From 07e0b5426e51ccb7d399850491d3b3b0c3cca36d Mon Sep 17 00:00:00 2001 From: Garrett Stevens Date: Tue, 20 Jan 2026 20:43:56 +0000 Subject: [PATCH 1/9] Pass feature instead of getting from model again --- .../src/extensions/annotationFromJBrowseFeature.ts | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/packages/jbrowse-plugin-apollo/src/extensions/annotationFromJBrowseFeature.ts b/packages/jbrowse-plugin-apollo/src/extensions/annotationFromJBrowseFeature.ts index b52584719..839aa4281 100644 --- a/packages/jbrowse-plugin-apollo/src/extensions/annotationFromJBrowseFeature.ts +++ b/packages/jbrowse-plugin-apollo/src/extensions/annotationFromJBrowseFeature.ts @@ -124,9 +124,10 @@ export function annotationFromJBrowseFeature( } return refSeqId }, - getAnnotationFeature(assembly: Assembly) { + getAnnotationFeature(assembly: Assembly, feature: Feature) { const refSeqId = self.getRefSeqId(assembly) - const sfeature: Feature = self.contextMenuFeature.data + // @ts-expect-error typing needs improvement + const sfeature: Feature = feature.data return jbrowseFeatureToAnnotationFeature(sfeature, refSeqId) }, })) @@ -156,7 +157,10 @@ export function annotationFromJBrowseFeature( handleClose: () => { doneCallback() }, - annotationFeature: self.getAnnotationFeature(assembly), + annotationFeature: self.getAnnotationFeature( + assembly, + feature, + ), assembly, refSeqId: self.getRefSeqId(assembly), region, From c4b2eae8d042b7763d3366d37f145c60eda54906 Mon Sep 17 00:00:00 2001 From: Garrett Stevens Date: Tue, 20 Jan 2026 20:46:34 +0000 Subject: [PATCH 2/9] Improve typing of JBrowse feature --- .../annotationFromJBrowseFeature.ts | 33 ++++++++++--------- 1 file changed, 17 insertions(+), 16 deletions(-) diff --git a/packages/jbrowse-plugin-apollo/src/extensions/annotationFromJBrowseFeature.ts b/packages/jbrowse-plugin-apollo/src/extensions/annotationFromJBrowseFeature.ts index 839aa4281..93985b9d9 100644 --- a/packages/jbrowse-plugin-apollo/src/extensions/annotationFromJBrowseFeature.ts +++ b/packages/jbrowse-plugin-apollo/src/extensions/annotationFromJBrowseFeature.ts @@ -24,23 +24,26 @@ function simpleFeatureToGFF3Feature( feature: Feature, refSeqId: string, ): GFF3Feature { - // eslint-disable-next-line unicorn/prefer-structured-clone - const xfeature = JSON.parse(JSON.stringify(feature)) - const children = xfeature.subfeatures + const children = feature.get('subfeatures') const gff3Feature = [ { - start: (xfeature.start as number) + 1, - end: xfeature.end as number, + start: feature.get('start') + 1, + end: feature.get('end'), seq_id: refSeqId, - source: xfeature.source ?? null, - type: xfeature.type ?? null, - score: xfeature.score ?? null, - strand: xfeature.strand ? (xfeature.strand === 1 ? '+' : '-') : null, + source: feature.get('source') ?? null, + type: feature.get('type') ?? null, + score: feature.get('score') ?? null, + strand: feature.get('strand') + ? // eslint-disable-next-line unicorn/no-nested-ternary + feature.get('strand') === 1 + ? '+' + : '-' + : null, phase: - xfeature.phase !== null || xfeature.phase !== undefined - ? (xfeature.phase as string) + feature.get('phase') !== null || feature.get('phase') !== undefined + ? (feature.get('phase') as string) : null, - attributes: convertFeatureAttributes(xfeature), + attributes: convertFeatureAttributes(feature), derived_features: [], child_features: children ? children.map((x: Feature) => simpleFeatureToGFF3Feature(x, refSeqId)) @@ -71,7 +74,7 @@ function convertFeatureAttributes(feature: Feature): Record { 'source', 'score', ]) - for (const [key, value] of Object.entries(feature)) { + for (const [key, value] of Object.entries(feature.toJSON())) { if (defaultFields.has(key)) { continue } @@ -126,9 +129,7 @@ export function annotationFromJBrowseFeature( }, getAnnotationFeature(assembly: Assembly, feature: Feature) { const refSeqId = self.getRefSeqId(assembly) - // @ts-expect-error typing needs improvement - const sfeature: Feature = feature.data - return jbrowseFeatureToAnnotationFeature(sfeature, refSeqId) + return jbrowseFeatureToAnnotationFeature(feature, refSeqId) }, })) .views((self) => { From 51ddddbbe21cb3e7b528fa8e706400ffbb6382c1 Mon Sep 17 00:00:00 2001 From: Garrett Stevens Date: Tue, 20 Jan 2026 20:47:05 +0000 Subject: [PATCH 3/9] Remove custom z-index that broke sub-menus --- .../src/LinearApolloDisplay/components/LinearApolloDisplay.tsx | 1 - 1 file changed, 1 deletion(-) diff --git a/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/components/LinearApolloDisplay.tsx b/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/components/LinearApolloDisplay.tsx index 3f7976ef0..bcb94f5da 100644 --- a/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/components/LinearApolloDisplay.tsx +++ b/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/components/LinearApolloDisplay.tsx @@ -156,7 +156,6 @@ export const LinearApolloDisplay = observer(function LinearApolloDisplay( ? { top: contextCoord[1], left: contextCoord[0] } : undefined } - style={{ zIndex: theme.zIndex.tooltip }} menuItems={contextMenuItems} /> From b8797dd8a3c5754833523a7db4643169415214e0 Mon Sep 17 00:00:00 2001 From: Garrett Stevens Date: Tue, 27 Jan 2026 19:27:02 +0000 Subject: [PATCH 4/9] Lots of dependency upgrades --- .github/workflows/pull_request.yml | 5 - .github/workflows/push.yml | 5 - .yarnrc.yml | 3 - package.json | 2 +- packages/apollo-cli/package.json | 2 +- .../apollo-collaboration-server/package.json | 18 +- .../src/changes/changes.service.ts | 2 +- .../apollo-collaboration-server/tsconfig.json | 1 + packages/apollo-common/package.json | 18 +- packages/apollo-mst/package.json | 8 +- .../apollo-mst/src/AnnotationFeatureModel.ts | 2 +- packages/apollo-mst/src/ApolloAssembly.ts | 2 +- packages/apollo-mst/src/ApolloRefSeq.ts | 2 +- packages/apollo-mst/src/CheckResult.ts | 2 +- packages/apollo-schemas/package.json | 2 +- packages/apollo-shared/package.json | 23 +- .../src/Changes/MergeTranscriptsChange.ts | 2 +- packages/jbrowse-plugin-apollo/package.json | 41 +- .../jbrowse-plugin-apollo/rollup.config.js | 2 +- .../components/AuthTypeSelector.tsx | 2 +- .../components/LoginButtons.tsx | 2 +- .../src/ApolloInternetAccount/configSchema.ts | 2 +- .../src/ApolloInternetAccount/model.ts | 8 +- .../src/ApolloJobModel.ts | 2 +- .../src/BackendDrivers/DesktopFileDriver.ts | 2 +- .../src/ChangeManager.ts | 2 +- .../ApolloFeatureDetailsWidget.tsx | 2 +- .../ApolloTranscriptDetailsWidget.tsx | 4 +- .../src/FeatureDetailsWidget/AttributeKey.tsx | 2 +- .../src/FeatureDetailsWidget/Attributes.tsx | 4 +- .../src/FeatureDetailsWidget/Sequence.tsx | 2 +- .../src/FeatureDetailsWidget/model.ts | 4 +- .../LinearApolloDisplay/stateModel/base.ts | 15 +- .../LinearApolloDisplay/stateModel/index.ts | 4 +- .../LinearApolloDisplay/stateModel/layouts.ts | 10 +- .../stateModel/mouseEvents.ts | 4 +- .../stateModel/rendering.ts | 4 +- .../stateModel/base.ts | 9 +- .../stateModel/index.ts | 4 +- .../stateModel/rendering.ts | 4 +- .../glyphs/GeneGlyph.ts | 2 +- .../stateModel/base.ts | 15 +- .../stateModel/index.ts | 4 +- .../stateModel/layouts.ts | 10 +- .../stateModel/mouseEvents.ts | 4 +- .../stateModel/rendering.ts | 4 +- .../src/OntologyManager/index.ts | 4 +- .../src/TabularEditor/HybridGrid/Feature.tsx | 2 +- .../HybridGrid/FeatureAttributes.tsx | 2 +- .../TabularEditor/HybridGrid/Highlight.tsx | 2 +- .../TabularEditor/HybridGrid/HybridGrid.tsx | 5 +- .../TabularEditor/HybridGrid/NumberCell.tsx | 2 +- .../src/TabularEditor/HybridGrid/ToolBar.tsx | 2 +- .../src/TabularEditor/model.ts | 5 +- .../src/components/AddAssembly.tsx | 4 +- .../src/components/CopyFeature.tsx | 2 +- .../src/components/CreateApolloAnnotation.tsx | 2 +- .../src/components/DeleteAssembly.tsx | 2 +- .../src/components/DeleteFeature.tsx | 2 +- .../src/components/Dialog.tsx | 2 +- .../src/components/DownloadGFF3.tsx | 2 +- .../src/components/LogOut.tsx | 2 +- .../src/components/ManageChecks.tsx | 2 +- .../src/components/ManageUsers.tsx | 2 +- .../src/components/MergeExons.tsx | 2 +- .../src/components/MergeTranscripts.tsx | 2 +- .../components/OntologyTermMultiSelect.tsx | 2 +- .../src/components/SplitExon.tsx | 2 +- .../src/components/ViewChangeLog.tsx | 4 +- .../src/components/ViewCheckResults.tsx | 2 +- packages/jbrowse-plugin-apollo/src/config.ts | 2 +- .../annotationFromJBrowseFeature.ts | 4 +- .../src/extensions/annotationFromPileup.ts | 8 +- .../src/makeDisplayComponent.tsx | 2 +- .../src/session/ClientDataStore.ts | 16 +- .../src/session/session.ts | 9 +- .../src/util/displayUtils.ts | 3 +- .../jbrowse-plugin-apollo/src/util/index.ts | 2 +- .../src/util/loadAssemblyIntoClient.ts | 2 +- packages/website/package.json | 2 +- yarn.lock | 1053 +++++++++-------- 81 files changed, 739 insertions(+), 697 deletions(-) diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml index aaab917fe..4ec216ec6 100644 --- a/.github/workflows/pull_request.yml +++ b/.github/workflows/pull_request.yml @@ -19,11 +19,6 @@ jobs: cache: yarn - name: Install run: yarn --immutable - # Have to build shared before linting so type-based lint rules can - # run correctly - - name: Build shared - run: yarn build - working-directory: packages/apollo-shared - name: Lint codebase run: yarn eslint --max-warnings 0 - name: Run Jest tests diff --git a/.github/workflows/push.yml b/.github/workflows/push.yml index d4797b503..204932ffb 100644 --- a/.github/workflows/push.yml +++ b/.github/workflows/push.yml @@ -40,11 +40,6 @@ jobs: cache: yarn - name: Install run: yarn --immutable - # Have to build shared before linting so type-based lint rules can - # run correctly - - name: Build shared - run: yarn build - working-directory: packages/apollo-shared - name: Lint codebase run: yarn eslint --max-warnings 0 docker: diff --git a/.yarnrc.yml b/.yarnrc.yml index 9ff5ea77c..5bc5a6ae6 100644 --- a/.yarnrc.yml +++ b/.yarnrc.yml @@ -5,9 +5,6 @@ enableGlobalCache: false npmMinimalAgeGate: 2880 packageExtensions: - "@jbrowse/cli@*": - dependencies: - tmp: ^0.2.1 "@jbrowse/core@*": peerDependencies: "@emotion/react": "*" diff --git a/package.json b/package.json index f05511fa6..27a841d18 100644 --- a/package.json +++ b/package.json @@ -41,7 +41,7 @@ "npm-run-all": "^4.1.5", "prettier": "^3.3.2", "prettier-plugin-packagejson": "^2.5.2", - "react": "^18.2.0", + "react": ">=18.0.0", "semver": "^7.6.3", "tslib": "^2.3.1", "tsx": "^4.6.2", diff --git a/packages/apollo-cli/package.json b/packages/apollo-cli/package.json index 5b4d42be4..2cdfca410 100644 --- a/packages/apollo-cli/package.json +++ b/packages/apollo-cli/package.json @@ -108,7 +108,7 @@ "oclif": "^4.4.2", "prettier": "^3.3.2", "react-dom": "^18.2.0", - "rxjs": "^7.4.0", + "rxjs": "^7.8.2", "serve": "^14.0.1", "shx": "^0.3.3", "ts-node": "^10.3.0", diff --git a/packages/apollo-collaboration-server/package.json b/packages/apollo-collaboration-server/package.json index 8523372f8..447eab23a 100644 --- a/packages/apollo-collaboration-server/package.json +++ b/packages/apollo-collaboration-server/package.json @@ -45,8 +45,9 @@ "@emotion/styled": "^11.10.6", "@gmod/gff": "^2.0.0", "@gmod/indexedfasta": "^2.0.4", - "@jbrowse/core": "^3.6.5", - "@mui/material": "^7.0.0", + "@jbrowse/core": "^4.1.1", + "@jbrowse/mobx-state-tree": "^5.5.0", + "@mui/material": "^7.3.7", "@nestjs/common": "^10.1.0", "@nestjs/config": "^3.0.0", "@nestjs/core": "^10.1.0", @@ -66,9 +67,8 @@ "https-proxy-agent": "^7.0.6", "joi": "^17.7.0", "material-ui-popup-state": "^5.0.4", - "mobx": "^6.6.1", - "mobx-react": "^7.2.1", - "mobx-state-tree": "^5.4.0", + "mobx": "^6.15.0", + "mobx-react": "^9.2.1", "mongoose": "^6.12.0", "mongoose-id-validator": "^0.6.0", "multer": "^1.4.5-lts.1", @@ -78,16 +78,14 @@ "passport-jwt": "^4.0.0", "passport-local": "^1.0.0", "passport-microsoft": "^1.0.0", - "prop-types": "^15.8.1", - "react": "^18.2.0", + "react": ">=18.0.0", "react-dom": "^18.2.0", "reflect-metadata": "^0.1.13", - "rxjs": "^7.4.0", + "rxjs": "^7.8.2", "sanitize-filename": "^1.6.3", "socket.io": "^4.5.3", "stream-concat": "^1.0.0", - "tslib": "^2.3.1", - "tss-react": "^4.6.1" + "tslib": "^2.3.1" }, "devDependencies": { "@apollo-annotation/mst": "workspace:^", diff --git a/packages/apollo-collaboration-server/src/changes/changes.service.ts b/packages/apollo-collaboration-server/src/changes/changes.service.ts index b1173f20d..460f8c6da 100644 --- a/packages/apollo-collaboration-server/src/changes/changes.service.ts +++ b/packages/apollo-collaboration-server/src/changes/changes.service.ts @@ -187,7 +187,7 @@ export class ChangesService { try { await this.featureModel.updateMany( { - $and: [{ status: -1, user: uniqUserId, _id: addedFeature._id }], + $and: [{ status: -1, user: uniqUserId, _id: addedFeature }], }, { $set: { status: 0 } }, ) diff --git a/packages/apollo-collaboration-server/tsconfig.json b/packages/apollo-collaboration-server/tsconfig.json index fda356433..153f44af7 100644 --- a/packages/apollo-collaboration-server/tsconfig.json +++ b/packages/apollo-collaboration-server/tsconfig.json @@ -17,6 +17,7 @@ }, "references": [ { "path": "../apollo-common" }, + { "path": "../apollo-mst" }, { "path": "../apollo-schemas" }, { "path": "../apollo-shared" }, ], diff --git a/packages/apollo-common/package.json b/packages/apollo-common/package.json index 43182fca3..3c2b0a3a9 100644 --- a/packages/apollo-common/package.json +++ b/packages/apollo-common/package.json @@ -12,7 +12,7 @@ }, "dependencies": { "@apollo-annotation/schemas": "workspace:^", - "@jbrowse/core": "^3.6.5", + "@jbrowse/core": "^4.1.1", "bson-objectid": "^2.0.4", "tslib": "^2.3.1" }, @@ -27,16 +27,14 @@ "typescript": "^5.5.3" }, "peerDependencies": { - "@mui/material": "^7.0.0", - "@mui/x-data-grid": "^8.0.0", - "mobx": "^6.6.1", - "mobx-react": "^7.2.1", - "mobx-state-tree": "^5.4.0", - "prop-types": "^15.8.1", - "react": "^18.2.0", + "@jbrowse/mobx-state-tree": "^5.5.0", + "@mui/material": "^7.3.7", + "@mui/x-data-grid": "^8.26.0", + "mobx": "^6.15.0", + "mobx-react": "^9.2.1", + "react": ">=18.0.0", "react-dom": "^18.2.0", - "rxjs": "^7.4.0", - "tss-react": "^4.6.1" + "rxjs": "^7.8.2" }, "publishConfig": { "access": "public" diff --git a/packages/apollo-mst/package.json b/packages/apollo-mst/package.json index 3e48cdb44..27fe6a4a3 100644 --- a/packages/apollo-mst/package.json +++ b/packages/apollo-mst/package.json @@ -6,11 +6,11 @@ "build": "tsc" }, "dependencies": { - "@jbrowse/core": "^3.6.5", - "mobx": "^6.6.1", - "mobx-state-tree": "^5.4.0", + "@jbrowse/core": "^4.1.1", + "@jbrowse/mobx-state-tree": "^5.5.0", + "mobx": "^6.15.0", "react-dom": "^18.2.0", - "rxjs": "^7.4.0", + "rxjs": "^7.8.2", "tslib": "^2.3.1" }, "devDependencies": { diff --git a/packages/apollo-mst/src/AnnotationFeatureModel.ts b/packages/apollo-mst/src/AnnotationFeatureModel.ts index cc7d38bf7..40df87fdb 100644 --- a/packages/apollo-mst/src/AnnotationFeatureModel.ts +++ b/packages/apollo-mst/src/AnnotationFeatureModel.ts @@ -12,7 +12,7 @@ import { getParentOfType, getSnapshot, types, -} from 'mobx-state-tree' +} from '@jbrowse/mobx-state-tree' import { ApolloAssembly } from '.' diff --git a/packages/apollo-mst/src/ApolloAssembly.ts b/packages/apollo-mst/src/ApolloAssembly.ts index 980d4e17d..733afb9f5 100644 --- a/packages/apollo-mst/src/ApolloAssembly.ts +++ b/packages/apollo-mst/src/ApolloAssembly.ts @@ -1,4 +1,4 @@ -import { type Instance, type SnapshotIn, types } from 'mobx-state-tree' +import { type Instance, type SnapshotIn, types } from '@jbrowse/mobx-state-tree' import { ApolloRefSeq } from './ApolloRefSeq' diff --git a/packages/apollo-mst/src/ApolloRefSeq.ts b/packages/apollo-mst/src/ApolloRefSeq.ts index aea3e081a..6b2709c1b 100644 --- a/packages/apollo-mst/src/ApolloRefSeq.ts +++ b/packages/apollo-mst/src/ApolloRefSeq.ts @@ -4,7 +4,7 @@ import { type SnapshotIn, type SnapshotOrInstance, types, -} from 'mobx-state-tree' +} from '@jbrowse/mobx-state-tree' import { type AnnotationFeature, diff --git a/packages/apollo-mst/src/CheckResult.ts b/packages/apollo-mst/src/CheckResult.ts index e2f541ca0..da72184cf 100644 --- a/packages/apollo-mst/src/CheckResult.ts +++ b/packages/apollo-mst/src/CheckResult.ts @@ -1,4 +1,4 @@ -import { type Instance, type SnapshotIn, types } from 'mobx-state-tree' +import { type Instance, type SnapshotIn, types } from '@jbrowse/mobx-state-tree' import { AnnotationFeatureModel } from './AnnotationFeatureModel' diff --git a/packages/apollo-schemas/package.json b/packages/apollo-schemas/package.json index 634026c4e..f8baf780a 100644 --- a/packages/apollo-schemas/package.json +++ b/packages/apollo-schemas/package.json @@ -11,7 +11,7 @@ "@nestjs/mongoose": "^10.0.0", "mongoose": "^6.12.0", "reflect-metadata": "^0.1.13", - "rxjs": "^7.4.0", + "rxjs": "^7.8.2", "tslib": "^2.3.1" }, "devDependencies": { diff --git a/packages/apollo-shared/package.json b/packages/apollo-shared/package.json index bab5643bc..83894334c 100644 --- a/packages/apollo-shared/package.json +++ b/packages/apollo-shared/package.json @@ -15,13 +15,14 @@ "@apollo-annotation/schemas": "workspace:^", "@gmod/gff": "^2.0.0", "@gmod/indexedfasta": "^2.0.4", - "@jbrowse/core": "^3.6.5", + "@jbrowse/core": "^4.1.1", "bson-objectid": "^2.0.4", "generic-filehandle": "^3.0.0", "jwt-decode": "^3.1.2", "tslib": "^2.3.1" }, "devDependencies": { + "@jbrowse/mobx-state-tree": "^5.5.0", "@nestjs/common": "^10.1.0", "@nestjs/core": "^10.1.0", "@types/chai": "^4.3.19", @@ -29,25 +30,23 @@ "chai": "^5.1.1", "chai-exclude": "^3.0.0", "glob": "^11.0.0", - "mobx": "^6.6.1", - "mobx-state-tree": "^5.4.0", + "mobx": "^6.15.0", "mongoose": "^6.12.0", "react-dom": "^18.2.0", "rimraf": "^3.0.2", - "rxjs": "^7.4.0", + "rxjs": "^7.8.2", "tsx": "^4.6.2", "typescript": "^5.5.3" }, "peerDependencies": { - "@mui/material": "^7.0.0", - "@mui/x-data-grid": "^8.0.0", - "mobx": "^6.6.1", - "mobx-react": "^7.2.1", - "mobx-state-tree": "^5.4.0", - "prop-types": "^15.8.1", - "react": "^18.2.0", + "@jbrowse/mobx-state-tree": "^5.5.0", + "@mui/material": "^7.3.7", + "@mui/x-data-grid": "^8.26.0", + "mobx": "^6.15.0", + "mobx-react": "^9.2.1", + "react": ">=18.0.0", "react-dom": "^18.2.0", - "rxjs": "^7.4.0" + "rxjs": "^7.8.2" }, "publishConfig": { "access": "public" diff --git a/packages/apollo-shared/src/Changes/MergeTranscriptsChange.ts b/packages/apollo-shared/src/Changes/MergeTranscriptsChange.ts index f74faba05..772743ac8 100644 --- a/packages/apollo-shared/src/Changes/MergeTranscriptsChange.ts +++ b/packages/apollo-shared/src/Changes/MergeTranscriptsChange.ts @@ -16,7 +16,7 @@ import { } from '@apollo-annotation/mst' import { type Feature } from '@apollo-annotation/schemas' import { doesIntersect2 } from '@jbrowse/core/util' -import { getSnapshot } from 'mobx-state-tree' +import { getSnapshot } from '@jbrowse/mobx-state-tree' import { attributesToRecords, stringifyAttributes } from '../util' diff --git a/packages/jbrowse-plugin-apollo/package.json b/packages/jbrowse-plugin-apollo/package.json index 223c58163..09bc7d4ae 100644 --- a/packages/jbrowse-plugin-apollo/package.json +++ b/packages/jbrowse-plugin-apollo/package.json @@ -13,6 +13,7 @@ }, "license": "Apache-2.0", "author": "JBrowse Team", + "type": "module", "main": "dist/index.js", "module": "dist/index.esm.js", "typings": "dist/index.d.ts", @@ -54,8 +55,8 @@ "@emotion/react": "^11.10.6", "@emotion/styled": "^11.10.6", "@gmod/gff": "^2.0.0", - "@jbrowse/plugin-authentication": "^3.6.5", - "@jbrowse/plugin-linear-genome-view": "^3.6.5", + "@jbrowse/plugin-authentication": "^4.1.1", + "@jbrowse/plugin-linear-genome-view": "^4.1.1", "@mui/icons-material": "^6.5.0", "@types/jsonpath": "^0.2.0", "autosuggest-highlight": "^3.3.4", @@ -71,12 +72,13 @@ "tslib": "^2.3.1" }, "devDependencies": { - "@jbrowse/cli": "^3.6.5", - "@jbrowse/core": "^3.6.5", + "@jbrowse/cli": "^4.1.1", + "@jbrowse/core": "^4.1.1", "@jbrowse/development-tools": "^2.2.1", + "@jbrowse/mobx-state-tree": "^5.5.0", "@jest/globals": "^29.0.3", - "@mui/material": "^7.0.0", - "@mui/x-data-grid": "^8.0.0", + "@mui/material": "^7.3.7", + "@mui/x-data-grid": "^8.26.0", "@types/autosuggest-highlight": "^3", "@types/file-saver": "^2", "@types/node": "^20.19.15", @@ -91,35 +93,30 @@ "jest": "^29.6.2", "jest-fetch-mock": "^3.0.3", "librpc-web-mod": "^1.1.9", - "mobx": "^6.6.1", - "mobx-react": "^7.2.1", - "mobx-state-tree": "^5.4.0", + "mobx": "^6.15.0", + "mobx-react": "^9.2.1", "npm-run-all": "^4.1.5", - "prop-types": "^15.8.1", - "react": "^18.2.0", + "react": ">=18.0.0", "react-dom": "^18.2.0", "rimraf": "^3.0.2", - "rollup": "^2.79.2", - "rxjs": "^7.4.0", + "rollup": "^3.29.5", + "rxjs": "^7.8.2", "serve": "^14.0.1", "shx": "^0.3.3", "start-server-and-test": "^1.11.7", "ts-jest": "^29.1.1", "ts-node": "^10.3.0", - "tss-react": "^4.6.1", "typescript": "^5.5.3" }, "peerDependencies": { - "@jbrowse/core": "^3.0.1", - "@mui/material": "^7.0.0", - "mobx": "^6.6.1", + "@jbrowse/core": "^4.1.1", + "@jbrowse/mobx-state-tree": "^5.5.0", + "@mui/material": "^7.3.7", + "mobx": "^6.15.0", "mobx-react": "^9.0.0", - "mobx-state-tree": "^5.4.0", - "prop-types": "^15.8.1", - "react": "^18.2.0", + "react": ">=18.0.0", "react-dom": "^18.2.0", - "rxjs": "^7.4.0", - "tss-react": "^4.6.1" + "rxjs": "^7.8.2" }, "publishConfig": { "access": "public" diff --git a/packages/jbrowse-plugin-apollo/rollup.config.js b/packages/jbrowse-plugin-apollo/rollup.config.js index 3c07910a1..b24a51f0d 100644 --- a/packages/jbrowse-plugin-apollo/rollup.config.js +++ b/packages/jbrowse-plugin-apollo/rollup.config.js @@ -32,7 +32,7 @@ for (const config of rollupConfig) { config.onwarn = (warning, warn) => { if ( warning.code === 'MODULE_LEVEL_DIRECTIVE' && - warning.message.includes(`'use client'`) + warning.message.includes(`use client`) ) { return } diff --git a/packages/jbrowse-plugin-apollo/src/ApolloInternetAccount/components/AuthTypeSelector.tsx b/packages/jbrowse-plugin-apollo/src/ApolloInternetAccount/components/AuthTypeSelector.tsx index b6387f9e8..5e80ee088 100644 --- a/packages/jbrowse-plugin-apollo/src/ApolloInternetAccount/components/AuthTypeSelector.tsx +++ b/packages/jbrowse-plugin-apollo/src/ApolloInternetAccount/components/AuthTypeSelector.tsx @@ -1,5 +1,6 @@ /* eslint-disable @typescript-eslint/use-unknown-in-catch-callback-variable */ import { isAbortException } from '@jbrowse/core/util/aborting' +import { makeStyles } from '@jbrowse/core/util/tss-react' import { Button, DialogActions, @@ -8,7 +9,6 @@ import { Divider, } from '@mui/material' import React, { useEffect, useState } from 'react' -import { makeStyles } from 'tss-react/mui' import { Dialog } from '../../components/Dialog' import { createFetchErrorMessage } from '../../util' diff --git a/packages/jbrowse-plugin-apollo/src/ApolloInternetAccount/components/LoginButtons.tsx b/packages/jbrowse-plugin-apollo/src/ApolloInternetAccount/components/LoginButtons.tsx index f7f60b63b..752f64b4d 100644 --- a/packages/jbrowse-plugin-apollo/src/ApolloInternetAccount/components/LoginButtons.tsx +++ b/packages/jbrowse-plugin-apollo/src/ApolloInternetAccount/components/LoginButtons.tsx @@ -1,7 +1,7 @@ +import { makeStyles } from '@jbrowse/core/util/tss-react' import AccountCircleIcon from '@mui/icons-material/AccountCircle' import { Button, type ButtonProps } from '@mui/material' import React from 'react' -import { makeStyles } from 'tss-react/mui' import { Google, Microsoft } from './LoginIcons' diff --git a/packages/jbrowse-plugin-apollo/src/ApolloInternetAccount/configSchema.ts b/packages/jbrowse-plugin-apollo/src/ApolloInternetAccount/configSchema.ts index 09e670135..f6092cbe8 100644 --- a/packages/jbrowse-plugin-apollo/src/ApolloInternetAccount/configSchema.ts +++ b/packages/jbrowse-plugin-apollo/src/ApolloInternetAccount/configSchema.ts @@ -1,6 +1,6 @@ import { ConfigurationSchema } from '@jbrowse/core/configuration' import { BaseInternetAccountConfig } from '@jbrowse/core/pluggableElementTypes' -import { type Instance } from 'mobx-state-tree' +import { type Instance } from '@jbrowse/mobx-state-tree' const ApolloConfigSchema = ConfigurationSchema( 'ApolloInternetAccount', diff --git a/packages/jbrowse-plugin-apollo/src/ApolloInternetAccount/model.ts b/packages/jbrowse-plugin-apollo/src/ApolloInternetAccount/model.ts index f474cc506..7cd37ee37 100644 --- a/packages/jbrowse-plugin-apollo/src/ApolloInternetAccount/model.ts +++ b/packages/jbrowse-plugin-apollo/src/ApolloInternetAccount/model.ts @@ -22,8 +22,14 @@ import { isAbstractMenuManager, isElectron, } from '@jbrowse/core/util' +import { + type Instance, + flow, + getRoot, + isAlive, + types, +} from '@jbrowse/mobx-state-tree' import { autorun } from 'mobx' -import { type Instance, flow, getRoot, isAlive, types } from 'mobx-state-tree' import { io } from 'socket.io-client' import { addTopLevelAdminMenus } from '../menus/topLevelMenuAdmin' diff --git a/packages/jbrowse-plugin-apollo/src/ApolloJobModel.ts b/packages/jbrowse-plugin-apollo/src/ApolloJobModel.ts index f59e0350f..30959765d 100644 --- a/packages/jbrowse-plugin-apollo/src/ApolloJobModel.ts +++ b/packages/jbrowse-plugin-apollo/src/ApolloJobModel.ts @@ -5,7 +5,7 @@ import { getSession, isSessionModelWithWidgets, } from '@jbrowse/core/util' -import { types } from 'mobx-state-tree' +import { types } from '@jbrowse/mobx-state-tree' interface JobsEntry { name: string diff --git a/packages/jbrowse-plugin-apollo/src/BackendDrivers/DesktopFileDriver.ts b/packages/jbrowse-plugin-apollo/src/BackendDrivers/DesktopFileDriver.ts index 2eb28c304..47d7afde3 100644 --- a/packages/jbrowse-plugin-apollo/src/BackendDrivers/DesktopFileDriver.ts +++ b/packages/jbrowse-plugin-apollo/src/BackendDrivers/DesktopFileDriver.ts @@ -16,7 +16,7 @@ import { import { type GFF3Item, formatSync } from '@gmod/gff' import { getConf } from '@jbrowse/core/configuration' import { type Region, getSession } from '@jbrowse/core/util' -import { getSnapshot } from 'mobx-state-tree' +import { getSnapshot } from '@jbrowse/mobx-state-tree' import { checkFeatures, loadAssemblyIntoClient } from '../util' diff --git a/packages/jbrowse-plugin-apollo/src/ChangeManager.ts b/packages/jbrowse-plugin-apollo/src/ChangeManager.ts index 2d11bcb0f..b5a474e02 100644 --- a/packages/jbrowse-plugin-apollo/src/ChangeManager.ts +++ b/packages/jbrowse-plugin-apollo/src/ChangeManager.ts @@ -11,7 +11,7 @@ import { validationRegistry, } from '@apollo-annotation/shared' import { getSession } from '@jbrowse/core/util' -import { type IAnyStateTreeNode } from 'mobx-state-tree' +import { type IAnyStateTreeNode } from '@jbrowse/mobx-state-tree' import { type ApolloSessionModel } from './session' diff --git a/packages/jbrowse-plugin-apollo/src/FeatureDetailsWidget/ApolloFeatureDetailsWidget.tsx b/packages/jbrowse-plugin-apollo/src/FeatureDetailsWidget/ApolloFeatureDetailsWidget.tsx index a4865a0c2..0c0478067 100644 --- a/packages/jbrowse-plugin-apollo/src/FeatureDetailsWidget/ApolloFeatureDetailsWidget.tsx +++ b/packages/jbrowse-plugin-apollo/src/FeatureDetailsWidget/ApolloFeatureDetailsWidget.tsx @@ -1,4 +1,5 @@ import { getSession } from '@jbrowse/core/util' +import { makeStyles } from '@jbrowse/core/util/tss-react' import ExpandMoreIcon from '@mui/icons-material/ExpandMore' import { Accordion, @@ -8,7 +9,6 @@ import { } from '@mui/material' import { observer } from 'mobx-react' import React, { useEffect, useState } from 'react' -import { makeStyles } from 'tss-react/mui' import { type ApolloSessionModel } from '../session' diff --git a/packages/jbrowse-plugin-apollo/src/FeatureDetailsWidget/ApolloTranscriptDetailsWidget.tsx b/packages/jbrowse-plugin-apollo/src/FeatureDetailsWidget/ApolloTranscriptDetailsWidget.tsx index b00cc311a..d2271604a 100644 --- a/packages/jbrowse-plugin-apollo/src/FeatureDetailsWidget/ApolloTranscriptDetailsWidget.tsx +++ b/packages/jbrowse-plugin-apollo/src/FeatureDetailsWidget/ApolloTranscriptDetailsWidget.tsx @@ -5,6 +5,8 @@ import { getEnv, getSession, } from '@jbrowse/core/util' +import { makeStyles } from '@jbrowse/core/util/tss-react' +import { getRoot } from '@jbrowse/mobx-state-tree' import ExpandMoreIcon from '@mui/icons-material/ExpandMore' import InfoIcon from '@mui/icons-material/Info' import { @@ -15,9 +17,7 @@ import { Typography, } from '@mui/material' import { observer } from 'mobx-react' -import { getRoot } from 'mobx-state-tree' import React, { useEffect, useState } from 'react' -import { makeStyles } from 'tss-react/mui' import { type ApolloInternetAccountModel } from '../ApolloInternetAccount/model' import { type ApolloSessionModel } from '../session' diff --git a/packages/jbrowse-plugin-apollo/src/FeatureDetailsWidget/AttributeKey.tsx b/packages/jbrowse-plugin-apollo/src/FeatureDetailsWidget/AttributeKey.tsx index 50133509a..c1b3d44df 100644 --- a/packages/jbrowse-plugin-apollo/src/FeatureDetailsWidget/AttributeKey.tsx +++ b/packages/jbrowse-plugin-apollo/src/FeatureDetailsWidget/AttributeKey.tsx @@ -4,10 +4,10 @@ import { isGFFColumnInternal, isGFFInternalAttribute, } from '@apollo-annotation/shared' +import { makeStyles } from '@jbrowse/core/util/tss-react' import InfoIcon from '@mui/icons-material/Info' import { Chip, Tooltip, Typography } from '@mui/material' import React from 'react' -import { makeStyles } from 'tss-react/mui' const useStyles = makeStyles()((theme) => ({ attributeKey: { diff --git a/packages/jbrowse-plugin-apollo/src/FeatureDetailsWidget/Attributes.tsx b/packages/jbrowse-plugin-apollo/src/FeatureDetailsWidget/Attributes.tsx index 2ff3c122e..2951224ec 100644 --- a/packages/jbrowse-plugin-apollo/src/FeatureDetailsWidget/Attributes.tsx +++ b/packages/jbrowse-plugin-apollo/src/FeatureDetailsWidget/Attributes.tsx @@ -1,6 +1,8 @@ import { type AnnotationFeature } from '@apollo-annotation/mst' import { FeatureAttributeChange } from '@apollo-annotation/shared' import { type AbstractSessionModel, getEnv } from '@jbrowse/core/util' +import { makeStyles } from '@jbrowse/core/util/tss-react' +import { getSnapshot } from '@jbrowse/mobx-state-tree' import DeleteIcon from '@mui/icons-material/Delete' import EditIcon from '@mui/icons-material/Edit' import MoreHorizIcon from '@mui/icons-material/MoreHoriz' @@ -18,9 +20,7 @@ import { } from '@mui/material' import { entries } from 'mobx' import { observer } from 'mobx-react' -import { getSnapshot } from 'mobx-state-tree' import React, { useState } from 'react' -import { makeStyles } from 'tss-react/mui' import { type ApolloSessionModel } from '../session' diff --git a/packages/jbrowse-plugin-apollo/src/FeatureDetailsWidget/Sequence.tsx b/packages/jbrowse-plugin-apollo/src/FeatureDetailsWidget/Sequence.tsx index 7662d423c..eb2b8abc6 100644 --- a/packages/jbrowse-plugin-apollo/src/FeatureDetailsWidget/Sequence.tsx +++ b/packages/jbrowse-plugin-apollo/src/FeatureDetailsWidget/Sequence.tsx @@ -1,9 +1,9 @@ /* eslint-disable @typescript-eslint/no-unnecessary-condition */ import { type AnnotationFeature } from '@apollo-annotation/mst' import { splitStringIntoChunks } from '@apollo-annotation/shared' +import { makeStyles } from '@jbrowse/core/util/tss-react' import { observer } from 'mobx-react' import React from 'react' -import { makeStyles } from 'tss-react/mui' import { type ApolloSessionModel } from '../session' diff --git a/packages/jbrowse-plugin-apollo/src/FeatureDetailsWidget/model.ts b/packages/jbrowse-plugin-apollo/src/FeatureDetailsWidget/model.ts index 7eb966e48..b79b57242 100644 --- a/packages/jbrowse-plugin-apollo/src/FeatureDetailsWidget/model.ts +++ b/packages/jbrowse-plugin-apollo/src/FeatureDetailsWidget/model.ts @@ -6,13 +6,13 @@ import { } from '@apollo-annotation/mst' import { getSession } from '@jbrowse/core/util' import { ElementId } from '@jbrowse/core/util/types/mst' -import { autorun } from 'mobx' import { type Instance, type SnapshotIn, addDisposer, types, -} from 'mobx-state-tree' +} from '@jbrowse/mobx-state-tree' +import { autorun } from 'mobx' import { type ApolloSessionModel } from '../session' diff --git a/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/base.ts b/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/base.ts index b506f2d48..450014c86 100644 --- a/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/base.ts +++ b/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/base.ts @@ -5,8 +5,11 @@ /* eslint-disable @typescript-eslint/no-unnecessary-condition */ import { type AnnotationFeature } from '@apollo-annotation/mst' import type PluginManager from '@jbrowse/core/PluginManager' -import { ConfigurationReference, getConf } from '@jbrowse/core/configuration' -import { type AnyConfigurationSchemaType } from '@jbrowse/core/configuration/configurationSchema' +import { + type AnyConfigurationSchemaType, + ConfigurationReference, + getConf, +} from '@jbrowse/core/configuration' import { BaseDisplay } from '@jbrowse/core/pluggableElementTypes' import { type AbstractSessionModel, @@ -16,9 +19,15 @@ import { } from '@jbrowse/core/util' import { getParentRenderProps } from '@jbrowse/core/util/tracks' // import type LinearGenomeViewPlugin from '@jbrowse/plugin-linear-genome-view' +import { + addDisposer, + cast, + getRoot, + getSnapshot, + types, +} from '@jbrowse/mobx-state-tree' import { type LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view' import { autorun } from 'mobx' -import { addDisposer, cast, getRoot, getSnapshot, types } from 'mobx-state-tree' import { type ApolloInternetAccountModel } from '../../ApolloInternetAccount/model' import { FilterFeatures } from '../../components/FilterFeatures' diff --git a/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/index.ts b/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/index.ts index f1131b62f..f745581f9 100644 --- a/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/index.ts +++ b/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/index.ts @@ -1,6 +1,6 @@ import type PluginManager from '@jbrowse/core/PluginManager' -import { type AnyConfigurationSchemaType } from '@jbrowse/core/configuration/configurationSchema' -import { type Instance, types } from 'mobx-state-tree' +import { type AnyConfigurationSchemaType } from '@jbrowse/core/configuration' +import { type Instance, types } from '@jbrowse/mobx-state-tree' import { TabularEditorStateModelType } from '../../TabularEditor' diff --git a/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/layouts.ts b/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/layouts.ts index 12c467570..e2af072b8 100644 --- a/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/layouts.ts +++ b/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/layouts.ts @@ -2,10 +2,10 @@ import { type AnnotationFeature } from '@apollo-annotation/mst' import type PluginManager from '@jbrowse/core/PluginManager' -import { type AnyConfigurationSchemaType } from '@jbrowse/core/configuration/configurationSchema' +import { type AnyConfigurationSchemaType } from '@jbrowse/core/configuration' import { type AbstractSessionModel, doesIntersect2 } from '@jbrowse/core/util' -import { autorun, observable } from 'mobx' -import { addDisposer, isAlive } from 'mobx-state-tree' +import { addDisposer, isAlive } from '@jbrowse/mobx-state-tree' +import { autorun, entries, observable } from 'mobx' import { type ApolloSessionModel } from '../../session' import { boxGlyph, geneGlyph, genericChildGlyph } from '../glyphs' @@ -91,7 +91,7 @@ export function layoutsModelFactory( // Track the occupied coordinates in each row const filledRowLocations = new Map() const { end, refName, start } = region - for (const [id, feature] of self.seenFeatures.entries()) { + for (const [id, feature] of entries(self.seenFeatures)) { if (!isAlive(feature)) { self.deleteSeenFeature(id) continue @@ -215,7 +215,7 @@ export function layoutsModelFactory( } // Clear out features that are no longer in the view and out of the cleanup boundary // cleanup boundary + region boundary + cleanup boundary - for (const [id, feature] of self.seenFeatures.entries()) { + for (const [id, feature] of entries(self.seenFeatures)) { let shouldKeep = false for (const region of self.regions) { const extendedStart = region.start - self.cleanupBoundary diff --git a/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/mouseEvents.ts b/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/mouseEvents.ts index d575e280f..b34cbdbe0 100644 --- a/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/mouseEvents.ts +++ b/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/mouseEvents.ts @@ -4,10 +4,10 @@ import { LocationStartChange, } from '@apollo-annotation/shared' import type PluginManager from '@jbrowse/core/PluginManager' -import { type AnyConfigurationSchemaType } from '@jbrowse/core/configuration/configurationSchema' +import { type AnyConfigurationSchemaType } from '@jbrowse/core/configuration' import { type MenuItem } from '@jbrowse/core/ui' +import { type Instance, addDisposer } from '@jbrowse/mobx-state-tree' import { autorun } from 'mobx' -import { type Instance, addDisposer } from 'mobx-state-tree' import { type CSSProperties } from 'react' import { diff --git a/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/rendering.ts b/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/rendering.ts index dddc3dec5..bf8acdccb 100644 --- a/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/rendering.ts +++ b/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/rendering.ts @@ -1,10 +1,10 @@ /* eslint-disable @typescript-eslint/no-unnecessary-condition */ import type PluginManager from '@jbrowse/core/PluginManager' -import { type AnyConfigurationSchemaType } from '@jbrowse/core/configuration/configurationSchema' +import { type AnyConfigurationSchemaType } from '@jbrowse/core/configuration' import { doesIntersect2 } from '@jbrowse/core/util' +import { type Instance, addDisposer, types } from '@jbrowse/mobx-state-tree' import { type Theme, createTheme } from '@mui/material' import { autorun } from 'mobx' -import { type Instance, addDisposer, types } from 'mobx-state-tree' import { type ApolloSessionModel } from '../../session' diff --git a/packages/jbrowse-plugin-apollo/src/LinearApolloReferenceSequenceDisplay/stateModel/base.ts b/packages/jbrowse-plugin-apollo/src/LinearApolloReferenceSequenceDisplay/stateModel/base.ts index 7af793c60..add1343f4 100644 --- a/packages/jbrowse-plugin-apollo/src/LinearApolloReferenceSequenceDisplay/stateModel/base.ts +++ b/packages/jbrowse-plugin-apollo/src/LinearApolloReferenceSequenceDisplay/stateModel/base.ts @@ -5,8 +5,11 @@ /* eslint-disable @typescript-eslint/no-unnecessary-condition */ import { type AnnotationFeature } from '@apollo-annotation/mst' import type PluginManager from '@jbrowse/core/PluginManager' -import { ConfigurationReference, getConf } from '@jbrowse/core/configuration' -import { type AnyConfigurationSchemaType } from '@jbrowse/core/configuration/configurationSchema' +import { + type AnyConfigurationSchemaType, + ConfigurationReference, + getConf, +} from '@jbrowse/core/configuration' import { BaseDisplay } from '@jbrowse/core/pluggableElementTypes' import { type AbstractSessionModel, @@ -15,9 +18,9 @@ import { } from '@jbrowse/core/util' import { getParentRenderProps } from '@jbrowse/core/util/tracks' // import type LinearGenomeViewPlugin from '@jbrowse/plugin-linear-genome-view' +import { addDisposer, getRoot, types } from '@jbrowse/mobx-state-tree' import { type LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view' import { autorun } from 'mobx' -import { addDisposer, getRoot, types } from 'mobx-state-tree' import { type ApolloInternetAccountModel } from '../../ApolloInternetAccount/model' import { type ApolloSessionModel, type HoveredFeature } from '../../session' diff --git a/packages/jbrowse-plugin-apollo/src/LinearApolloReferenceSequenceDisplay/stateModel/index.ts b/packages/jbrowse-plugin-apollo/src/LinearApolloReferenceSequenceDisplay/stateModel/index.ts index d61c257b3..49954d5bb 100644 --- a/packages/jbrowse-plugin-apollo/src/LinearApolloReferenceSequenceDisplay/stateModel/index.ts +++ b/packages/jbrowse-plugin-apollo/src/LinearApolloReferenceSequenceDisplay/stateModel/index.ts @@ -1,6 +1,6 @@ import type PluginManager from '@jbrowse/core/PluginManager' -import { type AnyConfigurationSchemaType } from '@jbrowse/core/configuration/configurationSchema' -import { type Instance } from 'mobx-state-tree' +import { type AnyConfigurationSchemaType } from '@jbrowse/core/configuration' +import { type Instance } from '@jbrowse/mobx-state-tree' import { renderingModelFactory } from './rendering' diff --git a/packages/jbrowse-plugin-apollo/src/LinearApolloReferenceSequenceDisplay/stateModel/rendering.ts b/packages/jbrowse-plugin-apollo/src/LinearApolloReferenceSequenceDisplay/stateModel/rendering.ts index 3a3a04da3..02e10b1ef 100644 --- a/packages/jbrowse-plugin-apollo/src/LinearApolloReferenceSequenceDisplay/stateModel/rendering.ts +++ b/packages/jbrowse-plugin-apollo/src/LinearApolloReferenceSequenceDisplay/stateModel/rendering.ts @@ -1,9 +1,9 @@ /* eslint-disable @typescript-eslint/no-unnecessary-condition */ import type PluginManager from '@jbrowse/core/PluginManager' -import { type AnyConfigurationSchemaType } from '@jbrowse/core/configuration/configurationSchema' +import { type AnyConfigurationSchemaType } from '@jbrowse/core/configuration' +import { type Instance, addDisposer } from '@jbrowse/mobx-state-tree' import { type Theme, createTheme } from '@mui/material' import { autorun } from 'mobx' -import { type Instance, addDisposer } from 'mobx-state-tree' import { drawSequenceOverlay } from '../drawSequenceOverlay' import { drawSequenceTrack } from '../drawSequenceTrack' diff --git a/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/glyphs/GeneGlyph.ts b/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/glyphs/GeneGlyph.ts index 373c131de..0cd64f97e 100644 --- a/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/glyphs/GeneGlyph.ts +++ b/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/glyphs/GeneGlyph.ts @@ -11,10 +11,10 @@ import { intersection2, measureText, } from '@jbrowse/core/util' +import { getSnapshot } from '@jbrowse/mobx-state-tree' import { type LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view' import { alpha } from '@mui/material' import equal from 'fast-deep-equal/es6' -import { getSnapshot } from 'mobx-state-tree' import { MergeExons, SplitExon } from '../../components' import { FilterTranscripts } from '../../components/FilterTranscripts' diff --git a/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/stateModel/base.ts b/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/stateModel/base.ts index 8f50b5196..86fb6f19b 100644 --- a/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/stateModel/base.ts +++ b/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/stateModel/base.ts @@ -5,8 +5,11 @@ /* eslint-disable @typescript-eslint/no-unnecessary-condition */ import { type AnnotationFeature } from '@apollo-annotation/mst' import type PluginManager from '@jbrowse/core/PluginManager' -import { ConfigurationReference, getConf } from '@jbrowse/core/configuration' -import { type AnyConfigurationSchemaType } from '@jbrowse/core/configuration/configurationSchema' +import { + type AnyConfigurationSchemaType, + ConfigurationReference, + getConf, +} from '@jbrowse/core/configuration' import { BaseDisplay } from '@jbrowse/core/pluggableElementTypes' import { type AbstractSessionModel, @@ -16,9 +19,15 @@ import { } from '@jbrowse/core/util' import { getParentRenderProps } from '@jbrowse/core/util/tracks' // import type LinearGenomeViewPlugin from '@jbrowse/plugin-linear-genome-view' +import { + addDisposer, + cast, + getRoot, + getSnapshot, + types, +} from '@jbrowse/mobx-state-tree' import { type LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view' import { autorun } from 'mobx' -import { addDisposer, cast, getRoot, getSnapshot, types } from 'mobx-state-tree' import { type ApolloInternetAccountModel } from '../../ApolloInternetAccount/model' import { FilterFeatures } from '../../components/FilterFeatures' diff --git a/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/stateModel/index.ts b/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/stateModel/index.ts index 980ffc9bc..301dcd311 100644 --- a/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/stateModel/index.ts +++ b/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/stateModel/index.ts @@ -1,6 +1,6 @@ import type PluginManager from '@jbrowse/core/PluginManager' -import { type AnyConfigurationSchemaType } from '@jbrowse/core/configuration/configurationSchema' -import { type Instance, types } from 'mobx-state-tree' +import { type AnyConfigurationSchemaType } from '@jbrowse/core/configuration' +import { type Instance, types } from '@jbrowse/mobx-state-tree' import { TabularEditorStateModelType } from '../../TabularEditor' diff --git a/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/stateModel/layouts.ts b/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/stateModel/layouts.ts index 3c2a0e461..101a114ed 100644 --- a/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/stateModel/layouts.ts +++ b/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/stateModel/layouts.ts @@ -2,14 +2,14 @@ import { type AnnotationFeature } from '@apollo-annotation/mst' import type PluginManager from '@jbrowse/core/PluginManager' -import { type AnyConfigurationSchemaType } from '@jbrowse/core/configuration/configurationSchema' +import { type AnyConfigurationSchemaType } from '@jbrowse/core/configuration' import { type AbstractSessionModel, doesIntersect2, getFrame, } from '@jbrowse/core/util' -import { autorun, observable } from 'mobx' -import { addDisposer, isAlive } from 'mobx-state-tree' +import { addDisposer, isAlive } from '@jbrowse/mobx-state-tree' +import { autorun, entries, observable } from 'mobx' import { type ApolloSessionModel } from '../../session' import { geneGlyph } from '../glyphs' @@ -48,7 +48,7 @@ export function layoutsModelFactory( let min: number | undefined let max: number | undefined const { end, refName, start } = region - for (const [, feature] of self.seenFeatures) { + for (const [, feature] of entries(self.seenFeatures)) { if ( refName !== assembly?.getCanonicalRefName(feature.refSeq) || !doesIntersect2(start, end, feature.min, feature.max) || @@ -107,7 +107,7 @@ export function layoutsModelFactory( return featureLayout } const { end, refName, start } = region - for (const [id, feature] of self.seenFeatures.entries()) { + for (const [id, feature] of entries(self.seenFeatures)) { if (!isAlive(feature)) { self.deleteSeenFeature(id) continue diff --git a/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/stateModel/mouseEvents.ts b/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/stateModel/mouseEvents.ts index e764ec683..192bedb37 100644 --- a/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/stateModel/mouseEvents.ts +++ b/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/stateModel/mouseEvents.ts @@ -4,11 +4,11 @@ import { LocationStartChange, } from '@apollo-annotation/shared' import type PluginManager from '@jbrowse/core/PluginManager' -import { type AnyConfigurationSchemaType } from '@jbrowse/core/configuration/configurationSchema' +import { type AnyConfigurationSchemaType } from '@jbrowse/core/configuration' import { type MenuItem } from '@jbrowse/core/ui' import { getFrame } from '@jbrowse/core/util' +import { type Instance, addDisposer, cast } from '@jbrowse/mobx-state-tree' import { autorun } from 'mobx' -import { type Instance, addDisposer, cast } from 'mobx-state-tree' import { type CSSProperties } from 'react' import { diff --git a/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/stateModel/rendering.ts b/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/stateModel/rendering.ts index 5d5622709..6a932bc24 100644 --- a/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/stateModel/rendering.ts +++ b/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/stateModel/rendering.ts @@ -1,15 +1,15 @@ /* eslint-disable @typescript-eslint/no-unnecessary-condition */ import type PluginManager from '@jbrowse/core/PluginManager' -import { type AnyConfigurationSchemaType } from '@jbrowse/core/configuration/configurationSchema' +import { type AnyConfigurationSchemaType } from '@jbrowse/core/configuration' import { defaultCodonTable, doesIntersect2, getFrame, revcom, } from '@jbrowse/core/util' +import { type Instance, addDisposer, types } from '@jbrowse/mobx-state-tree' import { type Theme, createTheme } from '@mui/material' import { autorun } from 'mobx' -import { type Instance, addDisposer, types } from 'mobx-state-tree' import { type ApolloSessionModel } from '../../session' import { codonColorCode } from '../../util/displayUtils' diff --git a/packages/jbrowse-plugin-apollo/src/OntologyManager/index.ts b/packages/jbrowse-plugin-apollo/src/OntologyManager/index.ts index 223ae8f8c..1b463d188 100644 --- a/packages/jbrowse-plugin-apollo/src/OntologyManager/index.ts +++ b/packages/jbrowse-plugin-apollo/src/OntologyManager/index.ts @@ -8,7 +8,6 @@ import { LocalPathLocation, UriLocation, } from '@jbrowse/core/util/types/mst' -import { autorun } from 'mobx' import { type Instance, addDisposer, @@ -17,7 +16,8 @@ import { getSnapshot, isAlive, types, -} from 'mobx-state-tree' +} from '@jbrowse/mobx-state-tree' +import { autorun } from 'mobx' import type ApolloPluginConfigurationSchema from '../config' import { type ApolloRootModel } from '../types' diff --git a/packages/jbrowse-plugin-apollo/src/TabularEditor/HybridGrid/Feature.tsx b/packages/jbrowse-plugin-apollo/src/TabularEditor/HybridGrid/Feature.tsx index c1980c940..1281ec3aa 100644 --- a/packages/jbrowse-plugin-apollo/src/TabularEditor/HybridGrid/Feature.tsx +++ b/packages/jbrowse-plugin-apollo/src/TabularEditor/HybridGrid/Feature.tsx @@ -3,9 +3,9 @@ import { type AnnotationFeature } from '@apollo-annotation/mst' import { type AbstractSessionModel } from '@jbrowse/core/util' +import { makeStyles } from '@jbrowse/core/util/tss-react' import { observer } from 'mobx-react' import React from 'react' -import { makeStyles } from 'tss-react/mui' import { isOntologyClass } from '../../OntologyManager' import type OntologyStore from '../../OntologyManager/OntologyStore' diff --git a/packages/jbrowse-plugin-apollo/src/TabularEditor/HybridGrid/FeatureAttributes.tsx b/packages/jbrowse-plugin-apollo/src/TabularEditor/HybridGrid/FeatureAttributes.tsx index 47872d503..6faa7b525 100644 --- a/packages/jbrowse-plugin-apollo/src/TabularEditor/HybridGrid/FeatureAttributes.tsx +++ b/packages/jbrowse-plugin-apollo/src/TabularEditor/HybridGrid/FeatureAttributes.tsx @@ -1,7 +1,7 @@ /* eslint-disable @typescript-eslint/restrict-template-expressions */ import { type AnnotationFeature } from '@apollo-annotation/mst' +import { getSnapshot } from '@jbrowse/mobx-state-tree' import { observer } from 'mobx-react' -import { getSnapshot } from 'mobx-state-tree' import React from 'react' import Highlight from './Highlight' diff --git a/packages/jbrowse-plugin-apollo/src/TabularEditor/HybridGrid/Highlight.tsx b/packages/jbrowse-plugin-apollo/src/TabularEditor/HybridGrid/Highlight.tsx index 03e973289..617d596c1 100644 --- a/packages/jbrowse-plugin-apollo/src/TabularEditor/HybridGrid/Highlight.tsx +++ b/packages/jbrowse-plugin-apollo/src/TabularEditor/HybridGrid/Highlight.tsx @@ -1,5 +1,5 @@ +import { makeStyles } from '@jbrowse/core/util/tss-react' import React from 'react' -import { makeStyles } from 'tss-react/mui' const useStyles = makeStyles()({ highlighted: { diff --git a/packages/jbrowse-plugin-apollo/src/TabularEditor/HybridGrid/HybridGrid.tsx b/packages/jbrowse-plugin-apollo/src/TabularEditor/HybridGrid/HybridGrid.tsx index b9658f306..45ade8019 100644 --- a/packages/jbrowse-plugin-apollo/src/TabularEditor/HybridGrid/HybridGrid.tsx +++ b/packages/jbrowse-plugin-apollo/src/TabularEditor/HybridGrid/HybridGrid.tsx @@ -1,8 +1,9 @@ import { Menu, type MenuItem } from '@jbrowse/core/ui' +import { makeStyles } from '@jbrowse/core/util/tss-react' import { useTheme } from '@mui/material' +import { entries } from 'mobx' import { observer } from 'mobx-react' import React, { useEffect, useRef, useState } from 'react' -import { makeStyles } from 'tss-react/mui' import { type DisplayStateModel } from '../types' @@ -81,7 +82,7 @@ const HybridGrid = observer(function HybridGrid({ - {[...seenFeatures.entries()] + {[...entries(seenFeatures)] .filter((entry) => { if (!filterText) { return true diff --git a/packages/jbrowse-plugin-apollo/src/TabularEditor/HybridGrid/NumberCell.tsx b/packages/jbrowse-plugin-apollo/src/TabularEditor/HybridGrid/NumberCell.tsx index b9c9ead33..2ed925f63 100644 --- a/packages/jbrowse-plugin-apollo/src/TabularEditor/HybridGrid/NumberCell.tsx +++ b/packages/jbrowse-plugin-apollo/src/TabularEditor/HybridGrid/NumberCell.tsx @@ -1,7 +1,7 @@ /* eslint-disable @typescript-eslint/unbound-method */ +import { makeStyles } from '@jbrowse/core/util/tss-react' import { observer } from 'mobx-react' import React, { useEffect, useState } from 'react' -import { makeStyles } from 'tss-react/mui' const useStyles = makeStyles()((theme) => ({ inputWrapper: { diff --git a/packages/jbrowse-plugin-apollo/src/TabularEditor/HybridGrid/ToolBar.tsx b/packages/jbrowse-plugin-apollo/src/TabularEditor/HybridGrid/ToolBar.tsx index f67db21c4..6ba70d146 100644 --- a/packages/jbrowse-plugin-apollo/src/TabularEditor/HybridGrid/ToolBar.tsx +++ b/packages/jbrowse-plugin-apollo/src/TabularEditor/HybridGrid/ToolBar.tsx @@ -1,10 +1,10 @@ /* eslint-disable @typescript-eslint/unbound-method */ +import { makeStyles } from '@jbrowse/core/util/tss-react' import ClearIcon from '@mui/icons-material/Clear' import UnfoldLessIcon from '@mui/icons-material/UnfoldLess' import { IconButton, InputAdornment, TextField, Tooltip } from '@mui/material' import { observer } from 'mobx-react' import React from 'react' -import { makeStyles } from 'tss-react/mui' import { type DisplayStateModel } from '../types' diff --git a/packages/jbrowse-plugin-apollo/src/TabularEditor/model.ts b/packages/jbrowse-plugin-apollo/src/TabularEditor/model.ts index 43ec657fc..6b67812a8 100644 --- a/packages/jbrowse-plugin-apollo/src/TabularEditor/model.ts +++ b/packages/jbrowse-plugin-apollo/src/TabularEditor/model.ts @@ -1,4 +1,5 @@ -import { type Instance, getParent, types } from 'mobx-state-tree' +import { type Instance, getParent, types } from '@jbrowse/mobx-state-tree' +import { entries } from 'mobx' import { type DisplayStateModel } from './types' @@ -21,7 +22,7 @@ export const TabularEditorStateModelType = types collapseAllFeatures() { // iterate over all seen features and set them to collapsed const display = getParent(self) - for (const [featureId] of display.seenFeatures.entries()) { + for (const [featureId] of entries(display.seenFeatures)) { self.featureCollapsed.set(featureId, true) } }, diff --git a/packages/jbrowse-plugin-apollo/src/components/AddAssembly.tsx b/packages/jbrowse-plugin-apollo/src/components/AddAssembly.tsx index 8f458a0fc..cb594346b 100644 --- a/packages/jbrowse-plugin-apollo/src/components/AddAssembly.tsx +++ b/packages/jbrowse-plugin-apollo/src/components/AddAssembly.tsx @@ -10,6 +10,8 @@ import { } from '@apollo-annotation/shared' import { readConfObject } from '@jbrowse/core/configuration' import { type AbstractSessionModel } from '@jbrowse/core/util' +import { makeStyles } from '@jbrowse/core/util/tss-react' +import { getRoot } from '@jbrowse/mobx-state-tree' import InfoIcon from '@mui/icons-material/Info' import LinkIcon from '@mui/icons-material/Link' import RadioButtonCheckedIcon from '@mui/icons-material/RadioButtonChecked' @@ -38,9 +40,7 @@ import { Typography, } from '@mui/material' import ObjectID from 'bson-objectid' -import { getRoot } from 'mobx-state-tree' import React, { useState } from 'react' -import { makeStyles } from 'tss-react/mui' import { type ApolloInternetAccountModel } from '../ApolloInternetAccount/model' import { type ChangeManager } from '../ChangeManager' diff --git a/packages/jbrowse-plugin-apollo/src/components/CopyFeature.tsx b/packages/jbrowse-plugin-apollo/src/components/CopyFeature.tsx index 064445957..f226dab4f 100644 --- a/packages/jbrowse-plugin-apollo/src/components/CopyFeature.tsx +++ b/packages/jbrowse-plugin-apollo/src/components/CopyFeature.tsx @@ -10,6 +10,7 @@ import { import { AddFeatureChange } from '@apollo-annotation/shared' import { readConfObject } from '@jbrowse/core/configuration' import { type AbstractSessionModel } from '@jbrowse/core/util' +import { getSnapshot } from '@jbrowse/mobx-state-tree' import { Button, DialogActions, @@ -22,7 +23,6 @@ import { } from '@mui/material' import ObjectID from 'bson-objectid' import { type IKeyValueMap } from 'mobx' -import { getSnapshot } from 'mobx-state-tree' import React, { useEffect, useState } from 'react' import { type ChangeManager } from '../ChangeManager' diff --git a/packages/jbrowse-plugin-apollo/src/components/CreateApolloAnnotation.tsx b/packages/jbrowse-plugin-apollo/src/components/CreateApolloAnnotation.tsx index 577de75a8..bd3861dd0 100644 --- a/packages/jbrowse-plugin-apollo/src/components/CreateApolloAnnotation.tsx +++ b/packages/jbrowse-plugin-apollo/src/components/CreateApolloAnnotation.tsx @@ -10,6 +10,7 @@ import { } from '@apollo-annotation/shared' import { type Assembly } from '@jbrowse/core/assemblyManager/assembly' import { type AbstractSessionModel } from '@jbrowse/core/util' +import { getSnapshot } from '@jbrowse/mobx-state-tree' import { Box, Button, @@ -26,7 +27,6 @@ import { Typography, } from '@mui/material' import ObjectID from 'bson-objectid' -import { getSnapshot } from 'mobx-state-tree' import React, { useEffect, useMemo, useState } from 'react' import { type ApolloSessionModel } from '../session' diff --git a/packages/jbrowse-plugin-apollo/src/components/DeleteAssembly.tsx b/packages/jbrowse-plugin-apollo/src/components/DeleteAssembly.tsx index 52d22e695..da16dc691 100644 --- a/packages/jbrowse-plugin-apollo/src/components/DeleteAssembly.tsx +++ b/packages/jbrowse-plugin-apollo/src/components/DeleteAssembly.tsx @@ -1,6 +1,7 @@ /* eslint-disable @typescript-eslint/unbound-method */ /* eslint-disable @typescript-eslint/no-misused-promises */ import { DeleteAssemblyChange } from '@apollo-annotation/shared' +import { getRoot } from '@jbrowse/mobx-state-tree' import { Button, Checkbox, @@ -13,7 +14,6 @@ import { Select, type SelectChangeEvent, } from '@mui/material' -import { getRoot } from 'mobx-state-tree' import React, { useState } from 'react' import { type ApolloInternetAccountModel } from '../ApolloInternetAccount/model' diff --git a/packages/jbrowse-plugin-apollo/src/components/DeleteFeature.tsx b/packages/jbrowse-plugin-apollo/src/components/DeleteFeature.tsx index aa2ff90f6..30538b363 100644 --- a/packages/jbrowse-plugin-apollo/src/components/DeleteFeature.tsx +++ b/packages/jbrowse-plugin-apollo/src/components/DeleteFeature.tsx @@ -6,13 +6,13 @@ import { LocationEndChange, LocationStartChange, } from '@apollo-annotation/shared' +import { getSnapshot } from '@jbrowse/mobx-state-tree' import { Button, DialogActions, DialogContent, DialogContentText, } from '@mui/material' -import { getSnapshot } from 'mobx-state-tree' import React, { useState } from 'react' import { type ChangeManager } from '../ChangeManager' diff --git a/packages/jbrowse-plugin-apollo/src/components/Dialog.tsx b/packages/jbrowse-plugin-apollo/src/components/Dialog.tsx index c0b0da54c..e31d9d1e2 100644 --- a/packages/jbrowse-plugin-apollo/src/components/Dialog.tsx +++ b/packages/jbrowse-plugin-apollo/src/components/Dialog.tsx @@ -1,10 +1,10 @@ /* eslint-disable @typescript-eslint/unbound-method */ import { Dialog as JBDialog } from '@jbrowse/core/ui' +import { makeStyles } from '@jbrowse/core/util/tss-react' import CloseIcon from '@mui/icons-material/Close' import { type DialogProps, DialogTitle, IconButton } from '@mui/material' import { observer } from 'mobx-react' import React from 'react' -import { makeStyles } from 'tss-react/mui' const useStyles = makeStyles()((theme) => ({ dialogTitle: { diff --git a/packages/jbrowse-plugin-apollo/src/components/DownloadGFF3.tsx b/packages/jbrowse-plugin-apollo/src/components/DownloadGFF3.tsx index 0c2d05b96..c9eab6506 100644 --- a/packages/jbrowse-plugin-apollo/src/components/DownloadGFF3.tsx +++ b/packages/jbrowse-plugin-apollo/src/components/DownloadGFF3.tsx @@ -8,6 +8,7 @@ import { annotationFeatureToGFF3 } from '@apollo-annotation/shared' import { type GFF3Item, formatSync } from '@gmod/gff' import { type Assembly } from '@jbrowse/core/assemblyManager/assembly' import { getConf } from '@jbrowse/core/configuration' +import { type IMSTMap, getSnapshot } from '@jbrowse/mobx-state-tree' import { Button, Checkbox, @@ -21,7 +22,6 @@ import { type SelectChangeEvent, } from '@mui/material' import { saveAs } from 'file-saver' -import { type IMSTMap, getSnapshot } from 'mobx-state-tree' import React, { useState } from 'react' import { diff --git a/packages/jbrowse-plugin-apollo/src/components/LogOut.tsx b/packages/jbrowse-plugin-apollo/src/components/LogOut.tsx index a6a5657ae..3f9a97282 100644 --- a/packages/jbrowse-plugin-apollo/src/components/LogOut.tsx +++ b/packages/jbrowse-plugin-apollo/src/components/LogOut.tsx @@ -1,4 +1,5 @@ /* eslint-disable @typescript-eslint/unbound-method */ +import { getRoot } from '@jbrowse/mobx-state-tree' import { Button, DialogActions, @@ -8,7 +9,6 @@ import { Select, type SelectChangeEvent, } from '@mui/material' -import { getRoot } from 'mobx-state-tree' import React, { useState } from 'react' import { type ApolloInternetAccountModel } from '../ApolloInternetAccount/model' diff --git a/packages/jbrowse-plugin-apollo/src/components/ManageChecks.tsx b/packages/jbrowse-plugin-apollo/src/components/ManageChecks.tsx index 88c591e71..27970c0d3 100644 --- a/packages/jbrowse-plugin-apollo/src/components/ManageChecks.tsx +++ b/packages/jbrowse-plugin-apollo/src/components/ManageChecks.tsx @@ -2,6 +2,7 @@ /* eslint-disable @typescript-eslint/unbound-method */ /* eslint-disable @typescript-eslint/no-misused-promises */ import { type AbstractSessionModel } from '@jbrowse/core/util' +import { getRoot } from '@jbrowse/mobx-state-tree' import { Button, Checkbox, @@ -19,7 +20,6 @@ import { TableHead, TableRow, } from '@mui/material' -import { getRoot } from 'mobx-state-tree' import React, { useEffect, useState } from 'react' import { type ApolloInternetAccountModel } from '../ApolloInternetAccount/model' diff --git a/packages/jbrowse-plugin-apollo/src/components/ManageUsers.tsx b/packages/jbrowse-plugin-apollo/src/components/ManageUsers.tsx index 3dfe8374c..aabbdf217 100644 --- a/packages/jbrowse-plugin-apollo/src/components/ManageUsers.tsx +++ b/packages/jbrowse-plugin-apollo/src/components/ManageUsers.tsx @@ -7,6 +7,7 @@ /* eslint-disable @typescript-eslint/no-unsafe-return */ import { DeleteUserChange, UserChange } from '@apollo-annotation/shared' import { type AbstractRootModel } from '@jbrowse/core/util' +import { getRoot } from '@jbrowse/mobx-state-tree' import DeleteIcon from '@mui/icons-material/Delete' import { Button, @@ -27,7 +28,6 @@ import { type GridRowParams, GridToolbar, } from '@mui/x-data-grid' -import { getRoot } from 'mobx-state-tree' import React, { useEffect, useState } from 'react' import { type ApolloInternetAccountModel } from '../ApolloInternetAccount/model' diff --git a/packages/jbrowse-plugin-apollo/src/components/MergeExons.tsx b/packages/jbrowse-plugin-apollo/src/components/MergeExons.tsx index 675b40609..8f9b6f92b 100644 --- a/packages/jbrowse-plugin-apollo/src/components/MergeExons.tsx +++ b/packages/jbrowse-plugin-apollo/src/components/MergeExons.tsx @@ -2,6 +2,7 @@ import { type AnnotationFeature } from '@apollo-annotation/mst' import { MergeExonsChange } from '@apollo-annotation/shared' +import { getSnapshot } from '@jbrowse/mobx-state-tree' import { Box, Button, @@ -14,7 +15,6 @@ import { RadioGroup, type SelectChangeEvent, } from '@mui/material' -import { getSnapshot } from 'mobx-state-tree' import React, { useState } from 'react' import { type ChangeManager } from '../ChangeManager' diff --git a/packages/jbrowse-plugin-apollo/src/components/MergeTranscripts.tsx b/packages/jbrowse-plugin-apollo/src/components/MergeTranscripts.tsx index 2de2b47b9..963916870 100644 --- a/packages/jbrowse-plugin-apollo/src/components/MergeTranscripts.tsx +++ b/packages/jbrowse-plugin-apollo/src/components/MergeTranscripts.tsx @@ -1,6 +1,7 @@ /* eslint-disable @typescript-eslint/unbound-method */ import { type AnnotationFeature } from '@apollo-annotation/mst' import { MergeTranscriptsChange } from '@apollo-annotation/shared' +import { getSnapshot } from '@jbrowse/mobx-state-tree' import { Box, Button, @@ -13,7 +14,6 @@ import { RadioGroup, type SelectChangeEvent, } from '@mui/material' -import { getSnapshot } from 'mobx-state-tree' import React, { useState } from 'react' import { type ChangeManager } from '../ChangeManager' diff --git a/packages/jbrowse-plugin-apollo/src/components/OntologyTermMultiSelect.tsx b/packages/jbrowse-plugin-apollo/src/components/OntologyTermMultiSelect.tsx index 184b721bf..43cabd0ce 100644 --- a/packages/jbrowse-plugin-apollo/src/components/OntologyTermMultiSelect.tsx +++ b/packages/jbrowse-plugin-apollo/src/components/OntologyTermMultiSelect.tsx @@ -2,6 +2,7 @@ /* eslint-disable @typescript-eslint/use-unknown-in-catch-callback-variable */ /* eslint-disable @typescript-eslint/no-unnecessary-condition */ import { isAbortException } from '@jbrowse/core/util/aborting' +import { getParent } from '@jbrowse/mobx-state-tree' import { Autocomplete, type AutocompleteRenderValueGetItemProps, @@ -14,7 +15,6 @@ import { import { debounce } from '@mui/material/utils' import highlightMatch from 'autosuggest-highlight/match' import highlightParse from 'autosuggest-highlight/parse' -import { getParent } from 'mobx-state-tree' import * as React from 'react' import { diff --git a/packages/jbrowse-plugin-apollo/src/components/SplitExon.tsx b/packages/jbrowse-plugin-apollo/src/components/SplitExon.tsx index 9d4586f12..e3874cf2c 100644 --- a/packages/jbrowse-plugin-apollo/src/components/SplitExon.tsx +++ b/packages/jbrowse-plugin-apollo/src/components/SplitExon.tsx @@ -5,6 +5,7 @@ import { type AnnotationFeatureSnapshot, } from '@apollo-annotation/mst' import { SplitExonChange } from '@apollo-annotation/shared' +import { getSnapshot } from '@jbrowse/mobx-state-tree' import { Button, DialogActions, @@ -12,7 +13,6 @@ import { DialogContentText, } from '@mui/material' import ObjectID from 'bson-objectid' -import { getSnapshot } from 'mobx-state-tree' import React, { useState } from 'react' import { type ChangeManager } from '../ChangeManager' diff --git a/packages/jbrowse-plugin-apollo/src/components/ViewChangeLog.tsx b/packages/jbrowse-plugin-apollo/src/components/ViewChangeLog.tsx index 320bcc9f0..8bed28af3 100644 --- a/packages/jbrowse-plugin-apollo/src/components/ViewChangeLog.tsx +++ b/packages/jbrowse-plugin-apollo/src/components/ViewChangeLog.tsx @@ -6,6 +6,8 @@ /* eslint-disable @typescript-eslint/no-unsafe-member-access */ /* eslint-disable @typescript-eslint/no-unsafe-return */ import { changeRegistry } from '@apollo-annotation/common' +import { makeStyles } from '@jbrowse/core/util/tss-react' +import { getRoot } from '@jbrowse/mobx-state-tree' import { Button, DialogActions, @@ -21,9 +23,7 @@ import { type GridRowsProp, GridToolbar, } from '@mui/x-data-grid' -import { getRoot } from 'mobx-state-tree' import React, { useEffect, useState } from 'react' -import { makeStyles } from 'tss-react/mui' import { type ApolloInternetAccountModel } from '../ApolloInternetAccount/model' import { diff --git a/packages/jbrowse-plugin-apollo/src/components/ViewCheckResults.tsx b/packages/jbrowse-plugin-apollo/src/components/ViewCheckResults.tsx index 2c9479a7d..0e8303dec 100644 --- a/packages/jbrowse-plugin-apollo/src/components/ViewCheckResults.tsx +++ b/packages/jbrowse-plugin-apollo/src/components/ViewCheckResults.tsx @@ -4,6 +4,7 @@ /* eslint-disable @typescript-eslint/no-unsafe-argument */ /* eslint-disable @typescript-eslint/no-unsafe-member-access */ /* eslint-disable @typescript-eslint/no-unsafe-return */ +import { getRoot } from '@jbrowse/mobx-state-tree' import { Button, DialogActions, @@ -19,7 +20,6 @@ import { type GridRowsProp, GridToolbar, } from '@mui/x-data-grid' -import { getRoot } from 'mobx-state-tree' import React, { useEffect, useState } from 'react' import { type ApolloInternetAccountModel } from '../ApolloInternetAccount/model' diff --git a/packages/jbrowse-plugin-apollo/src/config.ts b/packages/jbrowse-plugin-apollo/src/config.ts index 411223d52..0960d4bc5 100644 --- a/packages/jbrowse-plugin-apollo/src/config.ts +++ b/packages/jbrowse-plugin-apollo/src/config.ts @@ -1,5 +1,5 @@ import { ConfigurationSchema } from '@jbrowse/core/configuration' -import { types } from 'mobx-state-tree' +import { types } from '@jbrowse/mobx-state-tree' import { OntologyRecordConfiguration } from './OntologyManager' diff --git a/packages/jbrowse-plugin-apollo/src/extensions/annotationFromJBrowseFeature.ts b/packages/jbrowse-plugin-apollo/src/extensions/annotationFromJBrowseFeature.ts index 93985b9d9..899fed311 100644 --- a/packages/jbrowse-plugin-apollo/src/extensions/annotationFromJBrowseFeature.ts +++ b/packages/jbrowse-plugin-apollo/src/extensions/annotationFromJBrowseFeature.ts @@ -7,8 +7,8 @@ import { type AnnotationFeatureSnapshot } from '@apollo-annotation/mst' import { gff3ToAnnotationFeature } from '@apollo-annotation/shared' import { type GFF3Feature } from '@gmod/gff' import { type Assembly } from '@jbrowse/core/assemblyManager/assembly' +import { type PluggableElementType } from '@jbrowse/core/pluggableElementTypes' import type DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType' -import type PluggableElementBase from '@jbrowse/core/pluggableElementTypes/PluggableElementBase' import { type AbstractSessionModel, getContainingView, @@ -84,7 +84,7 @@ function convertFeatureAttributes(feature: Feature): Record { } export function annotationFromJBrowseFeature( - pluggableElement: PluggableElementBase, + pluggableElement: PluggableElementType, ) { if (pluggableElement.name !== 'LinearBasicDisplay') { return pluggableElement diff --git a/packages/jbrowse-plugin-apollo/src/extensions/annotationFromPileup.ts b/packages/jbrowse-plugin-apollo/src/extensions/annotationFromPileup.ts index c064996a8..090d41369 100644 --- a/packages/jbrowse-plugin-apollo/src/extensions/annotationFromPileup.ts +++ b/packages/jbrowse-plugin-apollo/src/extensions/annotationFromPileup.ts @@ -5,8 +5,10 @@ /* eslint-disable @typescript-eslint/no-unsafe-return */ import { type AnnotationFeatureSnapshot } from '@apollo-annotation/mst' import { type Assembly } from '@jbrowse/core/assemblyManager/assembly' -import { type DisplayType } from '@jbrowse/core/pluggableElementTypes' -import type PluggableElementBase from '@jbrowse/core/pluggableElementTypes/PluggableElementBase' +import { + type DisplayType, + type PluggableElementType, +} from '@jbrowse/core/pluggableElementTypes' import { type AbstractSessionModel, getContainingView, @@ -30,7 +32,7 @@ function parseCigar(cigar: string): [string, number][] { return result } -export function annotationFromPileup(pluggableElement: PluggableElementBase) { +export function annotationFromPileup(pluggableElement: PluggableElementType) { if (pluggableElement.name !