November 2009 - galaxy-dev - lists.galaxyproject.org

[hg] galaxy 2971: Fix bug in selecting a page.
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/9561573441a4 changeset: 2971:9561573441a4 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Thu Nov 05 16:28:38 2009 -0500 description: Fix bug in selecting a page. diffstat: templates/history/grid.mako | 6 +++--- 1 files changed, 3 insertions(+), 3 deletions(-) diffs (24 lines): diff -r 731875ce0a36 -r 9561573441a4 templates/history/grid.mako --- a/templates/history/grid.mako Thu Nov 05 14:19:45 2009 -0500 +++ b/templates/history/grid.mako Thu Nov 05 16:28:38 2009 -0500 @@ -126,9 +126,9 @@ // // Initiate navigation when user selects a page to view. // - function navigate_to_page() + function navigate_to_page(page_select) { - page_num = $(this).val(); + page_num = $(page_select).val(); <% url_args = {"page" : "PAGE"} %> var url_base = "${url( url_args )}"; var url = url_base.replace("PAGE", page_num); @@ -360,7 +360,7 @@ %endif ## Go to page select box. <span>| Select:</span> - <select id="page-select" onchange="navigate_to_page()"> + <select id="page-select" onchange="navigate_to_page(this)"> <option value=""></option> %for page_index in range(1, num_pages + 1): %if page_index == cur_page_num:

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[hg] galaxy 2968: Copy the sample universe_wsgi.ini for buildbot...
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/3adcadbe8b61 changeset: 2968:3adcadbe8b61 user: Nate Coraor <nate(a)bx.psu.edu> date: Thu Nov 05 09:29:03 2009 -0500 description: Copy the sample universe_wsgi.ini for buildbot so the new eggs code doesn't bomb diffstat: buildbot_setup.sh | 1 + 1 files changed, 1 insertions(+), 0 deletions(-) diffs (11 lines): diff -r f77f039c3697 -r 3adcadbe8b61 buildbot_setup.sh --- a/buildbot_setup.sh Wed Nov 04 16:23:23 2009 -0500 +++ b/buildbot_setup.sh Thu Nov 05 09:29:03 2009 -0500 @@ -25,6 +25,7 @@ SAMPLES=" datatypes_conf.xml.sample +universe_wsgi.ini.sample " DIRS="

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[hg] galaxy 2969: Run test webserver on a random port between 80...
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/c6a8bd78357a changeset: 2969:c6a8bd78357a user: Nate Coraor <nate(a)bx.psu.edu> date: Thu Nov 05 10:39:59 2009 -0500 description: Run test webserver on a random port between 8000 and 9999 instead of a fixed port, so multiple people can run tests at the same time w/o setting GALAXY_TEST_PORT manually diffstat: scripts/functional_tests.py | 32 +++++++++++++++++++++++++------- 1 files changed, 25 insertions(+), 7 deletions(-) diffs (71 lines): diff -r 3adcadbe8b61 -r c6a8bd78357a scripts/functional_tests.py --- a/scripts/functional_tests.py Thu Nov 05 09:29:03 2009 -0500 +++ b/scripts/functional_tests.py Thu Nov 05 10:39:59 2009 -0500 @@ -17,10 +17,10 @@ eggs.require( "PasteDeploy" ) eggs.require( "Cheetah" ) -import atexit, logging, os, sys, tempfile +import atexit, logging, os, os.path, sys, tempfile import twill, unittest, time -import os, os.path, subprocess, sys, threading -import httplib +import subprocess, sys, threading, random +import httplib, socket from paste import httpserver import galaxy.app from galaxy.app import UniverseApplication @@ -31,7 +31,8 @@ log = logging.getLogger( "functional_tests.py" ) default_galaxy_test_host = "localhost" -default_galaxy_test_port = "8777" +default_galaxy_test_port_min = 8000 +default_galaxy_test_port_max = 9999 default_galaxy_locales = 'en' default_galaxy_test_file_dir = "test-data" @@ -40,7 +41,7 @@ # ---- Configuration ------------------------------------------------------ galaxy_test_host = os.environ.get( 'GALAXY_TEST_HOST', default_galaxy_test_host ) - galaxy_test_port = os.environ.get( 'GALAXY_TEST_PORT', default_galaxy_test_port ) + galaxy_test_port = os.environ.get( 'GALAXY_TEST_PORT', None ) if 'HTTP_ACCEPT_LANGUAGE' not in os.environ: os.environ['HTTP_ACCEPT_LANGUAGE'] = default_galaxy_locales galaxy_test_file_dir = os.environ.get( 'GALAXY_TEST_FILE_DIR', default_galaxy_test_file_dir ) @@ -75,7 +76,6 @@ # What requires these? os.environ['GALAXY_TEST_HOST'] = galaxy_test_host - os.environ['GALAXY_TEST_PORT'] = galaxy_test_port