chore: update package versions and add trimAnnStartEndToFitSeqLength …

…utility function with tests, start to add protein editor test
TeselaGen · Jan 28, 2025 · a8fc851 · a8fc851
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Showing 9 changed files with 108 additions and 15 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -6,6 +6,8 @@ Generated by [`auto-changelog`](https://github.com/CookPete/auto-changelog).
 
 #### 0.2.0
 
+- feat: replace HTMLSelect with TgHTMLSelect to provide better disabled… [`#130`](https://github.com/TeselaGen/tg-oss/pull/130)
+- fix: Pass editor name to simplelinearcircularSequenceView component [`#129`](https://github.com/TeselaGen/tg-oss/pull/129)
 - Expose files in package to workaround multiple version of react [`#124`](https://github.com/TeselaGen/tg-oss/pull/124)
 - fix copy sequence [`#127`](https://github.com/TeselaGen/tg-oss/pull/127)
 - Refactor file imports and update version; make initial values not get overridden by default values; add DefaultVal demo component [`#125`](https://github.com/TeselaGen/tg-oss/pull/125)

diff --git a/packages/ove/cypress/e2e/proteinEditor.spec.js b/packages/ove/cypress/e2e/proteinEditor.spec.js
@@ -1,27 +1,27 @@
 describe("proteinEditor", function () {
-  beforeEach(() => {
-    cy.visit("/#/Editor?moleculeType=Protein");
-    // cy.get(`[data-test="moleculeType"]`).select('Protein')
-  });
   it(`annotations shouldn't have a strand field to edit and all annotations be 'forward'`, () => {
+    cy.visit("/#/Editor?moleculeType=Protein");
     cy.contains(".veRowViewPart", "Part 0").rightclick();
     cy.contains(".bp3-menu-item", "Edit Part").click();
     cy.contains(".bp3-dialog", "Add Note"); //dialog should exist, but strand shouldn't
     cy.contains(".bp3-dialog", "Strand").should("not.exist");
   });
   it(`should have non protein actions hidden from the menu search`, () => {
+    cy.visit("/#/Editor?moleculeType=Protein");
     cy.get("body").type("{meta}/");
     // eslint-disable-next-line cypress/no-unnecessary-waiting
     cy.wait(0);
     cy.focused().type("translation{enter}");
     cy.contains(".bp3-menu-item", "Translations").should("not.exist");
   });
   it(`should be able to toggle between protein and dna mode after firing some actions`, () => {
+    cy.visit("/#/Editor?moleculeType=Protein");
     cy.contains(".veLabelText", "Part 0").click();
     cy.get(`[data-test="moleculeType"]`).select("DNA");
     cy.contains("Length: 5299 bps").should("exist");
   });
   it(`feature/part add/edit should be AA indexed`, () => {
+    cy.visit("/#/Editor?moleculeType=Protein");
     cy.get(".tg-menu-bar").contains("Edit").click();
     cy.contains(".bp3-menu-item", "Create").click();
     cy.contains(".bp3-menu-item", "New Feature").click({ force: true });
@@ -57,6 +57,7 @@ describe("proteinEditor", function () {
     cy.get(`.tg-test-end [value="31"]`);
   });
   it(`should be able to insert AAs correctly via typing in the editor`, () => {
+    cy.visit("/#/Editor?moleculeType=Protein");
     cy.contains("Part - pj5_00001 - Start: 1 End: 1384");
     cy.contains(".veRowViewPrimaryProteinSequenceContainer svg g", "M").click({
       force: true
@@ -96,7 +97,25 @@ describe("proteinEditor", function () {
 
     cy.get(`[title="Selecting 2 AAs from 2 to 3"]`).should("exist");
   });
+  it.skip(`selection layer should be updated correctly if inserting at the end of an AA seq`, () => {
+    // TNWTODO
+    cy.visit("/#/Editor?shortSeq=true&moleculeType=Protein");
+    cy.contains(".veRowViewPrimaryProteinSequenceContainer svg g", "V").click({
+      force: true
+    });
+
+    cy.get(".veRowViewCaret:first").trigger("contextmenu", { force: true });
+    cy.contains(".bp3-menu-item", "Replace").click();
+    cy.contains("Press ENTER");
+    // eslint-disable-next-line cypress/no-unnecessary-waiting
+    cy.wait(0);
+    cy.get(".sequenceInputBubble input").type("rggta{enter}");
+    //we don't want to see the insert successful message because no bps were entered
+    cy.contains("Sequence Inserted Successfully");
+    cy.contains("Selecting 5 AAs from 14 to 18");
+  });
   it(`should be able to delete correctly when backspace/del pressed`, () => {
+    cy.visit("/#/Editor?moleculeType=Protein");
     cy.contains(".veRowViewPrimaryProteinSequenceContainer svg g", "M").click({
       force: true
     });
@@ -105,6 +124,7 @@ describe("proteinEditor", function () {
     cy.contains("Length: 1383 AAs");
   });
   it(`should be able to cut /* todo: and paste */ correctly`, () => {
+    cy.visit("/#/Editor?moleculeType=Protein");
     cy.get(".veRowViewPartsContainer")
       .contains("Part 0")
       .first()
@@ -134,7 +154,8 @@ describe("proteinEditor", function () {
   });
 