== 'LinearPileupDisplay') { return pluggableElement } diff --git a/packages/jbrowse-plugin-apollo/src/makeDisplayComponent.tsx b/packages/jbrowse-plugin-apollo/src/makeDisplayComponent.tsx index 3d82b9778..2e85b1567 100644 --- a/packages/jbrowse-plugin-apollo/src/makeDisplayComponent.tsx +++ b/packages/jbrowse-plugin-apollo/src/makeDisplayComponent.tsx @@ -1,11 +1,11 @@ /* eslint-disable @typescript-eslint/unbound-method */ import { getSession } from '@jbrowse/core/util' +import { makeStyles } from '@jbrowse/core/util/tss-react' import ExpandLessIcon from '@mui/icons-material/ExpandLess' import ExpandMoreIcon from '@mui/icons-material/ExpandMore' import { Alert, Typography, alpha } from '@mui/material' import { observer } from 'mobx-react' import React, { useCallback, useEffect, useRef } from 'react' -import { makeStyles } from 'tss-react/mui' import { LinearApolloDisplay } from './LinearApolloDisplay/components' import { type LinearApolloDisplay as LinearApolloDisplayI } from './LinearApolloDisplay/stateModel' diff --git a/packages/jbrowse-plugin-apollo/src/session/ClientDataStore.ts b/packages/jbrowse-plugin-apollo/src/session/ClientDataStore.ts index e22349fdc..33a8587c3 100644 --- a/packages/jbrowse-plugin-apollo/src/session/ClientDataStore.ts +++ b/packages/jbrowse-plugin-apollo/src/session/ClientDataStore.ts @@ -13,14 +13,16 @@ import { CheckResult, type CheckResultSnapshot, } from '@apollo-annotation/mst' -import { getConf, readConfObject } from '@jbrowse/core/configuration' -import { type ConfigurationModel } from '@jbrowse/core/configuration/types' +import { + type AnyConfigurationModel, + getConf, + readConfObject, +} from '@jbrowse/core/configuration' import { type Region, getSession, isElectron } from '@jbrowse/core/util' import { type LocalPathLocation, type UriLocation, } from '@jbrowse/core/util/types/mst' -import { autorun } from 'mobx' import { type Instance, addDisposer, @@ -29,7 +31,8 @@ import { getRoot, resolveIdentifier, types, -} from 'mobx-state-tree' +} from '@jbrowse/mobx-state-tree' +import { autorun } from 'mobx' import { type ApolloInternetAccount, @@ -41,7 +44,6 @@ import { import { ChangeManager } from '../ChangeManager' import { OntologyManagerType, - type OntologyRecordConfiguration, type TextIndexFieldDefinition, } from '../OntologyManager' import type ApolloPluginConfigurationSchema from '../config' @@ -177,9 +179,7 @@ export function clientDataStoreFactory( // take precedence over the ontologies in the configuration. const { ontologyManager, pluginConfiguration } = self const configuredOntologies = - pluginConfiguration.ontologies as ConfigurationModel< - typeof OntologyRecordConfiguration - >[] + pluginConfiguration.ontologies as AnyConfigurationModel[] for (const ont of configuredOntologies || []) { const [name, version, source, indexFields] = [ readConfObject(ont, 'name') as string, diff --git a/packages/jbrowse-plugin-apollo/src/session/session.ts b/packages/jbrowse-plugin-apollo/src/session/session.ts index bf983dcd6..e5a90425a 100644 --- a/packages/jbrowse-plugin-apollo/src/session/session.ts +++ b/packages/jbrowse-plugin-apollo/src/session/session.ts @@ -1,4 +1,3 @@ -/* eslint-disable @typescript-eslint/no-unsafe-return */ /* eslint-disable @typescript-eslint/no-unnecessary-condition */ /* eslint-disable @typescript-eslint/no-unsafe-assignment */ import { type ClientDataStore as ClientDataStoreType } from '@apollo-annotation/common' @@ -20,9 +19,6 @@ import { type AbstractSessionModel, type SessionWithAddTracks, } from '@jbrowse/core/util' -import { type LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view' -import SaveIcon from '@mui/icons-material/Save' -import { autorun, observable } from 'mobx' import { type Instance, type SnapshotOut, @@ -31,7 +27,10 @@ import { getRoot, getSnapshot, types, -} from 'mobx-state-tree' +} from '@jbrowse/mobx-state-tree' +import { type LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view' +import SaveIcon from '@mui/icons-material/Save' +import { autorun, observable } from 'mobx' import { type ApolloInternetAccountModel } from '../ApolloInternetAccount/model' import { ApolloJobModel } from '../ApolloJobModel' diff --git a/packages/jbrowse-plugin-apollo/src/util/displayUtils.ts b/packages/jbrowse-plugin-apollo/src/util/displayUtils.ts index 4883febb0..708f79d76 100644 --- a/packages/jbrowse-plugin-apollo/src/util/displayUtils.ts +++ b/packages/jbrowse-plugin-apollo/src/util/displayUtils.ts @@ -1,7 +1,6 @@ import { type CheckResultIdsType } from '@apollo-annotation/mst' +import { makeStyles } from '@jbrowse/core/util/tss-react' import { type Theme } from '@mui/material' -import { makeStyles } from 'tss-react/mui' - export { default as EditZoomThresholdDialog } from '../components/EditZoomThresholdDialog' export type Coord = [number, number] diff --git a/packages/jbrowse-plugin-apollo/src/util/index.ts b/packages/jbrowse-plugin-apollo/src/util/index.ts index 972f55b06..4f734d87b 100644 --- a/packages/jbrowse-plugin-apollo/src/util/index.ts +++ b/packages/jbrowse-plugin-apollo/src/util/index.ts @@ -1,4 +1,4 @@ -import { getParent } from 'mobx-state-tree' +import { getParent } from '@jbrowse/mobx-state-tree' import { type ApolloInternetAccountModel } from '../ApolloInternetAccount/model' import { type ApolloSessionModel } from '../session' diff --git a/packages/jbrowse-plugin-apollo/src/util/loadAssemblyIntoClient.ts b/packages/jbrowse-plugin-apollo/src/util/loadAssemblyIntoClient.ts index e6c0ec2b2..d211d57e5 100644 --- a/packages/jbrowse-plugin-apollo/src/util/loadAssemblyIntoClient.ts +++ b/packages/jbrowse-plugin-apollo/src/util/loadAssemblyIntoClient.ts @@ -10,7 +10,7 @@ import { type GFF3Sequence, parseStringSync, } from '@gmod/gff' -import { getSnapshot } from 'mobx-state-tree' +import { getSnapshot } from '@jbrowse/mobx-state-tree' export async function loadAssemblyIntoClient( assemblyId: string, diff --git a/packages/website/package.json b/packages/website/package.json index 7e4a2c9d3..4ce7cbfd0 100755 --- a/packages/website/package.json +++ b/packages/website/package.json @@ -19,7 +19,7 @@ "@mdx-js/react": "^3.0.0", "clsx": "^1.1.1", "prism-react-renderer": "^2.3.0", - "react": "^18.2.0", + "react": ">=18.0.0", "react-dom": "^18.2.0" }, "devDependencies": { diff --git a/yarn.lock b/yarn.lock index f7a98680f..011acc38f 100644 --- a/yarn.lock +++ b/yarn.lock @@ -350,7 +350,7 @@ __metadata: open: "npm:^10.1.0" prettier: "npm:^3.3.2" react-dom: "npm:^18.2.0" - rxjs: "npm:^7.4.0" + rxjs: "npm:^7.8.2" serve: "npm:^14.0.1" shx: "npm:^0.3.3" ts-node: "npm:^10.3.0" @@ -376,8 +376,9 @@ __metadata: "@emotion/styled": "npm:^11.10.6" "@gmod/gff": "npm:^2.0.0" "@gmod/indexedfasta": "npm:^2.0.4" - "@jbrowse/core": "npm:^3.6.5" - "@mui/material": "npm:^7.0.0" + "@jbrowse/core": "npm:^4.1.1" + "@jbrowse/mobx-state-tree": "npm:^5.5.0" + "@mui/material": "npm:^7.3.7" "@nestjs/cli": "npm:^10.1.10" "@nestjs/common": "npm:^10.1.0" "@nestjs/config": "npm:^3.0.0" @@ -414,9 +415,8 @@ __metadata: jest: "npm:^29.6.2" joi: "npm:^17.7.0" material-ui-popup-state: "npm:^5.0.4" - mobx: "npm:^6.6.1" - mobx-react: "npm:^7.2.1" - mobx-state-tree: "npm:^5.4.0" + mobx: "npm:^6.15.0" + mobx-react: "npm:^9.2.1" mongodb: "npm:^4.7.0" mongoose: "npm:^6.12.0" mongoose-id-validator: "npm:^0.6.0" @@ -427,12 +427,11 @@ __metadata: passport-jwt: "npm:^4.0.0" passport-local: "npm:^1.0.0" passport-microsoft: "npm:^1.0.0" - prop-types: "npm:^15.8.1" - react: "npm:^18.2.0" + react: "npm:>=18.0.0" react-dom: "npm:^18.2.0" reflect-metadata: "npm:^0.1.13" rimraf: "npm:^3.0.2" - rxjs: "npm:^7.4.0" + rxjs: "npm:^7.8.2" sanitize-filename: "npm:^1.6.3" serve: "npm:^14.0.1" socket.io: "npm:^4.5.3" @@ -445,7 +444,6 @@ __metadata: ts-node-dev: "npm:^1.1.8" tsconfig-paths: "npm:^3.11.0" tslib: "npm:^2.3.1" - tss-react: "npm:^4.6.1" typescript: "npm:^5.5.3" languageName: unknown linkType: soft @@ -457,7 +455,7 @@ __metadata: "@apollo-annotation/mst": "workspace:^" "@apollo-annotation/schemas": "workspace:^" "@gmod/gff": "npm:^2.0.0" - "@jbrowse/core": "npm:^3.6.5" + "@jbrowse/core": "npm:^4.1.1" "@nestjs/common": "npm:^10.1.0" "@nestjs/core": "npm:^10.1.0" "@types/node": "npm:^20.19.15" @@ -467,16 +465,14 @@ __metadata: tslib: "npm:^2.3.1" typescript: "npm:^5.5.3" peerDependencies: - "@mui/material": ^7.0.0 - "@mui/x-data-grid": ^8.0.0 - mobx: ^6.6.1 - mobx-react: ^7.2.1 - mobx-state-tree: ^5.4.0 - prop-types: ^15.8.1 - react: ^18.2.0 + "@jbrowse/mobx-state-tree": ^5.5.0 + "@mui/material": ^7.3.7 + "@mui/x-data-grid": ^8.26.0 + mobx: ^6.15.0 + mobx-react: ^9.2.1 + react: ">=18.0.0" react-dom: ^18.2.0 - rxjs: ^7.4.0 - tss-react: ^4.6.1 + rxjs: ^7.8.2 languageName: unknown linkType: soft @@ -490,15 +486,16 @@ __metadata: "@emotion/react": "npm:^11.10.6" "@emotion/styled": "npm:^11.10.6" "@gmod/gff": "npm:^2.0.0" - "@jbrowse/cli": "npm:^3.6.5" - "@jbrowse/core": "npm:^3.6.5" + "@jbrowse/cli": "npm:^4.1.1" + "@jbrowse/core": "npm:^4.1.1" "@jbrowse/development-tools": "npm:^2.2.1" - "@jbrowse/plugin-authentication": "npm:^3.6.5" - "@jbrowse/plugin-linear-genome-view": "npm:^3.6.5" + "@jbrowse/mobx-state-tree": "npm:^5.5.0" + "@jbrowse/plugin-authentication": "npm:^4.1.1" + "@jbrowse/plugin-linear-genome-view": "npm:^4.1.1" "@jest/globals": "npm:^29.0.3" "@mui/icons-material": "npm:^6.5.0" - "@mui/material": "npm:^7.0.0" - "@mui/x-data-grid": "npm:^8.0.0" + "@mui/material": "npm:^7.3.7" + "@mui/x-data-grid": "npm:^8.26.0" "@types/autosuggest-highlight": "npm:^3" "@types/file-saver": "npm:^2" "@types/jsonpath": "npm:^0.2.0" @@ -522,17 +519,15 @@ __metadata: jest-fetch-mock: "npm:^3.0.3" jsonpath: "npm:^1.1.1" librpc-web-mod: "npm:^1.1.9" - mobx: "npm:^6.6.1" - mobx-react: "npm:^7.2.1" - mobx-state-tree: "npm:^5.4.0" + mobx: "npm:^6.15.0" + mobx-react: "npm:^9.2.1" nanoid: "npm:^4.0.2" npm-run-all: "npm:^4.1.5" - prop-types: "npm:^15.8.1" - react: "npm:^18.2.0" + react: "npm:>=18.0.0" react-dom: "npm:^18.2.0" rimraf: "npm:^3.0.2" - rollup: "npm:^2.79.2" - rxjs: "npm:^7.4.0" + rollup: "npm:^3.29.5" + rxjs: "npm:^7.8.2" serve: "npm:^14.0.1" shx: "npm:^0.3.3" socket.io-client: "npm:^4.5.4" @@ -540,19 +535,16 @@ __metadata: ts-jest: "npm:^29.1.1" ts-node: "npm:^10.3.0" tslib: "npm:^2.3.1" - tss-react: "npm:^4.6.1" typescript: "npm:^5.5.3" peerDependencies: - "@jbrowse/core": ^3.0.1 - "@mui/material": ^7.0.0 - mobx: ^6.6.1 + "@jbrowse/core": ^4.1.1 + "@jbrowse/mobx-state-tree": ^5.5.0 + "@mui/material": ^7.3.7 + mobx: ^6.15.0 mobx-react: ^9.0.0 - mobx-state-tree: ^5.4.0 - prop-types: ^15.8.1 - react: ^18.2.0 + react: ">=18.0.0" react-dom: ^18.2.0 - rxjs: ^7.4.0 - tss-react: ^4.6.1 + rxjs: ^7.8.2 languageName: unknown linkType: soft @@ -560,11 +552,11 @@ __metadata: version: 0.0.0-use.local resolution: "@apollo-annotation/mst@workspace:packages/apollo-mst" dependencies: - "@jbrowse/core": "npm:^3.6.5" - mobx: "npm:^6.6.1" - mobx-state-tree: "npm:^5.4.0" + "@jbrowse/core": "npm:^4.1.1" + "@jbrowse/mobx-state-tree": "npm:^5.5.0" + mobx: "npm:^6.15.0" react-dom: "npm:^18.2.0" - rxjs: "npm:^7.4.0" + rxjs: "npm:^7.8.2" tslib: "npm:^2.3.1" typescript: "npm:^5.5.3" languageName: unknown @@ -581,7 +573,7 @@ __metadata: "@types/node": "npm:^20.19.15" mongoose: "npm:^6.12.0" reflect-metadata: "npm:^0.1.13" - rxjs: "npm:^7.4.0" + rxjs: "npm:^7.8.2" tslib: "npm:^2.3.1" typescript: "npm:^5.5.3" languageName: unknown @@ -596,7 +588,8 @@ __metadata: "@apollo-annotation/schemas": "workspace:^" "@gmod/gff": "npm:^2.0.0" "@gmod/indexedfasta": "npm:^2.0.4" - "@jbrowse/core": "npm:^3.6.5" + "@jbrowse/core": "npm:^4.1.1" + "@jbrowse/mobx-state-tree": "npm:^5.5.0" "@nestjs/common": "npm:^10.1.0" "@nestjs/core": "npm:^10.1.0" "@types/chai": "npm:^4.3.19" @@ -607,25 +600,23 @@ __metadata: generic-filehandle: "npm:^3.0.0" glob: "npm:^11.0.0" jwt-decode: "npm:^3.1.2" - mobx: "npm:^6.6.1" - mobx-state-tree: "npm:^5.4.0" + mobx: "npm:^6.15.0" mongoose: "npm:^6.12.0" react-dom: "npm:^18.2.0" rimraf: "npm:^3.0.2" - rxjs: "npm:^7.4.0" + rxjs: "npm:^7.8.2" tslib: "npm:^2.3.1" tsx: "npm:^4.6.2" typescript: "npm:^5.5.3" peerDependencies: - "@mui/material": ^7.0.0 - "@mui/x-data-grid": ^8.0.0 - mobx: ^6.6.1 - mobx-react: ^7.2.1 - mobx-state-tree: ^5.4.0 - prop-types: ^15.8.1 - react: ^18.2.0 + "@jbrowse/mobx-state-tree": ^5.5.0 + "@mui/material": ^7.3.7 + "@mui/x-data-grid": ^8.26.0 + mobx: ^6.15.0 + mobx-react: ^9.2.1 + react: ">=18.0.0" react-dom: ^18.2.0 - rxjs: ^7.4.0 + rxjs: ^7.8.2 languageName: unknown linkType: soft @@ -645,7 +636,7 @@ __metadata: "@types/react": "npm:^18.3.4" clsx: "npm:^1.1.1" prism-react-renderer: "npm:^2.3.0" - react: "npm:^18.2.0" + react: "npm:>=18.0.0" react-dom: "npm:^18.2.0" typescript: "npm:^5.5.3" languageName: unknown @@ -4651,7 +4642,7 @@ __metadata: languageName: node linkType: hard -"@babel/runtime@npm:^7.10.2, @babel/runtime@npm:^7.12.5, @babel/runtime@npm:^7.18.3, @babel/runtime@npm:^7.20.6, @babel/runtime@npm:^7.23.1, @babel/runtime@npm:^7.5.5, @babel/runtime@npm:^7.8.4, @babel/runtime@npm:^7.8.7": +"@babel/runtime@npm:^7.12.5, @babel/runtime@npm:^7.18.3, @babel/runtime@npm:^7.20.6, @babel/runtime@npm:^7.23.1, @babel/runtime@npm:^7.5.5, @babel/runtime@npm:^7.8.4, @babel/runtime@npm:^7.8.7": version: 7.23.1 resolution: "@babel/runtime@npm:7.23.1" dependencies: @@ -4660,13 +4651,20 @@ __metadata: 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"@emotion/cache": "npm:*" - "@emotion/serialize": "npm:*" - "@emotion/utils": "npm:*" - peerDependencies: - "@emotion/react": ^11.4.1 - "@emotion/server": ^11.4.0 - "@mui/material": ^5.0.0 - react: ^16.8.0 || ^17.0.2 || ^18.0.0 - peerDependenciesMeta: - "@emotion/server": - optional: true - "@mui/material": - optional: true - checksum: 10c0/edbb3679b493d7921a9c79be6c2e66112cd59760a6edeea67e2660c19e799726232ad56f93a124db39df761379e4d0cfb4878b2507475fb8b7a8379caa4b38d1 - languageName: node - linkType: hard - "tsx@npm:^4.6.2": version: 4.6.2 resolution: "tsx@npm:4.6.2" @@ -30978,7 +31011,7 @@ __metadata: languageName: node linkType: hard -"type-is@npm:^2.0.0, type-is@npm:^2.0.1": +"type-is@npm:^2.0.1": version: 2.0.1 resolution: "type-is@npm:2.0.1" dependencies: @@ -31779,12 +31812,12 @@ __metadata: languageName: node linkType: hard -"use-sync-external-store@npm:^1.5.0": - version: 1.5.0 - resolution: "use-sync-external-store@npm:1.5.0" +"use-sync-external-store@npm:^1.6.0": + version: 1.6.0 + resolution: "use-sync-external-store@npm:1.6.0" peerDependencies: react: ^16.8.0 || ^17.0.0 || ^18.0.0 || ^19.0.0 - checksum: 10c0/1b8663515c0be34fa653feb724fdcce3984037c78dd4a18f68b2c8be55cc1a1084c578d5b75f158d41b5ddffc2bf5600766d1af3c19c8e329bb20af2ec6f52f4 + checksum: 10c0/35e1179f872a53227bdf8a827f7911da4c37c0f4091c29b76b1e32473d1670ebe7bcd880b808b7549ba9a5605c233350f800ffab963ee4a4ee346ee983b6019b languageName: node linkType: hard From b5aeb5556fcc6afcce86f2e6229455196e9b964b Mon Sep 17 00:00:00 2001 From: Garrett Stevens Date: Tue, 27 Jan 2026 21:48:52 +0000 Subject: [PATCH 5/9] More strict react versions --- package.json | 2 +- packages/apollo-cli/README.md | 1255 ----------------- packages/apollo-cli/package.json | 2 +- .../apollo-collaboration-server/package.json | 4 +- packages/apollo-common/package.json | 4 +- packages/apollo-mst/package.json | 2 +- packages/apollo-shared/package.json | 6 +- packages/jbrowse-plugin-apollo/package.json | 6 +- packages/website/package.json | 4 +- 9 files changed, 15 insertions(+), 1270 deletions(-) diff --git a/package.json b/package.json index 27a841d18..47700df21 100644 --- a/package.json +++ b/package.json @@ -41,7 +41,7 @@ "npm-run-all": "^4.1.5", "prettier": "^3.3.2", "prettier-plugin-packagejson": "^2.5.2", - "react": ">=18.0.0", + "react": "^18.3.1", "semver": "^7.6.3", "tslib": "^2.3.1", "tsx": "^4.6.2", diff --git a/packages/apollo-cli/README.md b/packages/apollo-cli/README.md index 18e82a90d..06041d6de 100644 --- a/packages/apollo-cli/README.md +++ b/packages/apollo-cli/README.md @@ -29,972 +29,7 @@ USAGE -- [`apollo assembly add-from-fasta INPUT`](#apollo-assembly-add-from-fasta-input) -- [`apollo assembly add-from-gff INPUT-FILE`](#apollo-assembly-add-from-gff-input-file) -- [`apollo assembly check`](#apollo-assembly-check) -- [`apollo assembly delete`](#apollo-assembly-delete) -- [`apollo assembly get`](#apollo-assembly-get) -- [`apollo assembly sequence`](#apollo-assembly-sequence) -- [`apollo change get`](#apollo-change-get) -- [`apollo config [KEY] [VALUE]`](#apollo-config-key-value) -- [`apollo export gff3 ASSEMBLY`](#apollo-export-gff3-assembly) -- [`apollo feature add [FEATURE-JSON]`](#apollo-feature-add-feature-json) -- [`apollo feature add-child`](#apollo-feature-add-child) -- [`apollo feature check`](#apollo-feature-check) -- [`apollo feature copy`](#apollo-feature-copy) -- [`apollo feature delete`](#apollo-feature-delete) -- [`apollo feature edit`](#apollo-feature-edit) -- [`apollo feature edit-attribute`](#apollo-feature-edit-attribute) -- [`apollo feature edit-coords`](#apollo-feature-edit-coords) -- [`apollo feature edit-type`](#apollo-feature-edit-type) -- [`apollo feature get`](#apollo-feature-get) -- [`apollo feature get-id`](#apollo-feature-get-id) -- [`apollo feature get-indexed-id ID`](#apollo-feature-get-indexed-id-id) -- [`apollo feature import INPUT-FILE`](#apollo-feature-import-input-file) -- [`apollo feature search`](#apollo-feature-search) -- [`apollo file delete`](#apollo-file-delete) -- [`apollo file download`](#apollo-file-download) -- [`apollo file get`](#apollo-file-get) -- [`apollo file upload INPUT-FILE`](#apollo-file-upload-input-file) - [`apollo help [COMMANDS]`](#apollo-help-commands) -- [`apollo jbrowse desktop JBROWSEFILE`](#apollo-jbrowse-desktop-jbrowsefile) -- [`apollo jbrowse get-config`](#apollo-jbrowse-get-config) -- [`apollo jbrowse set-config INPUTFILE`](#apollo-jbrowse-set-config-inputfile) -- [`apollo login`](#apollo-login) -- [`apollo logout`](#apollo-logout) -- [`apollo refseq add-alias INPUT-FILE`](#apollo-refseq-add-alias-input-file) -- [`apollo refseq get`](#apollo-refseq-get) -- [`apollo status`](#apollo-status) -- [`apollo user get`](#apollo-user-get) - -## `apollo assembly add-from-fasta INPUT` - -Add a new assembly from fasta input - -``` -USAGE - $ apollo assembly add-from-fasta INPUT [--profile ] [--config-file ] [-a ] [-f] [-e] [--fai ] - [--gzi ] [-z | -d] - -ARGUMENTS - INPUT Input fasta file, local or remote, or id of a previously uploaded file. For local or remote files, it is - assumed the file is bgzip'd with `bgzip` and indexed with `samtools faidx`. The indexes are assumed to be at - .fai and .gzi unless the options --fai and --gzi are provided. A local file can be - uncompressed if the flag -e/--editable is set (but see below about using -e) - -FLAGS - -a, --assembly= Name for this assembly. Use the file name if omitted - -d, --decompressed For local file input: Override autodetection and instruct that input is decompressed - -e, --editable Instead of using indexed fasta lookup, the sequence is loaded into the Apollo database and - is editable. Use with caution, as editing the sequence often has unintended side effects. - -f, --force Delete existing assembly, if it exists - -z, --gzip For local file input: Override autodetection and instruct that input is gzip compressed - --config-file= Use this config file (mostly for testing) - --fai= Fasta index of the (not-editable) fasta file - --gzi= Gzi index of the (not-editable) fasta file - --profile= Use credentials from this profile - -DESCRIPTION - Add a new assembly from fasta input - - Add new assembly. The input fasta may be: - * A local file bgzip'd and indexed. It can be uncompressed if the -e/--editable is set (but see description of -e) - * An external fasta file bgzip'd and indexed - * The id of a file previously uploaded to Apollo - -EXAMPLES - From local file assuming indexes genome.gz.fai and genome.gz.gzi are present: - - $ apollo assembly add-from-fasta genome.fa.gz -a myAssembly - - Local file with editable sequence does not require compression and indexing: - - $ apollo assembly add-from-fasta genome.fa -a myAssembly - - From external source assuming there are also indexes https://.../genome.fa.gz.fai and https://.../genome.fa.gz.gzi: - - $ apollo assembly add-from-fasta https://.../genome.fa.gz -a myAssembly -``` - -_See code: -[src/commands/assembly/add-from-fasta.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/assembly/add-from-fasta.ts)_ - -## `apollo assembly add-from-gff INPUT-FILE` - -Add new assembly from gff or gft file - -``` -USAGE - $ apollo assembly add-from-gff INPUT-FILE [--profile ] [--config-file ] [-a ] [-o] [-f] - -ARGUMENTS - INPUT-FILE Input gff file - -FLAGS - -a, --assembly= Name for this assembly. Use the file name if omitted - -f, --force Delete existing assembly, if it exists - -o, --omit-features Do not import features, only upload the sequences - --config-file= Use this config file (mostly for testing) - --profile= Use credentials from this profile - -DESCRIPTION - Add new assembly from gff or gft file - - The gff file is expected to contain sequences as per gff specifications. Features are also imported by default. - -EXAMPLES - Import sequences and features: - - $ apollo assembly add-from-gff genome.gff -a myAssembly - - Import sequences only: - - $ apollo assembly add-from-gff genome.gff -a myAssembly -o -``` - -_See code: -[src/commands/assembly/add-from-gff.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/assembly/add-from-gff.ts)_ - -## `apollo assembly check` - -Add, view, or delete checks to assembly - -``` -USAGE - $ apollo assembly check [--profile ] [--config-file ] [-a ] [-c ] [-d] - -FLAGS - -a, --assembly= Manage checks in this assembly - -c, --check=... Add these check names or IDs. If unset, print the checks set for assembly - -d, --delete Delete (instead of adding) checks - --config-file= Use this config file (mostly for testing) - --profile= Use credentials from this profile - -DESCRIPTION - Add, view, or delete checks to assembly - - Manage checks, i.e. the rules ensuring features in an assembly are plausible. This command only sets the checks to - apply, to retrieve features flagged by these checks use `apollo feature check`. - -EXAMPLES - View available check types: - - $ apollo assembly check - - View checks set for assembly hg19: - - $ apollo assembly check -a hg19 - - Add checks to assembly: - - $ apollo assembly check -a hg19 -c CDSCheck - - Delete checks from assembly: - - $ apollo assembly check -a hg19 -c CDSCheck --delete -``` - -_See code: -[src/commands/assembly/check.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/assembly/check.ts)_ - -## `apollo assembly delete` - -Delete assemblies - -``` -USAGE - $ apollo assembly delete -a [--profile ] [--config-file ] [-v] - -FLAGS - -a, --assembly=... (required) Assembly names or IDs to delete - -v, --verbose Print to stdout the array of assemblies deleted - --config-file= Use this config file (mostly for testing) - --profile= Use credentials from this profile - -DESCRIPTION - Delete assemblies - - Assemblies to delete may be names or IDs - -EXAMPLES - Delete multiple assemblies using name or ID: - - $ apollo assembly delete -a mouse 6605826fbd0eee691f83e73f -``` - -_See code: -[src/commands/assembly/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/assembly/delete.ts)_ - -## `apollo assembly get` - -Get available assemblies - -``` -USAGE - $ apollo assembly get [--profile ] [--config-file ] [-a ] - -FLAGS - -a, --assembly=... Get assemblies in this list of names or IDs - --config-file= Use this config file (mostly for testing) - --profile= Use credentials from this profile - -DESCRIPTION - Get available assemblies - - Print to stdout the list of assemblies in json format -``` - -_See code: -[src/commands/assembly/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/assembly/get.ts)_ - -## `apollo assembly sequence` - -Get reference sequence in fasta format - -``` -USAGE - $ apollo assembly sequence [--profile ] [--config-file ] [-a ] [-r ] [-s ] [-e - ] - -FLAGS - -a, --assembly= Find input reference sequence in this assembly - -e, --end= End coordinate - -r, --refseq= Reference sequence. If unset, get all sequences - -s, --start= [default: 1] Start coordinate (1-based) - --config-file= Use this config file (mostly for testing) - --profile= Use credentials from this profile - -DESCRIPTION - Get reference sequence in fasta format - - Return the reference sequence for a given assembly and coordinates - -EXAMPLES - Get all sequences in myAssembly: - - $ apollo assembly sequence -a myAssembly - - Get sequence in coordinates chr1:1..1000: - - $ apollo assembly sequence -a myAssembly -r chr1 -s 1 -e 1000 -``` - -_See code: -[src/commands/assembly/sequence.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/assembly/sequence.ts)_ - -## `apollo change get` - -Get list of changes - -``` -USAGE - $ apollo change get [--profile ] [--config-file ] [-a ] - -FLAGS - -a, --assembly=... Get changes only for these assembly names or IDs (but see description) - --config-file= Use this config file (mostly for testing) - --profile= Use credentials from this profile - -DESCRIPTION - Get list of changes - - Return the change log in json format. Note that when an assembly is deleted the link between common name and ID is - lost (it can still be recovered by inspecting the change log but at present this task is left to the user). In such - cases you need to use the assembly ID. -``` - -_See code: -[src/commands/change/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/change/get.ts)_ - -## `apollo config [KEY] [VALUE]` - -Get or set apollo configuration options - -``` -USAGE - $ apollo config [KEY] [VALUE] [--profile ] [---file ] [--get-config-file] - -ARGUMENTS - KEY Name of configuration parameter - VALUE Parameter value - -FLAGS - --config-file= Use this config file (mostly for testing) - --get-config-file Return the path to the config file and exit (this file may not exist yet) - --profile= Profile to create or edit - -DESCRIPTION - Get or set apollo configuration options - - Use this command to create or edit a user profile with credentials to access Apollo. Configuration options are: - - - address: - Address and port e.g http://localhost:3999 - - - accessType: - How to access Apollo. accessType is typically one of: google, microsoft, guest, root. Allowed types depend on your - Apollo setup - - - accessToken: - Access token. Usually inserted by `apollo login` - - - rootPassword: - Password for root account. Only set this for "root" access type - -EXAMPLES - Interactive setup: - - $ apollo config - - Setup with key/value pairs: - - $ apollo config --profile admin address http://localhost:3999 - - Get current address for default profile: - - $ apollo config address -``` - -_See code: -[src/commands/config.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/config.ts)_ - -## `apollo export gff3 ASSEMBLY` - -Export the annotations for an assembly to stdout as gff3 - -``` -USAGE - $ apollo export gff3 ASSEMBLY [--profile ] [--config-file ] [--include-fasta] - -ARGUMENTS - ASSEMBLY Export annotations for this assembly name or id - -FLAGS - --config-file= Use this config file (mostly for testing) - --include-fasta Include fasta sequence in output - --profile= Use credentials from this profile - -DESCRIPTION - Export the annotations for an assembly to stdout as gff3 - -EXAMPLES - Export annotations for myAssembly: - - $ apollo export gff3 myAssembly > out.gff3 -``` - -_See code: -[src/commands/export/gff3.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/export/gff3.ts)_ - -## `apollo feature add [FEATURE-JSON]` - -Add one or more features to Apollo - -``` -USAGE - $ apollo feature add [FEATURE-JSON] [--profile ] [--config-file ] [-a ] [-r -s - -e -t ] [-F ] - -ARGUMENTS - FEATURE-JSON Inline JSON describing the feature(s) to add. Can also be provided via stdin. - -FLAGS - -F, --feature-json-file= File with JSON describing the feature(s) to add - -a, --assembly= Name or ID of target assembly. Not required if refseq is unique in the database - -e, --max= End position in target reference sequence - -r, --refSeq= Name or ID of target reference sequence - -s, --min= Start position in target reference sequence - -t, --type= Type of child feature - --config-file= Use this config file (mostly for testing) - --profile= Use credentials from this profile - -DESCRIPTION - Add one or more features to Apollo - - A single simple feature can be added using the --min, --max, etc. flags. - - To add multiple features, features with more details, or features with children, you can pass in JSON via argument or - stdin or use the --feature-json-file options. - - -EXAMPLES - Add a single feature by specifying its location and type - - $ apollo feature add --assembly hg19 --refSeq chr3 --min 1000 --max 5000 --type remark - - Add a single feature from inline JSON - - $ apollo feature add \ - '{"assembly":"","refseq":"","min":1,"max":100,"type":""}' - - Add mutilple features from stdin JSON - - echo '[{"assembly":"","refseq":"","min":1,"max":100,"type":""},{" \ - assembly":"","refseq":"","min":101,"max":200,"type":""}]' | \ - apollo feature add - - Add a feature with children from inline JSON - - $ apollo feature add '{"assembly":"","refseq":"","min":1,"max":100,"type":"","children":[{"min":1,"max":50,"type":""}]}' -``` - -_See code: -[src/commands/feature/add.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/feature/add.ts)_ - -## `apollo feature add-child` - -Add a child feature (e.g. add an exon to an mRNA) - -``` -USAGE - $ apollo feature add-child -s -e -t [--profile ] [--config-file ] [-i ] - -FLAGS - -e, --end= (required) End coordinate of the child feature (1-based) - -i, --feature-id= [default: -] Add a child to this feature ID; use - to read it from stdin - -s, --start= (required) Start coordinate of the child feature (1-based) - -t, --type= (required) Type of child feature - --config-file= Use this config file (mostly for testing) - --profile= Use credentials from this profile - -DESCRIPTION - Add a child feature (e.g. add an exon to an mRNA) - - See the other commands under `apollo feature` to retrive the parent ID of interest and to populate the child feature - with attributes. - -EXAMPLES - Add an exon at genomic coordinates 10..20 to this feature ID: - - $ apollo feature add-child -i 660...73f -t exon -s 10 -e 20 -``` - -_See code: -[src/commands/feature/add-child.