Merge pull request #434 from EI-CoreBioinformatics/issue-433-marshmallow

Issue #433 - changing the order of operations in printing out the fil…

Mikado/configuration/__init__.py

@@ -7,6 +7,7 @@
 import os
 from marshmallow import fields
 from .configuration import MikadoConfiguration
+from .configurator import load_and_validate_config
 from .daijin_configuration import DaijinConfiguration
 from . import configurator
 import itertools
@@ -55,6 +56,9 @@ def print_config(config: Union[MikadoConfiguration, DaijinConfiguration], out,
     if not full:
         config_dict = filter_config(config_dict, config)
 
+    assert isinstance(config_dict, dict)
+    # load_and_validate_config(config_dict)
+
     if output_format == "toml":
         print_toml_config(config_dict, config, out)
     elif output_format == "yaml":

Mikado/subprograms/configure.py

@@ -1,6 +1,8 @@
 #!/usr/bin/env python3
 
 """Stub of pre-configurer for Mikado"""
+import shutil
+
 import yaml
 import os
 import re
@@ -186,14 +188,6 @@ def create_config(args):
     config.check()
 
     # Check that the configuration file is correct
-    with tempfile.NamedTemporaryFile("wt", suffix=".json", delete=True) as tempcheck:
-        print_config(config, tempcheck, full=args.full, output_format="json")
-        tempcheck.flush()
-        try:
-            load_and_validate_config(tempcheck.name)
-        except InvalidConfiguration as exc:
-            raise InvalidConfiguration("Created an invalid configuration file! Error:\n{}".format(exc))
-
     # Print out the final configuration file
     if args.json is True or args.out.name.endswith("json"):
         format_name = "json"
@@ -202,7 +196,25 @@ def create_config(args):
     else:
         format_name = "toml"
 
+    with tempfile.NamedTemporaryFile("wt", suffix=f".{format_name}", delete=False,
+                                     dir=os.path.dirname(os.path.abspath(args.out.name))) as tempcheck:
+        print_config(config, tempcheck, full=args.full, output_format=format_name, no_files=args.no_files)
+        tempcheck.flush()
+        assert os.path.exists(tempcheck.name)
+        try:
+            load_and_validate_config(tempcheck.name)
+            os.remove(tempcheck.name)
+        except InvalidConfiguration as exc:
+            raise InvalidConfiguration(f"Created an invalid configuration file! Error:\n{exc}")
+
+    config = config.copy()
     print_config(config, args.out, output_format=format_name, no_files=args.no_files, full=args.full)
+    args.out.close()
+    try:
+        load_and_validate_config(args.out.name)
+    except InvalidConfiguration as exc:
+        os.remove(args.out.name)
+        raise InvalidConfiguration("Created an invalid configuration file! Error:\n{}".format(exc))
 
 
 def configure_parser():

Mikado/tests/test_configurators.py

@@ -3,11 +3,12 @@
 import marshmallow
 import tempfile
 import pkg_resources
-from ..configuration import configurator
+from ..configuration import configurator, print_config
 from .._transcripts.scoring_configuration import SizeFilter, TargetScore
 from ..configuration.configuration import *
 from ..loci.abstractlocus import Abstractlocus
 import pickle
+import io
 
 
 class TestConfigurator(unittest.TestCase):
@@ -119,3 +120,16 @@ def test_load_invalid_scoring(self):
                          pkg_resources.resource_filename("Mikado.configuration", os.path.join("scoring_files",
                                                                                               "plant.yaml")))
         os.chdir(current)
+
+    def test_create_config(self):
+        config = MikadoConfiguration()
+        self.assertIsInstance(config, MikadoConfiguration)
+        self.assertIsInstance(config.pick, PickConfiguration)
+        config.check()
+        buffer = io.StringIO()
+        print_config(config, buffer, output_format="json")
+        reading = buffer.getvalue()
+        self.assertGreater(len(reading), 0)
+        reloaded = json.loads(reading)
+        reloaded_config = MikadoConfiguration.Schema().load(reloaded)
+        self.assertEqual(reloaded_config, config)

requirements.txt

@@ -19,6 +19,6 @@ python-rapidjson>=1.0.0
 toml>=0.10.0
 pyfaidx>=0.5.8
 dataclasses; python_version < '3.7'
-marshmallow==3.14.1
-marshmallow-dataclass==8.5.3
+marshmallow>=3.14.1
+marshmallow-dataclass>=8.5.3
 typeguard  # Necessary for mashmallow apparently