March 2010 - galaxy-dev - lists.galaxyproject.org

[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 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-@1831_577_692_F3 -T01122320200330103121202301211100220 -+ -@B,@?@B(@A?@+@@>@+?=>@'=<@<=<9=?75< diff -r 19d8ba4269ba -r 8bd2ace6c92d test-data/fastq_combiner_no_qual_ascii_out_1.fastqcssanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastq_combiner_no_qual_ascii_out_1.fastqcssanger Tue Mar 02 10:47:23 2010 -0500 @@ -0,0 +1,576 @@ +@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 ++ 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++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@1831_576_266_F3 +T30322223101312011300311121221333223 ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@1831_576_327_F3 +T22112331301313021321001332120332130 ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@1831_576_331_F3 +T32012133301311223023011232112333030 ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@1831_576_387_F3 +T00101211032031120300200222001230022 ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@1831_576_406_F3 +T00223133010210122221320212103132011 ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@1831_576_449_F3 +T31312001121222231100020132132100220 ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@1831_576_519_F3 +T03011321130130133213131202130321131 ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@1831_576_603_F3 +T21003032313302312320131221001330311 ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@1831_576_655_F3 +T02001023130302322122200313123123102 ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@1831_576_677_F3 +T13330131023320301031013230210103022 ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@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?" ) )

1 0

[hg] galaxy 3455: Fix uploads not working
by Greg Von Kuster 03 Mar '10

03 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/c48de7f12e58 changeset: 3455:c48de7f12e58 user: Kanwei Li <kanwei(a)gmail.com> date: Mon Mar 01 17:47:28 2010 -0500 description: Fix uploads not working diffstat: lib/galaxy/jobs/__init__.py | 2 +- 1 files changed, 1 insertions(+), 1 deletions(-) diffs (12 lines): diff -r 29bb8ebb3a59 -r c48de7f12e58 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py Mon Mar 01 16:07:54 2010 -0500 +++ b/lib/galaxy/jobs/__init__.py Mon Mar 01 17:47:28 2010 -0500 @@ -155,7 +155,7 @@ run and dispatching if so. """ # HACK: Delay until after forking, we need a way to do post fork notification!!! - time.sleep( 1000 ) + time.sleep( 10 ) while self.running: try: self.__monitor_step()

1 0

[hg] galaxy 3454: Passwords are no longer changed ( sanitized ) ...
by Greg Von Kuster 03 Mar '10

03 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/29bb8ebb3a59 changeset: 3454:29bb8ebb3a59 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Mon Mar 01 16:07:54 2010 -0500 description: Passwords are no longer changed ( sanitized ) as part of processing the request. Enhanced functional tests to cover the scenario where passwords include chars that break in sanitization. diffstat: lib/galaxy/web/controllers/requests_admin.py | 4 +- lib/galaxy/web/controllers/user.py | 30 ++++++++++++++++----------- test/base/twilltestcase.py | 5 +++- test/functional/test_user_info.py | 7 ++++- 4 files changed, 29 insertions(+), 17 deletions(-) diffs (118 lines): diff -r 58ba6e72d803 -r 29bb8ebb3a59 lib/galaxy/web/controllers/requests_admin.py --- a/lib/galaxy/web/controllers/requests_admin.py Mon Mar 01 16:00:26 2010 -0500 +++ b/lib/galaxy/web/controllers/requests_admin.py Mon Mar 01 16:07:54 2010 -0500 @@ -1703,7 +1703,7 @@ # data transfer info rt.datatx_info = dict(host=util.restore_text( params.get( 'host', '' ) ), username=util.restore_text( params.get( 'username', '' ) ), - password=util.restore_text( params.get( 'password', '' ) ), + password=params.get( 'password', '' ), data_dir=util.restore_text( params.get( 'data_dir', '' ) )) trans.sa_session.add( rt ) trans.sa_session.flush() @@ -1775,7 +1775,7 @@ # data transfer info rt.datatx_info = dict(host=util.restore_text( params.get( 'host', '' ) ), username=util.restore_text( params.get( 'username', '' ) ), - password=util.restore_text( params.get( 'password', '' ) )) + password=params.get( 'password', '' )) trans.sa_session.add( rt ) trans.sa_session.flush() # set sample states diff -r 58ba6e72d803 -r 29bb8ebb3a59 lib/galaxy/web/controllers/user.py --- a/lib/galaxy/web/controllers/user.py Mon Mar 01 16:00:26 2010 -0500 +++ b/lib/galaxy/web/controllers/user.py Mon Mar 01 16:07:54 2010 -0500 @@ -167,12 +167,14 @@ @web.expose def create( self, trans, **kwd ): params = util.Params( kwd ) - email = util.restore_text( params.get('email', '') ) - username = util.restore_text( params.get('username', '') ) - password = util.restore_text( params.get('password', '') ) - confirm = util.restore_text( params.get('confirm', '') ) - subscribe = CheckboxField.is_checked( params.get('subscribe', '') ) - admin_view = params.get('admin_view', 'False') + email = util.restore_text( params.get( 'email', '' ) ) + username = util.restore_text( params.get( 'username', '' ) ) + # Do not sanitize passwords, so take from kwd + # instead of params ( which were sanitized ) + password = kwd.get( 'password', '' ) + confirm = kwd.get( 'confirm', '' ) + subscribe = CheckboxField.is_checked( params.get( 'subscribe', '' ) ) + admin_view = params.get( 'admin_view', 'False' ) msg = util.restore_text( params.get( 'msg', '' ) ) messagetype = params.get( 'messagetype', 'done' ) if trans.app.config.require_login: @@ -413,11 +415,11 @@ login_info = { 'Email': TextField( 'email', 40, util.restore_text( params.get('email', '') ) ), 'Public Username': TextField( 'username', 40, - util.restore_text( params.get('username', '') ) ), + util.restore_text( params.get( 'username', '' ) ) ), 'Password': PasswordField( 'password', 40, - util.restore_text( params.get('password', '') ) ), + params.get( 'password', '' ) ), 'Confirm': PasswordField( 'confirm', 40, - util.restore_text( params.get('confirm', '') ) ), + params.get( 'confirm', '' ) ), 'Subscribe To Mailing List': CheckboxField( 'subscribe', util.restore_text( params.get('subscribe', '') ) ) } # user information @@ -531,11 +533,15 @@ # Change password # elif params.get('change_password_button', None) == 'Save': - password = util.restore_text( params.get('password', '') ) - confirm = util.restore_text( params.get('confirm', '') ) + # Do not sanitize passwords, so get from kwd and not params + # ( which were sanitized ). + password = kwd.get( 'password', '' ) + confirm = kwd.get( 'confirm', '' ) # when from the user perspective, validate the current password if params.get('admin_view', 'False') == 'False': - current = util.restore_text( params.get('current', '') ) + # Do not sanitize passwords, so get from kwd and not params + # ( which were sanitized ). + current = kwd.get( 'current', '' ) if not trans.user.check_password( current ): return trans.response.send_redirect( web.url_for( controller='user', action='show_info', diff -r 58ba6e72d803 -r 29bb8ebb3a59 test/base/twilltestcase.py --- a/test/base/twilltestcase.py Mon Mar 01 16:00:26 2010 -0500 +++ b/test/base/twilltestcase.py Mon Mar 01 16:07:54 2010 -0500 @@ -745,7 +745,10 @@ self.create( email=email, password=password ) except: self.home() - self.visit_page( "user/login?email=%s&password=%s" % ( email, password ) ) + self.visit_url( "%s/user/login" % self.url ) + tc.fv( '1', 'email', email ) + tc.fv( '1', 'password', password ) + tc.submit( 'Login' ) self.check_page_for_string( "Now logged in as %s" %email ) self.home() def logout( self ): diff -r 58ba6e72d803 -r 29bb8ebb3a59 test/functional/test_user_info.py --- a/test/functional/test_user_info.py Mon Mar 01 16:00:26 2010 -0500 +++ b/test/functional/test_user_info.py Mon Mar 01 16:07:54 2010 -0500 @@ -20,7 +20,6 @@ return fdc.latest_form return None - class TestUserInfo( TwillTestCase ): def test_000_create_user_info_forms( self ): """Testing creating a new user info form and editing it""" @@ -127,7 +126,11 @@ user = sa_session.query( galaxy.model.User ) \ .filter( and_( galaxy.model.User.table.c.email=='test11(a)bx.psu.edu' ) ).first() self.edit_login_info( new_email='test11_new(a)bx.psu.edu', new_username='test11_new' ) - self.change_password('testuser', 'new_testuser') + self.change_password( 'testuser', 'testuser#' ) + self.logout() + self.login( email='test11_new(a)bx.psu.edu', password='testuser#' ) + self.edit_login_info( new_email='test11(a)bx.psu.edu', new_username='test11' ) + self.change_password( 'testuser#', 'testuser' ) self.edit_user_info( ['Research', 'PSU'] ) def test_020_create_user_as_admin( self ): ''' Testing creating users as an admin '''

1 0

[hg] galaxy 3453: update GeneTrack egg
by Greg Von Kuster 03 Mar '10

03 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/58ba6e72d803 changeset: 3453:58ba6e72d803 user: Nate Coraor <nate(a)bx.psu.edu> date: Mon Mar 01 16:00:26 2010 -0500 description: update GeneTrack egg diffstat: eggs.ini | 2 +- 1 files changed, 1 insertions(+), 1 deletions(-) diffs (12 lines): diff -r 0cb68935eede -r 58ba6e72d803 eggs.ini --- a/eggs.ini Mon Mar 01 15:41:30 2010 -0500 +++ b/eggs.ini Mon Mar 01 16:00:26 2010 -0500 @@ -60,7 +60,7 @@ pysqlite = _3.6.17_static MySQL_python = _5.1.41_static bx_python = _dev_3b9d30e47619 -GeneTrack = _dev_bf44f7054c30f19bd9f79106c1fd69849562b361 +GeneTrack = _dev_48da9e998f0caf01c5be731e926f4b0481f658f0 SQLAlchemy = _dev_r6498 pysam = _kanwei_90e03180969d

1 0

[hg] galaxy 3452: Egg support overhaul, introduces a number of f...
by Greg Von Kuster 03 Mar '10

