Merge pull request #57 from biothings/typescript

Support workspace/typescript migration
biothings · Oct 24, 2023 · e8a3085 · e8a3085
2 parents d6723f5 + d7c096e
commit e8a3085
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diff --git a/.github/workflows/test_and_coverage.yml b/.github/workflows/test_and_coverage.yml
diff --git a/.github/workflows/test_ws_codecov.yml b/.github/workflows/test_ws_codecov.yml
@@ -16,18 +16,24 @@ jobs:
     - uses: actions/checkout@v3
       with:
         repository: biothings/biothings_explorer
+        ref: ${{ steps.branch-name.outputs.current_branch }}
 
-    - name: Use Node.js 16.x
-      uses: actions/setup-node@v1
+    - name: Use Node.js 18.x
+      uses: actions/setup-node@v3
       with:
-        node-version: 16.x
+        node-version: 18.x
 
-    - name: npm install, generate coverage report
+    - name: Use pnpm
+      uses: pnpm/action-setup@v2
+      with:
+        version: 8
+
+    - name: pnpm install, generate coverage report
       run: |
-        npm run clone
-        npm run git checkout ${{ steps.branch-name.outputs.current_branch }}
-        npm i || true && npm i
-        npm run test-cov --workspace=@biothings-explorer/api-response-transform
+        pnpm run clone
+        pnpm run git checkout ${{ steps.branch-name.outputs.current_branch }}
+        pnpm i
+        pnpm --filter api-response-transform test-cov
 
     - name: Send coverage report to codecov for visualization
       uses: codecov/codecov-action@v3

diff --git a/.gitignore b/.gitignore
@@ -47,6 +47,9 @@ typings/
 # TypeScript cache
 *.tsbuildinfo
 
+# Turbo cache
+.turbo
+
 # Optional npm cache directory
 .npm
 
@@ -105,4 +108,4 @@ dist
 
 kevin.js
 
-/built
+/built
diff --git a/README.md b/README.md
@@ -16,7 +16,7 @@ A NodeJS module to transform the JSON output from APIs into BioLink-compatible J
 ## Install
 
 ```sh
-npm i @biothings-explorer/api-response-transform
+pnpm i @biothings-explorer/api-response-transform
 ```
 
 ## Usage
@@ -144,7 +144,7 @@ This package is desgined to be used as a downstream consumer of [@biothings-expl
 ## Run tests
 
 ```sh
-npm run test
+pnpm run test
 ```
 
 ## Author

diff --git a/__test__/base_transformer.test.ts b/__test__/base_transformer.test.ts
@@ -1,121 +1,118 @@
-import {describe, expect, test} from '@jest/globals';
-
 import base_tf from "../src/transformers/transformer";
 import fs from "fs";
 import path from "path";
-import { JSONDoc } from '../src/json_transform/types';
+import { JSONDoc } from "../src/json_transform/types";
 
 describe("test base transformer", () => {
+  let response;
+  let input;
 
-    let response;
-    let input;
-
-    beforeEach(() => {
-        const response_path = path.resolve(__dirname, './data/ols/response.json');
-        response = JSON.parse(fs.readFileSync(response_path, { encoding: 'utf8' }));
-        const edge_path = path.resolve(__dirname, './data/ols/edge.json');
-        const edge = JSON.parse(fs.readFileSync(edge_path, { encoding: 'utf8' }));
-        input = {
-            response,
-            edge
-        }
-    })
+  beforeEach(() => {
+    const response_path = path.resolve(__dirname, "./data/ols/response.json");
+    response = JSON.parse(fs.readFileSync(response_path, { encoding: "utf8" }));
+    const edge_path = path.resolve(__dirname, "./data/ols/edge.json");
+    const edge = JSON.parse(fs.readFileSync(edge_path, { encoding: "utf8" }));
+    input = {
+      response,
+      edge,
+    };
+  });
 
-    test("Test pairInputWithAPIResponse function", () => {
-        const tf = new base_tf(input, {});
-        const res = tf.pairCurieWithAPIResponse();
-        expect(res).toHaveProperty("DOID:9562");
-        expect(res["DOID:9562"]).toHaveLength(1);
-    })
+  test("Test pairInputWithAPIResponse function", () => {
+    const tf = new base_tf(input, {});
+    const res = tf.pairCurieWithAPIResponse();
+    expect(res).toHaveProperty("DOID:9562");
+    expect(res["DOID:9562"]).toHaveLength(1);
+  });
 
-    test("Test wrap function if response is not an array", () => {
-        const tf = new base_tf(input, {});
-        const res = tf.wrap(response);
-        expect(res).toHaveProperty("_embedded");
-    })
+  test("Test wrap function if response is not an array", () => {
+    const tf = new base_tf(input, {});
+    const res = tf.wrap(response);
+    expect(res).toHaveProperty("_embedded");
+  });
 
-    test("Test wrap function if response is an array", () => {
-        const tf = new base_tf(input, {});
-        const fake = ["1"]
-        const res = tf.wrap(fake);
-        expect(res).toHaveProperty("data");
-        expect(res.data).toEqual(["1"])
-    })
+  test("Test wrap function if response is an array", () => {
+    const tf = new base_tf(input, {});
+    const fake = ["1"];
+    const res = tf.wrap(fake);
+    expect(res).toHaveProperty("data");
+    expect(res.data).toEqual(["1"]);
+  });
 
