@teselagen/ove 0.7.30-beta.1 → 0.7.30-beta.2

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@teselagen/ove",
-  "version": "0.7.30-beta.1",
+  "version": "0.7.30-beta.2",
   "main": "./src/index.js",
   "type": "module",
   "exports": {
@@ -11,19 +11,22 @@
     "./*": "./*"
   },
   "dependencies": {
-    "@teselagen/sequence-utils": "0.3.32-beta.1",
-    "@teselagen/range-utils": "0.3.14-beta.1",
-    "@teselagen/ui": "0.8.6-beta.24",
-    "@teselagen/file-utils": "0.3.20",
-    "@teselagen/bio-parsers": "0.4.29-beta.1",
     "@blueprintjs/core": "3.54.0",
     "@hello-pangea/dnd": "16.2.0",
     "@risingstack/react-easy-state": "^6.3.0",
+    "@teselagen/bio-parsers": "0.4.29-beta.1",
+    "@teselagen/file-utils": "0.3.20",
+    "@teselagen/range-utils": "0.3.14-beta.1",
     "@teselagen/react-list": "0.8.18",
+    "@teselagen/sequence-utils": "0.3.32-beta.2",
+    "@teselagen/ui": "0.8.6-beta.27",
+    "@use-gesture/react": "10.3.0",
+    "biomsa": "^0.2.4",
     "classnames": "^2.3.2",
-    "color": "^3.2.1",
+    "color": "^5.0.0",
     "combokeys": "^3.0.1",
     "copy-to-clipboard": "^3.3.1",
+    "cypress-real-events": "^1.13.0",
     "deep-equal": "^1.1.1",
     "dom-to-image": "^2.6.0",
     "downloadjs": "^1.4.7",
@@ -58,11 +61,11 @@
     "to-regex-range": "5.0.1",
     "use-debounce": "^8.0.4",
     "validate.io-nonnegative-integer-array": "^1.0.1",
-    "cypress-real-events": "^1.13.0",
-    "biomsa": "^0.2.4",
-    "shortid": "2.2.16",
-    "@use-gesture/react": "10.3.0",
-    "@playwright/test": "^1.44.1"
+    "nanoid": "5.1.5"
+  },
+  "volta": {
+    "node": "18.18.0",
+    "yarn": "1.22.21"
   },
   "license": "MIT"
 }

package/selectors/orfsSelector.d.ts

@@ -7,7 +7,7 @@ declare const _default: ((state: any) => {
     forward: any;
     annotationTypePlural: string;
     isOrf: boolean;
-    id: any;
+    id: string;
 }[]) & import('reselect').OutputSelectorFields<(args_0: any, args_1: any, args_2: any, args_3: any) => {
     start: number;
     end: number;
@@ -17,7 +17,7 @@ declare const _default: ((state: any) => {
     forward: any;
     annotationTypePlural: string;
     isOrf: boolean;
-    id: any;
+    id: string;
 }[], {
     clearCache: () => void;
 }> & {

package/selectors/translationsSelector.d.ts

@@ -7,7 +7,7 @@ declare const _default: ((state: any) => any) & import('reselect').OutputSelecto
     forward: any;
     annotationTypePlural: string;
     isOrf: boolean;
-    id: any;
+    id: string;
 }[], args_4: any, args_5: any, args_6: any[], args_7: any, args_8: any, args_9: any, args_10: any, args_11: any, args_12: any) => any, {
     clearCache: () => void;
 }> & {

