[galaxy-commits] commit/galaxy-central: 6 new changesets

4 Sep 2014

6 new commits in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/a3c5b729592b/
Changeset:   a3c5b729592b
User:        natefoo
Date:        2014-09-03 00:20:23
Summary:     Remove the BuildSites class I recently created and merge its functionality back into util and the datatypes registry. As a result, the build_sites configuration moves to datatypes_conf.xml and display applications can now use configured build sites so that the path is not hardcoded into the individual committed display application files. `from_file` in the display applications is still supported.
Affected #:  25 files

diff -r 8e699330dfcd889b02acccb058f16b28c95ac848 -r a3c5b729592b9f1d18a9e911a0125ba10f74c68d datatypes_conf.xml.sample

--- a/datatypes_conf.xml.sample
+++ b/datatypes_conf.xml.sample
@@ -312,4 +312,12 @@
     <sniffer type="galaxy.datatypes.assembly:Amos"/>
     --></sniffers>
+  <build_sites>
+      <site type="ucsc" file="tool-data/shared/ucsc/ucsc_build_sites.txt"/>
+      <site type="gbrowse" file="tool-data/shared/gbrowse/gbrowse_build_sites.txt"/>
+      <site type="ensembl" file="tool-data/shared/ensembl/ensembl_sites.txt"/>
+      <site type="ensembl_data_url" file="tool-data/shared/ensembl/ensembl_sites_data_URL.txt"/>
+      <site type="igv" file="tool-data/shared/igv/igv_build_sites.txt"/>
+      <site type="rviewer" file="tool-data/shared/rviewer/rviewer_build_sites.txt"/>
+  </build_sites></datatypes>

diff -r 8e699330dfcd889b02acccb058f16b28c95ac848 -r a3c5b729592b9f1d18a9e911a0125ba10f74c68d display_applications/ensembl/ensembl_bam.xml
--- a/display_applications/ensembl/ensembl_bam.xml
+++ b/display_applications/ensembl/ensembl_bam.xml
@@ -1,7 +1,7 @@
 <display id="ensembl_bam" version="1.0.0" name="display at Ensembl"><!-- Current Ensembl method of attaching user data via URL; archives older than ~November 2008 will use a different method --><!-- Load links from file: one line to one link -->
-    <dynamic_links from_file="tool-data/shared/ensembl/ensembl_sites.txt" skip_startswith="#" id="0" name="1">
+    <dynamic_links site_type="ensembl" skip_startswith="#" id="0" name="1"><!-- Define parameters by column from file, allow splitting on builds --><dynamic_param name="site_id" value="0"/>

diff -r 8e699330dfcd889b02acccb058f16b28c95ac848 -r a3c5b729592b9f1d18a9e911a0125ba10f74c68d display_applications/ensembl/ensembl_gff.xml
--- a/display_applications/ensembl/ensembl_gff.xml
+++ b/display_applications/ensembl/ensembl_gff.xml
@@ -1,7 +1,7 @@
 <display id="ensembl_gff" version="1.0.0" name="display at Ensembl"><!-- Current Ensembl method of attaching user data via URL; archives older than ~November 2008 will use a different method --><!-- Load links from file: one line to one link -->
-    <dynamic_links from_file="tool-data/shared/ensembl/ensembl_sites.txt" skip_startswith="#" id="0" name="1">
+    <dynamic_links site_type="ensembl" skip_startswith="#" id="0" name="1"><!-- Define parameters by column from file, allow splitting on builds --><dynamic_param name="site_id" value="0"/>
@@ -41,7 +41,7 @@
 
     <!-- Old Ensembl method of attaching user data via URL --><!-- Load links from file: one line to one link -->
-    <dynamic_links from_file="tool-data/shared/ensembl/ensembl_sites_data_URL.txt" skip_startswith="#" id="0" name="1">
+    <dynamic_links site_type="ensembl_data_url" skip_startswith="#" id="0" name="1"><!-- Define parameters by column from file, allow splitting on builds --><dynamic_param name="site_id" value="0"/>

diff -r 8e699330dfcd889b02acccb058f16b28c95ac848 -r a3c5b729592b9f1d18a9e911a0125ba10f74c68d display_applications/ensembl/ensembl_interval_as_bed.xml
--- a/display_applications/ensembl/ensembl_interval_as_bed.xml
+++ b/display_applications/ensembl/ensembl_interval_as_bed.xml
@@ -1,7 +1,7 @@
 <display id="ensembl_interval" version="1.0.0" name="display at Ensembl"><!-- Current Ensembl method of attaching user data via URL; archives older than ~November 2008 will use a different method --><!-- Load links from file: one line to one link -->
-    <dynamic_links from_file="tool-data/shared/ensembl/ensembl_sites.txt" skip_startswith="#" id="0" name="1">
+    <dynamic_links site_type="ensembl" skip_startswith="#" id="0" name="1"><!-- Define parameters by column from file, allow splitting on builds --><dynamic_param name="site_id" value="0"/>
@@ -41,7 +41,7 @@
 
     <!-- Old Ensembl method of attaching user data via URL --><!-- Load links from file: one line to one link -->
-    <dynamic_links from_file="tool-data/shared/ensembl/ensembl_sites_data_URL.txt" skip_startswith="#" id="0" name="1">
+    <dynamic_links site_type="ensembl_data_url" skip_startswith="#" id="0" name="1"><!-- Define parameters by column from file, allow splitting on builds --><dynamic_param name="site_id" value="0"/>

diff -r 8e699330dfcd889b02acccb058f16b28c95ac848 -r a3c5b729592b9f1d18a9e911a0125ba10f74c68d display_applications/gbrowse/gbrowse_gff.xml
--- a/display_applications/gbrowse/gbrowse_gff.xml
+++ b/display_applications/gbrowse/gbrowse_gff.xml
@@ -1,6 +1,6 @@
 <display id="gbrowse_gff" version="1.0.0" name="display at GBrowse"><!-- Load links from file: one line to one link -->
-    <dynamic_links from_file="tool-data/shared/gbrowse/gbrowse_build_sites.txt" skip_startswith="#" id="0" name="1">
+    <dynamic_links site_type="gbrowse" skip_startswith="#" id="0" name="1"><!-- Define parameters by column from file, allow splitting on builds --><dynamic_param name="site_id" value="0"/>

diff -r 8e699330dfcd889b02acccb058f16b28c95ac848 -r a3c5b729592b9f1d18a9e911a0125ba10f74c68d display_applications/gbrowse/gbrowse_interval_as_bed.xml
--- a/display_applications/gbrowse/gbrowse_interval_as_bed.xml
+++ b/display_applications/gbrowse/gbrowse_interval_as_bed.xml
@@ -1,6 +1,6 @@
 <display id="gbrowse_interval_as_bed" version="1.0.0" name="display at GBrowse"><!-- Load links from file: one line to one link -->
-    <dynamic_links from_file="tool-data/shared/gbrowse/gbrowse_build_sites.txt" skip_startswith="#" id="0" name="1">
+    <dynamic_links site_type="gbrowse" skip_startswith="#" id="0" name="1"><!-- Define parameters by column from file, allow splitting on builds --><dynamic_param name="site_id" value="0"/>

diff -r 8e699330dfcd889b02acccb058f16b28c95ac848 -r a3c5b729592b9f1d18a9e911a0125ba10f74c68d display_applications/gbrowse/gbrowse_wig.xml
--- a/display_applications/gbrowse/gbrowse_wig.xml
+++ b/display_applications/gbrowse/gbrowse_wig.xml
@@ -1,6 +1,6 @@
 <display id="gbrowse_wig" version="1.0.0" name="display at GBrowse"><!-- Load links from file: one line to one link -->
-    <dynamic_links from_file="tool-data/shared/gbrowse/gbrowse_build_sites.txt" skip_startswith="#" id="0" name="1">
+    <dynamic_links site_type="gbrowse" skip_startswith="#" id="0" name="1"><!-- Define parameters by column from file, allow splitting on builds --><dynamic_param name="site_id" value="0"/>

diff -r 8e699330dfcd889b02acccb058f16b28c95ac848 -r a3c5b729592b9f1d18a9e911a0125ba10f74c68d display_applications/igv/bam.xml
--- a/display_applications/igv/bam.xml
+++ b/display_applications/igv/bam.xml
@@ -2,7 +2,7 @@
 <display id="igv_bam" version="1.0.0" name="display with IGV"><!-- Load links from file: one line to one link -->
-    <dynamic_links from_file="tool-data/shared/igv/igv_build_sites.txt" skip_startswith="#" id="0" name="1">
+    <dynamic_links site_type="igv" skip_startswith="#" id="0" name="1"><!-- Define parameters by column from file, allow splitting on builds --><dynamic_param name="site_id" value="0"/>
@@ -92,4 +92,4 @@
     
     
 </display>
-<!-- Dan Blankenberg -->
\ No newline at end of file
+<!-- Dan Blankenberg -->

diff -r 8e699330dfcd889b02acccb058f16b28c95ac848 -r a3c5b729592b9f1d18a9e911a0125ba10f74c68d display_applications/igv/vcf.xml
--- a/display_applications/igv/vcf.xml
+++ b/display_applications/igv/vcf.xml
@@ -2,7 +2,7 @@
 <display id="igv_vcf" version="1.0.0" name="display with IGV"><!-- Load links from file: one line to one link -->
-    <dynamic_links from_file="tool-data/shared/igv/igv_build_sites.txt" skip_startswith="#" id="0" name="1">
+    <dynamic_links site_type="igv" skip_startswith="#" id="0" name="1"><!-- Define parameters by column from file, allow splitting on builds --><dynamic_param name="site_id" value="0"/>
@@ -92,4 +92,4 @@
     
