Rename @annotations to @provenance

MaastrichtU-IDS · Sep 21, 2023 · 04c76a8 · 04c76a8
1 parent d7ccb17
commit 04c76a8
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Showing 3 changed files with 7 additions and 6 deletions.
diff --git a/astro-frontend/src/app/PageAnnotate.tsx b/astro-frontend/src/app/PageAnnotate.tsx
@@ -444,7 +444,7 @@ export default function PageAnnotate() {
     return {
       '@context': genericContext,
       '@graph': stmtJsonld,
-      '@annotations': {
+      '@provenance': {
         '@context': {
           tao: 'http://pubannotation.org/ontology/tao.owl#',
           rdfs: 'http://www.w3.org/2000/01/rdf-schema#'

diff --git a/backend/app/api/nanopub.py b/backend/app/api/nanopub.py
@@ -54,7 +54,7 @@ def get_np_config(user_id: str) -> NanopubConf:
     "rdf:subject": {"@id": "drugbank:DB00001"},
     "rdf:predicate": {"@id": "biolink:treats"},
     "rdf:object": {"@id": "MONDO:0004975"},
-    # "@annotations": {
+    # "@provenance": {
     #     "@context": {
     #         "ml": "https://w3id.org/YOUR_ML_SCHEMA/"
     #     },
@@ -115,9 +115,9 @@ async def publish_assertion(
     # nanopub_rdf = jsonld.expand(nanopub_rdf)
     # nanopub_rdf = json.dumps(nanopub_rdf, ensure_ascii=False).encode("utf-8")
 
-    annotations_rdf = nanopub_rdf["@annotations"]
+    annotations_rdf = nanopub_rdf["@provenance"]
 
-    del nanopub_rdf["@annotations"]
+    del nanopub_rdf["@provenance"]
     nanopub_rdf = json.dumps(nanopub_rdf)
 
     g = Graph()
@@ -173,7 +173,8 @@ async def publish_assertion(
 
     if annotations_rdf:
         # Make sure annotations have the assertion as subject
-        annotations_rdf["@id"] = np.assertion.identifier
+        if "@graph" not in annotations_rdf and "@id" not in annotations_rdf:
+            annotations_rdf["@id"] = str(np.assertion.identifier)
         np.provenance.parse(data=annotations_rdf, format="json-ld")
     if source:
         np.provenance.add((np.assertion.identifier, PROV.hadPrimarySource, URIRef(source)))

diff --git a/frontend/src/pages/annotate.tsx b/frontend/src/pages/annotate.tsx
@@ -463,7 +463,7 @@ export default function AnnotateText() {
     return {
       '@context': genericContext,
       '@graph': stmtJsonld,
-      '@annotations': {
+      '@provenance': {
         '@context': {
           tao: 'http://pubannotation.org/ontology/tao.owl#',
           rdfs: 'http://www.w3.org/2000/01/rdf-schema#'