03 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/0cb68935eede changeset: 3452:0cb68935eede user: Nate Coraor <nate(a)bx.psu.edu> date: Mon Mar 01 15:41:30 2010 -0500 description: Egg support overhaul, introduces a number of fixes to the ABI recognition, better build scripts, a rewrite of the eggs library and eliminition of the need for python -ES diffstat: dist-eggs.ini | 79 +- eggs.ini | 63 +- lib/galaxy/__init__.py | 78 +- lib/galaxy/eggs/__init__.py | 769 ++++++++-------------- lib/galaxy/eggs/dist.py | 86 ++ lib/galaxy/eggs/scramble.py | 234 ++++++ manage_db.sh | 2 +- run.sh | 8 +- run_functional_tests.sh | 10 +- run_reports.sh | 3 +- run_unit_tests.sh | 2 +- scripts/check_eggs.py | 10 +- scripts/check_python.py | 13 +- scripts/dist-scramble.py | 22 +- scripts/fetch_eggs.py | 56 +- scripts/get_platforms.py | 6 +- scripts/paster.py | 1 + scripts/scramble.py | 44 +- scripts/scramble/lib/get_platform.py | 18 - scripts/scramble/lib/scramble_lib.py | 164 ++++ scripts/scramble/patches/Cheetah/SetupConfig.py | 103 +++ scripts/scramble/patches/GeneTrack/setup.py | 15 + scripts/scramble/patches/MySQL_python/site.cfg | 18 + scripts/scramble/patches/PasteScript/setup.py | 145 ++++ scripts/scramble/patches/psycopg2/setup.py | 252 +++++++ scripts/scramble/scripts/Cheetah.py | 62 - scripts/scramble/scripts/DRMAA_python-macosx.py | 29 +- scripts/scramble/scripts/DRMAA_python-solaris.py | 44 +- scripts/scramble/scripts/DRMAA_python.py | 30 +- scripts/scramble/scripts/GeneTrack.py | 58 - scripts/scramble/scripts/MySQL_python-solaris.py | 81 ++ scripts/scramble/scripts/MySQL_python.py | 188 +--- scripts/scramble/scripts/PasteScript.py | 53 - scripts/scramble/scripts/generic.py | 28 +- scripts/scramble/scripts/pbs_python.py | 57 +- scripts/scramble/scripts/psycopg2-cygwin.py | 39 - scripts/scramble/scripts/psycopg2.py | 177 +--- scripts/scramble/scripts/pysam-solaris.py | 29 + scripts/scramble/scripts/pysqlite.py | 43 +- scripts/scramble/scripts/python_lzo.py | 129 --- set_metadata.sh | 2 +- setup.sh | 4 +- setup_paths.sh | 46 - 43 files changed, 1817 insertions(+), 1483 deletions(-) diffs (truncated from 3938 to 3000 lines): diff -r a6c9862ece3d -r 0cb68935eede dist-eggs.ini --- a/dist-eggs.ini Mon Mar 01 13:30:37 2010 -0500 +++ b/dist-eggs.ini Mon Mar 01 15:41:30 2010 -0500 @@ -1,9 +1,9 @@ ; ; Config for building eggs for distribution (via a site such as ; eggs.g2.bx.psu.edu) Probably only useful to Galaxy developers at -; Penn State. This file is used by dist-scramble.py +; Penn State. This file is used by scripts/dist-scramble.py ; -; More information: http://g2.trac.bx.psu.edu/wiki/GalaxyEggs +; More information: http://bitbucket.org/galaxy/galaxy-central/wiki/Config/Eggs ; [hosts] @@ -22,16 +22,32 @@ py2.4-macosx-10.3-fat-ucs2 = medeski.bx.psu.edu /usr/local/bin/python2.4 py2.5-macosx-10.3-fat-ucs2 = medeski.bx.psu.edu /usr/local/bin/python2.5 py2.6-macosx-10.3-fat-ucs2 = medeski.bx.psu.edu /usr/local/bin/python2.6 -py2.5-macosx-10.5-i386-ucs2 = lion.bx.psu.edu /usr/bin/python2.5 -py2.4-solaris-2.10-i86pc-ucs2 = thumper.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.10-i86pc-ucs2/bin/python2.4 -py2.5-solaris-2.10-i86pc-ucs2 = thumper.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.10-i86pc-ucs2/bin/python2.5 -py2.6-solaris-2.10-i86pc-ucs2 = thumper.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.10-i86pc-ucs2/bin/python2.6 -py2.4-solaris-2.11-i86pc-ucs2 = victory.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.11-i86pc-ucs2/bin/python2.4 -py2.5-solaris-2.11-i86pc-ucs2 = victory.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.11-i86pc-ucs2/bin/python2.5 -py2.6-solaris-2.11-i86pc-ucs2 = victory.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.11-i86pc-ucs2/bin/python2.6 -py2.4-solaris-2.10-sun4u-ucs2 = v880.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.10-sun4u-ucs2/bin/python2.4 -py2.5-solaris-2.10-sun4u-ucs2 = v880.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.10-sun4u-ucs2/bin/python2.5 -py2.6-solaris-2.10-sun4u-ucs2 = v880.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.10-sun4u-ucs2/bin/python2.6 +py2.6-macosx-10.6-universal-ucs2 = lion.bx.psu.edu /usr/bin/python2.6 +py2.4-solaris-2.10-i86pc_32-ucs2 = thumper.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.10-i86pc_32-ucs2/bin/python2.4 +py2.5-solaris-2.10-i86pc_32-ucs2 = thumper.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.10-i86pc_32-ucs2/bin/python2.5 +py2.6-solaris-2.10-i86pc_32-ucs2 = thumper.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.10-i86pc_32-ucs2/bin/python2.6 +py2.4-solaris-2.10-i86pc_64-ucs2 = thumper.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.10-i86pc_64-ucs2/bin/python2.4 +py2.5-solaris-2.10-i86pc_64-ucs2 = thumper.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.10-i86pc_64-ucs2/bin/python2.5 +py2.6-solaris-2.10-i86pc_64-ucs2 = thumper.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.10-i86pc_64-ucs2/bin/python2.6 +py2.4-solaris-2.8-sun4u_32-ucs2 = troegs.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.8-sun4u_32-ucs2/bin/python2.4 +py2.5-solaris-2.8-sun4u_32-ucs2 = troegs.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.8-sun4u_32-ucs2/bin/python2.5 +py2.6-solaris-2.8-sun4u_32-ucs2 = troegs.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.8-sun4u_32-ucs2/bin/python2.6 +py2.4-solaris-2.8-sun4u_64-ucs2 = troegs.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.8-sun4u_64-ucs2/bin/python2.4 +py2.5-solaris-2.8-sun4u_64-ucs2 = troegs.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.8-sun4u_64-ucs2/bin/python2.5 +py2.6-solaris-2.8-sun4u_64-ucs2 = troegs.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.8-sun4u_64-ucs2/bin/python2.6 + +; pysam doesn't build on solaris < 10, so for it alone we need these hosts +py2.4-solaris-2.10-sun4u_32-ucs2 = early.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.8-sun4u_32-ucs2/bin/python2.4 +py2.5-solaris-2.10-sun4u_32-ucs2 = early.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.8-sun4u_32-ucs2/bin/python2.5 +py2.6-solaris-2.10-sun4u_32-ucs2 = early.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.8-sun4u_32-ucs2/bin/python2.6 +py2.4-solaris-2.10-sun4u_64-ucs2 = early.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.8-sun4u_64-ucs2/bin/python2.4 +py2.5-solaris-2.10-sun4u_64-ucs2 = early.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.8-sun4u_64-ucs2/bin/python2.5 +py2.6-solaris-2.10-sun4u_64-ucs2 = early.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.8-sun4u_64-ucs2/bin/python2.6 + +; these hosts are used to build eggs with no C extensions +py2.4 = straub.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-x86_64-ucs4/bin/python2.4 +py2.5 = straub.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-x86_64-ucs4/bin/python2.5 +py2.6 = straub.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-x86_64-ucs4/bin/python2.6 [groups] py2.4-linux-i686 = py2.4-linux-i686-ucs2 py2.4-linux-i686-ucs4 @@ -47,20 +63,37 @@ linux-x86_64 = py2.4-linux-x86_64 py2.5-linux-x86_64 py2.6-linux-x86_64 linux = linux-i686 linux-x86_64 py2.4-macosx = py2.4-macosx-10.3-fat-ucs2 -py2.5-macosx = py2.5-macosx-10.3-fat-ucs2 py2.5-macosx-10.5-i386-ucs2 -py2.6-macosx = py2.6-macosx-10.3-fat-ucs2 +py2.5-macosx = py2.5-macosx-10.3-fat-ucs2 +py2.6-macosx = py2.6-macosx-10.3-fat-ucs2 py2.6-macosx-10.6-universal-ucs2 macosx = py2.4-macosx py2.5-macosx py2.6-macosx -py2.4-solaris = py2.4-solaris-2.10-i86pc-ucs2 py2.4-solaris-2.11-i86pc-ucs2 py2.4-solaris-2.10-sun4u-ucs2 -py2.5-solaris = py2.5-solaris-2.10-i86pc-ucs2 py2.5-solaris-2.11-i86pc-ucs2 py2.5-solaris-2.10-sun4u-ucs2 -py2.6-solaris = py2.6-solaris-2.10-i86pc-ucs2 py2.6-solaris-2.11-i86pc-ucs2 py2.6-solaris-2.10-sun4u-ucs2 -solaris = py2.4-solaris py2.5-solaris py2.6-solaris +py2.4-solaris-i86pc = py2.4-solaris-2.10-i86pc_32-ucs2 py2.4-solaris-2.10-i86pc_64-ucs2 +py2.5-solaris-i86pc = py2.5-solaris-2.10-i86pc_32-ucs2 py2.5-solaris-2.10-i86pc_64-ucs2 +py2.6-solaris-i86pc = py2.6-solaris-2.10-i86pc_32-ucs2 py2.6-solaris-2.10-i86pc_64-ucs2 +py2.4-solaris-sun4u = py2.4-solaris-2.8-sun4u_32-ucs2 py2.4-solaris-2.8-sun4u_64-ucs2 +py2.5-solaris-sun4u = py2.5-solaris-2.8-sun4u_32-ucs2 py2.5-solaris-2.8-sun4u_64-ucs2 +py2.6-solaris-sun4u = py2.6-solaris-2.8-sun4u_32-ucs2 py2.6-solaris-2.8-sun4u_64-ucs2 +py2.4-solaris = py2.4-solaris-i86pc py2.4-solaris-sun4u +py2.5-solaris = py2.5-solaris-i86pc py2.5-solaris-sun4u +py2.6-solaris = py2.6-solaris-i86pc py2.6-solaris-sun4u +solaris-i86pc = py2.4-solaris-i86pc py2.5-solaris-i86pc py2.6-solaris-i86pc +solaris-sun4u = py2.4-solaris-sun4u py2.5-solaris-sun4u py2.6-solaris-sun4u +solaris = solaris-i86pc solaris-sun4u py2.4-all = py2.4-linux py2.4-macosx py2.4-solaris py2.5-all = py2.5-linux py2.5-macosx py2.5-solaris py2.6-all = py2.6-linux py2.6-macosx py2.6-solaris -all = py2.4-all py2.5-all py2.6-all -; default hosts for platform-inspecific eggs -noplatform = py2.4-linux-i686-ucs4 py2.5-linux-i686-ucs4 py2.6-linux-i686-ucs4 +; group for building pysam on solaris 10 sparc +solaris-2.10-sun4u = py2.4-solaris-2.10-sun4u_32-ucs2 py2.5-solaris-2.10-sun4u_32-ucs2 py2.6-solaris-2.10-sun4u_32-ucs2 py2.4-solaris-2.10-sun4u_64-ucs2 py2.5-solaris-2.10-sun4u_64-ucs2 py2.6-solaris-2.10-sun4u_64-ucs2 + +; the 'all' key is used internally by the build system to specify which hosts +; to build on when no hosts are specified on the dist-eggs.py command line. +all = linux macosx solaris + +; the 'noplatform' key, likewise, is for which build hosts should be used when +; building pure python (noplatform) eggs. +noplatform = py2.4 py2.5 py2.6 + +; don't build these eggs on these platforms: [ignore] -; Don't build these eggs on these platforms: -GeneTrack = py2.4-noplatform +GeneTrack = py2.4 +pysam = py2.4-solaris-2.8-sun4u_32-ucs2 py2.5-solaris-2.8-sun4u_32-ucs2 py2.6-solaris-2.8-sun4u_32-ucs2 py2.4-solaris-2.8-sun4u_64-ucs2 py2.5-solaris-2.8-sun4u_64-ucs2 py2.6-solaris-2.8-sun4u_64-ucs2 diff -r a6c9862ece3d -r 0cb68935eede eggs.ini --- a/eggs.ini Mon Mar 01 13:30:37 2010 -0500 +++ b/eggs.ini Mon Mar 01 15:41:30 2010 -0500 @@ -3,11 +3,11 @@ ; ; This file is version controlled and should not be edited by hand! ; For more information, see: -; http://g2.trac.bx.psu.edu/wiki/GalaxyEggs +; http://bitbucket.org/galaxy/galaxy-central/wiki/Config/Eggs ; [general] -repository = http://eggs.g2.bx.psu.edu +repository = http://eggs.g2.bx.psu.edu/new ; these eggs must be scrambled for your local environment no_auto = pbs_python DRMAA_python @@ -15,13 +15,13 @@ bx_python = 0.5.0 Cheetah = 2.2.2 DRMAA_python = 0.2 -MySQL_python = 1.2.2 +MySQL_python = 1.2.3c1 pbs_python = 2.9.4 psycopg2 = 2.0.6 pycrypto = 2.0.1 pysam = 0.1.1 pysqlite = 2.5.6 -python_lzo = 1.08 +python_lzo = 1.08_2.03_static threadframe = 0.2 guppy = 0.1.8 @@ -33,10 +33,9 @@ elementtree = 1.2.6_20050316 GeneTrack = 2.0.0_beta_1 lrucache = 0.2 -;lsprof - james Mako = 0.2.5 nose = 0.11.1 -NoseHTML = 0.3 +NoseHTML = 0.3.1 Paste = 1.6 PasteDeploy = 1.3.3 PasteScript = 1.7.3 @@ -58,52 +57,16 @@ ; extra version information [tags] psycopg2 = _8.2.6_static -pysqlite = _static -MySQL_python = _5.0.67_static -python_lzo = _static +pysqlite = _3.6.17_static +MySQL_python = _5.1.41_static bx_python = _dev_3b9d30e47619 GeneTrack = _dev_bf44f7054c30f19bd9f79106c1fd69849562b361 SQLAlchemy = _dev_r6498 -; nose = .dev_r7156749efc58 +pysam = _kanwei_90e03180969d -; source location, necessary for scrambling +; dependency source urls, necessary for scrambling. for an explanation, see +; the wiki page above [source] -bx_python = http://bitbucket.org/james_taylor/bx-python/get/3b9d30e47619.bz2 -Cheetah = http://pypi.python.org/packages/source/C/Cheetah/Cheetah-2.2.2.tar.gz -DRMAA_python = http://gridengine.sunsource.net/files/documents/7/36/DRMAA-python-0.2.tar.gz -MySQL_python = http://downloads.sourceforge.net/project/mysql-python/mysql-python/1.2.2/My… http://downloads.mysql.com/archives/mysql-5.0/mysql-5.0.67.tar.gz -pbs_python = http://ftp.sara.nl/pub/outgoing/pbs_python-2.9.4.tar.gz -pexpect = http://pypi.python.org/packages/source/p/pexpect/pexpect-2.4.tar.gz -psycopg2 = http://initd.org/pub/software/psycopg/PSYCOPG-2-0/psycopg2-2.0.6.tar.gz ftp://ftp-archives.postgresql.org/pub/source/v8.2.6/postgresql-8.2.6.tar.bz2 -pycrypto = http://www.amk.ca/files/python/crypto/pycrypto-2.0.1.tar.gz -pysam = http://bitbucket.org/kanwei/kanwei-pysam/get/e3c601a062fd.gz -pysqlite = http://pypi.python.org/packages/source/p/pysqlite/pysqlite-2.5.6.tar.gz -python_lzo = http://www.oberhumer.com/opensource/lzo/download/LZO-v1/python-lzo-1.08.tar… http://www.oberhumer.com/opensource/lzo/download/LZO-v1/lzo-1.08.tar.gz -threadframe = http://www.majid.info/python/threadframe/threadframe-0.2.tar.gz -guppy = http://pypi.python.org/packages/source/g/guppy/guppy-0.1.8.tar.gz -amqplib = http://py-amqplib.googlecode.com/files/amqplib-0.6.1.tgz -Beaker = http://cheeseshop.python.org/packages/source/B/Beaker/Beaker-1.4.tar.gz -decorator = http://pypi.python.org/packages/source/d/decorator/decorator-3.1.2.tar.gz -docutils = http://downloads.sourceforge.net/docutils/docutils-0.4.tar.gz -elementtree = http://effbot.org/downloads/elementtree-1.2.6-20050316.tar.gz -GeneTrack = http://github.com/ialbert/genetrack-central/tarball/bf44f7054c30f19bd9f7910… -lrucache = http://evan.prodromou.name/lrucache/lrucache-0.2.tar.gz -Mako = http://www.makotemplates.org/downloads/Mako-0.2.5.tar.gz -nose = http://pypi.python.org/packages/source/n/nose/nose-0.11.1.tar.gz -NoseHTML = http://bitbucket.org/james_taylor/nosehtml/get/c46a54d569ae.bz2 -Paste = http://cheeseshop.python.org/packages/source/P/Paste/Paste-1.6.tar.gz -PasteDeploy = http://cheeseshop.python.org/packages/source/P/PasteDeploy/PasteDeploy-1.3.… -PasteScript = http://cheeseshop.python.org/packages/source/P/PasteScript/PasteScript-1.7.… -Routes = http://pypi.python.org/packages/source/R/Routes/Routes-1.11.tar.gz -simplejson = http://cheeseshop.python.org/packages/source/s/simplejson/simplejson-1.5.ta… -SQLAlchemy = http://dist.g2.bx.psu.edu/SQLAlchemy-0.5.6_r6498.tar.bz2 -sqlalchemy_migrate = http://pypi.python.org/packages/source/s/sqlalchemy-migrate/sqlalchemy-migr… -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 -WebHelpers = http://pypi.python.org/packages/source/W/WebHelpers/WebHelpers-0.2.tar.gz -WebOb = http://pypi.python.org/packages/source/W/WebOb/WebOb-0.8.5.tar.gz -wsgiref = http://pypi.python.org/packages/source/w/wsgiref/wsgiref-0.1.2.zip -Babel = http://ftp.edgewall.com/pub/babel/Babel-0.9.4.zip -wchartype = http://ginstrom.com/code/wchartype-0.1.zip -boto = http://boto.googlecode.com/files/boto-1.8d.tar.gz +MySQL_python = mysql-5.1.41 +psycopg2 = postgresql-8.2.6 +pysqlite = sqlite-amalgamation-3_6_17 diff -r a6c9862ece3d -r 0cb68935eede lib/galaxy/__init__.py --- a/lib/galaxy/__init__.py Mon Mar 01 13:30:37 2010 -0500 +++ b/lib/galaxy/__init__.py Mon Mar 01 15:41:30 2010 -0500 @@ -2,30 +2,62 @@ Galaxy root package -- this is a namespace package. """ -# Starting somewhere in 2.5.x, Python on Mac became broken - despite being fat, -# the machine portion of the platform is not set to 'fat'. -# -# For more, see: -# -# http://bugs.python.org/setuptools/issue19 -# -import os, sys -from distutils.sysconfig import get_config_vars +__import__( "pkg_resources" ).declare_namespace( __name__ ) -if sys.version_info[:2] == ( 2, 5 ) and \ +import os, sys, re +from distutils.sysconfig import get_config_var, get_config_vars + +import pkg_resources + +# patch get_platform() for better ABI recognition +def _get_build_platform(): + plat = pkg_resources._get_build_platform() + if sys.version_info[:2] == ( 2, 5 ) and \ ( ( os.uname()[-1] in ( 'i386', 'ppc' ) and sys.platform == 'darwin' and os.path.abspath( sys.prefix ).startswith( '/System' ) ) or \ ( sys.platform == 'darwin' and get_config_vars().get('UNIVERSALSDK', '').strip() ) ): - # Has to be before anything imports pkg_resources - def _get_platform_monkeypatch(): - plat = distutils.util._get_platform() - if plat.startswith( 'macosx-' ): - plat = 'macosx-10.3-fat' - return plat - import distutils.util - try: - assert distutils.util._get_platform - except: - distutils.util._get_platform = distutils.util.get_platform - distutils.util.get_platform = _get_platform_monkeypatch + plat = 'macosx-10.3-fat' + if sys.platform == "sunos5" and not (plat.endswith('_32') or plat.endswith('_64')): + if sys.maxint > 2**31: + plat += '_64' + else: + plat += '_32' + if not (plat.endswith('-ucs2') or plat.endswith('-ucs4')): + if sys.maxunicode > 2**16: + plat += '-ucs4' + else: + plat += '-ucs2' + return plat +try: + assert pkg_resources._get_build_platform +except: + pkg_resources._get_build_platform = pkg_resources.get_build_platform + pkg_resources.get_build_platform = _get_build_platform + pkg_resources.get_platform = _get_build_platform -__import__( "pkg_resources" ).declare_namespace( __name__ ) +# patch compatible_platforms() to allow for Solaris binary compatibility +solarisVersionString = re.compile(r"solaris-(\d)\.(\d+)-(.*)") +def _compatible_platforms(provided,required): + # this is a bit kludgey since we need to know a bit about what happened in + # the original method + if provided is None or required is None or provided==required: + return True # easy case + reqMac = pkg_resources.macosVersionString.match(required) + if reqMac: + return pkg_resources._compatible_platforms(provided,required) + reqSol = solarisVersionString.match(required) + if reqSol: + provSol = solarisVersionString.match(provided) + if not provSol: + return False + if provSol.group(1) != reqSol.group(1) or \ + provSol.group(3) != reqSol.group(3): + return False + if int(provSol.group(2)) > int(reqSol.group(2)): + return False + return True + return False +try: + assert pkg_resources._compatible_platforms +except: + pkg_resources._compatible_platforms = pkg_resources.compatible_platforms + pkg_resources.compatible_platforms = _compatible_platforms diff -r a6c9862ece3d -r 0cb68935eede lib/galaxy/eggs/__init__.py --- a/lib/galaxy/eggs/__init__.py Mon Mar 01 13:30:37 2010 -0500 +++ b/lib/galaxy/eggs/__init__.py Mon Mar 01 15:41:30 2010 -0500 @@ -2,17 +2,15 @@ Manage Galaxy eggs """ -import os, sys, shutil, tarfile, zipfile, zipimport, subprocess, ConfigParser, glob, urllib2, shutil -from types import ModuleType +import os, sys, glob, urllib, urllib2, ConfigParser, HTMLParser, zipimport, zipfile import logging log = logging.getLogger( __name__ ) import pkg_resources -# we MUST have the top level galaxy dir for automatic egg fetching -# within tools. i don't know of any way around this. -ndc -galaxy_dir = os.path.abspath( os.path.join( os.path.dirname( __file__ ), "..", "..", ".." ) ) +galaxy_dir = os.path.abspath( os.path.join( os.path.dirname( __file__ ), '..', '..', '..' ) ) +py = 'py%s' % sys.version[:3] class EggNotFetchable( Exception ): def __init__( self, eggs ): @@ -23,452 +21,287 @@ def __str__( self ): return ' '.join( self.eggs ) -class PlatformNotSupported( Exception ): - pass - -# TODO: we should really be using exceptions instead of returns for everything - # need the options to remain case sensitive -class CSConfigParser( ConfigParser.SafeConfigParser ): +class CaseSensitiveConfigParser( ConfigParser.SafeConfigParser ): def optionxform( self, optionstr ): return optionstr +# so we can actually detect failures +class URLRetriever( urllib.FancyURLopener ): + def http_error_default( *args ): + urllib.URLopener.http_error_default( *args ) + class Egg( object ): """ - Contains information about locating, downloading and scrambling eggs. + Contains information about locating and downloading eggs. """ - archive_dir = os.path.join( galaxy_dir, "scripts", "scramble", "archives" ) - script_dir = os.path.join( galaxy_dir, "scripts", "scramble", "scripts" ) - build_dir = os.path.join( galaxy_dir, "scripts", "scramble", "build" ) - ez_setup = os.path.join( galaxy_dir, "scripts", "scramble", "lib", "ez_setup.py" ) - ez_setup_url = "http://peak.telecommunity.com/dist/ez_setup.py" - def __init__( self ): - self.name = None - self.version = None - self.tag = None - self.sources = [] - self.platform = {} - self.url = None - self.have = False - self.path = None - self.doppelgangers = [] - self.buildpath = None + def __init__( self, name=None, version=None, tag=None, url=None, platform=None ): + self.name = name + self.version = version + self.tag = tag + self.url = url + self.platform = platform + self.distribution = None self.dir = None - self.build_host = None - self.python = sys.executable + if self.name is not None and self.version is not None: + self.set_distribution() def set_dir( self ): - if self.build_host is not None: - self.dir = os.path.join( galaxy_dir, "dist-eggs", self.platform['galaxy'] ) - else: - self.dir = os.path.join( galaxy_dir, "eggs", self.platform['galaxy'] ) - def get_namever( self ): - return( "%s-%s" %( self.name, self.version ) ) - def get_namevertag( self ): - if self.tag is None: - return( "%s-%s" %( self.name, self.version ) ) - else: - return( "%s-%s%s" %( self.name, self.version, self.tag ) ) - def get_vertag( self ): - if self.tag is None: - return self.version - else: - return( "%s%s" %( self.version, self.tag ) ) - def get_filename( self ): - if self.tag is None: - return( "%s-%s-%s.egg" %( self.name, self.version, self.platform['peak'] ) ) - else: - return( "%s-%s%s-%s.egg" %( self.name, self.version, self.tag, self.platform['peak'] ) ) - def find( self ): - # TODO: should be able to set a search path in eggs.ini + self.dir = os.path.join( galaxy_dir, 'eggs' ) + if not os.path.exists( self.dir ): + os.makedirs( self.dir ) + def set_distribution( self ): + """ + Stores a pkg_resources Distribution object for reference later + """ if self.dir is None: self.set_dir() - self.path = os.path.join( self.dir, self.get_filename() ) - self.doppelgangers = glob.glob( os.path.join( self.dir, "%s-*-%s.egg" % (self.name, self.platform['peak'] ) ) ) - if os.access( self.path, os.F_OK ): - self.have = True - self.doppelgangers.remove( self.path ) - def fetch( self ): - if self.path is None: - self.find() - if not self.have: - if not os.access( os.path.dirname( self.path ), os.F_OK ): - os.makedirs( os.path.dirname( self.path ) ) + tag = self.tag or '' + self.distribution = pkg_resources.Distribution.from_filename( + os.path.join( self.dir, '-'.join( ( self.name, self.version + tag, self.platform ) ) + '.egg' ) ) + @property + def path( self ): + """ + Return the path of the egg, if it exists, or None + """ + if env[self.distribution.project_name]: + return env[self.distribution.project_name][0].location + return None + def fetch( self, requirement ): + """ + fetch() serves as the install method to pkg_resources.working_set.resolve() + """ + def find_alternative(): + """ + Some platforms (e.g. Solaris) support eggs compiled on older platforms + """ + class LinkParser( HTMLParser.HTMLParser ): + """ + Finds links in what should be an Apache-style directory index + """ + def __init__( self ): + HTMLParser.HTMLParser.__init__( self ) + self.links = [] + def handle_starttag( self, tag, attrs ): + if tag == 'a' and 'href' in dict( attrs ): + self.links.append( dict( attrs )['href'] ) + parser = LinkParser() try: - inf = urllib2.urlopen( self.url ) - otf = open( self.path, 'wb' ) - otf.write( inf.read() ) - inf.close() - otf.close() - log.debug( "Fetched %s" % self.url ) + parser.feed( urllib2.urlopen( self.url + '/' ).read() ) except urllib2.HTTPError, e: - raise EggNotFetchable( self.name ) - #if e.code == 404: - # return False - self.unpack_if_needed() - for doppelganger in self.doppelgangers: - remove_file_or_path( doppelganger ) - log.debug( "Removed conflicting egg: %s" % doppelganger ) - return True + if e.code == 404: + return None + parser.close() + for link in parser.links: + file = urllib.unquote( link ).rsplit( '/', 1 )[-1] + tmp_dist = pkg_resources.Distribution.from_filename( file ) + if tmp_dist.platform is not None and \ + self.distribution.project_name == tmp_dist.project_name and \ + self.distribution.version == tmp_dist.version and \ + pkg_resources.compatible_platforms( tmp_dist.platform, pkg_resources.get_platform() ): + return file + return None + if self.url is None: + return None + alternative = None + try: + url = self.url + '/' + self.distribution.egg_name() + '.egg' + URLRetriever().retrieve( url, self.distribution.location ) + log.debug( "Fetched %s" % url ) + except IOError, e: + if e[1] == 404 and self.distribution.platform != py: + alternative = find_alternative() + if alternative is None: + return None + else: + return None + if alternative is not None: + try: + url = '/'.join( ( self.url, alternative ) ) + URLRetriever().retrieve( url, os.path.join( self.dir, alternative ) ) + log.debug( "Fetched %s" % url ) + except IOError, e: + return None + self.platform = alternative.split( '-', 2 )[-1].rsplit( '.egg', 1 )[0] + self.set_distribution() + self.unpack_if_needed() + self.remove_doppelgangers() + global env + env = get_env() # reset the global Environment object now that we've obtained a new egg + return self.distribution def unpack_if_needed( self ): - meta = pkg_resources.EggMetadata( zipimport.zipimporter( self.path ) ) + meta = pkg_resources.EggMetadata( zipimport.zipimporter( self.distribution.location ) ) if meta.has_metadata( 'not-zip-safe' ): - unpack_zipfile( self.path, self.path + "-tmp" ) - os.remove( self.path ) - os.rename( self.path + "-tmp", self.path ) - def scramble( self, dist=False ): - if self.path is None: - self.find() - if os.access( self.path, os.F_OK ): - log.warning( "scramble(): Egg already exists, remove to force rebuild:" ) - log.warning( " %s" % self.path ) - return True - self.fetch_source() - self.unpack_source() - self.copy_build_script() - if not os.access( Egg.ez_setup, os.F_OK ): - if not os.access( os.path.dirname( Egg.ez_setup ), os.F_OK ): - os.makedirs( os.path.dirname( Egg.ez_setup ) ) - inf = urllib2.urlopen( Egg.ez_setup_url ) - otf = open( Egg.ez_setup, 'wb' ) - otf.write( inf.read() ) - inf.close() - otf.close() - shutil.copyfile( Egg.ez_setup, os.path.join( self.buildpath, "ez_setup.py" ) ) - log.warning( "scramble(): Beginning build" ) - # subprocessed to sterilize the env - if self.build_host is not None: - cmd = "ssh %s 'cd %s; %s -ES %s'" % ( self.build_host, self.buildpath, self.python, "scramble.py" ) - else: - cmd = "%s -ES %s" % ( self.python, "scramble.py" ) - log.debug( 'Executing: %s' % cmd ) - p = subprocess.Popen( args = cmd, shell = True, cwd = self.buildpath ) - r = p.wait() - if r != 0: - log.error( "scramble(): Egg build failed for %s" % self.get_namevertag() ) - return False - new_egg = os.path.join( self.buildpath, "dist", os.path.basename( self.path ) ) - if not os.access( os.path.dirname( self.path ), os.F_OK ): - os.makedirs( os.path.dirname( self.path ) ) - shutil.copyfile( new_egg, self.path ) - log.warning( "scramble(): Copied egg to:" ) - log.warning( " %s" % self.path ) - if not dist: - self.unpack_if_needed() - for doppelganger in self.doppelgangers: + unpack_zipfile( self.distribution.location, self.distribution.location + "-tmp" ) + os.remove( self.distribution.location ) + os.rename( self.distribution.location + "-tmp", self.distribution.location ) + def remove_doppelgangers( self ): + doppelgangers = glob.glob( os.path.join( self.dir, "%s-*-%s.egg" % ( self.name, self.platform ) ) ) + if self.distribution.location in doppelgangers: + doppelgangers.remove( self.distribution.location ) + for doppelganger in doppelgangers: remove_file_or_path( doppelganger ) - log.warning( "Removed conflicting egg: %s" % doppelganger ) - return True - # scramble helper methods - def get_archive_path( self, url ): - return os.path.join( Egg.archive_dir, (url.rsplit( '/', 1 ))[1] ) - def get_tld( self, names ): - tld = names[0].split( os.path.sep, 1 )[0] - for name in names: - try: - assert tld == name.split( os.path.sep, 1 )[0] - except: - raise Exception( "get_tld(): Archive contains multiple top-level directories!" ) - return tld - def fetch_source( self ): - if not os.access( Egg.archive_dir, os.F_OK ): - os.makedirs( Egg.archive_dir ) - for source_url in self.sources: - source_path = self.get_archive_path( source_url ) - if os.access( source_path, os.F_OK ): - log.warning( "fetch_source(): Using existing source, remove to download again:" ) - log.warning( " %s" % source_path ) - continue - log.warning( "fetch_source(): Attempting to download" ) - log.warning( " %s" % source_url ) - inf = urllib2.urlopen( source_url ) - otf = open( source_path, 'wb' ) - otf.write( inf.read() ) - inf.close() - otf.close() - log.warning( "fetch_source(): Fetched %s" % source_url ) - def unpack_source( self ): - unpack_dir = os.path.join( Egg.build_dir, self.platform['galaxy'] ) - if not os.access( unpack_dir, os.F_OK ): - os.makedirs( unpack_dir ) - self.buildpath = os.path.join( unpack_dir, self.name ) - if os.access( self.buildpath, os.F_OK ): - log.warning( "Removing old build directory at:" ) - log.warning( " %s" % self.buildpath ) - shutil.rmtree( self.buildpath ) - source_path = self.get_archive_path( self.sources[0] ) - if tarfile.is_tarfile( source_path ): - self.unpack = self.unpack_tar - elif zipfile.is_zipfile( source_path ): - self.unpack = self.unpack_zip - else: - raise Exception( "unpack_source(): Unknown archive file type for %s" % source_path ) - self.unpack( source_path, unpack_dir ) - log.warning( "unpack_source(): Unpacked to:" ) - log.warning( " %s" % self.buildpath ) - def unpack_zip( self, source_path, unpack_path ): - z = zipfile.ZipFile( source_path, "r" ) - tld = self.get_tld( z.namelist() ) - cur = os.getcwd() - os.chdir( unpack_path ) - for fn in z.namelist(): - if "ez_setup" in fn: - continue - if not os.access( os.path.dirname( fn ), os.F_OK ): - os.makedirs( os.path.dirname( fn ) ) - otf = open( fn, "wb" ) - otf.write( z.read( fn ) ) - otf.close() - z.close() - os.rename( tld, self.name ) - os.chdir( cur ) - def unpack_tar( self, source_path, unpack_path ): - t = tarfile.open( source_path, "r" ) - members = filter( lambda x: "ez_setup" not in x.name and "pax_global_header" != x.name, t.getmembers() ) - tld = self.get_tld( [ x.name for x in members ] ) - cur = os.getcwd() - os.chdir( unpack_path ) - for member in members: - t.extract( member ) - t.close() - os.rename( tld, self.name ) - os.chdir( cur ) - def copy_build_script( self ): - peak_platform = get_platform( platform=True, peak=True ) - nopy_platform = ( peak_platform.split( "-", 1 ) )[1] - just_os = ( nopy_platform.split( "-", 1 ) )[0] - just_py = ( peak_platform.split( "-", 1 ) )[0] - # will try: - # bx_python-py2.4-solaris-2.11-i86pc.py - # bx_python-py2.4-solaris.py - # bx_python-solaris-2.11-i86pc.py - # bx_python-solaris.py - # bx_python-py2.4.py - # bx_python.py - # generic.py - build_scripts = [ - os.path.join( Egg.script_dir, "%s-%s.py" % ( self.name, peak_platform ) ), - os.path.join( Egg.script_dir, "%s-%s-%s.py" % ( self.name, just_py, just_os ) ), - os.path.join( Egg.script_dir, "%s-%s.py" % ( self.name, nopy_platform ) ), - os.path.join( Egg.script_dir, "%s-%s.py" % ( self.name, just_os ) ), - os.path.join( Egg.script_dir, "%s-%s.py" % ( self.name, just_py ) ), - os.path.join( Egg.script_dir, "%s.py" % self.name ), - os.path.join( Egg.script_dir, "generic.py" ) - ] - for build_script in build_scripts: - try: - f = open( build_script, "r" ) - f.close() - log.warning( "scramble(): Using build script %s" % build_script ) - break - except IOError: - pass - shutil.copyfile( build_script, os.path.join( self.buildpath, "scramble.py" ) ) - if self.tag is not None: - tagfile = open( os.path.join( self.buildpath, ".galaxy_tag" ), "w" ) - print >>tagfile, self.tag - tagfile.close() + log.debug( "Removed conflicting egg: %s" % doppelganger ) + def resolve( self ): + try: + return pkg_resources.working_set.resolve( ( self.distribution.as_requirement(), ), env, self.fetch ) + except pkg_resources.DistributionNotFound, e: + # If this statement is true, it means we do have the requested egg, + # just not one (or more) of its deps. + if e.args[0].project_name != self.distribution.project_name: + log.warning( "Warning: %s (a dependant egg of %s) cannot be fetched" % ( e.args[0].project_name, self.distribution.project_name ) ) + return ( self.distribution, ) + else: + raise EggNotFetchable( self ) + except pkg_resources.VersionConflict, e: + # there's a conflicting egg on the path, remove it + dist = e.args[0] + # use the canonical path for comparisons + location = os.path.realpath( dist.location ) + for entry in pkg_resources.working_set.entries: + if os.path.realpath( entry ) == location: + pkg_resources.working_set.entries.remove( entry ) + break + else: + location = entry = None + del pkg_resources.working_set.by_key[dist.key] + if entry is not None: + pkg_resources.working_set.entry_keys[entry] = [] + if entry in sys.path: + sys.path.remove(entry) + r = pkg_resources.working_set.resolve( ( self.distribution.as_requirement(), ), env, self.fetch ) + if location is not None and not location.endswith( '.egg' ): + # re-add the path if it's a non-egg dir, in case more deps live there + pkg_resources.working_set.entries.append( location ) + sys.path.append( location ) + return r + def require( self ): + try: + dists = self.resolve() + for dist in dists: + pkg_resources.working_set.add( dist ) + return dists + except: + raise class Crate( object ): """ - Reads the eggs.ini file for use with checking, fetching and scrambling eggs. + Reads the eggs.ini file for use with checking and fetching. """ - config_file = os.path.join( galaxy_dir, "eggs.ini" ) + config_file = os.path.join( galaxy_dir, 'eggs.ini' ) def __init__( self ): self.eggs = {} - self.config = CSConfigParser() + self.config = CaseSensitiveConfigParser() self.repo = None self.no_auto = [] - self.platform = { 'peak' : get_platform( platform=True, peak=True ), 'galaxy' : get_platform( platform=True, peak=False ) } - self.noplatform = { 'peak' : get_platform( platform=False, peak=True ), 'galaxy' : get_platform( platform=False, peak=False ) } + self.galaxy_config = GalaxyConfig() + self.parse() def parse( self ): - if self.config.read( Crate.config_file ) == []: - raise Exception( "unable to read egg config from %s" % Crate.config_file ) - try: - self.repo = self.config.get( "general", "repository" ) - self.no_auto = self.config.get( "general", "no_auto" ).split() - except ConfigParser.NoSectionError: - raise Exception( "eggs.ini is missing required section [general]" ) - #except ConfigParser.NoOptionError: - # raise Exception( "eggs.ini is missing required [general] option 'repository'" ) - try: - platform_eggs = self.config.items( "eggs:platform" ) - noplatform_eggs = self.config.items( "eggs:noplatform" ) - except ConfigParser.NoSectionError, e: - raise Exception( "eggs.ini is missing required section: %s" % e ) - self.parse_egg_section( platform_eggs, self.platform ) - self.parse_egg_section( noplatform_eggs, self.noplatform ) - def parse_egg_section( self, eggs, platform ): + self.config.read( Crate.config_file ) + self.repo = self.config.get( 'general', 'repository' ) + self.no_auto = self.config.get( 'general', 'no_auto' ).split() + self.parse_egg_section( self.config.items( 'eggs:platform' ), self.config.items( 'tags' ), True ) + self.parse_egg_section( self.config.items( 'eggs:noplatform' ), self.config.items( 'tags' ) ) + def parse_egg_section( self, eggs, tags, full_platform=False, egg_class=Egg ): for name, version in eggs: - egg = Egg() + tag = dict( tags ).get( name, '' ) + url = '/'.join( ( self.repo, name ) ) + if full_platform: + platform = '-'.join( ( py, pkg_resources.get_platform() ) ) + else: + platform = py + egg = egg_class( name, version, tag, url, platform ) + self.eggs[name] = egg + @property + def config_missing( self ): + """ + Return true if any eggs are missing, conditional on options set in the + Galaxy config file. + """ + for egg in self.config_eggs: + if not egg.path: + return True + return False + @property + def all_missing( self ): + """ + Return true if any eggs in the eggs config file are missing. + """ + for egg in self.all_eggs: + if not os.path.exists( egg.distribution.location ): + return True + return False + @property + def config_names( self ): + """ + Return a list of names of all eggs in the crate that are needed based + on the options set in the Galaxy config file. + """ + return [ egg.name for egg in self.config_eggs ] + @property + def all_names( self ): + """ + Return a list of names of all eggs in the crate. + """ + return [ egg.name for egg in self.all_eggs ] + @property + def config_eggs( self ): + """ + Return a list of all eggs in the crate that are needed based on the + options set in the Galaxy config file. + """ + return [ egg for egg in self.eggs.values() if self.galaxy_config.check_conditional( egg.name ) ] + @property + def all_eggs( self ): + """ + Return a list of all eggs in the crate. + """ + rval = [] + for egg in self.eggs.values(): + if egg.name not in self.galaxy_config.always_conditional: + rval.append( egg ) + elif self.galaxy_config.check_conditional( egg.name ): + rval.append( egg ) + return rval + def __getitem__( self, name ): + """ + Return a specific egg. + """ + name = name.replace( '-', '_' ) + return self.eggs[name] + def resolve( self, all=False ): + """ + Try to resolve (e.g. fetch) all eggs in the crate. + """ + if all: + eggs = self.all_eggs + else: + eggs = self.config_eggs + eggs = filter( lambda x: x.name not in self.no_auto, eggs ) + missing = [] + for egg in eggs: try: - egg.tag = self.config.get( "tags", name ) + egg.resolve() except: - egg.tag = None - try: - egg.sources = self.config.get( "source", name ).split() - except: - egg.sources = None - egg.name = name - egg.version = version - egg.platform['galaxy'] = platform['galaxy'] - egg.platform['peak'] = platform['peak'] - egg.url = "%s/%s/%s" %( self.repo, platform['galaxy'], egg.get_filename() ) - self.eggs[name] = egg - def find( self, ignore=None ): - missing = [] - for egg in self.eggs.itervalues(): - if ignore is not None: - if egg.name in ignore: - continue - egg.find() - if not egg.have: - missing.append( egg.name ) - if len( missing ): - return False - return True - def fetch( self, ignore=[] ): - """ - Fetch all eggs in the crate (ignoring any that you want to - ignore). If your platform isn't available, it'll attempt to - download all the noplatform eggs before failing. - """ - skip_platform = False - ignore.extend( self.no_auto ) - missing = [] - try: - f = urllib2.urlopen( "%s/%s" % ( self.repo, self.platform['galaxy'] ) ) - f.close() - except urllib2.HTTPError, e: - if e.code == 404: - skip_platform = True - for egg in self.eggs.itervalues(): - if ignore is not None: - if egg.name in ignore: - continue - if skip_platform and egg.platform['galaxy'] == self.platform['galaxy']: - missing.append( egg.name ) - continue - try: - egg.fetch() - except EggNotFetchable: - missing.append( egg.name ) - if skip_platform: - raise PlatformNotSupported( self.platform['galaxy'] ) + missing.append( egg ) if missing: raise EggNotFetchable( missing ) - return True - def scramble( self, ignore=None ): - # Crate-scrambling the no_auto eggs makes no sense - ignore.extend( self.no_auto ) - for egg in self.eggs.itervalues(): - if ignore is not None: - if egg.name in ignore: - continue - if not egg.scramble(): - return False - return True - def get_names( self ): - return self.eggs.keys() - def get( self, name ): - if self.eggs.has_key( name ): - return self.eggs[name] - else: - return None - def get_for_require( self, name ): - """ - return an egg based on a lowercase name comparo and with _ instead of -. used by require. - """ - for key in self.eggs.keys(): - if key.lower() == name.lower().replace( '-', '_' ): - return self.eggs[key] -class DistCrate( Crate ): - """ - A subclass of Crate that holds eggs with info on how to build them for distribution. - """ - dist_config_file = os.path.join( galaxy_dir, "dist-eggs.ini" ) - def __init__( self, build_on="all" ): - self.eggs = {} - self.config = CSConfigParser() - self.repo = None - self.build_on = build_on - self.platform = 'platform' - self.noplatform = 'noplatform' - def parse( self ): - if self.config.read( DistCrate.dist_config_file ) == []: - raise Exception( "unable to read dist egg config from %s" % DistCrate.dist_config_file ) - try: - self.hosts = dict( self.config.items( "hosts" ) ) - self.groups = dict( self.config.items( "groups" ) ) - self.ignore = dict( self.config.items( "ignore" ) ) - except ConfigParser.NoSectionError, e: - raise Exception( "eggs.ini is missing required section: %s" % e ) - self.platforms = self.get_platforms( self.build_on ) - self.noplatforms = self.get_platforms( 'noplatform' ) - Crate.parse( self ) - def get_platforms( self, wanted ): - # find all the members of a group and process them - if self.groups.has_key( wanted ): - platforms = [] - for name in self.groups[wanted].split(): - for platform in self.get_platforms( name ): - if platform not in platforms: - platforms.append( platform ) - return platforms - elif self.hosts.has_key( wanted ): - return [ wanted ] - else: - raise Exception( "unknown platform: %s" % wanted ) - def parse_egg_section( self, eggs, type ): - """ - Overrides the base class's method. Here we use the third arg - to find out what type of egg we'll be building. - """ - if type == "platform": - platforms = self.platforms - elif type == "noplatform": - platforms = self.noplatforms - for name, version in eggs: - for platform in platforms: - # can't use the regular methods here because we're not - # actually ON the target platform - if type == "platform": - gplat = platform - pplat = platform.rsplit('-', 1)[0] - elif type == "noplatform": - gplat = "%s-noplatform" % platform.split('-', 1)[0] - pplat = platform.split('-', 1)[0] - if name in self.ignore and gplat in self.ignore[name].split(): - continue - egg = Egg() - try: - egg.tag = self.config.get( "tags", name ) - except: - egg.tag = None - try: - egg.sources = self.config.get( "source", name ).split() - except: - egg.sources = None - egg.name = name - egg.version = version - egg.platform['galaxy'] = gplat - egg.platform['peak'] = pplat - egg.url = "%s/%s/%s" %( self.repo, gplat, egg.get_filename() ) - egg.build_host, egg.python = self.hosts[platform].split() - if not self.eggs.has_key( name ): - self.eggs[name] = [ egg ] - else: - self.eggs[name].append( egg ) - -class GalaxyConfig: +class GalaxyConfig( object ): config_file = os.path.join( galaxy_dir, "universe_wsgi.ini" ) - always_conditional = ( 'GeneTrack', ) + always_conditional = ( 'GeneTrack', 'pysam' ) def __init__( self ): self.config = ConfigParser.ConfigParser() if self.config.read( GalaxyConfig.config_file ) == []: raise Exception( "error: unable to read Galaxy config from %s" % GalaxyConfig.config_file ) - # TODO: conditionals should really be handled better than this def check_conditional( self, egg_name ): + def check_pysam(): + # can't build pysam on solaris < 10 + plat = pkg_resources.get_platform().split( '-' ) + if plat[0] == 'solaris': + minor = plat[1].split('.')[1] + if int( minor ) < 10: + return False + return True if egg_name == "pysqlite": # SQLite is different since it can be specified in two config vars and defaults to True try: @@ -484,102 +317,45 @@ "threadframe": lambda: self.config.get( "app:main", "use_heartbeat" ), "guppy": lambda: self.config.get( "app:main", "use_memdump" ), "GeneTrack": lambda: sys.version_info[:2] >= ( 2, 5 ), + "pysam": check_pysam() }.get( egg_name, lambda: True )() except: return False -def require( pkg ): - # add the egg dirs to sys.path if they're not already there - for platform in [ get_platform(), get_platform( platform=True ) ]: - path = os.path.join( galaxy_dir, "eggs", platform ) - if path not in sys.path: - new_path = [ path ] - new_path.extend( sys.path ) - sys.path = new_path - pkg_resources.working_set.add_entry(path) - name = pkg_resources.Requirement.parse( pkg ).project_name +def get_env(): + env = pkg_resources.Environment( platform=pkg_resources.get_platform() ) + for dist in pkg_resources.find_distributions( os.path.join( galaxy_dir, 'eggs' ), False ): + env.add( dist ) + return env +env = get_env() + +def require( req_str ): c = Crate() - c.parse() - egg = c.get_for_require( name ) + req = pkg_resources.Requirement.parse( req_str ) try: - if egg is None: - return pkg_resources.working_set.require( pkg ) - else: - return pkg_resources.working_set.require( "%s==%s" % ( name, egg.get_vertag() ) ) - except pkg_resources.VersionConflict, e: - # there's a conflicting egg on the pythonpath, remove it - dist = e.args[0] - working_set = pkg_resources.working_set - # use the canonical path for comparisons - location = os.path.realpath( dist.location ) - for entry in working_set.entries: - if os.path.realpath( entry ) == location: - working_set.entries.remove( entry ) - break - else: - location = None - del working_set.by_key[dist.key] - working_set.entry_keys[entry] = [] - try: - sys.path.remove(entry) - except ValueError: - raise Exception( "Cannot remove entry: %s" % str(entry) ) - r = require( pkg ) - if location is not None and not location.endswith( '.egg' ): - # re-add the path if it's a non-egg dir, in case more deps live there - working_set.entries.append( location ) # re-add to the set if it's a dir. - sys.path.append( location ) # re-add to the set if it's a dir. - return r - except pkg_resources.DistributionNotFound, e: - # the initial require itself is the first dep, but it can have - # multiple deps, which will be fetched by the require below. - dep = pkg_resources.Requirement.parse( str( e ) ).project_name - egg = c.get_for_require( dep ) - if egg is None: - # we don't have it and we can't get it - raise - egg.find() - if not egg.have: - if not egg.fetch(): - raise EggNotFetchable( egg.name ) - return require( pkg ) + return c[req.project_name].require() + except KeyError: + # not a galaxy-owned dependency + return pkg_resources.working_set.require( req_str ) + except EggNotFetchable, e: + raise EggNotFetchable( str( [ egg.name for egg in e.eggs ] ) ) +pkg_resources.require = require -# convenience stuff -def get_ucs(): - if sys.maxunicode > 65535: - return "ucs4" - else: - return "ucs2" - -def get_py(): - return "py%s" % sys.version[:3] - -def get_noplatform(): - return "%s-noplatform" % get_py() - -def get_platform( platform=False, peak=False ): - if platform: - if peak: - return "%s-%s" % ( get_py(), pkg_resources.get_platform() ) - else: - return "%s-%s-%s" % ( get_py(), pkg_resources.get_platform(), get_ucs() ) - else: - if peak: - return get_py() - else: - return "%s-noplatform" % get_py() - -def unpack_zipfile( filename, extract_dir): +def unpack_zipfile( filename, extract_dir, ignores=[] ): z = zipfile.ZipFile(filename) try: for info in z.infolist(): name = info.filename + perm = (info.external_attr >> 16L) & 0777 # don't extract absolute paths or ones with .. in them if name.startswith('/') or '..' in name: continue target = os.path.join(extract_dir, *name.split('/')) if not target: continue + for ignore in ignores: + if ignore in name: + continue if name.endswith('/'): # directory pkg_resources.ensure_directory(target) @@ -593,6 +369,11 @@ finally: f.close() del data + try: + if not os.path.islink(): + os.chmod(target, mode) + except: + pass finally: z.close() @@ -601,5 +382,3 @@ shutil.rmtree( f ) else: os.remove( f ) - -pkg_resources.require = require diff -r a6c9862ece3d -r 0cb68935eede lib/galaxy/eggs/dist.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/eggs/dist.py Mon Mar 01 15:41:30 2010 -0500 @@ -0,0 +1,86 @@ +""" +Manage Galaxy eggs +""" + +import os, sys, subprocess +from scramble import ScrambleEgg, ScrambleCrate, ScrambleFailure, galaxy_dir, py +from __init__ import Crate, CaseSensitiveConfigParser + +import logging +log = logging.getLogger( __name__ ) + +class DistScrambleEgg( ScrambleEgg ): + def set_dir( self ): + self.dir = os.path.join( galaxy_dir, 'dist-eggs', self.name ) + if not os.path.exists( self.dir ): + os.makedirs( self.dir ) + @property + def path( self ): + # don't look for compatible eggs, look for exact matches + if os.path.exists( self.distribution.location ): + return self.distribution.location + return None + def run_scramble_script( self ): + log.warning( "%s(): Beginning build" % sys._getframe().f_code.co_name ) + # subprocessed to sterilize the env + cmd = "ssh %s 'cd %s; %s -ES %s'" % ( self.build_host, self.buildpath, self.python, 'scramble.py' ) + log.debug( '%s(): Executing:' % sys._getframe().f_code.co_name ) + log.debug( ' %s' % cmd ) + p = subprocess.Popen( args = cmd, shell = True ) + r = p.wait() + if r != 0: + raise ScrambleFailure( "%s(): Egg build failed for %s %s" % ( sys._getframe().f_code.co_name, self.name, self.version ) ) + def unpack_if_needed( self ): + return # do not unpack dist eggs + +class DistScrambleCrate( ScrambleCrate ): + """ + Holds eggs with info on how to build them for distribution. + """ + dist_config_file = os.path.join( galaxy_dir, 'dist-eggs.ini' ) + def __init__( self, build_on='all' ): + self.dist_config = CaseSensitiveConfigParser() + self.build_on = build_on + ScrambleCrate.__init__( self ) + def parse( self ): + self.dist_config.read( DistScrambleCrate.dist_config_file ) + self.hosts = dict( self.dist_config.items( 'hosts' ) ) + self.groups = dict( self.dist_config.items( 'groups' ) ) + self.ignore = dict( self.dist_config.items( 'ignore' ) ) + self.platforms = self.get_platforms( self.build_on ) + self.noplatforms = self.get_platforms( 'noplatform' ) + Crate.parse( self ) + def get_platforms( self, wanted ): + # find all the members of a group and process them + if self.groups.has_key( wanted ): + platforms = [] + for name in self.groups[wanted].split(): + for platform in self.get_platforms( name ): + if platform not in platforms: + platforms.append( platform ) + return platforms + elif self.hosts.has_key( wanted ): + return [ wanted ] + else: + raise Exception( "unknown platform: %s" % wanted ) + def parse_egg_section( self, eggs, tags, full_platform=False ): + for name, version in eggs: + self.eggs[name] = [] + tag = dict( tags ).get( name, '' ) + url = '/'.join( ( self.repo, name ) ) + try: + sources = self.config.get( 'source', name ).split() + except: + sources = [] + if full_platform: + platforms = self.platforms + else: + platforms = self.noplatforms + for platform in platforms: + if name in self.ignore and platform in self.ignore[name].split(): + continue + egg = DistScrambleEgg( name, version, tag, url, platform ) + host_info = self.hosts[platform].split() + egg.build_host, egg.python = host_info[:2] + egg.sources = sources + self.eggs[name].append( egg ) diff -r a6c9862ece3d -r 0cb68935eede lib/galaxy/eggs/scramble.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/eggs/scramble.py Mon Mar 01 15:41:30 2010 -0500 @@ -0,0 +1,234 @@ +""" +Manage Galaxy eggs +""" + +import os, sys, shutil, tempfile, subprocess, urlparse, urllib +from __init__ import Egg, Crate, URLRetriever, galaxy_dir, py, unpack_zipfile +from distutils.sysconfig import get_config_var + +import tarfile, zipfile, zlib +arctypes = ( 'tar.gz', 'tgz', 'zip' ) + +import logging +log = logging.getLogger( __name__ ) + +import pkg_resources + +class ScrambleFailure( Exception ): + def __init__( self, eggs, msg=None ): + if type( eggs ) in ( list, tuple ): + self.eggs = eggs + else: + self.eggs = [ eggs ] + self.msg = msg + def __str__( self ): + return self.msg or ' '.join( self.eggs ) + +class ScrambleEgg( Egg ): + """ + Contains information about scrambling eggs. + """ + scramble_dir = os.path.join( galaxy_dir, 'scripts', 'scramble' ) + archive_dir = os.path.join( scramble_dir, 'archives' ) + script_dir = os.path.join( scramble_dir, 'scripts' ) + build_dir = os.path.join( scramble_dir, 'build' ) + ez_setup = os.path.join( scramble_dir, 'lib', 'ez_setup.py' ) + ez_setup_url = 'http://peak.telecommunity.com/dist/ez_setup.py' + def __init__( self, *args, **kwargs ): + Egg.__init__( self, *args, **kwargs ) + self.sources = [] + self.buildpath = None + self.source_path = None + self.py = py + self.build_host = None + self.python = sys.executable + def scramble( self ): + if self.path: + log.warning( "%s(): Egg already exists, remove to force rebuild:" % sys._getframe().f_code.co_name ) + log.warning( " %s" % self.path ) + return + self.fetch_source() + self.unpack_source() + self.copy_build_script() + if not os.path.exists( ScrambleEgg.ez_setup ): + URLRetriever().retrieve( ScrambleEgg.ez_setup_url, ScrambleEgg.ez_setup ) + shutil.copyfile( ScrambleEgg.ez_setup, os.path.join( self.buildpath, 'ez_setup.py' ) ) + 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 ) ) + 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 ) + self.unpack_if_needed() + self.remove_doppelgangers() + # scramble helper methods + def get_tld( self, names ): + tld = names[0].split( os.path.sep, 1 )[0] + for name in names: + try: + assert tld == name.split( os.path.sep, 1 )[0] + except: + raise Exception( "%s(): Archive contains multiple top-level directories!" % sys._getframe().f_code.co_name ) + return tld + def fetch_one( self, urls ): + """ + Fetches the first available archive out of a list. + """ + for url in urls: + file = os.path.join( ScrambleEgg.archive_dir, ( urllib.unquote( url ).rsplit( '/', 1 ) )[-1] ) + if os.path.exists( file ): + log.warning( "%s(): Using existing source, remove to download again:" % sys._getframe().f_code.co_name ) + log.warning( " %s" % file ) + return file + # if we don't have one, get one + for url in urls: + file = os.path.join( ScrambleEgg.archive_dir, ( urllib.unquote( url ).rsplit( '/', 1 ) )[-1] ) + try: + log.debug( "%s(): Trying to fetch:" % sys._getframe().f_code.co_name ) + log.debug( " %s" % url ) + URLRetriever().retrieve( url, file + '.download' ) + shutil.move( file + '.download', file ) + log.debug( "%s(): Fetched to:" % sys._getframe().f_code.co_name ) + log.debug( " %s" % file ) + return file + except IOError, e: + if e[1] != 404: + raise + else: + return None + def fetch_source( self ): + """ + Get egg (and dependent) source + """ + if not os.path.exists( ScrambleEgg.archive_dir ): + os.makedirs( ScrambleEgg.archive_dir ) + urls = [] + url_base = self.url + '/' + '-'.join( ( self.name, self.version ) ) + urls.extend( map( lambda x: '.'.join( ( url_base, x ) ), arctypes ) ) + if self.tag: + urls.extend( map( lambda x: '.'.join( ( url_base + self.tag, x ) ), arctypes ) ) + self.source_path = self.fetch_one( urls ) + if self.source_path is None: + raise Exception( "%s(): Couldn't find a suitable source archive for %s %s from %s" % ( sys._getframe().f_code.co_name, self.name, self.version, self.url ) ) + for url in self.sources: + if not urlparse.urlparse( url )[0]: + url = self.url + '/' + url.lstrip( '/' ) + urls = [ url ] + urls.extend( map( lambda x: '.'.join( ( url, x ) ), arctypes ) ) # allows leaving off the extension and we'll try to find one + file = self.fetch_one( urls ) + if file is None: + raise Exception( "%s(): Couldn't fetch extra source for %s, check path in %s. URL(s) attempted output above." % ( sys._getframe().f_code.co_name, self.name, Crate.config_file, ) ) + def unpack_source( self ): + unpack_dir = os.path.join( ScrambleEgg.build_dir, self.platform ) + if not os.path.exists( unpack_dir ): + os.makedirs( unpack_dir ) + self.buildpath = os.path.join( unpack_dir, self.name ) + if os.path.exists( self.buildpath ): + log.warning( "%s(): Removing old build directory at:" % sys._getframe().f_code.co_name ) + log.warning( " %s" % self.buildpath ) + shutil.rmtree( self.buildpath ) + if tarfile.is_tarfile( self.source_path ): + self.unpack_tar() + elif zipfile.is_zipfile( self.source_path ): + self.unpack_zip() + else: + raise Exception( "%s(): Unknown archive file type for %s" % ( sys._getframe().f_code.co_name, source_path ) ) + log.warning( "%s(): Unpacked to:" % sys._getframe().f_code.co_name ) + log.warning( " %s" % self.buildpath ) + def unpack_zip( self ): + unpack_path = os.path.dirname( self.buildpath ) + tld = self.get_tld( zipfile.ZipFile( self.source_path, 'r' ).namelist() ) + unpack_zipfile( self.source_path, unpack_path, ( 'ez_setup', ) ) + os.rename( os.path.join( unpack_path, tld ), self.buildpath ) + def unpack_tar( self ): + unpack_path = os.path.dirname( self.buildpath ) + t = tarfile.open( self.source_path, "r" ) + members = filter( lambda x: "ez_setup" not in x.name and "pax_global_header" != x.name, t.getmembers() ) + tld = self.get_tld( [ x.name for x in members ] ) + cur = os.getcwd() + os.chdir( unpack_path ) + for member in members: + t.extract( member ) + t.close() + os.rename( tld, self.name ) + os.chdir( cur ) + def copy_build_script( self ): + # will try: + # bx_python-py2.4-solaris-2.11-i86pc.py + # bx_python-py2.4-solaris.py + # bx_python-solaris-2.11-i86pc.py + # bx_python-solaris.py + # bx_python-py2.4.py + # bx_python.py + # generic.py + platform = self.platform.replace( '-ucs2', '' ).replace( '-ucs4', '' ) # ucs is unimportant here + build_scripts = ( + "%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( '-' )[0] ), + "%s.py" % self.name, + "generic.py" ) + for build_script in build_scripts: + build_script = os.path.join( ScrambleEgg.script_dir, build_script ) + if os.path.exists( build_script ): + log.warning( "%s(): Using build script %s" % ( sys._getframe().f_code.co_name, build_script ) ) + break + shutil.copyfile( build_script, os.path.join( self.buildpath, "scramble.py" ) ) + verfile = open( os.path.join( self.buildpath, ".galaxy_ver" ), "w" ) + verfile.write( self.version + '\n' ) + verfile.close() + if self.tag is not None: + tagfile = open( os.path.join( self.buildpath, ".galaxy_tag" ), "w" ) + tagfile.write( self.tag + '\n' ) + tagfile.close() + def run_scramble_script( self ): + log.warning( "%s(): Beginning build" % sys._getframe().f_code.co_name ) + # subprocessed to sterilize the env + cmd = "%s -ES %s" % ( self.python, "scramble.py" ) + log.debug( '%s(): Executing in %s:' % ( sys._getframe().f_code.co_name, self.buildpath ) ) + log.debug( ' %s' % cmd ) + p = subprocess.Popen( args = cmd, shell = True, cwd = self.buildpath ) + r = p.wait() + if r != 0: + if sys.platform == 'sunos5' and get_config_var('CC').endswith('pycc') and not os.environ.get( 'PYCC_CC', None ): + log.error( "%s(): Your python interpreter was compiled with Sun's pycc" % sys._getframe().f_code.co_name ) + log.error( " pseudo-compiler. You may need to set PYCC_CC and PYCC_CXX in your" ) + log.error( " environment if your compiler is in a non-standard location." ) + raise ScrambleFailure( self, "%s(): Egg build failed for %s %s" % ( sys._getframe().f_code.co_name, self.name, self.version ) ) + +class ScrambleCrate( Crate ): + """ + Reads the eggs.ini file for use with scrambling eggs. + """ + def parse( self ): + Crate.parse( self ) + # get dependency sources + for egg in self.eggs.values(): + try: + egg.sources = self.config.get( "source", egg.name ).split() + except: + egg.sources = [] + def parse_egg_section( self, *args, **kwargs ): + kwargs['egg_class'] = ScrambleEgg + Crate.parse_egg_section( self, *args, **kwargs ) + def scramble( self, all=False ): + if all: + eggs = self.all_eggs + else: + eggs = self.config_eggs + eggs = filter( lambda x: x.name not in self.no_auto, eggs ) + failed = [] + for egg in eggs: + try: + egg.scramble() + except Exception, e: + failed.append( egg ) + last_exc = e + if failed: + if len( failed ) == 1: + raise last_exc # only 1 failure out of the crate, be more informative + else: + raise ScrambleFailure( failed ) diff -r a6c9862ece3d -r 0cb68935eede manage_db.sh --- a/manage_db.sh Mon Mar 01 13:30:37 2010 -0500 +++ b/manage_db.sh Mon Mar 01 15:41:30 2010 -0500 @@ -6,4 +6,4 @@ ####### cd `dirname $0` -`python ./scripts/check_python.py` ./scripts/manage_db.py $@ +python ./scripts/manage_db.py $@ diff -r a6c9862ece3d -r 0cb68935eede run.sh --- a/run.sh Mon Mar 01 13:30:37 2010 -0500 +++ b/run.sh Mon Mar 01 15:41:30 2010 -0500 @@ -2,18 +2,16 @@ cd `dirname $0` -CLEAN_PYTHON=`python ./scripts/check_python.py` - # explicitly attempt to fetch eggs before running FETCH_EGGS=1 for arg in "$@"; do [ "$arg" = "--stop-daemon" ] && FETCH_EGGS=0; break done if [ $FETCH_EGGS -eq 1 ]; then - $CLEAN_PYTHON ./scripts/check_eggs.py quiet + python ./scripts/check_eggs.py quiet if [ $? -ne 0 ]; then echo "Some eggs are out of date, attempting to fetch..." - $CLEAN_PYTHON ./scripts/fetch_eggs.py + python ./scripts/fetch_eggs.py if [ $? -eq 0 ]; then echo "Fetch successful." else @@ -22,4 +20,4 @@ fi fi fi -$CLEAN_PYTHON ./scripts/paster.py serve universe_wsgi.ini $@ +python ./scripts/paster.py serve universe_wsgi.ini $@ diff -r a6c9862ece3d -r 0cb68935eede run_functional_tests.sh --- a/run_functional_tests.sh Mon Mar 01 13:30:37 2010 -0500 +++ b/run_functional_tests.sh Mon Mar 01 15:41:30 2010 -0500 @@ -4,10 +4,8 @@ rm -f run_functional_tests.log -CLEAN_PYTHON=`python ./scripts/check_python.py` - if [ ! $1 ]; then - $CLEAN_PYTHON ./scripts/functional_tests.py -v --with-nosehtml --html-report-file run_functional_tests.html --exclude="^get" functional + python ./scripts/functional_tests.py -v --with-nosehtml --html-report-file run_functional_tests.html --exclude="^get" functional elif [ $1 = 'help' ]; then echo "'run_functional_tests.sh' for testing all the tools in functional directory" echo "'run_functional_tests.sh aaa' for testing one test case of 'aaa' ('aaa' is the file name with path)" @@ -15,16 +13,16 @@ echo "'run_functional_tests.sh -sid ccc' for testing one section with sid 'ccc' ('ccc' is the string after 'section::')" echo "'run_functional_tests.sh -list' for listing all the tool ids" elif [ $1 = '-id' ]; then - $CLEAN_PYTHON ./scripts/functional_tests.py -v functional.test_toolbox:TestForTool_$2 --with-nosehtml --html-report-file run_functional_tests.html + python ./scripts/functional_tests.py -v functional.test_toolbox:TestForTool_$2 --with-nosehtml --html-report-file run_functional_tests.html elif [ $1 = '-sid' ]; then - $CLEAN_PYTHON ./scripts/functional_tests.py --with-nosehtml --html-report-file run_functional_tests.html -v `python tool_list.py $2` + python ./scripts/functional_tests.py --with-nosehtml --html-report-file run_functional_tests.html -v `python tool_list.py $2` elif [ $1 = '-list' ]; then python tool_list.py echo "===========================================================================================================================================" echo "'run_functional_tests.sh -id bbb' for testing one tool with id 'bbb' ('bbb' is the tool id)" echo "'run_functional_tests.sh -sid ccc' for testing one section with sid 'ccc' ('ccc' is the string after 'section::')" else - $CLEAN_PYTHON ./scripts/functional_tests.py -v --with-nosehtml --html-report-file run_functional_tests.html $1 + python ./scripts/functional_tests.py -v --with-nosehtml --html-report-file run_functional_tests.html $1 fi echo "'run_functional_tests.sh help' for help" diff -r a6c9862ece3d -r 0cb68935eede run_reports.sh --- a/run_reports.sh Mon Mar 01 13:30:37 2010 -0500 +++ b/run_reports.sh Mon Mar 01 15:41:30 2010 -0500 @@ -1,5 +1,4 @@ #!