Merge pull request #177 from biothings/up_dep_1

biothings · May 13, 2021 · 5087c27 · 5087c27
2 parents 7bca881 + 2a41515
commit 5087c27
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Showing 31 changed files with 87 additions and 87 deletions.
diff --git a/__test__/integration/TRAPIv1.test.js b/__test__/integration/TRAPIv1.test.js
@@ -16,9 +16,9 @@ describe("Testing endpoints", () => {
     const query_without_category = JSON.parse(fs.readFileSync(path.join(example_foler, 'query_without_input_category.json')))
     const expand_node = JSON.parse(fs.readFileSync(path.join(example_foler, 'query_with_node_to_be_expanded.json')))
 
-    test("GET /v1/predicates", async () => {
+    test("GET /v1/meta_knowledge_graph", async () => {
         await request(app)
-            .get("/v1/predicates")
+            .get("/v1/meta_knowledge_graph")
             .expect(200)
             .expect('Content-Type', /json/)
             .then((response) => {
@@ -28,9 +28,9 @@ describe("Testing endpoints", () => {
             })
     })
 
-    test("GET /v1/smartapi/{smartapi_id}/predicates", async () => {
+    test("GET /v1/smartapi/{smartapi_id}/meta_knowledge_graph", async () => {
         await request(app)
-            .get("/v1/smartapi/978fe380a147a8641caf72320862697b/predicates")
+            .get("/v1/smartapi/978fe380a147a8641caf72320862697b/meta_knowledge_graph")
             .expect(200)
             .expect('Content-Type', /json/)
             .then((response) => {

diff --git a/__test__/integration/routes/metakg.test.js b/__test__/integration/routes/metakg.test.js
@@ -86,7 +86,7 @@ describe("Test /metakg endpoint", () => {
             })
     })
 
-    test("Should return info from TRAPI /predicates endpoint", async () => {
+    test("Should return info from TRAPI /meta_knowledge_graph endpoint", async () => {
         await request(app)
             .get("/metakg")
             .expect(200)

diff --git a/__test__/integration/routes/v1predicates.test.js b/__test__/integration/routes/v1predicates.test.js
@@ -1,10 +1,10 @@
 const app = require("../../../src/app");
 const request = require('supertest');
 
-describe("Test /v1/predicates endpoint", () => {
+describe("Test /v1/meta_knowledge_graph endpoint", () => {
     test("Should return 200 with valid response", async () => {
         await request(app)
-            .get("/v1/predicates")
+            .get("/v1/meta_knowledge_graph")
             .expect(200)
             .expect('Content-Type', /json/)
             .then((response) => {

diff --git a/__test__/integration/routes/v1predicates_by_api.test.js b/__test__/integration/routes/v1predicates_by_api.test.js
@@ -1,10 +1,10 @@
 const app = require("../../../src/app");
 const request = require('supertest');
 
-describe("Test /v1/smartapi/{smartapi_id}/predicates endpoint", () => {
+describe("Test /v1/smartapi/{smartapi_id}/meta_knowledge_graph endpoint", () => {
     test("Query to Text Mining Targeted Association API Should return 200 with valid response", async () => {
         await request(app)
-            .get("/v1/smartapi/978fe380a147a8641caf72320862697b/predicates")
+            .get("/v1/smartapi/978fe380a147a8641caf72320862697b/meta_knowledge_graph")
             .expect(200)
             .expect('Content-Type', /json/)
             .then((response) => {
@@ -15,7 +15,7 @@ describe("Test /v1/smartapi/{smartapi_id}/predicates endpoint", () => {
 
     test("Query to Invalid API Should return 404 with error message included", async () => {
         await request(app)
-            .get("/v1/smartapi/78fe380a147a8641caf72320862697b/predicates")
+            .get("/v1/smartapi/78fe380a147a8641caf72320862697b/meta_knowledge_graph")
             .expect(404)
             .expect('Content-Type', /json/)
             .then((response) => {

diff --git a/__test__/integration/routes/v1predicates_by_team.test.js b/__test__/integration/routes/v1predicates_by_team.test.js
@@ -1,10 +1,10 @@
 const app = require("../../../src/app");
 const request = require('supertest');
 
