chore: merging in master

TeselaGen · May 6, 2024 · 8b83f4f · 8b83f4f
2 parents d5d24bf + df37053
commit 8b83f4f
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diff --git a/.vscode/tasks.json b/.vscode/tasks.json
@@ -0,0 +1,16 @@
+{
+  "version": "2.0.0",
+  "tasks": [
+    {
+      "type": "nx",
+      "project": "",
+      "command": "run-many",
+      "flags": [
+        "--target=publish",
+        "--projects=bio-parsers,ove,sequence-utils,ui"
+      ],
+      "problemMatcher": [],
+      "label": "nx: nx run-many --target=publish --projects=bio-parsers,ove,sequence-utils,ui"
+    }
+  ]
+}
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -35,5 +35,5 @@ Generated by [`auto-changelog`](https://github.com/CookPete/auto-changelog).
 - Added fix for clipboard commands when there are multiple editors on a page to resolve https://github.com/TeselaGen/tg-oss/issues/24 [`#24`](https://github.com/TeselaGen/tg-oss/issues/24)
 - closes #35 [`#35`](https://github.com/TeselaGen/tg-oss/issues/35)
 - updating yarn lock [`ff41df0`](https://github.com/TeselaGen/tg-oss/commit/ff41df0b49b8051fcba084f7eaa44cf23284926d)
-- updating table styling to remove table last row bottom margin, removing unused S3Download, removing axios dep, updating deps [`8a6fb1f`](https://github.com/TeselaGen/tg-oss/commit/8a6fb1f047550f617c3e56b8c3ebf145967076ef)
 - unifying the ui and ove demos [`f23237d`](https://github.com/TeselaGen/tg-oss/commit/f23237d4185830d94f362cbd1dae527ab59ad623)
+- Add example file [`79f356f`](https://github.com/TeselaGen/tg-oss/commit/79f356faac0dc5fa0afc882eccdbf9ed5f41d047)
diff --git a/package.json b/package.json
@@ -57,7 +57,7 @@
     "react-measure": "^2.5.2",
     "react-redux": "^8.0.5",
     "react-rnd": "^10.2.4",
-    "react-router-dom": "^4.3.1",
+    "react-router-dom": "^5.3.4",
     "react-sizeme": "^2.6.12",
     "react-sortable-hoc": "^0.6.8",
     "react-transition-group": "^2.4.0",
@@ -155,15 +155,14 @@
     "vite-plugin-eslint": "^1.8.1",
     "vite-plugin-libcss": "^1.1.1",
     "vite-plugin-static-copy": "^0.17.0",
-    "vite-plugin-virtual-html": "^1.1.10",
     "vite-tsconfig-paths": "^4.2.1",
     "vitest": "^0.34.6"
   },
   "workspaces": [
     "packages/*"
   ],
   "volta": {
-    "node": "16.20.2",
+    "node": "18.17.0",
     "yarn": "1.22.21"
   }
 }
diff --git a/packages/bio-parsers/package.json b/packages/bio-parsers/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@teselagen/bio-parsers",
-  "version": "0.4.10",
+  "version": "0.4.15",
   "type": "commonjs",
   "dependencies": {
     "@gmod/gff": "^1.2.1",

diff --git a/packages/bounce-loader/index.html b/packages/bounce-loader/index.html
@@ -0,0 +1,11 @@
+<!doctype html>
+<html lang="en">
+  <head>
+    <meta charset="UTF-8" />
+    <title>bounce-loader demo</title>
+    <script src="./demo/index.js" type="module"></script>
+  </head>
+  <body>
+    <div id="demo"></div>
+  </body>
+</html>
diff --git a/packages/ove/cypress/e2e/proteinEditor.spec.js b/packages/ove/cypress/e2e/proteinEditor.spec.js
@@ -90,11 +90,11 @@ describe("proteinEditor", function () {
     // eslint-disable-next-line cypress/no-unnecessary-waiting
     cy.wait(0);
     cy.get(".sequenceInputBubble input").type("{enter}");
-    cy.contains("Selecting 6 AAs from 1 to 6");
-    cy.contains("Length: 1391 AAs");
+    cy.contains("Selecting 7 AAs from 1 to 7");
+    cy.contains("Length: 1392 AAs");
     cy.get(`[data-test="ve-find-tool-toggle"]`).click().focused().type("ma");
 
