Model Job

galaxyproject · Dec 5, 2023 · 5d1a63d · 5d1a63d
1 parent 499f76d
commit 5d1a63d
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Showing 7 changed files with 806 additions and 27 deletions.
diff --git a/lib/galaxy/tool_util/schemas/.xsdata.xml b/lib/galaxy/tool_util/schemas/.xsdata.xml
@@ -2,5 +2,7 @@
 <Config xmlns="http://pypi.org/project/xsdata" version="23.6">
   <Extensions>
     <Extension type="class" class=".*" import=".config.BaseSetting" prepend="false" applyIfDerived="true"/>
+    <Extension type="class" class="TestOutput$" import=".config.ClassFileField" prepend="false" applyIfDerived="true"/>
+    <Extension type="class" class="TestOutputCollection" import=".config.ClassCollectionField" prepend="false" applyIfDerived="true"/>
   </Extensions>
 </Config>
diff --git a/lib/galaxy/tool_util/schemas/generated/config.py b/lib/galaxy/tool_util/schemas/generated/config.py
@@ -1,3 +1,12 @@
+from dataclasses import (
+    dataclass,
+    field,
+)
+from typing import (
+    Literal,
+    Optional,
+)
+
 from pydantic import ConfigDict
 
 alias_lookup = {
@@ -9,3 +18,14 @@ class BaseSetting:
     __pydantic_config__ = ConfigDict(
         extra="forbid", alias_generator=lambda field_name: alias_lookup.get(field_name, field_name)
     )
+
+
+@dataclass(kw_only=True)
+class ClassFileField:
+    class_: Optional[Literal["File"]] = field(default="File", metadata={"alias": "class"})
+    path: Optional[str] = None
+
+
+@dataclass(kw_only=True)
+class ClassCollectionField:
+    class_: Optional[Literal["Collection"]] = field(default="Collection", metadata={"alias": "class"})
diff --git a/lib/galaxy/tool_util/schemas/generated/galaxy.py b/lib/galaxy/tool_util/schemas/generated/galaxy.py
@@ -10,7 +10,11 @@
     Union,
 )
 
-from .config import BaseSetting
+from .config import (
+    BaseSetting,
+    ClassCollectionField,
+    ClassFileField,
+)
 
 
 class ActionType(Enum):
@@ -4966,7 +4970,7 @@ class ConditionalWhen(BaseSetting):
 
 
 @dataclass(kw_only=True)
-class TestOutput(BaseSetting):
+class TestOutput(BaseSetting, ClassFileField):
     """This tag set defines the variable that names the output dataset for the
     functional test framework. The functional test framework will execute the tool
     using the parameters defined in the ``&lt;param&gt;`` tag sets and generate a
@@ -5425,7 +5429,7 @@ class TestExtraFile(TestOutput, BaseSetting):
 
 
 @dataclass(kw_only=True)
-class TestOutputCollection(BaseSetting):
+class TestOutputCollection(BaseSetting, ClassCollectionField):
     """Define tests for extra datasets and metadata corresponding to an output
     collection.
 
@@ -5531,14 +5535,6 @@ class TestOutputCollection(BaseSetting):
     """
 
     element: Union[List[TestOutput], TestOutput] = field(default_factory=list, metadata={"type": "Element"})
-    type_value: Optional[str] = field(
-        default=None,
-        metadata={
-            "name": "type",
-            "type": "Attribute",
-            "description": "Expected collection type (``list`` or ``paired``), nested collections are specified as colon separated list (the most common types are ``list``, ``paired``, ``list:paired``, or ``list:list``).",
-        },
-    )
     count: Optional[int] = field(
         default=None, metadata={"type": "Attribute", "description": "Number of elements in output collection."}
     )

diff --git a/lib/galaxy/tool_util/schemas/postprocess_schema.py b/lib/galaxy/tool_util/schemas/postprocess_schema.py
@@ -33,6 +33,7 @@
 ]
 ATTRIBUTES_TO_DELETE = [
     "TestOutputCollection.name",
+    "TestOutputCollection.type_value",
     "TestOutput.element",
 ]
 

diff --git a/lib/galaxy/tool_util/schemas/test_file_from_xsd.py b/lib/galaxy/tool_util/schemas/test_file_from_xsd.py
@@ -13,6 +13,7 @@
     TestOutput,
     TestOutputCollection as TestOutputCollection_,
 )
+from job import Job
 from pydantic import (
     BaseModel,
     ConfigDict,
@@ -30,16 +31,17 @@ class TestOutputElement(TestOutput):
 @dataclass
 class TestOutputCollection(TestOutputCollection_):
     element_tests: dict[str, TestOutputElement | TestOutput]
+    collection_type: str | None = None
 
 
-AnyOutput = Union[TestOutputElement, TestOutput, TestOutputCollection]  # noqa: F405
+AnyOutput = Union[TestOutputElement, TestOutput, TestOutputCollection, str, int, float, bool]  # noqa: F405
 
 
 class Test(BaseModel):
     model_config = extra_forbidden
 
     doc: str
-    job: str
+    job: Job
     outputs: dict[str, AnyOutput]