This should be putting a huge dent in #158 - the config files now wil…

…l NOT duplicate information when the 'daijin' option is invoked

Mikado/configuration/configurator.py

@@ -68,12 +68,12 @@ def set_default(instance, properties, simple_comment=False):
         for prop, subschema in properties.items():
             if instance is None:
                 instance = dict()
-            if "$ref" in subschema:
-                # Automatically resolve and load the reference
-                assert resolver is not None
-                properties[prop] = resolver.resolve(subschema["$ref"])[1]
-                subschema = properties[prop]
-
+            # if "$ref" in subschema:
+            #     # Automatically resolve and load the reference
+            #     assert resolver is not None
+            #     properties[prop] = resolver.resolve(subschema["$ref"])[1]
+            #     subschema = properties[prop]
+            #
             if "default" in subschema:
                 instance.setdefault(prop, subschema["default"])
             elif prop not in instance:
@@ -107,7 +107,7 @@ def set_defaults(validator, properties, instance, schema):
         instance = set_default(instance, properties, simple_comment=simple)
 
     return jsonschema.validators.extend(
-        validator_class, {"properties": set_defaults},
+        validator_class, {"properties": set_defaults, "resolver": resolver},
     )
 
 

Mikado/configuration/daijin_configurator.py

@@ -12,6 +12,7 @@
 from ..exceptions import InvalidJson
 from ..utilities.log_utils import create_default_logger
 import sys
+import jsonref
 
 
 def _substitute_conf(schema):
@@ -29,21 +30,21 @@ def _substitute_conf(schema):
     return schema
 
 
-def create_daijin_validator():
+def create_daijin_validator(simple=True):
 
-    with io.TextIOWrapper(resource_stream("Mikado.configuration", "configuration_blueprint.json")) as _:
-        schema = json.load(_)
-
-    resolver = jsonschema.RefResolver.from_schema(schema)
+    cname = resource_filename("Mikado.configuration", "configuration_blueprint.json")
 
+    # We have to repeate twice the ending configuration (bug in jsonref?)
+    baseuri = "file://" +  os.path.join(os.path.dirname(cname), os.path.basename(os.path.dirname(cname)))
     with io.TextIOWrapper(resource_stream("Mikado.configuration",
                                           "daijin_schema.json")) as blue:
-        blue_print = json.load(blue)
+        blue_print = jsonref.load(blue,
+                                  jsonschema=True,
+                                  base_uri=baseuri)
 
-    _substitute_conf(blue_print)
-    validator = extend_with_default(jsonschema.Draft4Validator,
-                                    resolver=resolver,
-                                    simple=True)
+    # _substitute_conf(blue_print)
+    validator = extend_with_default(jsonschema.Draft7Validator,
+                                    simple=simple)
     validator = validator(blue_print)
 
     return validator
@@ -72,9 +73,9 @@ def check_config(config, logger=None):
         sys.exit(1)
 
 
-def create_daijin_base_config():
+def create_daijin_base_config(simple=True):
 
-    validator = create_daijin_validator()
+    validator = create_daijin_validator(simple=simple)
     conf = dict()
     validator.validate(conf)
 
@@ -200,7 +201,7 @@ def create_daijin_config(args, level="ERROR", piped=False):
 
     logger = create_default_logger("daijin_config", level=level)
 
-    config = create_daijin_base_config()
+    config = create_daijin_base_config(simple=(not args.full))
     assert "reference" in config, config.keys()
     # print(config)
     config["reference"]["genome"] = args.genome

Mikado/daijin/__init__.py

@@ -129,6 +129,7 @@ def create_config_parser():
     runtime.add_argument("-c", "--cluster_config",
                         type=str, default=None,
                         help="Cluster configuration file to write to.")
+    parser.add_argument("--full", action="store_true", default=False)
     runtime.add_argument("--threads", "-t", action="store", metavar="N", type=int, default=4,
                         help="""Maximum number of threads per job. Default: %(default)s""")
     runtime.add_argument("-od", "--out-dir", dest="out_dir", default=None, required=False,

Mikado/tests/test_system_calls.py

@@ -1023,6 +1023,7 @@ def test_daijin_config(self):
         namespace.transcriptome = ""
         namespace.name = "Daijin"
         namespace.threads = 1
+        namespace.full = False
 
         for iteration in range(20):
             with self.subTest(iteration=iteration):

requirements.txt

@@ -21,5 +21,6 @@ tabulate
 ujson
 simplejson
 pandas
+jsonref>=0.2
 pytest-cov
-pysam >= 0.15.1
+pysam>=0.15.1