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/feature/add-child.ts)_ - -## `apollo feature check` - -Get check results - -``` -USAGE - $ apollo feature check [--profile ] [--config-file ] [-i ] [-a ] - -FLAGS - -a, --assembly= Get checks for this assembly - -i, --feature-id=... Get checks for these feature identifiers - --config-file= Use this config file (mostly for testing) - --profile= Use credentials from this profile - -DESCRIPTION - Get check results - - Use this command to view which features fail checks along with the reason for failing.Use `apollo assembly check` for - managing which checks should be applied to an assembly - -EXAMPLES - Get all check results in the database: - - $ apollo feature check - - Get check results for assembly hg19: - - $ apollo feature check -a hg19 -``` - -_See code: -[src/commands/feature/check.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/feature/check.ts)_ - -## `apollo feature copy` - -Copy a feature to another location - -``` -USAGE - $ apollo feature copy -r -s [--profile ] [--config-file ] [-i ] [-a ] - -FLAGS - -a, --assembly= Name or ID of target assembly. Not required if refseq is unique in the database - -i, --feature-id= [default: -] Feature ID to copy to; use - to read it from stdin - -r, --refseq= (required) Name or ID of target reference sequence - -s, --start= (required) Start position in target reference sequence - --config-file= Use this config file (mostly for testing) - --profile= Use credentials from this profile - -DESCRIPTION - Copy a feature to another location - - The feature may be copied to the same or to a different assembly. The destination reference sequence may be selected - by name only if unique in the database or by name and assembly or by identifier. - -EXAMPLES - Copy this feature ID to chr1:100 in assembly hg38: - - $ apollo feature copy -i 6605826fbd0eee691f83e73f -r chr1 -s 100 -a hg38 -``` - -_See code: -[src/commands/feature/copy.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/feature/copy.ts)_ - -## `apollo feature delete` - -Delete one or more features by ID - -``` -USAGE - $ apollo feature delete [--profile ] [--config-file ] [-i ] [-f] [-n] - -FLAGS - -f, --force Ignore non-existing features - -i, --feature-id=... [default: -] Feature IDs to delete - -n, --dry-run Only show what would be delete - --config-file= Use this config file (mostly for testing) - --profile= Use credentials from this profile - -DESCRIPTION - Delete one or more features by ID - - Note that deleting a child feature after deleting its parent will result in an error unless you set -f/--force. -``` - -_See code: -[src/commands/feature/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/feature/delete.ts)_ - -## `apollo feature edit` - -Edit features using an appropiate json input - -``` -USAGE - $ apollo feature edit [--profile ] [--config-file ] [-j ] - -FLAGS - -j, --json-input= [default: -] Json string or json file or "-" to read json from stdin - --config-file= Use this config file (mostly for testing) - --profile= Use credentials from this profile - -DESCRIPTION - Edit features using an appropiate json input - - Edit a feature by submitting a json input with all the required attributes for Apollo to process it. This is a very - low level command which most users probably do not need. - - Input may be a json string or a json file and it may be an array of changes. This is an example input for editing - feature type: - - { - "typeName": "TypeChange", - "changedIds": [ - "6613f7d22c957525d631b1cc" - ], - "assembly": "6613f7d1360321540a11e5ed", - "featureId": "6613f7d22c957525d631b1cc", - "oldType": "BAC", - "newType": "G_quartet" - } - -EXAMPLES - Editing by passing a json to stdin: - - echo '{"typeName": ... "newType": "G_quartet"}' | apollo feature edit -j - -``` - -_See code: -[src/commands/feature/edit.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/feature/edit.ts)_ - -## `apollo feature edit-attribute` - -Add, edit, or view a feature attribute - -``` -USAGE - $ apollo feature edit-attribute -a [--profile ] [--config-file ] [-i ] [-v ] [-d] - -FLAGS - -a, --attribute= (required) Attribute key to add or edit - -d, --delete Delete this attribute - -i, --feature-id= [default: -] Feature ID to edit or "-" to read it from stdin - -v, --value=... New attribute value. Separated mutliple values by space to them as a list. If unset return - current value - --config-file= Use this config file (mostly for testing) - --profile= Use credentials from this profile - -DESCRIPTION - Add, edit, or view a feature attribute - - Be aware that there is no checking whether attributes names and values are valid. For example, you can create - non-unique ID attributes or you can set gene ontology terms to non-existing terms - -EXAMPLES - Add attribute "domains" with a list of values: - - $ apollo feature edit-attribute -i 66...3f -a domains -v ABC PLD - - Print values in "domains" as json array: - - $ apollo feature edit-attribute -i 66...3f -a domains - - Delete attribute "domains" - - $ apollo feature edit-attribute -i 66...3f -a domains -d -``` - -_See code: -[src/commands/feature/edit-attribute.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/feature/edit-attribute.ts)_ - -## `apollo feature edit-coords` - -Edit feature start and/or end coordinates - -``` -USAGE - $ apollo feature edit-coords [--profile ] [--config-file ] [-i ] [-s ] [-e ] - -FLAGS - -e, --end= New end coordinate (1-based) - -i, --feature-id= [default: -] Feature ID to edit or "-" to read it from stdin - -s, --start= New start coordinate (1-based) - --config-file= Use this config file (mostly for testing) - --profile= Use credentials from this profile - -DESCRIPTION - Edit feature start and/or end coordinates - - If editing a child feature that new coordinates must be within the parent's coordinates.To get the identifier of the - feature to edit consider using `apollo feature get` or `apollo feature search` - -EXAMPLES - Edit start and end: - - $ apollo feature edit-coords -i abc...xyz -s 10 -e 1000 - - Edit end and leave start as it is: - - $ apollo feature edit-coords -i abc...xyz -e 2000 -``` - -_See code: -[src/commands/feature/edit-coords.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/feature/edit-coords.ts)_ - -## `apollo feature edit-type` - -Edit or view feature type - -``` -USAGE - $ apollo feature edit-type [--profile ] [--config-file ] [-i ] [-t ] - -FLAGS - -i, --feature-id= [default: -] Feature ID to edit or "-" to read it from stdin - -t, --type= Assign feature to this type. If unset return the current type - --config-file= Use this config file (mostly for testing) - --profile= Use credentials from this profile - -DESCRIPTION - Edit or view feature type - - Feature type is column 3 in gff format.It must be a valid sequence ontology term although but the valifdity of the new - term is not checked. -``` - -_See code: -[src/commands/feature/edit-type.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/feature/edit-type.ts)_ - -## `apollo feature get` - -Get features in assembly, reference sequence or genomic window - -``` -USAGE - $ apollo feature get [--profile ] [--config-file ] [-a ] [-r ] [-s ] [-e - ] - -FLAGS - -a, --assembly= Find input reference sequence in this assembly - -e, --end= End coordinate - -r, --refseq= Reference sequence. If unset, query all sequences - -s, --start= [default: 1] Start coordinate (1-based) - --config-file= Use this config file (mostly for testing) - --profile= Use credentials from this profile - -DESCRIPTION - Get features in assembly, reference sequence or genomic window - -EXAMPLES - Get all features in myAssembly: - - $ apollo feature get -a myAssembly - - Get features intersecting chr1:1..1000. You can omit the assembly name if there are no other reference sequences - named chr1: - - $ apollo feature get -a myAssembly -r chr1 -s 1 -e 1000 -``` - -_See code: -[src/commands/feature/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/feature/get.ts)_ - -## `apollo feature get-id` - -Get features given their identifiers - -``` -USAGE - $ apollo feature get-id [--profile ] [--config-file ] [-i ] - -FLAGS - -i, --feature-id=... [default: -] Retrieves feature with these IDs. Use "-" to read IDs from stdin (one per - line) - --config-file= Use this config file (mostly for testing) - --profile= Use credentials from this profile - -DESCRIPTION - Get features given their identifiers - - Invalid identifiers or identifiers not found in the database will be silently ignored - -EXAMPLES - Get features for these identifiers: - - $ apollo feature get-id -i abc...zyz def...foo -``` - -_See code: -[src/commands/feature/get-id.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/feature/get-id.ts)_ - -## `apollo feature get-indexed-id ID` - -Get features given an indexed identifier - -``` -USAGE - $ apollo feature get-indexed-id ID [--profile ] [--config-file ] [-a ] [--topLevel] - -ARGUMENTS - ID Indexed identifier to search for - -FLAGS - -a, --assembly=... Assembly names or IDs to search; use "-" to read it from stdin. If omitted search all - assemblies - --config-file= Use this config file (mostly for testing) - --profile= Use credentials from this profile - --topLevel Return the top-level parent of the feature instead of the feature itself - -DESCRIPTION - Get features given an indexed identifier - - Get features that match a given indexed identifier, such as the ID of a feature from an imported GFF3 file - -EXAMPLES - Get features for this indexed identifier: - - $ apollo feature get-indexed-id -i abc...zyz def...foo -``` - -_See code: -[src/commands/feature/get-indexed-id.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/feature/get-indexed-id.ts)_ - -## `apollo feature import INPUT-FILE` - -Import features from local gff file - -``` -USAGE - $ apollo feature import INPUT-FILE -a [--profile ] [--config-file ] [-d] - -ARGUMENTS - INPUT-FILE Input gff file - -FLAGS - -a, --assembly= (required) Import into this assembly name or assembly ID - -d, --delete-existing Delete existing features before importing - --config-file= Use this config file (mostly for testing) - --profile= Use credentials from this profile - -DESCRIPTION - Import features from local gff file - - By default, features are added to the existing ones. - -EXAMPLES - Delete features in myAssembly and then import features.gff3: - - $ apollo feature import features.gff3 -d -a myAssembly -``` - -_See code: -[src/commands/feature/import.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/feature/import.ts)_ - -## `apollo feature search` - -Free text search for feature in one or more assemblies - -``` -USAGE - $ apollo feature search -t [--profile ] [--config-file ] [-a ] - -FLAGS - -a, --assembly=... Assembly names or IDs to search; use "-" to read it from stdin. If omitted search all - assemblies - -t, --text= (required) Search for this text query - --config-file= Use this config file (mostly for testing) - --profile= Use credentials from this profile - -DESCRIPTION - Free text search for feature in one or more assemblies - - Return features matching a query string. This command searches only in: - - - Attribute *values* (not attribute names) - - Source field (which in fact is stored as an attribute) - - Feature type - - The search mode is: - - - Case insensitive - - Match only full words, but not necessarily the full value - - Common words are ignored. E.g. "the", "with" - - For example, given this feature: - - chr1 example SNP 10 30 0.987 . . "someKey=Fingerprint BAC with reads" - - Queries "bac" or "mRNA" return the feature. Instead these queries will NOT match: - - - "someKey" - - "with" - - "Finger" - - "chr1" - - "0.987" - -EXAMPLES - Search "bac" in these assemblies: - - $ apollo feature search -a mm9 mm10 -t bac -``` - -_See code: -[src/commands/feature/search.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/feature/search.ts)_ - -## `apollo file delete` - -Delete files from the Apollo server - -``` -USAGE - $ apollo file delete [--profile ] [--config-file ] [-i ] - -FLAGS - -i, --file-id=... [default: -] IDs of the files to delete - --config-file= Use this config file (mostly for testing) - --profile= Use credentials from this profile - -DESCRIPTION - Delete files from the Apollo server - - Deleted files are printed to stdout. See also `apollo file get` to list the files on the server - -EXAMPLES - Delete file multiple files: - - $ apollo file delete -i 123...abc xyz...789 -``` - -_See code: -[src/commands/file/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/file/delete.ts)_ - -## `apollo file download` - -Download a file from the Apollo server - -``` -USAGE - $ apollo file download [--profile ] [--config-file ] [-i ] [-o ] - -FLAGS - -i, --file-id= [default: -] ID of the file to download - -o, --output= Write output to this file or "-" for stdout. Default to the name of the uploaded file. - --config-file= Use this config file (mostly for testing) - --profile= Use credentials from this profile - -DESCRIPTION - Download a file from the Apollo server - - See also `apollo file get` to list the files on the server - -EXAMPLES - Download file with id xyz - - $ apollo file download -i xyz -o genome.fa -``` - -_See code: -[src/commands/file/download.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/file/download.ts)_ - -## `apollo file get` - -Get list of files uploaded to the Apollo server - -``` -USAGE - $ apollo file get [--profile ] [--config-file ] [-i ] - -FLAGS - -i, --file-id=... Get files matching this IDs - --config-file= Use this config file (mostly for testing) - --profile= Use credentials from this profile - -DESCRIPTION - Get list of files uploaded to the Apollo server - - Print to stdout the list of files in json format - -EXAMPLES - Get files by id: - - $ apollo file get -i xyz abc -``` - -_See code: -[src/commands/file/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/file/get.ts)_ - -## `apollo file upload INPUT-FILE` - -Upload a local file to the Apollo server - -``` -USAGE - $ apollo file upload INPUT-FILE [--profile ] [--config-file ] [-t - text/x-fasta|text/x-gff3|application/x-bgzip-fasta|text/x-fai|application/x-gzi] [-z | -d] - -ARGUMENTS - INPUT-FILE Local file to upload - -FLAGS - -d, --decompressed Override autodetection and instruct that input is decompressed - -t, --type=