From 4da80ca9c17bdd28e2689895ab6acb1ec0c70d33 Mon Sep 17 00:00:00 2001
From: Munyoki Kilyungi
Date: Wed, 7 Jun 2023 09:39:58 +0300
Subject: Add publication end-point

* gn3/api/metadata.py: Import get_publication_metadata
(publication): New endpoint.
* gn3/db/rdf.py (get_dataset_metadata): New function.

Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
---
 gn3/api/metadata.py | 10 ++++++++++
 gn3/db/rdf.py       | 40 ++++++++++++++++++++++++++++++++++++++++
 2 files changed, 50 insertions(+)

(limited to 'gn3')

diff --git a/gn3/api/metadata.py b/gn3/api/metadata.py
index b54f032..1330b6f 100644
--- a/gn3/api/metadata.py
+++ b/gn3/api/metadata.py
@@ -9,6 +9,7 @@ from flask import current_app
 from SPARQLWrapper import SPARQLWrapper
 
 from gn3.db.rdf import get_dataset_metadata
+from gn3.db.rdf import get_publication_metadata
 from gn3.db.rdf import sparql_query
 from gn3.db.rdf import RDF_PREFIXES
 
@@ -31,9 +32,18 @@ def dataset(name):
         return jsonify({})
 
 
+@metadata.route("/publication/<name>", methods=["GET"])
+def publication(name):
+    """Fetch a dataset's metadata given it's ACCESSION_ID"""
     try:
+        if "unpublished" in name:
+            name = f"gn:{name}"
+        else:
+            name = f"publication:{name}"
         return jsonify(
+            get_publication_metadata(
                 SPARQLWrapper(current_app.config.get("SPARQL_ENDPOINT")),
+                name,
             ).data
         )
     # The virtuoso server is misconfigured or it isn't running at all
diff --git a/gn3/db/rdf.py b/gn3/db/rdf.py
index 5b62b46..c559774 100644
--- a/gn3/db/rdf.py
+++ b/gn3/db/rdf.py
@@ -156,6 +156,46 @@ CONSTRUCT {
         ):
             response[key] = value.map(get_url_local_name)  # type: ignore
     return response
+
+
+def get_publication_metadata(
+        sparql_conn: SPARQLWrapper, name: str
+):
+    """Return info about a publication with a given NAME"""
+    __metadata_query = """
+$prefix
+
+CONSTRUCT {
+    gn:publication ?publicationTerm ?publicationValue .
+    gn:publication ?predicate ?subject .
+} WHERE {
+    $name ?publicationTerm ?publicationValue .
+    ?publication ?publicationTerm ?publicationValue .
+    OPTIONAL {
+       ?subject ?predicate ?publication .
+    } .
+    VALUES ?publicationTerm {
+        gn:pubMedId gn:title gn:volume
+        gn:abstract gn:pages gn:month gn:year gn:author
+    }
+    VALUES ?predicate {
+        gn:phenotypeOfPublication
+    }
+}
+"""
+    response: MonadicDict = MonadicDict()
+
+    for key, value in sparql_query(
+            sparql_conn,
+            Template(__metadata_query)
+            .substitute(
+                prefix=RDF_PREFIXES,
+                name=name
+            )
+    )[0].items():
+        response[key] = value
+        if isinstance(value, str) and not key.endswith("pubMedId"):
+            response[key] = value.map(get_url_local_name)  # type: ignore
     return response
 
 
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