Refactor display_as URL generation for UCSC links and fix to remove double slashes in URL

Author: natefoo

lib/galaxy/datatypes/genetics.py

@@ -49,6 +49,7 @@
     unicodify,
 )
 from galaxy.util.compression_utils import FileObjType
+from .util.generic_util import display_as_url
 
 gal_Log = logging.getLogger(__name__)
 verbose = False
@@ -121,13 +122,7 @@ def ucsc_links(self, dataset: DatasetProtocol, type: str, app, base_url: str) ->
                         action="display_at",
                         filename=f"ucsc_{site_name}",
                     )
-                    display_url = "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at" % (
-                        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

@@ -52,6 +52,7 @@
     data,
     dataproviders,
 )
+from .util.generic_util import display_as_url
 
 log = logging.getLogger(__name__)
 
@@ -345,15 +346,7 @@ def ucsc_links(self, dataset: DatasetProtocol, type: str, app, base_url: str) ->
                 action="display_at",
                 filename="ucsc_" + site_name,
             )
-            display_url = quote_plus(
-                "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at"
-                % (
-                    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))
@@ -783,15 +776,7 @@ def _get_remote_call_url(
         """
         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(
-            "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at"
-            % (
-                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
 
@@ -1566,15 +1551,7 @@ def ucsc_links(self, dataset: DatasetProtocol, type: str, app, base_url: str) ->
             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(
-                        "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at"
-                        % (
-                            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

@@ -1,3 +1,9 @@
+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