Merge branch 'release_24.1' into dev

client/src/components/Workflow/Editor/Index.vue

@@ -355,6 +355,15 @@ export default {
         }
 
         const tags = ref([]);
+
+        watch(
+            () => props.workflowTags,
+            (newTags) => {
+                tags.value = [...newTags];
+            },
+            { immediate: true }
+        );
+
         const setTagsHandler = new SetValueActionHandler(
             undoRedoStore,
             (value) => (tags.value = structuredClone(value)),
@@ -792,12 +801,9 @@ export default {
             this.report.markdown = markdown;
         },
         onRun() {
-            const runUrl = `/workflows/run?id=${this.id}${
-                this.version !== undefined ? `&version=${this.version}` : ""
-            }`;
-            this.onNavigate(runUrl);
+            this.onNavigate(`/workflows/run?id=${this.id}`, false, false, true);
         },
-        async onNavigate(url, forceSave = false, ignoreChanges = false) {
+        async onNavigate(url, forceSave = false, ignoreChanges = false, appendVersion = false) {
             if (this.isNewTempWorkflow) {
                 await this.onCreate();
             } else if (this.hasChanges && !forceSave && !ignoreChanges) {
@@ -810,6 +816,9 @@ export default {
                 await this.onSave();
             }
 
+            if (appendVersion && this.version !== undefined) {
+                url += `&version=${this.version}`;
+            }
             this.hasChanges = false;
             await nextTick();
             this.$router.push(url);

client/src/components/Workflow/Editor/SaveChangesModal.vue

@@ -24,7 +24,7 @@ const busy = ref(false);
 
 const emit = defineEmits<{
     /** Proceed with or without saving the changes */
-    (e: "on-proceed", url: string, forceSave: boolean, ignoreChanges: boolean): void;
+    (e: "on-proceed", url: string, forceSave: boolean, ignoreChanges: boolean, appendVersion: boolean): void;
     /** Update the nav URL prop */
     (e: "update:nav-url", url: string): void;
     /** Update the show modal boolean prop */
@@ -49,13 +49,13 @@ function closeModal() {
 
 function dontSave() {
     busy.value = true;
-    emit("on-proceed", props.navUrl, false, true);
+    emit("on-proceed", props.navUrl, false, true, true);
 }
 
 function saveChanges() {
     busy.value = true;
     closeModal();
-    emit("on-proceed", props.navUrl, true, false);
+    emit("on-proceed", props.navUrl, true, false, true);
 }
 </script>
 

client/src/components/WorkflowInvocationState/WorkflowInvocationStep.vue

@@ -74,7 +74,7 @@
                                 </details>
                                 <ParameterStep
                                     v-else-if="workflowStepType == 'parameter_input'"
-                                    :parameters="[invocation.input_step_parameters[stepDetails.workflow_step_label]]" />
+                                    :parameters="[getParamInput(stepDetails)]" />
                                 <GenericHistoryItem
                                     v-else-if="
                                         isDataStep &&
@@ -209,6 +209,11 @@ export default {
                 this.fetchWorkflowForInstanceId(this.workflowStep.workflow_id);
             }
         },
+        getParamInput(stepDetails) {
+            return Object.values(this.invocation.input_step_parameters).find(
+                (param) => param.workflow_step_id === stepDetails.workflow_step_id
+            );
+        },
         showJob(id) {
             this.$emit("show-job", id);
         },

client/src/entry/analysis/router.js

@@ -622,7 +622,7 @@ export function getRouter(Galaxy) {
                         props: (route) => ({
                             invocationId: route.params.invocationId,
                             isFullPage: true,
-                            fromPanel: route.query.from_panel,
+                            fromPanel: Boolean(route.query.from_panel),
                         }),
                     },
                     {

lib/galaxy/model/__init__.py

@@ -8922,7 +8922,7 @@ def to_dict(self, view="collection", value_mapper=None, step_details=False, lega
             for input_step_parameter in self.input_step_parameters:
                 label = input_step_parameter.workflow_step.label
                 if not label:
-                    continue
+                    label = f"{input_step_parameter.workflow_step.order_index + 1}: Unnamed parameter"
                 input_parameters[label] = {
                     "parameter_value": input_step_parameter.parameter_value,
                     "label": label,

lib/galaxy/model/store/discover.py

@@ -38,6 +38,10 @@
 from galaxy.util.hash_util import HASH_NAME_MAP
 
 if TYPE_CHECKING:
+    from galaxy.job_execution.output_collect import (
+        DatasetCollector,
+        ToolMetadataDatasetCollector,
+    )
     from galaxy.model.store import ModelExportStore
 
 log = logging.getLogger(__name__)
@@ -50,7 +54,7 @@ class MaxDiscoveredFilesExceededError(ValueError):
     pass
 
