feat: Add new command sodar landing-zone-validate (#219)

Co-authored-by: your-highness <hiob@noisecore.org>

cubi_tk/sodar/__init__.py

@@ -18,7 +18,7 @@
 ``landing-zone-create``
     Create a landing zone.
 
-``landing-zone-validate`` (planned)
+``landing-zone-validate``
     Validate a landing zone.
 
 ``landing-zone-move``
@@ -61,6 +61,7 @@
 from .lz_create import setup_argparse as setup_argparse_lz_create
 from .lz_list import setup_argparse as setup_argparse_lz_list
 from .lz_move import setup_argparse as setup_argparse_lz_move
+from .lz_validate import setup_argparse as setup_argparse_lz_validate
 from .pull_raw_data import setup_argparse as setup_argparse_pull_raw_data
 from .upload_sheet import setup_argparse as setup_argparse_upload_sheet
 
@@ -86,6 +87,9 @@ def setup_argparse(parser: argparse.ArgumentParser) -> None:
     setup_argparse_lz_move(
         subparsers.add_parser("landing-zone-move", help="Submit landing zone for moving")
     )
+    setup_argparse_lz_validate(
+        subparsers.add_parser("landing-zone-validate", help="Submit landing zone for validation")
+    )
     setup_argparse_ingest_fastq(
         subparsers.add_parser(
             "ingest-fastq", help="Upload external files to SODAR (defaults for fastq)"

cubi_tk/sodar/lz_validate.py

@@ -0,0 +1,105 @@
+"""``cubi-tk sodar landing-zone-validate`` command line program
+"""
+
+import argparse
+import json
+import os
+import typing
+
+import cattr
+import logzero
+from logzero import logger
+from sodar_cli import api
+
+from ..common import load_toml_config
+
+# no-frills logger
+formatter = logzero.LogFormatter(fmt="%(message)s")
+output_logger = logzero.setup_logger(formatter=formatter)
+
+# for testing
+output_logger.propagate = True
+
+
+class ValidateLandingZoneCommand:
+    """Implementation of the ``landing-zone-validate`` command."""
+
+    def __init__(self, args):
+        #: Command line arguments.
+        self.args = args
+
+    @classmethod
+    def setup_argparse(cls, parser: argparse.ArgumentParser) -> None:
+        """Setup argument parser."""
+        parser.add_argument(
+            "--hidden-cmd", dest="sodar_cmd", default=cls.run, help=argparse.SUPPRESS
+        )
+
+        group_sodar = parser.add_argument_group("SODAR-related")
+        group_sodar.add_argument(
+            "--sodar-url",
+            default=os.environ.get("SODAR_URL", "https://sodar.bihealth.org/"),
+            help="URL to SODAR, defaults to SODAR_URL environment variable or fallback to https://sodar.bihealth.org/",
+        )
+        group_sodar.add_argument(
+            "--sodar-api-token",
+            default=os.environ.get("SODAR_API_TOKEN", None),
+            help="Authentication token when talking to SODAR.  Defaults to SODAR_API_TOKEN environment variable.",
+        )
+
+        parser.add_argument(
+            "--format",
+            dest="format_string",
+            default=None,
+            help="Format string for printing, e.g. %%(uuid)s",
+        )
+
+        parser.add_argument("landing_zone_uuid", help="UUID of landing zone to validate.")
+
+    @classmethod
+    def run(
+        cls, args, _parser: argparse.ArgumentParser, _subparser: argparse.ArgumentParser
+    ) -> typing.Optional[int]:
+        """Entry point into the command."""
+        return cls(args).execute()  # pragma: nocover
+
+    def check_args(self, args):
+        """Called for checking arguments, override to change behaviour."""
+        res = 0
+
+        toml_config = load_toml_config(args)
+        args.sodar_url = args.sodar_url or toml_config.get("global", {}).get("sodar_server_url")
+        args.sodar_api_token = args.sodar_api_token or toml_config.get("global", {}).get(
+            "sodar_api_token"
+        )
+
+        return res
+
+    def execute(self) -> typing.Optional[int]:
+        """Execute the landing zone validation."""
+        res = self.check_args(self.args)
+        if res:  # pragma: nocover
+            return res
+
+        logger.info("Starting cubi-tk sodar landing-zone-validate.")
+        logger.debug("args: %s", self.args)
+
+        landing_zone = api.landingzone.submit_validate(
+            sodar_url=self.args.sodar_url,
+            sodar_api_token=self.args.sodar_api_token,
+            landingzone_uuid=self.args.landing_zone_uuid,
+        )
+        values = cattr.unstructure(landing_zone)
+        if self.args.format_string:
+            logger.info("Formatted server response:")
+            output_logger.info(self.args.format_string.replace(r"\t", "\t") % values)
+        else:
+            logger.info("Server response:")
+            output_logger.info(json.dumps(values))
+
+        return 0
+
+
+def setup_argparse(parser: argparse.ArgumentParser) -> None:  # pragma: nocover
+    """Setup argument parser for ``cubi-tk sodar landing-zone-validate``."""
+    return ValidateLandingZoneCommand.setup_argparse(parser)

tests/test_sodar_lz.py

@@ -0,0 +1,36 @@
+"""``Tests for sodar_lz functions``"""
+from argparse import ArgumentParser
+from unittest.mock import patch
+
+from cubi_tk.sodar.lz_validate import ValidateLandingZoneCommand
+
+
+@patch("cubi_tk.sodar.lz_validate.api.landingzone.submit_validate")
+@patch("cubi_tk.sodar.lz_validate.load_toml_config")
+def test_validate(mocktoml, mockapi, caplog):
+    mockapi.return_value = {"a": 1, "b": 2}
+    argv = [
+        "--sodar-url",
+        "sodar_url",
+        "--sodar-api-token",
+        "token",
+        "u-u-i-d",
+    ]
+
+    parser = ArgumentParser()
+    ValidateLandingZoneCommand.setup_argparse(parser)
+
+    # No format string
+    args = parser.parse_args(argv)
+    ValidateLandingZoneCommand(args).execute()
+    mockapi.assert_called_with(
+        sodar_url="sodar_url", sodar_api_token="token", landingzone_uuid="u-u-i-d"
+    )
+    assert '{"a": 1, "b": 2}' in caplog.messages
+
+    # With format string
+    argv.insert(-1, "--format")
+    argv.insert(-1, "%(a)s")
+    args = parser.parse_args(argv)
+    ValidateLandingZoneCommand(args).execute()
+    assert "1" in caplog.messages