def ucsc_links( self, dataset, type, app, base_url ):
ret_val = []
if dataset.has_data:
viewport_tuple = self.get_estimated_display_viewport(dataset)
if viewport_tuple:
chrom = viewport_tuple[0]
start = viewport_tuple[1]
stop = viewport_tuple[2]
if start == '' or int(start) < 1:
start='1'
if stop == '' or int(stop) <= int(start):
stop = '%d' % (int(start) + 10000)
for site_name, site_url in util.get_ucsc_by_build(dataset.dbkey):
if site_name in app.config.ucsc_display_sites:
# HACK: UCSC doesn't support https, so force http even
# if our URL scheme is https. Making this work
# requires additional hackery in your upstream proxy.
# If UCSC ever supports https, remove this hack.
internal_url = "%s" % url_for( controller='dataset',
dataset_id=dataset.id, action='display_at', filename='ucsc_' + site_name )
if base_url.startswith( 'https://' ):
base_url = base_url.replace( 'https', 'http', 1 )
display_url = urllib.quote_plus( "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at" % (base_url, url_for( controller='root' ), dataset.id, type) )
redirect_url = urllib.quote_plus( "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" % (site_url, dataset.dbkey, chrom, start, stop) )
link = '%s?redirect_url=%s&display_url=%s' % ( internal_url, redirect_url, display_url )
ret_val.append( (site_name, link) )
else:
gal_Log.debug('@@@ gg ucsc_links - no viewport_tuple')
return ret_val
def ucsc_links( self, dataset, type, app, base_url ):
""" from the ever-helpful angie hinrichs [email protected]
a genome graphs call looks like this
http://genome.ucsc.edu/cgi-bin/hgGenome?clade=mammal&org=Human&db=hg18&hgGenome_dataSetName=dname
&hgGenome_dataSetDescription=test&hgGenome_formatType=best%20guess&hgGenome_markerType=best%20guess
&hgGenome_columnLabels=best%20guess&hgGenome_maxVal=&hgGenome_labelVals=
&hgGenome_maxGapToFill=25000000&hgGenome_uploadFile=http://galaxy.esphealth.org/datasets/333/display/index
&hgGenome_doSubmitUpload=submit
Galaxy gives this for an interval file
http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&position=chr1:1-1000&hgt.customText=
http%3A%2F%2Fgalaxy.esphealth.org%2Fdisplay_as%3Fid%3D339%26display_app%3Ducsc
"""
ret_val = []
ggtail = '&hgGenome_doSubmitUpload=submit'
if not dataset.dbkey:
dataset.dbkey = 'hg18' # punt!
if dataset.has_data:
for site_name, site_url in util.get_ucsc_by_build(dataset.dbkey):
if site_name in app.config.ucsc_display_sites:
site_url = site_url.replace('/hgTracks?','/hgGenome?') # for genome graphs
display_url = urllib.quote_plus( "%s%s/display_as?id=%i&display_app=%s" % (base_url, url_for( controller='root' ), dataset.id, type))
sl = ["%sdb=%s" % (site_url,dataset.dbkey ),]
sl.append("&hgGenome_dataSetName=%s&hgGenome_dataSetDescription=%s" % (dataset.name, 'GalaxyGG_data'))
sl.append("&hgGenome_formatType=best%20guess&hgGenome_markerType=best%20guess")
sl.append("&hgGenome_columnLabels=first%20row&hgGenome_maxVal=&hgGenome_labelVals=")
sl.append("&hgGenome_maxGapToFill=25000000&hgGenome_uploadFile=")
s = ''.join(sl)
link = "%s%s%s" % (s, display_url, ggtail )
ret_val.append( (site_name, link) )
return ret_val
def ucsc_links(self, dataset, type, app, base_url):
"""
from the ever-helpful angie hinrichs [email protected]
a genome graphs call looks like this
http://genome.ucsc.edu/cgi-bin/hgGenome?clade=mammal&org=Human&db=hg18&hgGenome_dataSetName=dname
&hgGenome_dataSetDescription=test&hgGenome_formatType=best%20guess&hgGenome_markerType=best%20guess
&hgGenome_columnLabels=best%20guess&hgGenome_maxVal=&hgGenome_labelVals=
&hgGenome_maxGapToFill=25000000&hgGenome_uploadFile=http://galaxy.esphealth.org/datasets/333/display/index
&hgGenome_doSubmitUpload=submit
Galaxy gives this for an interval file
http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&position=chr1:1-1000&hgt.customText=
http%3A%2F%2Fgalaxy.esphealth.org%2Fdisplay_as%3Fid%3D339%26display_app%3Ducsc
"""
ret_val = []
ggtail = 'hgGenome_doSubmitUpload=submit'
if not dataset.dbkey:
dataset.dbkey = 'hg18' # punt!