     
 </display>
-<!-- Dan Blankenberg -->
\ No newline at end of file
+<!-- Dan Blankenberg -->

diff -r 8e699330dfcd889b02acccb058f16b28c95ac848 -r a3c5b729592b9f1d18a9e911a0125ba10f74c68d display_applications/rviewer/bed.xml
--- a/display_applications/rviewer/bed.xml
+++ b/display_applications/rviewer/bed.xml
@@ -2,7 +2,7 @@
 <display id="rviewer_interval" version="1.0.0" name="display at RViewer"><!-- Load links from file: one line to one link -->
-    <dynamic_links from_file="tool-data/shared/rviewer/rviewer_build_sites.txt" skip_startswith="#" id="0" name="1">
+    <dynamic_links site_type="rviewer" skip_startswith="#" id="0" name="1"><!-- Define parameters by column from file, allow splitting on builds --><dynamic_param name="site_id" value="0"/>

diff -r 8e699330dfcd889b02acccb058f16b28c95ac848 -r a3c5b729592b9f1d18a9e911a0125ba10f74c68d display_applications/rviewer/vcf.xml
--- a/display_applications/rviewer/vcf.xml
+++ b/display_applications/rviewer/vcf.xml
@@ -2,7 +2,7 @@
 <display id="rviewer_vcf" version="1.0.0" name="display at RViewer"><!-- Load links from file: one line to one link -->
-    <dynamic_links from_file="tool-data/shared/rviewer/rviewer_build_sites.txt" skip_startswith="#" id="0" name="1">
+    <dynamic_links site_type="rviewer" skip_startswith="#" id="0" name="1"><!-- Define parameters by column from file, allow splitting on builds --><dynamic_param name="site_id" value="0"/>

diff -r 8e699330dfcd889b02acccb058f16b28c95ac848 -r a3c5b729592b9f1d18a9e911a0125ba10f74c68d display_applications/ucsc/bam.xml
--- a/display_applications/ucsc/bam.xml
+++ b/display_applications/ucsc/bam.xml
@@ -1,6 +1,6 @@
 <display id="ucsc_bam" version="1.0.0" name="display at UCSC"><!-- Load links from file: one line to one link -->
-    <dynamic_links from_file="tool-data/shared/ucsc/ucsc_build_sites.txt" skip_startswith="#" id="0" name="0">
+    <dynamic_links site_type="ucsc" skip_startswith="#" id="0" name="0"><!-- Define parameters by column from file, allow splitting on builds --><dynamic_param name="site_id" value="0"/><dynamic_param name="ucsc_link" value="1"/>

diff -r 8e699330dfcd889b02acccb058f16b28c95ac848 -r a3c5b729592b9f1d18a9e911a0125ba10f74c68d display_applications/ucsc/bigbed.xml
--- a/display_applications/ucsc/bigbed.xml
+++ b/display_applications/ucsc/bigbed.xml
@@ -1,6 +1,6 @@
 <display id="ucsc_bigbed" version="1.0.0" name="display at UCSC"><!-- Load links from file: one line to one link -->
-    <dynamic_links from_file="tool-data/shared/ucsc/ucsc_build_sites.txt" skip_startswith="#" id="0" name="0">
+    <dynamic_links site_type="ucsc" skip_startswith="#" id="0" name="0"><!-- Define parameters by column from file, allow splitting on builds --><dynamic_param name="site_id" value="0"/><dynamic_param name="ucsc_link" value="1"/>

diff -r 8e699330dfcd889b02acccb058f16b28c95ac848 -r a3c5b729592b9f1d18a9e911a0125ba10f74c68d display_applications/ucsc/bigwig.xml
--- a/display_applications/ucsc/bigwig.xml
+++ b/display_applications/ucsc/bigwig.xml
@@ -1,6 +1,6 @@
 <display id="ucsc_bigwig" version="1.0.0" name="display at UCSC"><!-- Load links from file: one line to one link -->
-    <dynamic_links from_file="tool-data/shared/ucsc/ucsc_build_sites.txt" skip_startswith="#" id="0" name="0">
+    <dynamic_links site_type="ucsc" skip_startswith="#" id="0" name="0"><!-- Define parameters by column from file, allow splitting on builds --><dynamic_param name="site_id" value="0"/><dynamic_param name="ucsc_link" value="1"/>

diff -r 8e699330dfcd889b02acccb058f16b28c95ac848 -r a3c5b729592b9f1d18a9e911a0125ba10f74c68d display_applications/ucsc/interval_as_bed.xml
--- a/display_applications/ucsc/interval_as_bed.xml
+++ b/display_applications/ucsc/interval_as_bed.xml
@@ -1,6 +1,6 @@
 <display id="ucsc_interval_as_bed" version="1.0.0" name="display at UCSC" inherit="True"><!-- Load links from file: one line to one link -->
-    <dynamic_links from_file="tool-data/shared/ucsc/ucsc_build_sites.txt" skip_startswith="#" id="0" name="0">
+    <dynamic_links site_type="ucsc" skip_startswith="#" id="0" name="0"><!-- Define parameters by column from file, allow splitting on builds --><dynamic_param name="site_id" value="0"/><dynamic_param name="ucsc_link" value="1"/>

diff -r 8e699330dfcd889b02acccb058f16b28c95ac848 -r a3c5b729592b9f1d18a9e911a0125ba10f74c68d display_applications/ucsc/maf_customtrack.xml
--- a/display_applications/ucsc/maf_customtrack.xml
+++ b/display_applications/ucsc/maf_customtrack.xml
@@ -1,6 +1,6 @@
 <display id="ucsc_maf_customtrack" version="1.0.0" name="display at UCSC" inherit="True"><!-- Load links from file: one line to one link -->
-    <dynamic_links from_file="tool-data/shared/ucsc/ucsc_build_sites.txt" skip_startswith="#" id="0" name="0">
+    <dynamic_links site_type="ucsc" skip_startswith="#" id="0" name="0"><!-- Define parameters by column from file, allow splitting on builds --><dynamic_param name="site_id" value="0"/><dynamic_param name="ucsc_link" value="1"/>

diff -r 8e699330dfcd889b02acccb058f16b28c95ac848 -r a3c5b729592b9f1d18a9e911a0125ba10f74c68d display_applications/ucsc/vcf.xml
--- a/display_applications/ucsc/vcf.xml
+++ b/display_applications/ucsc/vcf.xml
@@ -1,6 +1,6 @@
 <display id="ucsc_vcf" version="1.0.0" name="display at UCSC"><!-- Load links from file: one line to one link -->
-    <dynamic_links from_file="tool-data/shared/ucsc/ucsc_build_sites.txt" skip_startswith="#" id="0" name="0">
+    <dynamic_links site_type="ucsc" skip_startswith="#" id="0" name="0"><!-- Define parameters by column from file, allow splitting on builds --><dynamic_param name="site_id" value="0"/><dynamic_param name="ucsc_link" value="1"/>

diff -r 8e699330dfcd889b02acccb058f16b28c95ac848 -r a3c5b729592b9f1d18a9e911a0125ba10f74c68d lib/galaxy/app.py
--- a/lib/galaxy/app.py
+++ b/lib/galaxy/app.py
@@ -64,9 +64,6 @@
         # Load dbkey / genome build manager
         self._configure_genome_builds( data_table_name="__dbkeys__", load_old_style=True )
 
-        # Load build sites (old-style)
-        self._configure_build_sites()
-
         # Genomes
         self.genomes = Genomes( self )
         # Data providers registry.

diff -r 8e699330dfcd889b02acccb058f16b28c95ac848 -r a3c5b729592b9f1d18a9e911a0125ba10f74c68d lib/galaxy/config.py
--- a/lib/galaxy/config.py
+++ b/lib/galaxy/config.py
@@ -16,7 +16,6 @@
 from galaxy.util import string_as_bool
 from galaxy.util import listify
 from galaxy.util.dbkeys import GenomeBuilds
-from galaxy.util.build_sites import BuildSites
 from galaxy import eggs
 
 log = logging.getLogger( __name__ )
@@ -224,9 +223,7 @@
         self.sanitize_all_html = string_as_bool( kwargs.get( 'sanitize_all_html', True ) )
         self.serve_xss_vulnerable_mimetypes = string_as_bool( kwargs.get( 'serve_xss_vulnerable_mimetypes', False ) )
         self.enable_old_display_applications = string_as_bool( kwargs.get( "enable_old_display_applications", "True" ) )
-        self.ucsc_build_sites = resolve_path( kwargs.get( 'ucsc_build_sites', os.path.join( self.tool_data_path, 'shared', 'ucsc', 'ucsc_build_sites.txt') ), self.root )
         self.ucsc_display_sites = kwargs.get( 'ucsc_display_sites', "main,test,archaea,ucla" ).lower().split(",")
-        self.gbrowse_build_sites = resolve_path( kwargs.get( 'gbrowse_build_sites', os.path.join( self.tool_data_path, 'shared', 'gbrowse', 'gbrowse_build_sites.txt') ), self.root )
         self.gbrowse_display_sites = kwargs.get( 'gbrowse_display_sites', "modencode,sgd_yeast,tair,wormbase,wormbase_ws120,wormbase_ws140,wormbase_ws170,wormbase_ws180,wormbase_ws190,wormbase_ws200,wormbase_ws204,wormbase_ws210,wormbase_ws220,wormbase_ws225" ).lower().split(",")
         self.brand = kwargs.get( 'brand', None )
         self.welcome_url = kwargs.get( 'welcome_url', '/static/welcome.html' )
@@ -574,9 +571,6 @@
     def _configure_genome_builds( self, data_table_name="__dbkeys__", load_old_style=True ):
         self.genome_builds = GenomeBuilds( self, data_table_name=data_table_name, load_old_style=load_old_style )
 
-    def _configure_build_sites( self ):
-        self.build_sites = BuildSites( self )
-
     def _configure_toolbox( self ):
         # Initialize the tools, making sure the list of tool configs includes the reserved migrated_tools_conf.xml file.
         tool_configs = self.config.tool_configs

diff -r 8e699330dfcd889b02acccb058f16b28c95ac848 -r a3c5b729592b9f1d18a9e911a0125ba10f74c68d lib/galaxy/datatypes/display_applications/application.py
--- a/lib/galaxy/datatypes/display_applications/application.py
+++ b/lib/galaxy/datatypes/display_applications/application.py
@@ -81,9 +81,13 @@
 
 class DynamicDisplayApplicationBuilder( object ):
     @classmethod
-    def __init__( self, elem, display_application ):
+    def __init__( self, elem, display_application, build_sites ):
         rval = []
-        filename = elem.get( 'from_file', None )
+        filename = None
+        if elem.get( 'site_type', None ) is not None:
+            filename = build_sites.get( elem.get( 'site_type' ) )
+        else:
+            filename = elem.get( 'from_file', None )
         assert filename is not None, 'Filename and id attributes required for dynamic_links'
         skip_startswith = elem.get( 'skip_startswith', None )
         separator = elem.get( 'separator', '\t' )
@@ -176,7 +180,7 @@
             if link:
                 rval.links[ link.id ] = link
         for dynamic_links in elem.findall( 'dynamic_links' ):
-            for link in DynamicDisplayApplicationBuilder( dynamic_links, rval ):
+            for link in DynamicDisplayApplicationBuilder( dynamic_links, rval, datatypes_registry.build_sites ):
                 rval.links[ link.id ] = link
         return rval
     def __init__( self, display_id, name, datatypes_registry, version = None ):

diff -r 8e699330dfcd889b02acccb058f16b28c95ac848 -r a3c5b729592b9f1d18a9e911a0125ba10f74c68d lib/galaxy/datatypes/genetics.py
--- a/lib/galaxy/datatypes/genetics.py
+++ b/lib/galaxy/datatypes/genetics.py
@@ -85,7 +85,7 @@
         if not dataset.dbkey:
               dataset.dbkey = 'hg18' # punt!
         if dataset.has_data():
-              for site_name, site_url in app.build_sites.get_ucsc_sites_by_build(dataset.dbkey):
+              for site_name, site_url in app.datatypes_registry.get_legacy_sites_by_build('ucsc', dataset.dbkey):
                     if site_name in app.config.ucsc_display_sites:
                         site_url = site_url.replace('/hgTracks?','/hgGenome?') # for genome graphs
                         internal_url = "%s" % url_for( controller='dataset',