-describe("Test /v1/team/{team_name}/predicates endpoint", () => {
+describe("Test /v1/team/{team_name}/meta_knowledge_graph endpoint", () => {
     test("Query to Text Mining team Should return 200 with valid response", async () => {
         await request(app)
-            .get("/v1/team/Text Mining Provider/predicates")
+            .get("/v1/team/Text Mining Provider/meta_knowledge_graph")
             .expect(200)
             .expect('Content-Type', /json/)
             .then((response) => {
@@ -15,7 +15,7 @@ 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")
+            .get("/v1/team/wrong team/meta_knowledge_graph")
             .expect(404)
             .expect('Content-Type', /json/)
             .then((response) => {

diff --git a/__test__/unittest/routes/predicates.test.js b/__test__/unittest/routes/predicates.test.js
@@ -7,15 +7,15 @@ jest.mock('../../../src/controllers/predicates');
 
 
 
-describe("Test /v1/predicates endpoint", () => {
+describe("Test /v1/meta_knowledge_graph endpoint", () => {
 
 
     test("Should return 404 with valid response", async () => {
         pred.mockImplementation(() => {
             throw new PredicatesLoadingError();
         })
         await request(app)
-            .get("/v1/predicates")
+            .get("/v1/meta_knowledge_graph")
             .expect(404)
             .expect('Content-Type', /json/)
             .then(res => {

diff --git a/__test__/unittest/routes/predicates_team.test.js b/__test__/unittest/routes/predicates_team.test.js
@@ -7,15 +7,15 @@ jest.mock('../../../src/controllers/predicates');
 
 
 
-describe("Test /v1/predicates endpoint", () => {
+describe("Test /v1/meta_knowledge_graph endpoint", () => {
 
 
     test("Should return 404 with valid response", async () => {
         pred.mockImplementation(() => {
             throw new PredicatesLoadingError();
         })
         await request(app)
-            .get("/v1/team/Text Mining Provider/predicates")
+            .get("/v1/team/Text Mining Provider/meta_knowledge_graph")
             .expect(404)
             .expect('Content-Type', /json/)
             .then(res => {

diff --git a/docs/smartapi.yaml b/docs/smartapi.yaml
@@ -113,7 +113,7 @@ paths:
         return all associations
       tags:
       - metadata
-  /predicates:
+  /meta_knowledge_graph:
     get:
       responses:
         '200':
@@ -139,7 +139,7 @@ paths:
       tags:
       - metadata
       - 0.9.2
-  /v1/predicates:
+  /v1/meta_knowledge_graph:
     get:
       tags:
         - predicates
@@ -166,7 +166,7 @@ paths:
                     'biolink:Gene':
                       - biolink:directly_interacts_with
                       - biolink:decreases_activity_of
-  /v1/smartapi/{smartapi_id}/predicates:
+  /v1/smartapi/{smartapi_id}/meta_knowledge_graph:
     get:
       tags:
         - predicates
@@ -201,7 +201,7 @@ paths:
                     'biolink:Gene':
                       - biolink:directly_interacts_with
                       - biolink:decreases_activity_of
-  /v1/team/{team_name}/predicates:
+  /v1/team/{team_name}/meta_knowledge_graph:
     get:
       tags:
         - predicates

diff --git a/examples/v1/branched_query.json b/examples/v1/branched_query.json
@@ -3,14 +3,14 @@
         "query_graph": {
             "nodes": {
                 "n0": {
-                    "category": "biolink:Disease",
-                    "id": "MONDO:0005737"
+                    "categories": "biolink:Disease",
+                    "ids": "MONDO:0005737"
                 },
                 "n1": {
-                    "category": "biolink:Gene"
+                    "categories": "biolink:Gene"
                 },
                 "n2": {
-                    "category": "biolink:ChemicalSubstance"
+                    "categories": "biolink:ChemicalSubstance"
                 }
             },
             "edges": {

