Merge 9ffdc14 into 78c4320

biothings · Jun 16, 2021 · 5fbc8dc · 5fbc8dc
2 parents 78c4320 + 9ffdc14
commit 5fbc8dc
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Showing 6 changed files with 42 additions and 19 deletions.
diff --git a/__test__/integration/TRAPIv1.1.test.js b/__test__/integration/TRAPIv1.1.test.js
@@ -202,7 +202,7 @@ describe("Testing v1.1 endpoints", () => {
                 expect(response.body.message.knowledge_graph).toHaveProperty("edges");
                 expect(response.body.message.knowledge_graph.nodes).toHaveProperty("MONDO:0016575");
                 expect(response.body.message.knowledge_graph.nodes).toHaveProperty("UMLS:C0008780");
-                expect(response.body.message.knowledge_graph.nodes["UMLS:C0008780"]).toHaveProperty("category", "biolink:PhenotypicFeature");
+                expect(response.body.message.knowledge_graph.nodes["UMLS:C0008780"]).toHaveProperty("categories", ["biolink:PhenotypicFeature"]);
             })
     })
 

diff --git a/data/predicates.json b/data/predicates.json
diff --git a/data/smartapi_specs.json b/data/smartapi_specs.json
diff --git a/package-lock.json b/package-lock.json
diff --git a/package.json b/package.json
@@ -43,7 +43,7 @@
     "supertest": "^6.1.3"
   },
   "dependencies": {
-    "@biothings-explorer/query_graph_handler": "^1.17.1",
+    "@biothings-explorer/query_graph_handler": "^1.17.3",
     "@biothings-explorer/smartapi-kg": "^3.8.1",
     "axios": "^0.21.1",
     "body-parser": "^1.19.0",

diff --git a/src/controllers/cron/update_local_smartapi.js b/src/controllers/cron/update_local_smartapi.js
@@ -6,6 +6,7 @@ const cron = require('node-cron');
 
 const getTRAPIWithPredicatesEndpoint = (specs) => {
     const trapi = [];
+    let special_cases = []
     specs.map((spec) => {
         try {
             if (
@@ -16,7 +17,9 @@ const getTRAPIWithPredicatesEndpoint = (specs) => {
                 "/query" in spec.paths &&
                 "x-trapi" in spec.info &&
                 spec.servers.length &&
-                "/predicates" in spec.paths || "/meta_knowledge_graph" in spec.paths
+                "/predicates" in spec.paths || 
+                "/meta_knowledge_graph" in spec.paths ||
+                "/1.1/meta_knowledge_graph" in spec.paths
             ) {
                 let api = {
                     association: {
@@ -46,10 +49,25 @@ const getTRAPIWithPredicatesEndpoint = (specs) => {
                     //1.1
                     api['predicates_path'] = "/meta_knowledge_graph";
                     trapi.push(api);
+                }
+                if (
+                    "/1.1/meta_knowledge_graph" in spec.paths &&
+                    Object.prototype.hasOwnProperty.call(spec.info["x-trapi"], "version") &&
+                    spec.info["x-trapi"].version.includes("1.1")
+                ) {
+                    //1.1
+                    api['predicates_path'] = "/1.1/meta_knowledge_graph";
+                    trapi.push(api);
+                    special_cases.push({name: spec.info['title'], id: spec['_id']})
                 }else if("/predicates" in spec.paths ){
                     //1.0
                     api['predicates_path'] = "/predicates";
                     trapi.push(api);
+                }else{
+                    debug(
+                        `[error]: Unable to parse spec, ${spec ? spec.info.title : spec
+                        }. Endpoint required not found.`
+                    );
                 }
             }
         } catch (err) {
@@ -59,6 +77,12 @@ const getTRAPIWithPredicatesEndpoint = (specs) => {
             );
         }
     });
+    if (special_cases.length) {
+        debug(
+            `Found some APIs with unexpected endpoint "/1.1/meta_knowledge_graph":`
+        );
+        debug(`${JSON.stringify(special_cases)}`);
+    }
     return trapi;
 }
 
@@ -71,7 +95,7 @@ const constructQueryUrl = (serverUrl, path) => {
 
 const getPredicatesFromGraphData = (predicate_endpoint, data) => {
     //if /predicates just return normal response
-    if (predicate_endpoint !== '/meta_knowledge_graph') {
+    if (!['/meta_knowledge_graph', '/1.1/meta_knowledge_graph'].includes(predicate_endpoint)) {
         return data
     }
     // transform graph data to legacy format > object.subject : predicates