diff -r 8e699330dfcd889b02acccb058f16b28c95ac848 -r a3c5b729592b9f1d18a9e911a0125ba10f74c68d lib/galaxy/datatypes/interval.py
--- a/lib/galaxy/datatypes/interval.py
+++ b/lib/galaxy/datatypes/interval.py
@@ -234,7 +234,7 @@
         # Filter UCSC sites to only those that are supported by this build and
         # enabled.
         valid_sites = [ ( name, url )
-                        for name, url in app.build_sites.get_ucsc_sites_by_build( dataset.dbkey )
+                        for name, url in app.datatypes_registry.get_legacy_sites_by_build('ucsc', dataset.dbkey )
                         if name in app.config.ucsc_display_sites ]
         if not valid_sites:
             return []
@@ -750,7 +750,7 @@
         ret_val = []
         seqid, start, stop = self.get_estimated_display_viewport( dataset )
         if seqid is not None:
-            for site_name, site_url in app.build_sites.get_ucsc_sites_by_build( dataset.dbkey ):
+            for site_name, site_url in app.datatypes_registry.get_legacy_sites_by_build('ucsc', dataset.dbkey ):
                 if site_name in app.config.ucsc_display_sites:
                     redirect_url = urllib.quote_plus(
                             "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" %
@@ -762,7 +762,7 @@
         ret_val = []
         seqid, start, stop = self.get_estimated_display_viewport( dataset )
         if seqid is not None:
-            for site_name, site_url in app.build_sites.get_gbrowse_sites_by_build( dataset.dbkey ):
+            for site_name, site_url in app.datatypes_registry.get_legacy_sites_by_build('gbrowse', dataset.dbkey ):
                 if site_name in app.config.gbrowse_display_sites:
                     if seqid.startswith( 'chr' ) and len ( seqid ) > 3:
                         seqid = seqid[3:]
@@ -1091,7 +1091,7 @@
         ret_val = []
         chrom, start, stop = self.get_estimated_display_viewport( dataset )
         if chrom is not None:
-            for site_name, site_url in app.build_sites.get_gbrowse_sites_by_build( dataset.dbkey ):
+            for site_name, site_url in app.datatypes_registry.get_legacy_sites_by_build('gbrowse', dataset.dbkey ):
                 if site_name in app.config.gbrowse_display_sites:
                     if chrom.startswith( 'chr' ) and len ( chrom ) > 3:
                         chrom = chrom[3:]
@@ -1103,7 +1103,7 @@
         ret_val = []
         chrom, start, stop = self.get_estimated_display_viewport( dataset )
         if chrom is not None:
-            for site_name, site_url in app.build_sites.get_ucsc_sites_by_build( dataset.dbkey ):
+            for site_name, site_url in app.datatypes_registry.get_legacy_sites_by_build('ucsc', dataset.dbkey ):
                 if site_name in app.config.ucsc_display_sites:
                     redirect_url = urllib.quote_plus( "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" % ( site_url, dataset.dbkey, chrom, start, stop ) )
                     link = self._get_remote_call_url( redirect_url, site_name, dataset, type, app, base_url )
@@ -1285,7 +1285,7 @@
         ret_val = []
         chrom, start, stop = self.get_estimated_display_viewport(dataset)
         if chrom is not None:
-            for site_name, site_url in app.build_sites.get_ucsc_sites_by_build(dataset.dbkey):
+            for site_name, site_url in app.datatypes_registry.get_legacy_sites_by_build('ucsc',dataset.dbkey):
                 if site_name in app.config.ucsc_display_sites:
                     internal_url = "%s" % url_for( controller='dataset', dataset_id=dataset.id, action='display_at', filename='ucsc_' + site_name )
                     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) )

diff -r 8e699330dfcd889b02acccb058f16b28c95ac848 -r a3c5b729592b9f1d18a9e911a0125ba10f74c68d lib/galaxy/datatypes/registry.py
--- a/lib/galaxy/datatypes/registry.py
+++ b/lib/galaxy/datatypes/registry.py
@@ -69,6 +69,9 @@
         self.datatype_elems = []
         self.sniffer_elems = []
         self.xml_filename = None
+        # Build sites
+        self.build_sites = {}
+        self.legacy_build_sites = {}
 
     def load_datatypes( self, root_dir=None, config=None, deactivate=False, override=True ):
         """
@@ -285,6 +288,8 @@
                                          handling_proprietary_datatypes=handling_proprietary_datatypes,
                                          override=override )
             self.upload_file_formats.sort()
+            # Load build sites
+            self.load_build_sites( root )
             # Persist the xml form of the registry into a temporary file so that it can be loaded from the command line by tools and
             # set_metadata processing.
             self.to_xml_file()
@@ -303,6 +308,26 @@
                     self.sniff_order.append( datatype )
         append_to_sniff_order()
 
+    def load_build_sites( self, root ):
+        if root.find( 'build_sites' ):
+            for elem in root.find( 'build_sites' ).findall( 'site' ):
+                if not (elem.get( 'type' ) and elem.get( 'file' )):
+                    self.log.exception( "Site is missing required 'type' and 'file' attributes: %s" )
+                else:
+                    self.build_sites[elem.get( 'type' )] = elem.get( 'file' )
+                    self.log.debug( "Loaded build site '%s': %s", elem.get( 'type' ), elem.get( 'file' ) )
+        for site, file in self.build_sites.items():
+            if site in ( 'ucsc', 'gbrowse' ):
+                self.legacy_build_sites[site] = galaxy.util.read_build_sites( file )
+                self.log.debug( "Loaded legacy build site '%s': %s", site, file )
+
+    def get_legacy_sites_by_build( self, site_type, build ):
+        sites = []
+        for site in self.legacy_build_sites[site_type]:
+            if build in site['builds']:
+                sites.append((site['name'], site['url']))
+        return sites
+
     def load_datatype_sniffers( self, root, deactivate=False, handling_proprietary_datatypes=False, override=False ):
         """
         Process the sniffers element from a parsed a datatypes XML file located at root_dir/config (if processing the Galaxy

diff -r 8e699330dfcd889b02acccb058f16b28c95ac848 -r a3c5b729592b9f1d18a9e911a0125ba10f74c68d lib/galaxy/util/__init__.py
--- a/lib/galaxy/util/__init__.py
+++ b/lib/galaxy/util/__init__.py
@@ -829,6 +829,30 @@
     return db_names
 
 
+def read_build_sites( filename, check_builds=True ):
+    """ read db names to ucsc mappings from file, this file should probably be merged with the one above """
+    build_sites = []
+    try:
+        for line in open(filename):
+            try:
+                if line[0:1] == "#":
+                    continue
+                fields = line.replace("\r", "").replace("\n", "").split("\t")
+                site_name = fields[0]
+                site = fields[1]
+                if check_builds:
+                    site_builds = fields[2].split(",")
+                    site_dict = {'name': site_name, 'url': site, 'builds': site_builds}
+                else:
+                    site_dict = {'name': site_name, 'url': site}
+                build_sites.append( site_dict )
+            except:
+                continue
+    except:
+        print "ERROR: Unable to read builds for site file %s" % filename
+    return build_sites
+
+
 def relativize_symlinks( path, start=None, followlinks=False):
     for root, dirs, files in os.walk( path, followlinks=followlinks ):
         rel_start = None

diff -r 8e699330dfcd889b02acccb058f16b28c95ac848 -r a3c5b729592b9f1d18a9e911a0125ba10f74c68d lib/galaxy/util/build_sites.py
--- a/lib/galaxy/util/build_sites.py
+++ /dev/null
@@ -1,52 +0,0 @@
-"""
-Functionality for dealing with build sites for legacy display applications.
-"""
-import os.path
-
-
-class BuildSites( object ):
-
-    def __init__( self, app ):
-        self._app = app
-        self._build_sites = {}
-        self.load_build_sites()
-
-    def read_build_sites( self, filename, check_builds=True ):
-        """ read db names to ucsc mappings from file, this file should probably be merged with the one above """
-        build_sites = []
-        try:
-            for line in open(filename):
-                try:
-                    if line[0:1] == "#":
-                        continue
-                    fields = line.replace("\r", "").replace("\n", "").split("\t")
-                    site_name = fields[0]
-                    site = fields[1]
-                    if check_builds:
-                        site_builds = fields[2].split(",")
-                        site_dict = {'name': site_name, 'url': site, 'builds': site_builds}
-                    else:
-                        site_dict = {'name': site_name, 'url': site}
-                    build_sites.append( site_dict )
-                except:
-                    continue
-        except:
-            print "ERROR: Unable to read builds for site file %s" % filename
-        return build_sites
-
-    def load_build_sites( self ):
-        self._build_sites['ucsc'] = self.read_build_sites( self._app.config.ucsc_build_sites )
-        self._build_sites['gbrowse'] = self.read_build_sites( self._app.config.gbrowse_build_sites )
-
-    def _get_site_by_build( self, site_type, build ):
-        sites = []
-        for site in self._build_sites[site_type]:
-            if build in site['builds']:
-                sites.append((site['name'], site['url']))
-        return sites
-
-    def get_ucsc_sites_by_build( self, build ):
-        return self._get_site_by_build( 'ucsc', build )
-
-    def get_gbrowse_sites_by_build( self, build ):
-        return self._get_site_by_build( 'gbrowse', build )


https://bitbucket.org/galaxy/galaxy-central/commits/6347caa946d7/
Changeset:   6347caa946d7
User:        natefoo
Date:        2014-09-03 00:21:50
Summary:     Remove config options from sample.
Affected #:  1 file

diff -r a3c5b729592b9f1d18a9e911a0125ba10f74c68d -r 6347caa946d76480267766122718db064ac3e0a1 universe_wsgi.ini.sample
--- a/universe_wsgi.ini.sample
+++ b/universe_wsgi.ini.sample
@@ -364,12 +364,10 @@
 # which browsers should be available.  URLs and builds available at these
 # browsers are defined in the specifield files.
 
-# UCSC browsers:
-#ucsc_build_sites = tool-data/shared/ucsc/ucsc_build_sites.txt
+# UCSC browsers: tool-data/shared/ucsc/ucsc_build_sites.txt
 #ucsc_display_sites = main,test,archaea,ucla
 
-# GBrowse servers:
-#gbrowse_build_sites = tool-data/shared/gbrowse/gbrowse_build_sites.txt
+# GBrowse servers: tool-data/shared/gbrowse/gbrowse_build_sites.txt
 #gbrowse_display_sites = modencode,sgd_yeast,tair,wormbase,wormbase_ws120,wormbase_ws140,wormbase_ws170,wormbase_ws180,wormbase_ws190,wormbase_ws200,wormbase_ws204,wormbase_ws210,wormbase_ws220,wormbase_ws225
 
