release commit

biocypher/_config/__init__.py

@@ -0,0 +1,148 @@
+#!/usr/bin/env python
+
+#
+# Copyright 2021, Heidelberg University Clinic
+#
+# File author(s): Sebastian Lobentanzer
+#                 ...
+#
+# Distributed under MIT licence, see the file `LICENSE`.
+#
+"""
+Module data directory, including:
+
+* The BioLink database schema
+* The default config files
+"""
+
+from typing import Any, Optional
+import os
+import warnings
+
+import yaml
+import appdirs
+
+__all__ = ["module_data", "module_data_path", "read_config", "config", "reset"]
+
+_USER_CONFIG_DIR = appdirs.user_config_dir("biocypher", "saezlab")
+_USER_CONFIG_FILE = os.path.join(_USER_CONFIG_DIR, "conf.yaml")
+
+
+class MyLoader(yaml.SafeLoader):
+    def construct_scalar(self, node):
+        # Check if the scalar contains double quotes and an escape sequence
+        value = super().construct_scalar(node)
+        q = bool(node.style == '"')
+        b = bool("\\" in value.encode("unicode_escape").decode("utf-8"))
+        if q and b:
+            warnings.warn(
+                (
+                    "Double quotes detected in YAML configuration scalar: "
+                    f"{value.encode('unicode_escape')}. "
+                    "These allow escape sequences and may cause problems, for "
+                    "instance with the Neo4j admin import files (e.g. '\\t'). "
+                    "Make sure you wanted to do this, and use single quotes "
+                    "whenever possible."
+                ),
+                category=UserWarning,
+            )
+        return value
+
+
+def module_data_path(name: str) -> str:
+    """
+    Absolute path to a YAML file shipped with the module.
+    """
+
+    here = os.path.dirname(os.path.abspath(__file__))
+
+    return os.path.join(here, f"{name}.yaml")
+
+
+def module_data(name: str) -> Any:
+    """
+    Retrieve the contents of a YAML file shipped with this module.
+    """
+
+    path = module_data_path(name)
+
+    return _read_yaml(path)
+
+
+def _read_yaml(path: str) -> Optional[dict]:
+    if os.path.exists(path):
+        with open(path, "r") as fp:
+            return yaml.load(fp.read(), Loader=MyLoader)
+
+
+def read_config() -> dict:
+    """
+    Read the module config.
+
+    Read and merge the built-in default, the user level and directory level
+    configuration, with the later taking precendence over the former.
+
+    TODO explain path configuration
+    """
+
+    defaults = module_data("biocypher_config")
+    user = _read_yaml(_USER_CONFIG_FILE) or {}
+    # TODO account for .yml?
+    local = (
+        _read_yaml("biocypher_config.yaml")
+        or _read_yaml("config/biocypher_config.yaml")
+        or {}
+    )
+
+    for key in defaults:
+        value = (
+            local[key] if key in local else user[key] if key in user else None
+        )
+
+        if value is not None:
+            if isinstance(
+                defaults[key], str
+            ):  # first level config (like title)
+                defaults[key] = value
+            else:
+                defaults[key].update(value)
+
+    return defaults
+
+
+def config(*args, **kwargs) -> Optional[Any]:
+    """
+    Set or get module config parameters.
+    """
+
+    if args and kwargs:
+        raise ValueError(
+            "Setting and getting values in the same call is not allowed.",
+        )
+
+    if args:
+        result = tuple(globals()["_config"].get(key, None) for key in args)
+
+        return result[0] if len(result) == 1 else result
+
+    for key, value in kwargs.items():
+        globals()["_config"][key].update(value)
+
+
+def reset():
+    """
+    Reload configuration from the config files.
+    """
+
+    globals()["_config"] = read_config()
+
+
+reset()
+
+
+def update_from_file(path: str):
+    """
+    Update the module configuration from a YAML file.
+    """
+
+    config(**_read_yaml(path))