os.environ['GALAXY_TEST_FILE_DIR'] = galaxy_test_file_dir # ---- Build Application -------------------------------------------------- @@ -115,7 +115,25 @@ if start_server: webapp = buildapp.app_factory( dict(), use_translogger = False, app=app ) - server = httpserver.serve( webapp, host=galaxy_test_host, port=galaxy_test_port, start_loop=False ) + + if galaxy_test_port is not None: + server = httpserver.serve( webapp, host=galaxy_test_host, port=galaxy_test_port, start_loop=False ) + else: + random.seed() + for i in range( 0, 9 ): + try: + galaxy_test_port = str( random.randint( default_galaxy_test_port_min, default_galaxy_test_port_max ) ) + log.debug( "Attempting to serve app on randomly chosen port: %s" % galaxy_test_port ) + server = httpserver.serve( webapp, host=galaxy_test_host, port=galaxy_test_port, start_loop=False ) + break + except socket.error, e: + if e[0] == 98: + continue + raise + else: + raise Exception( "Unable to open a port between %s and %s to start Galaxy server" % ( default_galaxy_test_port_min, default_galaxy_test_port_max ) ) + os.environ['GALAXY_TEST_PORT'] = galaxy_test_port + t = threading.Thread( target=server.serve_forever ) t.start()

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[hg] galaxy 2966: Added several loc files to setup.sh and buildb...
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/e49c58ca5f17 changeset: 2966:e49c58ca5f17 user: Kelly Vincent <kpvincent(a)bx.psu.edu> date: Wed Nov 04 13:58:50 2009 -0500 description: Added several loc files to setup.sh and buildbot_setup.sh diffstat: buildbot_setup.sh | 5 +++++ setup.sh | 6 ++++++ 2 files changed, 11 insertions(+), 0 deletions(-) diffs (47 lines): diff -r 5658f18fe950 -r e49c58ca5f17 buildbot_setup.sh --- a/buildbot_setup.sh Wed Nov 04 13:52:13 2009 -0500 +++ b/buildbot_setup.sh Wed Nov 04 13:58:50 2009 -0500 @@ -5,6 +5,8 @@ LINKS=" /depot/data2/galaxy/alignseq.loc /depot/data2/galaxy/binned_scores.loc +/depot/data2/galaxy/blastdb.loc +/depot/data2/galaxy/bowtie_indices.loc /depot/data2/galaxy/encode_datasets.loc /home/universe/linux-i686/HYPHY /depot/data2/galaxy/liftOver.loc @@ -14,6 +16,9 @@ /depot/data2/galaxy/phastOdds.loc /depot/data2/galaxy/quality_scores.loc /depot/data2/galaxy/regions.loc +/depot/data2/galaxy/sam_fa_indices.loc +/depot/data2/galaxy/sequence_index_base.loc +/depot/data2/galaxy/sequence_index_color.loc /depot/data2/galaxy/taxonomy /depot/data2/galaxy/twobit.loc " diff -r 5658f18fe950 -r e49c58ca5f17 setup.sh --- a/setup.sh Wed Nov 04 13:52:13 2009 -0500 +++ b/setup.sh Wed Nov 04 13:58:50 2009 -0500 @@ -9,8 +9,11 @@ tool_conf.xml.sample universe_wsgi.ini.sample tool-data/alignseq.loc.sample +tool-data/annotation_profiler_options.xml.sample +tool-data/annotation_profiler_valid_builds.txt.sample tool-data/binned_scores.loc.sample tool-data/blastdb.loc.sample +tool-data/bowtie_indices.loc.sample tool-data/encode_datasets.loc.sample tool-data/liftOver.loc.sample tool-data/maf_index.loc.sample @@ -19,6 +22,9 @@ tool-data/phastOdds.loc.sample tool-data/quality_scores.loc.sample tool-data/regions.loc.sample +tool-data/sam_fa_indices.loc.sample +tool-data/sequence_index_base.loc.sample +tool-data/sequence_index_color.loc.sample tool-data/twobit.loc.sample "

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[hg] galaxy 2967: Fix for printing EggNotFetchable exceptions
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/f77f039c3697 changeset: 2967:f77f039c3697 user: Nate Coraor <nate(a)bx.psu.edu> date: Wed Nov 04 16:23:23 2009 -0500 description: Fix for printing EggNotFetchable exceptions diffstat: lib/galaxy/eggs/__init__.py | 2 ++ 1 files changed, 2 insertions(+), 0 deletions(-) diffs (12 lines): diff -r e49c58ca5f17 -r f77f039c3697 lib/galaxy/eggs/__init__.py --- a/lib/galaxy/eggs/__init__.py Wed Nov 04 13:58:50 2009 -0500 +++ b/lib/galaxy/eggs/__init__.py Wed Nov 04 16:23:23 2009 -0500 @@ -20,6 +20,8 @@ self.eggs = eggs else: self.eggs = [ eggs ] + def __str__( self ): + return ' '.join( self.eggs ) class PlatformNotSupported( Exception ): pass

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[hg] galaxy 2965: Fixed the bash script to reflect the change in...
