From 02549482eb0584b7353050edfce68ebb6dbfc237 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Mon, 5 May 2025 18:00:00 +0200
Subject: [PATCH 1/5] Improve tool output parsing defaults

---
 lib/galaxy/tool_util/parser/output_objects.py | 17 +++++++++--------
 lib/galaxy/tool_util_models/tool_outputs.py   |  1 +
 2 files changed, 10 insertions(+), 8 deletions(-)

diff --git a/lib/galaxy/tool_util/parser/output_objects.py b/lib/galaxy/tool_util/parser/output_objects.py
index 86a627d15de..fd52a7695c2 100644
--- a/lib/galaxy/tool_util/parser/output_objects.py
+++ b/lib/galaxy/tool_util/parser/output_objects.py
@@ -177,22 +177,23 @@ class ToolOutput(ToolOutputBase):
             format_source=self.format_source,
             metadata_source=self.metadata_source or None,  # model is decorated as Optional
             discover_datasets=[d.to_model() for d in self.dataset_collector_descriptions],
+            from_work_dir=self.from_work_dir,
         )
 
     @staticmethod
     def from_dict(name: str, output_dict: Dict[str, Any], app: Optional[ToolOutputActionApp] = None) -> "ToolOutput":
         output = ToolOutput(name)
-        output.format = output_dict.get("format", "data")
+        output.format = output_dict.get("format") or "data"
         output.change_format = []
-        output.format_source = output_dict.get("format_source", None)
-        output.default_identifier_source = output_dict.get("default_identifier_source", None)
-        output.metadata_source = output_dict.get("metadata_source", "")
-        output.parent = output_dict.get("parent", None)
-        output.label = output_dict.get("label", None)
+        output.format_source = output_dict.get("format_source")
+        output.default_identifier_source = output_dict.get("default_identifier_source")
+        output.metadata_source = output_dict.get("metadata_source") or ""
+        output.parent = output_dict.get("parent")
+        output.label = output_dict.get("label")
         output.count = output_dict.get("count", 1)
         output.filters = []
-        output.from_work_dir = output_dict.get("from_work_dir", None)
-        output.hidden = output_dict.get("hidden", False)
+        output.from_work_dir = output_dict.get("from_work_dir")
+        output.hidden = output_dict.get("hidden") or False
         # TODO: implement tool output action group fixes
         if app is not None:
             output.actions = ToolOutputActionGroup(app, None)
diff --git a/lib/galaxy/tool_util_models/tool_outputs.py b/lib/galaxy/tool_util_models/tool_outputs.py
index 322f338aa06..0c686fdfaa3 100644
--- a/lib/galaxy/tool_util_models/tool_outputs.py
+++ b/lib/galaxy/tool_util_models/tool_outputs.py
@@ -33,6 +33,7 @@ class ToolOutputDataset(ToolOutputBaseModel):
     format_source: Optional[str]
     metadata_source: Optional[str]
     discover_datasets: Optional[List["DatasetCollectionDescriptionT"]]
+    from_work_dir: Optional[str] = None
 
 
 class ToolOutputCollectionStructure(BaseModel):

From 83127ea44cc8c2af9622a9d8158ba6c5486c457d Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Mon, 5 May 2025 18:02:41 +0200
Subject: [PATCH 2/5] Use `None` instead of empty string as (default)
 metadata_source

---
 lib/galaxy/tool_util/parser/cwl.py            | 2 +-
 lib/galaxy/tool_util/parser/output_objects.py | 4 ++--
 lib/galaxy/tool_util/parser/xml.py            | 4 ++--
 lib/galaxy/tool_util/parser/yaml.py           | 2 +-
 4 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/lib/galaxy/tool_util/parser/cwl.py b/lib/galaxy/tool_util/parser/cwl.py
index 77066125dee..00ce4738eab 100644
--- a/lib/galaxy/tool_util/parser/cwl.py
+++ b/lib/galaxy/tool_util/parser/cwl.py
@@ -159,7 +159,7 @@ class CwlToolSource(ToolSource):
             output.format = "expression.json"
         output.change_format = []
         output.format_source = None
-        output.metadata_source = ""
+        output.metadata_source = None
         output.parent = None
         output.label = None
         output.count = None
diff --git a/lib/galaxy/tool_util/parser/output_objects.py b/lib/galaxy/tool_util/parser/output_objects.py
index fd52a7695c2..090b38ac63b 100644
--- a/lib/galaxy/tool_util/parser/output_objects.py
+++ b/lib/galaxy/tool_util/parser/output_objects.py
@@ -175,7 +175,7 @@ class ToolOutput(ToolOutputBase):
             hidden=self.hidden,
             format=self.format,
             format_source=self.format_source,
-            metadata_source=self.metadata_source or None,  # model is decorated as Optional
+            metadata_source=self.metadata_source,
             discover_datasets=[d.to_model() for d in self.dataset_collector_descriptions],
             from_work_dir=self.from_work_dir,
         )
@@ -187,7 +187,7 @@ class ToolOutput(ToolOutputBase):
         output.change_format = []
         output.format_source = output_dict.get("format_source")
         output.default_identifier_source = output_dict.get("default_identifier_source")
-        output.metadata_source = output_dict.get("metadata_source") or ""
+        output.metadata_source = output_dict.get("metadata_source")
         output.parent = output_dict.get("parent")
         output.label = output_dict.get("label")
         output.count = output_dict.get("count", 1)
diff --git a/lib/galaxy/tool_util/parser/xml.py b/lib/galaxy/tool_util/parser/xml.py
index bbff153fd55..f0a8fdcb30e 100644
--- a/lib/galaxy/tool_util/parser/xml.py
+++ b/lib/galaxy/tool_util/parser/xml.py
@@ -489,7 +489,7 @@ class XmlToolSource(ToolSource):
                 inherit_format = string_as_bool(collection_elem.get("inherit_format", None))
                 inherit_metadata = string_as_bool(collection_elem.get("inherit_metadata", None))
             default_format_source = collection_elem.get("format_source", None)
-            default_metadata_source = collection_elem.get("metadata_source", "")
+            default_metadata_source = collection_elem.get("metadata_source", None)
             filters = collection_elem.findall("filter")
 
             dataset_collector_descriptions = None
@@ -560,7 +560,7 @@ class XmlToolSource(ToolSource):
         app: Optional[ToolOutputActionApp] = None,
         default_format="data",
         default_format_source=None,
-        default_metadata_source="",
+        default_metadata_source=None,
         expression_type=None,
     ):
         from_expression = data_elem.get("from")
diff --git a/lib/galaxy/tool_util/parser/yaml.py b/lib/galaxy/tool_util/parser/yaml.py
index 4a553785c9b..c7f7eea3e08 100644
--- a/lib/galaxy/tool_util/parser/yaml.py
+++ b/lib/galaxy/tool_util/parser/yaml.py
@@ -180,7 +180,7 @@ class YamlToolSource(ToolSource):
             inherit_format = output_dict.get("inherit_format", None)
             inherit_metadata = output_dict.get("inherit_metadata", None)
         default_format_source = output_dict.get("format_source", None)
-        default_metadata_source = output_dict.get("metadata_source", "")
+        default_metadata_source = output_dict.get("metadata_source", None)
         filters = []
         dataset_collector_descriptions = dataset_collector_descriptions_from_output_dict(output_dict)
 

From 993b569e4aca3843360b6d207e1491f293f77496 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Mon, 5 May 2025 18:04:42 +0200
Subject: [PATCH 3/5] Fix dataset_collector_descriptions_from_output_dict

---
 lib/galaxy/tool_util/parser/output_collection_def.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/tool_util/parser/output_collection_def.py b/lib/galaxy/tool_util/parser/output_collection_def.py
index b588957d651..f5c279dd372 100644
--- a/lib/galaxy/tool_util/parser/output_collection_def.py
+++ b/lib/galaxy/tool_util/parser/output_collection_def.py
@@ -58,7 +58,7 @@ def dataset_collector_descriptions_from_elem(elem, legacy=True):
 
 
 def dataset_collector_descriptions_from_output_dict(as_dict):
-    discover_datasets_dicts = as_dict.get("discover_datasets", [])
+    discover_datasets_dicts = as_dict.get("discover_datasets") or []
     if is_dict(discover_datasets_dicts):
         discover_datasets_dicts = [discover_datasets_dicts]
     dataset_collector_descriptions = dataset_collector_descriptions_from_list(discover_datasets_dicts)