 # If use_remote_user = True, display application servers will be denied access


https://bitbucket.org/galaxy/galaxy-central/commits/4888400b34d1/
Changeset:   4888400b34d1
User:        natefoo
Date:        2014-09-03 18:25:22
Summary:     Move ucsc_display_sites and gbrowse_display_sites into datatypes_conf.xml's new <build_sites> section, as per the suggestion by @nsoranzo.
Affected #:  10 files

diff -r 6347caa946d76480267766122718db064ac3e0a1 -r 4888400b34d120140d163ea3d92d053ba04e2ffb datatypes_conf.xml.sample
--- a/datatypes_conf.xml.sample
+++ b/datatypes_conf.xml.sample
@@ -313,8 +313,18 @@
     --></sniffers><build_sites>
-      <site type="ucsc" file="tool-data/shared/ucsc/ucsc_build_sites.txt"/>
-      <site type="gbrowse" file="tool-data/shared/gbrowse/gbrowse_build_sites.txt"/>
+      <!--
+      Build sites define the builds (dbkeys) available at sites used by display
+      applications and the URL to those sites.
+
+      The `display` attributes on the `ucsc` and `gbrowse` sites replace the
+      `ucsc_display_sites` and `gbrowse_display_sites` options in
+      universe_wsgi.ini. Because these are used by "old-style" display
+      applications, their types cannot not change if you want the old-style
+      display links for these sites to work.
+      -->
+      <site type="ucsc" file="tool-data/shared/ucsc/ucsc_build_sites.txt" display="main,test,archaea,ucla"/>
+      <site type="gbrowse" file="tool-data/shared/gbrowse/gbrowse_build_sites.txt" display="modencode,sgd_yeast,tair,wormbase,wormbase_ws120,wormbase_ws140,wormbase_ws170,wormbase_ws180,wormbase_ws190,wormbase_ws200,wormbase_ws204,wormbase_ws210,wormbase_ws220,wormbase_ws225"/><site type="ensembl" file="tool-data/shared/ensembl/ensembl_sites.txt"/><site type="ensembl_data_url" file="tool-data/shared/ensembl/ensembl_sites_data_URL.txt"/><site type="igv" file="tool-data/shared/igv/igv_build_sites.txt"/>

diff -r 6347caa946d76480267766122718db064ac3e0a1 -r 4888400b34d120140d163ea3d92d053ba04e2ffb display_applications/gbrowse/gbrowse_gff.xml
--- a/display_applications/gbrowse/gbrowse_gff.xml
+++ b/display_applications/gbrowse/gbrowse_gff.xml
@@ -10,7 +10,7 @@
         <dynamic_param name="site_organisms" value="4" split="True" separator="," /><!-- Filter out some of the links based upon matching site_id to a Galaxy application configuration parameter and by dataset dbkey -->
-        <filter>${site_id in $APP.config.gbrowse_display_sites}</filter>
+        <filter>${site_id in $APP.datatypes_registry.get_display_sites('gbrowse')}</filter><filter>${dataset.dbkey in $site_dbkeys}</filter><!-- We define url and params as normal, but values defined in dynamic_param are available by specified name -->

diff -r 6347caa946d76480267766122718db064ac3e0a1 -r 4888400b34d120140d163ea3d92d053ba04e2ffb display_applications/gbrowse/gbrowse_interval_as_bed.xml
--- a/display_applications/gbrowse/gbrowse_interval_as_bed.xml
+++ b/display_applications/gbrowse/gbrowse_interval_as_bed.xml
@@ -10,7 +10,7 @@
         <dynamic_param name="site_organisms" value="4" split="True" separator="," /><!-- Filter out some of the links based upon matching site_id to a Galaxy application configuration parameter and by dataset dbkey -->
-        <filter>${site_id in $APP.config.gbrowse_display_sites}</filter>
+        <filter>${site_id in $APP.datatypes_registry.get_display_sites('gbrowse')}</filter><filter>${dataset.dbkey in $site_dbkeys}</filter><!-- We define url and params as normal, but values defined in dynamic_param are available by specified name -->

diff -r 6347caa946d76480267766122718db064ac3e0a1 -r 4888400b34d120140d163ea3d92d053ba04e2ffb display_applications/gbrowse/gbrowse_wig.xml
--- a/display_applications/gbrowse/gbrowse_wig.xml
+++ b/display_applications/gbrowse/gbrowse_wig.xml
@@ -10,7 +10,7 @@
         <dynamic_param name="site_organisms" value="4" split="True" separator="," /><!-- Filter out some of the links based upon matching site_id to a Galaxy application configuration parameter and by dataset dbkey -->
-        <filter>${site_id in $APP.config.gbrowse_display_sites}</filter>
+        <filter>${site_id in $APP.datatypes_registry.get_display_sites('gbrowse')}</filter><filter>${dataset.dbkey in $site_dbkeys}</filter><!-- We define url and params as normal, but values defined in dynamic_param are available by specified name -->

diff -r 6347caa946d76480267766122718db064ac3e0a1 -r 4888400b34d120140d163ea3d92d053ba04e2ffb lib/galaxy/config.py
--- a/lib/galaxy/config.py
+++ b/lib/galaxy/config.py
@@ -223,8 +223,6 @@
         self.sanitize_all_html = string_as_bool( kwargs.get( 'sanitize_all_html', True ) )
         self.serve_xss_vulnerable_mimetypes = string_as_bool( kwargs.get( 'serve_xss_vulnerable_mimetypes', False ) )
         self.enable_old_display_applications = string_as_bool( kwargs.get( "enable_old_display_applications", "True" ) )
-        self.ucsc_display_sites = kwargs.get( 'ucsc_display_sites', "main,test,archaea,ucla" ).lower().split(",")
-        self.gbrowse_display_sites = kwargs.get( 'gbrowse_display_sites', "modencode,sgd_yeast,tair,wormbase,wormbase_ws120,wormbase_ws140,wormbase_ws170,wormbase_ws180,wormbase_ws190,wormbase_ws200,wormbase_ws204,wormbase_ws210,wormbase_ws220,wormbase_ws225" ).lower().split(",")
         self.brand = kwargs.get( 'brand', None )
         self.welcome_url = kwargs.get( 'welcome_url', '/static/welcome.html' )
         # Configuration for the message box directly below the masthead.

diff -r 6347caa946d76480267766122718db064ac3e0a1 -r 4888400b34d120140d163ea3d92d053ba04e2ffb lib/galaxy/datatypes/genetics.py
--- a/lib/galaxy/datatypes/genetics.py
+++ b/lib/galaxy/datatypes/genetics.py
@@ -86,7 +86,7 @@
               dataset.dbkey = 'hg18' # punt!
         if dataset.has_data():
               for site_name, site_url in app.datatypes_registry.get_legacy_sites_by_build('ucsc', dataset.dbkey):
-                    if site_name in app.config.ucsc_display_sites:
+                    if site_name in datatypes_registry.get_display_sites('ucsc'):
                         site_url = site_url.replace('/hgTracks?','/hgGenome?') # for genome graphs
                         internal_url = "%s" % url_for( controller='dataset',
                                 dataset_id=dataset.id, action='display_at', filename='ucsc_' + site_name )

diff -r 6347caa946d76480267766122718db064ac3e0a1 -r 4888400b34d120140d163ea3d92d053ba04e2ffb lib/galaxy/datatypes/interval.py
--- a/lib/galaxy/datatypes/interval.py
+++ b/lib/galaxy/datatypes/interval.py
@@ -235,7 +235,7 @@
         # enabled.
         valid_sites = [ ( name, url )
                         for name, url in app.datatypes_registry.get_legacy_sites_by_build('ucsc', dataset.dbkey )
-                        if name in app.config.ucsc_display_sites ]
+                        if name in app.datatypes_registry.get_display_sites('ucsc') ]
         if not valid_sites:
             return []
         # If there are any valid sites, we need to generate the estimated
@@ -751,7 +751,7 @@
         seqid, start, stop = self.get_estimated_display_viewport( dataset )
         if seqid is not None:
             for site_name, site_url in app.datatypes_registry.get_legacy_sites_by_build('ucsc', dataset.dbkey ):
-                if site_name in app.config.ucsc_display_sites:
+                if site_name in app.datatypes_registry.get_display_sites('ucsc'):
                     redirect_url = urllib.quote_plus(
                             "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" %
                             ( site_url, dataset.dbkey, seqid, start, stop ) )
@@ -763,7 +763,7 @@
         seqid, start, stop = self.get_estimated_display_viewport( dataset )
         if seqid is not None:
             for site_name, site_url in app.datatypes_registry.get_legacy_sites_by_build('gbrowse', dataset.dbkey ):
-                if site_name in app.config.gbrowse_display_sites:
+                if site_name in app.datatypes_registry.get_display_sites('gbrowse'):
                     if seqid.startswith( 'chr' ) and len ( seqid ) > 3:
                         seqid = seqid[3:]
                     redirect_url = urllib.quote_plus( "%s/?q=%s:%s..%s&eurl=%%s" % ( site_url, seqid, start, stop ) )
@@ -1092,7 +1092,7 @@
         chrom, start, stop = self.get_estimated_display_viewport( dataset )
         if chrom is not None:
             for site_name, site_url in app.datatypes_registry.get_legacy_sites_by_build('gbrowse', dataset.dbkey ):
-                if site_name in app.config.gbrowse_display_sites:
+                if site_name in app.datatypes_registry.get_display_sites('gbrowse'):
                     if chrom.startswith( 'chr' ) and len ( chrom ) > 3:
                         chrom = chrom[3:]
                     redirect_url = urllib.quote_plus( "%s/?q=%s:%s..%s&eurl=%%s" % ( site_url, chrom, start, stop ) )
@@ -1104,7 +1104,7 @@
         chrom, start, stop = self.get_estimated_display_viewport( dataset )
         if chrom is not None:
             for site_name, site_url in app.datatypes_registry.get_legacy_sites_by_build('ucsc', dataset.dbkey ):
-                if site_name in app.config.ucsc_display_sites:
+                if site_name in app.datatypes_registry.get_display_sites('ucsc'):
                     redirect_url = urllib.quote_plus( "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" % ( site_url, dataset.dbkey, chrom, start, stop ) )
                     link = self._get_remote_call_url( redirect_url, site_name, dataset, type, app, base_url )
                     ret_val.append( ( site_name, link ) )
@@ -1286,7 +1286,7 @@
         chrom, start, stop = self.get_estimated_display_viewport(dataset)
         if chrom is not None:
             for site_name, site_url in app.datatypes_registry.get_legacy_sites_by_build('ucsc',dataset.dbkey):
-                if site_name in app.config.ucsc_display_sites:
+                if site_name in app.datatypes_registry.get_display_sites('ucsc'):
                     internal_url = "%s" % url_for( controller='dataset', dataset_id=dataset.id, action='display_at', filename='ucsc_' + site_name )
                     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 ) )

diff -r 6347caa946d76480267766122718db064ac3e0a1 -r 4888400b34d120140d163ea3d92d053ba04e2ffb lib/galaxy/datatypes/registry.py
--- a/lib/galaxy/datatypes/registry.py
+++ b/lib/galaxy/datatypes/registry.py
@@ -71,6 +71,7 @@
         self.xml_filename = None
         # Build sites
         self.build_sites = {}
+        self.display_sites = {}
         self.legacy_build_sites = {}
 
     def load_datatypes( self, root_dir=None, config=None, deactivate=False, override=True ):
@@ -314,20 +315,28 @@
                 if not (elem.get( 'type' ) and elem.get( 'file' )):
                     self.log.exception( "Site is missing required 'type' and 'file' attributes: %s" )
                 else:
-                    self.build_sites[elem.get( 'type' )] = elem.get( 'file' )
-                    self.log.debug( "Loaded build site '%s': %s", elem.get( 'type' ), elem.get( 'file' ) )
-        for site, file in self.build_sites.items():
-            if site in ( 'ucsc', 'gbrowse' ):
-                self.legacy_build_sites[site] = galaxy.util.read_build_sites( file )
-                self.log.debug( "Loaded legacy build site '%s': %s", site, file )
+                    site_type = elem.get( 'type' )
+                    file = elem.get( 'file' )
+                    self.build_sites[site_type] = file
+                    if site_type in ('ucsc', 'gbrowse'):
+                        self.legacy_build_sites[site_type] = galaxy.util.read_build_sites( file )
+                    if elem.get( 'display', None ):
+                        display = elem.get( 'display' )
+                        self.display_sites[site_type] = [ x.strip() for x in display.lower().split( ',' ) ]
+                        self.log.debug( "Loaded build site '%s': %s with display sites: %s", site_type, file, display )
+                    else:
+                        self.log.debug( "Loaded build site '%s': %s", site_type, file )
 
     def get_legacy_sites_by_build( self, site_type, build ):
         sites = []
-        for site in self.legacy_build_sites[site_type]:
+        for site in self.legacy_build_sites.get(site_type, []):
             if build in site['builds']:
                 sites.append((site['name'], site['url']))
         return sites
 
