From 6e58cb5ffe3b145aa6ba9b7a54672e7a7f18a0b7 Mon Sep 17 00:00:00 2001
From: Munyoki Kilyungi
Date: Wed, 12 Oct 2022 15:50:33 +0300
Subject: Re-implement RDF related code to use monads in its own module

* gn3/api/general.py: Replace gn3.db.datasets import with gn3.db.rdf.
(dataset_metadata) <jsonify>: Replace datasets.dataset_metadata with
rdf.get_dataset_metadata.
* gn3/db/datasets.py: Remove unused imports.
(sparql_query, dataset_metadata): Delete.
* gn3/db/rdf.py: (sparql_query, get_dataset_metadata): New functions.
---
 gn3/db/datasets.py | 104 ++---------------------------------------------------
 1 file changed, 2 insertions(+), 102 deletions(-)

(limited to 'gn3/db/datasets.py')

diff --git a/gn3/db/datasets.py b/gn3/db/datasets.py
index 1d2f071..bc5467b 100644
--- a/gn3/db/datasets.py
+++ b/gn3/db/datasets.py
@@ -1,11 +1,8 @@
 """
 This module contains functions relating to specific trait dataset manipulation
 """
-import re
-from string import Template
-from typing import Any, Dict, List, Optional
-from SPARQLWrapper import JSON, SPARQLWrapper
-from gn3.settings import SPARQL_ENDPOINT
+from typing import Any
+
 
 def retrieve_probeset_trait_dataset_name(
         threshold: int, name: str, connection: Any):
@@ -264,100 +261,3 @@ def retrieve_trait_dataset(trait_type, trait, threshold, conn):
         **dataset_fns[trait_type](),
         **group
     }
-
-def sparql_query(query: str) -> List[Dict[str, Any]]:
-    """Run a SPARQL query and return the bound variables."""
-    sparql = SPARQLWrapper(SPARQL_ENDPOINT)
-    sparql.setQuery(query)
-    sparql.setReturnFormat(JSON)
-    return sparql.queryAndConvert()['results']['bindings']  # type: ignore
-
-def dataset_metadata(accession_id: str) -> Optional[Dict[str, Any]]:
-    """Return info about dataset with ACCESSION_ID."""
-    # Check accession_id to protect against query injection.
-    # TODO: This function doesn't yet return the names of the actual dataset files.
-    pattern = re.compile(r'GN\d+', re.ASCII)
-    if not pattern.fullmatch(accession_id):
-        return None
-    # KLUDGE: We split the SPARQL query because virtuoso is very slow on a
-    # single large query.
-    queries = ["""
-PREFIX gn: <http://genenetwork.org/>
-SELECT ?name ?dataset_group ?status ?title ?geo_series
-WHERE {
-  ?dataset gn:accessionId "$accession_id" ;
-           rdf:type gn:dataset ;
-           gn:name ?name .
-  OPTIONAL { ?dataset gn:datasetGroup ?dataset_group } .
-  # FIXME: gn:datasetStatus should not be optional. But, some records don't
-  # have it.
-  OPTIONAL { ?dataset gn:datasetStatus ?status } .
-  OPTIONAL { ?dataset gn:title ?title } .
-  OPTIONAL { ?dataset gn:geoSeries ?geo_series } .
-}
-""",
-               """
-PREFIX gn: <http://genenetwork.org/>
-SELECT ?platform_name ?normalization_name ?species_name ?inbred_set_name ?tissue_name
-WHERE {
-  ?dataset gn:accessionId "$accession_id" ;
-           rdf:type gn:dataset ;
-           gn:normalization / gn:name ?normalization_name ;
-           gn:datasetOfSpecies / gn:menuName ?species_name ;
-           gn:datasetOfInbredSet / gn:name ?inbred_set_name .
-  OPTIONAL { ?dataset gn:datasetOfTissue / gn:name ?tissue_name } .
-  OPTIONAL { ?dataset gn:datasetOfPlatform / gn:name ?platform_name } .
-}
-""",
-               """
-PREFIX gn: <http://genenetwork.org/>
-SELECT ?specifics ?summary ?about_cases ?about_tissue ?about_platform
-       ?about_data_processing ?notes ?experiment_design ?contributors
-       ?citation ?acknowledgment
-WHERE {
-  ?dataset gn:accessionId "$accession_id" ;
-           rdf:type gn:dataset .
-  OPTIONAL { ?dataset gn:specifics ?specifics . }
-  OPTIONAL { ?dataset gn:summary ?summary . }
-  OPTIONAL { ?dataset gn:aboutCases ?about_cases . }
-  OPTIONAL { ?dataset gn:aboutTissue ?about_tissue . }
-  OPTIONAL { ?dataset gn:aboutPlatform ?about_platform . }
-  OPTIONAL { ?dataset gn:aboutDataProcessing ?about_data_processing . }
-  OPTIONAL { ?dataset gn:notes ?notes . }
-  OPTIONAL { ?dataset gn:experimentDesign ?experiment_design . }
-  OPTIONAL { ?dataset gn:contributors ?contributors . }
-  OPTIONAL { ?dataset gn:citation ?citation . }
-  OPTIONAL { ?dataset gn:acknowledgment ?acknowledgment . }
-}
-"""]
-    result: Dict[str, Any] = {'accession_id': accession_id,
-                              'investigator': {}}
-    query_result = {}
-    for query in queries:
-        if sparql_result := sparql_query(Template(query).substitute(accession_id=accession_id)):
-            query_result.update(sparql_result[0])
-        else:
-            return None
-    for key, value in query_result.items():
-        result[key] = value['value']
-    investigator_query_result = sparql_query(Template("""
-PREFIX gn: <http://genenetwork.org/>
-SELECT ?name ?address ?city ?state ?zip ?phone ?email ?country ?homepage
-WHERE {
-  ?dataset gn:accessionId "$accession_id" ;
-           rdf:type gn:dataset ;
-           gn:datasetOfInvestigator ?investigator .
-  OPTIONAL { ?investigator foaf:name ?name . }
-  OPTIONAL { ?investigator gn:address ?address . }
-  OPTIONAL { ?investigator gn:city ?city . }
-  OPTIONAL { ?investigator gn:state ?state . }
-  OPTIONAL { ?investigator gn:zipCode ?zip . }
-  OPTIONAL { ?investigator foaf:phone ?phone . }
-  OPTIONAL { ?investigator foaf:mbox ?email . }
-  OPTIONAL { ?investigator gn:country ?country . }
-  OPTIONAL { ?investigator foaf:homepage ?homepage . }
-}
-""").substitute(accession_id=accession_id))[0]
-    for key, value in investigator_query_result.items():
-        result['investigator'][key] = value['value']
-    return result
-- 
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