From bd05b3d0e149752b61aa3f043a470ea996f9f59e Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Mon, 5 May 2025 18:12:27 +0200
Subject: [PATCH 4/5] Settle on type instead of reftyp inside xref

We could also make it an alias, but it seems muich simpler to not refer
to the same attribute with different names. So far this has used
internally only.
---
 client/src/components/Tool/ToolFooter.vue                   | 6 +++---
 lib/galaxy/tool_util/linters/general.py                     | 2 +-
 lib/galaxy/tool_util/ontologies/ontology_data.py            | 6 +++---
 lib/galaxy/tool_util/parser/xml.py                          | 2 +-
 lib/galaxy/tool_util/parser/yaml.py                         | 2 +-
 lib/galaxy/tool_util_models/tool_source.py                  | 2 +-
 lib/galaxy_test/api/test_tools.py                           | 2 +-
 .../frontend/src/components/pages/ToolVersionPage.vue       | 6 +++---
 test/unit/tool_util/test_ontologies.py                      | 2 +-
 test/unit/tool_util/test_parsing.py                         | 4 ++--
 10 files changed, 17 insertions(+), 17 deletions(-)

diff --git a/client/src/components/Tool/ToolFooter.vue b/client/src/components/Tool/ToolFooter.vue
index 6766a8ffa0f..d7775129712 100644
--- a/client/src/components/Tool/ToolFooter.vue
+++ b/client/src/components/Tool/ToolFooter.vue
@@ -40,7 +40,7 @@
             <span v-localize class="footer-section-name">References</span>
             <div v-for="(xref, index) in xrefs" :key="index">
                 -
-                <template v-if="xref.reftype == 'bio.tools'">
+                <template v-if="xref.type == 'bio.tools'">
                     bio.tools: {{ xref.value }} (<a :href="`https://bio.tools/${xref.value}`" target="_blank"
                         >bio.tools
                         <FontAwesomeIcon
@@ -55,13 +55,13 @@
                             icon="external-link-alt" /> </a
                     >)
                 </template>
-                <template v-else-if="xref.reftype == 'bioconductor'">
+                <template v-else-if="xref.type == 'bioconductor'">
                     Bioconductor Package:
                     <a :href="`https://bioconductor.org/packages/${xref.value}/`" target="_blank"
                         >{{ xref.value }} (doi:10.18129/B9.bioc.{{ xref.value }})</a
                     >
                 </template>
-                <template v-else> {{ xref.reftype }}: {{ xref.value }} </template>
+                <template v-else> {{ xref.type }}: {{ xref.value }} </template>
             </div>
         </div>
         <div v-if="hasCreators" class="mb-1">
diff --git a/lib/galaxy/tool_util/linters/general.py b/lib/galaxy/tool_util/linters/general.py
index eb3a98fd3b8..cd726fa9d37 100644
--- a/lib/galaxy/tool_util/linters/general.py
+++ b/lib/galaxy/tool_util/linters/general.py
@@ -237,7 +237,7 @@ class BioToolsValid(Linter):
         _, tool_node = _tool_xml_and_root(tool_source)
         xrefs = tool_source.parse_xrefs()
         for xref in xrefs:
-            if xref["reftype"] != "bio.tools":
+            if xref["type"] != "bio.tools":
                 continue
             metadata_source = ApiBiotoolsMetadataSource()
             if not metadata_source.get_biotools_metadata(xref["value"]):
diff --git a/lib/galaxy/tool_util/ontologies/ontology_data.py b/lib/galaxy/tool_util/ontologies/ontology_data.py
index 65343a803c3..89ee0e72999 100644
--- a/lib/galaxy/tool_util/ontologies/ontology_data.py
+++ b/lib/galaxy/tool_util/ontologies/ontology_data.py
@@ -53,7 +53,7 @@ class OntologyData(NamedTuple):
 
 def biotools_reference(xrefs):
     for xref in xrefs:
-        if xref["reftype"] == "bio.tools":
+        if xref["type"] == "bio.tools":
             return xref["value"]
     return None
 