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/5658f18fe950 changeset: 2965:5658f18fe950 user: rc date: Wed Nov 04 13:52:13 2009 -0500 description: Fixed the bash script to reflect the change in the location of galaxy amq listener script diffstat: run_galaxy_listener.sh | 2 +- 1 files changed, 1 insertions(+), 1 deletions(-) diffs (11 lines): diff -r 0d534da7f0ff -r 5658f18fe950 run_galaxy_listener.sh --- a/run_galaxy_listener.sh Wed Nov 04 13:09:37 2009 -0500 +++ b/run_galaxy_listener.sh Wed Nov 04 13:52:13 2009 -0500 @@ -1,4 +1,4 @@ #!/bin/sh cd `dirname $0` -python scripts/galaxy_messaging/amqp_consumer.py >> galaxy_listener.log 2>&1 \ No newline at end of file +python scripts/galaxy_messaging/server/amqp_consumer.py >> galaxy_listener.log 2>&1 \ No newline at end of file

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[hg] galaxy 2964: Eliminate printing PYTHONPATH to stderr in the...
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/0d534da7f0ff changeset: 2964:0d534da7f0ff user: Greg Von Kuster <greg(a)bx.psu.edu> date: Wed Nov 04 13:09:37 2009 -0500 description: Eliminate printing PYTHONPATH to stderr in the cleanup_datasets.py script. diffstat: scripts/cleanup_datasets/cleanup_datasets.py | 1 - 1 files changed, 0 insertions(+), 1 deletions(-) diffs (11 lines): diff -r fdf07565eedf -r 0d534da7f0ff scripts/cleanup_datasets/cleanup_datasets.py --- a/scripts/cleanup_datasets/cleanup_datasets.py Wed Nov 04 12:58:48 2009 -0500 +++ b/scripts/cleanup_datasets/cleanup_datasets.py Wed Nov 04 13:09:37 2009 -0500 @@ -387,7 +387,6 @@ class CleanupDatasetsApplication( object ): """Encapsulates the state of a Universe application""" def __init__( self, database_connection=None, file_path=None ): - print >> sys.stderr, "python path is: " + ", ".join( sys.path ) if database_connection is None: raise Exception( "CleanupDatasetsApplication requires a database_connection value" ) if file_path is None:

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[hg] galaxy 2961: Quick fix for maf_utilities.src_split.