/bin/sh cd `dirname $0` - -`python ./scripts/check_python.py` ./scripts/paster.py serve reports_wsgi.ini --pid-file=reports_webapp.pid --log-file=reports_webapp.log $@ +python ./scripts/paster.py serve reports_wsgi.ini --pid-file=reports_webapp.pid --log-file=reports_webapp.log $@ diff -r a6c9862ece3d -r 0cb68935eede run_unit_tests.sh --- a/run_unit_tests.sh Mon Mar 01 13:30:37 2010 -0500 +++ b/run_unit_tests.sh Mon Mar 01 15:41:30 2010 -0500 @@ -2,6 +2,6 @@ ## Excluding controllers due to the problematic genetrack dependency -`python ./scripts/check_python.py` ./scripts/nosetests.py -v -w lib \ +python ./scripts/nosetests.py -v -w lib \ --with-nosehtml --html-report-file run_unit_tests.html \ --with-doctest --exclude=functional --exclude="^get" --exclude=controllers diff -r a6c9862ece3d -r 0cb68935eede scripts/check_eggs.py --- a/scripts/check_eggs.py Mon Mar 01 13:30:37 2010 -0500 +++ b/scripts/check_eggs.py Mon Mar 01 15:41:30 2010 -0500 @@ -17,16 +17,10 @@ except: quiet = False -from galaxy.eggs import * +from galaxy.eggs import Crate c = Crate() -c.parse() -galaxy_config = GalaxyConfig() -ignore = [] -for name in c.get_names(): - if not galaxy_config.check_conditional( name ): - ignore.append( name ) -if not c.find( ignore=ignore ): +if c.config_missing: if not quiet: print "Some of your Galaxy eggs are out of date. Please update them" print "by running:" diff -r a6c9862ece3d -r 0cb68935eede scripts/check_python.py --- a/scripts/check_python.py Mon Mar 01 13:30:37 2010 -0500 +++ b/scripts/check_python.py Mon Mar 01 15:41:30 2010 -0500 @@ -6,13 +6,6 @@ supported version is installed but is not your default, getgalaxy.org contains instructions on how to force Galaxy to use a different version.""" % sys.version[:3] -def check_virtualenv(): - try: - assert sys.real_prefix - return 'python -E' - except: - return 'python -ES' - def check_python(): try: assert sys.version_info[:2] >= ( 2, 4 ) and sys.version_info[:2] <= ( 2, 6 ) @@ -21,9 +14,9 @@ raise if __name__ == '__main__': + rval = 0 try: check_python() - print check_virtualenv() - sys.exit( 0 ) except StandardError: - sys.exit( 1 ) + rval = 1 + sys.exit( rval ) diff -r a6c9862ece3d -r 0cb68935eede scripts/dist-scramble.py --- a/scripts/dist-scramble.py Mon Mar 01 13:30:37 2010 -0500 +++ b/scripts/dist-scramble.py Mon Mar 01 15:41:30 2010 -0500 @@ -11,28 +11,30 @@ root.setLevel( 10 ) root.addHandler( logging.StreamHandler( sys.stdout ) ) -lib = os.path.abspath( os.path.join( os.path.dirname( __file__ ), "..", "lib" ) ) +lib = os.path.abspath( os.path.join( os.path.dirname( __file__ ), '..', 'lib' ) ) sys.path.append( lib ) -from galaxy.eggs import DistCrate +from galaxy.eggs.dist import DistScrambleCrate, ScrambleFailure if len( sys.argv ) > 3 or len( sys.argv ) < 2: print __doc__ sys.exit( 1 ) elif len( sys.argv ) == 3: - c = DistCrate( sys.argv[2] ) + c = DistScrambleCrate( sys.argv[2] ) else: - c = DistCrate() + c = DistScrambleCrate() -c.parse() -egg_list = c.get( sys.argv[1] ) -if egg_list is None: +try: + eggs = c[sys.argv[1]] +except: print "error: %s not in eggs.ini" % sys.argv[1] sys.exit( 1 ) failed = [] -for egg in egg_list: - if not egg.scramble( dist=True ): - failed.append( egg.platform['galaxy'] ) +for egg in eggs: + try: + egg.scramble() + except ScrambleFailure: + failed.append( egg.platform ) if len( failed ): print "" print "Scramble failed to build eggs on the following platforms (more details" diff -r a6c9862ece3d -r 0cb68935eede scripts/fetch_eggs.py --- a/scripts/fetch_eggs.py Mon Mar 01 13:30:37 2010 -0500 +++ b/scripts/fetch_eggs.py Mon Mar 01 15:41:30 2010 -0500 @@ -18,39 +18,43 @@ lib = os.path.abspath( os.path.join( os.path.dirname( __file__ ), "..", "lib" ) ) sys.path.append( lib ) -from galaxy.eggs import * +from galaxy.eggs import Crate, EggNotFetchable +import pkg_resources c = Crate() -if len( sys.argv ) == 3: - c.platform = { 'peak' : sys.argv[2].rsplit('-',1)[0], 'galaxy' : sys.argv[2] } -c.parse() try: - galaxy_config = GalaxyConfig() - names = [] + c.platform = sys.argv[2] +except: + pass +try: if len( sys.argv ) == 1: - names = c.get_names() + c.resolve() # Only fetch eggs required by the config elif sys.argv[1] == 'all': - names = galaxy_config.always_conditional + c.resolve( all=True ) # Fetch everything else: # Fetch a specific egg - egg = c.get( sys.argv[1] ) - if egg is None: - print "error: %s not in eggs.ini" % sys.argv[1] + name = sys.argv[1] + try: + egg = c[name] + except: + print "error: %s not in eggs.ini" % name sys.exit( 1 ) - egg.fetch() - sys.exit( 0 ) - ignore = filter( lambda x: not galaxy_config.check_conditional( x ), list( names ) ) - c.fetch( ignore ) + dist = egg.resolve()[0] + print "%s %s is installed at %s" % ( dist.project_name, dist.version, dist.location ) except EggNotFetchable, e: - print "One or more of the python eggs necessary to run Galaxy couldn't be" - print "downloaded automatically. You may want to try building them by" - print "hand with:" - for egg in e.eggs: - print " python scripts/scramble.py %s" % egg + try: + assert sys.argv[1] != 'all' + egg = e.eggs[0] + print "%s %s couldn't be downloaded automatically. You can try" % ( egg.name, egg.version ) + print "building it by hand with:" + print " python scripts/scramble.py %s" + except ( AssertionError, IndexError ): + print "One or more of the python eggs necessary to run Galaxy couldn't be" + print "downloaded automatically. You can try building them by hand (all" + print "at once) with:" + print " python scripts/scramble.py" + print "Or individually:" + for egg in e.eggs: + print " python scripts/scramble.py %s" % egg.name sys.exit( 1 ) -except PlatformNotSupported, e: - print "Your platform (%s) is not supported." % e - print "Pre-built galaxy eggs are not available from the Galaxy developers for" - print "your platform. You may be able to build them by hand with:" - print " python scripts/scramble.py" - sys.exit( 1 ) +sys.exit( 0 ) diff -r a6c9862ece3d -r 0cb68935eede scripts/get_platforms.py --- a/scripts/get_platforms.py Mon Mar 01 13:30:37 2010 -0500 +++ b/scripts/get_platforms.py Mon Mar 01 15:41:30 2010 -0500 @@ -7,6 +7,6 @@ lib = os.path.abspath( os.path.join( os.path.dirname( __file__ ), "..", "lib" ) ) sys.path.append( lib ) -from galaxy.eggs import get_platform -print get_platform() -print get_platform( True ) +import galaxy +import pkg_resources +print pkg_resources.get_platform() diff -r a6c9862ece3d -r 0cb68935eede scripts/paster.py --- a/scripts/paster.py Mon Mar 01 13:30:37 2010 -0500 +++ b/scripts/paster.py Mon Mar 01 15:41:30 2010 -0500 @@ -28,6 +28,7 @@ pkg_resources.require( "Paste" ) pkg_resources.require( "PasteScript" ) +pkg_resources.require( "PasteDeploy" ) from paste.script import command command.run() diff -r a6c9862ece3d -r 0cb68935eede scripts/scramble.py --- a/scripts/scramble.py Mon Mar 01 13:30:37 2010 -0500 +++ b/scripts/scramble.py Mon Mar 01 15:41:30 2010 -0500 @@ -14,23 +14,29 @@ lib = os.path.abspath( os.path.join( os.path.dirname( __file__ ), "..", "lib" ) ) sys.path.append( lib ) -from galaxy.eggs import Crate, GalaxyConfig +from galaxy.eggs.scramble import ScrambleCrate, ScrambleFailure -c = Crate() -c.parse() -galaxy_config = GalaxyConfig() -names = [] -if len( sys.argv ) == 1: - names = c.get_names() -elif sys.argv[1] == 'all': - names = galaxy_config.always_conditional -else: -# Scramble a specific egg - egg = c.get( sys.argv[1] ) - if egg is None: - print "error: %s not in eggs.ini" % sys.argv[1] - sys.exit( 1 ) - egg.scramble() - sys.exit( 0 ) -ignore = filter( lambda x: not galaxy_config.check_conditional( x ), list( names ) ) -c.scramble( ignore=ignore ) +c = ScrambleCrate() + +try: + if len( sys.argv ) == 1: + eggs = c.scramble() + elif sys.argv[1] == 'all': + c.scramble( all=True ) + else: + # Scramble a specific egg + name = sys.argv[1] + try: + egg = c[name] + except: + print "error: %s not in eggs.ini" % name + sys.exit( 1 ) + egg.scramble() + sys.exit( 0 ) +except ScrambleFailure, e: + if len( e.eggs ) == 1: + raise + else: + print 'Scrambling the following eggs failed:\n ', + print '\n '.join( [ egg.name for egg in e.eggs ] ) + sys.exit( 1 ) diff -r a6c9862ece3d -r 0cb68935eede scripts/scramble/lib/get_platform.py --- a/scripts/scramble/lib/get_platform.py Mon Mar 01 13:30:37 2010 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,18 +0,0 @@ -""" -Monkeypatch get_platform since it's broken on OS X versions of Python 2.5 -""" -import os, sys -from distutils.sysconfig import get_config_vars -if sys.platform == 'darwin' and get_config_vars().get('UNIVERSALSDK', '').strip(): - # Has to be before anything imports pkg_resources - def _get_platform_monkeypatch(): - plat = distutils.util._get_platform() - if plat.startswith( 'macosx-' ): - plat = 'macosx-10.3-fat' - return plat - import distutils.util - try: - assert distutils.util._get_platform - except: - distutils.util._get_platform = distutils.util.get_platform - distutils.util.get_platform = _get_platform_monkeypatch diff -r a6c9862ece3d -r 0cb68935eede scripts/scramble/lib/scramble_lib.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/scramble/lib/scramble_lib.py Mon Mar 01 15:41:30 2010 -0500 @@ -0,0 +1,164 @@ +""" +Various utilities for scrambling. +""" +import os, sys, errno, re, distutils.util, glob, shutil, subprocess, tarfile, zipfile +from distutils.sysconfig import get_config_var, get_config_vars + +try: + import zlib +except: + raise Exception( 'Cannot import zlib, which must exist to build eggs. If your python interpreter is truly missing it, you will need to recompile or (on supported platforms) download a binary version from python.org.' ) + +def get_tag(): + try: + return open( '.galaxy_tag', 'r' ).read().strip() + except: + return None + +def get_ver(): + try: + return open( '.galaxy_ver', 'r' ).read().strip() + except: + return None + +def clean( extra_dirs=[] ): + for dir in [ 'build', 'dist' ] + extra_dirs: + try: + shutil.rmtree( dir ) + except OSError, e: + if e.errno != errno.ENOENT: + raise + +def apply_patches(): + name = os.path.basename( os.getcwd() ) + for file in glob.glob( os.path.join( patches, name, '*' ) ): + shutil.copy( file, os.path.basename( file ) ) + +def get_archive( base ): + for arctype in ( 'tar.gz', 'tgz', 'zip' ): + archive = '.'.join( ( base, arctype ) ) + if os.path.exists( archive ): + return archive + else: + raise Exception( "%s(): Couldn't find a suitable archive for %s in %s" % ( sys._getframe().f_code.co_name, os.path.basename( base ), archives ) ) + +def compress( path, *files ): + tarcf( path, *files ) + +def uncompress( path ): + if path.endswith( '.zip' ): + unzip( path ) + else: + tarxf( path ) + +def unzip( zipf ): + z = zipfile.ZipFile( zipf ) + try: + for info in z.infolist(): + name = info.filename + mode = (info.external_attr >> 16L) & 0777 + # don't extract absolute paths or ones with .. in them + if name.startswith('/') or '..' in name: + continue + if not name: + continue + if name.endswith('/'): + # directory + pkg_resources.ensure_directory(name) + else: + # file + pkg_resources.ensure_directory(name) + data = z.read(info.filename) + f = open(name,'wb') + try: + f.write(data) + finally: + f.close() + del data + try: + if not os.path.islink( name ): + os.chmod(name,mode) + except: + pass + finally: + z.close() + +def tarxf( ball ): + t = tarfile.open( ball, 'r' ) + for fn in t.getnames(): + t.extract( fn ) + t.close() + +def tarcf( ball, *files ): + if ball.endswith( '.gz' ): + t = tarfile.open( ball, 'w:gz' ) + elif ball.endswith( '.bz2' ): + t = tarfile.open( ball, 'w:bz2' ) + else: + t = tarfile.open( ball, 'w' ) + for file in files: + t.add( file ) + t.close() + +def run( cmd, d, txt ): + p = subprocess.Popen( args = cmd, shell = True, cwd = d ) + r = p.wait() + if r != 0: + print '%s(): %s failed' % ( sys._getframe().f_code.co_name, txt ) + sys.exit( 1 ) + +def unpack_dep( source, prepped, builder, args={} ): + if prepped is not None and os.path.exists( prepped ): + print "%s(): Prepared dependency already exists at the following path, remove to force re-prep:" % sys._getframe().f_code.co_name + print " ", prepped + uncompress( prepped ) + else: + print "%s(): Prepared dependency does not exist, preparing now from source:" % sys._getframe().f_code.co_name + print " ", source + uncompress( source ) + builder( prepped, args ) + +def get_solaris_compiler(): + p = subprocess.Popen( '%s -V 2>&1' % get_config_var('CC'), shell = True, stdout = subprocess.PIPE ) + out = p.stdout.read() + p.wait() + if 'Sun C' in out: + return 'cc' + else: + return 'gcc' + +# Monkeypatch pkg_resources for better ABI recognition +def _get_platform(): + plat = distutils.util._get_platform() + if sys.version_info[:2] == ( 2, 5 ) and \ + ( ( os.uname()[-1] in ( 'i386', 'ppc' ) and sys.platform == 'darwin' and os.path.abspath( sys.prefix ).startswith( '/System' ) ) or \ + ( sys.platform == 'darwin' and get_config_vars().get('UNIVERSALSDK', '').strip() ) ): + plat = 'macosx-10.3-fat' + if sys.platform == "sunos5" and not (plat.endswith('_32') or plat.endswith('_64')): + if sys.maxint > 2**31: + plat += '_64' + else: + plat += '_32' + if not (plat.endswith('-ucs2') or plat.endswith('-ucs4')): + if sys.maxunicode > 2**16: + plat += '-ucs4' + else: + plat += '-ucs2' + return plat +try: + assert distutil.util._get_platform +except: + distutils.util._get_platform = distutils.util.get_platform + distutils.util.get_platform = _get_platform + +# get setuptools +from ez_setup import use_setuptools +use_setuptools( download_delay=8, to_dir=os.path.dirname( __file__ ) ) +from setuptools import * +import pkg_resources + +# some constants +root = os.path.abspath( os.path.join( os.path.dirname( __file__ ), '..' ) ) +archives = os.path.abspath( os.path.join( root, 'archives' ) ) +patches = os.path.abspath( os.path.join( root, 'patches' ) ) +platform_noucs = pkg_resources.get_platform().rsplit( '-', 1 )[0] diff -r a6c9862ece3d -r 0cb68935eede scripts/scramble/patches/Cheetah/SetupConfig.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/scramble/patches/Cheetah/SetupConfig.py Mon Mar 01 15:41:30 2010 -0500 @@ -0,0 +1,103 @@ +#-------Main Package Settings-----------# +import sys + +name = 'Cheetah' +from cheetah.Version import Version as version +maintainer = "R. Tyler Ballance" +author = "Tavis Rudd" +author_email = "cheetahtemplate-discuss(a)lists.sf.net" +url = "http://www.cheetahtemplate.org/" +packages = ['Cheetah', + 'Cheetah.Macros', + 'Cheetah.Templates', + 'Cheetah.Tests', + 'Cheetah.Tools', + 'Cheetah.Utils', + ] +classifiers = [line.strip() for line in '''\ + #Development Status :: 4 - Beta + Development Status :: 5 - Production/Stable + Intended Audience :: Developers + Intended Audience :: System Administrators + License :: OSI Approved :: MIT License + Operating System :: OS Independent + Programming Language :: Python + Topic :: Internet :: WWW/HTTP + Topic :: Internet :: WWW/HTTP :: Dynamic Content + Topic :: Internet :: WWW/HTTP :: Site Management + Topic :: Software Development :: Code Generators + Topic :: Software Development :: Libraries :: Python Modules + Topic :: Software Development :: User Interfaces + Topic :: Text Processing'''.splitlines() if not line.strip().startswith('#')] +del line + +package_dir = {'Cheetah':'cheetah'} + +import os +import os.path +from distutils.core import Extension + +ext_modules=[ + Extension("Cheetah._namemapper", + [os.path.join('cheetah', 'c', '_namemapper.c')]), + # Extension("Cheetah._verifytype", + # [os.path.join('cheetah', 'c', '_verifytype.c')]), + # Extension("Cheetah._filters", + # [os.path.join('cheetah', 'c', '_filters.c')]), + # Extension('Cheetah._template', + # [os.path.join('cheetah', 'c', '_template.c')]), + ] + +## Data Files and Scripts +scripts = ['bin/cheetah-compile', + 'bin/cheetah', + ] + +data_files = ['recursive: cheetah *.tmpl *.txt LICENSE README TODO CHANGES',] + +if not os.getenv('CHEETAH_INSTALL_WITHOUT_SETUPTOOLS'): + try: + from setuptools import setup +# install_requires = [ +# "Markdown >= 2.0.1", +# ] + if sys.platform == 'win32': + # use 'entry_points' instead of 'scripts' + del scripts + entry_points = { + 'console_scripts': [ + 'cheetah = Cheetah.CheetahWrapper:_cheetah', + 'cheetah-compile = Cheetah.CheetahWrapper:_cheetah_compile', + ] + } + except ImportError: + print 'Not using setuptools, so we cannot install the Markdown dependency' + + +description = "Cheetah is a template engine and code generation tool." + +long_description = '''Cheetah is an open source template engine and code generation tool. + +It can be used standalone or combined with other tools and frameworks. Web +development is its principle use, but Cheetah is very flexible and is also being +used to generate C++ game code, Java, sql, form emails and even Python code. + +Documentation +================================================================================ +For a high-level introduction to Cheetah please refer to the User\'s Guide +at http://www.cheetahtemplate.org/learn.html + +Mailing list +================================================================================ +cheetahtemplate-discuss(a)lists.sourceforge.net +Subscribe at http://lists.sourceforge.net/lists/listinfo/cheetahtemplate-discuss + +Credits +================================================================================ +http://www.cheetahtemplate.org/credits.html + +Recent Changes +================================================================================ +See http://www.cheetahtemplate.org/CHANGES.txt for full details + +''' diff -r a6c9862ece3d -r 0cb68935eede scripts/scramble/patches/GeneTrack/setup.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/scramble/patches/GeneTrack/setup.py Mon Mar 01 15:41:30 2010 -0500 @@ -0,0 +1,15 @@ +from os import walk +from os.path import join +from setuptools import setup, find_packages + +def walk_files( top ): + for dir, dirs, files in walk( top ): + yield( dir, [ join( dir, f ) for f in files ] ) + +setup( + name = "GeneTrack", + version = "2.0.0-beta-1", + packages = ['genetrack','genetrack.scripts'], + data_files = [ f for f in walk_files('tests') ], + zip_safe = False +) diff -r a6c9862ece3d -r 0cb68935eede scripts/scramble/patches/MySQL_python/site.cfg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/scramble/patches/MySQL_python/site.cfg Mon Mar 01 15:41:30 2010 -0500 @@ -0,0 +1,18 @@ +[options] +# embedded: link against the embedded server library +# threadsafe: use the threadsafe client +# static: link against a static library (probably required for embedded) + +embedded = False +threadsafe = True +static = True + +# The path to mysql_config. +# Only use this if mysql_config is not on your PATH, or you have some weird +# setup that requires it. +mysql_config = mysql/bin/mysql_config + +# The Windows registry key for MySQL. +# This has to be set for Windows builds to work. +# Only change this if you have a different version. +registry_key = SOFTWARE\MySQL AB\MySQL Server 5.0 diff -r a6c9862ece3d -r 0cb68935eede scripts/scramble/patches/PasteScript/setup.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/scramble/patches/PasteScript/setup.py Mon Mar 01 15:41:30 2010 -0500 @@ -0,0 +1,145 @@ +import ez_setup +ez_setup.use_setuptools() +from setuptools import setup, find_packages +import re, os + +version = '1.7.3' + +news = os.path.join(os.path.dirname(__file__), 'docs', 'news.txt') +news = open(news).read() +parts = re.split(r'([0-9\.]+)\s*\n\r?-+\n\r?', news) +found_news = '' +for i in range(len(parts)-1): + if parts[i] == version: + found_news = parts[i+i] + break +if not found_news: + print 'Warning: no news for this version found' + +long_description="""\ +This is a pluggable command-line tool. + +It includes some built-in features; + +* Create file layouts for packages. For instance, ``paste create + --template=basic_package MyPackage`` will create a `setuptools + <http://peak.telecommunity.com/DevCenter/setuptools>`_-ready + file layout. + +* Serving up web applications, with configuration based on + `paste.deploy <http://pythonpaste.org/deploy/paste-deploy.html>`_. + +The latest version is available in a `Subversion repository +<http://svn.pythonpaste.org/Paste/Script/trunk#egg=PasteScript-dev>`_. + +For the latest changes see the `news file +<http://pythonpaste.org/script/news.html>`_. +""" + +if found_news: + title = 'Changes in %s' % version + long_description += "\n%s\n%s\n" % (title, '-'*len(title)) + long_description += found_news + +setup( + name="PasteScript", + version=version, + description="A pluggable command-line frontend, including commands to setup package file layouts", + long_description=long_description, + classifiers=[ + "Development Status :: 5 - Production/Stable", + "Intended Audience :: Developers", + "License :: OSI Approved :: MIT License", + "Programming Language :: Python", + "Topic :: Internet :: WWW/HTTP", + "Topic :: Internet :: WWW/HTTP :: Dynamic Content", + "Topic :: Software Development :: Libraries :: Python Modules", + "Framework :: Paste", + ], + keywords='web wsgi setuptools framework command-line setup', + author="Ian Bicking", + author_email="ianb(a)colorstudy.com", + url="http://pythonpaste.org/script/", + namespace_packages=['paste'], + license='MIT', + packages=find_packages(exclude='tests'), + package_data={ + 'paste.script': ['paster-templates/basic_package/setup.*', + 'paster-templates/basic_package/tests/*.py', + # @@: docs/ doesn't have any files :( + 'paster-templates/basic_package/+package+/*.py'], + }, + zip_safe=False, + scripts=['scripts/paster'], + extras_require={ + 'Templating': [], + 'Cheetah': ['Cheetah'], + 'Config': ['PasteDeploy'], + 'WSGIUtils': ['WSGIUtils'], + 'Flup': ['Flup'], + # the Paste feature means the complete set of features; + # (other features are truly optional) + 'Paste': ['PasteDeploy', 'Cheetah'], + }, + entry_points=""" + [paste.global_paster_command] + help=paste.script.help:HelpCommand + create=paste.script.create_distro:CreateDistroCommand [Templating] + serve=paste.script.serve:ServeCommand [Config] + request=paste.script.request:RequestCommand [Config] + post=paste.script.request:RequestCommand [Config] + exe=paste.script.exe:ExeCommand + points=paste.script.entrypoints:EntryPointCommand + make-config=paste.script.appinstall:MakeConfigCommand + setup-app=paste.script.appinstall:SetupCommand + + [paste.paster_command] + grep = paste.script.grep:GrepCommand + + [paste.paster_create_template] + basic_package=paste.script.templates:BasicPackage + + [paste.server_runner] + wsgiutils=paste.script.wsgiutils_server:run_server [WSGIUtils] + flup_ajp_thread=paste.script.flup_server:run_ajp_thread [Flup] + flup_ajp_fork=paste.script.flup_server:run_ajp_fork [Flup] + flup_fcgi_thread=paste.script.flup_server:run_fcgi_thread [Flup] + flup_fcgi_fork=paste.script.flup_server:run_fcgi_fork [Flup] + flup_scgi_thread=paste.script.flup_server:run_scgi_thread [Flup] + flup_scgi_fork=paste.script.flup_server:run_scgi_fork [Flup] + cgi=paste.script.cgi_server:paste_run_cgi + cherrypy=paste.script.cherrypy_server:cpwsgi_server + twisted=paste.script.twisted_web2_server:run_twisted + + [paste.app_factory] + test=paste.script.testapp:make_test_application + + [paste.entry_point_description] + paste.entry_point_description = paste.script.epdesc:MetaEntryPointDescription + paste.paster_create_template = paste.script.epdesc:CreateTemplateDescription + paste.paster_command = paste.script.epdesc:PasterCommandDescription + paste.global_paster_command = paste.script.epdesc:GlobalPasterCommandDescription + paste.app_install = paste.script.epdesc:AppInstallDescription + + # These aren't part of Paste Script particularly, but + # we'll document them here + console_scripts = paste.script.epdesc:ConsoleScriptsDescription + # @@: Need non-console scripts... + distutils.commands = paste.script.epdesc:DistutilsCommandsDescription + distutils.setup_keywords = paste.script.epdesc:SetupKeywordsDescription + egg_info.writers = paste.script.epdesc:EggInfoWriters + # @@: Not sure what this does: + #setuptools.file_finders = paste.script.epdesc:SetuptoolsFileFinders + + [console_scripts] + paster=paste.script.command:run + + [distutils.setup_keywords] + paster_plugins = setuptools.dist:assert_string_list + + [egg_info.writers] + paster_plugins.txt = setuptools.command.egg_info:write_arg + """, + install_requires=[ + ], + ) diff -r a6c9862ece3d -r 0cb68935eede scripts/scramble/patches/psycopg2/setup.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/scramble/patches/psycopg2/setup.py Mon Mar 01 15:41:30 2010 -0500 @@ -0,0 +1,252 @@ +# 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 a6c9862ece3d -r 0cb68935eede scripts/scramble/scripts/Cheetah.py --- a/scripts/scramble/scripts/Cheetah.py Mon Mar 01 13:30:37 2010 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,62 +0,0 @@ -import os, sys, shutil - -# 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 ) -import get_platform # fixes fat python 2.5 -from ez_setup import use_setuptools -use_setuptools( download_delay=8, to_dir=scramble_lib ) -from setuptools import * - -# get the tag -if os.access( ".galaxy_tag", os.F_OK ): - tagfile = open( ".galaxy_tag", "r" ) - tag = tagfile.readline().strip() -else: - tag = None - -# in case you're running this by hand from a dirty module source dir -for dir in [ "build", "dist" ]: - if os.access( dir, os.F_OK ): - print "scramble_it.py: removing dir:", dir - shutil.rmtree( dir ) - -# patch -file = "SetupConfig.py" -if not os.access( "%s.orig" %file, os.F_OK ): - print "scramble.py(): Patching", file - shutil.copyfile( file, "%s.orig" %file ) - i = open( "%s.orig" %file, "r" ) - o = open( file, "w" ) - comment = False - for line in i.readlines(): - if line == " install_requires = [\n": - comment = True - print >>o, "#" + line, - elif comment and line == " ]\n": - comment = False - print >>o, "#" + line, - elif comment: - print >>o, "#" + line, - else: - print >>o, line, - i.close() - o.close() - -# reset args for distutils -me = sys.argv[0] -sys.argv = [ me ] -sys.argv.append( "egg_info" ) -if tag is not None: - #sys.argv.append( "egg_info" ) - sys.argv.append( "--tag-build=%s" %tag ) -# svn revision (if any) is handled directly in tag-build -sys.argv.append( "--no-svn-revision" ) -sys.argv.append( "bdist_egg" ) - -# do it -execfile( "setup.py", globals(), locals() ) diff -r a6c9862ece3d -r 0cb68935eede scripts/scramble/scripts/DRMAA_python-macosx.py --- a/scripts/scramble/scripts/DRMAA_python-macosx.py Mon Mar 01 13:30:37 2010 -0500 +++ b/scripts/scramble/scripts/DRMAA_python-macosx.py Mon Mar 01 15:41:30 2010 -0500 @@ -1,8 +1,8 @@ import os, sys, shutil if "SGE_ROOT" not in os.environ: - print "scramble(): Please set SGE_ROOT to the path of your SGE installation" - print "scramble(): before scrambling DRMAA_python" + print "main(): Please set SGE_ROOT to the path of your SGE installation" + print "main(): before scrambling DRMAA_python" sys.exit(1) # change back to the build dir @@ -10,27 +10,15 @@ os.chdir( os.path.dirname( sys.argv[0] ) ) # find setuptools -scramble_lib = os.path.join( "..", "..", "..", "lib" ) -sys.path.append( scramble_lib ) -import get_platform # fixes fat python 2.5 -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 +sys.path.append( os.path.join( '..', '..', '..', 'lib' ) ) +from scramble_lib import * -# clean, in case you're running this by hand from a dirty module source dir -for dir in [ "build", "dist", "gridengine" ]: - if os.access( dir, os.F_OK ): - print "scramble_it.py: removing dir:", dir - shutil.rmtree( dir ) +tag = get_tag() # get the tag +clean() # clean up any existing stuff (could happen if you run scramble.py by hand) # patch file = "setup.py" -print "scramble(): Patching", file +print "main(): Patching", file if not os.access( "%s.orig" %file, os.F_OK ): shutil.copyfile( file, "%s.orig" %file ) i = open( "%s.orig" %file, "r" ) @@ -44,7 +32,7 @@ i.close() o.close() -# go +# build me = sys.argv[0] sys.argv = [ me ] sys.argv.append( "build" ) @@ -55,6 +43,7 @@ libdrmaa = os.path.join(SGE6_ROOT, "lib", SGE6_ARCH, "libdrmaa.dylib.1.0" ) os.system( "install_name_tool -change libdrmaa.dylib.1.0 %s %s" % ( libdrmaa, so ) ) +# package sys.argv = [ me ] sys.argv.append( "bdist_egg" ) execfile( "setup.py", globals(), locals() ) diff -r a6c9862ece3d -r 0cb68935eede scripts/scramble/scripts/DRMAA_python-solaris.py --- a/scripts/scramble/scripts/DRMAA_python-solaris.py Mon Mar 01 13:30:37 2010 -0500 +++ b/scripts/scramble/scripts/DRMAA_python-solaris.py Mon Mar 01 15:41:30 2010 -0500 @@ -1,8 +1,8 @@ import os, sys, shutil if "SGE_ROOT" not in os.environ: - print "scramble(): Please set SGE_ROOT to the path of your SGE installation" - print "scramble(): before scrambling DRMAA_python" + print "main(): Please set SGE_ROOT to the path of your SGE installation" + print "main(): before scrambling DRMAA_python" sys.exit(1) # change back to the build dir @@ -10,22 +10,11 @@ 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 +sys.path.append( os.path.join( '..', '..', '..', 'lib' ) ) +from scramble_lib import * -# clean, in case you're running this by hand from a dirty module source dir -for dir in [ "build", "dist", "gridengine" ]: - if os.access( dir, os.F_OK ): - print "scramble_it.py: removing dir:", dir - shutil.rmtree( dir ) +tag = get_tag() # get the tag +clean() # clean up any existing stuff (could happen if you run scramble.py by hand) # if our python is 64 bit, use 64 bit sge... if sys.maxint < ( 2048 * 1024 * 1024 ): @@ -38,24 +27,13 @@ arch = "sparc64" else: arch = "amd64" - if not "CFLAGS" in os.environ: - os.environ["CFLAGS"] = "" - os.environ["CFLAGS"] += " -m64" # if we're using sun cc, drop the gcc -Wno-unused option -import distutils.sysconfig -cc = distutils.sysconfig.get_config_var('CC') -if os.popen( cc + ' --version 2>&1' ).read().strip().split('\n')[0].startswith('gcc'): - compiler = 'gcc' -elif os.popen( cc + ' -V 2>&1' ).read().strip().split('\n')[0].startswith('cc: Sun C'): - compiler = 'sun' -else: - print "scramble(): Unable to determine compiler" - sys.exit(1) +cc = get_solaris_compiler() # patch file = "setup.py" -print "scramble(): Patching", file +print "main(): Patching", file if not os.access( "%s.orig" %file, os.F_OK ): shutil.copyfile( file, "%s.orig" %file ) i = open( "%s.orig" %file, "r" ) @@ -68,14 +46,16 @@ elif line.startswith('link_args ='): line = 'link_args = [ "-L%s" % os.path.join(SGE6_ROOT, "lib", SGE6_ARCH), "-Wl,-R%s" % os.path.join(SGE6_ROOT, "lib", SGE6_ARCH), "-ldrmaa" ]\n' if line == " + [ '-Wno-unused' ]\n": - if compiler == 'sun': + if cc == 'cc': line = " #+ [ '-Wno-unused' ]\n" print >>o, line, i.close() o.close() -# go +# reset args for distutils me = sys.argv[0] sys.argv = [ me ] sys.argv.append( "bdist_egg" ) + +# do it execfile( "setup.py", globals(), locals() ) diff -r a6c9862ece3d -r 0cb68935eede scripts/scramble/scripts/DRMAA_python.py --- a/scripts/scramble/scripts/DRMAA_python.py Mon Mar 01 13:30:37 2010 -0500 +++ b/scripts/scramble/scripts/DRMAA_python.py Mon Mar 01 15:41:30 2010 -0500 @@ -1,8 +1,8 @@ import os, sys, shutil if "SGE_ROOT" not in os.environ: - print "scramble(): Please set SGE_ROOT to the path of your SGE installation" - print "scramble(): before scrambling DRMAA_python" + print "main(): Please set SGE_ROOT to the path of your SGE installation" + print "main(): before scrambling DRMAA_python" sys.exit(1) # change back to the build dir @@ -10,27 +10,15 @@ os.chdir( os.path.dirname( sys.argv[0] ) ) # find setuptools -scramble_lib = os.path.join( "..", "..", "..", "lib" ) -sys.path.append( scramble_lib ) -import get_platform # fixes fat python 2.5 -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 +sys.path.append( os.path.join( '..', '..', '..', 'lib' ) ) +from scramble_lib import * -# clean, in case you're running this by hand from a dirty module source dir -for dir in [ "build", "dist", "gridengine" ]: - if os.access( dir, os.F_OK ): - print "scramble_it.py: removing dir:", dir - shutil.rmtree( dir ) +tag = get_tag() # get the tag +clean() # clean up any existing stuff (could happen if you run scramble.py by hand) # patch file = "setup.py" -print "scramble(): Patching", file +print "main(): Patching", file if not os.access( "%s.orig" %file, os.F_OK ): shutil.copyfile( file, "%s.orig" %file ) i = open( "%s.orig" %file, "r" ) @@ -44,8 +32,10 @@ i.close() o.close() -# go +# reset args for distutils me = sys.argv[0] sys.argv = [ me ] sys.argv.append( "bdist_egg" ) + +# do it execfile( "setup.py", globals(), locals() ) diff -r a6c9862ece3d -r 0cb68935eede scripts/scramble/scripts/GeneTrack.py --- a/scripts/scramble/scripts/GeneTrack.py Mon Mar 01 13:30:37 2010 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,58 +0,0 @@ -import os, sys, shutil - -# 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 ) -from ez_setup import use_setuptools -use_setuptools( download_delay=8, to_dir=scramble_lib ) -from setuptools import * - -# get the tag -if os.access( ".galaxy_tag", os.F_OK ): - tagfile = open( ".galaxy_tag", "r" ) - tag = tagfile.readline().strip() -else: - tag = None - -# in case you're running this by hand from a dirty module source dir -for dir in [ "build", "dist" ]: - if os.access( dir, os.F_OK ): - print "scramble.py: removing dir:", dir - shutil.rmtree( dir ) - -# reset args for distutils -me = sys.argv[0] -sys.argv = [ me ] -sys.argv.append( "egg_info" ) -if tag is not None: - #sys.argv.append( "egg_info" ) - sys.argv.append( "--tag-build=%s" %tag ) -# svn revision (if any) is handled directly in tag-build -sys.argv.append( "--no-svn-revision" ) -sys.argv.append( "bdist_egg" ) - -if not os.access( 'setup.py', os.F_OK ): - print "scramble.py: Creating setup.py for GeneTrack" - setup_py = """from os import walk -from os.path import join -from setuptools import setup, find_packages -def walk_files( top ): - for dir, dirs, files in walk( top ): - yield( dir, [ join( dir, f ) for f in files ] ) -setup( - name = "GeneTrack", - version = "2.0.0-beta-1", - packages = ['genetrack','genetrack.scripts'], - data_files = [ f for f in walk_files('tests') ], - zip_safe = False -) -""" - open( 'setup.py', 'w' ).write( setup_py ) - - -# do it -execfile( "setup.py", globals(), locals() ) diff -r a6c9862ece3d -r 0cb68935eede scripts/scramble/scripts/MySQL_python-solaris.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/scramble/scripts/MySQL_python-solaris.py Mon Mar 01 15:41:30 2010 -0500 @@ -0,0 +1,81 @@ +import os, sys, shutil +from distutils.sysconfig import get_config_var + +def prep_mysql( prepped, args ): + + my_version = args['version'] + my_srcdir = os.path.join( os.getcwd(), "mysql-%s" % my_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/mysql --disable-dependency-tracking --enable-static --disable-shared --without-server --without-uca " %os.getcwd() + \ + "--without-libwrap --without-ssl --without-docs --without-man --enable-thread-safe-client --with-named-curses-libs=''", + my_srcdir, "Configuring mysql (./configure)" ) + + # compile + run( "make", os.path.join( my_srcdir, 'include' ), "Preparing mysql includes (cd include; make)" ) + run( "make link_sources", os.path.join( my_srcdir, 'libmysql' ), "Preparing libmysql (cd libmysql; make link_sources)" ) + run( "make link_sources", os.path.join( my_srcdir, 'libmysql_r' ), "Preparing libmysql_r (cd libmysql_r; make link_sources)" ) + run( "make", os.path.join( my_srcdir, 'libmysql_r' ), "Compiling libmysql_r (cd libmysql_r; make)" ) + run( "make", os.path.join( my_srcdir, 'scripts' ), "Preparing scripts (cd scripts; make)" ) + + # install + run( "make install", os.path.join( my_srcdir, 'include' ), "Installing mysql includes (cd include; make install)" ) + run( "make install", os.path.join( my_srcdir, 'libmysql_r' ), "Installing libmysql_r (cd libmysql_r; make install)" ) + run( "make install", os.path.join( my_srcdir, 'scripts' ), "Installing mysql scripts (cd scripts; make install)" ) + shutil.copy( os.path.join( my_srcdir, 'include', 'mysqld_error.h' ), os.path.join( 'mysql', 'include', 'mysql' ) ) + + # create prepped archive + print "%s(): Creating prepped archive for future builds at:" % sys._getframe().f_code.co_name + print " ", prepped + compress( prepped, + 'mysql/bin/mysql_config', + 'mysql/include', + 'mysql/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() + + my_version = ( tag.split( '_' ) )[1] + my_archive_base = os.path.join( archives, 'mysql-%s' % my_version ) + my_archive = get_archive( my_archive_base ) + my_archive_prepped = os.path.join( archives, 'mysql-%s-%s.tar.gz' % ( my_version, platform_noucs ) ) + + # clean up any existing stuff (could happen if you run scramble.py by hand) + clean( [ 'mysql-%s' % my_version, 'mysql' ] ) + + # unpack mysql + unpack_dep( my_archive, my_archive_prepped, prep_mysql, dict( version=my_version ) ) + + # get site.cfg + shutil.copy( os.path.join( patches, 'MySQL_python', 'site.cfg' ), 'site.cfg' ) + + # 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() )