@@ -69,11 +69,11 @@ def expand_ontology_data(
     tool_source: ToolSource, all_ids: List[str], biotools_metadata_source: Optional[BiotoolsMetadataSource]
 ) -> OntologyData:
     xrefs = tool_source.parse_xrefs()
-    has_biotools_reference = any(x["reftype"] == "bio.tools" for x in xrefs)
+    has_biotools_reference = any(x["type"] == "bio.tools" for x in xrefs)
     if not has_biotools_reference:
         for legacy_biotools_ref in legacy_biotools_external_reference(all_ids):
             if legacy_biotools_ref is not None:
-                xrefs.append({"value": legacy_biotools_ref, "reftype": "bio.tools"})
+                xrefs.append({"value": legacy_biotools_ref, "type": "bio.tools"})
 
     edam_operations = tool_source.parse_edam_operations()
     edam_topics = tool_source.parse_edam_topics()
diff --git a/lib/galaxy/tool_util/parser/xml.py b/lib/galaxy/tool_util/parser/xml.py
index f0a8fdcb30e..1b942b3070a 100644
--- a/lib/galaxy/tool_util/parser/xml.py
+++ b/lib/galaxy/tool_util/parser/xml.py
@@ -224,7 +224,7 @@ class XmlToolSource(ToolSource):
         if xrefs is None:
             return []
         return [
-            XrefDict(value=xref.text.strip(), reftype=str(xref.attrib["type"]))
+            XrefDict(value=xref.text.strip(), type=str(xref.attrib["type"]))
             for xref in xrefs.findall("xref")
             if xref.get("type") and xref.text
         ]
diff --git a/lib/galaxy/tool_util/parser/yaml.py b/lib/galaxy/tool_util/parser/yaml.py
index c7f7eea3e08..c883df1bc2e 100644
--- a/lib/galaxy/tool_util/parser/yaml.py
+++ b/lib/galaxy/tool_util/parser/yaml.py
@@ -85,7 +85,7 @@ class YamlToolSource(ToolSource):
 
     def parse_xrefs(self) -> List[XrefDict]:
         xrefs = self.root_dict.get("xrefs", [])
-        return [XrefDict(value=xref["value"], reftype=xref["type"]) for xref in xrefs if xref["type"]]
+        return [XrefDict(value=xref["value"], type=xref["type"]) for xref in xrefs if xref["type"]]
 
     def parse_sanitize(self):
         return self.root_dict.get("sanitize", True)
diff --git a/lib/galaxy/tool_util_models/tool_source.py b/lib/galaxy/tool_util_models/tool_source.py
index 487870895bd..d7bb207b58d 100644
--- a/lib/galaxy/tool_util_models/tool_source.py
+++ b/lib/galaxy/tool_util_models/tool_source.py
@@ -15,7 +15,7 @@ from typing_extensions import (
 
 class XrefDict(TypedDict):
     value: str
-    reftype: str
+    type: str
 
 
 class Citation(BaseModel):
diff --git a/lib/galaxy_test/api/test_tools.py b/lib/galaxy_test/api/test_tools.py
index bb7a2cb1330..59f34dd9b79 100644
--- a/lib/galaxy_test/api/test_tools.py
+++ b/lib/galaxy_test/api/test_tools.py
@@ -257,7 +257,7 @@ class TestToolsApi(ApiTestCase, TestsTools):
         assert "xrefs" in get_json
         assert len(get_json["xrefs"]) == 1
         xref = get_json["xrefs"][0]
-        assert xref["reftype"] == "bio.tools"
+        assert xref["type"] == "bio.tools"
         assert xref["value"] == "bwa"
 
