# HG changeset patch --
Bitbucket.org
# Project galaxy-dist
# URL
http://bitbucket.org/galaxy/galaxy-dist/overview
# User Nate Coraor <nate(a)bx.psu.edu>
# Date 1277829642 14400
# Node ID b4237641ca4d28631c9e65c726693057d4b8dab3
# Parent eea2c040ccb7bd0d2a7c6e5eab8e65f98a163009
Make the PSU BX browser a UCSC browser instead of being a different display type.
--- a/universe_wsgi.ini.sample
+++ b/universe_wsgi.ini.sample
@@ -105,8 +105,7 @@ mailing_join_addr = galaxy-user-join@bx.
# Use the new iframe / javascript based layout
use_new_layout = true
-# Comma separated list of bx / UCSC / gbrowse / GeneTrack browsers to use for viewing
-bx_display_sites = main
+# Comma separated list of UCSC / gbrowse / GeneTrack browsers to use for viewing
ucsc_display_sites = main,test,archaea,ucla
gbrowse_display_sites = wormbase,tair,modencode_worm,modencode_fly
# Define your GeneTrack servers in tool-data/shared/genetrack/genetrack_sites.txt
--- a/lib/galaxy/util/__init__.py
+++ b/lib/galaxy/util/__init__.py
@@ -278,12 +278,6 @@ def object_to_string( obj ):
def string_to_object( s ):
return pickle.loads( binascii.unhexlify( s ) )
-def get_bx_by_build(build):
- sites = []
- for site in bx_build_sites:
- if build in site['builds']:
- sites.append((site['name'],site['url']))
- return sites
def get_ucsc_by_build(build):
sites = []
for site in ucsc_build_sites:
@@ -484,7 +478,6 @@ def umask_fix_perms( path, umask, unmask
galaxy_root_path = os.path.join(__path__[0],
"..","..","..")
# The dbnames list is used in edit attributes and the upload tool
dbnames = read_dbnames( os.path.join( galaxy_root_path, "tool-data",
"shared", "ucsc", "builds.txt" ) )
-bx_build_sites = read_build_sites( os.path.join( galaxy_root_path, "tool-data",
"shared", "bx", "bx_build_sites.txt" ) )
ucsc_build_sites = read_build_sites( os.path.join( galaxy_root_path,
"tool-data", "shared", "ucsc",
"ucsc_build_sites.txt" ) )
gbrowse_build_sites = read_build_sites( os.path.join( galaxy_root_path,
"tool-data", "shared", "gbrowse",
"gbrowse_build_sites.txt" ) )
genetrack_sites = read_build_sites( os.path.join( galaxy_root_path,
"tool-data", "shared", "genetrack",
"genetrack_sites.txt" ), check_builds=False )
--- a/tool-data/shared/bx/bx_build_sites.txt
+++ /dev/null
@@ -1,1 +0,0 @@
-main
http://main.genome-browser.bx.psu.edu/cgi-bin/hgTracks? hg18,hg19,mm8,mm9 bx-main
--- a/lib/galaxy/datatypes/interval.py
+++ b/lib/galaxy/datatypes/interval.py
@@ -54,7 +54,6 @@ class Interval( Tabular ):
"""Initialize interval datatype, by adding UCSC display
apps"""
Tabular.__init__(self, **kwd)
self.add_display_app ( 'ucsc', 'display at UCSC',
'as_ucsc_display_file', 'ucsc_links' )
- self.add_display_app ( 'main', 'BX',
'as_ucsc_display_file', 'bx_links' )
def init_meta( self, dataset, copy_from=None ):
Tabular.init_meta( self, dataset, copy_from=copy_from )
@@ -247,29 +246,6 @@ class Interval( Tabular ):
link = '%s?redirect_url=%s&display_url=%s' % (
internal_url, redirect_url, display_url )
ret_val.append( (site_name, link) )
return ret_val
- def bx_links( self, dataset, type, app, base_url ):
- # TODO: abstract these methods to eliminate duplicate code.
- ret_val = []
- if dataset.has_data:
- viewport_tuple = self.get_estimated_display_viewport(dataset)
- if viewport_tuple:
- chrom = viewport_tuple[0]
- start = viewport_tuple[1]
- stop = viewport_tuple[2]
- for site_name, site_url in util.get_bx_by_build(dataset.dbkey):
- if site_name in app.config.bx_display_sites:
- # HACK: UCSC doesn't support https, so force http even
- # if our URL scheme is https. Making this work
- # requires additional hackery in your upstream proxy.
