adding the ability to set a specific biolink model version with an en…

…v var

README.md

@@ -34,3 +34,9 @@ qgraph = {
 
 cypher = get_query(qgraph)
 ```
+
+## Biolink Model
+This package uses the Biolink Model Toolkit to access the Biolink Model. Optionally, choose a specific version of the Biolink Model with the environment variable BL_VERSION. Otherwise, the latest version used by the Biolink Model Toolkit will be used.
+```commandline
+export BL_VERSION=4.1.6
+```

reasoner_transpiler/matching.py

@@ -1,4 +1,5 @@
 """MATCHing tools."""
+import os
 from typing import Dict, List
 
 from bmt import Toolkit
@@ -7,7 +8,12 @@
 from .nesting import Query
 from .util import ensure_list, snake_case, space_case, pascal_case
 
-bmt = Toolkit()
+
+BIOLINK_MODEL_VERSION = os.environ.get('BL_VERSION', '4.1.6')
+BIOLINK_MODEL_SCHEMA_URL = f"https://raw.githubusercontent.com/biolink/biolink-model/v{BIOLINK_MODEL_VERSION}/biolink-model.yaml"
+PREDICATE_MAP_URL = f"https://raw.githubusercontent.com/biolink/biolink-model/v{BIOLINK_MODEL_VERSION}/predicate_mapping.yaml"
+
+bmt = Toolkit(schema=BIOLINK_MODEL_SCHEMA_URL, predicate_map=PREDICATE_MAP_URL)
 ALL_BIOLINK_ENUMS = bmt.view.all_enums().keys()
 
 def cypher_prop_string(value):

setup.py

@@ -3,7 +3,7 @@
 
 setup(
     name="reasoner-transpiler",
-    version="2.0.6",
+    version="2.0.7",
     author="Patrick Wang",
     author_email="[email protected]",
     maintainer="Yaphet Kebede",