build: migration to pnpm+turbo

biothings · Oct 18, 2023 · dcd6b1b · dcd6b1b
1 parent 1691f63
commit dcd6b1b
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Showing 14 changed files with 5,420 additions and 566 deletions.
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/__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([]);
+  });
+});