Progress on workflow default files.

jmchilton · Nov 1, 2023 · 742f8d8 · 742f8d8
1 parent 5f4779c
commit 742f8d8
Show file tree

Hide file tree

Showing 4 changed files with 58 additions and 11 deletions.
diff --git a/lib/galaxy/tool_util/xsd/galaxy.xsd b/lib/galaxy/tool_util/xsd/galaxy.xsd
@@ -4123,7 +4123,8 @@ dataset for the contained input of the type specified using the ``type`` tag.
 </xs:documentation>
     </xs:annotation>
     <xs:sequence>
-      <xs:group ref="ParamDefaultCollectionElement" minOccurs="0" maxOccurs="unbounded"/>
+      <!-- can have zero or one collection elements -->
+      <xs:element name="element" type="ParamDefaultElement" minOccurs="0" maxOccurs="unbounded" />
     </xs:sequence>
     <xs:attribute name="collection_type" type="CollectionType" use="optional">
       <xs:annotation>
@@ -4135,21 +4136,52 @@ collection types (the most common types are ``list``, ``paired``,
         ]]></xs:documentation>
       </xs:annotation>
     </xs:attribute>
-    <xs:attribute name="location" type="xs:string" use="optional">
+
+    <xs:attribute name="location" type="xs:anyURI" gxdocs:added="23.2" use="optional">
       <xs:annotation>
         <xs:documentation xml:lang="en"><![CDATA[
-Galaxy-aware URI for the default file.
+Galaxy-aware URI for the default file. This should only be used with parameters of type "data".
         ]]></xs:documentation>
       </xs:annotation>
     </xs:attribute>
 
   </xs:complexType>
 
-  <xs:group name="ParamDefaultCollectionElement">
-    <xs:choice>
-      <xs:element name="element" type="OutputData" />
-    </xs:choice>
-  </xs:group>
+  <xs:complexType name="ParamDefaultCollection">
+    <xs:sequence>
+      <xs:element name="element" type="ParamDefaultElement" minOccurs="0" maxOccurs="unbounded" />
+    </xs:sequence>
+
+    <xs:attribute name="collection_type" type="CollectionType" use="optional">
+      <xs:annotation>
+        <xs:documentation xml:lang="en"><![CDATA[
+Collection type for default collection (if param type is data_collection). Simple collection types are
+either ``list`` or ``paired``, nested collections are specified as colon separated list of simple
+collection types (the most common types are ``list``, ``paired``,
+``list:paired``, or ``list:list``).
+        ]]></xs:documentation>
+      </xs:annotation>
+    </xs:attribute>
+
+  </xs:complexType>
+
+  <xs:complexType name="ParamDefaultElement">
+    <xs:sequence>
+      <xs:element name="collection" type="ParamDefaultCollection" minOccurs="0" maxOccurs="1" />
+    </xs:sequence>
+    <xs:attribute name="name" type="xs:string">
+      <xs:annotation>
+        <xs:documentation xml:lang="en">Name (and element identifier) for this element</xs:documentation>
+      </xs:annotation>
+    </xs:attribute>
+    <xs:attribute name="location" type="xs:anyURI" gxdocs:added="23.2" use="optional">
+      <xs:annotation>
+        <xs:documentation xml:lang="en"><![CDATA[
+Galaxy-aware URI for the default file for collection element.
+        ]]></xs:documentation>
+      </xs:annotation>
+    </xs:attribute>
+  </xs:complexType>
 
   <xs:complexType name="ParamOptions">
     <xs:annotation>

diff --git a/lib/galaxy/workflow/modules.py b/lib/galaxy/workflow/modules.py
@@ -99,6 +99,8 @@
 
 if TYPE_CHECKING:
     from galaxy.schema.invocation import InvocationMessageUnion
+    from galaxy.workflow.run import WorkflowProgress
+
 
 log = logging.getLogger(__name__)
 
@@ -176,7 +178,7 @@ def to_cwl(value, hda_references, step):
         return value
 
 
-def from_cwl(value, hda_references, progress):
+def from_cwl(value, hda_references, progress: WorkflowProgress):
     # TODO: turn actual files into HDAs here ... somehow I suppose. Things with
     # file:// locations for instance.
     if isinstance(value, dict) and "class" in value and "location" in value:

diff --git a/lib/galaxy/workflow/run.py b/lib/galaxy/workflow/run.py
@@ -328,6 +328,8 @@ def _invoke_step(self, invocation_step: WorkflowInvocationStep) -> Optional[bool
 
 
 class ModuleInjector(Protocol):
+    trans: "WorkRequestContext"
+
     def inject(self, step, step_args=None, steps=None, **kwargs):
         pass
 
@@ -699,6 +701,9 @@ def subworkflow_progress(
             when_values=when_values,
         )
 
+    def raw_to_galaxy(self, value: dict):
+        return raw_to_galaxy(self.module_injector.trans, value)
+
     def _recover_mapping(self, step_invocation: WorkflowInvocationStep) -> None:
         try:
             step_invocation.workflow_step.module.recover_mapping(step_invocation, self)

diff --git a/test/unit/workflows/test_workflow_progress.py b/test/unit/workflows/test_workflow_progress.py
@@ -1,9 +1,15 @@
+from typing import cast
+
 from galaxy import model
 from galaxy.model.base import transaction
 from galaxy.util.unittest import TestCase
-from galaxy.workflow.run import WorkflowProgress
+from galaxy.workflow.run import (
+    ModuleInjector,
+    WorkflowProgress,
+)
 from .workflow_support import (
     MockApp,
+    MockTrans,
     yaml_to_model,
 )
 
@@ -76,7 +82,8 @@ def _setup_workflow(self, workflow_yaml):
         self.invocation.workflow = workflow
 
     def _new_workflow_progress(self):
-        return WorkflowProgress(self.invocation, self.inputs_by_step_id, MockModuleInjector(self.progress), {})
+        mock_injector: ModuleInjector = cast(ModuleInjector, MockModuleInjector(self.progress))
+        return WorkflowProgress(self.invocation, self.inputs_by_step_id, mock_injector, {})
 
     def _set_previous_progress(self, outputs):
         for i, (step_id, step_value) in enumerate(outputs):
@@ -242,6 +249,7 @@ def compute_runtime_state(self, step, step_args=None):
 class MockModule:
     def __init__(self, progress):
         self.progress = progress
+        self.trans = MockTrans()
 
     def decode_runtime_state(self, step, runtime_state):
         return True