 
-CollectorT = Any  # TODO: setup an interface for these file collectors data classes.
+CollectorT = Union["DatasetCollector", "ToolMetadataDatasetCollector"]
 
 
 class ModelPersistenceContext(metaclass=abc.ABCMeta):
@@ -1058,19 +1062,21 @@ def name(self):
         return self.as_dict.get("name")
 
     @property
-    def dbkey(self):
-        return self.as_dict.get("dbkey", getattr(self.collector, "default_dbkey", "?"))
+    def dbkey(self) -> str:
+        return self.as_dict.get("dbkey", self.collector and self.collector.default_dbkey or "?")
 
     @property
-    def ext(self):
-        return self.as_dict.get("ext", getattr(self.collector, "default_ext", "data"))
+    def ext(self) -> str:
+        return self.as_dict.get("ext", self.collector and self.collector.default_ext or "data")
 
     @property
-    def visible(self):
+    def visible(self) -> bool:
         try:
             return self.as_dict["visible"].lower() == "visible"
         except KeyError:
-            return getattr(self.collector, "default_visible", True)
+            if self.collector and self.collector.default_visible is not None:
+                return self.collector.default_visible
+            return True
 
     @property
     def link_data(self):

lib/galaxy/tool_util/parser/output_collection_def.py

@@ -34,7 +34,13 @@ def dataset_collector_descriptions_from_elem(elem, legacy=True):
     if num_discover_dataset_blocks == 0 and legacy:
         collectors = [DEFAULT_DATASET_COLLECTOR_DESCRIPTION]
     else:
-        collectors = [dataset_collection_description(**e.attrib) for e in primary_dataset_elems]
+        default_format = elem.attrib.get("format")
+        collectors = []
+        for e in primary_dataset_elems:
+            description_attributes = e.attrib
+            if default_format and "format" not in description_attributes and "ext" not in description_attributes:
+                description_attributes["format"] = default_format
+            collectors.append(dataset_collection_description(**description_attributes))
 
     return _validate_collectors(collectors)
 

lib/galaxy/tool_util/xsd/galaxy.xsd

@@ -5641,11 +5641,13 @@ The default is ``galaxy.json``.
   <xs:attributeGroup name="OutputCommon">
     <xs:attribute name="format" type="xs:string">
       <xs:annotation>
-        <xs:documentation xml:lang="en">The short name for the output datatype.
-The valid values for format can be found in
+        <xs:documentation xml:lang="en"><![CDATA[
+The short name for the output datatype. The valid values for format can be found in
 [/config/datatypes_conf.xml.sample](https://github.com/galaxyproject/galaxy/blob/dev/config/datatypes_conf.xml.sample)
-(e.g. ``format="pdf"`` or ``format="fastqsanger"``). For collections this is the default format for all included
-elements. Note that the format specified here is ignored for discovered data sets.</xs:documentation>
+(e.g. ``format="pdf"`` or ``format="fastqsanger"``). For collections this is the default
+format for all included elements. Note that the format specified here is ignored for
+discovered data sets on Galaxy versions prior to 24.0 and should be specified using the ``<discovered_data>`` tag set.
+        ]]></xs:documentation>
       </xs:annotation>
     </xs:attribute>
     <xs:attribute name="format_source" type="xs:string">