1 0

[hg] galaxy 3451: UI tweaks
by Greg Von Kuster 03 Mar '10

03 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/a6c9862ece3d changeset: 3451:a6c9862ece3d user: James Taylor <james(a)jamestaylor.org> date: Mon Mar 01 13:30:37 2010 -0500 description: UI tweaks diffstat: templates/display_base.mako | 9 ++++----- templates/page/display.mako | 2 +- templates/user/info.mako | 15 ++++++++++++--- 3 files changed, 17 insertions(+), 9 deletions(-) diffs (80 lines): diff -r 71a525ae9426 -r a6c9862ece3d templates/display_base.mako --- a/templates/display_base.mako Mon Mar 01 12:46:54 2010 -0500 +++ b/templates/display_base.mako Mon Mar 01 13:30:37 2010 -0500 @@ -190,14 +190,13 @@ <div class="unified-panel-body"> <div style="overflow: auto; height: 100%;"> <div style="padding: 10px;"> + + <div style="float: right;"><img src="http://www.gravatar.com/avatar/${h.md5(item.user.email)}?d=identicon"></div> + <h4>Author</h4> <p>${item.user.username | h}</p> - - <div><img src="http://www.gravatar.com/avatar/${h.md5(item.user.email)}?d=identicon&s=150"></div> - - - + ## Page meta. <h4>Related ${item_plural}</h4> <p> diff -r 71a525ae9426 -r a6c9862ece3d templates/page/display.mako --- a/templates/page/display.mako Mon Mar 01 12:46:54 2010 -0500 +++ b/templates/page/display.mako Mon Mar 01 13:30:37 2010 -0500 @@ -20,7 +20,7 @@ if ( $.browser.mozilla ) { $(this).find( "pre.peek" ).css( "overflow", "hidden" ); } - $(this).slideUp( "fast" ); + $(this).hide(); }); }); diff -r 71a525ae9426 -r a6c9862ece3d templates/user/info.mako --- a/templates/user/info.mako Mon Mar 01 12:46:54 2010 -0500 +++ b/templates/user/info.mako Mon Mar 01 13:30:37 2010 -0500 @@ -56,6 +56,9 @@ <input type="submit" name="login_info_button" value="Save"> </div> </form> +</div> +<p></p> +<div class="toolForm"> <form name="change_password" id="change_password" action="${h.url_for( controller='user', action='edit_info', user_id=user.id, admin_view=admin_view )}" method="post" > <div class="toolFormTitle">Change Password</div> %if not admin_view: @@ -76,7 +79,10 @@ <input type="submit" name="change_password_button" value="Save"> </div> </form> - %if user.values or user_info_forms: +</div> +%if user.values or user_info_forms: +<p></p> +<div class="toolForm"> <form name="user_info" id="user_info" action="${h.url_for( controller='user', action='edit_info', user_id=user.id, admin_view=admin_view )}" method="post" > <div class="toolFormTitle">User information</div> %if user_info_select: @@ -104,7 +110,10 @@ <input type="submit" name="edit_user_info_button" value="Save"> </div> </form> - %endif +</div> +%endif +<p></p> +<div class="toolForm"> <form name="user_info" id="user_info" action="${h.url_for( controller='user', action='new_address', user_id=user.id, admin_view=admin_view )}" method="post" > <div class="toolFormTitle">User Addresses</div> <div class="toolFormBody"> @@ -160,7 +169,7 @@ </div> </div> </form> - +

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[hg] galaxy 3450: Page editor: use Galaxy styles for drop downs ...
by Greg Von Kuster 03 Mar '10

03 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/71a525ae9426 changeset: 3450:71a525ae9426 user: James Taylor <james(a)jamestaylor.org> date: Mon Mar 01 12:46:54 2010 -0500 description: Page editor: use Galaxy styles for drop downs in menubar diffstat: static/june_2007_style/base.css.tmpl | 12 +++++++-- static/june_2007_style/blue/base.css | 3 +- templates/page/editor.mako | 44 +++++++++++++---------------------- 3 files changed, 27 insertions(+), 32 deletions(-) diffs (118 lines): diff -r 405764879961 -r 71a525ae9426 static/june_2007_style/base.css.tmpl --- a/static/june_2007_style/base.css.tmpl Mon Mar 01 12:14:04 2010 -0500 +++ b/static/june_2007_style/base.css.tmpl Mon Mar 01 12:46:54 2010 -0500 @@ -507,9 +507,15 @@ } } -.menubutton.popup { - padding-right: 1.5em; - background: url(../images/dropdownarrow.png) no-repeat right 8px; +.menubutton.action-button { + border-color: #aaaaaa; +} + +.menubutton.popup, .action-button.popup { + padding-right: 20px; + background-image: url(../images/dropdownarrow.png); + background-repeat: no-repeat; + background-position: right 8px; } .menubutton:hover { diff -r 405764879961 -r 71a525ae9426 static/june_2007_style/blue/base.css --- a/static/june_2007_style/blue/base.css Mon Mar 01 12:14:04 2010 -0500 +++ b/static/june_2007_style/blue/base.css Mon Mar 01 12:46:54 2010 -0500 @@ -87,7 +87,8 @@ .action-button:active{color:white;background:#aaaaaa;} .menubutton{display:inline-block;cursor:pointer;position:relative;user-select:none;-moz-user-select:none;-webkit-user-select:none;border:solid transparent 1px;-moz-border-radius:0.5em;-webkit-border-radius:0.5em;border-radius:0.5em;padding:3px 0.5em;margin:-3px -0.5em;} .menubutton .label{position:relative;display:block;border-right:none;} -.menubutton.popup{padding-right:1.5em;background:url(../images/dropdownarrow.png) no-repeat right 8px;} +.menubutton.action-button{border-color:#aaaaaa;} +.menubutton.popup,.action-button.popup{padding-right:20px;background-image:url(../images/dropdownarrow.png);background-repeat:no-repeat;background-position:right 8px;} .menubutton:hover{border-color:#aaaaaa;} .menubutton.popup.split{padding-right:2em;} .menubutton.popup.split:hover{background:url(../images/ddarrowsplit.png) no-repeat right -38px;} diff -r 405764879961 -r 71a525ae9426 templates/page/editor.mako --- a/templates/page/editor.mako Mon Mar 01 12:14:04 2010 -0500 +++ b/templates/page/editor.mako Mon Mar 01 12:46:54 2010 -0500 @@ -534,7 +534,6 @@ boxHtml: "<table class='wym_box' width='100%' height='100%'>" + "<tr><td><div class='wym_area_top'>" + WYMeditor.TOOLS - + WYMeditor.CONTAINERS + "</div></td></tr>" + "<tr height='100%'><td>" + "<div class='wym_area_main' style='height: 100%;'>" @@ -559,11 +558,6 @@ {'name': 'Unlink', 'title': 'Unlink', 'css': 'wym_tools_unlink'}, {'name': 'InsertImage', 'title': 'Image', 'css': 'wym_tools_image'}, {'name': 'InsertTable', 'title': 'Table', 'css': 'wym_tools_table'}, - {'name': 'Insert Galaxy History Link', 'title' : 'Galaxy_History_Link', 'css' : 'galaxy_tools_insert_history_link'}, - {'name': 'Insert Galaxy Dataset Link', 'title' : 'Galaxy_Dataset_Link', 'css' : 'galaxy_tools_insert_dataset_link'}, - {'name': 'Insert Galaxy Workflow Link', 'title' : 'Galaxy_Workflow_Link', 'css' : 'galaxy_tools_insert_workflow_link'}, - {'name': 'Insert Galaxy Page Link', 'title' : 'Galaxy_Page_Link', 'css' : 'galaxy_tools_insert_page_link'}, - {'name': 'Annonate Galaxy History', 'title' : 'Annotate_Galaxy_History', 'css' : 'galaxy_tools_annotate_history'}, ] }); ## Get the editor object @@ -636,35 +630,29 @@ } }); - // Initialize 'Insert history link' button. - $('.galaxy_tools_insert_history_link').children().click( function() { - editor.dialog(Galaxy.DIALOG_HISTORY_LINK); - }); - // Initialize 'Insert dataset link' button. - $('.galaxy_tools_insert_dataset_link').children().click( function() { - editor.dialog(Galaxy.DIALOG_DATASET_LINK); - }); - // Initialize 'Insert workflow link' button. - $('.galaxy_tools_insert_workflow_link').children().click( function() { - editor.dialog(Galaxy.DIALOG_WORKFLOW_LINK); - }); - // Initialize 'Insert page link' button. - $('.galaxy_tools_insert_page_link').children().click( function() { - editor.dialog(Galaxy.DIALOG_PAGE_LINK); - }); - // Initialize 'Annotate history' button. - $('.galaxy_tools_annotate_history').children().click( function() { - editor.dialog(Galaxy.DIALOG_ANNOTATE_HISTORY); - }); // Initialize galaxy elements. //init_galaxy_elts(editor); // + // Containers, Galaxy style + // + var containers_menu = $("<div class='galaxy-page-editor-button'><a id='insert-galaxy-link' class='action-button popup' href='#'>${_('Paragraph type')}</a></div>"); + $(".wym_area_top").append( containers_menu ); + + // Add menu options. + var items = {} + $.each( editor._options.containersItems, function( k, v ) { + var tagname = v.name; + items[ v.title.replace( '_', ' ' ) ] = function() { editor.container( tagname ) } + }); + make_popupmenu( containers_menu, items); + + // // Create 'Insert Link to Galaxy Object' menu. // // Add menu button. - var insert_link_menu_button = $("<div><a id='insert-galaxy-link' class='panel-header-button popup' href='#'>${_('Insert Link to Galaxy Object')}</a></div>").addClass('galaxy-page-editor-button'); + var insert_link_menu_button = $("<div><a id='insert-galaxy-link' class='action-button popup' href='#'>${_('Insert Link to Galaxy Object')}</a></div>").addClass('galaxy-page-editor-button'); $(".wym_area_top").append(insert_link_menu_button); // Add menu options. @@ -688,7 +676,7 @@ // // Add menu button. - var embed_object_button = $("<div><a id='embed-galaxy-object' class='panel-header-button popup' href='#'>${_('Embed Galaxy Object')}</a></div>").addClass('galaxy-page-editor-button'); + var embed_object_button = $("<div><a id='embed-galaxy-object' class='action-button popup' href='#'>${_('Embed Galaxy Object')}</a></div>").addClass('galaxy-page-editor-button'); $(".wym_area_top").append(embed_object_button); // Add menu options.

1 0

[hg] galaxy 3449: Ran optipng on sprite images
by Greg Von Kuster 03 Mar '10

03 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/405764879961 changeset: 3449:405764879961 user: James Taylor <james(a)jamestaylor.org> date: Mon Mar 01 12:14:04 2010 -0500 description: Ran optipng on sprite images diffstat: static/june_2007_style/blue/fugue.png | 0 static/june_2007_style/blue/history-buttons.png | 0 static/june_2007_style/blue/history-states.png | 0 3 files changed, 0 insertions(+), 0 deletions(-) diffs (6 lines): diff -r d3f94b7aa60f -r 405764879961 static/june_2007_style/blue/fugue.png Binary file static/june_2007_style/blue/fugue.png has changed diff -r d3f94b7aa60f -r 405764879961 static/june_2007_style/blue/history-buttons.png Binary file static/june_2007_style/blue/history-buttons.png has changed diff -r d3f94b7aa60f -r 405764879961 static/june_2007_style/blue/history-states.png Binary file static/june_2007_style/blue/history-states.png has changed

1 0

[hg] galaxy 3448: fix: menu border opacity
by Greg Von Kuster 03 Mar '10

03 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/d3f94b7aa60f changeset: 3448:d3f94b7aa60f user: James Taylor <james(a)jamestaylor.org> date: Mon Mar 01 12:09:38 2010 -0500 description: fix: menu border opacity diffstat: static/june_2007_style/blue/base.css | 2 +- 1 files changed, 1 insertions(+), 1 deletions(-) diffs (12 lines): diff -r f5d383525d68 -r d3f94b7aa60f static/june_2007_style/blue/base.css --- a/static/june_2007_style/blue/base.css Mon Mar 01 12:01:50 2010 -0500 +++ b/static/june_2007_style/blue/base.css Mon Mar 01 12:09:38 2010 -0500 @@ -91,7 +91,7 @@ .menubutton:hover{border-color:#aaaaaa;} .menubutton.popup.split{padding-right:2em;} .menubutton.popup.split:hover{background:url(../images/ddarrowsplit.png) no-repeat right -38px;} -.overlay-border{position:absolute;top:0;left:0;height:100%;width:100%;padding:1em;margin:-1em;background-color:rgba(0,0,0,0.8);-moz-border-radius:1em;-webkit-border-radius:1em;z-index:-1;} +.overlay-border{position:absolute;top:0;left:0;height:100%;width:100%;padding:1em;margin:-1em;background-color:rgba(0,0,0,0.5);-moz-border-radius:1em;-webkit-border-radius:1em;z-index:-1;} div.popmenu-wrapper{position:absolute;top:100%;z-index:20000;} div.popmenu-wrapper ul{display:block;margin:0;padding:0;background:white;color:#333;font-weight:bold;font-style:normal;white-space:nowrap;border:solid #aaaaaa 1px;padding:3px 0;-moz-border-radius:0.5em;-webkit-border-radius:0.5em;border-radius:0.5em;user-select:none;-moz-user-select:none;-webkit-user-select:none;} div.popmenu-wrapper ul li{display:block;padding:3px 1em;cursor:pointer;border-top:solid transparent 1px;border-bottom:solid transparent 1px;}

1 0

[hg] galaxy 3447: 1) Jquery 1.4 again, with fixed tooltips; 2) S...
by Greg Von Kuster 03 Mar '10