   it(`goTo, rotateTo work
-  -can't go to a position outside of the sequence
+  cy.visit("/#/Editor?moleculeType=Protein");
+    -can't go to a position outside of the sequence
   -can go to a position inside the sequence
   // -can rotate the sequence to that position
   `, () => {
@@ -157,14 +178,16 @@ describe("proteinEditor", function () {
   });
 
   it(`can move the caret around correctly`, () => {
+    cy.visit("/#/Editor?moleculeType=Protein");
     cy.contains(".veRowViewPrimaryProteinSequenceContainer svg g", "M").click({
       force: true
     });
     cy.focused().type("{rightarrow}{rightarrow}{rightarrow}");
     cy.contains("Caret Between AAs 3 and 4");
   });
   it(`
-  -can find AA's by default in the search bar
+  cy.visit("/#/Editor?moleculeType=Protein");
+    -can find AA's by default in the search bar
 
   `, () => {
     cy.get(`[data-test="ve-find-tool-toggle"]`).click().focused().type("mmh");
@@ -183,7 +206,8 @@ describe("proteinEditor", function () {
     cy.contains("Selecting 5 AAs from 1 to 5");
   });
   it(`should
-  -has 1, 5, 10 AA's in the rowview axis
+  cy.visit("/#/Editor?moleculeType=Protein");
+    -has 1, 5, 10 AA's in the rowview axis
   -can click an AA and have the selecting message display correctly
   -not show circularity/cutsite/orf/translations tools or properties
   `, () => {
@@ -227,7 +251,8 @@ describe("proteinEditor", function () {
   });
 
   it(`should
-  -show the AA count
+  cy.visit("/#/Editor?moleculeType=Protein");
+    -show the AA count
   -the protein seq should be the primary sequence displayed
   -not show any dna sequence by default
   -should not show options to update restriction enzymes or simulate digestion

diff --git a/packages/ove/demo/src/EditorDemo/index.js b/packages/ove/demo/src/EditorDemo/index.js
@@ -32,6 +32,15 @@ import _chromData from "../../../scratch/ab1ParsedGFPvv50.json";
 import { convertBasePosTraceToPerBpTrace } from "@teselagen/bio-parsers";
 import { defaultToolList } from "../../../src/ToolBar";
 const chromData = convertBasePosTraceToPerBpTrace(_chromData);
+const exampleProteinDataShort = {
+  name: "exampleProteinDataShort",
+  isProtein: true,
+  proteinSequence: "mmhlrlfcillaavs"
+};
+const exampleSequenceDataShort = {
+  name: "exampleSequenceDataShort",
+  sequence: "gtagagagagcc"
+};
 
 const MyCustomTab = connectToEditor(({ sequenceData = {} }) => {
   //you can optionally grab additional editor data using the exported connectToEditor function
@@ -100,6 +109,7 @@ const defaultState = {
   beforeSequenceInsertOrDelete: false,
   beforeSequenceInsertOrDeleteAsync: false,
   maintainOriginSplit: false,
+  shortSeq: false,
   maxAnnotationsToDisplayAdjustment: false,
   truncateLabelsThatDoNotFit: true,
   withPartTags: true,
@@ -468,6 +478,10 @@ This feature requires beforeSequenceInsertOrDelete toggle to be true to be enabl
 \`\`\`
 `
       }),
+      renderToggle({
+        that: this,
+        type: "shortSeq"
+      }),
       renderToggle({
         that: this,
         type: "onCopy"
@@ -700,9 +714,14 @@ certain dna specific tools and annotations are automatically disabled when isPro
                   if (val === "Protein") {
                     updateEditor(store, "DemoEditor", {
                       readOnly: false,
-                      sequenceData: tidyUpSequenceData(exampleProteinData, {
-                        convertAnnotationsFromAAIndices: true
-                      })
+                      sequenceData: tidyUpSequenceData(
+                        this.state.shortSeq
+                          ? exampleProteinDataShort
+                          : exampleProteinData,
+                        {
+                          convertAnnotationsFromAAIndices: true
+                        }
+                      )
                     });
                   } else if (val === "RNA") {
                     updateEditor(store, "DemoEditor", {
@@ -738,7 +757,9 @@ certain dna specific tools and annotations are automatically disabled when isPro
                     ) {
                       updateEditor(store, "DemoEditor", {
                         readOnly: false,
-                        sequenceData: exampleSequenceData
+                        sequenceData: this.state.shortSeq
+                          ? exampleSequenceDataShort
+                          : exampleSequenceData
                       });
                     }
                   }