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/adfcd8bb13d1 changeset: 2961:adfcd8bb13d1 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Wed Nov 04 12:21:13 2009 -0500 description: Quick fix for maf_utilities.src_split. diffstat: lib/galaxy/tools/util/maf_utilities.py | 2 +- 1 files changed, 1 insertions(+), 1 deletions(-) diffs (12 lines): diff -r 91a3bbb52d7a -r adfcd8bb13d1 lib/galaxy/tools/util/maf_utilities.py --- a/lib/galaxy/tools/util/maf_utilities.py Wed Nov 04 12:15:53 2009 -0500 +++ b/lib/galaxy/tools/util/maf_utilities.py Wed Nov 04 12:21:13 2009 -0500 @@ -23,7 +23,7 @@ fields = src.split( SRC_SPLIT_CHAR, 1 ) spec = fields.pop( 0 ) if fields: - chrom = fields + chrom = fields.pop( 0 ) else: chrom = spec return spec, chrom

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[hg] galaxy 2962: Fixed a bug in user info - adding new address
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/92d395c8614b changeset: 2962:92d395c8614b user: rc date: Wed Nov 04 12:30:36 2009 -0500 description: Fixed a bug in user info - adding new address diffstat: lib/galaxy/web/controllers/user.py | 114 +++++++++++++++++++++++--------------- templates/user/edit_address.mako | 2 +- templates/user/info.mako | 2 +- templates/user/new_address.mako | 33 +++++++++++ 4 files changed, 104 insertions(+), 47 deletions(-) diffs (200 lines): diff -r adfcd8bb13d1 -r 92d395c8614b lib/galaxy/web/controllers/user.py --- a/lib/galaxy/web/controllers/user.py Wed Nov 04 12:21:13 2009 -0500 +++ b/lib/galaxy/web/controllers/user.py Wed Nov 04 12:30:36 2009 -0500 @@ -272,7 +272,7 @@ user_address.country = util.restore_text(params.get('field_%i_country' % index, '')) user_address.phone = util.restore_text(params.get('field_%i_phone' % index, '')) user_address.flush() - trans.user.refresh() + trans.sa_session.refresh( user ) values.append(int(user_address.id)) elif value == unicode('none'): values.append('') @@ -618,57 +618,81 @@ # User not logged in, history group must be only public return trans.show_error_message( "You must be logged in to change your default permitted actions." ) @web.expose - def new_address( self, trans, short_desc='', name='', institution='', address1='', - address2='', city='', state='', postal_code='', country='', phone='' ): - if trans.app.config.require_login: - refresh_frames = [ 'masthead', 'history', 'tools' ] - else: - refresh_frames = [ 'masthead', 'history' ] + def new_address( self, trans, **kwd ): + params = util.Params( kwd ) + msg = util.restore_text( params.get( 'msg', '' ) ) + messagetype = params.get( 'messagetype', 'done' ) + admin_view = params.get( 'admin_view', 'False' ) + error = '' + user = trans.sa_session.query( trans.app.model.User ).get( int( params.get( 'user_id', None ) ) ) if not trans.app.config.allow_user_creation and not trans.user_is_admin(): return trans.show_error_message( 'User registration is disabled. Please contact your Galaxy administrator for an account.' ) - short_desc_error = name_error = institution_error = address1_error = city_error = None - address2_error = state_error = postal_code_error = country_error = phone_error = None - if short_desc: - if not len( short_desc ): - short_desc_error = 'Enter a short description for this address' - elif not len( name ): - name_error = 'Enter the full name' - elif not len( institution ): - institution_error = 'Enter the institution associated with the user' - elif not len ( address1 ): - address1_error = 'Enter the address' - elif not len( city ): - city_error = 'Enter the city' - elif not len( state ): - state_error = 'Enter the state/province/region' - elif not len( postal_code ): - postal_code_error = 'Enter the postal code' - elif not len( country ): - country_error = 'Enter the country' + if params.get( 'save_new_address_button', None ) == 'Save': + if not len( util.restore_text( params.get( 'short_desc', '' ) ) ): + error = 'Enter a short description for this address' + elif not len( util.restore_text( params.get( 'name', '' ) ) ): + error = 'Enter the full name' + elif not len( util.restore_text( params.get( 'institution', '' ) ) ): + error = 'Enter the institution associated with the user' + elif not len ( util.restore_text( params.get( 'address1', '' ) ) ): + error = 'Enter the address' + elif not len( util.restore_text( params.get( 'city', '' ) ) ): + error = 'Enter the city' + elif not len( util.restore_text( params.get( 'state', '' ) ) ): + error = 'Enter the state/province/region' + elif not len( util.restore_text( params.get( 'postal_code', '' ) ) ): + error = 'Enter the postal code' + elif not len( util.restore_text( params.get( 'country', '' ) ) ): + error = 'Enter the country' else: - user_address = trans.app.model.UserAddress( user=trans.user, desc=short_desc, - name=name, institution=institution, - address=address1+' '+address2, city=city, - state=state, postal_code=postal_code, - country=country, phone=phone) + user_address = trans.app.model.UserAddress( user=user ) + user_address.desc = util.restore_text( params.get( 'short_desc', '' ) ) + user_address.name = util.restore_text( params.get( 'name', '' ) ) + user_address.institution = util.restore_text( params.get( 'institution', '' ) ) + user_address.address = util.restore_text( params.get( 'address1', '' ) )+' '+util.restore_text( params.get( 'address2', '' ) ) + user_address.city = util.restore_text( params.get( 'city', '' ) ) + user_address.state = util.restore_text( params.get( 'state', '' ) ) + user_address.postal_code = util.restore_text( params.get( 'postal_code', '' ) ) + user_address.country = util.restore_text( params.get( 'country', '' ) ) + user_address.phone = util.restore_text( params.get( 'phone', '' ) ) user_address.flush() + msg = 'Address <b>%s</b> has been added' % user_address.desc + if admin_view == 'True': + return trans.response.send_redirect( web.url_for( controller='user', + action='show_info', + admin_view=True, + user_id=user.id, + msg=msg, + messagetype='done') ) return trans.response.send_redirect( web.url_for( controller='user', action='show_info', - msg='Address <b>%s</b> has been added' % user_address.desc, + msg=msg, messagetype='done') ) - - return trans.show_form( - web.FormBuilder( web.url_for(), "New address", submit_text="Save" ) - .add_text( "short_desc", "Short address description", value=short_desc, error=short_desc_error ) - .add_text( "name", "Name", value=name, error=name_error ) - .add_text( "institution", "Institution", value=institution, error=institution_error ) - .add_text( "address1", "Address Line 1", value=address1, error=address1_error ) - .add_text( "address2", "Address Line 2", value=address2, error=address2_error ) - .add_text( "city", "City", value=city, error=city_error ) - .add_text( "state", "State/Province/Region", value=state, error=state_error ) - .add_text( "postal_code", "Postal Code", value=postal_code, error=postal_code_error ) - .add_text( "country", "Country", value=country, error=country_error ) - .add_text( "phone", "Phone", value=phone, error=phone_error ) ) + else: + # show the address form with the current values filled in + # create the widgets for each address field + widgets = [] + widgets.append(dict(label='Short description', + widget=TextField( 'short_desc', 40, '' ) ) ) + widgets.append(dict(label='Name', + widget=TextField( 'name', 40, '' ) ) ) + widgets.append(dict(label='Institution', + widget=TextField( 'institution', 40, '' ) ) ) + widgets.append(dict(label='Address Line 1', + widget=TextField( 'address1', 40, '' ) ) ) + widgets.append(dict(label='City', + widget=TextField( 'city', 40, '' ) ) ) + widgets.append(dict(label='State', + widget=TextField( 'state', 40, '' ) ) ) + widgets.append(dict(label='Postal Code', + widget=TextField( 'postal_code', 40, '' ) ) ) + widgets.append(dict(label='Country', + widget=TextField( 'country', 40, '' ) ) ) + widgets.append(dict(label='Phone', + widget=TextField( 'phone', 40, '' ) ) ) + return trans.fill_template( 'user/new_address.mako', user=user, + admin_view=admin_view, + widgets=widgets, msg=msg, messagetype=messagetype) @web.expose def edit_address( self, trans, **kwd ): params = util.Params( kwd ) diff -r adfcd8bb13d1 -r 92d395c8614b templates/user/edit_address.mako --- a/templates/user/edit_address.mako Wed Nov 04 12:21:13 2009 -0500 +++ b/templates/user/edit_address.mako Wed Nov 04 12:30:36 2009 -0500 @@ -11,7 +11,7 @@ <ul class="manage-table-actions"> <li> - <a class="action-button" href="${h.url_for( controller='user', action='show_info')}"> + <a class="action-button" href="${h.url_for( controller='user', action='show_info', admin_view=admin_view, user_id=user.id)}"> <span>Manage User Information</span></a> </li> </ul> diff -r adfcd8bb13d1 -r 92d395c8614b templates/user/info.mako --- a/templates/user/info.mako Wed Nov 04 12:21:13 2009 -0500 +++ b/templates/user/info.mako Wed Nov 04 12:30:36 2009 -0500 @@ -99,7 +99,7 @@ </div> </form> %endif - <form name="user_info" id="user_info" action="${h.url_for( controller='user', action='new_address' )}" method="post" > + <form name="user_info" id="user_info" action="${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"> %if user.addresses: diff -r adfcd8bb13d1 -r 92d395c8614b templates/user/new_address.mako --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/templates/user/new_address.mako Wed Nov 04 12:30:36 2009 -0500 @@ -0,0 +1,33 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> + + +%if msg: + ${render_msg( msg, messagetype )} +%endif +</br> +</br> +<h3>New address</h3> + +<ul class="manage-table-actions"> + <li> + <a class="action-button" href="${h.url_for( controller='user', action='show_info', admin_view=admin_view, user_id=user.id)}"> + <span>Manage User Information</span></a> + </li> +</ul> +<div class="toolForm"> +<form name="login_info" id="login_info" action="${h.url_for( controller='user', action='new_address', admin_view=admin_view, user_id=user.id )}" method="post" > + <div class="toolFormTitle">New address</div> + <div class="toolFormBody"> + %for field in widgets: + <div class="form-row"> + <label>${field[ 'label' ]}</label> + ${field[ 'widget' ].get_html()} + </div> + %endfor + <div class="form-row"> + <input type="submit" name="save_new_address_button" value="Save"> + </div> + </div> +</form> +</div> \ No newline at end of file

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[hg] galaxy 2963: Add the GeneTrack egg. Also includes some enh...
