Lift get_config_data from npg_notifications. Improve error handling b…

…y checking for a necessary config file. Use a dataclass to validate all properties are set in conf.

src/npg_porch_cli/config.py

@@ -0,0 +1,98 @@
+import configparser
+from dataclasses import dataclass
+import json
+import pathlib
+
+"""Common utility functions for the package."""
+
+DEFAULT_CONF_FILE_TYPE = "ini"
+
+
+def get_config_data(conf_file_path: str, conf_file_section: str = None):
+    """
+    Parses a configuration file and returns its content.
+
+    Allows for two types of configuration files, 'ini' and 'json'. The type of
+    the file is determined from the extension of the file name. In case of no
+    extension an 'ini' type is assumed.
+
+    The content of the file is not cached, so subsequent calls to get data from
+    the same configuration file result in re-reading and re-parsing of the file.
+
+    Args:
+
+      conf_file_path:
+        A configuration file with database connection details.
+      conf_file_section:
+        The section of the configuration file. Optional. Should be defined
+        for 'ini' files.
+
+    Returns:
+      For an 'ini' file returns the content of the given section of the file as
+      a dictionary.
+      For a 'json' file, if the conf_file_section argument is not defined, the
+      content of a file as a Python object is returned. If the conf_file_section
+      argument is defined, the object returned by the parser is assumed to be
+      a dictionary that has the value of the 'conf_file_section' argument as a key.
+      The value corresponding to this key is returned.
+    """
+
+    path = pathlib.Path(conf_file_path)
+
+    conf_file_extension = path.suffix
+    if conf_file_extension:
+        conf_file_extension = conf_file_extension[1:]
+    else:
+        conf_file_extension = DEFAULT_CONF_FILE_TYPE
+
+    if conf_file_extension == DEFAULT_CONF_FILE_TYPE:
+        if not conf_file_section:
+            raise Exception(
+                "'conf_file_section' argument is not given, "
+                "it should be defined for '{DEFAULT_CONF_FILE_TYPE}' "
+                "configuration file."
+            )
+
+        config = configparser.ConfigParser()
+        with open(conf_file_path) as cf:
+            if not cf.readable():
+                raise Exception(f"{path} has a permissions issue")
+
+            config.read_file(cf)
+
+        return {i[0]: i[1] for i in config[conf_file_section].items()}
+
+    elif conf_file_extension == "json":
+        conf: dict = json.load(conf_file_path)
+        if conf_file_section:
+            if isinstance(conf, dict) is False:
+                raise Exception(f"{conf_file_path} does not have sections.")
+            if conf_file_section in conf.keys:
+                conf = conf[conf_file_section]
+            else:
+                raise Exception(
+                    f"{conf_file_path} does not contain {conf_file_section} key"
+                )
+
+        return conf
+
+    else:
+        raise Exception(f"Parsing for '{conf_file_extension}' files is not implemented")
+
+
+@dataclass(frozen=True, kw_only=True)
+class PorchClientConfig:
+    """
+    Suggested config file content for interacting with a Porch server instance
+    """
+
+    api_url: str
+    pipeline_name: str
+    pipeline_uri: str
+    pipeline_version: str
+    npg_porch_token: str
+
+    @classmethod
+    def from_config_file(cls, conf_file_path: str, conf_file_section: str = "PORCH"):
+        conf = get_config_data(conf_file_path, conf_file_section=conf_file_section)
+        return cls(**conf)

tests/data/conf.ini

@@ -0,0 +1,17 @@
+[STUFF]
+
+logging = INFO
+
+[PORCH]
+
+api_url = https://porch.dnapipelines.sanger.ac.uk
+pipeline_name = test_pipeline
+pipeline_uri = https://test.pipeline.com
+pipeline_version = 9.9.9
+npg_porch_token = 0123456789abcdef0123456789abcdef
+
+[PARTIALPORCH]
+
+api_url = https://porch.dnapipelines.sanger.ac.uk
+pipeline_name = test_pipeline
+pipeline_uri = https://test.pipeline.com

tests/test_porch_client_config.py

@@ -0,0 +1,36 @@
+from pytest import raises
+from npg_porch_cli.config import get_config_data, PorchClientConfig
+
+
+def test_config_file_reading():
+    conf = get_config_data(
+        conf_file_path="tests/data/conf.ini", conf_file_section="STUFF"
+    )
+
+    assert conf == {"logging": "INFO"}
+
+
+def test_conf_obj():
+    config_obj = PorchClientConfig.from_config_file("tests/data/conf.ini")
+    assert config_obj.pipeline_name == "test_pipeline"
+    assert config_obj.pipeline_version == "9.9.9"
+
+    with raises(Exception):
+        PorchClientConfig.from_config_file(
+            "tests/data/conf.ini", conf_file_section="ABSENT"
+        )
+
+    with raises(Exception):
+        PorchClientConfig.from_config_file("notafile", conf_file_section="ABSENT")
+
+    with raises(TypeError) as e:
+        PorchClientConfig.from_config_file(
+            "tests/data/conf.ini", conf_file_section="STUFF"
+        )
+    assert e.match("unexpected keyword argument 'logging'")
+
+    with raises(Exception) as e:
+        PorchClientConfig.from_config_file(
+            "tests/data/conf.ini", conf_file_section="PARTIALPORCH"
+        )
+    assert e.match("missing 2 required keyword-only arguments")