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"lint": "eslint --ext .js,.jsx,.ts,.tsx,.json, ." + }, + "devDependencies": { + "@cypress/mount-utils": "0.0.0-development", + "@cypress/react": "0.0.0-development", + "@rollup/plugin-commonjs": "^17.1.0", + "@rollup/plugin-node-resolve": "^11.1.1", + "@types/react": "^16", + "@types/react-dom": "^16", + "cypress": "0.0.0-development", + "react": "^16", + "react-dom": "^16", + "rollup": "3.7.3", + "rollup-plugin-typescript2": "^0.29.0", + "typescript": "^4.7.4" + }, + "peerDependencies": { + "@types/react": "^18", + "@types/react-dom": "^18", + "cypress": "*", + "react": "^18", + "react-dom": "^18" + }, + "files": [ + "dist" + ], + "types": "dist/index.d.ts", + "license": "MIT", + "repository": { + "type": "git", + "url": "https://github.com/cypress-io/cypress.git" + }, + "homepage": "https://github.com/cypress-io/cypress/blob/develop/npm/react18/#readme", + "bugs": 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diff --git a/.yarn/unplugged/cypress-npm-12.17.3-602acfb08c/node_modules/cypress/vue/package.json b/.yarn/unplugged/cypress-npm-12.17.3-602acfb08c/node_modules/cypress/vue/package.json new file mode 100644 index 000000000..a22f0588f --- /dev/null +++ b/.yarn/unplugged/cypress-npm-12.17.3-602acfb08c/node_modules/cypress/vue/package.json @@ -0,0 +1,85 @@ +{ + "name": "@cypress/vue", + "version": "0.0.0-development", + "description": "Browser-based Component Testing for Vue.js with Cypress.io ✌️🌲", + "main": "dist/cypress-vue.cjs.js", + "scripts": { + "build-prod": "yarn build", + "cy:open": "node ../../scripts/cypress.js open --component --project ${PWD}", + "cy:run": "node ../../scripts/cypress.js run --component --project ${PWD}", + "build": "rimraf dist && rollup -c rollup.config.mjs", + "postbuild": "node ../../scripts/sync-exported-npm-with-cli.js", + "typecheck": "yarn tsd && vue-tsc --noEmit", + "check-ts": "yarn tsd && vue-tsc --noEmit", + "lint": "eslint --ext .js,.jsx,.ts,.tsx,.json,.vue .", + "test": "yarn cy:run", + "tsd": "yarn build && yarn tsc -p test-tsd/tsconfig.tsd.json", + "watch": "yarn build --watch --watch.exclude ./dist/**/*" + }, + "devDependencies": { + "@cypress/mount-utils": "0.0.0-development", + "@vitejs/plugin-vue": "4.2.0", + "@vue/compiler-sfc": "3.2.47", + "@vue/test-utils": "2.3.2", + "axios": "0.21.2", + "cypress": "0.0.0-development", + "debug": "^4.3.4", + "globby": "^11.0.1", + "tailwindcss": "1.1.4", + "typescript": "^4.7.4", + "vite": "4.3.2", + "vue": "3.2.47", + "vue-i18n": "9.0.0-rc.6", + "vue-router": "^4.0.0", + "vue-tsc": "^0.3.0", + "vuex": "^4.0.0" + }, + "peerDependencies": { + "@cypress/webpack-dev-server": "*", + "cypress": ">=7.0.0", + "vue": ">=3.0.0" + }, + "files": [ + "dist/**/*", + "src/**/*.js" + ], + "engines": { + "node": ">=8" + }, + "types": "dist/index.d.ts", + "license": "MIT", + "repository": { + "type": "git", + "url": "https://github.com/cypress-io/cypress.git" + }, + "homepage": 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b/.yarn/unplugged/cypress-npm-12.17.3-602acfb08c/node_modules/cypress/vue2/package.json @@ -0,0 +1,53 @@ +{ + "name": "@cypress/vue2", + "version": "0.0.0-development", + "description": "Browser-based Component Testing for Vue.js@2 with Cypress.io ✌️🌲", + "main": "dist/cypress-vue2.cjs.js", + "scripts": { + "typecheck": "tsc --noEmit", + "build": "rimraf dist && yarn rollup -c rollup.config.mjs", + "postbuild": "node ../../scripts/sync-exported-npm-with-cli.js", + "build-prod": "yarn build", + "test": "echo \"Tests for @cypress/vue2 are run from system-tests\"", + "watch": "yarn build --watch --watch.exclude ./dist/**/*", + "lint": "eslint --ext .js,.jsx,.ts,.tsx,.json,.vue .", + "test-ci": "node ../../scripts/run-ct-examples.js --examplesList=./examples.env" + }, + "devDependencies": { + "@cypress/mount-utils": "0.0.0-development", + "@rollup/plugin-json": "^4.1.0", + "@rollup/plugin-replace": "^2.3.1", + "@vue/test-utils": "^1.3.1", + "tslib": "^2.1.0", + "typescript": "^4.7.4", + 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b/.yarn/unplugged/esbuild-npm-0.18.20-004a76d281/node_modules/esbuild/package.json @@ -0,0 +1,42 @@ +{ + "name": "esbuild", + "version": "0.18.20", + "description": "An extremely fast JavaScript and CSS bundler and minifier.", + "repository": "https://github.com/evanw/esbuild", + "scripts": { + "postinstall": "node install.js" + }, + "main": "lib/main.js", + "types": "lib/main.d.ts", + "engines": { + "node": ">=12" + }, + "bin": { + "esbuild": "bin/esbuild" + }, + "optionalDependencies": { + "@esbuild/android-arm": "0.18.20", + "@esbuild/android-arm64": "0.18.20", + "@esbuild/android-x64": "0.18.20", + "@esbuild/darwin-arm64": "0.18.20", + "@esbuild/darwin-x64": "0.18.20", + "@esbuild/freebsd-arm64": "0.18.20", + "@esbuild/freebsd-x64": "0.18.20", + "@esbuild/linux-arm": "0.18.20", + "@esbuild/linux-arm64": "0.18.20", + "@esbuild/linux-ia32": "0.18.20", + "@esbuild/linux-loong64": "0.18.20", + "@esbuild/linux-mips64el": "0.18.20", + "@esbuild/linux-ppc64": "0.18.20", + 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(https://github.com/dominictarr)", + "Max Ogden (https://github.com/maxogden)", + "Lars-Magnus Skog (https://github.com/ralphtheninja)", + "David Björklund (https://github.com/kesla)", + "Julian Gruber (https://github.com/juliangruber)", + "Paolo Fragomeni (https://github.com/hij1nx)", + "Anton Whalley (https://github.com/No9)", + "Matteo Collina (https://github.com/mcollina)", + "Pedro Teixeira (https://github.com/pgte)", + "James Halliday (https://github.com/substack)" + ], + "repository": { + "type": "git", + "url": "https://github.com/rvagg/node-levelup.git" + }, + "homepage": "https://github.com/rvagg/node-levelup", + "keywords": [ + "leveldb", + "stream", + "database", + "db", + "store", + "storage", + "json" + ], + "main": "lib/levelup.js", + "dependencies": { + "bl": "~0.8.1", + "deferred-leveldown": "~0.2.0", + "errno": "~0.1.1", + "prr": "~0.0.0", + "readable-stream": "~1.0.26", + "semver": "~2.3.1", + "xtend": "~3.0.0" + }, + "devDependencies": { + "leveldown": "~0.10.0", + 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+1,50 @@ +{ + "name": "node-gyp", + "description": "Node.js native addon build tool", + "license": "MIT", + "keywords": [ + "native", + "addon", + "module", + "c", + "c++", + "bindings", + "gyp" + ], + "version": "8.4.1", + "installVersion": 9, + "author": "Nathan Rajlich (http://tootallnate.net)", + "repository": { + "type": "git", + "url": "git://github.com/nodejs/node-gyp.git" + }, + "preferGlobal": true, + "bin": "./bin/node-gyp.js", + "main": "./lib/node-gyp.js", + "dependencies": { + "env-paths": "^2.2.0", + "glob": "^7.1.4", + "graceful-fs": "^4.2.6", + "make-fetch-happen": "^9.1.0", + "nopt": "^5.0.0", + "npmlog": "^6.0.0", + "rimraf": "^3.0.2", + "semver": "^7.3.5", + "tar": "^6.1.2", + "which": "^2.0.2" + }, + "engines": { + "node": ">= 