-    cy.get(`[title="Selecting 2 AAs from 1 to 2"]`).should("exist");
+    cy.get(`[title="Selecting 2 AAs from 2 to 3"]`).should("exist");
   });
   it(`should be able to delete correctly when backspace/del pressed`, () => {
     cy.contains(".veRowViewPrimaryProteinSequenceContainer svg g", "M").click({

diff --git a/packages/ove/demo/src/SimpleCircularOrLinearViewDemo.js b/packages/ove/demo/src/SimpleCircularOrLinearViewDemo.js
@@ -84,6 +84,7 @@ export default class SimpleCircularOrLinearViewDemo extends React.Component {
             })}
             {renderToggle({ that: this, type: "togglePartColor" })}
             {renderToggle({ that: this, type: "isOligo" })}
+            {renderToggle({ that: this, type: "isProtein" })}
             {renderToggle({
               that: this,
               type: "toggleNoRedux",
@@ -126,21 +127,26 @@ export default class SimpleCircularOrLinearViewDemo extends React.Component {
                       size: this.state.superLongSequence
                         ? 1640
                         : this.state.limitLengthTo50Bps
-                        ? 50
-                        : 164
+                          ? 50
+                          : 164
                     }
                   : {
                       sequence: this.state.superLongSequence
                         ? "GGGAAAagagagtgagagagtagagagagaccacaccccccGGGAAAagagagtgagagagtagagagagaccacaccccccGGGAAAagagagtgagagagtagagagagaccacaccccccGGGAAAagagagtgagagagtagagagagaccacaccccccGGGAAAagagagtgagagagtagagagagaccacaccccccGGGAAAagagagtgagagagtagagagagaccacaccccccGGGAAAagagagtgagagagtagagagagaccacaccccccGGGAAAagagagtgagagagtagagagagaccacaccccccGGGAAAagagagtgagagagtagagagagaccacaccccccGGGAAAagagagtgagagagtagagagagaccacaccccccGGGAAAagagagtgagagagtagagagagaccacaccccccGGGAAAagagagtgagagagtagagagagaccacaccccccGGGAAAagagagtgagagagtagagagagaccacaccccccGGGAAAagagagtgagagagtagagagagaccacaccccccGGGAAAagagagtgagagagtagagagagaccacaccccccGGGAAAagagagtgagagagtagagagagaccacaccccccGGGAAAagagagtgagagagtagagagagaccacaccccccGGGAAAagagagtgagagagtagagagagaccacaccccccGGGAAAagagagtgagagagtagagagagaccacaccccccGGGAAAagagagtgagagagtagagagagaccacaccccccGGGAAAagagagtgagagagtagagagagaccacaccccccGGGAAAagagagtgagagagtagagagagaccacaccccccGGGAAAagagagtgagagagtagagagagaccacaccccccGGGAAAagagagtgagagagtagagagagaccacaccccccGGGAAAagagagtgagagagtagagagagaccacaccccccGGGAAAagagagtgagagagtagagagagaccacaccccccGGGAAAagagagtgagagagtagagagagaccacaccccccGGGAAAagagagtgagagagtagagagagaccacaccccccGGGAAAagagagtgagagagtagagagagaccacaccccccGGGAAAagagagtgagagagtagagagagaccacaccccccGGGAAAagagagtgagagagtagagagagaccacaccccccGGGAAAagagagtgagagagtagagagagaccacaccccccGGGAAAagagagtgagagagtagagagagaccacaccccccGGGAAAagagagtgagagagtagagagagaccacaccccccGGGAAAagagagtgagagagtagagagagaccacaccccccGGGAAAagagagtgagagagtagagagagaccacaccccccGGGAAAagagagtgagagagtagagagagaccacaccccccGGGAAAagagagtgagagagtagagagagaccacaccccccGGGAAAagagagtgagagagtagagagagaccacaccccccGGGAAAagagagtgagagagtagagagagaccacacccccc"
                         : this.state.limitLengthTo50Bps
-                        ? "GGGAAAagagagtgagagagtagagagagaccacaccccccGGGAAAaga"
-                        : "GGGAAAagagagtgagagagtagagagagaccacaccccccGGGAAAagagagtgagagagtagagagagaccacaccccccGGGAAAagagagtgagagagtagagagagaccacaccccccGGGAAAagagagtgagagagtagagagagaccacacccccc"
+                          ? "GGGAAAagagagtgagagagtagagagagaccacaccccccGGGAAAaga"
+                          : "GGGAAAagagagtgagagagtagagagagaccacaccccccGGGAAAagagagtgagagagtagagagagaccacaccccccGGGAAAagagagtgagagagtagagagagaccacaccccccGGGAAAagagagtgagagagtagagagagaccacacccccc"
                     }),
                 ...(this.state.isOligo
                   ? {
                       isOligo: true
                     }
                   : {}),
+                ...(this.state.isProtein
+                  ? {
+                      isProtein: true
+                    }
+                  : {}),
                 name: "Test Seq",
                 circular: this.state.circular, //toggle to true to change this!
                 features: [