03 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/f5d383525d68 changeset: 3447:f5d383525d68 user: James Taylor <james(a)jamestaylor.org> date: Mon Mar 01 12:01:50 2010 -0500 description: 1) Jquery 1.4 again, with fixed tooltips; 2) Style changes for history, icons and editable text areas. diffstat: lib/galaxy/jobs/__init__.py | 2 +- static/images/fugue/arrow-circle.png | 0 static/images/fugue/bug.png | 0 static/images/fugue/chevron-expand.png | 0 static/images/fugue/chevron.png | 0 static/images/fugue/cross-button.png | 0 static/images/fugue/cross.png | 0 static/images/fugue/disk.png | 0 static/images/fugue/eye.png | 0 static/images/fugue/pencil-small.png | 0 static/images/fugue/pencil.png | 0 static/june_2007_style/base.css.tmpl | 51 +- static/june_2007_style/blue/base.css | 19 +- static/june_2007_style/blue/fugue.png | 0 static/june_2007_style/blue/history.css | 2 +- static/june_2007_style/history.css.tmpl | 3 +- static/june_2007_style/make_style.py | 2 +- static/june_2007_style/process_css.py | 27 +- static/scripts/jquery.js | 7076 +++++++++++++++++++----------- static/scripts/jquery.tipsy.js | 25 +- static/scripts/packed/jquery.js | 17 +- static/scripts/packed/jquery.tipsy.js | 2 +- templates/root/history.mako | 92 +- templates/root/history_common.mako | 191 +- 24 files changed, 4715 insertions(+), 2794 deletions(-) diffs (truncated from 9068 to 3000 lines): diff -r 143c920af25c -r f5d383525d68 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py Sun Feb 28 22:19:56 2010 -0500 +++ b/lib/galaxy/jobs/__init__.py Mon Mar 01 12:01:50 2010 -0500 @@ -155,7 +155,7 @@ run and dispatching if so. """ # HACK: Delay until after forking, we need a way to do post fork notification!!! - time.sleep( 10 ) + time.sleep( 1000 ) while self.running: try: self.__monitor_step() diff -r 143c920af25c -r f5d383525d68 static/images/fugue/arrow-circle.png Binary file static/images/fugue/arrow-circle.png has changed diff -r 143c920af25c -r f5d383525d68 static/images/fugue/bug.png Binary file static/images/fugue/bug.png has changed diff -r 143c920af25c -r f5d383525d68 static/images/fugue/chevron-expand.png Binary file static/images/fugue/chevron-expand.png has changed diff -r 143c920af25c -r f5d383525d68 static/images/fugue/chevron.png Binary file static/images/fugue/chevron.png has changed diff -r 143c920af25c -r f5d383525d68 static/images/fugue/cross-button.png Binary file static/images/fugue/cross-button.png has changed diff -r 143c920af25c -r f5d383525d68 static/images/fugue/cross.png Binary file static/images/fugue/cross.png has changed diff -r 143c920af25c -r f5d383525d68 static/images/fugue/disk.png Binary file static/images/fugue/disk.png has changed diff -r 143c920af25c -r f5d383525d68 static/images/fugue/eye.png Binary file static/images/fugue/eye.png has changed diff -r 143c920af25c -r f5d383525d68 static/images/fugue/pencil-small.png Binary file static/images/fugue/pencil-small.png has changed diff -r 143c920af25c -r f5d383525d68 static/images/fugue/pencil.png Binary file static/images/fugue/pencil.png has changed diff -r 143c920af25c -r f5d383525d68 static/june_2007_style/base.css.tmpl --- a/static/june_2007_style/base.css.tmpl Sun Feb 28 22:19:56 2010 -0500 +++ b/static/june_2007_style/base.css.tmpl Mon Mar 01 12:01:50 2010 -0500 @@ -720,57 +720,70 @@ -sprite-group: history-buttons; -sprite-image: eye_icon.png; } - .icon-button.display:hover { -sprite-group: history-buttons; -sprite-image: eye_icon_dark.png; } - .icon-button.delete { -sprite-group: history-buttons; -sprite-image: delete_icon.png; } - .icon-button.delete:hover { -sprite-group: history-buttons; -sprite-image: delete_icon_dark.png; } - .icon-button.edit { -sprite-group: history-buttons; -sprite-image: pencil_icon.png; } - .icon-button.edit:hover { -sprite-group: history-buttons; -sprite-image: pencil_icon_dark.png; } .icon-button.tag { - background-image: url(/static/images/fugue/tag-label.png); + -sprite-group: fugue; + -sprite-image: fugue/tag-label.png; } - .icon-button.tags { - background-image: url(/static/images/fugue/tags.png); + -sprite-group: fugue; + -sprite-image: fugue/tags.png; } - .icon-button.tag--plus { - background-image: url(/static/images/fugue/tag--plus.png); + -sprite-group: fugue; + -sprite-image: fugue/tag--plus.png; } - .icon-button.toggle-expand { - background-image:url(/static/images/fugue/toggle-expand.png); + -sprite-group: fugue; + -sprite-image: fugue/toggle-expand.png; } - +.icon-button.toggle { + -sprite-group: fugue; + -sprite-image: fugue/toggle.png; +} .icon-button.toggle-contract { - background-image:url(/static/images/fugue/toggle.png); + -sprite-group: fugue; + -sprite-image: fugue/toggle.png; } - +.icon-button.arrow-circle { + -sprite-group: fugue; + -sprite-image: fugue/arrow-circle.png; +} +.icon-button.chevron { + -sprite-group: fugue; + -sprite-image: fugue/chevron.png; +} +.icon-button.bug { + -sprite-group: fugue; + -sprite-image: fugue/bug.png; +} +.icon-button.disk { + -sprite-group: fugue; + -sprite-image: fugue/disk.png; +} .icon-button.annotate { - background-image:url(/static/images/fugue/sticky-note-text.png); - background-repeat:no-repeat; - background-position:center; - padding: 0; + -sprite-group: fugue; + -sprite-image: fugue/sticky-note-text.png; } .tipsy { diff -r 143c920af25c -r f5d383525d68 static/june_2007_style/blue/base.css --- a/static/june_2007_style/blue/base.css Sun Feb 28 22:19:56 2010 -0500 +++ b/static/june_2007_style/blue/base.css Mon Mar 01 12:01:50 2010 -0500 @@ -91,7 +91,7 @@ .menubutton:hover{border-color:#aaaaaa;} .menubutton.popup.split{padding-right:2em;} .menubutton.popup.split:hover{background:url(../images/ddarrowsplit.png) no-repeat right -38px;} -.overlay-border{position:absolute;top:0;left:0;height:100%;width:100%;padding:1em;margin:-1em;background-color:rgba(0,0,0,0.5);-moz-border-radius:1em;-webkit-border-radius:1em;z-index:-1;} +.overlay-border{position:absolute;top:0;left:0;height:100%;width:100%;padding:1em;margin:-1em;background-color:rgba(0,0,0,0.8);-moz-border-radius:1em;-webkit-border-radius:1em;z-index:-1;} div.popmenu-wrapper{position:absolute;top:100%;z-index:20000;} div.popmenu-wrapper ul{display:block;margin:0;padding:0;background:white;color:#333;font-weight:bold;font-style:normal;white-space:nowrap;border:solid #aaaaaa 1px;padding:3px 0;-moz-border-radius:0.5em;-webkit-border-radius:0.5em;border-radius:0.5em;user-select:none;-moz-user-select:none;-webkit-user-select:none;} div.popmenu-wrapper ul li{display:block;padding:3px 1em;cursor:pointer;border-top:solid transparent 1px;border-bottom:solid transparent 1px;} @@ -124,12 +124,17 @@ .icon-button.delete:hover{background:url(history-buttons.png) no-repeat 0px -78px;} .icon-button.edit{background:url(history-buttons.png) no-repeat 0px -104px;} .icon-button.edit:hover{background:url(history-buttons.png) no-repeat 0px -130px;} -.icon-button.tag{background-image:url(/static/images/fugue/tag-label.png);} -.icon-button.tags{background-image:url(/static/images/fugue/tags.png);} -.icon-button.tag--plus{background-image:url(/static/images/fugue/tag--plus.png);} -.icon-button.toggle-expand{background-image:url(/static/images/fugue/toggle-expand.png);} -.icon-button.toggle-contract{background-image:url(/static/images/fugue/toggle.png);} -.icon-button.annotate{background-image:url(/static/images/fugue/sticky-note-text.png);background-repeat:no-repeat;background-position:center;padding:0;} +.icon-button.tag{background:url(fugue.png) no-repeat 0px -0px;} +.icon-button.tags{background:url(fugue.png) no-repeat 0px -26px;} +.icon-button.tag--plus{background:url(fugue.png) no-repeat 0px -52px;} +.icon-button.toggle-expand{background:url(fugue.png) no-repeat 0px -78px;} +.icon-button.toggle{background:url(fugue.png) no-repeat 0px -104px;} +.icon-button.toggle-contract{background:url(fugue.png) no-repeat 0px -104px;} +.icon-button.arrow-circle{background:url(fugue.png) no-repeat 0px -130px;} +.icon-button.chevron{background:url(fugue.png) no-repeat 0px -156px;} +.icon-button.bug{background:url(fugue.png) no-repeat 0px -182px;} +.icon-button.disk{background:url(fugue.png) no-repeat 0px -208px;} +.icon-button.annotate{background:url(fugue.png) no-repeat 0px -234px;} .tipsy{padding:5px;font-size:10px;filter:alpha(opacity=80);background-repeat:no-repeat;background-image:url(../images/tipsy.gif);} .tipsy-inner{padding:5px 8px 4px 8px;background-color:black;color:white;max-width:200px;text-align:center;} .tipsy-north{background-position:top center;} diff -r 143c920af25c -r f5d383525d68 static/june_2007_style/blue/fugue.png Binary file static/june_2007_style/blue/fugue.png has changed diff -r 143c920af25c -r f5d383525d68 static/june_2007_style/blue/history.css --- a/static/june_2007_style/blue/history.css Sun Feb 28 22:19:56 2010 -0500 +++ b/static/june_2007_style/blue/history.css Mon Mar 01 12:01:50 2010 -0500 @@ -1,6 +1,6 @@ body{background:#C1C9E5;color:#303030;background-image:url(menu_bg.png);background-repeat:repeat-x;background-position:top;margin:5px;border:0;padding:0;} a{color:#303030;} -div.historyLinks{padding:5px;margin:5px 0 5px 0;} +div.historyLinks{margin:5px 5px;} div.historyItem{margin:5px -5px 5px 0px;padding:5px 11px 5px 5px;border:solid #888888 1px;border-left:solid #888888 5px;border-right:none;background:#EEEEEE;} div.historyItem .state-icon{display:inline-block;vertical-align:middle;width:16px;height:16px;background-position:0 1px;background-repeat:no-repeat;} div.historyItem .historyItemTitle{font-weight:bold;line-height:16px;} diff -r 143c920af25c -r f5d383525d68 static/june_2007_style/history.css.tmpl --- a/static/june_2007_style/history.css.tmpl Sun Feb 28 22:19:56 2010 -0500 +++ b/static/june_2007_style/history.css.tmpl Mon Mar 01 12:01:50 2010 -0500 @@ -15,8 +15,7 @@ ## Control links at top of history div.historyLinks { - padding: 5px; - margin: 5px 0 5px 0; + margin: 5px 5px; } ## Default history item appearance diff -r 143c920af25c -r f5d383525d68 static/june_2007_style/make_style.py --- a/static/june_2007_style/make_style.py Sun Feb 28 22:19:56 2010 -0500 +++ b/static/june_2007_style/make_style.py Mon Mar 01 12:01:50 2010 -0500 @@ -66,7 +66,7 @@ for input, output in templates: print input ,"->", output - subprocess.call( "./process_css.py %s %s < %s > %s" % ( vars, out_dir, input, os.path.join( out_dir, output ) ), shell=True ) + subprocess.call( "./process_css.py %s %s:../images %s < %s > %s" % ( vars, out_dir, out_dir, input, os.path.join( out_dir, output ) ), shell=True ) """ diff -r 143c920af25c -r f5d383525d68 static/june_2007_style/process_css.py --- a/static/june_2007_style/process_css.py Sun Feb 28 22:19:56 2010 -0500 +++ b/static/june_2007_style/process_css.py Mon Mar 01 12:01:50 2010 -0500 @@ -35,6 +35,20 @@ digits[i] = wheels[i].next() else: break + +def find_file( path, fname ): + # Path can be a single directory or a ':' separated list + if ':' in path: + paths = path.split( ':' ) + else: + paths = [ path ] + # Check in each directory + for path in paths: + fullname = os.path.join( path, fname ) + if os.path.exists( fullname ): + return fullname + # Not found + raise IOError( "File '%s' not found in path '%s'" % ( fname, paths ) ) def build_stylesheet_parser(): """ @@ -87,7 +101,7 @@ class CSSProcessor( object ): - def process( self, file, out, variables, image_dir ): + def process( self, file, out, variables, image_dir, out_dir ): # Build parse tree results = stylesheet_parser.parseFile( sys.stdin, parseAll=True ) # Expand rules (elimimate recursion and resolve mixins) @@ -95,7 +109,7 @@ # Expand variables (inplace) self.expand_variables( rules, variables ) # Do sprites - self.make_sprites( rules, image_dir ) + self.make_sprites( rules, image_dir, out_dir ) # Print self.print_rules( rules, out ) @@ -139,7 +153,7 @@ for p in properties: p[1] = string.Template( p[1] ).substitute( context ).strip() - def make_sprites( self, rules, image_dir ): + def make_sprites( self, rules, image_dir, out_dir ): pad = 10 @@ -159,7 +173,7 @@ class Sprite( object ): def __init__( self, fname, offset ): self.fname = fname - self.image = Image.open( os.path.join( image_dir, fname ) ) + self.image = Image.open( find_file( image_dir, fname ) ) self.offset = offset sprite_groups = {} @@ -200,7 +214,7 @@ for sprite in group.sprites.itervalues(): master.paste( sprite.image, (0,offset) ) offset += sprite.image.size[1] + pad - master.save( os.path.join( image_dir, group.name + ".png" ) ) + master.save( os.path.join( out_dir, group.name + ".png" ) ) def print_rules( self, rules, file ): for selectors, properties in rules: @@ -223,11 +237,12 @@ context[key] = value image_dir = sys.argv[2] + out_dir = sys.argv[3] try: processor = CSSProcessor() - processor.process( sys.stdin, sys.stdout, context, image_dir ) + processor.process( sys.stdin, sys.stdout, context, image_dir, out_dir ) except ParseException, e: diff -r 143c920af25c -r f5d383525d68 static/scripts/jquery.js --- a/static/scripts/jquery.js Sun Feb 28 22:19:56 2010 -0500 +++ b/static/scripts/jquery.js Mon Mar 01 12:01:50 2010 -0500 @@ -1,567 +1,310 @@ -/*! - * jQuery JavaScript Library v1.3.2 +/* + * jQuery JavaScript Library v1.4.2 * http://jquery.com/ * - * Copyright (c) 2009 John Resig - * Dual licensed under the MIT and GPL licenses. - * http://docs.jquery.com/License + * Copyright 2010, John Resig + * Dual licensed under the MIT or GPL Version 2 licenses. + * http://jquery.org/license * - * Date: 2009-02-19 17:34:21 -0500 (Thu, 19 Feb 2009) - * Revision: 6246 + * Includes Sizzle.js + * http://sizzlejs.com/ + * Copyright 2010, The Dojo Foundation + * Released under the MIT, BSD, and GPL Licenses. + * + * Date: Sat Feb 13 22:33:48 2010 -0500 */ -(function(){ - -var - // Will speed up references to window, and allows munging its name. - window = this, - // Will speed up references to undefined, and allows munging its name. - undefined, - // Map over jQuery in case of overwrite - _jQuery = window.jQuery, - // Map over the $ in case of overwrite - _$ = window.$, - - jQuery = window.jQuery = window.$ = function( selector, context ) { +(function( window, undefined ) { + +// Define a local copy of jQuery +var jQuery = function( selector, context ) { // The jQuery object is actually just the init constructor 'enhanced' return new jQuery.fn.init( selector, context ); }, + // Map over jQuery in case of overwrite + _jQuery = window.jQuery, + + // Map over the $ in case of overwrite + _$ = window.$, + + // Use the correct document accordingly with window argument (sandbox) + document = window.document, + + // A central reference to the root jQuery(document) + rootjQuery, + // A simple way to check for HTML strings or ID strings // (both of which we optimize for) - quickExpr = /^[^<]*(<(.|\s)+>)[^>]*$|^#([\w-]+)$/, + quickExpr = /^[^<]*(<[\w\W]+>)[^>]*$|^#([\w-]+)$/, + // Is it a simple selector - isSimple = /^.[^:#\[\.,]*$/; + isSimple = /^.[^:#\[\.,]*$/, + + // Check if a string has a non-whitespace character in it + rnotwhite = /\S/, + + // Used for trimming whitespace + rtrim = /^(\s|\u00A0)+|(\s|\u00A0)+$/g, + + // Match a standalone tag + rsingleTag = /^<(\w+)\s*\/?>(?:<\/\1>)?$/, + + // Keep a UserAgent string for use with jQuery.browser + userAgent = navigator.userAgent, + + // For matching the engine and version of the browser + browserMatch, + + // Has the ready events already been bound? + readyBound = false, + + // The functions to execute on DOM ready + readyList = [], + + // The ready event handler + DOMContentLoaded, + + // Save a reference to some core methods + toString = Object.prototype.toString, + hasOwnProperty = Object.prototype.hasOwnProperty, + push = Array.prototype.push, + slice = Array.prototype.slice, + indexOf = Array.prototype.indexOf; jQuery.fn = jQuery.prototype = { init: function( selector, context ) { - // Make sure that a selection was provided - selector = selector || document; + var match, elem, ret, doc; + + // Handle $(""), $(null), or $(undefined) + if ( !selector ) { + return this; + } // Handle $(DOMElement) if ( selector.nodeType ) { - this[0] = selector; + this.context = this[0] = selector; this.length = 1; - this.context = selector; return this; } + + // The body element only exists once, optimize finding it + if ( selector === "body" && !context ) { + this.context = document; + this[0] = document.body; + this.selector = "body"; + this.length = 1; + return this; + } + // Handle HTML strings if ( typeof selector === "string" ) { // Are we dealing with HTML string or an ID? - var match = quickExpr.exec( selector ); + match = quickExpr.exec( selector ); // Verify a match, and that no context was specified for #id if ( match && (match[1] || !context) ) { // HANDLE: $(html) -> $(array) - if ( match[1] ) - selector = jQuery.clean( [ match[1] ], context ); - + if ( match[1] ) { + doc = (context ? context.ownerDocument || context : document); + + // If a single string is passed in and it's a single tag + // just do a createElement and skip the rest + ret = rsingleTag.exec( selector ); + + if ( ret ) { + if ( jQuery.isPlainObject( context ) ) { + selector = [ document.createElement( ret[1] ) ]; + jQuery.fn.attr.call( selector, context, true ); + + } else { + selector = [ doc.createElement( ret[1] ) ]; + } + + } else { + ret = buildFragment( [ match[1] ], [ doc ] ); + selector = (ret.cacheable ? ret.fragment.cloneNode(true) : ret.fragment).childNodes; + } + + return jQuery.merge( this, selector ); + // HANDLE: $("#id") - else { - var elem = document.getElementById( match[3] ); - - // Handle the case where IE and Opera return items - // by name instead of ID - if ( elem && elem.id != match[3] ) - return jQuery().find( selector ); - - // Otherwise, we inject the element directly into the jQuery object - var ret = jQuery( elem || [] ); - ret.context = document; - ret.selector = selector; - return ret; + } else { + elem = document.getElementById( match[2] ); + + if ( elem ) { + // Handle the case where IE and Opera return items + // by name instead of ID + if ( elem.id !== match[2] ) { + return rootjQuery.find( selector ); + } + + // Otherwise, we inject the element directly into the jQuery object + this.length = 1; + this[0] = elem; + } + + this.context = document; + this.selector = selector; + return this; } - // HANDLE: $(expr, [context]) - // (which is just equivalent to: $(content).find(expr) - } else + // HANDLE: $("TAG") + } else if ( !context && /^\w+$/.test( selector ) ) { + this.selector = selector; + this.context = document; + selector = document.getElementsByTagName( selector ); + return jQuery.merge( this, selector ); + + // HANDLE: $(expr, $(...)) + } else if ( !context || context.jquery ) { + return (context || rootjQuery).find( selector ); + + // HANDLE: $(expr, context) + // (which is just equivalent to: $(context).find(expr) + } else { return jQuery( context ).find( selector ); + } // HANDLE: $(function) // Shortcut for document ready - } else if ( jQuery.isFunction( selector ) ) - return jQuery( document ).ready( selector ); - - // Make sure that old selector state is passed along - if ( selector.selector && selector.context ) { + } else if ( jQuery.isFunction( selector ) ) { + return rootjQuery.ready( selector ); + } + + if (selector.selector !== undefined) { this.selector = selector.selector; this.context = selector.context; } - return this.setArray(jQuery.isArray( selector ) ? - selector : - jQuery.makeArray(selector)); + return jQuery.makeArray( selector, this ); }, // Start with an empty selector selector: "", // The current version of jQuery being used - jquery: "1.3.2", + jquery: "1.4.2", + + // The default length of a jQuery object is 0 + length: 0, // The number of elements contained in the matched element set size: function() { return this.length; }, + toArray: function() { + return slice.call( this, 0 ); + }, + // Get the Nth element in the matched element set OR // Get the whole matched element set as a clean array get: function( num ) { - return num === undefined ? + return num == null ? // Return a 'clean' array - Array.prototype.slice.call( this ) : + this.toArray() : // Return just the object - this[ num ]; + ( num < 0 ? this.slice(num)[ 0 ] : this[ num ] ); }, // Take an array of elements and push it onto the stack // (returning the new matched element set) pushStack: function( elems, name, selector ) { // Build a new jQuery matched element set - var ret = jQuery( elems ); + var ret = jQuery(); + + if ( jQuery.isArray( elems ) ) { + push.apply( ret, elems ); + + } else { + jQuery.merge( ret, elems ); + } // Add the old object onto the stack (as a reference) ret.prevObject = this; ret.context = this.context; - if ( name === "find" ) + if ( name === "find" ) { ret.selector = this.selector + (this.selector ? " " : "") + selector; - else if ( name ) + } else if ( name ) { ret.selector = this.selector + "." + name + "(" + selector + ")"; + } // Return the newly-formed element set return ret; }, - // Force the current matched set of elements to become - // the specified array of elements (destroying the stack in the process) - // You should use pushStack() in order to do this, but maintain the stack - setArray: function( elems ) { - // Resetting the length to 0, then using the native Array push - // is a super-fast way to populate an object with array-like properties - this.length = 0; - Array.prototype.push.apply( this, elems ); - - return this; - }, - // Execute a callback for every element in the matched set. // (You can seed the arguments with an array of args, but this is // only used internally.) each: function( callback, args ) { return jQuery.each( this, callback, args ); }, - - // Determine the position of an element within - // the matched set of elements - index: function( elem ) { - // Locate the position of the desired element - return jQuery.inArray( - // If it receives a jQuery object, the first element is used - elem && elem.jquery ? elem[0] : elem - , this ); - }, - - attr: function( name, value, type ) { - var options = name; - - // Look for the case where we're accessing a style value - if ( typeof name === "string" ) - if ( value === undefined ) - return this[0] && jQuery[ type || "attr" ]( this[0], name ); - - else { - options = {}; - options[ name ] = value; - } - - // Check to see if we're setting style values - return this.each(function(i){ - // Set all the styles - for ( name in options ) - jQuery.attr( - type ? - this.style : - this, - name, jQuery.prop( this, options[ name ], type, i, name ) - ); - }); - }, - - css: function( key, value ) { - // ignore negative width and height values - if ( (key == 'width' || key == 'height') && parseFloat(value) < 0 ) - value = undefined; - return this.attr( key, value, "curCSS" ); - }, - - text: function( text ) { - if ( typeof text !== "object" && text != null ) - return this.empty().append( (this[0] && this[0].ownerDocument || document).createTextNode( text ) ); - - var ret = ""; - - jQuery.each( text || this, function(){ - jQuery.each( this.childNodes, function(){ - if ( this.nodeType != 8 ) - ret += this.nodeType != 1 ? - this.nodeValue : - jQuery.fn.text( [ this ] ); - }); - }); - - return ret; - }, - - wrapAll: function( html ) { - if ( this[0] ) { - // The elements to wrap the target around - var wrap = jQuery( html, this[0].ownerDocument ).clone(); - - if ( this[0].parentNode ) - wrap.insertBefore( this[0] ); - - wrap.map(function(){ - var elem = this; - - while ( elem.firstChild ) - elem = elem.firstChild; - - return elem; - }).append(this); + + ready: function( fn ) { + // Attach the listeners + jQuery.bindReady(); + + // If the DOM is already ready + if ( jQuery.isReady ) { + // Execute the function immediately + fn.call( document, jQuery ); + + // Otherwise, remember the function for later + } else if ( readyList ) { + // Add the function to the wait list + readyList.push( fn ); } return this; }, - - wrapInner: function( html ) { - return this.each(function(){ - jQuery( this ).contents().wrapAll( html ); - }); + + eq: function( i ) { + return i === -1 ? + this.slice( i ) : + this.slice( i, +i + 1 ); }, - wrap: function( html ) { - return this.each(function(){ - jQuery( this ).wrapAll( html ); - }); + first: function() { + return this.eq( 0 ); }, - append: function() { - return this.domManip(arguments, true, function(elem){ - if (this.nodeType == 1) - this.appendChild( elem ); - }); + last: function() { + return this.eq( -1 ); }, - prepend: function() { - return this.domManip(arguments, true, function(elem){ - if (this.nodeType == 1) - this.insertBefore( elem, this.firstChild ); - }); + slice: function() { + return this.pushStack( slice.apply( this, arguments ), + "slice", slice.call(arguments).join(",") ); }, - before: function() { - return this.domManip(arguments, false, function(elem){ - this.parentNode.insertBefore( elem, this ); - }); - }, - - after: function() { - return this.domManip(arguments, false, function(elem){ - this.parentNode.insertBefore( elem, this.nextSibling ); - }); - }, - - end: function() { - return this.prevObject || jQuery( [] ); - }, - - // For internal use only. - // Behaves like an Array's method, not like a jQuery method. - push: [].push, - sort: [].sort, - splice: [].splice, - - find: function( selector ) { - if ( this.length === 1 ) { - var ret = this.pushStack( [], "find", selector ); - ret.length = 0; - jQuery.find( selector, this[0], ret ); - return ret; - } else { - return this.pushStack( jQuery.unique(jQuery.map(this, function(elem){ - return jQuery.find( selector, elem ); - })), "find", selector ); - } - }, - - clone: function( events ) { - // Do the clone - var ret = this.map(function(){ - if ( !jQuery.support.noCloneEvent && !jQuery.isXMLDoc(this) ) { - // IE copies events bound via attachEvent when - // using cloneNode. Calling detachEvent on the - // clone will also remove the events from the orignal - // In order to get around this, we use innerHTML. - // Unfortunately, this means some modifications to - // attributes in IE that are actually only stored - // as properties will not be copied (such as the - // the name attribute on an input). - var html = this.outerHTML; - if ( !html ) { - var div = this.ownerDocument.createElement("div"); - div.appendChild( this.cloneNode(true) ); - html = div.innerHTML; - } - - return jQuery.clean([html.replace(/ jQuery\d+="(?:\d+|null)"/g, "").replace(/^\s*/, "")])[0]; - } else - return this.cloneNode(true); - }); - - // Copy the events from the original to the clone - if ( events === true ) { - var orig = this.find("*").andSelf(), i = 0; - - ret.find("*").andSelf().each(function(){ - if ( this.nodeName !== orig[i].nodeName ) - return; - - var events = jQuery.data( orig[i], "events" ); - - for ( var type in events ) { - for ( var handler in events[ type ] ) { - jQuery.event.add( this, type, events[ type ][ handler ], events[ type ][ handler ].data ); - } - } - - i++; - }); - } - - // Return the cloned set - return ret; - }, - - filter: function( selector ) { - return this.pushStack( - jQuery.isFunction( selector ) && - jQuery.grep(this, function(elem, i){ - return selector.call( elem, i ); - }) || - - jQuery.multiFilter( selector, jQuery.grep(this, function(elem){ - return elem.nodeType === 1; - }) ), "filter", selector ); - }, - - closest: function( selector ) { - var pos = jQuery.expr.match.POS.test( selector ) ? jQuery(selector) : null, - closer = 0; - - return this.map(function(){ - var cur = this; - while ( cur && cur.ownerDocument ) { - if ( pos ? pos.index(cur) > -1 : jQuery(cur).is(selector) ) { - jQuery.data(cur, "closest", closer); - return cur; - } - cur = cur.parentNode; - closer++; - } - }); - }, - - not: function( selector ) { - if ( typeof selector === "string" ) - // test special case where just one selector is passed in - if ( isSimple.test( selector ) ) - return this.pushStack( jQuery.multiFilter( selector, this, true ), "not", selector ); - else - selector = jQuery.multiFilter( selector, this ); - - var isArrayLike = selector.length && selector[selector.length - 1] !== undefined && !selector.nodeType; - return this.filter(function() { - return isArrayLike ? jQuery.inArray( this, selector ) < 0 : this != selector; - }); - }, - - add: function( selector ) { - return this.pushStack( jQuery.unique( jQuery.merge( - this.get(), - typeof selector === "string" ? - jQuery( selector ) : - jQuery.makeArray( selector ) - ))); - }, - - is: function( selector ) { - return !!selector && jQuery.multiFilter( selector, this ).length > 0; - }, - - hasClass: function( selector ) { - return !!selector && this.is( "." + selector ); - }, - - val: function( value ) { - if ( value === undefined ) { - var elem = this[0]; - - if ( elem ) { - if( jQuery.nodeName( elem, 'option' ) ) - return (elem.attributes.value || {}).specified ? elem.value : elem.text; - - // We need to handle select boxes special - if ( jQuery.nodeName( elem, "select" ) ) { - var index = elem.selectedIndex, - values = [], - options = elem.options, - one = elem.type == "select-one"; - - // Nothing was selected - if ( index < 0 ) - return null; - - // Loop through all the selected options - for ( var i = one ? index : 0, max = one ? index + 1 : options.length; i < max; i++ ) { - var option = options[ i ]; - - if ( option.selected ) { - // Get the specifc value for the option - value = jQuery(option).val(); - - // We don't need an array for one selects - if ( one ) - return value; - - // Multi-Selects return an array - values.push( value ); - } - } - - return values; - } - - // Everything else, we just grab the value - return (elem.value || "").replace(/\r/g, ""); - - } - - return undefined; - } - - if ( typeof value === "number" ) - value += ''; - - return this.each(function(){ - if ( this.nodeType != 1 ) - return; - - if ( jQuery.isArray(value) && /radio|checkbox/.test( this.type ) ) - this.checked = (jQuery.inArray(this.value, value) >= 0 || - jQuery.inArray(this.name, value) >= 0); - - else if ( jQuery.nodeName( this, "select" ) ) { - var values = jQuery.makeArray(value); - - jQuery( "option", this ).each(function(){ - this.selected = (jQuery.inArray( this.value, values ) >= 0 || - jQuery.inArray( this.text, values ) >= 0); - }); - - if ( !values.length ) - this.selectedIndex = -1; - - } else - this.value = value; - }); - }, - - html: function( value ) { - return value === undefined ? - (this[0] ? - this[0].innerHTML.replace(/ jQuery\d+="(?:\d+|null)"/g, "") : - null) : - this.empty().append( value ); - }, - - replaceWith: function( value ) { - return this.after( value ).remove(); - }, - - eq: function( i ) { - return this.slice( i, +i + 1 ); - }, - - slice: function() { - return this.pushStack( Array.prototype.slice.apply( this, arguments ), - "slice", Array.prototype.slice.call(arguments).join(",") ); - }, - map: function( callback ) { - return this.pushStack( jQuery.map(this, function(elem, i){ + return this.pushStack( jQuery.map(this, function( elem, i ) { return callback.call( elem, i, elem ); })); }, - - andSelf: function() { - return this.add( this.prevObject ); + + end: function() { + return this.prevObject || jQuery(null); }, - domManip: function( args, table, callback ) { - if ( this[0] ) { - var fragment = (this[0].ownerDocument || this[0]).createDocumentFragment(), - scripts = jQuery.clean( args, (this[0].ownerDocument || this[0]), fragment ), - first = fragment.firstChild; - - if ( first ) - for ( var i = 0, l = this.length; i < l; i++ ) - callback.call( root(this[i], first), this.length > 1 || i > 0 ? - fragment.cloneNode(true) : fragment ); - - if ( scripts ) - jQuery.each( scripts, evalScript ); - } - - return this; - - function root( elem, cur ) { - return table && jQuery.nodeName(elem, "table") && jQuery.nodeName(cur, "tr") ? - (elem.getElementsByTagName("tbody")[0] || - elem.appendChild(elem.ownerDocument.createElement("tbody"))) : - elem; - } - } + // For internal use only. + // Behaves like an Array's method, not like a jQuery method. + push: push, + sort: [].sort, + splice: [].splice }; // Give the init function the jQuery prototype for later instantiation jQuery.fn.init.prototype = jQuery.fn; -function evalScript( i, elem ) { - if ( elem.src ) - jQuery.ajax({ - url: elem.src, - async: false, - dataType: "script" - }); - - else - jQuery.globalEval( elem.text || elem.textContent || elem.innerHTML || "" ); - - if ( elem.parentNode ) - elem.parentNode.removeChild( elem ); -} - -function now(){ - return +new Date; -} - jQuery.extend = jQuery.fn.extend = function() { // copy reference to target object - var target = arguments[0] || {}, i = 1, length = arguments.length, deep = false, options; + var target = arguments[0] || {}, i = 1, length = arguments.length, deep = false, options, name, src, copy; // Handle a deep copy situation if ( typeof target === "boolean" ) { @@ -572,58 +315,137 @@ } // Handle case when target is a string or something (possible in deep copy) - if ( typeof target !== "object" && !jQuery.isFunction(target) ) + if ( typeof target !== "object" && !jQuery.isFunction(target) ) { target = {}; + } // extend jQuery itself if only one argument is passed - if ( length == i ) { + if ( length === i ) { target = this; --i; } - for ( ; i < length; i++ ) + for ( ; i < length; i++ ) { // Only deal with non-null/undefined values - if ( (options = arguments[ i ]) != null ) + if ( (options = arguments[ i ]) != null ) { // Extend the base object - for ( var name in options ) { - var src = target[ name ], copy = options[ name ]; + for ( name in options ) { + src = target[ name ]; + copy = options[ name ]; // Prevent never-ending loop - if ( target === copy ) + if ( target === copy ) { continue; - - // Recurse if we're merging object values - if ( deep && copy && typeof copy === "object" && !copy.nodeType ) - target[ name ] = jQuery.extend( deep, - // Never move original objects, clone them - src || ( copy.length != null ? [ ] : { } ) - , copy ); + } + + // Recurse if we're merging object literal values or arrays + if ( deep && copy && ( jQuery.isPlainObject(copy) || jQuery.isArray(copy) ) ) { + var clone = src && ( jQuery.isPlainObject(src) || jQuery.isArray(src) ) ? src + : jQuery.isArray(copy) ? [] : {}; + + // Never move original objects, clone them + target[ name ] = jQuery.extend( deep, clone, copy ); // Don't bring in undefined values - else if ( copy !== undefined ) + } else if ( copy !== undefined ) { target[ name ] = copy; - - } + } + } + } + } // Return the modified object return target; }; -// exclude the following css properties to add px -var exclude = /z-?index|font-?weight|opacity|zoom|line-?height/i, - // cache defaultView - defaultView = document.defaultView || {}, - toString = Object.prototype.toString; - jQuery.extend({ noConflict: function( deep ) { window.$ = _$; - if ( deep ) + if ( deep ) { window.jQuery = _jQuery; + } return jQuery; }, + + // Is the DOM ready to be used? Set to true once it occurs. + isReady: false, + + // Handle when the DOM is ready + ready: function() { + // Make sure that the DOM is not already loaded + if ( !jQuery.isReady ) { + // Make sure body exists, at least, in case IE gets a little overzealous (ticket #5443). + if ( !document.body ) { + return setTimeout( jQuery.ready, 13 ); + } + + // Remember that the DOM is ready + jQuery.isReady = true; + + // If there are functions bound, to execute + if ( readyList ) { + // Execute all of them + var fn, i = 0; + while ( (fn = readyList[ i++ ]) ) { + fn.call( document, jQuery ); + } + + // Reset the list of functions + readyList = null; + } + + // Trigger any bound ready events + if ( jQuery.fn.triggerHandler ) { + jQuery( document ).triggerHandler( "ready" ); + } + } + }, + + bindReady: function() { + if ( readyBound ) { + return; + } + + readyBound = true; + + // Catch cases where $(document).ready() is called after the + // browser event has already occurred. + if ( document.readyState === "complete" ) { + return jQuery.ready(); + } + + // Mozilla, Opera and webkit nightlies currently support this event + if ( document.addEventListener ) { + // Use the handy event callback + document.addEventListener( "DOMContentLoaded", DOMContentLoaded, false ); + + // A fallback to window.onload, that will always work + window.addEventListener( "load", jQuery.ready, false ); + + // If IE event model is used + } else if ( document.attachEvent ) { + // ensure firing before onload, + // maybe late but safe also for iframes + document.attachEvent("onreadystatechange", DOMContentLoaded); + + // A fallback to window.onload, that will always work + window.attachEvent( "onload", jQuery.ready ); + + // If IE and not a frame + // continually check to see if the document is ready + var toplevel = false; + + try { + toplevel = window.frameElement == null; + } catch(e) {} + + if ( document.documentElement.doScroll && toplevel ) { + doScrollCheck(); + } + } + }, // See test/unit/core.js for details concerning isFunction. // Since version 1.3, DOM methods and functions like alert @@ -636,27 +458,84 @@ return toString.call(obj) === "[object Array]"; }, - // check if an element is in a (or is an) XML document - isXMLDoc: function( elem ) { - return elem.nodeType === 9 && elem.documentElement.nodeName !== "HTML" || - !!elem.ownerDocument && jQuery.isXMLDoc( elem.ownerDocument ); + isPlainObject: function( obj ) { + // Must be an Object. + // Because of IE, we also have to check the presence of the constructor property. + // Make sure that DOM nodes and window objects don't pass through, as well + if ( !obj || toString.call(obj) !== "[object Object]" || obj.nodeType || obj.setInterval ) { + return false; + } + + // Not own constructor property must be Object + if ( obj.constructor + && !hasOwnProperty.call(obj, "constructor") + && !hasOwnProperty.call(obj.constructor.prototype, "isPrototypeOf") ) { + return false; + } + + // Own properties are enumerated firstly, so to speed up, + // if last one is own, then all properties are own. + + var key; + for ( key in obj ) {} + + return key === undefined || hasOwnProperty.call( obj, key ); }, + isEmptyObject: function( obj ) { + for ( var name in obj ) { + return false; + } + return true; + }, + + error: function( msg ) { + throw msg; + }, + + parseJSON: function( data ) { + if ( typeof data !== "string" || !data ) { + return null; + } + + // Make sure leading/trailing whitespace is removed (IE can't handle it) + data = jQuery.trim( data ); + + // Make sure the incoming data is actual JSON + // Logic borrowed from http://json.org/json2.js + if ( /^[\],:{}\s]*$/.test(data.replace(/\\(?:["\\\/bfnrt]|u[0-9a-fA-F]{4})/g, "@") + .replace(/"[^"\\\n\r]*"|true|false|null|-?\d+(?:\.\d*)?(?:[eE][+\-]?\d+)?/g, "]") + .replace(/(?:^|:|,)(?:\s*\[)+/g, "")) ) { + + // Try to use the native JSON parser first + return window.JSON && window.JSON.parse ? + window.JSON.parse( data ) : + (new Function("return " + data))(); + + } else { + jQuery.error( "Invalid JSON: " + data ); + } + }, + + noop: function() {}, + // Evalulates a script in a global context globalEval: function( data ) { - if ( data && /\S/.test(data) ) { + if ( data && rnotwhite.test(data) ) { // Inspired by code by Andrea Giammarchi // http://webreflection.blogspot.com/2007/08/global-scope-evaluation-and-dom.h… var head = document.getElementsByTagName("head")[0] || document.documentElement, script = document.createElement("script"); script.type = "text/javascript"; - if ( jQuery.support.scriptEval ) + + if ( jQuery.support.scriptEval ) { script.appendChild( document.createTextNode( data ) ); - else + } else { script.text = data; - - // Use insertBefore instead of appendChild to circumvent an IE6 bug. + } + + // Use insertBefore instead of appendChild to circumvent an IE6 bug. // This arises when a base node is used (#2709). head.insertBefore( script, head.firstChild ); head.removeChild( script ); @@ -664,785 +543,2130 @@ }, nodeName: function( elem, name ) { - return elem.nodeName && elem.nodeName.toUpperCase() == name.toUpperCase(); + return elem.nodeName && elem.nodeName.toUpperCase() === name.toUpperCase(); }, // args is for internal usage only each: function( object, callback, args ) { - var name, i = 0, length = object.length; + var name, i = 0, + length = object.length, + isObj = length === undefined || jQuery.isFunction(object); if ( args ) { - if ( length === undefined ) { - for ( name in object ) - if ( callback.apply( object[ name ], args ) === false ) + if ( isObj ) { + for ( name in object ) { + if ( callback.apply( object[ name ], args ) === false ) { break; - } else - for ( ; i < length; ) - if ( callback.apply( object[ i++ ], args ) === false ) + } + } + } else { + for ( ; i < length; ) { + if ( callback.apply( object[ i++ ], args ) === false ) { break; + } + } + } // A special, fast, case for the most common use of each } else { - if ( length === undefined ) { - for ( name in object ) - if ( callback.call( object[ name ], name, object[ name ] ) === false ) + if ( isObj ) { + for ( name in object ) { + if ( callback.call( object[ name ], name, object[ name ] ) === false ) { break; - } else + } + } + } else { for ( var value = object[0]; - i < length && callback.call( value, i, value ) !== false; value = object[++i] ){} + i < length && callback.call( value, i, value ) !== false; value = object[++i] ) {} + } } return object; }, - prop: function( elem, value, type, i, name ) { - // Handle executable functions - if ( jQuery.isFunction( value ) ) - value = value.call( elem, i ); - - // Handle passing in a number to a CSS property - return typeof value === "number" && type == "curCSS" && !exclude.test( name ) ? - value + "px" : - value; + trim: function( text ) { + return (text || "").replace( rtrim, "" ); }, - className: { - // internal only, use addClass("class") - add: function( elem, classNames ) { - jQuery.each((classNames || "").split(/\s+/), function(i, className){ - if ( elem.nodeType == 1 && !jQuery.className.has( elem.className, className ) ) - elem.className += (elem.className ? " " : "") + className; - }); - }, - - // internal only, use removeClass("class") - remove: function( elem, classNames ) { - if (elem.nodeType == 1) - elem.className = classNames !