10.12.0" + }, + "devDependencies": { + "bindings": "^1.5.0", + "nan": "^2.14.2", + "require-inject": "^1.4.4", + "standard": "^14.3.4", + "tap": "^12.7.0" + }, + "scripts": { + "lint": "standard */*.js test/**/*.js", + "test": "npm run lint && tap --timeout=120 test/test-*" + } +} diff --git a/.yarn/unplugged/node-gyp-npm-9.4.0-ebf5f5573e/node_modules/node-gyp/package.json b/.yarn/unplugged/node-gyp-npm-9.4.0-ebf5f5573e/node_modules/node-gyp/package.json new file mode 100644 index 000000000..7e9fb648a --- /dev/null +++ b/.yarn/unplugged/node-gyp-npm-9.4.0-ebf5f5573e/node_modules/node-gyp/package.json @@ -0,0 +1,51 @@ +{ + "name": "node-gyp", + "description": "Node.js native addon build tool", + "license": "MIT", + "keywords": [ + "native", + "addon", + "module", + "c", + "c++", + "bindings", + "gyp" + ], + "version": "9.4.0", + "installVersion": 11, + "author": "Nathan Rajlich (http://tootallnate.net)", + "repository": { + "type": "git", + "url": "git://github.com/nodejs/node-gyp.git" + }, + "preferGlobal": true, + "bin": "./bin/node-gyp.js", + "main": "./lib/node-gyp.js", + "dependencies": { + "env-paths": "^2.2.0", + "exponential-backoff": "^3.1.1", + "glob": "^7.1.4", + "graceful-fs": "^4.2.6", + "make-fetch-happen": 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"./index.mjs" + }, + "./*": "./*", + "./doc": { + "types": "./doc.d.ts", + "require": "./doc.js", + "default": "./doc.mjs" + }, + "./standalone": { + "types": "./standalone.d.ts", + "require": "./standalone.js", + "default": "./standalone.mjs" + }, + "./plugins/estree": { + "types": "./plugins/estree.d.ts", + "require": "./plugins/estree.js", + "default": "./plugins/estree.mjs" + }, + "./plugins/babel": { + "types": "./plugins/babel.d.ts", + "require": "./plugins/babel.js", + "default": "./plugins/babel.mjs" + }, + "./plugins/flow": { + "types": "./plugins/flow.d.ts", + "require": "./plugins/flow.js", + "default": "./plugins/flow.mjs" + }, + "./plugins/typescript": { + "types": "./plugins/typescript.d.ts", + "require": "./plugins/typescript.js", + "default": "./plugins/typescript.mjs" + }, + "./plugins/acorn": { + "types": "./plugins/acorn.d.ts", + "require": "./plugins/acorn.js", + "default": "./plugins/acorn.mjs" + }, + "./plugins/meriyah": { + "types": "./plugins/meriyah.d.ts", + 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"./plugins/yaml.js", + "default": "./plugins/yaml.mjs" + }, + "./esm/standalone.mjs": "./standalone.mjs", + "./parser-babel": "./plugins/babel.js", + "./parser-babel.js": "./plugins/babel.js", + "./esm/parser-babel.mjs": "./plugins/babel.mjs", + "./parser-flow": "./plugins/flow.js", + "./parser-flow.js": "./plugins/flow.js", + "./esm/parser-flow.mjs": "./plugins/flow.mjs", + "./parser-typescript": "./plugins/typescript.js", + "./parser-typescript.js": "./plugins/typescript.js", + "./esm/parser-typescript.mjs": "./plugins/typescript.mjs", + "./parser-espree": "./plugins/acorn.js", + "./parser-espree.js": "./plugins/acorn.js", + "./esm/parser-espree.mjs": "./plugins/acorn.mjs", + "./parser-meriyah": "./plugins/meriyah.js", + "./parser-meriyah.js": "./plugins/meriyah.js", + "./esm/parser-meriyah.mjs": "./plugins/meriyah.mjs", + "./parser-angular": "./plugins/angular.js", + "./parser-angular.js": "./plugins/angular.js", + "./esm/parser-angular.mjs": "./plugins/angular.mjs", + "./parser-postcss": "./plugins/postcss.js", + "./parser-postcss.js": "./plugins/postcss.js", + "./esm/parser-postcss.mjs": "./plugins/postcss.mjs", + "./parser-graphql": "./plugins/graphql.js", + "./parser-graphql.js": "./plugins/graphql.js", + "./esm/parser-graphql.mjs": "./plugins/graphql.mjs", + "./parser-markdown": "./plugins/markdown.js", + "./parser-markdown.js": "./plugins/markdown.js", + "./esm/parser-markdown.mjs": "./plugins/markdown.mjs", + "./parser-glimmer": "./plugins/glimmer.js", + "./parser-glimmer.js": "./plugins/glimmer.js", + "./esm/parser-glimmer.mjs": "./plugins/glimmer.mjs", + "./parser-html": "./plugins/html.js", + "./parser-html.js": "./plugins/html.js", + "./esm/parser-html.mjs": "./plugins/html.mjs", + "./parser-yaml": "./plugins/yaml.js", + "./parser-yaml.js": "./plugins/yaml.js", + "./esm/parser-yaml.mjs": "./plugins/yaml.mjs" + }, + "engines": { + "node": ">=14" + }, + "files": [ + "LICENSE", + "README.md", + "bin/prettier.cjs", + "doc.d.ts", + "doc.js", + "doc.mjs", + "index.cjs", + "index.d.ts", + "index.d.ts", + "index.mjs", + "internal/cli.mjs", + "package.json", + "plugins/acorn.d.ts", + "plugins/acorn.js", + "plugins/acorn.mjs", + "plugins/angular.d.ts", + "plugins/angular.js", + "plugins/angular.mjs", + "plugins/babel.d.ts", + "plugins/babel.js", + "plugins/babel.mjs", + "plugins/estree.d.ts", + "plugins/estree.js", + "plugins/estree.mjs", + "plugins/flow.d.ts", + "plugins/flow.js", + "plugins/flow.mjs", + "plugins/glimmer.d.ts", + "plugins/glimmer.js", + "plugins/glimmer.mjs", + "plugins/graphql.d.ts", + "plugins/graphql.js", + "plugins/graphql.mjs", + "plugins/html.d.ts", + "plugins/html.js", + "plugins/html.mjs", + "plugins/markdown.d.ts", + "plugins/markdown.js", + "plugins/markdown.mjs", + "plugins/meriyah.d.ts", + "plugins/meriyah.js", + "plugins/meriyah.mjs", + "plugins/postcss.d.ts", + "plugins/postcss.js", + "plugins/postcss.mjs", + "plugins/typescript.d.ts", + "plugins/typescript.js", + "plugins/typescript.mjs", + "plugins/yaml.d.ts", + "plugins/yaml.js", + "plugins/yaml.mjs", + "standalone.d.ts", + "standalone.js", + "standalone.mjs" + ], + "preferUnplugged": true +} \ No newline at end of file diff --git a/.yarn/unplugged/term-size-npm-2.2.1-77ce7141d0/node_modules/term-size/package.json b/.yarn/unplugged/term-size-npm-2.2.1-77ce7141d0/node_modules/term-size/package.json new file mode 100644 index 000000000..a070eb93f --- /dev/null +++ b/.yarn/unplugged/term-size-npm-2.2.1-77ce7141d0/node_modules/term-size/package.json @@ -0,0 +1,43 @@ +{ + "name": "term-size", + "version": "2.2.1", + "description": "Reliably get the terminal window size (columns & rows)", + "license": "MIT", + "repository": "sindresorhus/term-size", + "funding": "https://github.com/sponsors/sindresorhus", + "author": { + "name": "Sindre Sorhus", + "email": "sindresorhus@gmail.com", + "url": "https://sindresorhus.com" + }, + "engines": { + "node": ">=8" + }, + "scripts": { + "test": "xo && ava && tsd" + }, + "files": [ + "index.js", + "index.d.ts", + "vendor" + ], + "keywords": [ + "terminal", + "size", + "console", + "window", + "width", + "height", + "columns", + "rows", + "lines", + "tty", + "redirected" + ], + "devDependencies": { + "ava": "^2.4.0", + "execa": "^3.4.0", + "tsd": "^0.11.0", + "xo": "^0.25.3" + } +} diff --git a/packages/apollo-cli/README.md