diff --git a/examples/v1/invalid/query_graph_with_edges_not_specified.json b/examples/v1/invalid/query_graph_with_edges_not_specified.json
@@ -3,11 +3,11 @@
         "query_graph": {
             "nodes": {
                 "n0": {
-                    "category": "biolink:Gene",
-                    "id": "NCBIGene:1017"
+                    "categories": "biolink:Gene",
+                    "ids": "NCBIGene:1017"
                 },
                 "n1": {
-                    "category": "biolink:ChemicalSubstance"
+                    "categories": "biolink:ChemicalSubstance"
                 }
             },
             "edges": {}

diff --git a/examples/v1/invalid/query_graph_with_nodes_and_edges_not_match.json b/examples/v1/invalid/query_graph_with_nodes_and_edges_not_match.json
@@ -3,18 +3,18 @@
         "query_graph": {
             "nodes": {
                 "n0": {
-                    "category": "biolink:Gene",
-                    "id": "NCBIGene:1017"
+                    "categories": "biolink:Gene",
+                    "ids": "NCBIGene:1017"
                 },
                 "n2": {
-                    "category": "biolink:ChemicalSubstance"
+                    "categories": "biolink:ChemicalSubstance"
                 }
             },
             "edges": {
                 "e01": {
                     "subject": "n0",
                     "object": "n1",
-                    "predicate": "biolink:physically_interacts_with"
+                    "predicates": "biolink:physically_interacts_with"
                 }
             }
         }

diff --git a/examples/v1/invalid/query_graph_with_nodes_not_specified.json b/examples/v1/invalid/query_graph_with_nodes_not_specified.json
@@ -6,7 +6,7 @@
                 "e01": {
                     "subject": "n0",
                     "object": "n1",
-                    "predicate": "biolink:physically_interacts_with"
+                    "predicates": "biolink:physically_interacts_with"
                 }
             }
         }

diff --git a/examples/v1/multiomics/clinical_risk_kp/query_attribute_to_disease.json b/examples/v1/multiomics/clinical_risk_kp/query_attribute_to_disease.json
@@ -3,11 +3,11 @@
         "query_graph": {
             "nodes": {
                 "n0": {
-                    "category": "biolink:Attribute",
-                    "id": "NCIT:C28421"
+                    "categories": "biolink:Attribute",
+                    "ids": "NCIT:C28421"
                 },
                 "n3": {
-                    "category": "biolink:DiseaseOrPhenotypicFeature"
+                    "categories": "biolink:DiseaseOrPhenotypicFeature"
                 }
             },
             "edges": {

diff --git a/examples/v1/multiomics/clinical_risk_kp/query_disease_to_disease.json b/examples/v1/multiomics/clinical_risk_kp/query_disease_to_disease.json
@@ -3,11 +3,11 @@
         "query_graph": {
             "nodes": {
                 "n0": {
-                    "category": "biolink:DiseaseOrPhenotypicFeature",
-                    "id": "MONDO:0005015"
+                    "categories": "biolink:DiseaseOrPhenotypicFeature",
+                    "ids": "MONDO:0005015"
                 },
                 "n3": {
-                    "category": "biolink:DiseaseOrPhenotypicFeature"
+                    "categories": "biolink:DiseaseOrPhenotypicFeature"
                 }
             },
             "edges": {

diff --git a/examples/v1/multiomics/clinical_risk_kp/query_drug_to_disease.json b/examples/v1/multiomics/clinical_risk_kp/query_drug_to_disease.json
@@ -3,11 +3,11 @@
         "query_graph": {
             "nodes": {
                 "n0": {
-                    "category": "biolink:Drug",
-                    "id": "CHEBI:86990"
+                    "categories": "biolink:Drug",
+                    "ids": "CHEBI:86990"
                 },
                 "n3": {
-                    "category": "biolink:Disease"
+                    "categories": "biolink:Disease"
                 }
             },
             "edges": {