     @skip_without_tool("test_data_source")
diff --git a/lib/tool_shed/webapp/frontend/src/components/pages/ToolVersionPage.vue b/lib/tool_shed/webapp/frontend/src/components/pages/ToolVersionPage.vue
index 1adaa1b5c52..7ebe291bc1b 100644
--- a/lib/tool_shed/webapp/frontend/src/components/pages/ToolVersionPage.vue
+++ b/lib/tool_shed/webapp/frontend/src/components/pages/ToolVersionPage.vue
@@ -156,11 +156,11 @@ const linkedFromOlderRevision = computed(() => {
                 <q-list bordered separator>
                     <q-item v-for="xref in xrefs" :key="xref.value">
                         <q-item-section>
-                            <q-item-label overline>REFERENCE {{ xref.reftype }}</q-item-label>
-                            <q-item-label v-if="xref.reftype == 'bio.tools'">
+                            <q-item-label overline>REFERENCE {{ xref.type }}</q-item-label>
+                            <q-item-label v-if="xref.type == 'bio.tools'">
                                 <bio-tools-link :id="xref.value" />
                             </q-item-label>
-                            <q-item-label v-else-if="xref.reftype == 'bioconductor'">
+                            <q-item-label v-else-if="xref.type == 'bioconductor'">
                                 <bioconductor-link :id="xref.value" />
                             </q-item-label>
                             <q-item-label v-else>
diff --git a/test/unit/tool_util/test_ontologies.py b/test/unit/tool_util/test_ontologies.py
index 5c1faca4771..15873910a77 100644
--- a/test/unit/tool_util/test_ontologies.py
+++ b/test/unit/tool_util/test_ontologies.py
@@ -87,7 +87,7 @@ def test_parse_edam_mapping_operations_legacy():
 def test_parse_biotools_default_mapping():
     test_source = get_test_tool_source(source_file_name="testtool.yml", source_contents=TOOL_YAML_NO_EXPLICIT_XREFS)
     ontology_data = expand_ontology_data(test_source, ["cheetah_problem_unbound_var_input"], None)
-    assert ontology_data.xrefs[0]["reftype"] == "bio.tools"
+    assert ontology_data.xrefs[0]["type"] == "bio.tools"
     assert ontology_data.xrefs[0]["value"] == "bwa"
 
     test_source = get_test_tool_source(source_file_name="testtool.yml", source_contents=TOOL_YAML_NO_EXPLICIT_XREFS)
diff --git a/test/unit/tool_util/test_parsing.py b/test/unit/tool_util/test_parsing.py
index 2c57377db14..8698be752fe 100644
--- a/test/unit/tool_util/test_parsing.py
+++ b/test/unit/tool_util/test_parsing.py
@@ -416,7 +416,7 @@ class TestXmlLoader(BaseLoaderTestCase):
 
     def test_xrefs(self):
         xrefs = self._tool_source.parse_xrefs()
-        assert xrefs == [{"value": "bwa", "reftype": "bio.tools"}]
+        assert xrefs == [{"value": "bwa", "type": "bio.tools"}]
 
     def test_exit_code(self):
         tool_source = self._get_tool_source(
@@ -622,7 +622,7 @@ class TestYamlLoader(BaseLoaderTestCase):
 
     def test_xrefs(self):
         xrefs = self._tool_source.parse_xrefs()
-        assert xrefs == [{"value": "bwa", "reftype": "bio.tools"}]
+        assert xrefs == [{"value": "bwa", "type": "bio.tools"}]
 
     def test_sanitize(self):
         assert self._tool_source.parse_sanitize() is True

From 386742d12e79272bd198d6ef6171422a787f8e85 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Mon, 5 May 2025 18:18:26 +0200
Subject: [PATCH 5/5] rebuild schema

---
 lib/tool_shed/webapp/frontend/src/schema/schema.ts | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/lib/tool_shed/webapp/frontend/src/schema/schema.ts b/lib/tool_shed/webapp/frontend/src/schema/schema.ts
index d78c4048d87..52b5aaaec81 100644
--- a/lib/tool_shed/webapp/frontend/src/schema/schema.ts
+++ b/lib/tool_shed/webapp/frontend/src/schema/schema.ts
@@ -2727,6 +2727,8 @@ export interface components {
             format: string
             /** Format Source */
             format_source: string | null
+            /** From Work Dir */
+            from_work_dir?: string | null
             /** Hidden */
             hidden: boolean
             /** Label */
@@ -3006,8 +3008,8 @@ export interface components {
         }
         /** XrefDict */
         XrefDict: {
-            /** Reftype */
-            reftype: string
+            /** Type */
+            type: string
             /** Value */
             value: string
         }