b/packages/apollo-cli/README.md index 1be041ec1..2420e6a5f 100644 --- a/packages/apollo-cli/README.md +++ b/packages/apollo-cli/README.md @@ -16,7 +16,7 @@ $ npm install -g @apollo-annotation/cli $ apollo COMMAND running command... $ apollo (--version) -@apollo-annotation/cli/0.1.18 linux-x64 node-v20.14.0 +@apollo-annotation/cli/0.1.19 linux-x64 node-v20.14.0 $ apollo --help [COMMAND] USAGE $ apollo COMMAND diff --git a/packages/apollo-cli/package.json b/packages/apollo-cli/package.json index 1a53265d6..8a9526601 100644 --- a/packages/apollo-cli/package.json +++ b/packages/apollo-cli/package.json @@ -1,7 +1,7 @@ { "name": "@apollo-annotation/cli", "description": "Command line interface for the Apollo annotation server", - "version": "0.1.18", + "version": "0.1.19", "author": "Apollo Team", "repository": { "type": "git", diff --git a/packages/apollo-collaboration-server/package.json b/packages/apollo-collaboration-server/package.json index 39ab7526d..0fb68dd7a 100644 --- a/packages/apollo-collaboration-server/package.json +++ b/packages/apollo-collaboration-server/package.json @@ -1,6 +1,6 @@ { "name": "@apollo-annotation/collaboration-server", - "version": "0.1.18", + "version": "0.1.19", "description": "", "author": "", "license": "Apache-2.0", diff --git a/packages/apollo-common/package.json b/packages/apollo-common/package.json index 8c21a079e..6c1d5cc1c 100644 --- a/packages/apollo-common/package.json +++ b/packages/apollo-common/package.json @@ -1,6 +1,6 @@ { "name": "@apollo-annotation/common", - "version": "0.1.18", + "version": "0.1.19", "repository": { "type": "git", "url": "https://github.com/GMOD/Apollo3.git", diff --git a/packages/apollo-mst/package.json b/packages/apollo-mst/package.json index 3960481b6..f295fabcc 100644 --- a/packages/apollo-mst/package.json +++ b/packages/apollo-mst/package.json @@ -1,6 +1,6 @@ { "name": "@apollo-annotation/mst", - "version": "0.1.18", + "version": "0.1.19", "main": "./dist/index.js", "scripts": { "build": "tsc" diff --git a/packages/apollo-schemas/package.json b/packages/apollo-schemas/package.json index 44d28762f..0dbb3df95 100644 --- a/packages/apollo-schemas/package.json +++ b/packages/apollo-schemas/package.json @@ -1,6 +1,6 @@ { "name": "@apollo-annotation/schemas", - "version": "0.1.18", + "version": "0.1.19", "main": "./dist/index.js", "scripts": { "build": "tsc" diff --git a/packages/apollo-shared/package.json b/packages/apollo-shared/package.json index 8377c44f5..76aab1fcd 100644 --- a/packages/apollo-shared/package.json +++ b/packages/apollo-shared/package.json @@ -1,6 +1,6 @@ { "name": "@apollo-annotation/shared", - "version": "0.1.18", + "version": "0.1.19", "main": "./dist/index.js", "scripts": { "start": "tsc --build --watch", diff --git a/packages/jbrowse-plugin-apollo/package.json b/packages/jbrowse-plugin-apollo/package.json index d85f3da05..3dd4ce879 100644 --- a/packages/jbrowse-plugin-apollo/package.json +++ b/packages/jbrowse-plugin-apollo/package.json @@ -1,6 +1,6 @@ { "name": "@apollo-annotation/jbrowse-plugin-apollo", - "version": "0.1.18", + "version": "0.1.19", "description": "Apollo plugin for JBrowse 2", "repository": { "type": "git", From 42712d55f567716060317659b1434ae57f50b602 Mon Sep 17 00:00:00 2001 From: Garrett Stevens Date: Tue, 27 Aug 2024 17:30:44 +0000 Subject: [PATCH 02/12] Restore missing commands to README --- packages/apollo-cli/README.md | 906 ++++++++++++++++++++++++++++++++++ 1 file changed, 906 insertions(+) diff --git a/packages/apollo-cli/README.md b/packages/apollo-cli/README.md index 2420e6a5f..79aea0e6e 100644 --- a/packages/apollo-cli/README.md +++ b/packages/apollo-cli/README.md @@ -29,7 +29,720 @@ USAGE +- [`apollo assembly add-fasta`](#apollo-assembly-add-fasta) +- [`apollo assembly add-gff`](#apollo-assembly-add-gff) +- [`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 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 import`](#apollo-feature-import) +- [`apollo feature search`](#apollo-feature-search) - [`apollo help [COMMANDS]`](#apollo-help-commands) +- [`apollo login`](#apollo-login) +- [`apollo logout`](#apollo-logout) +- [`apollo refseq add-alias`](#apollo-refseq-add-alias) +- [`apollo refseq get`](#apollo-refseq-get) +- [`apollo status`](#apollo-status) +- [`apollo user get`](#apollo-user-get) + +## `apollo assembly add-fasta` + +Add new assembly from local or external fasta file + +``` +USAGE + $ apollo assembly add-fasta -i [--profile ] [--config-file ] [-a ] [-x ] [-f] + +FLAGS + -a, --assembly= Name for this assembly. Use the file name if omitted + -f, --force Delete existing assembly, if it exists + -i, --input-file= (required) Input fasta file + -x, --index= URL of the index. Required if input is an external source and ignored if input is a local + file + --config-file= Use this config file (mostly for testing) + --profile= Use credentials from this profile + +DESCRIPTION + Add new assembly from local or external fasta file + +EXAMPLES + From local file: + + $ apollo assembly add-fasta -i genome.fa -a myAssembly + + From external source we also need the URL of the index: + + $ apollo assembly add-fasta -i https://.../genome.fa -x https://.../genome.fa.fai -a myAssembly +``` + +_See code: +[src/commands/assembly/add-fasta.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/assembly/add-fasta.ts)_ + +## `apollo assembly add-gff` + +Add new assembly from gff or gft file + +``` +USAGE + $ apollo assembly add-gff -i [--profile ] [--config-file ] [-a ] [-o] [-f] + +FLAGS + -a, --assembly= Name for this assembly. Use the file name if omitted + -f, --force Delete existing assembly, if it exists + -i, --input-file= (required) Input gff or gtf file + -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-gff -i genome.gff -a myAssembly + + Import sequences only: + + $ apollo assembly add-gff -i genome.gff -a myAssembly -o +``` + +_See code: +[src/commands/assembly/add-gff.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/assembly/add-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/v0.1.19/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/v0.1.19/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/v0.1.19/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/v0.1.19/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/v0.1.19/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` + + - rootCredentials.username: + Username of root account. Only set this for "root" access type + + - rootCredentials.password: + 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/v0.1.19/packages/apollo-cli/src/commands/config.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 6605826fbd0eee691f83e73f -t exon -s 10 -e 20 +``` + +_See code: +[src/commands/feature/add-child.