== undefined ? - jQuery.grep(elem.className.split(/\s+/), function(className){ - return !jQuery.className.has( classNames, className ); - }).join(" ") : - ""; - }, - - // internal only, use hasClass("class") - has: function( elem, className ) { - return elem && jQuery.inArray( className, (elem.className || elem).toString().split(/\s+/) ) > -1; - } - }, - - // A method for quickly swapping in/out CSS properties to get correct calculations - swap: function( elem, options, callback ) { - var old = {}; - // Remember the old values, and insert the new ones - for ( var name in options ) { - old[ name ] = elem.style[ name ]; - elem.style[ name ] = options[ name ]; - } - - callback.call( elem ); - - // Revert the old values - for ( var name in options ) - elem.style[ name ] = old[ name ]; - }, - - css: function( elem, name, force, extra ) { - if ( name == "width" || name == "height" ) { - var val, props = { position: "absolute", visibility: "hidden", display:"block" }, which = name == "width" ? [ "Left", "Right" ] : [ "Top", "Bottom" ]; - - function getWH() { - val = name == "width" ? elem.offsetWidth : elem.offsetHeight; - - if ( extra === "border" ) - return; - - jQuery.each( which, function() { - if ( !extra ) - val -= parseFloat(jQuery.curCSS( elem, "padding" + this, true)) || 0; - if ( extra === "margin" ) - val += parseFloat(jQuery.curCSS( elem, "margin" + this, true)) || 0; - else - val -= parseFloat(jQuery.curCSS( elem, "border" + this + "Width", true)) || 0; - }); - } - - if ( elem.offsetWidth !== 0 ) - getWH(); - else - jQuery.swap( elem, props, getWH ); - - return Math.max(0, Math.round(val)); - } - - return jQuery.curCSS( elem, name, force ); - }, - - curCSS: function( elem, name, force ) { - var ret, style = elem.style; - - // We need to handle opacity special in IE - if ( name == "opacity" && !jQuery.support.opacity ) { - ret = jQuery.attr( style, "opacity" ); - - return ret == "" ? - "1" : - ret; - } - - // Make sure we're using the right name for getting the float value - if ( name.match( /float/i ) ) - name = styleFloat; - - if ( !force && style && style[ name ] ) - ret = style[ name ]; - - else if ( defaultView.getComputedStyle ) { - - // Only "float" is needed here - if ( name.match( /float/i ) ) - name = "float"; - - name = name.replace( /([A-Z])/g, "-$1" ).toLowerCase(); - - var computedStyle = defaultView.getComputedStyle( elem, null ); - - if ( computedStyle ) - ret = computedStyle.getPropertyValue( name ); - - // We should always get a number back from opacity - if ( name == "opacity" && ret == "" ) - ret = "1"; - - } else if ( elem.currentStyle ) { - var camelCase = name.replace(/\-(\w)/g, function(all, letter){ - return letter.toUpperCase(); - }); - - ret = elem.currentStyle[ name ] || elem.currentStyle[ camelCase ]; - - // From the awesome hack by Dean Edwards - // http://erik.eae.net/archives/2007/07/27/18.54.15/#comment-102291 - - // If we're not dealing with a regular pixel number - // but a number that has a weird ending, we need to convert it to pixels - if ( !/^\d+(px)?$/i.test( ret ) && /^\d/.test( ret ) ) { - // Remember the original values - var left = style.left, rsLeft = elem.runtimeStyle.left; - - // Put in the new values to get a computed value out - elem.runtimeStyle.left = elem.currentStyle.left; - style.left = ret || 0; - ret = style.pixelLeft + "px"; - - // Revert the changed values - style.left = left; - elem.runtimeStyle.left = rsLeft; + // results is for internal usage only + makeArray: function( array, results ) { + var ret = results || []; + + if ( array != null ) { + // The window, strings (and functions) also have 'length' + // The extra typeof function check is to prevent crashes + // in Safari 2 (See: #3039) + if ( array.length == null || typeof array === "string" || jQuery.isFunction(array) || (typeof array !== "function" && array.setInterval) ) { + push.call( ret, array ); + } else { + jQuery.merge( ret, array ); } } return ret; }, - clean: function( elems, context, fragment ) { - context = context || document; - - // !context.createElement fails in IE with an error but returns typeof 'object' - if ( typeof context.createElement === "undefined" ) - context = context.ownerDocument || context[0] && context[0].ownerDocument || document; - - // If a single string is passed in and it's a single tag - // just do a createElement and skip the rest - if ( !fragment && elems.length === 1 && typeof elems[0] === "string" ) { - var match = /^<(\w+)\s*\/?>$/.exec(elems[0]); - if ( match ) - return [ context.createElement( match[1] ) ]; - } - - var ret = [], scripts = [], div = context.createElement("div"); - - jQuery.each(elems, function(i, elem){ - if ( typeof elem === "number" ) - elem += ''; - - if ( !elem ) - return; - - // Convert html string into DOM nodes - if ( typeof elem === "string" ) { - // Fix "XHTML"-style tags in all browsers - elem = elem.replace(/(<(\w+)[^>]*?)\/>/g, function(all, front, tag){ - return tag.match(/^(abbr|br|col|img|input|link|meta|param|hr|area|embed)$/i) ? - all : - front + "></" + tag + ">"; - }); - - // Trim whitespace, otherwise indexOf won't work as expected - var tags = elem.replace(/^\s+/, "").substring(0, 10).toLowerCase(); - - var wrap = - // option or optgroup - !tags.indexOf("<opt") && - [ 1, "<select multiple='multiple'>", "</select>" ] || - - !tags.indexOf("<leg") && - [ 1, "<fieldset>", "</fieldset>" ] || - - tags.match(/^<(thead|tbody|tfoot|colg|cap)/) && - [ 1, "<table>", "</table>" ] || - - !tags.indexOf("<tr") && - [ 2, "<table><tbody>", "</tbody></table>" ] || - - // <thead> matched above - (!tags.indexOf("<td") || !tags.indexOf("<th")) && - [ 3, "<table><tbody><tr>", "</tr></tbody></table>" ] || - - !tags.indexOf("<col") && - [ 2, "<table><tbody></tbody><colgroup>", "</colgroup></table>" ] || - - // IE can't serialize <link> and <script> tags normally - !jQuery.support.htmlSerialize && - [ 1, "div<div>", "</div>" ] || - - [ 0, "", "" ]; - - // Go to html and back, then peel off extra wrappers - div.innerHTML = wrap[1] + elem + wrap[2]; - - // Move to the right depth - while ( wrap[0]-- ) - div = div.lastChild; - - // Remove IE's autoinserted <tbody> from table fragments - if ( !jQuery.support.tbody ) { - - // String was a <table>, *may* have spurious <tbody> - var hasBody = /<tbody/i.test(elem), - tbody = !tags.indexOf("<table") && !hasBody ? - div.firstChild && div.firstChild.childNodes : - - // String was a bare <thead> or <tfoot> - wrap[1] == "<table>" && !hasBody ? - div.childNodes : - []; - - for ( var j = tbody.length - 1; j >= 0 ; --j ) - if ( jQuery.nodeName( tbody[ j ], "tbody" ) && !tbody[ j ].childNodes.length ) - tbody[ j ].parentNode.removeChild( tbody[ j ] ); - - } - - // IE completely kills leading whitespace when innerHTML is used - if ( !jQuery.support.leadingWhitespace && /^\s/.test( elem ) ) - div.insertBefore( context.createTextNode( elem.match(/^\s*/)[0] ), div.firstChild ); - - elem = jQuery.makeArray( div.childNodes ); - } - - if ( elem.nodeType ) - ret.push( elem ); - else - ret = jQuery.merge( ret, elem ); - - }); - - if ( fragment ) { - for ( var i = 0; ret[i]; i++ ) { - if ( jQuery.nodeName( ret[i], "script" ) && (!ret[i].type || ret[i].type.toLowerCase() === "text/javascript") ) { - scripts.push( ret[i].parentNode ? ret[i].parentNode.removeChild( ret[i] ) : ret[i] ); - } else { - if ( ret[i].nodeType === 1 ) - ret.splice.apply( ret, [i + 1, 0].concat(jQuery.makeArray(ret[i].getElementsByTagName("script"))) ); - fragment.appendChild( ret[i] ); - } - } - - return scripts; + inArray: function( elem, array ) { + if ( array.indexOf ) { + return array.indexOf( elem ); + } + + for ( var i = 0, length = array.length; i < length; i++ ) { + if ( array[ i ] === elem ) { + return i; + } + } + + return -1; + }, + + merge: function( first, second ) { + var i = first.length, j = 0; + + if ( typeof second.length === "number" ) { + for ( var l = second.length; j < l; j++ ) { + first[ i++ ] = second[ j ]; + } + + } else { + while ( second[j] !== undefined ) { + first[ i++ ] = second[ j++ ]; + } + } + + first.length = i; + + return first; + }, + + grep: function( elems, callback, inv ) { + var ret = []; + + // Go through the array, only saving the items + // that pass the validator function + for ( var i = 0, length = elems.length; i < length; i++ ) { + if ( !inv !== !callback( elems[ i ], i ) ) { + ret.push( elems[ i ] ); + } } return ret; }, - attr: function( elem, name, value ) { - // don't set attributes on text and comment nodes - if (!elem || elem.nodeType == 3 || elem.nodeType == 8) - return undefined; - - var notxml = !jQuery.isXMLDoc( elem ), - // Whether we are setting (or getting) - set = value !== undefined; - - // Try to normalize/fix the name - name = notxml && jQuery.props[ name ] || name; - - // Only do all the following if this is a node (faster for style) - // IE elem.getAttribute passes even for style - if ( elem.tagName ) { - - // These attributes require special treatment - var special = /href|src|style/.test( name ); - - // Safari mis-reports the default selected property of a hidden option - // Accessing the parent's selectedIndex property fixes it - if ( name == "selected" && elem.parentNode ) - elem.parentNode.selectedIndex; - - // If applicable, access the attribute via the DOM 0 way - if ( name in elem && notxml && !special ) { - if ( set ){ - // We can't allow the type property to be changed (since it causes problems in IE) - if ( name == "type" && jQuery.nodeName( elem, "input" ) && elem.parentNode ) - throw "type property can't be changed"; - - elem[ name ] = value; - } - - // browsers index elements by id/name on forms, give priority to attributes. - if( jQuery.nodeName( elem, "form" ) && elem.getAttributeNode(name) ) - return elem.getAttributeNode( name ).nodeValue; - - // elem.tabIndex doesn't always return the correct value when it hasn't been explicitly set - // http://fluidproject.org/blog/2008/01/09/getting-setting-and-removing-tabind… - if ( name == "tabIndex" ) { - var attributeNode = elem.getAttributeNode( "tabIndex" ); - return attributeNode && attributeNode.specified - ? attributeNode.value - : elem.nodeName.match(/(button|input|object|select|textarea)/i) - ? 0 - : elem.nodeName.match(/^(a|area)$/i) && elem.href - ? 0 - : undefined; - } - - return elem[ name ]; - } - - if ( !jQuery.support.style && notxml && name == "style" ) - return jQuery.attr( elem.style, "cssText", value ); - - if ( set ) - // convert the value to a string (all browsers do this but IE) see #1070 - elem.setAttribute( name, "" + value ); - - var attr = !jQuery.support.hrefNormalized && notxml && special - // Some attributes require a special call on IE - ? elem.getAttribute( name, 2 ) - : elem.getAttribute( name ); - - // Non-existent attributes return null, we normalize to undefined - return attr === null ? undefined : attr; - } - - // elem is actually elem.style ... set the style - - // IE uses filters for opacity - if ( !jQuery.support.opacity && name == "opacity" ) { - if ( set ) { - // IE has trouble with opacity if it does not have layout - // Force it by setting the zoom level - elem.zoom = 1; - - // Set the alpha filter to set the opacity - elem.filter = (elem.filter || "").replace( /alpha$[^)]*$/, "" ) + - (parseInt( value ) + '' == "NaN" ? "" : "alpha(opacity=" + value * 100 + ")"); - } - - return elem.filter && elem.filter.indexOf("opacity=") >= 0 ? - (parseFloat( elem.filter.match(/opacity=([^)]*)/)[1] ) / 100) + '': - ""; - } - - name = name.replace(/-([a-z])/ig, function(all, letter){ - return letter.toUpperCase(); - }); - - if ( set ) - elem[ name ] = value; - - return elem[ name ]; - }, - - trim: function( text ) { - return (text || "").replace( /^\s+|\s+$/g, "" ); - }, - - makeArray: function( array ) { - var ret = []; - - if( array != null ){ - var i = array.length; - // The window, strings (and functions) also have 'length' - if( i == null || typeof array === "string" || jQuery.isFunction(array) || array.setInterval ) - ret[0] = array; - else - while( i ) - ret[--i] = array[i]; - } - - return ret; - }, - - inArray: function( elem, array ) { - for ( var i = 0, length = array.length; i < length; i++ ) - // Use === because on IE, window == document - if ( array[ i ] === elem ) - return i; - - return -1; - }, - - merge: function( first, second ) { - // We have to loop this way because IE & Opera overwrite the length - // expando of getElementsByTagName - var i = 0, elem, pos = first.length; - // Also, we need to make sure that the correct elements are being returned - // (IE returns comment nodes in a '*' query) - if ( !jQuery.support.getAll ) { - while ( (elem = second[ i++ ]) != null ) - if ( elem.nodeType != 8 ) - first[ pos++ ] = elem; - - } else - while ( (elem = second[ i++ ]) != null ) - first[ pos++ ] = elem; - - return first; - }, - - unique: function( array ) { - var ret = [], done = {}; - - try { - - for ( var i = 0, length = array.length; i < length; i++ ) { - var id = jQuery.data( array[ i ] ); - - if ( !done[ id ] ) { - done[ id ] = true; - ret.push( array[ i ] ); - } - } - - } catch( e ) { - ret = array; - } - - return ret; - }, - - grep: function( elems, callback, inv ) { - var ret = []; - - // Go through the array, only saving the items - // that pass the validator function - for ( var i = 0, length = elems.length; i < length; i++ ) - if ( !inv != !callback( elems[ i ], i ) ) - ret.push( elems[ i ] ); - - return ret; - }, - - map: function( elems, callback ) { - var ret = []; + // arg is for internal usage only + map: function( elems, callback, arg ) { + var ret = [], value; // Go through the array, translating each of the items to their // new value (or values). for ( var i = 0, length = elems.length; i < length; i++ ) { - var value = callback( elems[ i ], i ); - - if ( value != null ) + value = callback( elems[ i ], i, arg ); + + if ( value != null ) { ret[ ret.length ] = value; + } } return ret.concat.apply( [], ret ); + }, + + // A global GUID counter for objects + guid: 1, + + proxy: function( fn, proxy, thisObject ) { + if ( arguments.length === 2 ) { + if ( typeof proxy === "string" ) { + thisObject = fn; + fn = thisObject[ proxy ]; + proxy = undefined; + + } else if ( proxy && !jQuery.isFunction( proxy ) ) { + thisObject = proxy; + proxy = undefined; + } + } + + if ( !proxy && fn ) { + proxy = function() { + return fn.apply( thisObject || this, arguments ); + }; + } + + // Set the guid of unique handler to the same of original handler, so it can be removed + if ( fn ) { + proxy.guid = fn.guid = fn.guid || proxy.guid || jQuery.guid++; + } + + // So proxy can be declared as an argument + return proxy; + }, + + // Use of jQuery.browser is frowned upon. + // More details: http://docs.jquery.com/Utilities/jQuery.browser + uaMatch: function( ua ) { + ua = ua.toLowerCase(); + + var match = /(webkit)[ \/]([\w.]+)/.exec( ua ) || + /(opera)(?:.*version)?[ \/]([\w.]+)/.exec( ua ) || + /(msie) ([\w.]+)/.exec( ua ) || + !/compatible/.test( ua ) && /(mozilla)(?:.*? rv:([\w.]+))?/.exec( ua ) || + []; + + return { browser: match[1] || "", version: match[2] || "0" }; + }, + + browser: {} +}); + +browserMatch = jQuery.uaMatch( userAgent ); +if ( browserMatch.browser ) { + jQuery.browser[ browserMatch.browser ] = true; + jQuery.browser.version = browserMatch.version; +} + +// Deprecated, use jQuery.browser.webkit instead +if ( jQuery.browser.webkit ) { + jQuery.browser.safari = true; +} + +if ( indexOf ) { + jQuery.inArray = function( elem, array ) { + return indexOf.call( array, elem ); + }; +} + +// All jQuery objects should point back to these +rootjQuery = jQuery(document); + +// Cleanup functions for the document ready method +if ( document.addEventListener ) { + DOMContentLoaded = function() { + document.removeEventListener( "DOMContentLoaded", DOMContentLoaded, false ); + jQuery.ready(); + }; + +} else if ( document.attachEvent ) { + DOMContentLoaded = function() { + // Make sure body exists, at least, in case IE gets a little overzealous (ticket #5443). + if ( document.readyState === "complete" ) { + document.detachEvent( "onreadystatechange", DOMContentLoaded ); + jQuery.ready(); + } + }; +} + +// The DOM ready check for Internet Explorer +function doScrollCheck() { + if ( jQuery.isReady ) { + return; + } + + try { + // If IE is used, use the trick by Diego Perini + // http://javascript.nwbox.com/IEContentLoaded/ + document.documentElement.doScroll("left"); + } catch( error ) { + setTimeout( doScrollCheck, 1 ); + return; + } + + // and execute any waiting functions + jQuery.ready(); +} + +function evalScript( i, elem ) { + if ( elem.src ) { + jQuery.ajax({ + url: elem.src, + async: false, + dataType: "script" + }); + } else { + jQuery.globalEval( elem.text || elem.textContent || elem.innerHTML || "" ); + } + + if ( elem.parentNode ) { + elem.parentNode.removeChild( elem ); + } +} + +// Mutifunctional method to get and set values to a collection +// The value/s can be optionally by executed if its a function +function access( elems, key, value, exec, fn, pass ) { + var length = elems.length; + + // Setting many attributes + if ( typeof key === "object" ) { + for ( var k in key ) { + access( elems, k, key[k], exec, fn, value ); + } + return elems; + } + + // Setting one attribute + if ( value !== undefined ) { + // Optionally, function values get executed if exec is true + exec = !pass && exec && jQuery.isFunction(value); + + for ( var i = 0; i < length; i++ ) { + fn( elems[i], key, exec ? value.call( elems[i], i, fn( elems[i], key ) ) : value, pass ); + } + + return elems; + } + + // Getting an attribute + return length ? fn( elems[0], key ) : undefined; +} + +function now() { + return (new Date).getTime(); +} +(function() { + + jQuery.support = {}; + + var root = document.documentElement, + script = document.createElement("script"), + div = document.createElement("div"), + id = "script" + now(); + + div.style.display = "none"; + div.innerHTML = " <link/><table></table><a href='/a' style='color:red;float:left;opacity:.55;'>a</a><input type='checkbox'/>"; + + var all = div.getElementsByTagName("*"), + a = div.getElementsByTagName("a")[0]; + + // Can't get basic test support + if ( !all || !all.length || !a ) { + return; + } + + jQuery.support = { + // IE strips leading whitespace when .innerHTML is used + leadingWhitespace: div.firstChild.nodeType === 3, + + // Make sure that tbody elements aren't automatically inserted + // IE will insert them into empty tables + tbody: !div.getElementsByTagName("tbody").length, + + // Make sure that link elements get serialized correctly by innerHTML + // This requires a wrapper element in IE + htmlSerialize: !!div.getElementsByTagName("link").length, + + // Get the style information from getAttribute + // (IE uses .cssText insted) + style: /red/.test( a.getAttribute("style") ), + + // Make sure that URLs aren't manipulated + // (IE normalizes it by default) + hrefNormalized: a.getAttribute("href") === "/a", + + // Make sure that element opacity exists + // (IE uses filter instead) + // Use a regex to work around a WebKit issue. See #5145 + opacity: /^0.55$/.test( a.style.opacity ), + + // Verify style float existence + // (IE uses styleFloat instead of cssFloat) + cssFloat: !!a.style.cssFloat, + + // Make sure that if no value is specified for a checkbox + // that it defaults to "on". + // (WebKit defaults to "" instead) + checkOn: div.getElementsByTagName("input")[0].value === "on", + + // Make sure that a selected-by-default option has a working selected property. + // (WebKit defaults to false instead of true, IE too, if it's in an optgroup) + optSelected: document.createElement("select").appendChild( document.createElement("option") ).selected, + + parentNode: div.removeChild( div.appendChild( document.createElement("div") ) ).parentNode === null, + + // Will be defined later + deleteExpando: true, + checkClone: false, + scriptEval: false, + noCloneEvent: true, + boxModel: null + }; + + script.type = "text/javascript"; + try { + script.appendChild( document.createTextNode( "window." + id + "=1;" ) ); + } catch(e) {} + + root.insertBefore( script, root.firstChild ); + + // Make sure that the execution of code works by injecting a script + // tag with appendChild/createTextNode + // (IE doesn't support this, fails, and uses .text instead) + if ( window[ id ] ) { + jQuery.support.scriptEval = true; + delete window[ id ]; + } + + // Test to see if it's possible to delete an expando from an element + // Fails in Internet Explorer + try { + delete script.test; + + } catch(e) { + jQuery.support.deleteExpando = false; + } + + root.removeChild( script ); + + if ( div.attachEvent && div.fireEvent ) { + div.attachEvent("onclick", function click() { + // Cloning a node shouldn't copy over any + // bound event handlers (IE does this) + jQuery.support.noCloneEvent = false; + div.detachEvent("onclick", click); + }); + div.cloneNode(true).fireEvent("onclick"); + } + + div = document.createElement("div"); + div.innerHTML = "<input type='radio' name='radiotest' checked='checked'/>"; + + var fragment = document.createDocumentFragment(); + fragment.appendChild( div.firstChild ); + + // WebKit doesn't clone checked state correctly in fragments + jQuery.support.checkClone = fragment.cloneNode(true).cloneNode(true).lastChild.checked; + + // Figure out if the W3C box model works as expected + // document.body must exist before we can do this + jQuery(function() { + var div = document.createElement("div"); + div.style.width = div.style.paddingLeft = "1px"; + + document.body.appendChild( div ); + jQuery.boxModel = jQuery.support.boxModel = div.offsetWidth === 2; + document.body.removeChild( div ).style.display = 'none'; + + div = null; + }); + + // Technique from Juriy Zaytsev + // http://thinkweb2.com/projects/prototype/detecting-event-support-without-bro… + var eventSupported = function( eventName ) { + var el = document.createElement("div"); + eventName = "on" + eventName; + + var isSupported = (eventName in el); + if ( !isSupported ) { + el.setAttribute(eventName, "return;"); + isSupported = typeof el[eventName] === "function"; + } + el = null; + + return isSupported; + }; + + jQuery.support.submitBubbles = eventSupported("submit"); + jQuery.support.changeBubbles = eventSupported("change"); + + // release memory in IE + root = script = div = all = a = null; +})(); + +jQuery.props = { + "for": "htmlFor", + "class": "className", + readonly: "readOnly", + maxlength: "maxLength", + cellspacing: "cellSpacing", + rowspan: "rowSpan", + colspan: "colSpan", + tabindex: "tabIndex", + usemap: "useMap", + frameborder: "frameBorder" +}; +var expando = "jQuery" + now(), uuid = 0, windowData = {}; + +jQuery.extend({ + cache: {}, + + expando:expando, + + // The following elements throw uncatchable exceptions if you + // attempt to add expando properties to them. + noData: { + "embed": true, + "object": true, + "applet": true + }, + + data: function( elem, name, data ) { + if ( elem.nodeName && jQuery.noData[elem.nodeName.toLowerCase()] ) { + return; + } + + elem = elem == window ? + windowData : + elem; + + var id = elem[ expando ], cache = jQuery.cache, thisCache; + + if ( !id && typeof name === "string" && data === undefined ) { + return null; + } + + // Compute a unique ID for the element + if ( !id ) { + id = ++uuid; + } + + // Avoid generating a new cache unless none exists and we + // want to manipulate it. + if ( typeof name === "object" ) { + elem[ expando ] = id; + thisCache = cache[ id ] = jQuery.extend(true, {}, name); + + } else if ( !cache[ id ] ) { + elem[ expando ] = id; + cache[ id ] = {}; + } + + thisCache = cache[ id ]; + + // Prevent overriding the named cache with undefined values + if ( data !== undefined ) { + thisCache[ name ] = data; + } + + return typeof name === "string" ? thisCache[ name ] : thisCache; + }, + + removeData: function( elem, name ) { + if ( elem.nodeName && jQuery.noData[elem.nodeName.toLowerCase()] ) { + return; + } + + elem = elem == window ? + windowData : + elem; + + var id = elem[ expando ], cache = jQuery.cache, thisCache = cache[ id ]; + + // If we want to remove a specific section of the element's data + if ( name ) { + if ( thisCache ) { + // Remove the section of cache data + delete thisCache[ name ]; + + // If we've removed all the data, remove the element's cache + if ( jQuery.isEmptyObject(thisCache) ) { + jQuery.removeData( elem ); + } + } + + // Otherwise, we want to remove all of the element's data + } else { + if ( jQuery.support.deleteExpando ) { + delete elem[ jQuery.expando ]; + + } else if ( elem.removeAttribute ) { + elem.removeAttribute( jQuery.expando ); + } + + // Completely remove the data cache + delete cache[ id ]; + } } }); -// Use of jQuery.browser is deprecated. -// It's included for backwards compatibility and plugins, -// although they should work to migrate away. - -var userAgent = navigator.userAgent.toLowerCase(); - -// Figure out what browser is being used -jQuery.browser = { - version: (userAgent.match( /.+(?:rv|it|ra|ie)[\/: ]([\d.]+)/ ) || [0,'0'])[1], - safari: /webkit/.test( userAgent ), - opera: /opera/.test( userAgent ), - msie: /msie/.test( userAgent ) && !/opera/.test( userAgent ), - mozilla: /mozilla/.test( userAgent ) && !/(compatible|webkit)/.test( userAgent ) +jQuery.fn.extend({ + data: function( key, value ) { + if ( typeof key === "undefined" && this.length ) { + return jQuery.data( this[0] ); + + } else if ( typeof key === "object" ) { + return this.each(function() { + jQuery.data( this, key ); + }); + } + + var parts = key.split("."); + parts[1] = parts[1] ? "." + parts[1] : ""; + + if ( value === undefined ) { + var data = this.triggerHandler("getData" + parts[1] + "!", [parts[0]]); + + if ( data === undefined && this.length ) { + data = jQuery.data( this[0], key ); + } + return data === undefined && parts[1] ? + this.data( parts[0] ) : + data; + } else { + return this.trigger("setData" + parts[1] + "!", [parts[0], value]).each(function() { + jQuery.data( this, key, value ); + }); + } + }, + + removeData: function( key ) { + return this.each(function() { + jQuery.removeData( this, key ); + }); + } +}); +jQuery.extend({ + queue: function( elem, type, data ) { + if ( !elem ) { + return; + } + + type = (type || "fx") + "queue"; + var q = jQuery.data( elem, type ); + + // Speed up dequeue by getting out quickly if this is just a lookup + if ( !data ) { + return q || []; + } + + if ( !q || jQuery.isArray(data) ) { + q = jQuery.data( elem, type, jQuery.makeArray(data) ); + + } else { + q.push( data ); + } + + return q; + }, + + dequeue: function( elem, type ) { + type = type || "fx"; + + var queue = jQuery.queue( elem, type ), fn = queue.shift(); + + // If the fx queue is dequeued, always remove the progress sentinel + if ( fn === "inprogress" ) { + fn = queue.shift(); + } + + if ( fn ) { + // Add a progress sentinel to prevent the fx queue from being + // automatically dequeued + if ( type === "fx" ) { + queue.unshift("inprogress"); + } + + fn.call(elem, function() { + jQuery.dequeue(elem, type); + }); + } + } +}); + +jQuery.fn.extend({ + queue: function( type, data ) { + if ( typeof type !== "string" ) { + data = type; + type = "fx"; + } + + if ( data === undefined ) { + return jQuery.queue( this[0], type ); + } + return this.each(function( i, elem ) { + var queue = jQuery.queue( this, type, data ); + + if ( type === "fx" && queue[0] !== "inprogress" ) { + jQuery.dequeue( this, type ); + } + }); + }, + dequeue: function( type ) { + return this.each(function() { + jQuery.dequeue( this, type ); + }); + }, + + // Based off of the plugin by Clint Helfers, with permission. + // http://blindsignals.com/index.php/2009/07/jquery-delay/ + delay: function( time, type ) { + time = jQuery.fx ? jQuery.fx.speeds[time] || time : time; + type = type || "fx"; + + return this.queue( type, function() { + var elem = this; + setTimeout(function() { + jQuery.dequeue( elem, type ); + }, time ); + }); + }, + + clearQueue: function( type ) { + return this.queue( type || "fx", [] ); + } +}); +var rclass = /[\n\t]/g, + rspace = /\s+/, + rreturn = /\r/g, + rspecialurl = /href|src|style/, + rtype = /(button|input)/i, + rfocusable = /(button|input|object|select|textarea)/i, + rclickable = /^(a|area)$/i, + rradiocheck = /radio|checkbox/; + +jQuery.fn.extend({ + attr: function( name, value ) { + return access( this, name, value, true, jQuery.attr ); + }, + + removeAttr: function( name, fn ) { + return this.each(function(){ + jQuery.attr( this, name, "" ); + if ( this.nodeType === 1 ) { + this.removeAttribute( name ); + } + }); + }, + + addClass: function( value ) { + if ( jQuery.isFunction(value) ) { + return this.each(function(i) { + var self = jQuery(this); + self.addClass( value.call(this, i, self.attr("class")) ); + }); + } + + if ( value && typeof value === "string" ) { + var classNames = (value || "").split( rspace ); + + for ( var i = 0, l = this.length; i < l; i++ ) { + var elem = this[i]; + + if ( elem.nodeType === 1 ) { + if ( !elem.className ) { + elem.className = value; + + } else { + var className = " " + elem.className + " ", setClass = elem.className; + for ( var c = 0, cl = classNames.length; c < cl; c++ ) { + if ( className.indexOf( " " + classNames[c] + " " ) < 0 ) { + setClass += " " + classNames[c]; + } + } + elem.className = jQuery.trim( setClass ); + } + } + } + } + + return this; + }, + + removeClass: function( value ) { + if ( jQuery.isFunction(value) ) { + return this.each(function(i) { + var self = jQuery(this); + self.removeClass( value.call(this, i, self.attr("class")) ); + }); + } + + if ( (value && typeof value === "string") || value === undefined ) { + var classNames = (value || "").split(rspace); + + for ( var i = 0, l = this.length; i < l; i++ ) { + var elem = this[i]; + + if ( elem.nodeType === 1 && elem.className ) { + if ( value ) { + var className = (" " + elem.className + " ").replace(rclass, " "); + for ( var c = 0, cl = classNames.length; c < cl; c++ ) { + className = className.replace(" " + classNames[c] + " ", " "); + } + elem.className = jQuery.trim( className ); + + } else { + elem.className = ""; + } + } + } + } + + return this; + }, + + toggleClass: function( value, stateVal ) { + var type = typeof value, isBool = typeof stateVal === "boolean"; + + if ( jQuery.isFunction( value ) ) { + return this.each(function(i) { + var self = jQuery(this); + self.toggleClass( value.call(this, i, self.attr("class"), stateVal), stateVal ); + }); + } + + return this.each(function() { + if ( type === "string" ) { + // toggle individual class names + var className, i = 0, self = jQuery(this), + state = stateVal, + classNames = value.split( rspace ); + + while ( (className = classNames[ i++ ]) ) { + // check each className given, space seperated list + state = isBool ? state : !self.hasClass( className ); + self[ state ? "addClass" : "removeClass" ]( className ); + } + + } else if ( type === "undefined" || type === "boolean" ) { + if ( this.className ) { + // store className if set + jQuery.data( this, "__className__", this.className ); + } + + // toggle whole className + this.className = this.className || value === false ? "" : jQuery.data( this, "__className__" ) || ""; + } + }); + }, + + hasClass: function( selector ) { + var className = " " + selector + " "; + for ( var i = 0, l = this.length; i < l; i++ ) { + if ( (" " + this[i].className + " ").replace(rclass, " ").indexOf( className ) > -1 ) { + return true; + } + } + + return false; + }, + + val: function( value ) { + if ( value === undefined ) { + var elem = this[0]; + + if ( elem ) { + if ( jQuery.nodeName( elem, "option" ) ) { + return (elem.attributes.value || {}).specified ? elem.value : elem.text; + } + + // We need to handle select boxes special + if ( jQuery.nodeName( elem, "select" ) ) { + var index = elem.selectedIndex, + values = [], + options = elem.options, + one = elem.type === "select-one"; + + // Nothing was selected + if ( index < 0 ) { + return null; + } + + // Loop through all the selected options + for ( var i = one ? index : 0, max = one ? index + 1 : options.length; i < max; i++ ) { + var option = options[ i ]; + + if ( option.selected ) { + // Get the specifc value for the option + value = jQuery(option).val(); + + // We don't need an array for one selects + if ( one ) { + return value; + } + + // Multi-Selects return an array + values.push( value ); + } + } + + return values; + } + + // Handle the case where in Webkit "" is returned instead of "on" if a value isn't specified + if ( rradiocheck.test( elem.type ) && !jQuery.support.checkOn ) { + return elem.getAttribute("value") === null ? "on" : elem.value; + } + + + // Everything else, we just grab the value + return (elem.value || "").replace(rreturn, ""); + + } + + return undefined; + } + + var isFunction = jQuery.isFunction(value); + + return this.each(function(i) { + var self = jQuery(this), val = value; + + if ( this.nodeType !== 1 ) { + return; + } + + if ( isFunction ) { + val = value.call(this, i, self.val()); + } + + // Typecast each time if the value is a Function and the appended + // value is therefore different each time. + if ( typeof val === "number" ) { + val += ""; + } + + if ( jQuery.isArray(val) && rradiocheck.test( this.type ) ) { + this.checked = jQuery.inArray( self.val(), val ) >= 0; + + } else if ( jQuery.nodeName( this, "select" ) ) { + var values = jQuery.makeArray(val); + + jQuery( "option", this ).each(function() { + this.selected = jQuery.inArray( jQuery(this).val(), values ) >= 0; + }); + + if ( !values.length ) { + this.selectedIndex = -1; + } + + } else { + this.value = val; + } + }); + } +}); + +jQuery.extend({ + attrFn: { + val: true, + css: true, + html: true, + text: true, + data: true, + width: true, + height: true, + offset: true + }, + + attr: function( elem, name, value, pass ) { + // don't set attributes on text and comment nodes + if ( !elem || elem.nodeType === 3 || elem.nodeType === 8 ) { + return undefined; + } + + if ( pass && name in jQuery.attrFn ) { + return jQuery(elem)[name](value); + } + + var notxml = elem.nodeType !== 1 || !jQuery.isXMLDoc( elem ), + // Whether we are setting (or getting) + set = value !== undefined; + + // Try to normalize/fix the name + name = notxml && jQuery.props[ name ] || name; + + // Only do all the following if this is a node (faster for style) + if ( elem.nodeType === 1 ) { + // These attributes require special treatment + var special = rspecialurl.test( name ); + + // Safari mis-reports the default selected property of an option + // Accessing the parent's selectedIndex property fixes it + if ( name === "selected" && !jQuery.support.optSelected ) { + var parent = elem.parentNode; + if ( parent ) { + parent.selectedIndex; + + // Make sure that it also works with optgroups, see #5701 + if ( parent.parentNode ) { + parent.parentNode.selectedIndex; + } + } + } + + // If applicable, access the attribute via the DOM 0 way + if ( name in elem && notxml && !special ) { + if ( set ) { + // We can't allow the type property to be changed (since it causes problems in IE) + if ( name === "type" && rtype.test( elem.nodeName ) && elem.parentNode ) { + jQuery.error( "type property can't be changed" ); + } + + elem[ name ] = value; + } + + // browsers index elements by id/name on forms, give priority to attributes. + if ( jQuery.nodeName( elem, "form" ) && elem.getAttributeNode(name) ) { + return elem.getAttributeNode( name ).nodeValue; + } + + // elem.tabIndex doesn't always return the correct value when it hasn't been explicitly set + // http://fluidproject.org/blog/2008/01/09/getting-setting-and-removing-tabind… + if ( name === "tabIndex" ) { + var attributeNode = elem.getAttributeNode( "tabIndex" ); + + return attributeNode && attributeNode.specified ? + attributeNode.value : + rfocusable.test( elem.nodeName ) || rclickable.test( elem.nodeName ) && elem.href ? + 0 : + undefined; + } + + return elem[ name ]; + } + + if ( !jQuery.support.style && notxml && name === "style" ) { + if ( set ) { + elem.style.cssText = "" + value; + } + + return elem.style.cssText; + } + + if ( set ) { + // convert the value to a string (all browsers do this but IE) see #1070 + elem.setAttribute( name, "" + value ); + } + + var attr = !jQuery.support.hrefNormalized && notxml && special ? + // Some attributes require a special call on IE + elem.getAttribute( name, 2 ) : + elem.getAttribute( name ); + + // Non-existent attributes return null, we normalize to undefined + return attr === null ? undefined : attr; + } + + // elem is actually elem.style ... set the style + // Using attr for specific style information is now deprecated. Use style instead. + return jQuery.style( elem, name, value ); + } +}); +var rnamespaces = /\.(.*)$/, + fcleanup = function( nm ) { + return nm.replace(/[^\w\s\.\|`]/g, function( ch ) { + return "\\" + ch; + }); + }; + +/* + * A number of helper functions used for managing events. + * Many of the ideas behind this code originated from + * Dean Edwards' addEvent library. + */ +jQuery.event = { + + // Bind an event to an element + // Original by Dean Edwards + add: function( elem, types, handler, data ) { + if ( elem.nodeType === 3 || elem.nodeType === 8 ) { + return; + } + + // For whatever reason, IE has trouble passing the window object + // around, causing it to be cloned in the process + if ( elem.setInterval && ( elem !== window && !elem.frameElement ) ) { + elem = window; + } + + var handleObjIn, handleObj; + + if ( handler.handler ) { + handleObjIn = handler; + handler = handleObjIn.handler; + } + + // Make sure that the function being executed has a unique ID + if ( !handler.guid ) { + handler.guid = jQuery.guid++; + } + + // Init the element's event structure + var elemData = jQuery.data( elem ); + + // If no elemData is found then we must be trying to bind to one of the + // banned noData elements + if ( !elemData ) { + return; + } + + var events = elemData.events = elemData.events || {}, + eventHandle = elemData.handle, eventHandle; + + if ( !eventHandle ) { + elemData.handle = eventHandle = function() { + // Handle the second event of a trigger and when + // an event is called after a page has unloaded + return typeof jQuery !== "undefined" && !jQuery.event.triggered ? + jQuery.event.handle.apply( eventHandle.elem, arguments ) : + undefined; + }; + } + + // Add elem as a property of the handle function + // This is to prevent a memory leak with non-native events in IE. + eventHandle.elem = elem; + + // Handle multiple events separated by a space + // jQuery(...).bind("mouseover mouseout", fn); + types = types.split(" "); + + var type, i = 0, namespaces; + + while ( (type = types[ i++ ]) ) { + handleObj = handleObjIn ? + jQuery.extend({}, handleObjIn) : + { handler: handler, data: data }; + + // Namespaced event handlers + if ( type.indexOf(".") > -1 ) { + namespaces = type.split("."); + type = namespaces.shift(); + handleObj.namespace = namespaces.slice(0).sort().join("."); + + } else { + namespaces = []; + handleObj.namespace = ""; + } + + handleObj.type = type; + handleObj.guid = handler.guid; + + // Get the current list of functions bound to this event + var handlers = events[ type ], + special = jQuery.event.special[ type ] || {}; + + // Init the event handler queue + if ( !handlers ) { + handlers = events[ type ] = []; + + // Check for a special event handler + // Only use addEventListener/attachEvent if the special + // events handler returns false + if ( !special.setup || special.setup.call( elem, data, namespaces, eventHandle ) === false ) { + // Bind the global event handler to the element + if ( elem.addEventListener ) { + elem.addEventListener( type, eventHandle, false ); + + } else if ( elem.attachEvent ) { + elem.attachEvent( "on" + type, eventHandle ); + } + } + } + + if ( special.add ) { + special.add.call( elem, handleObj ); + + if ( !handleObj.handler.guid ) { + handleObj.handler.guid = handler.guid; + } + } + + // Add the function to the element's handler list + handlers.push( handleObj ); + + // Keep track of which events have been used, for global triggering + jQuery.event.global[ type ] = true; + } + + // Nullify elem to prevent memory leaks in IE + elem = null; + }, + + global: {}, + + // Detach an event or set of events from an element + remove: function( elem, types, handler, pos ) { + // don't do events on text and comment nodes + if ( elem.nodeType === 3 || elem.nodeType === 8 ) { + return; + } + + var ret, type, fn, i = 0, all, namespaces, namespace, special, eventType, handleObj, origType, + elemData = jQuery.data( elem ), + events = elemData && elemData.events; + + if ( !elemData || !events ) { + return; + } + + // types is actually an event object here + if ( types && types.type ) { + handler = types.handler; + types = types.type; + } + + // Unbind all events for the element + if ( !types || typeof types === "string" && types.charAt(0) === "." ) { + types = types || ""; + + for ( type in events ) { + jQuery.event.remove( elem, type + types ); + } + + return; + } + + // Handle multiple events separated by a space + // jQuery(...).unbind("mouseover mouseout", fn); + types = types.split(" "); + + while ( (type = types[ i++ ]) ) { + origType = type; + handleObj = null; + all = type.indexOf(".") < 0; + namespaces = []; + + if ( !all ) { + // Namespaced event handlers + namespaces = type.split("."); + type = namespaces.shift(); + + namespace = new RegExp("(^|\\.)" + + jQuery.map( namespaces.slice(0).sort(), fcleanup ).join("\\.(?:.*\\.)?") + "(\\.|$)") + } + + eventType = events[ type ]; + + if ( !eventType ) { + continue; + } + + if ( !handler ) { + for ( var j = 0; j < eventType.length; j++ ) { + handleObj = eventType[ j ]; + + if ( all || namespace.test( handleObj.namespace ) ) { + jQuery.event.remove( elem, origType, handleObj.handler, j ); + eventType.splice( j--, 1 ); + } + } + + continue; + } + + special = jQuery.event.special[ type ] || {}; + + for ( var j = pos || 0; j < eventType.length; j++ ) { + handleObj = eventType[ j ]; + + if ( handler.guid === handleObj.guid ) { + // remove the given handler for the given type + if ( all || namespace.test( handleObj.namespace ) ) { + if ( pos == null ) { + eventType.splice( j--, 1 ); + } + + if ( special.remove ) { + special.remove.call( elem, handleObj ); + } + } + + if ( pos != null ) { + break; + } + } + }

