Restructure RDF module.

* gn3/api/metadata.py: Import constants from gn3.db.rdf
* gn3/api/metadata_api/wiki.py: Ditto.  Import
"get_wiki_entries_by_symbol" from gn3.db.rdf.wiki.
* gn3/db/constants.py: Delete file and move all constants ...
* gn3/db/rdf.py: ... and functions ...
* gn3/db/rdf/__init__.py: ... here.

Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>

4 files changed, 44 insertions, 41 deletions

diff --git a/gn3/api/metadata.py b/gn3/api/metadata.py
index 3f28f5d..6110880 100644
--- a/gn3/api/metadata.py
+++ b/gn3/api/metadata.py
@@ -15,7 +15,7 @@ from gn3.db.datasets import (retrieve_metadata,
                              get_history)
 from gn3.db.rdf import (query_frame_and_compact,
                         query_and_compact)
-from gn3.db.constants import (
+from gn3.db.rdf import (
     RDF_PREFIXES, BASE_CONTEXT,
     DATASET_CONTEXT,
     DATASET_SEARCH_CONTEXT, PUBLICATION_CONTEXT,
diff --git a/gn3/api/metadata_api/wiki.py b/gn3/api/metadata_api/wiki.py
index a4abef6..b9942a0 100644
--- a/gn3/api/metadata_api/wiki.py
+++ b/gn3/api/metadata_api/wiki.py
@@ -5,8 +5,8 @@ from typing import Any, Dict
 from flask import Blueprint, request, jsonify, current_app, make_response
 from gn3 import db_utils
 from gn3.db import wiki
-from gn3.db.rdf import (query_frame_and_compact,
-                        get_wiki_entries_by_symbol)
+from gn3.db.rdf import query_frame_and_compact
+from gn3.db.rdf.wiki import get_wiki_entries_by_symbol
 
 
 wiki_blueprint = Blueprint("wiki", __name__, url_prefix="wiki")
diff --git a/gn3/db/constants.py b/gn3/db/rdf/__init__.py
index 45e3bfc..c763810 100644
--- a/gn3/db/constants.py
+++ b/gn3/db/rdf/__init__.py
@@ -1,6 +1,15 @@
+"""RDF
+
+Constants for prefixes and contexts; and wrapper functions around
+creating contexts to be used by jsonld when framing and/or compacting.
+
 """
-This module contains some constants used in other modules.
-"""
+import json
+
+from SPARQLWrapper import SPARQLWrapper
+from pyld import jsonld  # type: ignore
+
+
 PREFIXES = {
     "dcat": "http://www.w3.org/ns/dcat#",
     "dct": "http://purl.org/dc/terms/",
@@ -150,3 +159,30 @@ PHENOTYPE_CONTEXT = BASE_CONTEXT | PUBLICATION_CONTEXT | {
     "species": "gnt:belongsToSpecies",
     "group": "gnt:belongsToGroup",
 }
+
+
+def sparql_construct_query(query: str, endpoint: str) -> dict:
+    """Query virtuoso using a CONSTRUCT query and return a json-ld
+    dictionary"""
+    sparql = SPARQLWrapper(endpoint)
+    sparql.setQuery(query)
+    results = sparql.queryAndConvert()
+    return json.loads(results.serialize(format="json-ld"))  # type: ignore
+
+
+def query_frame_and_compact(query: str, context: dict, endpoint: str) -> dict:
+    """Frame and then compact the results given a context"""
+    results = sparql_construct_query(query, endpoint)
+    return jsonld.compact(jsonld.frame(results, context), context)
+
+
+def query_and_compact(query: str, context: dict, endpoint: str) -> dict:
+    """Compact the results given a context"""
+    results = sparql_construct_query(query, endpoint)
+    return jsonld.compact(results, context)
+
+
+def query_and_frame(query: str, context: dict, endpoint: str) -> dict:
+    """Frame the results given a context"""
+    results = sparql_construct_query(query, endpoint)
+    return jsonld.frame(results, context)
diff --git a/gn3/db/rdf.py b/gn3/db/rdf/wiki.py
index 5a95683..1fc3130 100644
--- a/gn3/db/rdf.py
+++ b/gn3/db/rdf/wiki.py
@@ -1,42 +1,9 @@
-"""RDF utilities
-
-This module is a collection of functions that handle SPARQL queries.
+"""Sparql queries to get metadata about WIKI and RIF metadata.
 
 """
-import json
 from string import Template
-from SPARQLWrapper import SPARQLWrapper
-from pyld import jsonld  # type: ignore
-from gn3.db.constants import (
-    RDF_PREFIXES, BASE_CONTEXT
-)
-
-
-def sparql_construct_query(query: str, endpoint: str) -> dict:
-    """Query virtuoso using a CONSTRUCT query and return a json-ld
-    dictionary"""
-    sparql = SPARQLWrapper(endpoint)
-    sparql.setQuery(query)
-    results = sparql.queryAndConvert()
-    return json.loads(results.serialize(format="json-ld"))  # type: ignore
-
-
-def query_frame_and_compact(query: str, context: dict, endpoint: str) -> dict:
-    """Frame and then compact the results given a context"""
-    results = sparql_construct_query(query, endpoint)
-    return jsonld.compact(jsonld.frame(results, context), context)
-
-
-def query_and_compact(query: str, context: dict, endpoint: str) -> dict:
-    """Compact the results given a context"""
-    results = sparql_construct_query(query, endpoint)
-    return jsonld.compact(results, context)
-
-
-def query_and_frame(query: str, context: dict, endpoint: str) -> dict:
-    """Frame the results given a context"""
-    results = sparql_construct_query(query, endpoint)
-    return jsonld.frame(results, context)
+from gn3.db.rdf import (BASE_CONTEXT, RDF_PREFIXES,
+                        query_frame_and_compact)
 
 
 def get_wiki_entries_by_symbol(symbol: str, sparql_uri: str) -> dict: