/scramble/patches/pbs_python/setup.py | 64 ++++++++++++++++++++++++++++ scripts/scramble/scripts/pbs_python.py | 7 +- 2 files changed, 68 insertions(+), 3 deletions(-) diffs (102 lines): diff -r 182a7947e63a -r cb10a08016eb scripts/scramble/patches/pbs_python/setup.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/scramble/patches/pbs_python/setup.py Tue Mar 02 11:37:55 2010 -0500 @@ -0,0 +1,64 @@ +#!/usr/bin/env python +# +# $Id: setup.py 434 2005-11-04 15:02:07Z bas $ +# +# set ts=4 +# + +import sys +import os + +from distutils.core import setup, Extension + +# Try some usefule defaults if not set +# +PBS_LIB_DIR='/opt/local/lib' +NEW_BUILD_SYSTEM=1 + +if not PBS_LIB_DIR: + for dir in ['/usr/lib', '/usr/local/lib', '/opt/pbs/usr/lib', '/usr/lib/torque', '/opt/pbs/lib', '/opt/torque/lib' ]: + dummy_new = os.path.join(dir, 'libtorque.so') + dummy_old = os.path.join(dir, 'libpbs.a') + if os.path.exists(dummy_new): + PBS_LIB_DIR=dir + break + elif os.path.exists(dummy_old): + PBS_LIB_DIR=dir + NEW_BUILD_SYSTEM=0 + break + +if not PBS_LIB_DIR: + print 'Please specify where the PBS libraries are!!' + print 'edit setup.py and fill in the PBS_LIB_DIR variable' + sys.exit(1) + +# Test if we have all the libs: +# +if NEW_BUILD_SYSTEM: + LIBS = ['torque'] +else: + LIBS = ['log', 'net', 'pbs'] + for lib in LIBS: + library = 'lib%s.a' %(lib) + dummy = os.path.join(PBS_LIB_DIR, library) + if not os.path.exists(dummy): + print 'You need to install "%s" in %s' %(library, PBS_LIB_DIR) + sys.exit(1) + +setup ( name = 'pbs_python', + version = '2.9.4', + description = 'openpbs/torque python interface', + author = 'Bas van der Vlies', + author_email = 'basv(a)sara.nl', + url = 'http://www.sara.nl/index_eng.html', + + extra_path = 'pbs', + package_dir = { '' : 'src' }, + py_modules = [ 'pbs', 'PBSQuery' ], + + ext_modules = [ + Extension( '_pbs', ['src/pbs_wrap.c'], + library_dirs = [ PBS_LIB_DIR ], + libraries = LIBS) + ] +) diff -r 182a7947e63a -r cb10a08016eb scripts/scramble/scripts/pbs_python.py --- a/scripts/scramble/scripts/pbs_python.py Tue Mar 02 11:17:05 2010 -0500 +++ b/scripts/scramble/scripts/pbs_python.py Tue Mar 02 11:37:55 2010 -0500 @@ -1,4 +1,4 @@ -import os, sys +import os, sys, shutil if "LIBTORQUE_DIR" not in os.environ: print "main(): Please set LIBTORQUE_DIR to the path of the" @@ -13,13 +13,15 @@ sys.path.append( os.path.join( '..', '..', '..', 'lib' ) ) from scramble_lib import * -ver = get_ver() # get the version tag = get_tag() # get the tag clean() # clean up any existing stuff (could happen if you run scramble.py by hand) # the build process doesn't set an rpath for libtorque os.environ['LD_RUN_PATH'] = os.environ['LIBTORQUE_DIR'] +# patch setup.py +shutil.copy( os.path.join( patches, 'pbs_python', 'setup.py' ), 'setup.py' ) + # run the config script run( 'sh configure --with-pbsdir=%s' % os.environ['LIBTORQUE_DIR'], os.getcwd(), 'Running pbs_python configure script' ) @@ -27,7 +29,6 @@ me = sys.argv[0] sys.argv = [ me ] sys.argv.append( "egg_info" ) -sys.argv.append( "--version=%s" % ver ) if tag is not None: sys.argv.append( "--tag-build=%s" %tag ) # svn revision (if any) is handled directly in tag-build

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[hg] galaxy 3460: Fix bug that prevents new Galaxy visitors from...
by Greg Von Kuster 03 Mar '10

03 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/182a7947e63a changeset: 3460:182a7947e63a user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Tue Mar 02 11:17:05 2010 -0500 description: Fix bug that prevents new Galaxy visitors from viewing an accessible/published workflow. Viewing an accessible/published workflow requires a history because rendering parameters require a history, so a history is now created for visitors that do not already have one. diffstat: templates/workflow/display.mako | 5 +++++ 1 files changed, 5 insertions(+), 0 deletions(-) diffs (15 lines): diff -r 8bd2ace6c92d -r 182a7947e63a templates/workflow/display.mako --- a/templates/workflow/display.mako Tue Mar 02 10:47:23 2010 -0500 +++ b/templates/workflow/display.mako Tue Mar 02 11:17:05 2010 -0500 @@ -85,6 +85,11 @@ </%def> <%def name="render_item( workflow, steps )"> + <% + # HACK: Rendering workflow steps requires that trans have a history; however, if a user's first visit to Galaxy is here, he won't have a history + # and an error will occur. To prevent this error, make sure user has a history. + trans.get_history( create=True ) + %> <table class="annotated-item"> <tr><th>Step</th><th class="annotation">Description/Notes</th></tr> %for i, step in enumerate( steps ):

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[hg] galaxy 3459: Change color space FASTA file type from fastqs...
