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[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()

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[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 '''

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[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

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[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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