- # If UCSC ever supports https, remove this hack.
- internal_url = "%s" % url_for(
controller='dataset', dataset_id=dataset.id, action='display_at',
filename='bx_' + site_name )
- if base_url.startswith( 'https://' ):
- base_url = base_url.replace( 'https', 'http',
1 )
- display_url = urllib.quote_plus(
"%s%s/display_as?id=%i&display_app=%s&authz_method=display_at" %
(base_url, url_for( controller='root' ), dataset.id, type) )
- redirect_url = urllib.quote_plus(
"%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" % (site_url,
dataset.dbkey, chrom, start, stop ) )
- link = '%s?redirect_url=%s&display_url=%s' % (
internal_url, redirect_url, display_url )
- ret_val.append( (site_name, link) )
- return ret_val
def validate( self, dataset ):
"""Validate an interval file using the bx
GenomicIntervalReader"""
--- a/tool-data/shared/ucsc/ucsc_build_sites.txt
+++ b/tool-data/shared/ucsc/ucsc_build_sites.txt
@@ -5,3 +5,4 @@ archaea
http://archaea.ucsc.edu/cgi-bin/
#Harvested from
http://genome-test.cse.ucsc.edu/cgi-bin/das/dsn
test
http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks? anoCar1,ce4,ce3,ce2,ce1,loxAfr1,rn2,eschColi_O157H7_1,rn4,droYak1,heliPylo_J99_1,droYak2,dp3,dp2,caeRem2,caeRem1,oryLat1,eschColi_K12_1,homIni13,homIni14,droAna1,droAna2,oryCun1,sacCer1,heliHepa1,droGri1,sc1,dasNov1,choHof1,tupBel1,mm9,mm8,vibrChol1,mm5,mm4,mm7,mm6,mm3,mm2,rn3,venter1,galGal3,galGal2,ornAna1,equCab1,cioSav2,rheMac2,eutHer13,droPer1,droVir2,droVir1,heliPylo_26695_1,euaGli13,calJac1,campJeju1,droSim1,hg13,hg15,hg16,hg17,monDom1,monDom4,droMoj1,petMar1,droMoj2,vibrChol_MO10_1,vibrPara1,gliRes13,vibrVuln_YJ016_1,braFlo1,cioSav1,lauRas13,dm1,canFam1,canFam2,ci1,echTel1,ci2,caePb1,dm3,ponAbe2,falciparum,xenTro1,xenTro2,nonAfr13,fr2,fr1,gasAcu1,dm2,apiMel1,apiMel2,eschColi_O157H7EDL933_1,priPac1,panTro1,hg18,panTro2,campJeju_RM1221_1,canHg12,vibrChol_O395_1,vibrFisc_ES114_1,danRer5,danRer4,danRer3,danRer2,danRer1,tetNig1,afrOth13,bosTau1,eschColi_CFT073_1,bosTau3,bosTau2,bosTau4,rodEnt13,droEre1,priMat13,vibrVu
ln_CMCP6_1,cb2,cb3,cb1,borEut13,droSec1,felCat3,strPur1,strPur2,otoGar1,catArr1,anoGam1,triCas2
ucla
http://epigenomics.mcdb.ucla.edu/cgi-bin/hgTracks? araTha1
+psu bx main
http://main.genome-browser.bx.psu.edu/cgi-bin/hgTracks? hg18,hg19,mm8,mm9
--- a/lib/galaxy/config.py
+++ b/lib/galaxy/config.py
@@ -83,7 +83,6 @@ class Configuration( object ):
self.log_memory_usage = string_as_bool( kwargs.get( 'log_memory_usage',
'False' ) )
self.log_actions = string_as_bool( kwargs.get( 'log_actions',
'False' ) )
self.log_events = string_as_bool( kwargs.get( 'log_events',
'False' ) )
- self.bx_display_sites = kwargs.get( 'bx_display_sites', "main"
).lower().split(",")
self.ucsc_display_sites = kwargs.get( 'ucsc_display_sites',
"main,test,archaea,ucla" ).lower().split(",")
self.gbrowse_display_sites = kwargs.get( 'gbrowse_display_sites',
"wormbase,tair,modencode_worm,modencode_fly" ).lower().split(",")
self.genetrack_display_sites = kwargs.get( 'genetrack_display_sites',
"main,test" ).lower().split(",")