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[hg] galaxy 3446: Clean up pages:
by Greg Von Kuster 03 Mar '10

03 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/143c920af25c changeset: 3446:143c920af25c user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Sun Feb 28 22:19:56 2010 -0500 description: Clean up pages: -remove unused code; -show annotation field when creating a page; -fix bug when filtering pages by sharing status. diffstat: lib/galaxy/web/controllers/page.py | 57 +++++++++---------------------------- 1 files changed, 14 insertions(+), 43 deletions(-) diffs (115 lines): diff -r 5ffd16fb6a12 -r 143c920af25c lib/galaxy/web/controllers/page.py --- a/lib/galaxy/web/controllers/page.py Thu Feb 25 23:20:19 2010 -0500 +++ b/lib/galaxy/web/controllers/page.py Sun Feb 28 22:19:56 2010 -0500 @@ -24,13 +24,13 @@ use_panels = True title = "Pages" model_class = model.Page - default_filter = { "published" : "All", "tags" : "All", "title" : "All"} + default_filter = { "published" : "All", "tags" : "All", "title" : "All", "sharing" : "All" } default_sort_key = "-create_time" columns = [ grids.TextColumn( "Title", key="title", model_class=model.Page, attach_popup=True, filterable="advanced" ), URLColumn( "Public URL" ), grids.IndividualTagsColumn( "Tags", "tags", model.Page, model.PageTagAssociation, filterable="advanced", grid_name="PageListGrid" ), - grids.SharingStatusColumn( "Sharing", key="sharing", model_class=model.History, filterable="advanced", sortable=False ), + grids.SharingStatusColumn( "Sharing", key="sharing", model_class=model.Page, filterable="advanced", sortable=False ), grids.GridColumn( "Created", key="create_time", format=time_ago ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), ] @@ -79,40 +79,7 @@ return session.query( self.model_class ).join( model.User.table ) def apply_default_filter( self, trans, query, **kwargs ): return query.filter( self.model_class.deleted==False ).filter( self.model_class.published==True ) - -class HistorySelectionGrid( grids.Grid ): - # Custom columns. - class NameColumn( grids.TextColumn ): - def get_value(self, trans, grid, history): - return history.get_display_name() - - # Grid definition. - title = "Saved Histories" - template = "/page/select_histories_grid.mako" - async_template = "/page/select_histories_grid_async.mako" - model_class = model.History - default_filter = { "deleted" : "False" , "shared" : "All" } - default_sort_key = "-update_time" - use_async = True - use_paging = True - num_rows_per_page = 10 - columns = [ - NameColumn( "Name", key="name", model_class=model.History, filterable="advanced" ), - grids.IndividualTagsColumn( "Tags", "tags", model.History, model.HistoryTagAssociation, filterable="advanced"), - grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), - # Columns that are valid for filtering but are not visible. - grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ), - grids.SharingStatusColumn( "Sharing", key="sharing", model_class=model.History, filterable="advanced", sortable=False, visible=False ), - ] - columns.append( - grids.MulticolFilterColumn( - "Search", - cols_to_filter=[ columns[0], columns[1] ], - key="free-text-search", visible=False, filterable="standard" ) - ) - def apply_default_filter( self, trans, query, **kwargs ): - return query.filter_by( user=trans.user, purged=False ) - + class ItemSelectionGrid( grids.Grid ): """ Base class for pages' item selection grids. """ # Custom columns. @@ -339,12 +306,12 @@ @web.expose @web.require_login( "create pages" ) - def create( self, trans, page_title="", page_slug="" ): + def create( self, trans, page_title="", page_slug="", page_annotation="" ): """ Create a new page """ user = trans.get_user() - page_title_err = page_slug_err = "" + page_title_err = page_slug_err = page_annotation_err = "" if trans.request.method == "POST": if not page_title: page_title_err = "Page name is required" @@ -355,12 +322,14 @@ elif trans.sa_session.query( model.Page ).filter_by( user=user, slug=page_slug, deleted=False ).first(): page_slug_err = "Page id must be unique" else: - # Create the new stored workflow + # Create the new stored page page = model.Page() page.title = page_title page.slug = page_slug + page_annotation = sanitize_html( page_annotation, 'utf-8', 'text/html' ) + self.add_item_annotation( trans, page, page_annotation ) page.user = user - # And the first (empty) workflow revision + # And the first (empty) page revision page_revision = model.PageRevision() page_revision.title = page_title page_revision.page = page @@ -381,8 +350,10 @@ public links to this page. A default is generated from the page title, but can be edited. This field must contain only lowercase letters, numbers, and - the '-' character.""" ), - template="page/create.mako" ) + the '-' character.""" ) + .add_text( "page_annotation", "Page annotation", value=page_annotation, error=page_annotation_err, + help="A description of the page; annotation is shown alongside published pages."), + template="page/create.mako" ) @web.expose @web.require_login( "create pages" ) @@ -432,7 +403,7 @@ must contain only lowercase letters, numbers, and the '-' character.""" ) .add_text( "page_annotation", "Page annotation", value=page_annotation, error=page_annotation_err, - help="A description of or notes about the page. Annotation is shown alongside published pages."), + help="A description of the page; annotation is shown alongside published pages."), template="page/create.mako" ) @web.expose

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[hg] galaxy 3445: Fixed dbkey's in sam_pileup and sam_to_bam too...
by Greg Von Kuster 03 Mar '10

03 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/5ffd16fb6a12 changeset: 3445:5ffd16fb6a12 user: Kelly Vincent <kpvincent(a)bx.psu.edu> date: Thu Feb 25 23:20:19 2010 -0500 description: Fixed dbkey's in sam_pileup and sam_to_bam tools in tests so they will pass diffstat: tools/samtools/sam_pileup.xml | 4 ++-- tools/samtools/sam_to_bam.xml | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diffs (42 lines): diff -r 294b1283ea56 -r 5ffd16fb6a12 tools/samtools/sam_pileup.xml --- a/tools/samtools/sam_pileup.xml Thu Feb 25 14:59:43 2010 -0500 +++ b/tools/samtools/sam_pileup.xml Thu Feb 25 23:20:19 2010 -0500 @@ -82,7 +82,7 @@ --> <param name="reference" value="history" /> <param name="input1" value="sam_pileup_in1.bam" ftype="bam" /> - <param name="ownFile" value="chr_m.fasta" ftype="fasta" /> + <param name="ownFile" value="chr_m.fasta" ftype="fasta" dbkey="equCab2" /> <param name="lastCol" value="no" /> <param name="indels" value="no" /> <param name="mapCap" value="60" /> @@ -96,7 +96,7 @@ chr_m.fasta is the prefix of the index --> <param name="reference" value="indexed" /> - <param name="input1" value="sam_pileup_in1.bam" ftype="bam" dbkey="chrM" /> + <param name="input1" value="sam_pileup_in1.bam" ftype="bam" dbkey="equCab2" /> <param name="lastCol" value="no" /> <param name="indels" value="no" /> <param name="mapCap" value="60" /> diff -r 294b1283ea56 -r 5ffd16fb6a12 tools/samtools/sam_to_bam.xml --- a/tools/samtools/sam_to_bam.xml Thu Feb 25 14:59:43 2010 -0500 +++ b/tools/samtools/sam_to_bam.xml Thu Feb 25 23:20:19 2010 -0500 @@ -41,7 +41,7 @@ --> <param name="index_source" value="history" /> <param name="input1" value="3.sam" ftype="sam" /> - <param name="ref_file" value="chr_m.fasta" ftype="fasta" /> + <param name="ref_file" value="chr_m.fasta" ftype="fasta" dbkey="equCab2" /> <output name="output1" file="sam_to_bam_out1.bam" /> </test> <test> @@ -53,7 +53,7 @@ should be in the same directory --> <param name="index_source" value="cached" /> - <param name="input1" value="3.sam" ftype="sam" dbkey="chrM" /> + <param name="input1" value="3.sam" ftype="sam" dbkey="equCab2" /> <param name="output1" file="sam_to_bam_out2.bam" /> </test> </tests>

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User customization in the Galaxy tool pane
by H. Mei 02 Mar '10

02 Mar '10

Dear colleagues, We are installing a local Galaxy server for a few groups working on high throughput sequencing. Some users like to customize their tool pane when they log in, e.g., by hiding certain tools that they do not need. I searched through the email list and noticed a somehow similar request: http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-January/001619.html Kanwei (Galaxy developer) mentioned that this is possible via user preference table (http://bitbucket.org/galaxy/galaxy-central/issue/286/user-customization-in-…) However, I can't find it in the current Galaxy server. Will this be included in the upcoming releases? Is there a time line? Thanks, Leon

2 1

MySQL database dump import
by Dijk, F van 02 Mar '10

02 Mar '10

Hello, I'm trying to transfer the data from the SQLite database Galaxy uses to a MySQL database we have running locally. I made a database dump from the SQLite database and tried to import into our MySQL database. This results in the following error message: ERROR 1059 (42000) at line 77132: Identifier name 'ix_history_dataset_association_display_at_authorization_history_dataset _association_id' is too long Do you know a way to solve this? Or should I perform an other action to transfer the SQLite database to our own MySQL database? I hope to hear from you soon. Sincerely, Freerk van Dijk University Medical Center Groningen De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht. The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.

1 0

Some data link problems on the wiki
by Iwe Muiser 02 Mar '10

02 Mar '10

Hello Galaxy team, Mainly the wiki on the local setup of NGS is a bit uncomplete. The download links to the built indexes do not seem to function on http://bitbucket.org/galaxy/galaxy-central/wiki/NGSLocalSetup My box somehow can't make the index files with BWA. This is probably due to memory shortage al though the tool does not specify. The tool just tells me: $ ./bwa index -a bwtsw -p test /home/muiser/data/Human_data/hg18/chromosomes/hg18.fa [bwa_index] fail to open file '/home/muiser/data/Human_data/hg18/chromosomes/hg18.fa'. Abort! Aborted It would be great if the files can be downloaded somewhere. Greetings, Iwe -- Iwe EC Muiser Master student NTNU - Department of Cancer Research and Molecular Medicine Bioinformatics & Gene Regulation Group Laboratory Centre, 5th floor. Erling Skjalgssons gt. 1 Trondheim +4594157082

1 0

LIMS Demo stalled
by nsfox＠uwaterloo.ca 01 Mar '10

01 Mar '10

Hi, I have setup up Galaxy on my computer following the instructions and then proceeded to run the LIMS Demo script following the instructions on the wiki. The setup stalled ending with the following: galaxy.jobs INFO 2010-03-01 10:51:36,928 job scheduler policy is galaxy.jobs.schedulingpolicy.roundrobin:UserRoundRobin galaxy.jobs INFO 2010-03-01 10:51:36,929 job manager started galaxy.jobs INFO 2010-03-01 10:51:37,036 job stopper started Traceback (most recent call last): File "setup_lims_demo.py", line 184, in <module> main() File "setup_lims_demo.py", line 137, in main user_list.append( create_user( app, admin_user_email, 'testuser' ) ) File "setup_lims_demo.py", line 43, in create_user user.flush() AttributeError: 'User' object has no attribute 'flush' The error suggests to me that I missed downloading some methods or something. I have not worked with python before so I am unfamiliar as to where I would look for the flush method or how I would import/use it to make it available. I was wondering if you have any suggestions as to what I could be missing or what I could do to fix the error, please let me know. Any help is greatly appreciated. Thanks, Natalie Fox

2 1

Where to place google analytics tracking code
by Martin Aryee 01 Mar '10

01 Mar '10

Hi, I'd like to use Google Analytics to track visits to our galaxy instance. It involves placing a <script></script> block (example below) on all the site's pages. The recommended location is just before the </body> tag. I'd like to insert the code snippet in one of the mako templates and am wondering which template would be most appropriate? Thanks, Martin. <script type="text/javascript"> var gaJsHost = (("https:" == document.location.protocol) ? "https://ssl." : "http://www."); document.write(unescape("%3Cscript src='" + gaJsHost + " google-analytics.com/ga.js' type='text/javascript'%3E%3C/script%3E")); </script> <script type="text/javascript"> try{ var pageTracker = _gat._getTracker("UA-xxxxxx-x"); pageTracker._trackPageview(); } catch(err) {} </script>

2 2