test/functional/tools/discover_default_ext.xml

@@ -0,0 +1,52 @@
+<tool id="discover_default_ext" name="discover_default_ext" version="0.1.0">
+    <command><![CDATA[
+echo 1 > 1.txt;
+]]></command>
+    <inputs />
+    <outputs>
+        <collection name="collection_with_default_ext" type="list" label="with default format" format="fasta">
+            <discover_datasets pattern="__name_and_ext__" />
+        </collection>
+        <collection name="collection_default_ext_and_explicit_format" type="list" label="with default format and static element format" format="fasta">
+            <discover_datasets pattern="__name__" format="txt" />
+        </collection>
+        <collection name="collection_default_ext_used" type="list" label="with default format and no override" format="fasta">
+            <discover_datasets pattern="__name__" />
+        </collection>
+        <collection name="collection_without_default_ext" type="list" label="wihtout default ext, should be data">
+            <discover_datasets pattern="__name__" />
+        </collection>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="4">
+            <output_collection name="collection_with_default_ext" type="list" count="1">
+                <element name="1" ftype="txt">
+                    <assert_contents>
+                        <has_text text="1" />
+                    </assert_contents>
+                </element>
+            </output_collection>
+            <output_collection name="collection_default_ext_and_explicit_format" type="list" count="1">
+                <element name="1.txt" ftype="txt">
+                    <assert_contents>
+                        <has_text text="1" />
+                    </assert_contents>
+                </element>
+            </output_collection>
+            <output_collection name="collection_default_ext_used" type="list" count="1">
+                <element name="1.txt" ftype="fasta">
+                    <assert_contents>
+                        <has_text text="1" />
+                    </assert_contents>
+                </element>
+            </output_collection>
+            <output_collection name="collection_without_default_ext" type="list" count="1">
+                <element name="1.txt" ftype="data">
+                    <assert_contents>
+                        <has_text text="1" />
+                    </assert_contents>
+                </element>
+            </output_collection>
+        </test>
+    </tests>
+</tool>

test/functional/tools/sample_tool_conf.xml

@@ -208,6 +208,7 @@
   <tool file="collection_cat_group_tag.xml" />
   <tool file="collection_cat_group_tag_multiple.xml" />
   <tool file="discover_sort_by.xml" />
+  <tool file="discover_default_ext.xml" />
   <tool file="expression_forty_two.xml" />
   <tool file="expression_pick_larger_file.xml" />
   <tool file="expression_parse_int.xml" />

test/unit/app/tools/test_collect_primary_datasets.py

@@ -128,6 +128,20 @@ def test_collect_multiple_recurse_dict(self):
         created_hda_3 = datasets[DEFAULT_TOOL_OUTPUT]["test3"]
         assert_created_with_path(self.app.object_store, created_hda_3.dataset, path3)
 
+    def test_collect_collection_default_format(self):
+        self._replace_output_collectors(
+            """<dataset_collection name="parent" format="abcdef">
+            <discover_datasets pattern="__name__" directory="subdir_for_name_discovery" sort_by="reverse_filename" />
+        </dataset_collection>"""
+        )
+        self._setup_extra_file(subdir="subdir_for_name_discovery", filename="test1")
+        self._setup_extra_file(subdir="subdir_for_name_discovery", filename="test2")
+
+        datasets = self._collect()
+        assert DEFAULT_TOOL_OUTPUT in datasets
+        for dataset in datasets[DEFAULT_TOOL_OUTPUT].values():
+            assert dataset.ext == "abcdef"
+
     def test_collect_sorted_reverse(self):
         self._replace_output_collectors(
             """<output>

test/unit/app/tools/test_parameter_validation.py

@@ -219,11 +219,13 @@ def test_InRangeValidator(self):
         )
         p.validate(10)
         with self.assertRaisesRegex(
-            ValueError, r"Parameter blah: Value \('15'\) must not fulfill float\('10'\) < float\(value\) <= float\('20'\)"
+            ValueError,
+            r"Parameter blah: Value \('15'\) must not fulfill float\('10'\) < float\(value\) <= float\('20'\)",
         ):
             p.validate(15)
         with self.assertRaisesRegex(
-            ValueError, r"Parameter blah: Value \('20'\) must not fulfill float\('10'\) < float\(value\) <= float\('20'\)"
+            ValueError,
+            r"Parameter blah: Value \('20'\) must not fulfill float\('10'\) < float\(value\) <= float\('20'\)",
         ):
             p.validate(20)
         p.validate(21)