Try to update test instance

setup.py

@@ -39,6 +39,9 @@ def get_var(var_name):
         install_tool_deps=ephemeris.install_tool_deps:main
         install-tool-deps=ephemeris.install_tool_deps:main
         set-library-permissions=ephemeris.set_library_permissions:main
+        _idc-lint=ephemeris._idc_lint:main
+        _idc-split-data-manager-genomes=ephemeris._idc_split_data_manager_genomes:main
+        _idc-data-managers-to-tools=ephemeris._idc_data_managers_to_tools:main
 '''
 PACKAGE_DATA = {
     # Be sure to update MANIFEST.in for source dist.

src/ephemeris/__init__.py

@@ -1,4 +1,5 @@
 # -*- coding: utf-8 -*-
+import os
 
 import yaml
 from bioblend import galaxy
@@ -16,6 +17,14 @@
 )
 
 
+def get_or_create_history(history_name: str, gi: galaxy.GalaxyInstance):
+    histories = gi.histories.get_histories(name=history_name)
+    if histories:
+        return histories[0]
+    else:
+        return gi.histories.create_history(name=history_name)
+
+
 def check_url(url, log=None):
     if not url.startswith("http"):
         if log:
@@ -39,7 +48,7 @@ def get_galaxy_connection(args, file=None, log=None, login_required=True):
 
     url = args.galaxy or file_content.get("galaxy_instance")
     galaxy_url = check_url(url, log)
-    api_key = args.api_key or file_content.get("api_key")
+    api_key = args.api_key or file_content.get("api_key") or os.environ.get("EPHEMERIS_API_KEY")
 
     if args.user and args.password:
         return galaxy.GalaxyInstance(

src/ephemeris/_config_models.py

@@ -0,0 +1,83 @@
+from pathlib import Path
+from typing import (
+    Dict,
+    List,
+    Optional,
+    Union,
+)
+
+import yaml
+from pydantic import (
+    BaseModel,
+    Extra,
+)
+
+
+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
+
+
+class DataManagers(BaseModel, extra=Extra.forbid):
+    __root__: Dict[str, DataManager]
+
+
+class Genome(BaseModel):
+    id: str  # The unique id of the data in Galaxy
+    description: str  # The description of the data, including its taxonomy, version and date
+    dbkey: Optional[str]
+    source: Optional[str]  # The source of the data. Can be: 'ucsc', an NCBI accession number or a URL to a fasta file.
+
+    # The following fields are currently purely for human consumption and unused by
+    # IDC infrastructure.
+    doi: Optional[str]  # Any DOI associated with the data
+    blob: Optional[str]  # A blob for any other pertinent information
+    checksum: Optional[str]  # A SHA256 checksum of the original
+    version: Optional[str]  # Any version information associated with the data
+
+    # Description of actions (data managers) to run on target genome.
+    indexers: Optional[List[str]]  # indexers to run - keyed on repository name - see data_managers.yml for how to resolve these to tools
+    skiplist: Optional[List[str]]  # unimplemented: but if we implement classes of indexers, these will be ones to skip
+
+
+class Genomes(BaseModel):
+    genomes: List[Genome]
+
+
+def _read_yaml(path: StrOrPath):
+    with open(path, "r") as f:
+        return yaml.safe_load(f)
+
+
+def read_data_managers(path: StrOrPath) -> DataManagers:
+    return DataManagers(__root__=_read_yaml(path))
+
+
+def read_genomes(path: StrOrPath) -> Genomes:
+    return Genomes(**_read_yaml(path))
+
+
+def read_tools(path: StrOrPath) -> RepositoryInstallTargets:
+    return RepositoryInstallTargets(**_read_yaml(path))