Merge pull request #17236 from mvdbeek/fix_schema_integrity

[23.1] Separate collection and non-collection data element
galaxyproject · Jan 2, 2024 · d0a7562 · d0a7562
2 parents 687bcf9 + 4027c99
commit d0a7562
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Showing 2 changed files with 21 additions and 8 deletions.
diff --git a/lib/galaxy/tool_util/xsd/galaxy.xsd b/lib/galaxy/tool_util/xsd/galaxy.xsd
@@ -5282,12 +5282,20 @@ on Human (hg18)``.
 
   <xs:group name="OutputCollectionElement">
     <xs:choice>
-      <xs:element name="data" type="OutputData" />
+      <xs:element name="data" type="OutputCollectionDataElement" />
       <xs:element name="discover_datasets" type="OutputCollectionDiscoverDatasets" />
       <xs:element name="filter" type="OutputFilter" />
     </xs:choice>
   </xs:group>
 
+  <xs:complexType name="OutputCollectionDataElement">
+    <xs:sequence>
+      <xs:group ref="OutputCollectionElement" minOccurs="0" maxOccurs="unbounded" />
+    </xs:sequence>
+    <xs:attributeGroup ref="OutputCommon" />
+    <xs:attributeGroup ref="OutputDataAttributes" />
+  </xs:complexType>
+
   <xs:complexType name="OutputCollection">
     <xs:annotation>
       <xs:documentation xml:lang="en"><![CDATA[
@@ -5335,7 +5343,6 @@ This tag describes an output to the tool.
     </xs:annotation>
     <xs:sequence>
       <xs:group ref="OutputDataElement" minOccurs="0" maxOccurs="unbounded" />
-      <xs:group ref="OutputCollectionElement" minOccurs="0" maxOccurs="unbounded" />
     </xs:sequence>
     <xs:attributeGroup ref="OutputCommon"/>
     <xs:attributeGroup ref="OutputCollectionAttributes"/>

diff --git a/test/unit/files/test_ftp.py b/test/unit/files/test_ftp.py
@@ -1,5 +1,8 @@
 import os
 
+import pytest
+from fs.errors import RemoteConnectionError
+
 from ._util import (
     assert_realizes_contains,
     configured_file_sources,
@@ -19,12 +22,15 @@ def test_file_source_ftp_specific():
     assert file_source_pair.path == test_url
     assert file_source_pair.file_source.id == "test1"
 
-    assert_realizes_contains(
-        file_sources,
-        test_url,
-        "This is ftp.gnu.org, the FTP server of the the GNU project.",
-        user_context=user_context,
-    )
+    try:
+        assert_realizes_contains(
+            file_sources,
+            test_url,
+            "This is ftp.gnu.org, the FTP server of the the GNU project.",
+            user_context=user_context,
+        )
+    except RemoteConnectionError:
+        pytest.skip("ftp.gnu.org not available")
 
 
 def test_file_source_ftp_generic():