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/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/v0.1.19/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. he 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/v0.1.19/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/v0.1.19/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/v0.1.19/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/v0.1.19/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/v0.1.19/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/v0.1.19/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/v0.1.19/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/v0.1.19/packages/apollo-cli/src/commands/feature/get-id.ts)_ + +## `apollo feature import` + +Import features from local gff file + +``` +USAGE + $ apollo feature import -i -a [--profile ] [--config-file ] [-d] + +FLAGS + -a, --assembly= (required) Import into this assembly name or assembly ID + -d, --delete-existing Delete existing features before importing + -i, --input-file= (required) Input gff or gtf file + --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 -d -i features.gff3 -a myAssembly +``` + +_See code: +[src/commands/feature/import.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/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/v0.1.19/packages/apollo-cli/src/commands/feature/search.ts)_ ## `apollo help [COMMANDS]` @@ -52,4 +765,197 @@ DESCRIPTION _See code: [@oclif/plugin-help](https://github.com/oclif/plugin-help/blob/v6.0.8/src/commands/help.ts)_ +## `apollo login` + +Login to Apollo + +``` +USAGE + $ apollo login [--profile ] [--config-file ] [-a ] [-u ] [-p ] [-f] + [--port ] + +FLAGS + -a, --address= Address of Apollo server + -f, --force Force re-authentication even if user is already logged in + -p, --password= Password for + -u, --username= Username for root login + --config-file= Use this config file (mostly for testing) + --port= [default: 3000] Get token by listening to this port number (usually this is >= 1024 and < + 65536) + --profile= Use credentials from this profile + +DESCRIPTION + Login to Apollo + + Use the provided credentials to obtain and save the token to access Apollo. Once + the token for the given profile has been saved in the configuration file, users + do not normally need to execute this command again unless the token has expired. + To setup a new profile use "apollo config" + +EXAMPLES + The most basic and probably most typical usage is to login using the default + profile in configuration file: + + $ apollo login + + Login with a different profile: + + $ apollo login --profile my-profile +``` + +_See code: +[src/commands/login.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/login.ts)_ + +## `apollo logout` + +Logout of Apollo + +``` +USAGE + $ apollo logout [--profile ] [--config-file ] + +FLAGS + --config-file= Use this config file (mostly for testing) + --profile= Use credentials from this profile + +DESCRIPTION + Logout of Apollo + + Logout by removing the access token from the selected profile + +EXAMPLES + Logout default profile: + + $ apollo logout + + Logout selected profile + + $ apollo logout --profile my-profile +``` + +_See code: +[src/commands/logout.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/logout.ts)_ + +## `apollo refseq add-alias` + +Add reference name aliases from a file + +``` +USAGE + $ apollo refseq add-alias -i -a [--profile ] [--config-file ] + +FLAGS + -a, --assembly= (required) Name for this assembly. + -i, --input-file= (required) Input refname alias file + --config-file= Use this config file (mostly for testing) + --profile= Use credentials from this profile + +DESCRIPTION + Add reference name aliases from a file + + Reference name aliasing is a process to make chromosomes that are named slightly + differently but which refer to the same thing render properly. This command + reads a file with reference name aliases and adds them to the database. + +EXAMPLES + Add reference name aliases: + + $ apollo refseq add-alias -i alias.txt -a myAssembly +``` + +_See code: +[src/commands/refseq/add-alias.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/refseq/add-alias.ts)_ + +## `apollo refseq get` + +Get reference sequences + +``` +USAGE + $ apollo refseq get [--profile ] [--config-file ] [-a ] + +FLAGS + -a, --assembly=... Get reference sequences for these assembly names or IDs; use - to read it from stdin + --config-file= Use this config file (mostly for testing) + --profile= Use credentials from this profile + +DESCRIPTION + Get reference sequences + + Output the reference sequences in one or more assemblies in json format. This + command returns the sequence characteristics (e.g., name, ID, etc), not the DNA + sequences. Use `assembly sequence` for that. + +EXAMPLES + All sequences in the database: + + $ apollo refseq get + + Only sequences for these assemblies: + + $ apollo refseq get -a mm9 mm10 +``` + +_See code: +[src/commands/refseq/get.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/refseq/get.ts)_ + +## `apollo status` + +View authentication status + +``` +USAGE + $ apollo status [--profile ] [--config-file ] + +FLAGS + --config-file= Use this config file (mostly for testing) + --profile= Use credentials from this profile + +DESCRIPTION + View authentication status + + This command returns ": Logged in" if the selected profile has an + access token and ": Logged out" otherwise. Note that this command does + not check the validity of the access token. +``` + +_See code: +[src/commands/status.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/status.ts)_ + +## `apollo user get` + +Get list of users + +``` +USAGE + $ apollo user get [--profile ] [--config-file ] [-u ] [-r ] + +FLAGS + -r, --role= Get users with this role + -u, --username= Find this username + --config-file= Use this config file (mostly for testing) + --profile= Use credentials from this profile + +DESCRIPTION + Get list of users + + If set, filters username and role must be both satisfied to return an entry + +EXAMPLES + By username: + + $ apollo user get -u Guest + + By role: + + $ apollo user get -r admin + + Use jq for more control: + + $ apollo user get | jq '.[] | select(.createdAt > "2024-03-18")' +``` + +_See code: +[src/commands/user/get.