+    def get_display_sites( self, site_type ):
+        return self.display_sites.get( site_type, [] )
+
     def load_datatype_sniffers( self, root, deactivate=False, handling_proprietary_datatypes=False, override=False ):
         """
         Process the sniffers element from a parsed a datatypes XML file located at root_dir/config (if processing the Galaxy

diff -r 6347caa946d76480267766122718db064ac3e0a1 -r 4888400b34d120140d163ea3d92d053ba04e2ffb lib/galaxy/web/framework/__init__.py
--- a/lib/galaxy/web/framework/__init__.py
+++ b/lib/galaxy/web/framework/__init__.py
@@ -926,7 +926,7 @@
                 url_for( controller='dataset', action='list' )
             )
             display_as = url_for( controller='root', action='display_as' )
-            if self.app.config.ucsc_display_sites and self.request.path == display_as:
+            if self.app.datatypes_registry.get_display_sites('ucsc') and self.request.path == display_as:
                 try:
                     host = socket.gethostbyaddr( self.environ[ 'REMOTE_ADDR' ] )[0]
                 except( socket.error, socket.herror, socket.gaierror, socket.timeout ):

diff -r 6347caa946d76480267766122718db064ac3e0a1 -r 4888400b34d120140d163ea3d92d053ba04e2ffb universe_wsgi.ini.sample
--- a/universe_wsgi.ini.sample
+++ b/universe_wsgi.ini.sample
@@ -364,12 +364,6 @@
 # which browsers should be available.  URLs and builds available at these
 # browsers are defined in the specifield files.
 
-# UCSC browsers: tool-data/shared/ucsc/ucsc_build_sites.txt
-#ucsc_display_sites = main,test,archaea,ucla
-
-# GBrowse servers: tool-data/shared/gbrowse/gbrowse_build_sites.txt
-#gbrowse_display_sites = modencode,sgd_yeast,tair,wormbase,wormbase_ws120,wormbase_ws140,wormbase_ws170,wormbase_ws180,wormbase_ws190,wormbase_ws200,wormbase_ws204,wormbase_ws210,wormbase_ws220,wormbase_ws225
-
 # If use_remote_user = True, display application servers will be denied access
 # to Galaxy and so displaying datasets in these sites will fail.
 # display_servers contains a list of hostnames which should be allowed to


https://bitbucket.org/galaxy/galaxy-central/commits/608391566ac8/
Changeset:   608391566ac8
User:        natefoo
Date:        2014-09-03 18:27:01
Summary:     Fix nonstandard indentation.
Affected #:  1 file

diff -r 4888400b34d120140d163ea3d92d053ba04e2ffb -r 608391566ac80318f703ddf9b8f9506fc46dc866 lib/galaxy/datatypes/genetics.py
--- a/lib/galaxy/datatypes/genetics.py
+++ b/lib/galaxy/datatypes/genetics.py
@@ -83,29 +83,31 @@
         ret_val = []
         ggtail = 'hgGenome_doSubmitUpload=submit'
         if not dataset.dbkey:
-              dataset.dbkey = 'hg18' # punt!
+            dataset.dbkey = 'hg18' # punt!
         if dataset.has_data():
-              for site_name, site_url in app.datatypes_registry.get_legacy_sites_by_build('ucsc', dataset.dbkey):
-                    if site_name in datatypes_registry.get_display_sites('ucsc'):
-                        site_url = site_url.replace('/hgTracks?','/hgGenome?') # for genome graphs
-                        internal_url = "%s" % url_for( controller='dataset',
-                                dataset_id=dataset.id, action='display_at', filename='ucsc_' + site_name )
-                        display_url = "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at" % (base_url, url_for( controller='root' ), dataset.id, type)
-                        display_url = urllib.quote_plus( display_url )
-                        # was display_url = urllib.quote_plus( "%s/display_as?id=%i&display_app=%s" % (base_url, dataset.id, type) )
-                        #redirect_url = urllib.quote_plus( "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" % (site_url, dataset.dbkey, chrom, start, stop) )
-                        sl = ["%sdb=%s" % (site_url,dataset.dbkey ),]
-                        #sl.append("&hgt.customText=%s")
-                        sl.append("&hgGenome_dataSetName=%s&hgGenome_dataSetDescription=%s" % (dataset.name, 'GalaxyGG_data'))
-                        sl.append("&hgGenome_formatType=best guess&hgGenome_markerType=best guess")
-                        sl.append("&hgGenome_columnLabels=first row&hgGenome_maxVal=&hgGenome_labelVals=")
-                        sl.append("&hgGenome_doSubmitUpload=submit")
-                        sl.append("&hgGenome_maxGapToFill=25000000&hgGenome_uploadFile=%s" % display_url)
-                        s = ''.join(sl)
-                        s = urllib.quote_plus(s)
-                        redirect_url = s
-                        link = '%s?redirect_url=%s&display_url=%s' % ( internal_url, redirect_url, display_url )
-                        ret_val.append( (site_name, link) )
+            for site_name, site_url in app.datatypes_registry.get_legacy_sites_by_build('ucsc', dataset.dbkey):
+                if site_name in datatypes_registry.get_display_sites('ucsc'):
+                    site_url = site_url.replace('/hgTracks?','/hgGenome?') # for genome graphs
+                    internal_url = "%s" % url_for( controller='dataset',
+                                                   dataset_id=dataset.id,
+                                                   action='display_at',
+                                                   filename='ucsc_' + site_name )
+                    display_url = "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at" % (base_url, url_for( controller='root' ), dataset.id, type)
+                    display_url = urllib.quote_plus( display_url )
+                    # was display_url = urllib.quote_plus( "%s/display_as?id=%i&display_app=%s" % (base_url, dataset.id, type) )
+                    #redirect_url = urllib.quote_plus( "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" % (site_url, dataset.dbkey, chrom, start, stop) )
+                    sl = ["%sdb=%s" % (site_url,dataset.dbkey ),]
+                    #sl.append("&hgt.customText=%s")
+                    sl.append("&hgGenome_dataSetName=%s&hgGenome_dataSetDescription=%s" % (dataset.name, 'GalaxyGG_data'))
+                    sl.append("&hgGenome_formatType=best guess&hgGenome_markerType=best guess")
+                    sl.append("&hgGenome_columnLabels=first row&hgGenome_maxVal=&hgGenome_labelVals=")
+                    sl.append("&hgGenome_doSubmitUpload=submit")
+                    sl.append("&hgGenome_maxGapToFill=25000000&hgGenome_uploadFile=%s" % display_url)
+                    s = ''.join(sl)
+                    s = urllib.quote_plus(s)
+                    redirect_url = s
+                    link = '%s?redirect_url=%s&display_url=%s' % ( internal_url, redirect_url, display_url )
+                    ret_val.append( (site_name, link) )
         return ret_val
 
     def make_html_table( self, dataset, skipchars=[] ):


https://bitbucket.org/galaxy/galaxy-central/commits/f7e396d29268/
Changeset:   f7e396d29268
User:        natefoo
Date:        2014-09-03 19:13:48
Summary:     Fix typo in sample config.
Affected #:  1 file

diff -r 608391566ac80318f703ddf9b8f9506fc46dc866 -r f7e396d292685cd03145225f40ad7eb6f74b9408 datatypes_conf.xml.sample
--- a/datatypes_conf.xml.sample
+++ b/datatypes_conf.xml.sample
@@ -320,8 +320,8 @@
       The `display` attributes on the `ucsc` and `gbrowse` sites replace the
       `ucsc_display_sites` and `gbrowse_display_sites` options in
       universe_wsgi.ini. Because these are used by "old-style" display
-      applications, their types cannot not change if you want the old-style
-      display links for these sites to work.
+      applications, their types cannot change if you want the old-style display
+      links for these sites to work.
       --><site type="ucsc" file="tool-data/shared/ucsc/ucsc_build_sites.txt" display="main,test,archaea,ucla"/><site type="gbrowse" file="tool-data/shared/gbrowse/gbrowse_build_sites.txt" display="modencode,sgd_yeast,tair,wormbase,wormbase_ws120,wormbase_ws140,wormbase_ws170,wormbase_ws180,wormbase_ws190,wormbase_ws200,wormbase_ws204,wormbase_ws210,wormbase_ws220,wormbase_ws225"/>


https://bitbucket.org/galaxy/galaxy-central/commits/9b6cccb3af2d/
Changeset:   9b6cccb3af2d
User:        natefoo
Date:        2014-09-04 17:38:26
Summary:     Merged in natefoo/galaxy-central (pull request #481)

Make build sites files configurable
Affected #:  27 files

diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 datatypes_conf.xml.sample
--- a/datatypes_conf.xml.sample
+++ b/datatypes_conf.xml.sample
@@ -312,4 +312,22 @@
     <sniffer type="galaxy.datatypes.assembly:Amos"/>
     --></sniffers>
+  <build_sites>
+      <!--
+      Build sites define the builds (dbkeys) available at sites used by display
+      applications and the URL to those sites.
+
+      The `display` attributes on the `ucsc` and `gbrowse` sites replace the
+      `ucsc_display_sites` and `gbrowse_display_sites` options in
+      universe_wsgi.ini. Because these are used by "old-style" display
+      applications, their types cannot change if you want the old-style display
+      links for these sites to work.
+      -->
+      <site type="ucsc" file="tool-data/shared/ucsc/ucsc_build_sites.txt" display="main,test,archaea,ucla"/>
+      <site type="gbrowse" file="tool-data/shared/gbrowse/gbrowse_build_sites.txt" display="modencode,sgd_yeast,tair,wormbase,wormbase_ws120,wormbase_ws140,wormbase_ws170,wormbase_ws180,wormbase_ws190,wormbase_ws200,wormbase_ws204,wormbase_ws210,wormbase_ws220,wormbase_ws225"/>
+      <site type="ensembl" file="tool-data/shared/ensembl/ensembl_sites.txt"/>
+      <site type="ensembl_data_url" file="tool-data/shared/ensembl/ensembl_sites_data_URL.txt"/>
+      <site type="igv" file="tool-data/shared/igv/igv_build_sites.txt"/>
+      <site type="rviewer" file="tool-data/shared/rviewer/rviewer_build_sites.txt"/>
+  </build_sites></datatypes>

diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 display_applications/ensembl/ensembl_bam.xml
--- a/display_applications/ensembl/ensembl_bam.xml
+++ b/display_applications/ensembl/ensembl_bam.xml
@@ -1,7 +1,7 @@
 <display id="ensembl_bam" version="1.0.0" name="display at Ensembl"><!-- Current Ensembl method of attaching user data via URL; archives older than ~November 2008 will use a different method --><!-- Load links from file: one line to one link -->
-    <dynamic_links from_file="tool-data/shared/ensembl/ensembl_sites.txt" skip_startswith="#" id="0" name="1">
+    <dynamic_links site_type="ensembl" skip_startswith="#" id="0" name="1"><!-- Define parameters by column from file, allow splitting on builds --><dynamic_param name="site_id" value="0"/>

diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 display_applications/ensembl/ensembl_gff.xml
--- a/display_applications/ensembl/ensembl_gff.xml
+++ b/display_applications/ensembl/ensembl_gff.xml
@@ -1,7 +1,7 @@
 <display id="ensembl_gff" version="1.0.0" name="display at Ensembl"><!-- Current Ensembl method of attaching user data via URL; archives older than ~November 2008 will use a different method --><!-- Load links from file: one line to one link -->
-    <dynamic_links from_file="tool-data/shared/ensembl/ensembl_sites.txt" skip_startswith="#" id="0" name="1">
+    <dynamic_links site_type="ensembl" skip_startswith="#" id="0" name="1"><!-- Define parameters by column from file, allow splitting on builds --><dynamic_param name="site_id" value="0"/>
@@ -41,7 +41,7 @@
 