diff --git a/packages/ove/package.json b/packages/ove/package.json
@@ -1,15 +1,12 @@
 {
   "name": "@teselagen/ove",
-  "version": "0.4.6",
+  "version": "0.4.10",
   "main": "./src/index.js",
   "exports": {
     ".": {
       "import": "./index.es.js",
       "require": "./index.cjs.js"
     },
     "./style.css": "./style.css"
-  },
-  "volta": {
-    "node": "16.20.2"
   }
 }
diff --git a/packages/ove/src/withEditorInteractions/index.js b/packages/ove/src/withEditorInteractions/index.js
@@ -286,7 +286,11 @@ function VectorInteractionHOC(Component /* options */) {
               }
             }
           ),
-        { doNotRemoveInvalidChars: true, annotationsAsObjects: true }
+        {
+          doNotRemoveInvalidChars: true,
+          annotationsAsObjects: true,
+          includeProteinSequence: true
+        }
       );
 
       if (
@@ -308,7 +312,6 @@ function VectorInteractionHOC(Component /* options */) {
             : seqData.sequence;
 
       seqData.textToCopy = textToCopy;
-
       clipboardData.setData("text/plain", textToCopy);
       clipboardData.setData("application/json", JSON.stringify(seqData));
       e.preventDefault();

diff --git a/packages/sequence-utils/package.json b/packages/sequence-utils/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@teselagen/sequence-utils",
-  "version": "0.3.19",
+  "version": "0.3.24",
   "type": "commonjs",
   "dependencies": {
     "bson-objectid": "^2.0.4",

diff --git a/packages/sequence-utils/src/bioData.js b/packages/sequence-utils/src/bioData.js
@@ -2,7 +2,7 @@
 
 export const protein_letters = "ACDEFGHIKLMNPQRSTVWY";
 export const protein_letters_withUandX = "ACDEFGHIKLMNPQRSTVWYUX";
-export const extended_protein_letters = "ACDEFGHIKLMNPQRSTVWYBXZJUO";
+export const extended_protein_letters = "ACDEFGHIKLMNPQRSTVWYBXZJUO*";
 export const ambiguous_dna_letters = "GATCRYWSMKHBVDN";
 export const unambiguous_dna_letters = "GATC";
 export const ambiguous_rna_letters = "GAUCRYWSMKHBVDN";

diff --git a/packages/sequence-utils/src/filterSequenceString.test.js b/packages/sequence-utils/src/filterSequenceString.test.js
@@ -77,6 +77,6 @@ describe("filterSequenceString", () => {
       }
     );
 