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/user/get.ts)_ + From 7fab7c504c76ea1f71172535b7985bbeaba2b0f3 Mon Sep 17 00:00:00 2001 From: Garrett Stevens Date: Tue, 27 Aug 2024 17:32:14 +0000 Subject: [PATCH 03/12] Remove accidentally committed unplugged files --- .../@esbuild/linux-x64/package.json | 17 -- .../node_modules/@nestjs/core/package.json | 60 ------ .../node_modules/@nestjs/core/package.json | 60 ------ .../node_modules/@nestjs/core/package.json | 60 ------ .../node_modules/@nestjs/core/package.json | 60 ------ .../quickjs-emscripten/package.json | 60 ------ .../node_modules/clipboardy/package.json | 57 ----- .../node_modules/cypress/angular/package.json | 69 ------ .../cypress/mount-utils/package.json | 37 ---- .../node_modules/cypress/package.json | 151 ------------- .../node_modules/cypress/react/package.json | 98 --------- .../node_modules/cypress/react18/package.json | 61 ------ .../node_modules/cypress/svelte/package.json | 44 ---- .../node_modules/cypress/vue/package.json | 85 -------- .../node_modules/cypress/vue2/package.json | 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delete mode 100644 .yarn/unplugged/@tootallnate-quickjs-emscripten-npm-0.23.0-a889ea7aeb/node_modules/@tootallnate/quickjs-emscripten/package.json delete mode 100644 .yarn/unplugged/clipboardy-npm-3.0.0-4025981f4b/node_modules/clipboardy/package.json delete mode 100644 .yarn/unplugged/cypress-npm-12.17.3-602acfb08c/node_modules/cypress/angular/package.json delete mode 100644 .yarn/unplugged/cypress-npm-12.17.3-602acfb08c/node_modules/cypress/mount-utils/package.json delete mode 100644 .yarn/unplugged/cypress-npm-12.17.3-602acfb08c/node_modules/cypress/package.json delete mode 100644 .yarn/unplugged/cypress-npm-12.17.3-602acfb08c/node_modules/cypress/react/package.json delete mode 100644 .yarn/unplugged/cypress-npm-12.17.3-602acfb08c/node_modules/cypress/react18/package.json delete mode 100644 .yarn/unplugged/cypress-npm-12.17.3-602acfb08c/node_modules/cypress/svelte/package.json delete mode 100644 .yarn/unplugged/cypress-npm-12.17.3-602acfb08c/node_modules/cypress/vue/package.json delete mode 100644 .yarn/unplugged/cypress-npm-12.17.3-602acfb08c/node_modules/cypress/vue2/package.json delete mode 100644 .yarn/unplugged/esbuild-npm-0.18.20-004a76d281/node_modules/esbuild/package.json delete mode 100644 .yarn/unplugged/levelup-npm-0.18.6-d181e19f2e/node_modules/levelup/package.json delete mode 100644 .yarn/unplugged/node-gyp-npm-8.4.1-13c90a9c9b/node_modules/node-gyp/package.json delete mode 100644 .yarn/unplugged/node-gyp-npm-9.4.0-ebf5f5573e/node_modules/node-gyp/package.json delete mode 100644 .yarn/unplugged/node-gyp-npm-9.4.1-15a6f0e8e4/node_modules/node-gyp/package.json delete mode 100644 .yarn/unplugged/open-npm-10.1.0-612222a007/node_modules/open/package.json delete mode 100644 .yarn/unplugged/prettier-npm-3.3.2-efeafcaa4b/node_modules/prettier/package.json delete mode 100644 .yarn/unplugged/term-size-npm-2.2.1-77ce7141d0/node_modules/term-size/package.json diff --git a/.yarn/unplugged/@esbuild-linux-x64-npm-0.18.20-de8e99b449/node_modules/@esbuild/linux-x64/package.json b/.yarn/unplugged/@esbuild-linux-x64-npm-0.18.20-de8e99b449/node_modules/@esbuild/linux-x64/package.json deleted file mode 100644 index e1392a248..000000000 --- a/.yarn/unplugged/@esbuild-linux-x64-npm-0.18.20-de8e99b449/node_modules/@esbuild/linux-x64/package.json +++ /dev/null @@ -1,17 +0,0 @@ -{ - "name": "@esbuild/linux-x64", - "version": "0.18.20", - "description": "The Linux 64-bit binary for esbuild, a JavaScript bundler.", - "repository": "https://github.com/evanw/esbuild", - "license": "MIT", - "preferUnplugged": true, - "engines": { - "node": ">=12" - }, - "os": [ - "linux" - ], - "cpu": [ - "x64" - ] -} diff --git a/.yarn/unplugged/@nestjs-core-virtual-39adde589b/node_modules/@nestjs/core/package.json b/.yarn/unplugged/@nestjs-core-virtual-39adde589b/node_modules/@nestjs/core/package.json deleted file mode 100644 index 776e0ca21..000000000 --- a/.yarn/unplugged/@nestjs-core-virtual-39adde589b/node_modules/@nestjs/core/package.json +++ /dev/null @@ -1,60 +0,0 @@ -{ - "name": "@nestjs/core", - "version": "10.2.7", - "description": "Nest - modern, fast, powerful node.js web framework (@core)", - "author": "Kamil Mysliwiec", - "license": "MIT", - "homepage": "https://nestjs.com", - "funding": { - "type": "opencollective", - "url": "https://opencollective.com/nest" - }, - "repository": { - "type": "git", - "url": "https://github.com/nestjs/nest.git", - "directory": "packages/core" - }, - "publishConfig": { - "access": "public" - }, - "scripts": { - "postinstall": "opencollective || exit 0" - }, - "collective": { - "type": "opencollective", - "url": "https://opencollective.com/nest", - "donation": { - "text": "Become a partner:" - } - }, - "dependencies": { - "@nuxtjs/opencollective": "0.3.2", - "fast-safe-stringify": "2.1.1", - "iterare": "1.2.1", - "path-to-regexp": "3.2.0", - "tslib": "2.6.2", - "uid": "2.0.2" - }, - 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a/.yarn/unplugged/@nestjs-core-virtual-e6912399bc/node_modules/@nestjs/core/package.json b/.yarn/unplugged/@nestjs-core-virtual-e6912399bc/node_modules/@nestjs/core/package.json deleted file mode 100644 index 776e0ca21..000000000 --- a/.yarn/unplugged/@nestjs-core-virtual-e6912399bc/node_modules/@nestjs/core/package.json +++ /dev/null @@ -1,60 +0,0 @@ -{ - "name": "@nestjs/core", - "version": "10.2.7", - "description": "Nest - modern, fast, powerful node.js web framework (@core)", - "author": "Kamil Mysliwiec", - "license": "MIT", - "homepage": "https://nestjs.com", - "funding": { - "type": "opencollective", - "url": "https://opencollective.com/nest" - }, - "repository": { - "type": "git", - "url": "https://github.com/nestjs/nest.git", - "directory": "packages/core" - }, - "publishConfig": { - "access": "public" - }, - "scripts": { - "postinstall": "opencollective || exit 0" - }, - "collective": { - "type": "opencollective", - "url": "https://opencollective.com/nest", - "donation": { - 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39c152b01..000000000 --- a/.yarn/unplugged/@tootallnate-quickjs-emscripten-npm-0.23.0-a889ea7aeb/node_modules/@tootallnate/quickjs-emscripten/package.json +++ /dev/null @@ -1,60 +0,0 @@ -{ - "name": "@tootallnate/quickjs-emscripten", - "version": "0.23.0", - "main": "dist/index.js", - "sideEffects": false, - "license": "MIT", - "keywords": [ - "eval", - "quickjs", - "vm", - "interpreter", - "runtime", - "safe", - "emscripten", - "wasm" - ], - "repository": { - "type": "git", - "url": "https://github.com/justjake/quickjs-emscripten" - }, - "files": [ - "c/interface.c", - "dist/**/*", - "!dist/*.test.js", - "!dist/*.tsbuildinfo" - ], - "scripts": { - "tarball": "make build/quickjs-emscripten.tgz", - "clean": "make clean", - "tsc": "node_modules/.bin/tsc", - "build": "make dist", - "doc": "typedoc", - "test": "TS_NODE_TRANSPILE_ONLY=true mocha 'ts/**/*.test.ts'", - "test-dist": "cd dist && TS_NODE_TRANSPILE_ONLY=true mocha --require source-map-support/register *.test.js", - "test-fast": "TEST_NO_ASYNC=true yarn test 'ts/**/*.test.ts'", - "test-all": "TEST_LEAK=1 yarn test && TEST_LEAK=1 yarn test-dist", - "prettier": "prettier --write .", - "prettier-check": "prettier --check .", - "update-quickjs": "git subtree pull --prefix=quickjs --squash