Handle directories with percents in export_remote.xml.

lib/galaxy/tools/parameters/basic.py

@@ -2669,6 +2669,14 @@ class DirectoryUriToolParameter(SimpleTextToolParameter):
         if not user_has_access:
             raise ParameterValueError(f"The user cannot access {value}.", self.name)
 
+    def to_param_dict_string(self, value, other_values=None) -> str:
+        """Called via __str__ when used in the Cheetah template"""
+        if value is None:
+            value = ""
+        elif not isinstance(value, str):
+            value = str(value)
+        return value
+
 
 class RulesListToolParameter(BaseJsonToolParameter):
     """

test/integration/test_remote_files.py

@@ -205,6 +205,46 @@ class TestRemoteFilesIntegration(ConfiguresRemoteFilesIntegrationTestCase):
             with open(os.path.join(ftp_dir, "my_cool", "utf8_name_😻.txt")) as f:
                 assert "example content\n" == f.read()
 
+    def test_export_remote_tool_with_space(self):
+        dataset_populator = self.dataset_populator
+        ftp_dir = self.user_ftp_dir
+        _write_file_fixtures(self.root, ftp_dir)
+        dir_with_space = os.path.join(ftp_dir, "space dir")
+        os.makedirs(dir_with_space)
+        with dataset_populator.test_history() as history_id:
+            dataset = dataset_populator.new_dataset(history_id, content="example content", wait=True, name="foo")
+            infile = {"src": "hda", "id": dataset["id"]}
+            inputs = {
+                "d_uri": "gxftp://space dir/",
+                "export_type|export_type_selector": "datasets_named",
+                "export_type|datasets_0|infile": infile,
+                "export_type|datasets_0|name": ".my_cool/utf8_name_😻.txt",
+            }
+            response = dataset_populator.run_tool("export_remote", inputs, history_id)
+            dataset_populator.wait_for_job(response["jobs"][0]["id"], assert_ok=True)
+            with open(os.path.join(ftp_dir, "space dir", "my_cool", "utf8_name_😻.txt")) as f:
+                assert "example content\n" == f.read()
+
+    def test_export_remote_tool_with_space_encoded(self):
+        dataset_populator = self.dataset_populator
+        ftp_dir = self.user_ftp_dir
+        _write_file_fixtures(self.root, ftp_dir)
+        dir_with_space = os.path.join(ftp_dir, "space%20dir")
+        os.makedirs(dir_with_space)
+        with dataset_populator.test_history() as history_id:
+            dataset = dataset_populator.new_dataset(history_id, content="example content", wait=True, name="foo")
+            infile = {"src": "hda", "id": dataset["id"]}
+            inputs = {
+                "d_uri": "gxftp://space%20dir/",
+                "export_type|export_type_selector": "datasets_named",
+                "export_type|datasets_0|infile": infile,
+                "export_type|datasets_0|name": ".my_cool/utf8_name_😻.txt",
+            }
+            response = dataset_populator.run_tool("export_remote", inputs, history_id)
+            dataset_populator.wait_for_job(response["jobs"][0]["id"], assert_ok=True)
+            with open(os.path.join(ftp_dir, "space%20dir", "my_cool", "utf8_name_😻.txt")) as f:
+                assert "example content\n" == f.read()
+
     def test_export_remote_tool_default_duplicate_name_fails(self):
         dataset_populator = self.dataset_populator
         ftp_dir = self.user_ftp_dir

tools/data_export/export_remote.py

@@ -35,15 +35,23 @@ def write_if_not_exists(file_sources, target_uri, real_data_path):
     file_source.write_from(file_source_path.path, real_data_path)
 
 
+def get_directory_uri(args):
+    directory_uri = args.directory_uri
+    if not directory_uri:
+        inputs = json.load(open(args.inputs, "r"))
+        directory_uri = inputs["d_uri"]
+    if not directory_uri.endswith("/"):
+        directory_uri = f"{directory_uri}/"
+    return directory_uri
+
+
 def main(argv=None):
     if argv is None:
         argv = sys.argv[1:]
     args = _parser().parse_args(argv)
     exit_code = 0
     file_sources = get_file_sources(args.file_sources)
-    directory_uri = args.directory_uri
-    if not directory_uri.endswith("/"):
-        directory_uri = f"{directory_uri}/"
+    directory_uri = get_directory_uri(args)
     export_metadata_files = args.export_metadata_files
     with open(args.files_to_export) as f:
         files_to_export = json.load(f)
@@ -68,6 +76,8 @@ def main(argv=None):
 
 def _parser():
     parser = argparse.ArgumentParser()
+    parser.add_argument("--inputs", type=str, help="galaxy inputs")
+    # post 2026.XX drop the directory-uri argument and just assume inputs always contains d_uri.
     parser.add_argument("--directory-uri", type=str, help="directory target URI")
     parser.add_argument("--file-sources", type=str, help="file sources json")
     parser.add_argument("--files-to-export", type=str, help="files to export")

tools/data_export/export_remote.xml

@@ -8,7 +8,7 @@
     <command><![CDATA[
 python '$__tool_directory__/export_remote.py'
     --file-sources '$file_sources'
-    --directory-uri '$d_uri'
+    --inputs '$inputs'
     --files-to-export '$files_to_export'
     #if $include_metadata_files:
         --export-metadata-files $include_metadata_files
@@ -17,6 +17,7 @@ python '$__tool_directory__/export_remote.py'
     ]]></command>
     <configfiles>
         <file_sources name="file_sources"/>
+        <inputs name="inputs" />
         <configfile name="files_to_export">#import json
 #from galaxy.util import filesystem_safe_string
 #if $export_type.export_type_selector == "datasets_auto":