1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/5f663734a26e/ Changeset: 5f663734a26e User: natefoo Date: 2014-08-07 17:35:20 Summary: Bug fix for display site changes. Affected #: 3 files
diff -r 103697ebdd339377424063fba0459cb3cc2b707c -r 5f663734a26e8e2d1c462320741c86c9b5d9aef6 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_by_build(dataset.dbkey): + 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',
diff -r 103697ebdd339377424063fba0459cb3cc2b707c -r 5f663734a26e8e2d1c462320741c86c9b5d9aef6 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_by_build( dataset.dbkey ) + for name, url in app.build_sites.get_ucsc_sites_by_build( 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_by_build( dataset.dbkey ): + 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: redirect_url = urllib.quote_plus( "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" % @@ -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_by_build( dataset.dbkey ): + 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: 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_by_build(dataset.dbkey): + 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: 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 103697ebdd339377424063fba0459cb3cc2b707c -r 5f663734a26e8e2d1c462320741c86c9b5d9aef6 lib/galaxy/util/build_sites.py --- a/lib/galaxy/util/build_sites.py +++ b/lib/galaxy/util/build_sites.py @@ -38,7 +38,7 @@ 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 ): + def _get_site_by_build( self, site_type, build ): sites = [] for site in self._build_sites[site_type]: if build in site['builds']:
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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