git@github.com:bellard/quickjs.git master", - "smoketest-node": "yarn tarball && ./scripts/smoketest-node.sh", - "smoketest-cra": "yarn tarball && ./scripts/smoketest-website.sh" - }, - "devDependencies": { - "@types/emscripten": "^1.38.0", - "@types/fs-extra": "^9.0.13", - "@types/mocha": "^5.2.7", - "@types/node": "^13.1.4", - "fs-extra": "^10.0.1", - "markserv": "^1.17.4", - "mocha": "7.2.0", - "node-fetch-commonjs": "^3.1.1", - "prettier": "2.8.4", - "source-map-support": "^0.5.21", - "ts-node": "^10.9.1", - "typedoc": "^0.22.0", - "typedoc-plugin-inline-sources": "^1.0.1", - "typedoc-plugin-markdown": "^3.11.12", - "typescript": "^4.9.5" - } -} diff --git a/.yarn/unplugged/clipboardy-npm-3.0.0-4025981f4b/node_modules/clipboardy/package.json b/.yarn/unplugged/clipboardy-npm-3.0.0-4025981f4b/node_modules/clipboardy/package.json deleted file mode 100644 index a99b3314f..000000000 --- a/.yarn/unplugged/clipboardy-npm-3.0.0-4025981f4b/node_modules/clipboardy/package.json +++ /dev/null @@ -1,57 +0,0 @@ -{ - "name": "clipboardy", - "version": "3.0.0", - "description": "Access the system clipboard (copy/paste)", - "license": "MIT", - "repository": "sindresorhus/clipboardy", - "funding": "https://github.com/sponsors/sindresorhus", - "author": { - "name": "Sindre Sorhus", - "email": "sindresorhus@gmail.com", - "url": "https://sindresorhus.com" - }, - "type": "module", - "exports": { - "node": "./index.js", - "default": "./browser.js" - }, - "engines": { - "node": "^12.20.0 || ^14.13.1 || >=16.0.0" - }, - "scripts": { - "test": "xo && ava && tsd" - }, - "files": [ - "index.js", - "index.d.ts", - "browser.js", - "lib", - "fallbacks" - ], - 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"keywords": [ - "angular", - "cypress", - "cypress-io", - "test", - "testing" - ], - "contributors": [ - { - "name": "Jordan Powell", - "social": "@jordanpowell88" - }, - { - "name": "Zach Williams", - "social": "@ZachJW34" - } - ], - "module": "dist/index.js", - "publishConfig": { - "access": "public" - }, - "standard": { - "globals": [ - "Cypress", - "cy", - "expect" - ] - } -} diff --git a/.yarn/unplugged/cypress-npm-12.17.3-602acfb08c/node_modules/cypress/mount-utils/package.json b/.yarn/unplugged/cypress-npm-12.17.3-602acfb08c/node_modules/cypress/mount-utils/package.json deleted file mode 100644 index 791a5066d..000000000 --- a/.yarn/unplugged/cypress-npm-12.17.3-602acfb08c/node_modules/cypress/mount-utils/package.json +++ /dev/null @@ -1,37 +0,0 @@ -{ - "name": "@cypress/mount-utils", - "version": "0.0.0-development", - "description": "Shared utilities for the various component testing adapters", - "main": "dist/index.js", - "scripts": { - "build": "tsc || echo 'built, with type 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b/.yarn/unplugged/cypress-npm-12.17.3-602acfb08c/node_modules/cypress/package.json deleted file mode 100644 index a6a01196d..000000000 --- a/.yarn/unplugged/cypress-npm-12.17.3-602acfb08c/node_modules/cypress/package.json +++ /dev/null @@ -1,151 +0,0 @@ -{ - "name": "cypress", - "version": "12.17.3", - "main": "index.js", - "scripts": { - "postinstall": "node index.js --exec install", - "size": "t=\"$(npm pack .)\"; wc -c \"${t}\"; tar tvf \"${t}\"; rm \"${t}\";" - }, - "dependencies": { - "@cypress/request": "^2.88.11", - "@cypress/xvfb": "^1.2.4", - "@types/node": "^16.18.39", - "@types/sinonjs__fake-timers": "8.1.1", - "@types/sizzle": "^2.3.2", - "arch": "^2.2.0", - "blob-util": "^2.0.2", - "bluebird": "^3.7.2", - "buffer": "^5.6.0", - "cachedir": "^2.3.0", - "chalk": "^4.1.0", - "check-more-types": "^2.24.0", - "cli-cursor": "^3.1.0", - "cli-table3": "~0.6.1", - "commander": "^6.2.1", - "common-tags": "^1.8.0", - "dayjs": "^1.10.4", - "debug": "^4.3.4", - "enquirer": "^2.3.6", - 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"types": "./svelte/dist/index.d.ts", - "import": "./svelte/dist/cypress-svelte.esm-bundler.js", - "require": "./svelte/dist/cypress-svelte.cjs.js" - } - }, - "buildInfo": { - "commitBranch": "main", - "commitSha": "14a7416e126f6b296a2da037ae257c27e7915d5b", - "commitDate": "2023-08-01T19:13:43.000Z", - "stable": true - }, - "description": "Cypress is a next generation front end testing tool built for the modern web", - "homepage": "https://github.com/cypress-io/cypress", - "license": "MIT", - "bugs": { - "url": "https://github.com/cypress-io/cypress/issues" - }, - "repository": { - "type": "git", - "url": "https://github.com/cypress-io/cypress.git" - }, - "keywords": [ - "automation", - "browser", - "cypress", - "cypress.io", - "e2e", - "end-to-end", - "integration", - "component", - "mocks", - "runner", - "spies", - "stubs", - "test", - "testing" - ] -} \ No newline at end of file diff --git a/.yarn/unplugged/cypress-npm-12.17.3-602acfb08c/node_modules/cypress/react/package.json b/.yarn/unplugged/cypress-npm-12.17.3-602acfb08c/node_modules/cypress/react/package.json deleted file mode 100644 index e7b2505aa..000000000 --- a/.yarn/unplugged/cypress-npm-12.17.3-602acfb08c/node_modules/cypress/react/package.json +++ /dev/null @@ -1,98 +0,0 @@ -{ - "name": "@cypress/react", - "version": "0.0.0-development", - "description": "Test React components using Cypress", - "main": "dist/cypress-react.cjs.js", - "scripts": { - "build": "rimraf dist && rollup -c rollup.config.mjs", - "postbuild": "node ../../scripts/sync-exported-npm-with-cli.js", - "build-prod": "yarn build", - "cy:open": "node ../../scripts/cypress.js open --component", - "cy:open:debug": "node --inspect-brk ../../scripts/start.js --component-testing --run-project ${PWD}", - "cy:run": "node ../../scripts/cypress.js run --component", - "cy:run:debug": "node --inspect-brk ../../scripts/start.js --component-testing --run-project ${PWD}", - "test": "yarn cy:run", - "lint": "eslint --ext .js,.jsx,.ts,.tsx,.json, 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b/.yarn/unplugged/cypress-npm-12.17.3-602acfb08c/node_modules/cypress/react18/package.json deleted file mode 100644 index 2ffc31d89..000000000 --- a/.yarn/unplugged/cypress-npm-12.17.3-602acfb08c/node_modules/cypress/react18/package.json +++ /dev/null @@ -1,61 +0,0 @@ -{ - "name": "@cypress/react18", - "version": "0.0.0-development", - "description": "Test React components using Cypress", - "main": "dist/cypress-react.cjs.js", - "scripts": { - "build": "rimraf dist && rollup -c rollup.config.mjs", - "postbuild": "node ../../scripts/sync-exported-npm-with-cli.js", - "build-prod": "yarn build", - "watch": "yarn build --watch --watch.exclude ./dist/**/*", - "lint": "eslint --ext .js,.jsx,.ts,.tsx,.json, ." - }, - "devDependencies": { - "@cypress/mount-utils": "0.0.0-development", - "@cypress/react": "0.0.0-development", - "@rollup/plugin-commonjs": "^17.1.0", - "@rollup/plugin-node-resolve": "^11.1.1", - "@types/react": "^16", - "@types/react-dom": "^16", - "cypress": "0.0.0-development", 