diff --git a/examples/v1/multiomics/clinical_risk_kp/query_observation_to_disease.json b/examples/v1/multiomics/clinical_risk_kp/query_observation_to_disease.json
@@ -3,11 +3,11 @@
         "query_graph": {
             "nodes": {
                 "n0": {
-                    "category": "biolink:Observation",
-                    "id": "NCIT:C110935"
+                    "categories": "biolink:Observation",
+                    "ids": "NCIT:C110935"
                 },
                 "n3": {
-                    "category": "biolink:DiseaseOrPhenotypicFeature"
+                    "categories": "biolink:DiseaseOrPhenotypicFeature"
                 }
             },
             "edges": {

diff --git a/examples/v1/query_chemicals_physically_interacts_with_genes.json b/examples/v1/query_chemicals_physically_interacts_with_genes.json
@@ -3,18 +3,18 @@
         "query_graph": {
             "nodes": {
                 "n0": {
-                    "category": "biolink:Gene",
-                    "id": "NCBIGene:1017"
+                    "categories": "biolink:Gene",
+                    "ids": "NCBIGene:1017"
                 },
                 "n1": {
-                    "category": "biolink:ChemicalSubstance"
+                    "categories": "biolink:ChemicalSubstance"
                 }
             },
             "edges": {
                 "e01": {
                     "subject": "n0",
                     "object": "n1",
-                    "predicate": "biolink:physically_interacts_with"
+                    "predicates": "biolink:physically_interacts_with"
                 }
             }
         }

diff --git a/examples/v1/query_disease_has_phenotype.json b/examples/v1/query_disease_has_phenotype.json
@@ -3,18 +3,18 @@
         "query_graph": {
             "nodes": {
                 "n0": {
-                    "category": "biolink:Disease",
-                    "id": "MONDO:0016575"
+                    "categories": "biolink:Disease",
+                    "ids": "MONDO:0016575"
                 },
                 "n1": {
-                    "category": "biolink:PhenotypicFeature"
+                    "categories": "biolink:PhenotypicFeature"
                 }
             },
             "edges": {
                 "e01": {
                     "subject": "n0",
                     "object": "n1",
-                    "predicate": "biolink:has_phenotype"
+                    "predicates": "biolink:has_phenotype"
                 }
             }
         }

diff --git a/examples/v1/query_genes_relate_to_disease.json b/examples/v1/query_genes_relate_to_disease.json
@@ -3,11 +3,11 @@
         "query_graph": {
             "nodes": {
                 "n0": {
-                    "category": "biolink:Disease",
-                    "id": "MONDO:0005737"
+                    "categories": "biolink:Disease",
+                    "ids": "MONDO:0005737"
                 },
                 "n1": {
-                    "category": "biolink:Gene"
+                    "categories": "biolink:Gene"
                 }
             },
             "edges": {

diff --git a/examples/v1/query_multihop_disease_gene_chemical.json b/examples/v1/query_multihop_disease_gene_chemical.json
@@ -3,14 +3,14 @@
         "query_graph": {
             "nodes": {
                 "n0": {
-                    "category": "biolink:Disease",
-                    "id": "MONDO:0005737"
+                    "categories": "biolink:Disease",
+                    "ids": "MONDO:0005737"
                 },
                 "n1": {
-                    "category": "biolink:Gene"
+                    "categories": "biolink:Gene"
                 },
                 "n2": {
-                    "category": "biolink:ChemicalSubstance"
+                    "categories": "biolink:ChemicalSubstance"
                 }
             },
             "edges": {

diff --git a/examples/v1/query_with_category_as_list.json b/examples/v1/query_with_category_as_list.json
@@ -3,11 +3,11 @@
         "query_graph": {
             "nodes": {
                 "n0": {
-                    "id": "UMLS:C0008780",
-                    "category": "biolink:PhenotypicFeature"
+                    "ids": "UMLS:C0008780",
+                    "categories": "biolink:PhenotypicFeature"
                 },
                 "n1": {
-                    "category": [
+                    "categories": [
                         "biolink:Disease",
                         "biolink:BiologicalProcess",
                         "biolink:Pathway"