Support for string workflow parameter

Author: suecharo

pyproject.toml

@@ -47,7 +47,15 @@ Documentation = "https://github.com/sapporo-wes/sapporo-service/blob/main/README
 Repository = "https://github.com/sapporo-wes/sapporo-service.git"
 
 [project.optional-dependencies]
-tests = ["isort", "mypy", "pylint", "pytest-cov", "pytest-mock", "pytest"]
+tests = [
+    "isort",
+    "mypy",
+    "pylint",
+    "pytest-cov",
+    "pytest-mock",
+    "pytest",
+    "types-PyYAML",
+]
 
 [project.scripts]
 sapporo = "sapporo.app:main"

sapporo/run.py

@@ -59,7 +59,10 @@ def write_file(run_id: str, key: RunDirStructureKeys, content: Any) -> None:
     file.parent.mkdir(parents=True, exist_ok=True)
     with file.open(mode="w", encoding="utf-8") as f:
         if file.suffix == ".json":
-            content = json.dumps(content, indent=2)
+            if key == "wf_params" and isinstance(content, str):
+                pass
+            else:
+                content = json.dumps(content, indent=2)
         elif key == "state":
             content = content.value
         else:

sapporo/schemas.py

@@ -294,9 +294,14 @@ class RunListResponse(BaseModel):
 
 
 class RunRequest(BaseModel):
-    workflow_params: Dict[str, Any] = Field(
+    workflow_params: Union[Dict[str, Any], str] = Field(
         ...,
-        description=GA4GH_WES_SCHEMAS["RunRequest"]["properties"]["workflow_params"]["description"],
+        description=GA4GH_WES_SCHEMAS["RunRequest"]["properties"]["workflow_params"]["description"] + """\n
+**sapporo-wes-2.0.0 extension:**
+
+- original wes-1.1.0: Dict[str, Any]
+- sapporo-wes-2.0.0: Union[Dict[str, Any], str]
+""",
     )
     workflow_type: str = Field(
         ...,