Do not ignore module-level SLME parameters.

Declare the module-level `module_type_slme` and `slme_individuals`
options to be None by default.

This way, we can detect whether those options have been explicitly set
for a given individual module, and if so, use their values instead of
using the values from the group level.

Then, we can detect whether the SLME type of an individual module is
different from the group-level SLME type, and make sure we generate a
specific rule for that module in that case.

closes #1204

Author: gouttegd

odk/odk.py

@@ -144,13 +144,13 @@ class ImportProduct(Product):
     module_type : Optional[str] = None
     """Module type. Supported: slme, minimal, custom, mirror"""
 
-    module_type_slme : str = "BOT"
+    module_type_slme : Optional[str] = None
     """SLME module type. Supported: BOT, TOP, STAR"""
 
     annotation_properties : List[str] = field(default_factory=lambda: ['rdfs:label', 'IAO:0000115', 'OMO:0002000'])
     """Define which annotation properties to pull in."""
 
-    slme_individuals : str = "include"
+    slme_individuals : Optional[str] = None
     """See http://robot.obolibrary.org/extract#syntactic-locality-module-extractor-slme"""
 
     use_base: bool = False
@@ -388,17 +388,22 @@ def _derive_fields(self):
         self.special_products = []
         for p in self.products:
             if p.module_type is None:
-                # Use group-level parameters
+                # Use group-level module type
                 p.module_type = self.module_type
-                p.module_type_slme = self.module_type_slme
-                p.slme_individuals = self.slme_individuals
             elif p.module_type == 'fast_slme':
                 # Accept fast_slme as a synonym for slme, for backwards
                 # compatibility
                 p.module_type = 'slme'
+            if p.module_type == 'slme':
+                # Use group-level SLME parameters unless overriden
+                if p.module_type_slme is None:
+                    p.module_type_slme = self.module_type_slme
+                if p.slme_individuals is None:
+                    p.slme_individuals = self.slme_individuals
             if p.base_iris is None:
                 p.base_iris = [ 'http://purl.obolibrary.org/obo/' + p.id.upper() ]
-            if p.is_large or p.module_type != self.module_type:
+            if (p.is_large or p.module_type != self.module_type or
+                (p.module_type == 'slme' and p.module_type_slme != self.module_type_slme)):
                 # This module will require a distinct rule
                 self.special_products.append(p)