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a/.yarn/unplugged/cypress-npm-12.17.3-602acfb08c/node_modules/cypress/svelte/package.json b/.yarn/unplugged/cypress-npm-12.17.3-602acfb08c/node_modules/cypress/svelte/package.json deleted file mode 100644 index e061dec3b..000000000 --- a/.yarn/unplugged/cypress-npm-12.17.3-602acfb08c/node_modules/cypress/svelte/package.json +++ /dev/null @@ -1,44 +0,0 @@ -{ - "name": "@cypress/svelte", - "version": "0.0.0-development", - "description": "Browser-based Component Testing for Svelte.js with Cypress.io 🧡", - "main": "dist/cypress-svelte.cjs.js", - "scripts": { - "prebuild": "rimraf dist", - "build": "rollup -c rollup.config.mjs", - "postbuild": "node ../../scripts/sync-exported-npm-with-cli.js", - "build-prod": "yarn build", - "lint": "eslint --ext .js,.jsx,.ts,.tsx,.json, .", - "check-ts": "tsc --noEmit" - }, - "devDependencies": { - "@cypress/mount-utils": "0.0.0-development", - "svelte": "^3.49.0", - "typescript": "^4.7.4" - }, - "peerDependencies": { - "cypress": ">=10.6.0", - "svelte": 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"0.0.0-development", - "description": "Browser-based Component Testing for Vue.js with Cypress.io ✌️🌲", - "main": "dist/cypress-vue.cjs.js", - "scripts": { - "build-prod": "yarn build", - "cy:open": "node ../../scripts/cypress.js open --component --project ${PWD}", - "cy:run": "node ../../scripts/cypress.js run --component --project ${PWD}", - "build": "rimraf dist && rollup -c rollup.config.mjs", - "postbuild": "node ../../scripts/sync-exported-npm-with-cli.js", - "typecheck": "yarn tsd && vue-tsc --noEmit", - "check-ts": "yarn tsd && vue-tsc --noEmit", - "lint": "eslint --ext .js,.jsx,.ts,.tsx,.json,.vue .", - "test": "yarn cy:run", - "tsd": "yarn build && yarn tsc -p test-tsd/tsconfig.tsd.json", - "watch": "yarn build --watch --watch.exclude ./dist/**/*" - }, - "devDependencies": { - "@cypress/mount-utils": "0.0.0-development", - "@vitejs/plugin-vue": "4.2.0", - "@vue/compiler-sfc": "3.2.47", - "@vue/test-utils": "2.3.2", - "axios": "0.21.2", - "cypress": "0.0.0-development", - 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"build-prod": "yarn build", - "test": "echo \"Tests for @cypress/vue2 are run from system-tests\"", - "watch": "yarn build --watch --watch.exclude ./dist/**/*", - "lint": "eslint --ext .js,.jsx,.ts,.tsx,.json,.vue .", - "test-ci": "node ../../scripts/run-ct-examples.js --examplesList=./examples.env" - }, - "devDependencies": { - "@cypress/mount-utils": "0.0.0-development", - "@rollup/plugin-json": "^4.1.0", - "@rollup/plugin-replace": "^2.3.1", - "@vue/test-utils": "^1.3.1", - "tslib": "^2.1.0", - "typescript": "^4.7.4", - "vue": "2.6.12" - }, - "peerDependencies": { - "cypress": ">=4.5.0", - "vue": "^2.0.0" - }, - "files": [ - "dist/**/*", - "src/**/*.js" - ], - "engines": { - "node": ">=8" - }, - "types": "dist/index.d.ts", - "license": "MIT", - "repository": { - "type": "git", - "url": "https://github.com/cypress-io/cypress.git" - }, - "homepage": "https://github.com/cypress-io/cypress/blob/develop/npm/vue/#readme", - "bugs": 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b/.yarn/unplugged/levelup-npm-0.18.6-d181e19f2e/node_modules/levelup/package.json deleted file mode 100644 index cea9e8524..000000000 --- a/.yarn/unplugged/levelup-npm-0.18.6-d181e19f2e/node_modules/levelup/package.json +++ /dev/null @@ -1,73 +0,0 @@ -{ - "name": "levelup", - "description": "Fast & simple storage - a Node.js-style LevelDB wrapper", - "version": "0.18.6", - "contributors": [ - "Rod Vagg (https://github.com/rvagg)", - "John Chesley (https://github.com/chesles/)", - "Jake Verbaten (https://github.com/raynos)", - "Dominic Tarr (https://github.com/dominictarr)", - "Max Ogden (https://github.com/maxogden)", - "Lars-Magnus Skog (https://github.com/ralphtheninja)", - "David Björklund (https://github.com/kesla)", - "Julian Gruber (https://github.com/juliangruber)", - "Paolo Fragomeni (https://github.com/hij1nx)", - "Anton Whalley (https://github.com/No9)", - "Matteo Collina (https://github.com/mcollina)", - "Pedro Teixeira (https://github.com/pgte)", - "James Halliday (https://github.com/substack)" - ], - "repository": { - "type": "git", - "url": "https://github.com/rvagg/node-levelup.git" - }, - "homepage": "https://github.com/rvagg/node-levelup", - "keywords": [ - "leveldb", - "stream", - "database", - "db", - "store", - "storage", - "json" - ], - "main": "lib/levelup.js", - "dependencies": { - "bl": "~0.8.1", - "deferred-leveldown": "~0.2.0", - "errno": "~0.1.1", - "prr": "~0.0.0", - "readable-stream": "~1.0.26", - "semver": "~2.3.1", - "xtend": "~3.0.0" - }, - "devDependencies": { - "leveldown": "~0.10.0", - "bustermove": "*", - "tap": "*", - "referee": "*", - "rimraf": "*", - "async": "*", - "fstream": "*", - "tar": "*", - "mkfiletree": "*", - "readfiletree": "*", - "slow-stream": ">=0.0.4", - "delayed": "*", - "boganipsum": "*", - "du": "*", - "memdown": "*", - "msgpack-js": "*" - }, - "browser": { - "leveldown": false, - "leveldown/package": false, - "semver": false - }, - "scripts": { - "test": "tap test/*-test.js --stderr", - "functionaltests": "node ./test/functional/fstream-test.js && node ./test/functional/binary-data-test.js && node ./test/functional/compat-test.js", - "alltests": "npm test && npm run-script functionaltests" - }, - "license": "MIT" -} diff --git a/.yarn/unplugged/node-gyp-npm-8.4.1-13c90a9c9b/node_modules/node-gyp/package.json b/.yarn/unplugged/node-gyp-npm-8.4.1-13c90a9c9b/node_modules/node-gyp/package.json deleted file mode 100644 index fbeae5e20..000000000 --- a/.yarn/unplugged/node-gyp-npm-8.4.1-13c90a9c9b/node_modules/node-gyp/package.json +++ /dev/null @@ -1,50 +0,0 @@ -{ - "name": "node-gyp", - "description": "Node.js native addon build tool", - "license": "MIT", - "keywords": [ - "native", - "addon", - "module", - "c", - "c++", - "bindings", - "gyp" - ], - "version": "8.4.1", - "installVersion": 9, - "author": "Nathan Rajlich (http://tootallnate.net)", - "repository": { - "type": "git", - "url": "git://github.com/nodejs/node-gyp.git" - }, - "preferGlobal": true, - "bin": "./bin/node-gyp.js", - "main": "./lib/node-gyp.js", - "dependencies": { - "env-paths": "^2.2.0", - "glob": "^7.1.4", - "graceful-fs": "^4.2.6", - "make-fetch-happen": "^9.1.0", - "nopt": "^5.0.0", - "npmlog": "^6.0.0", - "rimraf": "^3.0.2", - "semver": "^7.3.5", - "tar": "^6.1.2", - "which": "^2.0.2" - }, - "engines": { - "node": ">= 10.12.0" - }, - "devDependencies": { - "bindings": "^1.5.0", - "nan": "^2.14.2", - "require-inject": "^1.4.4", - "standard": "^14.3.4", - "tap": "^12.7.0" - }, - "scripts": { - "lint": "standard */*.js test/**/*.js", - "test": "npm run lint && tap --timeout=120 