-    expect(str).toBe("BXZJUObbbxtgalbmfwkqespvicyhrnd");
+    expect(str).toBe("BXZJUO*bbbxtgalbmfwkqespvicyhrnd");
   });
 });
diff --git a/packages/sequence-utils/src/insertSequenceDataAtPositionOrRange.test.js b/packages/sequence-utils/src/insertSequenceDataAtPositionOrRange.test.js
@@ -83,6 +83,28 @@ describe("insertSequenceData", () => {
     postInsertSeq.sequence.should.equal("atgatagatagggagaaa");
     postInsertSeq.proteinSequence.should.equal("MIDREK");
   });
+  it("inserts protein seq into a dna seq correctly", () => {
+    const sequenceToInsert = {
+      isProtein: true,
+      sequence: "atagatagg",
+      proteinSequence: "IDR"
+    };
+    const sequenceToInsertInto = {
+      //  012345
+      isProtein: false,
+      sequence: "atgagagagaaa",
+      proteinSequence: "MREK"
+    };
+    const range = { start: 3, end: 5 };
+    const postInsertSeq = insertSequenceDataAtPositionOrRange(
+      sequenceToInsert,
+      sequenceToInsertInto,
+      range
+    );
+    postInsertSeq.sequence.should.equal("atgatagatagggagaaa");
+    postInsertSeq.isProtein.should.equal(false);
+    postInsertSeq.proteinSequence.should.equal("MIDREK");
+  });
   it("inserts characters at correct range and computes the new size correctly", () => {
     const sequenceToInsert = {
       sequence: "rrrrrrr"

diff --git a/packages/sequence-utils/src/tidyUpSequenceData.js b/packages/sequence-utils/src/tidyUpSequenceData.js
@@ -8,6 +8,7 @@ import filterSequenceString from "./filterSequenceString";
 import tidyUpAnnotation from "./tidyUpAnnotation";
 import getDegenerateDnaStringFromAaString from "./getDegenerateDnaStringFromAAString";
 import { getFeatureTypes } from "./featureTypesAndColors";
+import getAminoAcidStringFromSequenceString from "./getAminoAcidStringFromSequenceString";
 
 export default function tidyUpSequenceData(pSeqData, options = {}) {
   const {
@@ -16,6 +17,7 @@ export default function tidyUpSequenceData(pSeqData, options = {}) {
     doNotRemoveInvalidChars,
     additionalValidChars,
     noTranslationData,
+    includeProteinSequence,
     doNotProvideIdsForAnnotations,
     noCdsTranslations,
     convertAnnotationsFromAAIndices,
@@ -55,7 +57,8 @@ export default function tidyUpSequenceData(pSeqData, options = {}) {
   if (!doNotRemoveInvalidChars) {
     if (seqData.isProtein) {
       const [newSeq] = filterSequenceString(seqData.proteinSequence, {
-        ...(topLevelSeqData || seqData)
+        ...(topLevelSeqData || seqData),
+        isProtein: true
       });
       seqData.proteinSequence = newSeq;
     } else {
@@ -79,6 +82,10 @@ export default function tidyUpSequenceData(pSeqData, options = {}) {
       null,
       true
     );
+  } else if (includeProteinSequence) {
+    seqData.proteinSequence = getAminoAcidStringFromSequenceString(
+      seqData.sequence
+    );
   }
 
   seqData.size = seqData.noSequence ? seqData.size : seqData.sequence.length;