by Greg Von Kuster 03 Mar '10

03 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/8bd2ace6c92d changeset: 3459:8bd2ace6c92d user: Dan Blankenberg <dan(a)bx.psu.edu> date: Tue Mar 02 10:47:23 2010 -0500 description: Change color space FASTA file type from fastqsolid to fastqcssanger. Cripple accepted tool input formats for many of the FASTQ tools to only allow only fastqsanger and fastqcssanger to be used. diffstat: datatypes_conf.xml.sample | 2 +- lib/galaxy/datatypes/sequence.py | 6 +- lib/galaxy_utils/sequence/fasta.py | 2 +- lib/galaxy_utils/sequence/fastq.py | 6 +- test-data/combine_phiX_out_1.fastqcssanger | 576 +++++++++++++ test-data/combine_phiX_out_1.fastqsolid | 576 ------------- test-data/combine_phiX_out_2.fastqcssanger | 576 +++++++++++++ test-data/combine_phiX_out_2.fastqsolid | 576 ------------- test-data/fastq_combiner_no_qual_ascii_out_1.fastqcssanger | 576 +++++++++++++ test-data/fastq_combiner_no_qual_ascii_out_1.fastqsolid | 576 ------------- test-data/illumina_full_range_as_cssanger.fastqcssanger | 8 + test-data/illumina_full_range_as_solid.fastqsolid | 8 - test-data/sanger_full_range_as_cssanger.fastqcssanger | 8 + test-data/sanger_full_range_as_solid.fastqsolid | 8 - test-data/solexa_full_range_as_cssanger.fastqcssanger | 8 + test-data/solexa_full_range_as_solid.fastqsolid | 8 - tool_conf.xml.sample | 19 +- tools/fastq/fastq_combiner.py | 2 +- tools/fastq/fastq_combiner.xml | 15 +- tools/fastq/fastq_filter.xml | 32 +- tools/fastq/fastq_groomer.xml | 50 +- tools/fastq/fastq_manipulation.xml | 19 +- tools/fastq/fastq_paired_end_joiner.xml | 4 +- tools/fastq/fastq_paired_end_splitter.xml | 2 +- tools/fastq/fastq_stats.xml | 12 +- tools/fastq/fastq_to_fasta.xml | 2 +- tools/fastq/fastq_trimmer.xml | 12 +- 27 files changed, 1848 insertions(+), 1841 deletions(-) diffs (truncated from 4157 to 3000 lines): diff -r 19d8ba4269ba -r 8bd2ace6c92d datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample Tue Mar 02 09:51:05 2010 -0500 +++ b/datatypes_conf.xml.sample Tue Mar 02 10:47:23 2010 -0500 @@ -35,7 +35,7 @@ <datatype extension="fastq" type="galaxy.datatypes.sequence:Fastq" display_in_upload="true"/> <datatype extension="fastqsanger" type="galaxy.datatypes.sequence:FastqSanger" display_in_upload="true"/> <datatype extension="fastqsolexa" type="galaxy.datatypes.sequence:FastqSolexa" display_in_upload="true"/> - <datatype extension="fastqsolid" type="galaxy.datatypes.sequence:FastqSolid" display_in_upload="true"/> + <datatype extension="fastqcssanger" type="galaxy.datatypes.sequence:FastqCSSanger" display_in_upload="true"/> <datatype extension="fastqillumina" type="galaxy.datatypes.sequence:FastqIllumina" display_in_upload="true"/> <datatype extension="genetrack" type="galaxy.datatypes.tracks:GeneTrack">  diff -r 19d8ba4269ba -r 8bd2ace6c92d lib/galaxy/datatypes/sequence.py --- a/lib/galaxy/datatypes/sequence.py Tue Mar 02 09:51:05 2010 -0500 +++ b/lib/galaxy/datatypes/sequence.py Tue Mar 02 10:47:23 2010 -0500 @@ -224,9 +224,9 @@ """Class representing a FASTQ sequence ( the Illumina 1.3+ variant )""" file_ext = "fastqillumina" -class FastqSolid( Fastq ): - """Class representing a FASTQ sequence ( the SOLiD (color space) variant )""" - file_ext = "fastqsolid" +class FastqCSSanger( Fastq ): + """Class representing a Color Space FASTQ sequence ( e.g a SOLiD variant )""" + file_ext = "fastqcssanger" try: from galaxy import eggs diff -r 19d8ba4269ba -r 8bd2ace6c92d lib/galaxy_utils/sequence/fasta.py --- a/lib/galaxy_utils/sequence/fasta.py Tue Mar 02 09:51:05 2010 -0500 +++ b/lib/galaxy_utils/sequence/fasta.py Tue Mar 02 10:47:23 2010 -0500 @@ -104,7 +104,7 @@ def __init__( self, fh ): self.file = fh def write( self, fastq_read ): - #this will include SOLiD adapter base if applicable + #this will include color space adapter base if applicable self.file.write( ">%s\n%s\n" % ( fastq_read.identifier[1:], fastq_read.sequence ) ) def close( self ): return self.file.close() diff -r 19d8ba4269ba -r 8bd2ace6c92d lib/galaxy_utils/sequence/fastq.py --- a/lib/galaxy_utils/sequence/fastq.py Tue Mar 02 09:51:05 2010 -0500 +++ b/lib/galaxy_utils/sequence/fastq.py Tue Mar 02 10:47:23 2010 -0500 @@ -176,8 +176,8 @@ score_system = 'solexa' sequence_space = 'base' -class fastqSolidRead( fastqSequencingRead ): - format = 'solid' #color space +class fastqCSSangerRead( fastqSequencingRead ): + format = 'cssanger' #color space ascii_min = 33 ascii_max = 126 quality_min = 0 @@ -260,7 +260,7 @@ FASTQ_FORMATS = {} -for format in [ fastqIlluminaRead, fastqSolexaRead, fastqSangerRead, fastqSolidRead ]: +for format in [ fastqIlluminaRead, fastqSolexaRead, fastqSangerRead, fastqCSSangerRead ]: FASTQ_FORMATS[ format.format ] = format diff -r 19d8ba4269ba -r 8bd2ace6c92d test-data/combine_phiX_out_1.fastqcssanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/combine_phiX_out_1.fastqcssanger Tue Mar 02 10:47:23 2010 -0500 @@ -0,0 +1,576 @@ +@1831_573_1004_F3 +T00030133312212111300011021310132222 ++ +4 29 27 34 5 5 24 24 20 17 10 34 29 20 27 13 30 27 22 24 11 28 19 17 27 17 24 17 25 27 7 24 14 12 22 +@1831_573_1050_F3 +T03330322230322112131010221102122113 ++ +8 26 31 31 16 22 30 31 28 29 22 30 30 31 32 23 30 28 28 31 19 32 30 32 19 8 5 10 13 6 5 10 6 16 11 +@1831_573_1067_F3 +T00023032023103330112220321200200002 ++ +13 10 10 2 4 7 6 11 4 14 3 11 10 5 16 2 5 8 11 8 5 10 6 9 6 9 4 2 3 5 2 4 7 6 3 +@1831_573_1219_F3 +T11211130300300301021212330201121310 ++ +31 31 31 28 19 14 10 8 20 8 19 15 23 30 6 21 21 20 29 9 14 20 30 27 21 16 6 26 27 18 11 25 11 20 12 +@1831_573_1242_F3 +T02132003121011302100130302112221121 ++ +29 29 29 25 25 29 16 22 28 32 20 30 31 31 28 26 22 32 28 26 17 13 21 15 29 23 17 27 23 28 22 19 10 26 26 +@1831_573_1333_F3 +T00200312330110101013212313222303112 ++ +8 28 6 31 2 4 18 28 13 29 8 14 18 19 9 16 16 22 11 11 14 21 12 19 10 13 24 22 19 17 19 20 21 27 8 +@1831_573_1362_F3 +T21203131001102231121211101111321131 ++ +34 33 31 31 30 31 31 30 31 34 31 33 32 30 31 29 31 27 31 23 32 31 30 31 6 13 23 6 30 16 22 25 11 10 30 +@1831_573_1448_F3 +T23101211223113320132212331313312022 ++ +22 22 28 32 8 30 11 13 31 32 31 31 25 31 31 27 28 14 22 8 31 27 12 2 23 21 21 17 4 24 21 16 18 5 10 +@1831_573_1490_F3 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+T00332022110020300332022020202002232 ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@1831_577_281_F3 +T03032301231212301013112222111210000 ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@1831_577_288_F3 +T01031120221303100221230021013201130 ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@1831_577_322_F3 +T12003213220230103303201000130312202 ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@1831_577_362_F3 +T31203302330110131230331210121110220 ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@1831_577_382_F3 +T32312123033111120321303230201332100 ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@1831_577_464_F3 +T13020221011130013102221333131203302 ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@1831_577_488_F3 +T13200302330322110200323132101120301 ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@1831_577_511_F3 +T32232133031023313331312220133230333 ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@1831_577_545_F3 +T00112131333222303222210031322103233 ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@1831_577_559_F3 +T32321101303233120102011130022122002 ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@1831_577_562_F3 +T32331101301233110121000220031120031 ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@1831_577_637_F3 +T22113312122202103031023120301031110 ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@1831_577_641_F3 +T13031301101121223221212020032131113 ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@1831_577_692_F3 +T01122320200330103121202301211100220 ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ diff -r 19d8ba4269ba -r 8bd2ace6c92d test-data/fastq_combiner_no_qual_ascii_out_1.fastqsolid --- a/test-data/fastq_combiner_no_qual_ascii_out_1.fastqsolid Tue Mar 02 09:51:05 2010 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,576 +0,0 @@ -@1831_573_1004_F3 -T00030133312212111300011021310132222 -+ -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -@1831_573_1050_F3 -T03330322230322112131010221102122113 -+ -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -@1831_573_1067_F3 -T00023032023103330112220321200200002 -+ -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -@1831_573_1219_F3 -T11211130300300301021212330201121310 -+ -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -@1831_573_1242_F3 -T02132003121011302100130302112221121 -+ -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -@1831_573_1333_F3 -T00200312330110101013212313222303112 -+ -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -@1831_573_1362_F3 -T21203131001102231121211101111321131 -+ -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -@1831_573_1448_F3 -T23101211223113320132212331313312022 -+ -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -@1831_573_1490_F3

1 0

[hg] galaxy 3458: Fix bug that prevented tags with capital lette...
