- Internal class hierarchy restructured for logical clarity in recent…

… releases, formally highlighted in this release - Most visible TRAPIResponseValidator class (previously) moved from the **`reasoner_validator.__init__.py`** package module, into its own **`reasoner_validator.validator`** module - Some documentation repair
NCATSTranslator · Aug 7, 2023 · 04bdf56 · 04bdf56
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -2,10 +2,14 @@
 
 The Reasoner Validator package is evolving along with progress in TRAPI and Biolink Model standards within the NCATS Biomedical Knowledge Translator.
 
+## 3.8.0
+- Internal class hierarchy restructured for logical clarity in recent releases, formally highlighted in this release
+- Most visible TRAPIResponseValidator class (previously) moved from the **`reasoner_validator.__init__.py`** package module, into its own  **`reasoner_validator.validator`** module
+- Some documentation repair
+
 ## 3.7.6
 - TRAPI qualifier validation enhanced by use of biolink:Association subclass slot_usage driven constraints (leveraging novel Biolink Model Toolkit 1.1.1 methods)
-- Validation made TRAPI Response (TRAPI) schema_version and biolink_version aware, taking precedence over default (non-overridden) values of these version parameters.
-
+- Validation made TRAPI Response (TRAPI) **`schema_version`** and **`biolink_version`** aware, taking precedence over default (non-overridden) values of these version parameters.
 
 ## 3.7.5
 - Added TRAPI Response schema version and biolink version validation warning codes

diff --git a/README.md b/README.md
@@ -150,7 +150,7 @@ The web service has a single POST endpoint `/validate` taking a simple JSON requ
     "kp_source_type": "primary"
   },
   "strict_validation": true,
-  "response": {<some full JSON object of a TRAPI query Response...>}
+  "response": "{<some full JSON object of a TRAPI query Response...>}"
 }
 ```
 
@@ -230,27 +230,30 @@ one should typically get a response body something like the following JSON valid
   "trapi_version": "1.4.1",
   "biolink_version": "3.2.1",
   "messages": {
-    # some categories of messages may be absent, hence, empty dictionaries
+    "_comment": "some categories of messages may be absent, hence, empty dictionaries",
     "critical": {},
     "errors": {
       "error.knowledge_graph.node.category.missing": {
-          # this message template does not have any additional parameters
-          # other than identifier hence it just has the unique identifier 
-          # value as a dictionary key, with associated value None
-           "MONDO:0005148": None
+          "_comment": "source scope of the validation error ('global' or some knowledge source path string)",
+          "global": {
+              "_comment": "this message template does not have any additional parameters other than identifier hence it just has the unique identifier  value as a dictionary key, with associated value None",
+               "MONDO:0005148": null            
+          }
         }
     },
     "warnings": {
-      # validation code
+      "_comment": "validation code",
       "warning.knowledge_graph.node.unmapped_prefix": {
-          # template identifier field value
-          "CHEBI:6801": [  
-              {
-                # additional message template field values, if applicable
-                "categories": "['biolink:Drug']"  
-              }
-          ]
-
+          "global": {
+              "_comment": "template identifier field value",
+              "CHEBI:6801": [  
+                  {
+                    "_comment": "additional message template field values, if applicable",
+                    "categories": "['biolink:Drug']"  
+                  }
+              ]       
+          }
+
         }
     },
     "information": {},

diff --git a/docs/index.rst b/docs/index.rst
@@ -129,7 +129,7 @@ in a dictionary looking something like the following (as an example):
     messages: Dict[str, List[Dict[str,str]]] = {
         "information": {
             "info.excluded": {
-                # source scope of the validation error ("global" or some knowledge source path string
+                # source scope of the validation error ("global" or some knowledge source path string)
                 "global": {
                     # the uniquely discriminating 'identifier' here is the edge_id
                     "(ZFIN:ZDB-GENE-060825-345$biolink:Gene)--[biolink:active_in]->(GO:0042645$biolink:CellularComponent)": None
@@ -246,24 +246,24 @@ The web service has a single POST endpoint `/validate` taking a simple JSON requ
 .. code-block:: json
 
     {
-        # If the TRAPI version is omitted or set to None, then the 'latest' TRAPI version is used.
+        "_comment": "If the TRAPI version is omitted or set to None, then the 'latest' TRAPI version is used.
 
         # Note: for TRAPI releases from 1.4.0 onwards, the Response message will state the assumed 'schema_version'.
         # This modifies slightly the interpretation of this parameter, as follows:
         # If the following trapi_version parameter is given, then it overrides the TRAPI Response 'schema_version';
-        # Otherwise, a TRAPI 1.4.0 Response embedded 'schema_version' (not 'latest') becomes the default validation version.
+        # Otherwise, a TRAPI 1.4.0 Response embedded 'schema_version' (not 'latest') becomes the default validation version."
 
-        trapi_version="1.4.2",
+        "trapi_version": "1.4.2",
 
-        # If the Biolink Model version is omitted or set to None, then the current Biolink Model Toolkit is used.
+        "_comment": "If the Biolink Model version is omitted or set to None, then the current Biolink Model Toolkit is used.
 
         # Note: for TRAPI releases from 1.4.0 onwards, the Response message will state the assumed 'biolink_version'.
         # This modifies slightly the interpretation of this parameter, as follows:
         # If the 'biolink_version' given here is assumed, which overrides the TRAPI Response stated 'biolink_version';
         # Otherwise, a TRAPI 1.4.0 Response embedded 'biolink_version' (not BMT) becomes the default validation version.
-        # The biolink_version may also be set to the string 'suppress', in which case, most Biolink Model validation is NOT done during the validation of a TRAPI Response.
+        # The biolink_version may also be set to the string 'suppress', in which case, most Biolink Model validation is NOT done during the validation of a TRAPI Response."
 
-        biolink_version="3.5.0",
+        "biolink_version": "3.5.0",
 
         "sources": {
             "ara_source": "infores:aragorn",

diff --git a/poetry.lock b/poetry.lock
diff --git a/pyproject.toml b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "reasoner-validator"
-version = "3.7.6"
+version = "3.8.0"
 description = "Validation tools for Reasoner API"
 authors = [
     "Richard Bruskiewich <richard.bruskiewich@delphinai.com>",