-    test("Test jsonTransform function", () => {
-        const tf = new base_tf(input, {});
-        const res: JSONDoc = tf.jsonTransform(response);
-        expect(res).toHaveProperty("has_subclass");
-        expect(res.has_subclass[0]).toHaveProperty("DOID");
-        expect(res.has_subclass[0].DOID).toEqual("DOID:0110596");
-        expect(res.has_subclass[0].name).toEqual("primary ciliary dyskinesia 21");
-        expect(res.has_subclass[0].description).toEqual([
-            "A primary ciliary dyskinesia that is characterized by autosomal recessive inheritance with a missing Nexin link, infantile onset of chronic sinopulmonary infections, and has_material_basis_in homozygous mutation in the DRC1 gene on chromosome 2p23."
-        ]);
-    })
+  test("Test jsonTransform function", () => {
+    const tf = new base_tf(input, {});
+    const res: JSONDoc = tf.jsonTransform(response);
+    expect(res).toHaveProperty("has_subclass");
+    expect(res.has_subclass[0]).toHaveProperty("DOID");
+    expect(res.has_subclass[0].DOID).toEqual("DOID:0110596");
+    expect(res.has_subclass[0].name).toEqual("primary ciliary dyskinesia 21");
+    expect(res.has_subclass[0].description).toEqual([
+      "A primary ciliary dyskinesia that is characterized by autosomal recessive inheritance with a missing Nexin link, infantile onset of chronic sinopulmonary infections, and has_material_basis_in homozygous mutation in the DRC1 gene on chromosome 2p23.",
+    ]);
+  });
 
-    test("Test _updatePublications function if pubmed id is prefixed", () => {
-        const tf = new base_tf(input, {});
-        const fake = {
-            ref_pmid: "PMID:1233"
-        }
-        const res = tf._updatePublications(fake);
-        expect(res).not.toHaveProperty('ref_pmid');
-        expect(res.publications).toEqual(["PMID:1233"]);
-    })
+  test("Test _updatePublications function if pubmed id is prefixed", () => {
+    const tf = new base_tf(input, {});
+    const fake = {
+      ref_pmid: "PMID:1233",
+    };
+    const res = tf._updatePublications(fake);
+    expect(res).not.toHaveProperty("ref_pmid");
+    expect(res.publications).toEqual(["PMID:1233"]);
+  });
 
-    test("Test _updatePublications function if pubmed id is NOT prefixed", () => {
-        const tf = new base_tf(input, {});
-        const fake = {
-            ref_pmid: 1233
-        }
-        const res = tf._updatePublications(fake);
-        expect(res).not.toHaveProperty('ref_pmid');
-        expect(res.publications).toEqual(["PMID:1233"])
-    })
+  test("Test _updatePublications function if pubmed id is NOT prefixed", () => {
+    const tf = new base_tf(input, {});
+    const fake = {
+      ref_pmid: 1233,
+    };
+    const res = tf._updatePublications(fake);
+    expect(res).not.toHaveProperty("ref_pmid");
+    expect(res.publications).toEqual(["PMID:1233"]);
+  });
 
-    test("Test _updatePublications function if pmc id is prefixed", () => {
-        const tf = new base_tf(input, {});
-        const fake = {
-            ref_pmcid: "PMCID:1233"
-        }
-        const res = tf._updatePublications(fake);
-        expect(res).not.toHaveProperty('ref_pmcid');
-        expect(res.publications).toEqual(["PMCID:1233"]);
-    })
+  test("Test _updatePublications function if pmc id is prefixed", () => {
+    const tf = new base_tf(input, {});
+    const fake = {
+      ref_pmcid: "PMCID:1233",
+    };
+    const res = tf._updatePublications(fake);
+    expect(res).not.toHaveProperty("ref_pmcid");
+    expect(res.publications).toEqual(["PMCID:1233"]);
+  });
 
-    test("Test _updatePublications function if pmc id is NOT prefixed", () => {
-        const tf = new base_tf(input, {});
-        const fake = {
-            ref_pmcid: 123
-        }
-        const res = tf._updatePublications(fake);
-        expect(res).not.toHaveProperty('ref_pmcid');
-        expect(res.publications).toEqual(["PMCID:123"])
-    })
+  test("Test _updatePublications function if pmc id is NOT prefixed", () => {
+    const tf = new base_tf(input, {});
+    const fake = {
+      ref_pmcid: 123,
+    };
+    const res = tf._updatePublications(fake);
+    expect(res).not.toHaveProperty("ref_pmcid");
+    expect(res.publications).toEqual(["PMCID:123"]);
+  });
 
-    test("Test extractObjectIDs function if output id type not in result", () => {
-        const tf = new base_tf(input, {});
-        const fake = {
-            kk: 1
-        };
-        const res = tf.extractObjectIDs(fake);
-        expect(res).toEqual([]);
-    })
+  test("Test extractObjectIDs function if output id type not in result", () => {
+    const tf = new base_tf(input, {});
+    const fake = {
+      kk: 1,
+    };
+    const res = tf.extractObjectIDs(fake);
+    expect(res).toEqual([]);
+  });
 
-    test("Test extractObjectIDs function if output id type is in result", () => {
-        const tf = new base_tf(input, {});
-        const fake = {
-            DOID: 1
-        };
-        const res = tf.extractObjectIDs(fake);
-        expect(res).toEqual(["DOID:1"]);
-    })
+  test("Test extractObjectIDs function if output id type is in result", () => {
+    const tf = new base_tf(input, {});
+    const fake = {
+      DOID: 1,
+    };
+    const res = tf.extractObjectIDs(fake);
+    expect(res).toEqual(["DOID:1"]);
+  });
 
-    test("Test formatRecords function if result is empty", async () => {
-        const tf = new base_tf(input, {});
-        const fake = {};
-        const res = await tf.formatRecords("NCBIGene:1017", fake);
-        expect(res).toEqual([]);
-    })
-})
+  test("Test formatRecords function if result is empty", async () => {
+    const tf = new base_tf(input, {});
+    const fake = {};
+    const res = await tf.formatRecords("NCBIGene:1017", fake);
+    expect(res).toEqual([]);
+  });
+});