package/src/AutoAnnotate.js

@@ -4,7 +4,7 @@
 import { unparse } from "papaparse";
 import pluralize from "pluralize";
 import { SubmissionError, reduxForm } from "redux-form";
-import shortid from "shortid";
+import { nanoid } from "nanoid";
 import CreateAnnotationsPage from "./CreateAnnotationsPage";
 import { formName } from "./constants";
 import { AutoAnnotateBpMatchingDialog } from "./AutoAnnotateBpMatchingDialog";
@@ -403,7 +403,7 @@ FRT	GAAGTTCCTATTCTCTAGAAAGTATAGGAACTTC	misc_recomb	orchid	pink	0	0`,
               if (ann.matchType === "protein") {
                 ann.sequence = convertProteinSeqToDNAIupac(ann.sequence);
               }
-              const id = shortid();
+              const id = nanoid();
               annotationsToCheckById[id] = {
                 ...ann,
                 sequence: ann.isRegex
@@ -428,7 +428,7 @@ FRT	GAAGTTCCTATTCTCTAGAAAGTATAGGAACTTC	misc_recomb	orchid	pink	0	0`,
                     ...annotationsToCheckById[a.id],
                     ...a,
                     forward: a.strand !== -1,
-                    id: shortid()
+                    id: nanoid()
                   };
                   toRet.color =
                     toRet.color || getFeatureToColorMap()[toRet.type];

package/src/GlobalDialogUtils.js

@@ -1,4 +1,4 @@
-import shortid from "shortid";
+import { nanoid } from "nanoid";
 
 import { cloneDeep, startCase } from "lodash-es";
 import { convertRangeTo1Based } from "@teselagen/range-utils";
@@ -36,7 +36,7 @@ export function showDialog({
   dialogHolder.CustomModalComponent = ModalComponent;
   dialogHolder.props = props;
   dialogHolder.overrideName = overrideName;
-  dialogHolder.setUniqKeyToForceRerender(shortid());
+  dialogHolder.setUniqKeyToForceRerender(nanoid());
 }
 export function hideDialog() {
   delete dialogHolder.dialogType;

package/src/ToolBar/alignmentTool.js

@@ -10,7 +10,7 @@ import {
 import { reduxForm, FieldArray } from "redux-form";
 import { anyToJson } from "@teselagen/bio-parsers";
 import { flatMap } from "lodash-es";
-import uniqid from "shortid";
+import { nanoid } from "nanoid";
 import { cloneDeep } from "lodash-es";
 import classNames from "classnames";
 
@@ -155,7 +155,7 @@ class AlignmentTool extends React.Component {
     }
 
     hideModal();
-    const alignmentId = uniqid();
+    const alignmentId = nanoid();
     // const alignmentIdMismatches = uniqid();
     createNewAlignment({
       id: alignmentId,

package/src/helperComponents/MergeFeaturesDialog/index.js

@@ -1,5 +1,5 @@
 import React from "react";
-import uuid from "shortid";
+import { nanoid } from "nanoid";
 
 import { reduxForm } from "redux-form";
 
@@ -58,7 +58,7 @@ class MergeFeaturesDialog extends React.Component {
             upsertFeature(
               {
                 ...feat1,
-                id: uuid(),
+                id: nanoid(),
                 start: start - 1,
                 end: end - 1,
                 name

package/src/redux/alignments.js

@@ -3,7 +3,7 @@ import {
   condensePairwiseAlignmentDifferences
 } from "@teselagen/sequence-utils";
 import { convertBasePosTraceToPerBpTrace } from "@teselagen/bio-parsers";
-import shortid from "shortid";
+import { nanoid } from "nanoid";
 
 import addDashesForMatchStartAndEndForTracks from "./utils/addDashesForMatchStartAndEndForTracks";
 
@@ -149,7 +149,7 @@ export default (state = {}, { payload = {}, type }) => {
   if (type === "UPSERT_ALIGNMENT_RUN") {
     const { id } = payload;
     const payloadToUse = {
-      stateTrackingId: state[id]?.stateTrackingId ? shortid() : "initialLoadId",
+      stateTrackingId: state[id]?.stateTrackingId ? nanoid() : "initialLoadId",
       alignmentType: state[id]?.alignmentType,
       ...payload,
       //assign default visibilities

package/src/redux/sequenceData/index.js

@@ -1,6 +1,6 @@
 import deepEqual from "deep-equal";
 import { tidyUpSequenceData } from "@teselagen/sequence-utils";
-import uuid from "shortid";
+import { nanoid } from "nanoid";
 
 import createAction from "../utils/createMetaAction";
 import features from "./features";
@@ -75,7 +75,7 @@ export default function (state, action) {
     return {
       // ...cloneDeep(newState),
       ...newState,
-      stateTrackingId: newState.stateTrackingId ? uuid() : "initialLoadId"
+      stateTrackingId: newState.stateTrackingId ? nanoid() : "initialLoadId"
     };
   }
 }

package/src/redux/sequenceData/upsertDeleteActionGenerator.js

@@ -1,5 +1,5 @@
 import omit from "lodash/omit";
-import uuid from "shortid";
+import { nanoid } from "nanoid";
 
