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import shutil
from pathlib import Path
from typing import Any, Optional, cast
from schema_salad import codegen
from schema_salad.schema import load_schema
from .util import cwl_file_uri, get_path, metaschema_file_uri
def test_cwl_gen(tmp_path: Path) -> None:
topmed_example_path = get_path("tests/test_real_cwl/topmed/topmed_variant_calling_pipeline.cwl")
target_dir = tmp_path / "target"
examples_dir = tmp_path / "examples"
target_dir.mkdir()
examples_dir.mkdir()
shutil.copyfile(topmed_example_path, examples_dir / "valid_topmed.cwl")
java_codegen(cwl_file_uri, target_dir, examples=examples_dir)
pom_xml_path = target_dir / "pom.xml"
assert pom_xml_path.exists()
tests_dir = target_dir / "src" / "test" / "java" / "org" / "w3id" / "cwl" / "cwl" / "utils"
assert tests_dir.exists()
with open(tests_dir / "ExamplesTest.java") as f:
assert "topmed" in f.read()
def test_meta_schema_gen(tmp_path: Path) -> None:
target_dir = tmp_path / "target"
target_dir.mkdir()
java_codegen(metaschema_file_uri, target_dir)
pom_xml_path = target_dir / "pom.xml"
assert pom_xml_path.exists()
src_dir = target_dir / "src" / "main" / "java" / "org" / "w3id" / "cwl" / "salad"
assert src_dir.exists()
def java_codegen(file_uri: str, target: Path, examples: Optional[Path] = None) -> None:
document_loader, avsc_names, schema_metadata, metaschema_loader = load_schema(file_uri)
schema_raw_doc = metaschema_loader.fetch(file_uri)
schema_doc, schema_metadata = metaschema_loader.resolve_all(schema_raw_doc, file_uri)
codegen.codegen(
"java",
cast(list[dict[str, Any]], schema_doc),
schema_metadata,
document_loader,
target=str(target),
examples=str(examples) if examples else None,
)
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