Drop redundant data manager parsing

Author: mvdbeek

src/ephemeris/_idc_data_managers_to_tools.py

@@ -7,11 +7,6 @@
 """
 import argparse
 import logging
-from typing import (
-    Dict,
-    List,
-    NamedTuple,
-)
 
 import yaml
 
@@ -29,29 +24,10 @@
 )
 
 
-class DataManager(NamedTuple):
-    tool_id: str
-    repository_name: str
-    tags: List[str]
-
-
-def read_data_managers_configuration(path: str) -> Dict[str, DataManager]:
-    raw_data_managers = read_data_managers(path)
-    data_managers: Dict[str, DataManager] = {}
-    for repository_name, data_manager_configuration in raw_data_managers.__root__.items():
-        data_manager = DataManager(
-            tool_id=data_manager_configuration.tool_id,
-            repository_name=repository_name,
-            tags=data_manager_configuration.tags or [],
-        )
-        data_managers[repository_name] = data_manager
-    return data_managers
-
-
 def build_shed_install_conf(path: str) -> dict:
-    data_managers = read_data_managers_configuration(path)
+    data_managers = read_data_managers(path)
     tools = []
-    for data_manager in data_managers.values():
+    for data_manager in data_managers.__root__.values():
         tool_id = data_manager.tool_id
         tool_id_parts = tool_id.split("/")
         repo_owner = tool_id_parts[2]

src/ephemeris/_idc_split_data_manager_genomes.py

@@ -35,9 +35,9 @@
     )
 
 from . import get_galaxy_connection
-from ._idc_data_managers_to_tools import (
-    DataManager,
-    read_data_managers_configuration,
+from ._config_models import (
+    DataManagers,
+    read_data_managers,
 )
 from .common_parser import get_common_args
 from .ephemeris_log import (
@@ -77,8 +77,8 @@ class SplitOptions:
     filters: Filters = Filters()
 
 
-def tool_id_for(indexer: str, data_managers: Dict[str, DataManager], mode: str) -> str:
-    data_manager = data_managers[indexer]
+def tool_id_for(indexer: str, data_managers: DataManagers, mode: str) -> str:
+    data_manager = data_managers.__root__[indexer]
     assert data_manager, f"Could not find a target data manager for indexer name {indexer}"
     tool_shed_guid = data_manager.tool_id
     if mode == "short":
@@ -151,7 +151,7 @@ def write_run_data_manager_to_file(run_data_manager: RunDataManager, path: str):
 
 
 def walk_over_incomplete_runs(split_options: SplitOptions):
-    data_managers = read_data_managers_configuration(split_options.data_managers_path)
+    data_managers = read_data_managers(split_options.data_managers_path)
     with open(split_options.merged_genomes_path) as f:
         genomes_all = yaml.safe_load(f)
     genomes = genomes_all["genomes"]