by Greg Von Kuster 03 Mar '10

03 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/19d8ba4269ba changeset: 3458:19d8ba4269ba user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Tue Mar 02 09:51:05 2010 -0500 description: Fix bug that prevented tags with capital letters from being deleted. diffstat: lib/galaxy/model/__init__.py | 3 --- lib/galaxy/tags/tag_handler.py | 10 +++++----- 2 files changed, 5 insertions(+), 8 deletions(-) diffs (34 lines): diff -r 144c01a8db6e -r 19d8ba4269ba lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py Tue Mar 02 00:38:57 2010 -0500 +++ b/lib/galaxy/model/__init__.py Tue Mar 02 09:51:05 2010 -0500 @@ -1537,9 +1537,6 @@ self.value = None self.user_value = None - def __str__ ( self ): - return "%s(item_id=%s, item_tag=%s, user_tname=%s, value=%s, user_value=%s)" % (self.__class__.__name__, self.item_id, self.tag_id, self.user_tname, self.value. self.user_value ) - class HistoryTagAssociation ( ItemTagAssociation ): pass diff -r 144c01a8db6e -r 19d8ba4269ba lib/galaxy/tags/tag_handler.py --- a/lib/galaxy/tags/tag_handler.py Tue Mar 02 00:38:57 2010 -0500 +++ b/lib/galaxy/tags/tag_handler.py Tue Mar 02 09:51:05 2010 -0500 @@ -211,12 +211,12 @@ return tag - def _get_item_tag_assoc(self, user, item, tag_name): - """Return ItemTagAssociation object for an item and a tag string; returns None if there is - no such tag.""" - scrubbed_tag_name = self._scrub_tag_name(tag_name) + def _get_item_tag_assoc( self, user, item, tag_name ): + """Return ItemTagAssociation object for a user, item, and tag string; returns None if there is + no such association.""" + scrubbed_tag_name = self._scrub_tag_name( tag_name ) for item_tag_assoc in item.tags: - if ( item_tag_assoc.user == user ) and ( item_tag_assoc.tag.name == scrubbed_tag_name ): + if ( item_tag_assoc.user == user ) and ( item_tag_assoc.user_tname == scrubbed_tag_name ): return item_tag_assoc return None

1 0

[hg] galaxy 3457: psycopg2 scramble fix
by Greg Von Kuster 03 Mar '10

03 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/144c01a8db6e changeset: 3457:144c01a8db6e user: Nate Coraor <nate(a)bx.psu.edu> date: Tue Mar 02 00:38:57 2010 -0500 description: psycopg2 scramble fix diffstat: lib/galaxy/eggs/scramble.py | 2 +- scripts/scramble/patches/psycopg2/setup.py | 252 --------------------------- scripts/scramble/scripts/psycopg2-linux.py | 79 ++++++++ scripts/scramble/scripts/psycopg2-solaris.py | 81 ++++++++ scripts/scramble/scripts/psycopg2.py | 45 ++-- 5 files changed, 184 insertions(+), 275 deletions(-) diffs (515 lines): diff -r 2f3b76827743 -r 144c01a8db6e lib/galaxy/eggs/scramble.py --- a/lib/galaxy/eggs/scramble.py Thu Feb 11 00:17:04 2010 -0500 +++ b/lib/galaxy/eggs/scramble.py Tue Mar 02 00:38:57 2010 -0500 @@ -167,7 +167,7 @@ "%s-%s.py" % ( self.name, platform ), "%s-%s.py" % ( self.name, '-'.join( platform.split( '-' )[:2] ) ), "%s-%s.py" % ( self.name, '-'.join( platform.split( '-' )[1:] ) ), - "%s-%s.py" % ( self.name, self.py ), + "%s-%s.py" % ( self.name, platform.split( '-' )[:2][-1] ), "%s-%s.py" % ( self.name, platform.split( '-' )[0] ), "%s.py" % self.name, "generic.py" ) diff -r 2f3b76827743 -r 144c01a8db6e scripts/scramble/patches/psycopg2/setup.py --- a/scripts/scramble/patches/psycopg2/setup.py Thu Feb 11 00:17:04 2010 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,252 +0,0 @@ -# setup.py - distutils packaging -# -# Copyright (C) 2003-2004 Federico Di Gregorio <fog(a)debian.org> -# -# This program is free software; you can redistribute it and/or modify -# it under the terms of the GNU General Public License as published by the -# Free Software Foundation; either version 2, or (at your option) any later -# version. -# -# This program is distributed in the hope that it will be useful, but -# WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTIBILITY -# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License -# for more details. - -"""Python-PostgreSQL Database Adapter - -psycopg is a PostgreSQL database adapter for the Python programming -language. This is version 2, a complete rewrite of the original code to -provide new-style classes for connection and cursor objects and other sweet -candies. Like the original, psycopg 2 was written with the aim of being -very small and fast, and stable as a rock. - -psycopg is different from the other database adapter because it was -designed for heavily multi-threaded applications that create and destroy -lots of cursors and make a conspicuous number of concurrent INSERTs or -UPDATEs. psycopg 2 also provide full asycronous operations for the really -brave programmer. -""" - -classifiers = """\ -Development Status :: 4 - Beta -Intended Audience :: Developers -License :: OSI Approved :: GNU General Public License (GPL) -License :: OSI Approved :: Zope Public License -Programming Language :: Python -Programming Language :: C -Programming Language :: SQL -Topic :: Database -Topic :: Database :: Front-Ends -Topic :: Software Development -Topic :: Software Development :: Libraries :: Python Modules -Operating System :: Microsoft :: Windows -Operating System :: Unix -""" - -import os -import os.path -import sys -import popen2 -import ConfigParser -from glob import glob -from distutils.core import setup, Extension -from distutils.errors import DistutilsFileError -from distutils.command.build_ext import build_ext -from distutils.sysconfig import get_python_inc -from distutils.ccompiler import get_default_compiler - -assert sys.version_info[:2] >= ( 2, 4 ) - -PSYCOPG_VERSION = '2.0.6' -version_flags = [] - -PG_VERSION = '8.2.6' - -class psycopg_build_ext(build_ext): - """Conditionally complement the setup.cfg options file. - - This class configures the include_dirs, libray_dirs, libraries - options as required by the system. Most of the configuration happens - in finalize_options() method. - - If you want to set up the build step for a peculiar platform, add a - method finalize_PLAT(), where PLAT matches your sys.platform. - """ - user_options = build_ext.user_options[:] - user_options.extend([ - ('use-pydatetime', None, - "Use Python datatime objects for date and time representation."), - ('use-decimal', None, - "Use Decimal type even on Python 2.3 if the module is provided."), - ]) - - boolean_options = build_ext.boolean_options[:] - boolean_options.extend(('use-pydatetime', 'use-decimal', 'have-ssl')) - - def initialize_options(self): - build_ext.initialize_options(self) - self.use_pg_dll = 1 - self.pgdir = None - self.mx_include_dir = None - - def get_compiler(self): - """Return the name of the C compiler used to compile extensions. - - If a compiler was not explicitely set (on the command line, for - example), fall back on the default