fix nameResolution (the API response format changed)

MaastrichtU-IDS · Nov 8, 2023 · f671a52 · f671a52
1 parent 5c05596
commit f671a52
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Showing 2 changed files with 24 additions and 24 deletions.
diff --git a/backend/app/api/ner.py b/backend/app/api/ner.py
@@ -114,22 +114,22 @@ async def get_entities_relations(
                 status_code=400,
                 detail="the SRI NameResolution API is down (https://name-resolution-sri.renci.org)",
             )
-        if len(name_res.keys()) > 0:
+        if len(name_res) > 0:
             # entity['curies'] = name_res
-            for curie, labels in name_res.items():
+            for match in name_res:
                 alt_label = None
-                if len(labels) > 1:
-                    alt_label = labels[1]
+                if len(match["synonyms"]) > 1:
+                    alt_label = match["synonyms"][0]
                 entity["curies"].append(
                     {
-                        "curie": curie,
-                        "label": labels[0],
+                        "curie": match["curie"],
+                        "label": match["label"],
                         "altLabel": alt_label,
                     }
                 )
-            entity["id_curie"] = list(name_res.keys())[0]
-            entity["id_label"] = name_res[list(name_res.keys())[0]][0]
-            entity["id_uri"] = curie_to_uri(list(name_res.keys())[0])
+            entity["id_curie"] = entity["curies"][0]["curie"]
+            entity["id_label"] = entity["curies"][0]["label"]
+            entity["id_uri"] = curie_to_uri(entity["id_curie"])
 
         # else:
         # If not ID found with NCATS API, check RXCUIS: https://rxnav.nlm.nih.gov/REST/rxcui.json?name=Xyrem

diff --git a/frontend/src/pages/annotate.tsx b/frontend/src/pages/annotate.tsx
@@ -198,12 +198,12 @@ export default function AnnotateText() {
             }
             const entityCuries: any = await getEntityCuries(label)
             ent['curies'] = []
-            if (entityCuries && Object.keys(entityCuries).length > 0) {
-              Object.keys(entityCuries).map((curie: any) => {
+            if (entityCuries.length > 0) {
+              entityCuries.map((match: any) => {
                 const addEnt: any = {
-                  curie: curie,
-                  label: entityCuries[curie][0],
-                  altLabel: entityCuries[curie][1]
+                  curie: match["curie"],
+                  label: match["label"],
+                  altLabel: match["synonyms"][0]
                 }
                 ent['curies'].push(addEnt)
               })
@@ -586,12 +586,12 @@ export default function AnnotateText() {
         props: []
       }
       const entityCuries = await getEntityCuries(text)
-      if (entityCuries && Object.keys(entityCuries).length > 0) {
-        Object.keys(entityCuries).map((curie: any) => {
+      if (entityCuries.length > 0) {
+        entityCuries.map((match: any) => {
           const addEnt: any = {
-            curie: curie,
-            label: entityCuries[curie][0],
-            altLabel: entityCuries[curie][1]
+            curie: match["curie"],
+            label: match["label"],
+            altLabel: match["synonyms"][0]
           }
           newEntity['curies'].push(addEnt)
         })
@@ -836,13 +836,13 @@ export default function AnnotateText() {
                     // and update the "curies" options from the result for the autocomplete
                     if (newInputValue && typeof newInputValue === 'string' && newInputValue.length > 2) {
                       const entityCuries = await getEntityCuries(newInputValue)
-                      if (entityCuries && Object.keys(entityCuries).length > 0) {
+                      if (entityCuries.length > 0) {
                         tagSelected.curies = []
-                        Object.keys(entityCuries).map((curie: any) => {
+                        entityCuries.map((match: any) => {
                           const addEnt: any = {
-                            curie: curie,
-                            label: entityCuries[curie][0],
-                            altLabel: entityCuries[curie][1]
+                            curie: match["curie"],
+                            label: match["label"],
+                            altLabel: match["synonyms"][0]
                           }
                           tagSelected.curies.push(addEnt)
                         })