Test case for data manager tools YAML generation.

src/ephemeris/_config_models.py

@@ -16,6 +16,25 @@
 StrOrPath = Union[Path, str]
 
 
+class RepositoryInstallTarget(BaseModel):
+    name: str
+    owner: str
+    tool_shed_url: Optional[str]
+    tool_panel_section_id: Optional[str]
+    tool_panel_section_label: Optional[str]
+    revisions: Optional[List[str]]
+    install_tool_dependencies: Optional[bool]
+    install_repository_dependencies: Optional[bool]
+    install_resolver_dependencies: Optional[bool]
+
+
+class RepositoryInstallTargets(BaseModel):
+    """ """
+    api_key: Optional[str]
+    galaxy_instance: Optional[str]
+    tools: List[RepositoryInstallTarget]
+
+
 class DataManager(BaseModel, extra=Extra.forbid):
     tags: List[str]
     tool_id: str
@@ -58,3 +77,7 @@ def read_data_managers(path: StrOrPath) -> DataManagers:
 
 def read_genomes(path: StrOrPath) -> Genomes:
     return Genomes(**_read_yaml(path))
+
+
+def read_tools(path: StrOrPath) -> RepositoryInstallTargets:
+    return RepositoryInstallTargets(**_read_yaml(path))

src/ephemeris/_idc_data_managers_to_tools.py

@@ -15,7 +15,10 @@
 
 import yaml
 
-from ._config_models import read_data_managers
+from ._config_models import (
+    read_data_managers,
+    RepositoryInstallTargets,
+)
 from .common_parser import (
     add_log_file_argument,
     add_verbosity_argument,
@@ -66,6 +69,10 @@ def build_shed_install_conf(path: str) -> dict:
 
 def write_shed_install_conf(data_manager_conf_path: str, output_path: str) -> None:
     tools_yaml = build_shed_install_conf(data_manager_conf_path)
+
+    # validate generated dict to ensure we're writing out valid file
+    RepositoryInstallTargets(**tools_yaml)
+
     with open(output_path, "w") as f:
         yaml.safe_dump(tools_yaml, f)
 

tests/test_idc_data_managers_to_tools.py

@@ -0,0 +1,13 @@
+from pathlib import Path
+
+from ephemeris._config_models import read_tools
+from ephemeris._idc_data_managers_to_tools import write_shed_install_conf
+from .test_split_genomes import setup_mock_idc_dir
+
+
+def test_idc_lint_valid(tmp_path: Path):
+    setup_mock_idc_dir(tmp_path)
+    output_path = tmp_path / "output.yaml"
+    write_shed_install_conf(tmp_path / "data_managers.yml", output_path)
+    # validate the generated tools file...
+    read_tools(output_path)