compiler. - """ - if self.compiler: - # distutils doesn't keep the type of self.compiler uniform; we - # compensate: - if isinstance(self.compiler, str): - name = self.compiler - else: - name = self.compiler.compiler_type - else: - name = get_default_compiler() - return name - - def finalize_darwin(self): - """Finalize build system configuration on darwin platform.""" - self.libraries.append('ssl') - self.libraries.append('crypto') - - def finalize_options(self): - """Complete the build system configuation.""" - build_ext.finalize_options(self) - - self.include_dirs.append(".") - self.include_dirs.append("postgresql-8.2.6/src/interfaces/libpq") - self.include_dirs.append("postgresql-8.2.6/src/include") - self.include_dirs.append("postgresql-8.2.6/src/port") - pgmajor, pgminor, pgpatch = PG_VERSION.split('.') - define_macros.append(("PG_MAJOR_VERSION", pgmajor)) - define_macros.append(("PG_MINOR_VERSION", pgminor)) - define_macros.append(("PG_PATCH_VERSION", pgpatch)) - - if hasattr(self, "finalize_" + sys.platform): - getattr(self, "finalize_" + sys.platform)() - -# let's start with macro definitions (the ones not already in setup.cfg) -define_macros = [] -include_dirs = [] - -# python version -define_macros.append(('PY_MAJOR_VERSION', str(sys.version_info[0]))) -define_macros.append(('PY_MINOR_VERSION', str(sys.version_info[1]))) - -# some macros related to python versions and features -if sys.version_info[0] >= 2 and sys.version_info[1] >= 3: - define_macros.append(('HAVE_PYBOOL','1')) - -# gather information to build the extension module -ext = [] ; data_files = [] - -# sources - -sources = [ - 'psycopgmodule.c', 'pqpath.c', 'typecast.c', - 'microprotocols.c', 'microprotocols_proto.c', - 'connection_type.c', 'connection_int.c', 'cursor_type.c', 'cursor_int.c', - 'adapter_qstring.c', 'adapter_pboolean.c', 'adapter_binary.c', - 'adapter_asis.c', 'adapter_list.c'] - -parser = ConfigParser.ConfigParser() -parser.read('setup.cfg') - -# Choose if to use Decimal type -use_decimal = int(parser.get('build_ext', 'use_decimal')) -if sys.version_info[0] >= 2 and ( - sys.version_info[1] >= 4 or (sys.version_info[1] == 3 and use_decimal)): - define_macros.append(('HAVE_DECIMAL','1')) - version_flags.append('dec') - -# Choose a datetime module -have_pydatetime = False -have_mxdatetime = False -use_pydatetime = int(parser.get('build_ext', 'use_pydatetime')) - -# check for mx package -if parser.has_option('build_ext', 'mx_include_dir'): - mxincludedir = parser.get('build_ext', 'mx_include_dir') -else: - mxincludedir = os.path.join(get_python_inc(plat_specific=1), "mx") -if os.path.exists(mxincludedir): - include_dirs.append(mxincludedir) - define_macros.append(('HAVE_MXDATETIME','1')) - sources.append('adapter_mxdatetime.c') - have_mxdatetime = True - version_flags.append('mx') - -# check for python datetime package -if os.path.exists(os.path.join(get_python_inc(plat_specific=1),"datetime.h")): - define_macros.append(('HAVE_PYDATETIME','1')) - sources.append('adapter_datetime.c') - have_pydatetime = True - version_flags.append('dt') - -# now decide which package will be the default for date/time typecasts -if have_pydatetime and use_pydatetime \ - or have_pydatetime and not have_mxdatetime: - define_macros.append(('PSYCOPG_DEFAULT_PYDATETIME','1')) -elif have_mxdatetime: - define_macros.append(('PSYCOPG_DEFAULT_MXDATETIME','1')) -else: - def e(msg): - sys.stderr.write("error: " + msg + "\n") - e("psycopg requires a datetime module:") - e(" mx.DateTime module not found") - e(" python datetime module not found") - e("Note that psycopg needs the module headers and not just the module") - e("itself. If you installed Python or mx.DateTime from a binary package") - e("you probably need to install its companion -dev or -devel package.") - sys.exit(1) - -# generate a nice version string to avoid confusion when users report bugs -for have in parser.get('build_ext', 'define').split(','): - if have == 'PSYCOPG_EXTENSIONS': - version_flags.append('ext') - elif have == 'HAVE_PQPROTOCOL3': - version_flags.append('pq3') -if version_flags: - PSYCOPG_VERSION_EX = PSYCOPG_VERSION + " (%s)" % ' '.join(version_flags) -else: - PSYCOPG_VERSION_EX = PSYCOPG_VERSION - -define_macros.append(('PSYCOPG_VERSION', '"'+PSYCOPG_VERSION_EX+'"')) - -if parser.has_option('build_ext', 'have_ssl'): - have_ssl = int(parser.get('build_ext', 'have_ssl')) -else: - have_ssl = 0 - -# build the extension - -sources = map(lambda x: os.path.join('psycopg', x), sources) -sources.append( 'postgresql-%s/src/port/pgstrcasecmp.c' % PG_VERSION ) -sources.append( 'postgresql-%s/src/backend/libpq/md5.c' % PG_VERSION ) -sources.extend( glob('postgresql-%s/src/interfaces/libpq/*.c' % PG_VERSION) ) - -ext.append(Extension("psycopg2._psycopg", sources, - define_macros=define_macros, - include_dirs=include_dirs, - undef_macros=[])) -setup(name="psycopg2", - version=PSYCOPG_VERSION, - maintainer="Federico Di Gregorio", - maintainer_email="fog(a)initd.org", - author="Federico Di Gregorio", - author_email="fog(a)initd.org", - url="http://initd.org/tracker/psycopg", - download_url = "http://initd.org/pub/software/psycopg2", - license="GPL with exceptions or ZPL", - platforms = ["any"], - description=__doc__.split("\n")[0], - long_description="\n".join(__doc__.split("\n")[2:]), - classifiers=filter(None, classifiers.split("\n")), - data_files=data_files, - package_dir={'psycopg2':'lib'}, - packages=['psycopg2'], - cmdclass={ 'build_ext': psycopg_build_ext }, - ext_modules=ext) - diff -r 2f3b76827743 -r 144c01a8db6e scripts/scramble/scripts/psycopg2-linux.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/scramble/scripts/psycopg2-linux.py Tue Mar 02 00:38:57 2010 -0500 @@ -0,0 +1,79 @@ +import os, sys, shutil +from distutils.sysconfig import get_config_var + +def prep_postgres( prepped, args ): + + pg_version = args['version'] + pg_srcdir = os.path.join( os.getcwd(), "postgresql-%s" % pg_version ) + + # set up environment + os.environ['CC'] = get_config_var('CC') + os.environ['CFLAGS'] = get_config_var('CFLAGS') + os.environ['LDFLAGS'] = get_config_var('LDFLAGS') + + if '-fPIC' not in os.environ['CFLAGS']: + os.environ['CFLAGS'] += ' -fPIC' + + # run configure + run( "./configure --prefix=%s/postgres --disable-dependency-tracking --enable-static --disable-shared --without-readline --with-thread-safety" % os.getcwd(), + os.path.join( os.getcwd(), "postgresql-%s" % pg_version ), + "Configuring postgres (./configure)" ) + + # compile + run( "make", os.path.join( pg_srcdir, 'src', 'interfaces', 'libpq' ), "Compiling libpq (cd src/interfaces/libpq; make)" ) + run( "make", os.path.join( pg_srcdir, 'src', 'bin', 'pg_config' ), "Compiling pg_config (cd src/bin/pg_config; make)" ) + + # install + run( "make install", os.path.join( pg_srcdir, 'src', 'interfaces', 'libpq' ), "Compiling libpq (cd src/interfaces/libpq; make install)" ) + run( "make install", os.path.join( pg_srcdir, 'src', 'bin', 'pg_config' ), "Compiling pg_config (cd src/bin/pg_config; make install)" ) + run( "make install", os.path.join( pg_srcdir, 'src', 'include' ), "Compiling pg_config (cd src/include; make install)" ) + + # create prepped archive + print "%s(): Creating prepped archive for future builds at:" % sys._getframe().f_code.co_name + print " ", prepped + compress( prepped, + 'postgres/bin', + 'postgres/include', + 'postgres/lib' ) + +if __name__ == '__main__': + + # change back to the build dir + if os.path.dirname( sys.argv[0] ) != "": + os.chdir( os.path.dirname( sys.argv[0] ) ) + + # find setuptools + sys.path.append( os.path.abspath( os.path.join( '..', '..', '..', 'lib' ) ) ) + from scramble_lib import * + + tag = get_tag() + + pg_version = ( tag.split( "_" ) )[1] + pg_archive_base = os.path.join( archives, "postgresql-%s" % pg_version ) + pg_archive = get_archive( pg_archive_base ) + pg_archive_prepped = os.path.join( archives, "postgresql-%s-%s.tar.gz" % ( pg_version, platform_noucs ) ) + + # clean up any existing stuff (could happen if you run scramble.py by hand) + clean( [ 'postgresql-%s' % pg_version ] ) + + # unpack postgres + unpack_dep( pg_archive, pg_archive_prepped, prep_postgres, dict( version=pg_version ) ) + + # localize setup.cfg + if not os.path.exists( 'setup.cfg.orig' ): + shutil.copy( 'setup.cfg', 'setup.cfg.orig' ) + f = open( 'setup.cfg', 'a' ) + f.write( '\npg_config=postgres/bin/pg_config\n' ) + f.write( '\nlibraries=crypt\n' ) + f.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 2f3b76827743 -r 144c01a8db6e scripts/scramble/scripts/psycopg2-solaris.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/scramble/scripts/psycopg2-solaris.py Tue Mar 02 00:38:57 2010 -0500 @@ -0,0 +1,81 @@ +import os, sys, shutil +from distutils.sysconfig import get_config_var + +def prep_postgres( prepped, args ): + + pg_version = args['version'] + pg_srcdir = os.path.join( os.getcwd(), "postgresql-%s" % pg_version ) + + # set up environment + os.environ['CC'] = get_config_var('CC') + os.environ['CFLAGS'] = get_config_var('CFLAGS') + os.environ['LDFLAGS'] = get_config_var('LDFLAGS') + + cc = get_solaris_compiler() + if cc == 'cc': + os.environ['CFLAGS'] += ' -KPIC' + elif cc == 'gcc': + os.environ['CFLAGS'] += ' -fPIC -DPIC' + + # run configure + run( "./configure --prefix=%s/postgres --disable-dependency-tracking --enable-static --disable-shared --without-readline --with-thread-safety" % os.getcwd(), + os.path.join( os.getcwd(), "postgresql-%s" % pg_version ), + "Configuring postgres (./configure)" ) + + # compile + run( "gmake", os.path.join( pg_srcdir, 'src', 'interfaces', 'libpq' ), "Compiling libpq (cd src/interfaces/libpq; gmake)" ) + run( "gmake", os.path.join( pg_srcdir, 'src', 'bin', 'pg_config' ), "Compiling pg_config (cd src/bin/pg_config; gmake)" ) + + # install + run( "gmake install", os.path.join( pg_srcdir, 'src', 'interfaces', 'libpq' ), "Compiling libpq (cd src/interfaces/libpq; gmake install)" ) + run( "gmake install", os.path.join( pg_srcdir, 'src', 'bin', 'pg_config' ), "Compiling pg_config (cd src/bin/pg_config; gmake install)" ) + run( "gmake install", os.path.join( pg_srcdir, 'src', 'include' ), "Compiling pg_config (cd src/include; gmake install)" ) + + # create prepped archive + print "%s(): Creating prepped archive for future builds at:" % sys._getframe().f_code.co_name + print " ", prepped + compress( prepped, + 'postgres/bin', + 'postgres/include', + 'postgres/lib' ) + +if __name__ == '__main__': + + # change back to the build dir + if os.path.dirname( sys.argv[0] ) != "": + os.chdir( os.path.dirname( sys.argv[0] ) ) + + # find setuptools + sys.path.append( os.path.abspath( os.path.join( '..', '..', '..', 'lib' ) ) ) + from scramble_lib import * + + tag = get_tag() + + pg_version = ( tag.split( "_" ) )[1] + pg_archive_base = os.path.join( archives, "postgresql-%s" % pg_version ) + pg_archive = get_archive( pg_archive_base ) + pg_archive_prepped = os.path.join( archives, "postgresql-%s-%s.tar.gz" % ( pg_version, platform_noucs ) ) + + # clean up any existing stuff (could happen if you run scramble.py by hand) + clean( [ 'postgresql-%s' % pg_version ] ) + + # unpack postgres + unpack_dep( pg_archive, pg_archive_prepped, prep_postgres, dict( version=pg_version ) ) + + # localize setup.cfg + if not os.path.exists( 'setup.cfg.orig' ): + shutil.copy( 'setup.cfg', 'setup.cfg.orig' ) + f = open( 'setup.cfg', 'a' ) + f.write( '\npg_config=postgres/bin/pg_config\n' ) + f.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 2f3b76827743 -r 144c01a8db6e scripts/scramble/scripts/psycopg2.py --- a/scripts/scramble/scripts/psycopg2.py Thu Feb 11 00:17:04 2010 -0500 +++ b/scripts/scramble/scripts/psycopg2.py Tue Mar 02 00:38:57 2010 -0500 @@ -1,43 +1,40 @@ -import os, sys, subprocess, tarfile, shutil, glob +import os, sys, shutil from distutils.sysconfig import get_config_var def prep_postgres( prepped, args ): pg_version = args['version'] - if pkg_resources.get_platform().startswith('solaris'): - make = 'gmake' - else: - make = 'make' + pg_srcdir = os.path.join( os.getcwd(), "postgresql-%s" % pg_version ) # set up environment os.environ['CC'] = get_config_var('CC') os.environ['CFLAGS'] = get_config_var('CFLAGS') os.environ['LDFLAGS'] = get_config_var('LDFLAGS') - # run configure (to generate pg_config.h) - run( "./configure --without-readline", + if '-fPIC' not in os.environ['CFLAGS']: + os.environ['CFLAGS'] += ' -fPIC' + + # run configure + run( "./configure --prefix=%s/postgres --disable-dependency-tracking --enable-static --disable-shared --without-readline --with-thread-safety" % os.getcwd(), os.path.join( os.getcwd(), "postgresql-%s" % pg_version ), "Configuring postgres (./configure)" ) - # create src/port/pg_config_paths.h - run( "%s pg_config_paths.h" % make, - os.path.join( os.getcwd(), "postgresql-%s" % pg_version, "src", "port" ), - "Creating postgresql-%s/src/port/pg_config_paths.h" % pg_version ) + # compile + run( "make", os.path.join( pg_srcdir, 'src', 'interfaces', 'libpq' ), "Compiling libpq (cd src/interfaces/libpq; make)" ) + run( "make", os.path.join( pg_srcdir, 'src', 'bin', 'pg_config' ), "Compiling pg_config (cd src/bin/pg_config; make)" ) - # remove win32 crap in libpq dir - for file in glob.glob( "postgresql-%s/src/interfaces/libpq/*win32*" % pg_version ): - print "prep_postgres(): Removing %s" % file - os.unlink( file ) + # install + run( "make install", os.path.join( pg_srcdir, 'src', 'interfaces', 'libpq' ), "Compiling libpq (cd