Issue 91

CONTRIBUTING.md

@@ -67,3 +67,23 @@ Or
 Nx: run-many
 publish
 Execute: nx run-many --target=publish
+
+## Other
+
+### Running OVE unit tests
+
+In addition to cypress e2e tests, there are a few unit tests in OVE. To run them:
+
+- You must start the dev server, even if the tests don't load the page.
+- You have to be in the directory `packages/ove`
+
+```bash
+# Run the dev server (you can do this from any directory)
+yarn nx run ove:start
+
+# Move the package directory
+cd packages/ove
+
+# Run the unit test
+yarn cypress run --spec cypress/e2e/unit/getStructuredBases.spec.js
+```

cypress.config.ts

@@ -18,15 +18,23 @@ export default ({
         runMode: 3,
         openMode: 0
       },
-      // setupNodeEvents(on, config) {
-      //   on(
-      //     "file:preprocessor",
-      //     vitePreprocessor({
-      //       // configFile: "./vite.config.js",
-      //       configFile: path.resolve(__dirname, "./vite.config.js"),
-      //       mode: "development"
-      //     })
-      //   );
+      // Allow logging in the Cypress test runner
+      // calling cy.task('log', 'message') will log the message to the console
+      setupNodeEvents(on, config) {
+        on("task", {
+          log(message) {
+            console.log(message);
+            return null;
+          }
+        });
+        // on(
+        //   "file:preprocessor",
+        //   vitePreprocessor({
+        //     // configFile: "./vite.config.js",
+        //     configFile: path.resolve(__dirname, "./vite.config.js"),
+        //     mode: "development"
+        //   })
+      },
 
       //   // return require("./cypress/plugins/index.js")(on, config);
       // },

packages/ove/cypress/e2e/unit/getStructuredBases.spec.js

@@ -0,0 +1,81 @@
+import { getStructuredBases } from "../../../src/RowItem/StackedAnnotations/getStructuredBases";
+
+describe("getStructuredBases", () => {
+  it.skip("works for non origin-spanning case", () => {
+    const fullSequence = "ACGTCCACGT";
+    let primerSeq = "ACGT";
+    const start = 0;
+    const end = 3;
+    let { allBasesWithMetaData } = getStructuredBases({
+      annotationRange: { start, end },
+      forward: true,
+      bases: primerSeq,
+      start: start,
+      end: end,
+      fullSequence,
+      primerBindsOn: "3prime",
+      sequenceLength: fullSequence.length
+    });
+
+    let expected = [true, true, true, true];
+    assert.deepEqual(
+      allBasesWithMetaData.map(({ isMatch }) => isMatch),
+      expected
+    );
+
+    primerSeq = "CCGT";
+    ({ allBasesWithMetaData } = getStructuredBases({
+      annotationRange: { start, end },
+      forward: true,
+      bases: primerSeq,
+      start: start,
+      end: end,
+      fullSequence,
+      primerBindsOn: "3prime",
+      sequenceLength: fullSequence.length
+    }));
+    expected = [false, true, true, true];
+    assert.deepEqual(
+      allBasesWithMetaData.map(({ isMatch }) => isMatch),
+      expected
+    );
+  });
+  it("works for origin-spanning case", () => {
+    const fullSequence = "ACGTCCACGT";
+    let primerSeq = "TACGT";
+    const start = 9;
+    const end = 3;
+    let { allBasesWithMetaData } = getStructuredBases({
+      annotationRange: { start, end },
+      forward: true,
+      bases: primerSeq,
+      start: start,
+      end: end,
+      fullSequence,
+      primerBindsOn: "3prime",
+      sequenceLength: fullSequence.length
+    });
+    let expected = [true, true, true, true, true];
+    assert.deepEqual(
+      allBasesWithMetaData.map(({ isMatch }) => isMatch),
+      expected
+    );
+    primerSeq = "AACGT";
+    expected = [false, true, true, true, true];
+    ({ allBasesWithMetaData } = getStructuredBases({
+      annotationRange: { start, end },
+      forward: true,
+      bases: primerSeq,
+      start: start,
+      end: end,
+      fullSequence,
+      primerBindsOn: "3prime",
+      sequenceLength: fullSequence.length
+    }));
+    cy.task("log", allBasesWithMetaData);
+    assert.deepEqual(
+      allBasesWithMetaData.map(({ isMatch }) => isMatch),
+      expected
+    );
+  });
+});

packages/ove/demo/src/exampleData/exampleSequenceData.js

@@ -28,28 +28,48 @@ export default {
     }
   ],
   primers: [
+    // {
+    //   name: "Example Primer 1",
+    //   start: 280,
+    //   end: 300,
+    //   type: "primer_bind",
+    //   forward: true
+    // },
+    // {
+    //   name: "Blue primer",
+    //   start: 1,
+    //   end: 20,
+    //   type: "primer_bind",
+    //   forward: true,
+    //   color: "blue"
+    // },
+    // {
+    //   name: "Red primer",
+    //   start: 21,
+    //   end: 30,
+    //   type: "primer_bind",
+    //   forward: true,
+    //   color: "red"
+    // },
+    // {
+    //   name: "Normal primer",
+    //   start: 1,
+    //   end: 4,
+    //   type: "primer_bind",
+    //   forward: true,
+    //   color: "blue",
+    //   primerBindsOn: '3prime',
+    //   bases: "acgt"
+    // },
     {
-      name: "Example Primer 1",
-      start: 280,
-      end: 300,
-      type: "primer_bind",
-      forward: true
-    },
-    {
-      name: "Blue primer",
-      start: 1,
-      end: 20,
-      type: "primer_bind",
-      forward: true,
-      color: "blue"
-    },
-    {
-      name: "Red primer",
-      start: 21,
-      end: 30,
+      name: "Origin-spanning primer",
+      start: 5297,
+      end: 4,
       type: "primer_bind",
       forward: true,
-      color: "red"
+      color: "red",
+      primerBindsOn: "3prime",
+      bases: "tcgacgt"
     }
   ],
   afeatures: [

packages/ove/src/RowItem/StackedAnnotations/getStructuredBases.js

@@ -4,7 +4,7 @@ import { getComplementSequenceString } from "@teselagen/sequence-utils";
 import { bioData } from "@teselagen/sequence-utils";
 const { ambiguous_dna_values } = bioData;
 export function getStructuredBases({
-  annotationRange,
+  // annotationRange,
   forward,
   bases = "",
   start,
@@ -29,9 +29,8 @@ export function getStructuredBases({
     }
   }
   const aRange = {
-    //tnr: this probably needs to be changed in case annotation wraps origin
-    start: annotationRange.start - start,
-    end: annotationRange.end - start
+    start: 0,
+    end: basesToUse.length
   };
   const r = {
     aRange,
@@ -63,7 +62,7 @@ export function getStructuredBases({
     forward ? r.basesNoInserts : r.basesNoInserts.split("").reverse().join("")
   );
   r.basesNoInsertsWithMetaData = basesForRange.split("").map((b, i) => {
-    const indexOfBase = i + annotationRange.start;
+    const indexOfBase = (i + start) % sequenceLength;
     let seqForBase = (fullSequence && fullSequence[indexOfBase]) || "";
     if (!forward) {
       seqForBase = getComplementSequenceString(seqForBase);