     <!-- Old Ensembl method of attaching user data via URL --><!-- Load links from file: one line to one link -->
-    <dynamic_links from_file="tool-data/shared/ensembl/ensembl_sites_data_URL.txt" skip_startswith="#" id="0" name="1">
+    <dynamic_links site_type="ensembl_data_url" skip_startswith="#" id="0" name="1"><!-- Define parameters by column from file, allow splitting on builds --><dynamic_param name="site_id" value="0"/>

diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 display_applications/ensembl/ensembl_interval_as_bed.xml
--- a/display_applications/ensembl/ensembl_interval_as_bed.xml
+++ b/display_applications/ensembl/ensembl_interval_as_bed.xml
@@ -1,7 +1,7 @@
 <display id="ensembl_interval" version="1.0.0" name="display at Ensembl"><!-- Current Ensembl method of attaching user data via URL; archives older than ~November 2008 will use a different method --><!-- Load links from file: one line to one link -->
-    <dynamic_links from_file="tool-data/shared/ensembl/ensembl_sites.txt" skip_startswith="#" id="0" name="1">
+    <dynamic_links site_type="ensembl" skip_startswith="#" id="0" name="1"><!-- Define parameters by column from file, allow splitting on builds --><dynamic_param name="site_id" value="0"/>
@@ -41,7 +41,7 @@
 
     <!-- Old Ensembl method of attaching user data via URL --><!-- Load links from file: one line to one link -->
-    <dynamic_links from_file="tool-data/shared/ensembl/ensembl_sites_data_URL.txt" skip_startswith="#" id="0" name="1">
+    <dynamic_links site_type="ensembl_data_url" skip_startswith="#" id="0" name="1"><!-- Define parameters by column from file, allow splitting on builds --><dynamic_param name="site_id" value="0"/>

diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 display_applications/gbrowse/gbrowse_gff.xml
--- a/display_applications/gbrowse/gbrowse_gff.xml
+++ b/display_applications/gbrowse/gbrowse_gff.xml
@@ -1,6 +1,6 @@
 <display id="gbrowse_gff" version="1.0.0" name="display at GBrowse"><!-- Load links from file: one line to one link -->
-    <dynamic_links from_file="tool-data/shared/gbrowse/gbrowse_build_sites.txt" skip_startswith="#" id="0" name="1">
+    <dynamic_links site_type="gbrowse" skip_startswith="#" id="0" name="1"><!-- Define parameters by column from file, allow splitting on builds --><dynamic_param name="site_id" value="0"/>
@@ -10,7 +10,7 @@
         <dynamic_param name="site_organisms" value="4" split="True" separator="," /><!-- Filter out some of the links based upon matching site_id to a Galaxy application configuration parameter and by dataset dbkey -->
-        <filter>${site_id in $APP.config.gbrowse_display_sites}</filter>
+        <filter>${site_id in $APP.datatypes_registry.get_display_sites('gbrowse')}</filter><filter>${dataset.dbkey in $site_dbkeys}</filter><!-- We define url and params as normal, but values defined in dynamic_param are available by specified name -->

diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 display_applications/gbrowse/gbrowse_interval_as_bed.xml
--- a/display_applications/gbrowse/gbrowse_interval_as_bed.xml
+++ b/display_applications/gbrowse/gbrowse_interval_as_bed.xml
@@ -1,6 +1,6 @@
 <display id="gbrowse_interval_as_bed" version="1.0.0" name="display at GBrowse"><!-- Load links from file: one line to one link -->
-    <dynamic_links from_file="tool-data/shared/gbrowse/gbrowse_build_sites.txt" skip_startswith="#" id="0" name="1">
+    <dynamic_links site_type="gbrowse" skip_startswith="#" id="0" name="1"><!-- Define parameters by column from file, allow splitting on builds --><dynamic_param name="site_id" value="0"/>
@@ -10,7 +10,7 @@
         <dynamic_param name="site_organisms" value="4" split="True" separator="," /><!-- Filter out some of the links based upon matching site_id to a Galaxy application configuration parameter and by dataset dbkey -->
-        <filter>${site_id in $APP.config.gbrowse_display_sites}</filter>
+        <filter>${site_id in $APP.datatypes_registry.get_display_sites('gbrowse')}</filter><filter>${dataset.dbkey in $site_dbkeys}</filter><!-- We define url and params as normal, but values defined in dynamic_param are available by specified name -->

diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 display_applications/gbrowse/gbrowse_wig.xml
--- a/display_applications/gbrowse/gbrowse_wig.xml
+++ b/display_applications/gbrowse/gbrowse_wig.xml
@@ -1,6 +1,6 @@
 <display id="gbrowse_wig" version="1.0.0" name="display at GBrowse"><!-- Load links from file: one line to one link -->
-    <dynamic_links from_file="tool-data/shared/gbrowse/gbrowse_build_sites.txt" skip_startswith="#" id="0" name="1">
+    <dynamic_links site_type="gbrowse" skip_startswith="#" id="0" name="1"><!-- Define parameters by column from file, allow splitting on builds --><dynamic_param name="site_id" value="0"/>
@@ -10,7 +10,7 @@
         <dynamic_param name="site_organisms" value="4" split="True" separator="," /><!-- Filter out some of the links based upon matching site_id to a Galaxy application configuration parameter and by dataset dbkey -->
-        <filter>${site_id in $APP.config.gbrowse_display_sites}</filter>
+        <filter>${site_id in $APP.datatypes_registry.get_display_sites('gbrowse')}</filter><filter>${dataset.dbkey in $site_dbkeys}</filter><!-- We define url and params as normal, but values defined in dynamic_param are available by specified name -->

diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 display_applications/igv/bam.xml
--- a/display_applications/igv/bam.xml
+++ b/display_applications/igv/bam.xml
@@ -2,7 +2,7 @@
 <display id="igv_bam" version="1.0.0" name="display with IGV"><!-- Load links from file: one line to one link -->
-    <dynamic_links from_file="tool-data/shared/igv/igv_build_sites.txt" skip_startswith="#" id="0" name="1">
+    <dynamic_links site_type="igv" skip_startswith="#" id="0" name="1"><!-- Define parameters by column from file, allow splitting on builds --><dynamic_param name="site_id" value="0"/>
@@ -92,4 +92,4 @@
     
     
 </display>
-<!-- Dan Blankenberg -->
\ No newline at end of file
+<!-- Dan Blankenberg -->

diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 display_applications/igv/vcf.xml
--- a/display_applications/igv/vcf.xml
+++ b/display_applications/igv/vcf.xml
@@ -2,7 +2,7 @@
 <display id="igv_vcf" version="1.0.0" name="display with IGV"><!-- Load links from file: one line to one link -->
-    <dynamic_links from_file="tool-data/shared/igv/igv_build_sites.txt" skip_startswith="#" id="0" name="1">
+    <dynamic_links site_type="igv" skip_startswith="#" id="0" name="1"><!-- Define parameters by column from file, allow splitting on builds --><dynamic_param name="site_id" value="0"/>
@@ -92,4 +92,4 @@
     
     
 </display>
-<!-- Dan Blankenberg -->
\ No newline at end of file
+<!-- Dan Blankenberg -->

diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 display_applications/rviewer/bed.xml
--- a/display_applications/rviewer/bed.xml
+++ b/display_applications/rviewer/bed.xml
@@ -2,7 +2,7 @@
 <display id="rviewer_interval" version="1.0.0" name="display at RViewer"><!-- Load links from file: one line to one link -->
-    <dynamic_links from_file="tool-data/shared/rviewer/rviewer_build_sites.txt" skip_startswith="#" id="0" name="1">
+    <dynamic_links site_type="rviewer" skip_startswith="#" id="0" name="1"><!-- Define parameters by column from file, allow splitting on builds --><dynamic_param name="site_id" value="0"/>

diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 display_applications/rviewer/vcf.xml
--- a/display_applications/rviewer/vcf.xml
+++ b/display_applications/rviewer/vcf.xml
@@ -2,7 +2,7 @@
 <display id="rviewer_vcf" version="1.0.0" name="display at RViewer"><!-- Load links from file: one line to one link -->
-    <dynamic_links from_file="tool-data/shared/rviewer/rviewer_build_sites.txt" skip_startswith="#" id="0" name="1">
+    <dynamic_links site_type="rviewer" skip_startswith="#" id="0" name="1"><!-- Define parameters by column from file, allow splitting on builds --><dynamic_param name="site_id" value="0"/>

diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 display_applications/ucsc/bam.xml
--- a/display_applications/ucsc/bam.xml
+++ b/display_applications/ucsc/bam.xml
@@ -1,6 +1,6 @@
 <display id="ucsc_bam" version="1.0.0" name="display at UCSC"><!-- Load links from file: one line to one link -->
-    <dynamic_links from_file="tool-data/shared/ucsc/ucsc_build_sites.txt" skip_startswith="#" id="0" name="0">
+    <dynamic_links site_type="ucsc" skip_startswith="#" id="0" name="0"><!-- Define parameters by column from file, allow splitting on builds --><dynamic_param name="site_id" value="0"/><dynamic_param name="ucsc_link" value="1"/>

diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 display_applications/ucsc/bigbed.xml
--- a/display_applications/ucsc/bigbed.xml
+++ b/display_applications/ucsc/bigbed.xml
@@ -1,6 +1,6 @@
 <display id="ucsc_bigbed" version="1.0.0" name="display at UCSC"><!-- Load links from file: one line to one link -->
-    <dynamic_links from_file="tool-data/shared/ucsc/ucsc_build_sites.txt" skip_startswith="#" id="0" name="0">
+    <dynamic_links site_type="ucsc" skip_startswith="#" id="0" name="0"><!-- Define parameters by column from file, allow splitting on builds --><dynamic_param name="site_id" value="0"/><dynamic_param name="ucsc_link" value="1"/>

diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 display_applications/ucsc/bigwig.xml
--- a/display_applications/ucsc/bigwig.xml
+++ b/display_applications/ucsc/bigwig.xml
@@ -1,6 +1,6 @@
 <display id="ucsc_bigwig" version="1.0.0" name="display at UCSC"><!-- Load links from file: one line to one link -->
-    <dynamic_links from_file="tool-data/shared/ucsc/ucsc_build_sites.txt" skip_startswith="#" id="0" name="0">
+    <dynamic_links site_type="ucsc" skip_startswith="#" id="0" name="0"><!-- Define parameters by column from file, allow splitting on builds --><dynamic_param name="site_id" value="0"/><dynamic_param name="ucsc_link" value="1"/>

diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 display_applications/ucsc/interval_as_bed.xml
--- a/display_applications/ucsc/interval_as_bed.xml
+++ b/display_applications/ucsc/interval_as_bed.xml
@@ -1,6 +1,6 @@
 <display id="ucsc_interval_as_bed" version="1.0.0" name="display at UCSC" inherit="True"><!-- Load links from file: one line to one link -->
-    <dynamic_links from_file="tool-data/shared/ucsc/ucsc_build_sites.txt" skip_startswith="#" id="0" name="0">
+    <dynamic_links site_type="ucsc" skip_startswith="#" id="0" name="0"><!-- Define parameters by column from file, allow splitting on builds --><dynamic_param name="site_id" value="0"/><dynamic_param name="ucsc_link" value="1"/>

diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 display_applications/ucsc/maf_customtrack.xml
--- a/display_applications/ucsc/maf_customtrack.xml
+++ b/display_applications/ucsc/maf_customtrack.xml
@@ -1,6 +1,6 @@
 <display id="ucsc_maf_customtrack" version="1.0.0" name="display at UCSC" inherit="True"><!-- Load links from file: one line to one link -->
-    <dynamic_links from_file="tool-data/shared/ucsc/ucsc_build_sites.txt" skip_startswith="#" id="0" name="0">
+    <dynamic_links site_type="ucsc" skip_startswith="#" id="0" name="0"><!-- Define parameters by column from file, allow splitting on builds --><dynamic_param name="site_id" value="0"/><dynamic_param name="ucsc_link" value="1"/>

diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 display_applications/ucsc/vcf.xml
--- a/display_applications/ucsc/vcf.xml
+++ b/display_applications/ucsc/vcf.xml
@@ -1,6 +1,6 @@
 <display id="ucsc_vcf" version="1.0.0" name="display at UCSC"><!-- Load links from file: one line to one link -->
-    <dynamic_links from_file="tool-data/shared/ucsc/ucsc_build_sites.txt" skip_startswith="#" id="0" name="0">
+    <dynamic_links site_type="ucsc" skip_startswith="#" id="0" name="0"><!-- Define parameters by column from file, allow splitting on builds --><dynamic_param name="site_id" value="0"/><dynamic_param name="ucsc_link" value="1"/>

diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 lib/galaxy/app.py
--- a/lib/galaxy/app.py
+++ b/lib/galaxy/app.py
@@ -64,9 +64,6 @@
         # Load dbkey / genome build manager
         self._configure_genome_builds( data_table_name="__dbkeys__", load_old_style=True )
 
-        # Load build sites (old-style)
-        self._configure_build_sites()
-
         # Genomes
         self.genomes = Genomes( self )
         # Data providers registry.

diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 lib/galaxy/config.py
--- a/lib/galaxy/config.py
+++ b/lib/galaxy/config.py
@@ -16,7 +16,6 @@
 from galaxy.util import string_as_bool
 from galaxy.util import listify
 from galaxy.util.dbkeys import GenomeBuilds
-from galaxy.util.build_sites import BuildSites
 from galaxy import eggs
 
 log = logging.getLogger( __name__ )
@@ -224,10 +223,6 @@
         self.sanitize_all_html = string_as_bool( kwargs.get( 'sanitize_all_html', True ) )
         self.serve_xss_vulnerable_mimetypes = string_as_bool( kwargs.get( 'serve_xss_vulnerable_mimetypes', False ) )
         self.enable_old_display_applications = string_as_bool( kwargs.get( "enable_old_display_applications", "True" ) )
-        self.ucsc_build_sites = resolve_path( kwargs.get( 'ucsc_build_sites', os.path.join( self.tool_data_path, 'shared', 'ucsc', 'ucsc_build_sites.txt') ), self.root )
-        self.ucsc_display_sites = kwargs.get( 'ucsc_display_sites', "main,test,archaea,ucla" ).lower().split(",")
-        self.gbrowse_build_sites = resolve_path( kwargs.get( 'gbrowse_build_sites', os.path.join( self.tool_data_path, 'shared', 'gbrowse', 'gbrowse_build_sites.txt') ), self.root )
-        self.gbrowse_display_sites = kwargs.get( 'gbrowse_display_sites', "modencode,sgd_yeast,tair,wormbase,wormbase_ws120,wormbase_ws140,wormbase_ws170,wormbase_ws180,wormbase_ws190,wormbase_ws200,wormbase_ws204,wormbase_ws210,wormbase_ws220,wormbase_ws225" ).lower().split(",")
         self.brand = kwargs.get( 'brand', None )
         self.welcome_url = kwargs.get( 'welcome_url', '/static/welcome.html' )
         # Configuration for the message box directly below the masthead.
@@ -575,9 +570,6 @@
     def _configure_genome_builds( self, data_table_name="__dbkeys__", load_old_style=True ):
         self.genome_builds = GenomeBuilds( self, data_table_name=data_table_name, load_old_style=load_old_style )
 
-    def _configure_build_sites( self ):
-        self.build_sites = BuildSites( self )
-
     def _configure_toolbox( self ):
         # Initialize the tools, making sure the list of tool configs includes the reserved migrated_tools_conf.xml file.
         tool_configs = self.config.tool_configs

diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 lib/galaxy/datatypes/display_applications/application.py
--- a/lib/galaxy/datatypes/display_applications/application.py
+++ b/lib/galaxy/datatypes/display_applications/application.py
@@ -81,9 +81,13 @@
 
 class DynamicDisplayApplicationBuilder( object ):
     @classmethod
-    def __init__( self, elem, display_application ):
+    def __init__( self, elem, display_application, build_sites ):
         rval = []
-        filename = elem.get( 'from_file', None )
+        filename = None
+        if elem.get( 'site_type', None ) is not None:
+            filename = build_sites.get( elem.get( 'site_type' ) )
+        else:
+            filename = elem.get( 'from_file', None )
         assert filename is not None, 'Filename and id attributes required for dynamic_links'
         skip_startswith = elem.get( 'skip_startswith', None )
         separator = elem.get( 'separator', '\t' )
@@ -176,7 +180,7 @@
             if link:
                 rval.links[ link.id ] = link
         for dynamic_links in elem.findall( 'dynamic_links' ):
-            for link in DynamicDisplayApplicationBuilder( dynamic_links, rval ):
+            for link in DynamicDisplayApplicationBuilder( dynamic_links, rval, datatypes_registry.build_sites ):
                 rval.links[ link.id ] = link
         return rval
     def __init__( self, display_id, name, datatypes_registry, version = None ):

diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 lib/galaxy/datatypes/genetics.py
--- a/lib/galaxy/datatypes/genetics.py
+++ b/lib/galaxy/datatypes/genetics.py
@@ -83,29 +83,31 @@
         ret_val = []
         ggtail = 'hgGenome_doSubmitUpload=submit'
         if not dataset.dbkey:
-              dataset.dbkey = 'hg18' # punt!
+            dataset.dbkey = 'hg18' # punt!
         if dataset.has_data():
-              for site_name, site_url in app.build_sites.get_ucsc_sites_by_build(dataset.dbkey):
-                    if site_name in app.config.ucsc_display_sites:
-                        site_url = site_url.replace('/hgTracks?','/hgGenome?') # for genome graphs
-                        internal_url = "%s" % url_for( controller='dataset',
-                                dataset_id=dataset.id, action='display_at', filename='ucsc_' + site_name )
-                        display_url = "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at" % (base_url, url_for( controller='root' ), dataset.id, type)
-                        display_url = urllib.quote_plus( display_url )
-                        # was display_url = urllib.quote_plus( "%s/display_as?id=%i&display_app=%s" % (base_url, dataset.id, type) )
-                        #redirect_url = urllib.quote_plus( "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" % (site_url, dataset.dbkey, chrom, start, stop) )
-                        sl = ["%sdb=%s" % (site_url,dataset.dbkey ),]
-                        #sl.append("&hgt.customText=%s")
-                        sl.append("&hgGenome_dataSetName=%s&hgGenome_dataSetDescription=%s" % (dataset.name, 'GalaxyGG_data'))
-                        sl.append("&hgGenome_formatType=best guess&hgGenome_markerType=best guess")
-                        sl.append("&hgGenome_columnLabels=first row&hgGenome_maxVal=&hgGenome_labelVals=")
-                        sl.append("&hgGenome_doSubmitUpload=submit")
-                        sl.append("&hgGenome_maxGapToFill=25000000&hgGenome_uploadFile=%s" % display_url)
-                        s = ''.join(sl)
-                        s = urllib.quote_plus(s)
-                        redirect_url = s
-                        link = '%s?redirect_url=%s&display_url=%s' % ( internal_url, redirect_url, display_url )
-                        ret_val.append( (site_name, link) )
+            for site_name, site_url in app.datatypes_registry.get_legacy_sites_by_build('ucsc', dataset.dbkey):
+                if site_name in datatypes_registry.get_display_sites('ucsc'):
+                    site_url = site_url.replace('/hgTracks?','/hgGenome?') # for genome graphs
+                    internal_url = "%s" % url_for( controller='dataset',
+                                                   dataset_id=dataset.id,
+                                                   action='display_at',
+                                                   filename='ucsc_' + site_name )
+                    display_url = "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at" % (base_url, url_for( controller='root' ), dataset.id, type)
+                    display_url = urllib.quote_plus( display_url )
+                    # was display_url = urllib.quote_plus( "%s/display_as?id=%i&display_app=%s" % (base_url, dataset.id, type) )
+                    #redirect_url = urllib.quote_plus( "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" % (site_url, dataset.dbkey, chrom, start, stop) )
+                    sl = ["%sdb=%s" % (site_url,dataset.dbkey ),]
+                    #sl.append("&hgt.customText=%s")
+                    sl.append("&hgGenome_dataSetName=%s&hgGenome_dataSetDescription=%s" % (dataset.name, 'GalaxyGG_data'))
+                    sl.append("&hgGenome_formatType=best guess&hgGenome_markerType=best guess")
+                    sl.append("&hgGenome_columnLabels=first row&hgGenome_maxVal=&hgGenome_labelVals=")
+                    sl.append("&hgGenome_doSubmitUpload=submit")
+                    sl.append("&hgGenome_maxGapToFill=25000000&hgGenome_uploadFile=%s" % display_url)
+                    s = ''.join(sl)
+                    s = urllib.quote_plus(s)
+                    redirect_url = s
+                    link = '%s?redirect_url=%s&display_url=%s' % ( internal_url, redirect_url, display_url )
+                    ret_val.append( (site_name, link) )
         return ret_val
 
     def make_html_table( self, dataset, skipchars=[] ):

diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 lib/galaxy/datatypes/interval.py
--- a/lib/galaxy/datatypes/interval.py
+++ b/lib/galaxy/datatypes/interval.py
@@ -234,8 +234,8 @@
         # Filter UCSC sites to only those that are supported by this build and
         # enabled.
         valid_sites = [ ( name, url )
-                        for name, url in app.build_sites.get_ucsc_sites_by_build( dataset.dbkey )
-                        if name in app.config.ucsc_display_sites ]
+                        for name, url in app.datatypes_registry.get_legacy_sites_by_build('ucsc', dataset.dbkey )
+                        if name in app.datatypes_registry.get_display_sites('ucsc') ]
         if not valid_sites:
             return []
         # If there are any valid sites, we need to generate the estimated
@@ -750,8 +750,8 @@
         ret_val = []
         seqid, start, stop = self.get_estimated_display_viewport( dataset )
         if seqid is not None:
-            for site_name, site_url in app.build_sites.get_ucsc_sites_by_build( dataset.dbkey ):
-                if site_name in app.config.ucsc_display_sites:
+            for site_name, site_url in app.datatypes_registry.get_legacy_sites_by_build('ucsc', dataset.dbkey ):
+                if site_name in app.datatypes_registry.get_display_sites('ucsc'):
                     redirect_url = urllib.quote_plus(
                             "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" %
                             ( site_url, dataset.dbkey, seqid, start, stop ) )
@@ -762,8 +762,8 @@
         ret_val = []
         seqid, start, stop = self.get_estimated_display_viewport( dataset )
         if seqid is not None:
-            for site_name, site_url in app.build_sites.get_gbrowse_sites_by_build( dataset.dbkey ):
-                if site_name in app.config.gbrowse_display_sites:
+            for site_name, site_url in app.datatypes_registry.get_legacy_sites_by_build('gbrowse', dataset.dbkey ):
+                if site_name in app.datatypes_registry.get_display_sites('gbrowse'):
                     if seqid.startswith( 'chr' ) and len ( seqid ) > 3:
                         seqid = seqid[3:]
                     redirect_url = urllib.quote_plus( "%s/?q=%s:%s..%s&eurl=%%s" % ( site_url, seqid, start, stop ) )
@@ -1091,8 +1091,8 @@
         ret_val = []
         chrom, start, stop = self.get_estimated_display_viewport( dataset )
         if chrom is not None:
-            for site_name, site_url in app.build_sites.get_gbrowse_sites_by_build( dataset.dbkey ):
-                if site_name in app.config.gbrowse_display_sites:
+            for site_name, site_url in app.datatypes_registry.get_legacy_sites_by_build('gbrowse', dataset.dbkey ):
+                if site_name in app.datatypes_registry.get_display_sites('gbrowse'):
                     if chrom.startswith( 'chr' ) and len ( chrom ) > 3:
                         chrom = chrom[3:]
                     redirect_url = urllib.quote_plus( "%s/?q=%s:%s..%s&eurl=%%s" % ( site_url, chrom, start, stop ) )
@@ -1103,8 +1103,8 @@
         ret_val = []
         chrom, start, stop = self.get_estimated_display_viewport( dataset )
         if chrom is not None:
-            for site_name, site_url in app.build_sites.get_ucsc_sites_by_build( dataset.dbkey ):
-                if site_name in app.config.ucsc_display_sites:
+            for site_name, site_url in app.datatypes_registry.get_legacy_sites_by_build('ucsc', dataset.dbkey ):
+                if site_name in app.datatypes_registry.get_display_sites('ucsc'):
                     redirect_url = urllib.quote_plus( "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" % ( site_url, dataset.dbkey, chrom, start, stop ) )
                     link = self._get_remote_call_url( redirect_url, site_name, dataset, type, app, base_url )
                     ret_val.append( ( site_name, link ) )
@@ -1285,8 +1285,8 @@
         ret_val = []
         chrom, start, stop = self.get_estimated_display_viewport(dataset)
         if chrom is not None:
-            for site_name, site_url in app.build_sites.get_ucsc_sites_by_build(dataset.dbkey):
-                if site_name in app.config.ucsc_display_sites:
+            for site_name, site_url in app.datatypes_registry.get_legacy_sites_by_build('ucsc',dataset.dbkey):
+                if site_name in app.datatypes_registry.get_display_sites('ucsc'):
                     internal_url = "%s" % url_for( controller='dataset', dataset_id=dataset.id, action='display_at', filename='ucsc_' + site_name )
                     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 ) )

diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 lib/galaxy/datatypes/registry.py
--- a/lib/galaxy/datatypes/registry.py
+++ b/lib/galaxy/datatypes/registry.py
@@ -69,6 +69,10 @@
         self.datatype_elems = []
         self.sniffer_elems = []
         self.xml_filename = None
+        # Build sites
+        self.build_sites = {}
+        self.display_sites = {}
+        self.legacy_build_sites = {}
 
     def load_datatypes( self, root_dir=None, config=None, deactivate=False, override=True ):
         """
@@ -285,6 +289,8 @@
                                          handling_proprietary_datatypes=handling_proprietary_datatypes,
                                          override=override )
             self.upload_file_formats.sort()
+            # Load build sites
+            self.load_build_sites( root )
             # Persist the xml form of the registry into a temporary file so that it can be loaded from the command line by tools and
             # set_metadata processing.
             self.to_xml_file()
@@ -303,6 +309,34 @@
                     self.sniff_order.append( datatype )
         append_to_sniff_order()
 
+    def load_build_sites( self, root ):
+        if root.find( 'build_sites' ):
+            for elem in root.find( 'build_sites' ).findall( 'site' ):
+                if not (elem.get( 'type' ) and elem.get( 'file' )):
+                    self.log.exception( "Site is missing required 'type' and 'file' attributes: %s" )
+                else:
+                    site_type = elem.get( 'type' )
+                    file = elem.get( 'file' )
+                    self.build_sites[site_type] = file
+                    if site_type in ('ucsc', 'gbrowse'):
+                        self.legacy_build_sites[site_type] = galaxy.util.read_build_sites( file )
+                    if elem.get( 'display', None ):
+                        display = elem.get( 'display' )
+                        self.display_sites[site_type] = [ x.strip() for x in display.lower().split( ',' ) ]
+                        self.log.debug( "Loaded build site '%s': %s with display sites: %s", site_type, file, display )
+                    else:
+                        self.log.debug( "Loaded build site '%s': %s", site_type, file )
+
+    def get_legacy_sites_by_build( self, site_type, build ):
+        sites = []
+        for site in self.legacy_build_sites.get(site_type, []):
+            if build in site['builds']:
+                sites.append((site['name'], site['url']))
+        return sites
+
+    def get_display_sites( self, site_type ):
+        return self.display_sites.get( site_type, [] )
+
     def load_datatype_sniffers( self, root, deactivate=False, handling_proprietary_datatypes=False, override=False ):
         """
         Process the sniffers element from a parsed a datatypes XML file located at root_dir/config (if processing the Galaxy

diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 lib/galaxy/util/__init__.py
--- a/lib/galaxy/util/__init__.py
+++ b/lib/galaxy/util/__init__.py
@@ -844,6 +844,30 @@
     return db_names
 
 
+def read_build_sites( filename, check_builds=True ):
+    """ read db names to ucsc mappings from file, this file should probably be merged with the one above """
+    build_sites = []
+    try:
+        for line in open(filename):
+            try:
+                if line[0:1] == "#":
+                    continue
+                fields = line.replace("\r", "").replace("\n", "").split("\t")
+                site_name = fields[0]
+                site = fields[1]
+                if check_builds:
+                    site_builds = fields[2].split(",")
+                    site_dict = {'name': site_name, 'url': site, 'builds': site_builds}
+                else:
+                    site_dict = {'name': site_name, 'url': site}
+                build_sites.append( site_dict )
+            except:
+                continue
+    except:
+        print "ERROR: Unable to read builds for site file %s" % filename
+    return build_sites
+
+
 def relativize_symlinks( path, start=None, followlinks=False):
     for root, dirs, files in os.walk( path, followlinks=followlinks ):
         rel_start = None

diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 lib/galaxy/util/build_sites.py
--- a/lib/galaxy/util/build_sites.py
+++ /dev/null
@@ -1,52 +0,0 @@
-"""
-Functionality for dealing with build sites for legacy display applications.
-"""
-import os.path
-
-
-class BuildSites( object ):
-
-    def __init__( self, app ):
-        self._app = app
-        self._build_sites = {}
-        self.load_build_sites()
-
-    def read_build_sites( self, filename, check_builds=True ):
-        """ read db names to ucsc mappings from file, this file should probably be merged with the one above """
-        build_sites = []
-        try:
-            for line in open(filename):
-                try:
-                    if line[0:1] == "#":
-                        continue
-                    fields = line.replace("\r", "").replace("\n", "").split("\t")
-                    site_name = fields[0]
-                    site = fields[1]
-                    if check_builds:
-                        site_builds = fields[2].split(",")
-                        site_dict = {'name': site_name, 'url': site, 'builds': site_builds}
-                    else:
-                        site_dict = {'name': site_name, 'url': site}
-                    build_sites.append( site_dict )
-                except:
-                    continue
-        except:
-            print "ERROR: Unable to read builds for site file %s" % filename
-        return build_sites
-
-    def load_build_sites( self ):
-        self._build_sites['ucsc'] = self.read_build_sites( self._app.config.ucsc_build_sites )
-        self._build_sites['gbrowse'] = self.read_build_sites( self._app.config.gbrowse_build_sites )
-
-    def _get_site_by_build( self, site_type, build ):
-        sites = []
-        for site in self._build_sites[site_type]:
-            if build in site['builds']:
-                sites.append((site['name'], site['url']))
-        return sites
-
-    def get_ucsc_sites_by_build( self, build ):
-        return self._get_site_by_build( 'ucsc', build )
-
-    def get_gbrowse_sites_by_build( self, build ):
-        return self._get_site_by_build( 'gbrowse', build )

diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 lib/galaxy/web/framework/__init__.py
--- a/lib/galaxy/web/framework/__init__.py
+++ b/lib/galaxy/web/framework/__init__.py
@@ -926,7 +926,7 @@
                 url_for( controller='dataset', action='list' )
             )
             display_as = url_for( controller='root', action='display_as' )
-            if self.app.config.ucsc_display_sites and self.request.path == display_as:
+            if self.app.datatypes_registry.get_display_sites('ucsc') and self.request.path == display_as:
                 try:
                     host = socket.gethostbyaddr( self.environ[ 'REMOTE_ADDR' ] )[0]
                 except( socket.error, socket.herror, socket.gaierror, socket.timeout ):

diff -r 9fdca7477f44165ae894177a2fef78a4ff9dc5bf -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 universe_wsgi.ini.sample
--- a/universe_wsgi.ini.sample
+++ b/universe_wsgi.ini.sample
@@ -364,14 +364,6 @@
 # which browsers should be available.  URLs and builds available at these
 # browsers are defined in the specifield files.
 
-# UCSC browsers:
-#ucsc_build_sites = tool-data/shared/ucsc/ucsc_build_sites.txt
-#ucsc_display_sites = main,test,archaea,ucla
-
-# GBrowse servers:
-#gbrowse_build_sites = tool-data/shared/gbrowse/gbrowse_build_sites.txt
-#gbrowse_display_sites = modencode,sgd_yeast,tair,wormbase,wormbase_ws120,wormbase_ws140,wormbase_ws170,wormbase_ws180,wormbase_ws190,wormbase_ws200,wormbase_ws204,wormbase_ws210,wormbase_ws220,wormbase_ws225
-
 # If use_remote_user = True, display application servers will be denied access
 # to Galaxy and so displaying datasets in these sites will fail.
 # display_servers contains a list of hostnames which should be allowed to

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[galaxy-commits] commit/galaxy-central: 6 new changesets

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