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Add workflow test schema #17128

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Add workflow test schema #17128

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2638de3
Add partially auto-generated test file schema
mvdbeek Dec 4, 2023
ddf0301
Delete TestOutputCollection.name
mvdbeek Dec 5, 2023
9947446
Delete element from TestOutput
mvdbeek Dec 5, 2023
4be6465
Add workflow test specific TestOutputCollection and TestOutputElement
mvdbeek Dec 5, 2023
d36643c
Model Job
mvdbeek Dec 5, 2023
c747343
Make TestAssertions optional
mvdbeek Dec 5, 2023
2de7445
Fix typing in postprocess_schema.py
mvdbeek Dec 6, 2023
4cbb24f
Use pydantic dataclass instead of stdlib dataclass
mvdbeek Dec 6, 2023
05a6e9c
Allow location and path to be set
mvdbeek Dec 7, 2023
b0a9dc0
Allow reference to external job file
mvdbeek Dec 7, 2023
bb325ec
Mark TestOutputCollection.element_tests as deprecated, use TestOutput…
mvdbeek Dec 7, 2023
8d7d63b
Add composite_data key to job schema, array-style inputs
mvdbeek Dec 8, 2023
41c8b5c
Add job schema
mvdbeek Dec 8, 2023
805f429
Use new optional syntax
mvdbeek Jan 11, 2024
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Model Job
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@mvdbeek
mvdbeek committed Jan 11, 2024
commit d36643c4bde351915f5f62a299fc8d24b25d238e
2 changes: 2 additions & 0 deletions lib/galaxy/tool_util/schemas/.xsdata.xml
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Expand Up @@ -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>
20 changes: 20 additions & 0 deletions lib/galaxy/tool_util/schemas/generated/config.py
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Original file line number Diff line number Diff line change
@@ -1,3 +1,12 @@
from dataclasses import (
dataclass,
field,
)
from typing import (
Literal,
Optional,
)

from pydantic import ConfigDict

alias_lookup = {
Expand All @@ -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"})
18 changes: 7 additions & 11 deletions lib/galaxy/tool_util/schemas/generated/galaxy.py
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Expand Up @@ -10,7 +10,11 @@
Union,
)

from .config import BaseSetting
from .config import (
BaseSetting,
ClassCollectionField,
ClassFileField,
)


class ActionType(Enum):
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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.

Expand Down Expand Up @@ -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."}
)
Expand Down
1 change: 1 addition & 0 deletions lib/galaxy/tool_util/schemas/postprocess_schema.py
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Expand Up @@ -33,6 +33,7 @@
]
ATTRIBUTES_TO_DELETE = [
"TestOutputCollection.name",
"TestOutputCollection.type_value",
"TestOutput.element",
]

Expand Down
6 changes: 4 additions & 2 deletions lib/galaxy/tool_util/schemas/test_file_from_xsd.py
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Expand Up @@ -13,6 +13,7 @@
TestOutput,
TestOutputCollection as TestOutputCollection_,
)
from job import Job
from pydantic import (
BaseModel,
ConfigDict,
Expand All @@ -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]


Expand Down
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