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/fdf07565eedf changeset: 2963:fdf07565eedf user: Nate Coraor <nate(a)bx.psu.edu> date: Wed Nov 04 12:58:48 2009 -0500 description: Add the GeneTrack egg. Also includes some enhancements and cleanup of the eggs/fetch/scramble code. diffstat: dist-eggs.ini | 4 + eggs.ini | 5 +- lib/galaxy/config.py | 13 +++ lib/galaxy/eggs/__init__.py | 149 ++++++++++++++---------------------- scripts/fetch_eggs.py | 36 ++++---- scripts/scramble.py | 28 +++--- scripts/scramble/scripts/GeneTrack.py | 52 +++++++++++++ 7 files changed, 164 insertions(+), 123 deletions(-) diffs (490 lines): diff -r 92d395c8614b -r fdf07565eedf dist-eggs.ini --- a/dist-eggs.ini Wed Nov 04 12:30:36 2009 -0500 +++ b/dist-eggs.ini Wed Nov 04 12:58:48 2009 -0500 @@ -57,3 +57,7 @@ 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 + +[ignore] +; Don't build these eggs on these platforms: +GeneTrack = py2.4-noplatform diff -r 92d395c8614b -r fdf07565eedf eggs.ini --- a/eggs.ini Wed Nov 04 12:30:36 2009 -0500 +++ b/eggs.ini Wed Nov 04 12:58:48 2009 -0500 @@ -9,7 +9,7 @@ [general] repository = http://eggs.g2.bx.psu.edu ; these eggs must be scrambled for your local environment -no_download = pbs_python DRMAA_python +no_auto = pbs_python DRMAA_python [eggs:platform] bx_python = 0.5.0 @@ -31,6 +31,7 @@ decorator = 3.1.2 docutils = 0.4 elementtree = 1.2.6_20050316 +GeneTrack = 2.0.0_beta_1 lrucache = 0.2 ;lsprof - james Mako = 0.2.5 @@ -61,6 +62,7 @@ python_lzo = _static flup = .dev_r2311 bx_python = _dev_r4bf1f32e6b76 +GeneTrack = _dev_raa786e9fc131d998e532a1aef39d108850c9e93d ; nose = .dev_r7156749efc58 ; source location, necessary for scrambling @@ -81,6 +83,7 @@ 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/aa786e9fc131d998e532a1a… lrucache = http://evan.prodromou.name/lrucache/lrucache-0.2.tar.gz Mako = http://www.makotemplates.org/downloads/Mako-0.2.5.tar.gz MyghtyUtils = http://cheeseshop.python.org/packages/source/M/MyghtyUtils/MyghtyUtils-0.52… diff -r 92d395c8614b -r fdf07565eedf lib/galaxy/config.py --- a/lib/galaxy/config.py Wed Nov 04 12:30:36 2009 -0500 +++ b/lib/galaxy/config.py Wed Nov 04 12:58:48 2009 -0500 @@ -8,6 +8,9 @@ import ConfigParser from galaxy.util import string_as_bool +from galaxy import eggs +import pkg_resources + log = logging.getLogger( __name__ ) def resolve_path( path, root ): @@ -126,6 +129,16 @@ for path in self.tool_config, self.datatypes_config: if not os.path.isfile(path): raise ConfigurationError("File not found: %s" % path ) + # Check job runners so the admin can scramble dependent egg. + if self.start_job_runners is not None: + runner_to_egg = dict( pbs = 'pbs_python', sge = 'DRMAA_python' ) + for runner in self.start_job_runners.split( ',' ): + try: + pkg_resources.require( runner_to_egg[runner] ) + except eggs.EggNotFetchable, e: + raise eggs.EggNotFetchable( 'You must scramble the %s egg to use the %s job runner. Instructions are available at:\n http://bitbucket.org/galaxy/galaxy-central/wiki/Config/Cluster' % ( runner_to_egg[runner], runner ) ) + except KeyError: + raise Exception( 'No such job runner: %s. Please double-check the value of start_job_runners in universe_wsgi.ini' % runner ) def is_admin_user( self,user ): """ diff -r 92d395c8614b -r fdf07565eedf lib/galaxy/eggs/__init__.py --- a/lib/galaxy/eggs/__init__.py Wed Nov 04 12:30:36 2009 -0500 +++ b/lib/galaxy/eggs/__init__.py Wed Nov 04 12:58:48 2009 -0500 @@ -14,11 +14,12 @@ # within tools. i don't know of any way around this. -ndc galaxy_dir = os.path.abspath( os.path.join( os.path.dirname( __file__ ), "..", "..", ".." ) ) -class NewEgg( Exception ): - pass - class EggNotFetchable( Exception ): - pass + def __init__( self, eggs ): + if type( eggs ) in ( list, tuple ): + self.eggs = eggs + else: + self.eggs = [ eggs ] class PlatformNotSupported( Exception ): pass @@ -157,6 +158,14 @@ # 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 ) @@ -195,7 +204,7 @@ log.warning( " %s" % self.buildpath ) def unpack_zip( self, source_path, unpack_path ): z = zipfile.ZipFile( source_path, "r" ) - tld = ( z.namelist()[0].split( os.path.sep, 1 ) )[0] + tld = self.get_tld( z.namelist() ) cur = os.getcwd() os.chdir( unpack_path ) for fn in z.namelist(): @@ -211,12 +220,12 @@ os.chdir( cur ) def unpack_tar( self, source_path, unpack_path ): t = tarfile.open( source_path, "r" ) - tld = ( t.getnames()[0].split( os.path.sep, 1 ) )[0] + 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 t.getmembers(): - if "ez_setup" not in member.name: - t.extract( member ) + for member in members: + t.extract( member ) t.close() os.rename( tld, self.name ) os.chdir( cur ) @@ -265,7 +274,7 @@ self.eggs = {} self.config = CSConfigParser() self.repo = None - self.no_download = [] + 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 ) } def parse( self ): @@ -273,7 +282,7 @@ raise Exception( "unable to read egg config from %s" % Crate.config_file ) try: self.repo = self.config.get( "general", "repository" ) - self.no_download = self.config.get( "general", "no_download" ).split() + 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: @@ -316,19 +325,19 @@ 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. + 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_download ) + 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 - missing = [] for egg in self.eggs.itervalues(): if ignore is not None: if egg.name in ignore: @@ -336,11 +345,18 @@ if skip_platform and egg.platform['galaxy'] == self.platform['galaxy']: missing.append( egg.name ) continue - egg.fetch() + try: + egg.fetch() + except EggNotFetchable: + missing.append( egg.name ) if skip_platform: raise PlatformNotSupported( self.platform['galaxy'] ) + 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: @@ -379,21 +395,14 @@ 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 = self.dictize_list_of_tuples( self.config.items( "hosts" ) ) - self.groups = self.dictize_list_of_tuples( self.config.items( "groups" ) ) + 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 dictize_list_of_tuples( self, lot ): - """ - Makes a list of 2-value tuples into a dict. - """ - d = {} - for k, v in lot: - d[k] = v - return d def get_platforms( self, wanted ): # find all the members of a group and process them if self.groups.has_key( wanted ): @@ -409,8 +418,8 @@ 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. + 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 @@ -418,14 +427,16 @@ 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 + # 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 ) @@ -448,75 +459,31 @@ class GalaxyConfig: config_file = os.path.join( galaxy_dir, "universe_wsgi.ini" ) + always_conditional = ( 'GeneTrack', ) 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 ): - if egg_name == "psycopg2": + if egg_name == "pysqlite": + # SQLite is different since it can be specified in two config vars and defaults to True try: - if self.config.get( "app:main", "database_connection" ).startswith( "postgres://" ): - return True - else: - return False + return self.config.get( "app:main", "database_connection" ).startswith( "sqlite://" ) + except: + return True + else: + try: + return { "psycopg2": lambda: self.config.get( "app:main", "database_connection" ).startswith( "postgres://" ), + "MySQL_python": lambda: self.config.get( "app:main", "database_connection" ).startswith( "mysql://" ), + "DRMAA_python": lambda: "sge" in self.config.get( "app:main", "start_job_runners" ).split(","), + "pbs_python": lambda: "pbs" in self.config.get( "app:main", "start_job_runners" ).split(","), + "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 ), + }.get( egg_name, lambda: True )() except: return False - elif egg_name == "pysqlite": - try: - # database connection is the sqlite alchemy dialect (not really - # a documented usage in Galaxy, but it would work) - if