src/interfaces/libpq; make install)" ) + run( "make install", os.path.join( pg_srcdir, 'src', 'bin', 'pg_config' ), "Compiling pg_config (cd src/bin/pg_config; make install)" ) + run( "make install", os.path.join( pg_srcdir, 'src', 'include' ), "Compiling pg_config (cd src/include; make install)" ) # create prepped archive print "%s(): Creating prepped archive for future builds at:" % sys._getframe().f_code.co_name print " ", prepped compress( prepped, - "postgresql-%s/src/include" % pg_version, - "postgresql-%s/src/port/pg_config_paths.h" % pg_version, - "postgresql-%s/src/port/pgstrcasecmp.c" % pg_version, - "postgresql-%s/src/backend/libpq/md5.c" % pg_version, - "postgresql-%s/src/interfaces/libpq" % pg_version ) + 'postgres/bin', + 'postgres/include', + 'postgres/lib' ) if __name__ == '__main__': @@ -62,8 +59,12 @@ # unpack postgres unpack_dep( pg_archive, pg_archive_prepped, prep_postgres, dict( version=pg_version ) ) - # get setup.py - shutil.copy( os.path.join( patches, 'psycopg2', 'setup.py' ), 'setup.py' ) + # localize setup.cfg + if not os.path.exists( 'setup.cfg.orig' ): + shutil.copy( 'setup.cfg', 'setup.cfg.orig' ) + f = open( 'setup.cfg', 'a' ) + f.write( '\npg_config=postgres/bin/pg_config\n' ) + f.close() # tag me = sys.argv[0]

1 0

[hg] galaxy 3456: [mq] workflow-invocation: Track workflow invoc...
by Greg Von Kuster 03 Mar '10

03 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/2f3b76827743 changeset: 3456:2f3b76827743 user: James Taylor <james(a)jamestaylor.org> date: Thu Feb 11 00:17:04 2010 -0500 description: [mq] workflow-invocation: Track workflow invocations in database, provide a view of the history grouped by workflow and job diffstat: lib/galaxy/model/__init__.py | 6 + lib/galaxy/model/mapping.py | 68 +++++++--- lib/galaxy/model/migrate/versions/0041_workflow_invocation.py | 52 ++++++++ lib/galaxy/tools/__init__.py | 2 +- lib/galaxy/tools/actions/__init__.py | 6 +- lib/galaxy/tools/actions/metadata.py | 2 +- lib/galaxy/tools/actions/upload.py | 2 +- lib/galaxy/tools/actions/upload_common.py | 7 +- lib/galaxy/web/controllers/history.py | 67 ++++++++++ lib/galaxy/web/controllers/workflow.py | 19 ++- lib/galaxy/workflow/modules.py | 2 +- scripts/manage_db.py | 1 + templates/root/index.mako | 3 + 13 files changed, 204 insertions(+), 33 deletions(-) diffs (426 lines): diff -r c48de7f12e58 -r 2f3b76827743 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py Mon Mar 01 17:47:28 2010 -0500 +++ b/lib/galaxy/model/__init__.py Thu Feb 11 00:17:04 2010 -0500 @@ -1217,6 +1217,12 @@ self.user = None self.order_index = None +class WorkflowInvocation( object ): + pass + +class WorkflowInvocationStep( object ): + pass + class MetadataFile( object ): def __init__( self, dataset = None, name = None ): if isinstance( dataset, HistoryDatasetAssociation ): diff -r c48de7f12e58 -r 2f3b76827743 lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py Mon Mar 01 17:47:28 2010 -0500 +++ b/lib/galaxy/model/mapping.py Thu Feb 11 00:17:04 2010 -0500 @@ -558,6 +558,22 @@ Column( "input_name", TEXT) ) +WorkflowInvocation.table = Table( "workflow_invocation", metadata, + Column( "id", Integer, primary_key=True ), + Column( "create_time", DateTime, default=now ), + Column( "update_time", DateTime, default=now, onupdate=now ), + Column( "workflow_id", Integer, ForeignKey( "workflow.id" ), index=True, nullable=False ) + ) + +WorkflowInvocationStep.table = Table( "workflow_invocation_step", metadata, + Column( "id", Integer, primary_key=True ), + Column( "create_time", DateTime, default=now ), + Column( "update_time", DateTime, default=now, onupdate=now ), + Column( "workflow_invocation_id", Integer, ForeignKey( "workflow_invocation.id" ), index=True, nullable=False ), + Column( "workflow_step_id", Integer, ForeignKey( "workflow_step.id" ), index=True, nullable=False ), + Column( "job_id", Integer, ForeignKey( "job.id" ), index=True, nullable=False ) + ) + StoredWorkflowUserShareAssociation.table = Table( "stored_workflow_user_share_connection", metadata, Column( "id", Integer, primary_key=True ), Column( "stored_workflow_id", Integer, ForeignKey( "stored_workflow.id" ), index=True ), @@ -1215,27 +1231,6 @@ HistoryDatasetAssociation.mapper.add_property( "creating_job_associations", relation( JobToOutputDatasetAssociation ) ) -assign_mapper( context, Workflow, Workflow.table, - properties=dict( steps=relation( WorkflowStep, backref='workflow', - order_by=asc(WorkflowStep.table.c.order_index), - cascade="all, delete-orphan", - lazy=False ), - tags=relation(WorkflowTagAssociation, order_by=WorkflowTagAssociation.table.c.id, backref="workflows") - ) ) - - -assign_mapper( context, WorkflowStep, WorkflowStep.table, - properties=dict( - tags=relation(WorkflowStepTagAssociation, order_by=WorkflowStepTagAssociation.table.c.id, backref="workflow_steps"), - annotations=relation( WorkflowStepAnnotationAssociation, order_by=WorkflowStepAnnotationAssociation.table.c.id, backref="workflow_steps" ) ) - ) - -assign_mapper( context, WorkflowStepConnection, WorkflowStepConnection.table, - properties=dict( input_step=relation( WorkflowStep, backref="input_connections", cascade="all", - primaryjoin=( WorkflowStepConnection.table.c.input_step_id == WorkflowStep.table.c.id ) ), - output_step=relation( WorkflowStep, backref="output_connections", cascade="all", - primaryjoin=( WorkflowStepConnection.table.c.output_step_id == WorkflowStep.table.c.id ) ) ) ) - # vvvvvvvvvvvvvvvv Start cloud table mappings vvvvvvvvvvvvvvvv assign_mapper( context, CloudImage, CloudImage.table ) @@ -1272,6 +1267,27 @@ ) ) # ^^^^^^^^^^^^^^^ End cloud table mappings ^^^^^^^^^^^^^^^^^^ +assign_mapper( context, Workflow, Workflow.table, + properties=dict( steps=relation( WorkflowStep, backref='workflow', + order_by=asc(WorkflowStep.table.c.order_index), + cascade="all, delete-orphan", + lazy=False ), + tags=relation(WorkflowTagAssociation, order_by=WorkflowTagAssociation.table.c.id, backref="workflows") + ) ) + +assign_mapper( context, WorkflowStep, WorkflowStep.table, + properties=dict( + tags=relation(WorkflowStepTagAssociation, order_by=WorkflowStepTagAssociation.table.c.id, backref="workflow_steps"), + annotations=relation( WorkflowStepAnnotationAssociation, order_by=WorkflowStepAnnotationAssociation.table.c.id, backref="workflow_steps" ) ) + ) + +assign_mapper( context, WorkflowStepConnection, WorkflowStepConnection.table, + properties=dict( input_step=relation( WorkflowStep, backref="input_connections", cascade="all", + primaryjoin=( WorkflowStepConnection.table.c.input_step_id == WorkflowStep.table.c.id ) ), + output_step=relation( WorkflowStep, backref="output_connections", cascade="all", + primaryjoin=( WorkflowStepConnection.table.c.output_step_id == WorkflowStep.table.c.id ) ) ) ) + + assign_mapper( context, StoredWorkflow, StoredWorkflow.table, properties=dict( user=relation( User ), workflows=relation( Workflow, backref='stored_workflow', @@ -1297,6 +1313,16 @@ assign_mapper( context, StoredWorkflowMenuEntry, StoredWorkflowMenuEntry.table, properties=dict( stored_workflow=relation( StoredWorkflow ) ) ) +assign_mapper( context, WorkflowInvocation, WorkflowInvocation.table, + properties=dict( + steps=relation( WorkflowInvocationStep, backref='workflow_invocation', lazy=False ), + workflow=relation( Workflow ) ) ) + +assign_mapper( context, WorkflowInvocationStep, WorkflowInvocationStep.table, + properties=dict( + workflow_step = relation( WorkflowStep ), + job = relation( Job, backref=backref( 'workflow_invocation_step', uselist=False ) ) ) ) + assign_mapper( context, MetadataFile, MetadataFile.table, properties=dict( history_dataset=relation( HistoryDatasetAssociation ), library_dataset=relation( LibraryDatasetDatasetAssociation ) ) ) diff -r c48de7f12e58 -r 2f3b76827743 lib/galaxy/model/migrate/versions/0041_workflow_invocation.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/model/migrate/versions/0041_workflow_invocation.py Thu Feb 11 00:17:04 2010 -0500 @@ -0,0 +1,52 @@ +""" +Migration script to create tables for tracking workflow invocations. +""" + +from sqlalchemy import * +from sqlalchemy.orm import * +from migrate import * +from migrate.changeset import * + +import logging +logging.basicConfig( level=logging.DEBUG ) +log = logging.getLogger( __name__ ) + +import datetime +now = datetime.datetime.utcnow + +metadata = MetaData( migrate_engine ) +db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) + +WorkflowInvocation_table = Table( "workflow_invocation", metadata, + Column( "id", Integer, primary_key=True ), + Column( "create_time", DateTime, default=now ), + Column( "update_time", DateTime, default=now, onupdate=now ), + Column( "workflow_id", Integer, ForeignKey( "workflow.id" ), index=True, nullable=False ) + ) + +WorkflowInvocationStep_table = Table( "workflow_invocation_step", metadata, + Column( "id", Integer, primary_key=True ), + Column( "create_time", DateTime, default=now ), + Column( "update_time", DateTime, default=now, onupdate=now ), + Column( "workflow_invocation_id", Integer, ForeignKey( "workflow_invocation.id" ), index=True, nullable=False ), + Column( "workflow_step_id", Integer, ForeignKey( "workflow_step.id" ), index=True, nullable=False ), + Column( "job_id", Integer, ForeignKey( "job.id" ), index=True, nullable=False ) + ) + +tables = [ WorkflowInvocation_table, WorkflowInvocationStep_table ] + +def upgrade(): + print __doc__ + metadata.reflect() + + for table in tables: + try: + table.create() + except: + log.warn( "Failed to create table '%s', ignoring (might result in wrong schema)" % table.name ) + +def downgrade(): + metadata.reflect() + + for table in tables: + table.drop() \ No newline at end of file diff -r c48de7f12e58 -r 2f3b76827743 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py Mon Mar 01 17:47:28 2010 -0500 +++ b/lib/galaxy/tools/__init__.py Thu Feb 11 00:17:04 2010 -0500 @@ -789,7 +789,7 @@ return "tool_form.mako", dict( errors=errors, tool_state=state, incoming=incoming, error_message=error_message ) # If we've completed the last page we can execute the tool elif state.page == self.last_page: - out_data = self.execute( trans, incoming=params ) + _, out_data = self.execute( trans, incoming=params ) try: assert isinstance( out_data, odict ) return 'tool_executed.mako', dict( out_data=out_data ) diff -r c48de7f12e58 -r 2f3b76827743 lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py Mon Mar 01 17:47:28 2010 -0500 +++ b/lib/galaxy/tools/actions/__init__.py Thu Feb 11 00:17:04 2010 -0500 @@ -17,7 +17,7 @@ The actions to be taken when a tool is run (after parameters have been converted and validated). """ - def execute( self, tool, trans, incoming={} ): + def execute( self, tool, trans, incoming={}, set_output_hid=True ): raise TypeError("Abstract method") class DefaultToolAction( object ): @@ -101,7 +101,7 @@ tool.visit_inputs( param_values, visitor ) return input_datasets - def execute(self, tool, trans, incoming={}, set_output_hid=True ): + def execute(self, tool, trans, incoming={}, return_job=False, set_output_hid=True ): def make_dict_copy( from_dict ): """ Makes a copy of input dictionary from_dict such that all values that are dictionaries @@ -332,4 +332,4 @@ # Queue the job for execution trans.app.job_queue.put( job.id, tool ) trans.log_event( "Added job to the job queue, id: %s" % str(job.id), tool_id=job.tool_id ) - return out_data + return job, out_data diff -r c48de7f12e58 -r 2f3b76827743 lib/galaxy/tools/actions/metadata.py --- a/lib/galaxy/tools/actions/metadata.py Mon Mar 01 17:47:28 2010 -0500 +++ b/lib/galaxy/tools/actions/metadata.py Thu Feb 11 00:17:04 2010 -0500 @@ -60,4 +60,4 @@ # Queue the job for execution trans.app.job_queue.put( job.id, tool ) trans.log_event( "Added set external metadata job to the job queue, id: %s" % str(job.id), tool_id=job.tool_id ) - return odict() + return job, odict() diff -r c48de7f12e58 -r 2f3b76827743 lib/galaxy/tools/actions/upload.py --- a/lib/galaxy/tools/actions/upload.py Mon Mar 01 17:47:28 2010 -0500 +++ b/lib/galaxy/tools/actions/upload.py Thu Feb 11 00:17:04 2010 -0500 @@ -23,4 +23,4 @@ json_file_path = upload_common.create_paramfile( trans, uploaded_datasets ) data_list = [ ud.data for ud in uploaded_datasets ] - return upload_common.create_job( trans, incoming, tool, json_file_path, data_list ) + return upload_common.create_job( trans, incoming, tool, json_file_path, data_list, return_job=True ) diff -r c48de7f12e58 -r 2f3b76827743 lib/galaxy/tools/actions/upload_common.py --- a/lib/galaxy/tools/actions/upload_common.py Mon Mar 01 17:47:28 2010 -0500 +++ b/lib/galaxy/tools/actions/upload_common.py Thu Feb 11 00:17:04 2010 -0500 @@ -292,7 +292,7 @@ json_file.write( to_json_string( json ) + '\n' ) json_file.close() return json_file_path -def create_job( trans, params, tool, json_file_path, data_list, folder=None ): +def create_job( trans, params, tool, json_file_path, data_list, folder=None, return_job=False ): """ Create the upload job. """ @@ -329,7 +329,10 @@ output = odict() for i, v in enumerate( data_list ): output[ 'output%i' % i ] = v - return output + if return_job: + return job, output + else: + return output def active_folders( trans, folder ): # Stolen from galaxy.web.controllers.library_common (importing from which causes a circular issues). # Much faster way of retrieving all active sub-folders within a given folder than the diff -r c48de7f12e58 -r 2f3b76827743 lib/galaxy/web/controllers/history.py --- a/lib/galaxy/web/controllers/history.py Mon Mar 01 17:47:28 2010 -0500 +++ b/lib/galaxy/web/controllers/history.py Thu Feb 11 00:17:04 2010 -0500 @@ -295,6 +295,7 @@ trans.set_history( new_history ) # No message return None, None + @web.expose @web.require_login( "work with shared histories" ) def list_shared( self, trans, **kwargs ): @@ -329,6 +330,70 @@ status = 'done' # Render the list view return self.shared_list_grid( trans, status=status, message=message, **kwargs ) + + @web.expose + def display_structured( self, trans, id=None ): + """ + Display a history as a nested structure showing the jobs and workflow + invocations that created each dataset (if any). + """ + # Get history + if id is None: + history = trans.history + else: + id = trans.security.decode_id( id ) + history = trans.sa_session.query( model.History ).get( id ) + assert history + assert history.user and ( history.user == trans.user ) or ( history == trans.history ) + # Resolve jobs and workflow invocations for the datasets in the history + # items is filled with items (hdas, jobs, or workflows) that go at the + # top level + items = [] + # First go through and group hdas by job, if there is no job they get + # added directly to items + jobs = dict() + for hda in history.active_datasets: + # Follow "copied from ..." association until we get to the original + # instance of the dataset + original_hda = hda + while original_hda.copied_from_history_dataset_association: + original_hda = original_hda.copied_from_history_dataset_association + # Check if the job has a creating job, most should, datasets from + # before jobs were tracked, or from the upload tool before it + # created a job, may not + if not original_hda.creating_job_associations: + items.append( ( hda, None ) ) + # Attach hda to correct job + # -- there should only be one creating_job_association, so this + # loop body should only be hit once + for assoc in original_hda.creating_job_associations: + job = assoc.job + if job in jobs: + jobs[ job ].append( ( hda, None ) ) + else: + jobs[ job ] = [ ( hda, None ) ] + # Second, go through the jobs and connect to workflows + wf_invocations = dict() + for job, hdas in jobs.iteritems(): + # Job is attached to a workflow step, follow it to the + # workflow_invocation and group + if job.workflow_invocation_step: + wf_invocation = job.workflow_invocation_step.workflow_invocation + if wf_invocation in wf_invocations: + wf_invocations[ wf_invocation ].append( ( job, hdas ) ) + else: + wf_invocations[ wf_invocation ] = [ ( job, hdas ) ] + # Not attached to a workflow, add to items + else: + items.append( ( job, hdas ) ) + # Finally, add workflow invocations to items, which should now + # contain all hdas with some level of grouping + items.extend( wf_invocations.items() ) + # Sort items by age + items.sort( key=( lambda x: x[0].create_time ), reverse=True ) + # + return trans.fill_template( "history/display_structured.mako", items=items ) + @web.expose def delete_current( self, trans ): """Delete just the active history -- this does not require a logged in user.""" @@ -343,6 +408,7 @@ # Regardless of whether it was previously deleted, we make a new history active trans.new_history() return trans.show_ok_message( "History deleted, a new history is active", refresh_frames=['history'] ) + @web.expose def rename_async( self, trans, id=None, new_name=None ): history = self.get_history( trans, id ) @@ -493,6 +559,7 @@ Warning! If you import this history, you will lose your current history. Click <a href="%s">here</a> to confirm. """ % web.url_for( id=id, confirm=True ) ) + @web.expose def view( self, trans, id=None ): """View a history. If a history is importable, then it is viewable by any user.""" diff -r c48de7f12e58 -r 2f3b76827743 lib/galaxy/web/controllers/workflow.py --- a/lib/galaxy/web/controllers/workflow.py Mon Mar 01 17:47:28 2010 -0500 +++ b/lib/galaxy/web/controllers/workflow.py Thu Feb 11 00:17:04 2010 -0500 @@ -865,8 +865,12 @@ errors[step.id] = state.inputs["__errors__"] = step_errors if 'run_workflow' in kwargs and not errors: # Run each step, connecting outputs to inputs + workflow_invocation = model.WorkflowInvocation() + workflow_invocation.workflow = workflow outputs = odict() for i, step in enumerate( workflow.steps ): + # Execute module + job = None if step.type == 'tool' or step.type is None: tool = trans.app.toolbox.tools_by_id[ step.tool_id ] input_values = step.state.inputs @@ -878,10 +882,19 @@ return outputs[ conn.output_step.id ][ conn.output_name ] visit_input_values( tool.inputs, step.state.inputs, callback ) # Execute it - outputs[ step.id ] = tool.execute( trans, step.state.inputs ) + job, out_data = tool.execute( trans, step.state.inputs ) + outputs[ step.id ] = out_data else: - outputs[ step.id ] = step.module.execute( trans, step.state ) - + job, out_data = step.module.execute( trans, step.state ) + outputs[ step.id ] = out_data + # Record invocation + workflow_invocation_step = model.WorkflowInvocationStep() + workflow_invocation_step.workflow_invocation = workflow_invocation + workflow_invocation_step.workflow_step = step + workflow_invocation_step.job = job + # All jobs ran sucessfully, so we can save now + trans.sa_session.add( workflow_invocation ) + trans.sa_session.flush() return trans.fill_template( "workflow/run_complete.mako", workflow=stored, outputs=outputs ) diff -r c48de7f12e58 -r 2f3b76827743 lib/galaxy/workflow/modules.py --- a/lib/galaxy/workflow/modules.py Mon Mar 01 17:47:28 2010 -0500 +++ b/lib/galaxy/workflow/modules.py Thu Feb 11 00:17:04 2010 -0500 @@ -153,7 +153,7 @@ return errors def execute( self, trans, state ): - return dict( output=state.inputs['input']) + return None, dict( output=state.inputs['input']) class ToolModule( WorkflowModule ): diff -r c48de7f12e58 -r 2f3b76827743 scripts/manage_db.py --- a/scripts/manage_db.py Mon Mar 01 17:47:28 2010 -0500 +++ b/scripts/manage_db.py Thu Feb 11 00:17:04 2010 -0500 @@ -12,6 +12,7 @@ from migrate.versioning.shell import main from ConfigParser import SafeConfigParser + log = logging.getLogger( __name__ ) cp = SafeConfigParser() diff -r c48de7f12e58 -r 2f3b76827743 templates/root/index.mako --- a/templates/root/index.mako Mon Mar 01 17:47:28 2010 -0500 +++ b/templates/root/index.mako Thu Feb 11 00:17:04 2010 -0500 @@ -35,6 +35,9 @@ "Show Deleted Datasets": function() { galaxy_history.location = "${h.url_for( controller='root', action='history', show_deleted=True)}"; }, + "Show structure": function() { + galaxy_main.location = "${h.url_for( controller='history', action='display_structured' )}"; + }, "Delete": function() { if ( confirm( "Really delete the current history?" ) )

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