diff --git a/packages/sequence-utils/src/tidyUpSequenceData.test.js b/packages/sequence-utils/src/tidyUpSequenceData.test.js
@@ -65,18 +65,18 @@ describe("tidyUpSequenceData", () => {
     res.should.containSubset({
       aminoAcidDataForEachBaseOfDNA: [],
       isProtein: true,
-      size: 54, //size should refer to the DNA length
-      proteinSize: 18, //proteinSize should refer to the amino acid length
-      sequence: "ggngcnggnathtgacaytggggngcnggngcnytngcnwsnhtnggnytnhtn", //degenerate sequence
-      proteinSequence: "gagiuhwgagalasjglj",
+      size: 57, //size should refer to the DNA length
+      proteinSize: 19, //proteinSize should refer to the amino acid length
+      sequence: "ggngcnggnathtgacaytggggngcnggngcnytngcnwsnhtnggnytnhtntrr", //degenerate sequence
+      proteinSequence: "gagiuhwgagalasjglj*",
       circular: false,
       features: [
         { start: 9, end: 32, forward: true },
-        { start: 30, end: 53, forward: true },
+        { start: 30, end: 56, forward: true },
         {
           name: "iDon'tFit",
-          start: 51,
-          end: 53,
+          start: 54,
+          end: 56,
           forward: true
         }
       ]

diff --git a/packages/ui/package.json b/packages/ui/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@teselagen/ui",
-  "version": "0.3.79",
+  "version": "0.3.83",
   "main": "./src/index.js",
   "exports": {
     ".": {

diff --git a/packages/ui/src/DataTable/utils/queryParams.js b/packages/ui/src/DataTable/utils/queryParams.js
@@ -833,7 +833,7 @@ export function getQueryParams({
             console.error(
               "No schema for field found!",
               ccDisplayName,
-              schema.fields
+              JSON.stringify(schema.fields, null, 2)
             );
         }
       });

diff --git a/packages/ui/src/toastr.js b/packages/ui/src/toastr.js
@@ -82,7 +82,10 @@ const generateToast = intent => (message, options) => {
       timeout:
         options.timeout ||
         updatedTimeout ||
-        (!window.Cypress && intent === Intent.DANGER ? 60000 : undefined),
+        (!window.Cypress &&
+        (intent === Intent.DANGER || intent === Intent.WARNING)
+          ? 60000
+          : undefined),
       action: options.action,
       icon: options.icon,
       className: classNames("preserve-newline", options.className)

diff --git a/tools/scripts/publish.mjs b/tools/scripts/publish.mjs
@@ -115,5 +115,5 @@ execSync(
   `npm publish --access public --registry https://registry.npmjs.org/ --tag ${tag}`
 );
 
-execSync(`git commit -am "chore: publish ${name}@${version}"`);
-execSync(`git push`);
+// execSync(`git commit -am "chore: publish ${name}@${version}"`);
+// execSync(`git push`);
diff --git a/vite.react.config.ts b/vite.react.config.ts
@@ -4,7 +4,6 @@ import fs from "node:fs";
 import react from "@vitejs/plugin-react";
 import viteTsConfigPaths from "vite-tsconfig-paths";
 import * as esbuild from "esbuild";
-// import vitePluginVirtualHtml from "vite-plugin-virtual-html";
 import libCss from "vite-plugin-libcss";
 import { camelCase } from "lodash";
 import { getPort } from "./getPort";
@@ -87,19 +86,7 @@ export default ({ name }: { name: string; dir: string }) =>
                 ]
               })
             ]
-          : [
-              //   vitePluginVirtualHtml({
-              //     pages: {
-              //       index: {
-              //         entry: "./demo/index.js", // MUST
-              //         title: `${name} demo`, // optional, default: ''
-              //         body: `
-              //         <div id="demo"></div>
-              // ` // optional, default: '<div id="app"></div>'
-              //       }
-              //     }
-              //   })
-            ])
+          : [])
       ],
       esbuild: {
         loader: "jsx",
-Original file line number
+Diff line change
@@ Expand Up / @@ -77,6 +77,6 @@ describe("filterSequenceString", () => { @@
           }
         );
-        expect(str).toBe("BXZJUObbbxtgalbmfwkqespvicyhrnd");
+        expect(str).toBe("BXZJUO*bbbxtgalbmfwkqespvicyhrnd");
       });
     });