 // ------------------------------------
 // Reducer
@@ -10,7 +10,7 @@ export default function upsertDeleteActionGenerator(
 ) {
   return {
     [upsertAction]: (state, payload) => {
-      const idToUse = payload.id || uuid();
+      const idToUse = payload.id || nanoid();
       return {
         ...state,
         [idToUse]: { ...(state[idToUse] || {}), ...payload, id: idToUse }

package/src/selectors/cutsitesSelector.js

@@ -1,4 +1,4 @@
-import shortid from "shortid";
+import { nanoid } from "nanoid";
 import circularSelector from "./circularSelector";
 import sequenceSelector from "./sequenceSelector";
 import restrictionEnzymesSelector from "./restrictionEnzymesSelector";
@@ -20,7 +20,7 @@ function cutsitesSelector(sequence, circular, enzymeList, cutsiteLabelColors) {
     const cutsitesForEnzyme = cutsitesByName[enzymeName];
     cutsitesForEnzyme.forEach(function (cutsite) {
       const numberOfCuts = cutsitesByName[enzymeName].length;
-      const uniqueId = shortid();
+      const uniqueId = nanoid();
       cutsite.id = uniqueId;
       cutsite.numberOfCuts = numberOfCuts;
       cutsite.annotationType = "cutsite";

package/src/selectors/translationsSelector.js

@@ -1,5 +1,5 @@
 import { reduce } from "lodash-es";
-import uuid from "shortid";
+import { nanoid } from "nanoid";
 import sequenceSelector from "./sequenceSelector";
 import orfsSelector from "./orfsSelector";
 import { createSelector } from "reselect";
@@ -28,7 +28,7 @@ function translationsSelector(
   const translationsToPass = {
     ...translationSearchMatches.reduce((acc, match) => {
       if (!match) return acc;
-      const id = match.id || uuid();
+      const id = match.id || nanoid();
       acc[id] = {
         ...match,
         id,
@@ -79,7 +79,7 @@ function translationsSelector(
       (acc, isActive, frameName) => {
         const frameOffset = Number(frameName);
         if (isActive) {
-          const id = uuid();
+          const id = nanoid();
           acc[id] = {
             id,
             start:

package/src/utils/cleanSequenceData_DEPRECATED/arrayToObjWithIds.js

@@ -1,6 +1,6 @@
 //helper function to make sure any arrays coming in
 
-import shortid from "shortid";
+import { nanoid } from "nanoid";
 
 //get converted to objects with unique ids
 export default function arrayToObjWithIds(array) {
@@ -8,7 +8,7 @@ export default function arrayToObjWithIds(array) {
   array.forEach(function (item) {
     const newItem = {
       ...item,
-      id: item.id || shortid()
+      id: item.id || nanoid()
     };
     newObj[newItem.id] = newItem;
   });

package/src/withEditorProps/index.js

@@ -27,7 +27,7 @@ import {
   invertRange,
   normalizeRange
 } from "@teselagen/range-utils";
-import shortid from "shortid";
+import { nanoid } from "nanoid";
 
 import addMetaToActionCreators from "../redux/utils/addMetaToActionCreators";
 import { actions, editorReducer } from "../redux";
@@ -268,7 +268,7 @@ export const importSequenceFromFile =
       }
 
       if (seqData) {
-        seqData.stateTrackingId = shortid();
+        seqData.stateTrackingId = nanoid();
         updateEditor(
           {
             getState: () => ({ VectorEditor: { [props.editorName]: props } }),