self.config.get( "app:main", "database_connection" ).startswith( "sqlite://" ): - return True - else: - return False - # database connection is unset, so sqlite is the default - except: - return True - elif egg_name == "DRMAA_python": - try: - runners = self.config.get( "app:main", "start_job_runners" ).split(",") - if "sge" in runners: - return True - else: - return False - except: - return False - elif egg_name == "pbs_python": - try: - runners = self.config.get( "app:main", "start_job_runners" ).split(",") - if "pbs" in runners: - return True - else: - return False - except: - return False - elif egg_name == "threadframe": - try: - if self.config.get( "app:main", "use_heartbeat" ): - return True - else: - return False - except: - return False - elif egg_name == "guppy": - try: - if self.config.get( "app:main", "use_memdump" ): - return True - else: - return False - except: - return False - elif egg_name == "MySQL_python": - try: - if self.config.get( "app:main", "database_connection" ).startswith( "mysql://" ): - return True - else: - return False - except: - return False - else: - return True def require( pkg ): # add the egg dirs to sys.path if they're not already there diff -r 92d395c8614b -r fdf07565eedf scripts/fetch_eggs.py --- a/scripts/fetch_eggs.py Wed Nov 04 12:30:36 2009 -0500 +++ b/scripts/fetch_eggs.py Wed Nov 04 12:58:48 2009 -0500 @@ -25,26 +25,28 @@ c.platform = { 'peak' : sys.argv[2].rsplit('-',1)[0], 'galaxy' : sys.argv[2] } c.parse() try: + galaxy_config = GalaxyConfig() + names = [] if len( sys.argv ) == 1: - galaxy_config = GalaxyConfig() - ignore = [] - for name in c.get_names(): - if not galaxy_config.check_conditional( name ): - ignore.append( name ) - c.fetch( ignore=ignore ) + names = c.get_names() + elif sys.argv[1] == 'all': + names = galaxy_config.always_conditional else: - if sys.argv[1] == 'all': - c.fetch() - else: - egg = c.get( sys.argv[1] ) - if egg is None: - print "error: %s not in eggs.ini" % sys.argv[1] - sys.exit( 1 ) - egg.fetch() + # Fetch 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.fetch() + sys.exit( 0 ) + ignore = filter( lambda x: not galaxy_config.check_conditional( x ), list( names ) ) + c.fetch( ignore ) except EggNotFetchable, e: - print "One of the python eggs necessary to run Galaxy couldn't be downloaded" - print "automatically. You may want to try building it by hand with:" - print " python scripts/scramble.py %s" % 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 sys.exit( 1 ) except PlatformNotSupported, e: print "Your platform (%s) is not supported." % e diff -r 92d395c8614b -r fdf07565eedf scripts/scramble.py --- a/scripts/scramble.py Wed Nov 04 12:30:36 2009 -0500 +++ b/scripts/scramble.py Wed Nov 04 12:58:48 2009 -0500 @@ -18,19 +18,19 @@ c = Crate() c.parse() +galaxy_config = GalaxyConfig() +names = [] if len( sys.argv ) == 1: - galaxy_config = GalaxyConfig() - ignore = [] - for name in c.get_names(): - if not galaxy_config.check_conditional( name ): - ignore.append( name ) - c.scramble( ignore=ignore ) + names = c.get_names() +elif sys.argv[1] == 'all': + names = galaxy_config.always_conditional else: - if sys.argv[1] == 'all': - c.scramble() - else: - 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() +# 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 ) diff -r 92d395c8614b -r fdf07565eedf scripts/scramble/scripts/GeneTrack.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/scramble/scripts/GeneTrack.py Wed Nov 04 12:58:48 2009 -0500 @@ -0,0 +1,52 @@ +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" ) + +print "scramble.py: Creating setup.py for GeneTrack" +setup_py = """from setuptools import setup, find_packages +setup( + name = "GeneTrack", + version = "2.0.0-beta-1", + package_data = {'':["*.*"]}, + packages = find_packages(), + zip_safe = True, +) +""" +open( 'setup.py', 'w' ).write( setup_py ) + + +# do it +execfile( "setup.py", globals(), locals() )

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