diff --git a/packages/ove/package.json b/packages/ove/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@teselagen/ove",
-  "version": "0.7.15",
+  "version": "0.7.16",
   "main": "./src/index.js",
   "type": "module",
   "exports": {

diff --git a/packages/range-utils/package.json b/packages/range-utils/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@teselagen/range-utils",
-  "version": "0.3.7",
+  "version": "0.3.9",
   "type": "module",
   "dependencies": {
     "lodash-es": "^4.17.21"

diff --git a/packages/range-utils/src/index.js b/packages/range-utils/src/index.js
@@ -49,3 +49,4 @@ export { default as trimRangeByAnotherRange } from "./trimRangeByAnotherRange";
 export { default as zeroSubrangeByContainerRange } from "./zeroSubrangeByContainerRange";
 export { default as adjustRangeToRotation } from "./adjustRangeToRotation";
 export { default as getZeroedRangeOverlaps } from "./getZeroedRangeOverlaps";
+export { default as trimAnnStartEndToFitSeqLength } from "./trimAnnStartEndToFitSeqLength";
diff --git a/packages/range-utils/src/trimAnnStartEndToFitSeqLength.js b/packages/range-utils/src/trimAnnStartEndToFitSeqLength.js
@@ -0,0 +1,9 @@
+export default function trimAnnStartEndToFitSeqLength(
+  annStartOrEnd,
+  sequenceLength
+) {
+  return Math.max(
+    0,
+    Math.min(annStartOrEnd || 0, Math.max(sequenceLength - 1, 0))
+  );
+}
diff --git a/packages/range-utils/src/trimAnnStartEndToFitSeqLength.test.js b/packages/range-utils/src/trimAnnStartEndToFitSeqLength.test.js
@@ -0,0 +1,35 @@
+import trimAnnStartEndToFitSeqLength from "./trimAnnStartEndToFitSeqLength";
+
+describe("trimAnnStartEndToFitSeqLength", () => {
+  test("should return 0 if annStartOrEnd is undefined", () => {
+    expect(trimAnnStartEndToFitSeqLength(undefined, 10)).toBe(0);
+  });
+
+  test("should return 0 if annStartOrEnd is null", () => {
+    expect(trimAnnStartEndToFitSeqLength(null, 10)).toBe(0);
+  });
+
+  test("should return 0 if annStartOrEnd is less than 0", () => {
+    expect(trimAnnStartEndToFitSeqLength(-5, 10)).toBe(0);
+  });
+
+  test("should return annStartOrEnd if it is within the sequence length", () => {
+    expect(trimAnnStartEndToFitSeqLength(5, 10)).toBe(5);
+  });
+
+  test("should return sequenceLength - 1 if annStartOrEnd is greater than sequenceLength", () => {
+    expect(trimAnnStartEndToFitSeqLength(15, 10)).toBe(9);
+  });
+
+  test("should return 0 if sequenceLength is 0", () => {
+    expect(trimAnnStartEndToFitSeqLength(5, 0)).toBe(0);
+  });
+
+  test("should return 0 if sequenceLength is negative", () => {
+    expect(trimAnnStartEndToFitSeqLength(5, -10)).toBe(0);
+  });
+
+  test("should return 0 if annStartOrEnd is 0", () => {
+    expect(trimAnnStartEndToFitSeqLength(0, 10)).toBe(0);
+  });
+});
diff --git a/packages/ui/package.json b/packages/ui/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@teselagen/ui",
-  "version": "0.7.17",
+  "version": "0.7.18",
   "main": "./src/index.js",
   "type": "module",
   "exports": {