From c4b77143cd763d70931871645d6eb976272d3165 Mon Sep 17 00:00:00 2001
From: Munyoki Kilyungi
Date: Fri, 20 Oct 2023 16:37:56 +0300
Subject: Implement "GET /metadata/phenotypes/:name".

* gn3/api/metadata.py: Delete gn3.db.rdf.get_phenotype_metadata.
(phenotype): Rename this to ...
(phenotypes): ...  this and implement update logic.
* gn3/db/rdf.py (get_phenotype_metadata): Delete.

Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
---
 gn3/db/rdf.py | 47 -----------------------------------------------
 1 file changed, 47 deletions(-)

(limited to 'gn3/db')

diff --git a/gn3/db/rdf.py b/gn3/db/rdf.py
index ae0ec29..c8a5017 100644
--- a/gn3/db/rdf.py
+++ b/gn3/db/rdf.py
@@ -85,50 +85,3 @@ def get_url_local_name(string: str) -> str:
         url = urlparse(string)
         return unquote(url.path).rpartition("/")[-1]
     return string
-
-
-def get_phenotype_metadata(
-        sparql_conn: SPARQLWrapper, name: str
-):
-    """Return info about a phenotype with a given NAME"""
-    __metadata_query = """
-$prefix
-
-CONSTRUCT {
-    ?phenotype ?pPredicate ?pValue .
-    ?phenotype ?publicationTerm ?publicationValue .
-    ?phenotype gn:speciesName ?speciesName .
-    ?phenotype gn:inbredSetName ?inbredSetBinomialName .
-    ?phenotype gn:datasetName ?datasetFullName .
-} WHERE {
-    ?phenotype ?pPredicate ?pValue .
-    OPTIONAL {
-        ?phenotype gn:phenotypeOfPublication ?publication .
-        ?publication ?publicationTerm ?publicationValue .
-    } .
-    OPTIONAL {
-        ?phenotype gn:phenotypeOfDataset ?dataset .
-        ?dataset gn:name ?datasetFullName .
-        ?dataset gn:datasetOfInbredSet ?inbredSet .
-        ?inbredSet gn:binomialName ?inbredSetBinomialName .
-        ?inbredSet gn:inbredSetOfSpecies ?species .
-        ?species gn:displayName ?speciesName .
-    } .
-    FILTER( ?phenotype = phenotype:$name ) .
-    MINUS {
-         ?phenotype rdf:type ?pValue .
-    }
-    MINUS {
-         ?publication rdf:type ?publicationValue .
-    }
-}
-"""
-    result: MonadicDict = MonadicDict()
-    for key, value in sparql_query(
-            sparql_conn,
-            Template(__metadata_query)
-            .substitute(name=name,
-                        prefix=RDF_PREFIXES)
-    )[0].items():
-        result[key] = value
-    return result
-- 
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