Merge 5c1dc8a into 919bb1b

CHANGELOG.md

@@ -2,6 +2,30 @@
 
 All notable changes to this project will be documented in this file. See [standard-version](https://github.com/conventional-changelog/standard-version) for commit guidelines.
 
+## [2.1.0](https://github.com/biothings/BioThings_Explorer_TRAPI/compare/v2.0.1...v2.1.0) (2021-04-02)
+
+
+### Features
+
+* :sparkles: add /test/query endpoint to support user specified smartapi spec ([c75e44d](https://github.com/biothings/BioThings_Explorer_TRAPI/commits/c75e44db6b79ccd2ef7b3f6f5cfd2cc448fd2814))
+* :sparkles: add additional node attributes to knowledge graph ([4fb93e3](https://github.com/biothings/BioThings_Explorer_TRAPI/commits/4fb93e37c8a16bc2ae9381747ba56a4e13aa33ed))
+* :sparkles: add cron job to periodically pull from /predicates endpoint ([94461b1](https://github.com/biothings/BioThings_Explorer_TRAPI/commits/94461b1a7c96b9b7ea66b4f5eb41f55b1a87dcb9))
+* :sparkles: add num_of_participants property for pathway ([3d9f820](https://github.com/biothings/BioThings_Explorer_TRAPI/commits/3d9f8209134a5625f2940500a65bf0fd277cb457))
+* :sparkles: have bte only use a specified number of APIs ([7fa1732](https://github.com/biothings/BioThings_Explorer_TRAPI/commits/7fa17323faa8e457a60a6df4dea508cc0489a061))
+* :sparkles: support restricting /predicates to only api names provide ([9260ec9](https://github.com/biothings/BioThings_Explorer_TRAPI/commits/9260ec969b4244f878f8a0a6c360b04a7dfde8dd))
+* :sparkles: update local predicates file and smartapi specs ([425093e](https://github.com/biothings/BioThings_Explorer_TRAPI/commits/425093ee3e96af0b969620805bf796ffe592a6fc))
+
+
+### Bug Fixes
+
+* :bug: add support for resolving protein ids ([500161a](https://github.com/biothings/BioThings_Explorer_TRAPI/commits/500161ac8357cb89739da58189f73afd1f91cb58))
+* :bug: fix api_response_transform bug ([4d911d6](https://github.com/biothings/BioThings_Explorer_TRAPI/commits/4d911d6aa91120775b3d2b70c71fbd1a8e2feefb))
+* :bug: fix cache related bug causing query failure ([3bd87ae](https://github.com/biothings/BioThings_Explorer_TRAPI/commits/3bd87aec0283b12dfe1676e9fc7e2b57dd51c41e))
+* :bug: fix id resolver failure issue ([eecbe4f](https://github.com/biothings/BioThings_Explorer_TRAPI/commits/eecbe4f163d535a3a0f589d98fbdc0d76d8dd86d))
+* :bug: fix missing biolink prefix issue ([153b601](https://github.com/biothings/BioThings_Explorer_TRAPI/commits/153b6011641263bd1d420defa0c881b62b0741a2))
+* :bug: fix typo ([5b32009](https://github.com/biothings/BioThings_Explorer_TRAPI/commits/5b320097664afb438f6b9e2fc11b7dc232069b3e))
+* :bug: fix wrong edge id in query results ([4bb1aa7](https://github.com/biothings/BioThings_Explorer_TRAPI/commits/4bb1aa7e3e98da8cd713f89236840f91439d00cb))
+
 ### [2.0.1](https://github.com/biothings/BioThings_Explorer_TRAPI/compare/v2.0.0...v2.0.1) (2021-03-12)
 
 

README.md

@@ -115,3 +115,13 @@ Public Docker image located at [link](https://hub.docker.com/repository/docker/b
 ## Usage
 
 `http://<HOST>:3000`
+
+## Test with local SmartAPI spec
+
+The TRAPI interface has `/test/query` endpoint which uses a SmartAPI spec stored at **test** folder named **smartapi.json**
+
+If you would like to use the `/test/query` endpoint to test a local SmartAPI spec, you can mount the your local folder containing the SmartAPI spec to the folder **/home/nodde/app/test** in the container. [Note: The SmartAPI spec must be named **smartapi.json**]
+
+You could do so using the following command:
+
+`docker run -p 3000:3000 -v [local_folder_contain_smartapi_spec]:/home/node/app/test -d biothings/bte_reasoner_api`

__test__/integration/controllers/predicates.test.js

@@ -36,8 +36,7 @@ describe("Test Predicates Module", () => {
 
         test("If invalid team name is provided, should return an empty list", async () => {
             const handler = new pred();
-            const res = await handler._loadMetaKG(undefined, 'Multiomics Provider1');
-            expect(res.ops).toEqual([])
+            await expect(handler._loadMetaKG(undefined, 'Multiomics Provider1')).rejects.toThrow('Failed to Load MetaKG');
         })
 
         test("By default, should return all ops", async () => {

__test__/integration/routes/metakg.test.js

@@ -85,4 +85,16 @@ describe("Test /metakg endpoint", () => {
                 expect(subjs).toEqual(['ChemicalSubstance']);
             })
     })
+
+    test("Should return info from TRAPI /predicates endpoint", async () => {
+        await request(app)
+            .get("/metakg")
+            .expect(200)
+            .expect('Content-Type', /json/)
+            .then((response) => {
+                expect(response.body).toHaveProperty("associations");
+                const apis = Array.from(new Set(response.body.associations.map(item => item.api.name)));
+                expect(apis).toContain("Automat Pharos");
+            })
+    })
 })

__test__/integration/routes/v1predicates_by_team.test.js

@@ -16,10 +16,13 @@ describe("Test /v1/team/{team_name}/predicates endpoint", () => {
     test("Query to Invalid team Should return 200 with empty response", async () => {
         await request(app)
             .get("/v1/team/wrong team/predicates")
-            .expect(200)
+            .expect(404)
             .expect('Content-Type', /json/)
             .then((response) => {
-                expect(response.body).toEqual({});
+                expect(response.body).toEqual({
+                    "error": "Unable to load predicates",
+                    "more_info": "Failed to Load MetaKG",
+                });
             })
     })