Merge branch 'release_24.2' into release_25.0 (a92286ba) · Commits · NDIP / Galaxy

lib/galaxy/datatypes/genetics.py

+2 −7

Original line number	Diff line number	Diff line
		@@ -49,6 +49,7 @@ from galaxy.util import (
		unicodify,
		)
		from galaxy.util.compression_utils import FileObjType
		from .util.generic_util import display_as_url

		log = logging.getLogger(__name__)
		verbose = False
		@@ -121,13 +122,7 @@ class GenomeGraphs(Tabular):
		action="display_at",
		filename=f"ucsc_{site_name}",
		)
		display_url = "{}{}/display_as?id={}&display_app={}&authz_method=display_at".format(
		base_url,
		app.url_for(controller="root"),
		dataset.id,
		type,
		)
		display_url = quote_plus(display_url)
		display_url = display_as_url(app, base_url, str(dataset.id), type)
		# was display_url = quote_plus( "%s/display_as?id=%i&display_app=%s" % (base_url, dataset.id, type) )
		# redirect_url = quote_plus( "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" % (site_url, dataset.dbkey, chrom, start, stop) )
		sl = [

lib/galaxy/datatypes/interval.py

+4 −24

Original line number	Diff line number	Diff line
		@@ -52,6 +52,7 @@ from . import (
		data,
		dataproviders,
		)
		from .util.generic_util import display_as_url

		log = logging.getLogger(__name__)

		@@ -340,14 +341,7 @@ class Interval(Tabular):
		action="display_at",
		filename="ucsc_" + site_name,
		)
		display_url = quote_plus(
		"{}{}/display_as?id={}&display_app={}&authz_method=display_at".format(
		base_url,
		app.url_for(controller="root"),
		dataset.id,
		type,
		)
		)
		display_url = display_as_url(app, base_url, str(dataset.id), type)
		redirect_url = quote_plus(f"{site_url}db={dataset.dbkey}&position={chrom}:{start}-{stop}&hgt.customText=%s")
		link = f"{internal_url}?redirect_url={redirect_url}&display_url={display_url}"
		ret_val.append((site_name, link))
		@@ -777,14 +771,7 @@ class _RemoteCallMixin:
		"""
		internal_url = f"{app.url_for(controller='dataset', dataset_id=dataset.id, action='display_at', filename=f'{type}_{site_name}')}"
		base_url = app.config.get("display_at_callback", base_url)
		display_url = quote_plus(
		"{}{}/display_as?id={}&display_app={}&authz_method=display_at".format(
		base_url,
		app.url_for(controller="root"),
		dataset.id,
		type,
		)
		)
		display_url = display_as_url(app, base_url, str(dataset.id), type)
		link = f"{internal_url}?redirect_url={redirect_url}&display_url={display_url}"
		return link

		@@ -1559,14 +1546,7 @@ class CustomTrack(Tabular):
		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 = f"{app.url_for(controller='dataset', dataset_id=dataset.id, action='display_at', filename='ucsc_' + site_name)}"
		display_url = quote_plus(
		"{}{}/display_as?id={}&display_app={}&authz_method=display_at".format(
		base_url,
		app.url_for(controller="root"),
		dataset.id,
		type,
		)
		)
		display_url = display_as_url(app, base_url, str(dataset.id), type)
		redirect_url = quote_plus(
		f"{site_url}db={dataset.dbkey}&position={chrom}:{start}-{stop}&hgt.customText=%s"
		)

lib/galaxy/datatypes/util/generic_util.py

+20 −0

Original line number	Diff line number	Diff line
		from urllib.parse import (
		quote_plus,
		urlencode,
		urljoin,
		)

		from galaxy.util import commands


		@@ -16,3 +22,17 @@ def count_special_lines(word, filename, invert=False):
		except commands.CommandLineException:
		return 0
		return int(out)


		def display_as_url(app, base_url: str, dataset_id: str, display_app: str) -> str:
		"""Generate a link to the ``display_as`` action the the ``root`` controller, encoded for use as a query param."""
		display_base_url = urljoin(base_url, app.url_for(controller="root", action="display_as"))
		display_query = urlencode(
		{
		"id": dataset_id,
		"display_app": display_app,
		"authz_method": "display_at",
		}
		)
		display_url = quote_plus(f"{display_base_url}?{display_query}")
		return display_url

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