if dataset.has_data():
for site_name, site_url in util.get_ucsc_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))
return ret_val
def ucsc_links( self, dataset, type, app, base_url ):
ret_val = []
chrom, start, stop = self._get_viewer_range( dataset )
if chrom is not None:
for site_name, site_url in util.get_ucsc_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 )
ret_val.append( ( site_name, link ) )
return ret_val
def ucsc_links( self, dataset, type, app, base_url ):
ret_val = []
if dataset.has_data:
seqid, start, stop = self.get_estimated_display_viewport( dataset )
if seqid and start and stop:
for site_name, site_url in util.get_ucsc_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, seqid, start, stop ) )
link = self._get_remote_call_url( redirect_url, site_name, dataset, type, app, base_url )
ret_val.append( ( site_name, link ) )
return ret_val
def ucsc_links( self, dataset, type, app, base_url ):
ret_val = []
if dataset.has_data:
viewport_tuple = self.get_estimated_display_viewport(dataset)
if viewport_tuple:
chrom = viewport_tuple[0]
start = viewport_tuple[1]
stop = viewport_tuple[2]
for site_name, site_url in util.get_ucsc_by_build(dataset.dbkey):
if site_name in app.config.ucsc_display_sites:
display_url = urllib.quote_plus( "%s%s/display_as?id=%i&display_app=%s" % (base_url, url_for( controller='root' ), dataset.id, type) )
link = "%sdb=%s&position=%s:%s-%s&hgt.customText=%s" % (site_url, dataset.dbkey, chrom, start, stop, display_url )
ret_val.append( (site_name, link) )
return ret_val
def ucsc_links( self, dataset, type, app, base_url ):
ret_val = []
if dataset.has_data:
viewport_tuple = self.get_estimated_display_viewport(dataset)
if viewport_tuple:
chrom = viewport_tuple[0]
start = viewport_tuple[1]
stop = viewport_tuple[2]
for site_name, site_url in util.get_ucsc_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 )
if base_url.startswith( 'https://' ):
base_url = base_url.replace( 'https', 'http', 1 )
display_url = urllib.quote_plus( "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at" % (base_url, url_for( controller='root' ), dataset.id, type) )
redirect_url = urllib.quote_plus( "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" % (site_url, dataset.dbkey, chrom, start, stop ) )
link = '%s?redirect_url=%s&display_url=%s' % ( internal_url, redirect_url, display_url )
ret_val.append( (site_name, link) )
return ret_val
def ucsc_links( self, dataset, type, app, base_url ):
"""
from the ever-helpful angie hinrichs [email protected]
a genome graphs call looks like this
http://genome.ucsc.edu/cgi-bin/hgGenome?clade=mammal&org=Human&db=hg18&hgGenome_dataSetName=dname
&hgGenome_dataSetDescription=test&hgGenome_formatType=best%20guess&hgGenome_markerType=best%20guess
&hgGenome_columnLabels=best%20guess&hgGenome_maxVal=&hgGenome_labelVals=
&hgGenome_maxGapToFill=25000000&hgGenome_uploadFile=http://galaxy.esphealth.org/datasets/333/display/index
&hgGenome_doSubmitUpload=submit
Galaxy gives this for an interval file
http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&position=chr1:1-1000&hgt.customText=
http%3A%2F%2Fgalaxy.esphealth.org%2Fdisplay_as%3Fid%3D339%26display_app%3Ducsc
"""
ret_val = []
ggtail = 'hgGenome_doSubmitUpload=submit'
if not dataset.dbkey:
dataset.dbkey = 'hg18' # punt!
if dataset.has_data:
for site_name, site_url in util.get_ucsc_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 )
if base_url.startswith( 'https://' ):
base_url = base_url.replace( 'https', 'http', 1 )
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
log.debug('## rg gg ucsc rdurl=%s; s = %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 ucsc_links( self, dataset, type, app, base_url ):
ret_val = []
if dataset.has_data:
viewport_tuple = self.get_estimated_display_viewport(dataset)
if viewport_tuple:
chrom = viewport_tuple[0]
start = viewport_tuple[1]
stop = viewport_tuple[2]
for site_name, site_url in util.get_ucsc_by_build(dataset.dbkey):
if site_name in app.config.ucsc_display_sites:
# HACK: UCSC doesn't support https, so force http even
# if our URL scheme is https. Making this work
# requires additional hackery in your upstream proxy.
# If UCSC ever supports https, remove this hack.
if base_url.startswith( 'https://' ):
base_url = base_url.replace( 'https', 'http', 1 )
display_url = urllib.quote_plus( "%s%s/display_as?id=%i&display_app=%s" % (base_url, url_for( controller='root' ), dataset.id, type) )
link = "%sdb=%s&position=%s:%s-%s&hgt.customText=%s" % (site_url, dataset.dbkey, chrom, start, stop, display_url )
ret_val.append( (site_name, link) )
return ret_val
def ucsc_links(self, dataset, type, app, base_url):
ret_val = []
if dataset.has_data:
viewport_tuple = self.get_estimated_display_viewport(dataset)
if viewport_tuple:
chrom = viewport_tuple[0]
start = viewport_tuple[1]
stop = viewport_tuple[2]
if start == '' or int(start) < 1:
start = '1'
if stop == '' or int(stop) <= start:
stop = '%d' % (int(start) + 10000)
for site_name, site_url in util.get_ucsc_by_build(
dataset.dbkey):
if site_name in app.config.ucsc_display_sites:
# HACK: UCSC doesn't support https, so force http even
# if our URL scheme is https. Making this work
# requires additional hackery in your upstream proxy.
# If UCSC ever supports https, remove this hack.
internal_url = "%s" % url_for(
controller='dataset',
dataset_id=dataset.id,
action='display_at',
filename='ucsc_' + site_name)
if base_url.startswith('https://'):
base_url = base_url.replace('https', 'http', 1)
display_url = urllib.quote_plus(
"%s%s/display_as?id=%i&display_app=%s&authz_method=display_at"
% (base_url, url_for(controller='root'),
dataset.id, type))
redirect_url = urllib.quote_plus(
"%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" %
(site_url, dataset.dbkey, chrom, start, stop))
link = '%s?redirect_url=%s&display_url=%s' % (
internal_url, redirect_url, display_url)
ret_val.append((site_name, link))
else:
log.debug('@@@ gg ucsc_links - no viewport_tuple')
return ret_val
def get_ucsc_sites(self, dataset):
return util.get_ucsc_by_build(dataset.dbkey)
def get_ucsc_sites(self, dataset):
return util.get_ucsc_by_build(dataset.dbkey)