test/test-*" - } -} diff --git a/.yarn/unplugged/node-gyp-npm-9.4.0-ebf5f5573e/node_modules/node-gyp/package.json b/.yarn/unplugged/node-gyp-npm-9.4.0-ebf5f5573e/node_modules/node-gyp/package.json deleted file mode 100644 index 7e9fb648a..000000000 --- a/.yarn/unplugged/node-gyp-npm-9.4.0-ebf5f5573e/node_modules/node-gyp/package.json +++ /dev/null @@ -1,51 +0,0 @@ -{ - "name": "node-gyp", - "description": "Node.js native addon build tool", - "license": "MIT", - "keywords": [ - "native", - "addon", - "module", - "c", - "c++", - "bindings", - "gyp" - ], - "version": "9.4.0", - "installVersion": 11, - "author": "Nathan Rajlich (http://tootallnate.net)", - "repository": { - "type": "git", - "url": "git://github.com/nodejs/node-gyp.git" - }, - "preferGlobal": true, - "bin": "./bin/node-gyp.js", - "main": "./lib/node-gyp.js", - "dependencies": { - "env-paths": "^2.2.0", - "exponential-backoff": "^3.1.1", - "glob": "^7.1.4", - "graceful-fs": "^4.2.6", - "make-fetch-happen": "^11.0.3", - "nopt": "^6.0.0", - "npmlog": "^6.0.0", - "rimraf": "^3.0.2", - "semver": "^7.3.5", - "tar": "^6.1.2", - "which": "^2.0.2" - }, - "engines": { - "node": "^12.13 || ^14.13 || >=16" - }, - "devDependencies": { - "bindings": "^1.5.0", - "mocha": "^10.2.0", - "nan": "^2.14.2", - "require-inject": "^1.4.4", - "standard": "^14.3.4" - }, - "scripts": { - "lint": "standard */*.js test/**/*.js", - "test": "npm run lint && mocha --reporter=test/reporter.js test/test-download.js test/test-*" - } -} diff --git a/.yarn/unplugged/node-gyp-npm-9.4.1-15a6f0e8e4/node_modules/node-gyp/package.json b/.yarn/unplugged/node-gyp-npm-9.4.1-15a6f0e8e4/node_modules/node-gyp/package.json deleted file mode 100644 index 38359c300..000000000 --- a/.yarn/unplugged/node-gyp-npm-9.4.1-15a6f0e8e4/node_modules/node-gyp/package.json +++ /dev/null @@ -1,51 +0,0 @@ -{ - "name": "node-gyp", - "description": "Node.js native addon build tool", - "license": "MIT", - "keywords": [ - "native", - "addon", - "module", - "c", - "c++", - "bindings", - "gyp" - ], - "version": "9.4.1", - "installVersion": 11, - "author": "Nathan Rajlich (http://tootallnate.net)", - "repository": { - "type": "git", - "url": "git://github.com/nodejs/node-gyp.git" - }, - "preferGlobal": true, - "bin": "./bin/node-gyp.js", - "main": "./lib/node-gyp.js", - "dependencies": { - "env-paths": "^2.2.0", - "exponential-backoff": "^3.1.1", - "glob": 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Cross-platform.", - "license": "MIT", - "repository": "sindresorhus/open", - "funding": "https://github.com/sponsors/sindresorhus", - "author": { - "name": "Sindre Sorhus", - "email": "sindresorhus@gmail.com", - "url": "https://sindresorhus.com" - }, - "type": "module", - "exports": { - "types": "./index.d.ts", - "default": "./index.js" - }, - "sideEffects": false, - "engines": { - "node": ">=18" - }, - "scripts": { - "test": "xo && tsd" - }, - "files": [ - "index.js", - "index.d.ts", - "xdg-open" - ], - "keywords": [ - "app", - "open", - "opener", - "opens", - "launch", - "start", - "xdg-open", - "xdg", - "default", - "cmd", - "browser", - "editor", - "executable", - "exe", - "url", - "urls", - "arguments", - "args", - "spawn", - "exec", - "child", - "process", - "website", - "file" - ], - "dependencies": { - "default-browser": "^5.2.1", - "define-lazy-prop": "^3.0.0", - "is-inside-container": "^1.0.0", - "is-wsl": "^3.1.0" - }, - "devDependencies": { - "@types/node": "^20.10.5", - "ava": "^6.0.1", - "tsd": "^0.30.1", - "xo": "^0.56.0" - } -} diff --git a/.yarn/unplugged/prettier-npm-3.3.2-efeafcaa4b/node_modules/prettier/package.json b/.yarn/unplugged/prettier-npm-3.3.2-efeafcaa4b/node_modules/prettier/package.json deleted file mode 100644 index 1152d245d..000000000 --- a/.yarn/unplugged/prettier-npm-3.3.2-efeafcaa4b/node_modules/prettier/package.json +++ /dev/null @@ -1,198 +0,0 @@ -{ - "name": "prettier", - "version": "3.3.2", - "description": "Prettier is an opinionated code formatter", - "bin": "./bin/prettier.cjs", - "repository": "prettier/prettier", - "funding": "https://github.com/prettier/prettier?sponsor=1", - "homepage": "https://prettier.io", - "author": "James Long", - "license": "MIT", - "main": "./index.cjs", - "browser": "./standalone.js", - "unpkg": "./standalone.js", - "exports": { - ".": { - "types": "./index.d.ts", - "require": "./index.cjs", - "browser": { - "import": "./standalone.mjs", - "default": "./standalone.js" - }, - "default": "./index.mjs" - }, - "./*": "./*", - "./doc": { - "types": "./doc.d.ts", - "require": "./doc.js", - "default": "./doc.mjs" - }, - "./standalone": { - "types": "./standalone.d.ts", - "require": "./standalone.js", - "default": "./standalone.mjs" - }, - "./plugins/estree": { - "types": "./plugins/estree.d.ts", - "require": "./plugins/estree.js", - "default": "./plugins/estree.mjs" - }, - "./plugins/babel": { - "types": "./plugins/babel.d.ts", - "require": "./plugins/babel.js", - "default": "./plugins/babel.mjs" - }, - "./plugins/flow": { - "types": "./plugins/flow.d.ts", - "require": "./plugins/flow.js", - "default": "./plugins/flow.mjs" - }, - "./plugins/typescript": { - "types": "./plugins/typescript.d.ts", - "require": "./plugins/typescript.js", - "default": "./plugins/typescript.mjs" - }, - "./plugins/acorn": { - "types": "./plugins/acorn.d.ts", - "require": "./plugins/acorn.js", - "default": "./plugins/acorn.mjs" - }, - "./plugins/meriyah": { - "types": "./plugins/meriyah.d.ts", - "require": "./plugins/meriyah.js", - "default": "./plugins/meriyah.mjs" - }, - "./plugins/angular": { - "types": "./plugins/angular.d.ts", - "require": "./plugins/angular.js", - "default": "./plugins/angular.mjs" - }, - "./plugins/postcss": { - "types": "./plugins/postcss.d.ts", - "require": "./plugins/postcss.js", - "default": "./plugins/postcss.mjs" - }, - "./plugins/graphql": { - "types": "./plugins/graphql.d.ts", - "require": "./plugins/graphql.js", - "default": "./plugins/graphql.mjs" - }, - "./plugins/markdown": { - "types": "./plugins/markdown.d.ts", - "require": "./plugins/markdown.js", - "default": "./plugins/markdown.mjs" - }, - "./plugins/glimmer": { - "types": "./plugins/glimmer.d.ts", - "require": "./plugins/glimmer.js", - "default": "./plugins/glimmer.mjs" - }, - "./plugins/html": { - "types": "./plugins/html.d.ts", - "require": "./plugins/html.js", - "default": "./plugins/html.mjs" - }, - "./plugins/yaml": { - "types": "./plugins/yaml.d.ts", - "require": "./plugins/yaml.js", - "default": "./plugins/yaml.mjs" - }, - "./esm/standalone.mjs": "./standalone.mjs", - "./parser-babel": "./plugins/babel.js", - "./parser-babel.js": "./plugins/babel.js", - "./esm/parser-babel.mjs": "./plugins/babel.mjs", - "./parser-flow": "./plugins/flow.js", - "./parser-flow.js": "./plugins/flow.js", - "./esm/parser-flow.mjs": "./plugins/flow.mjs", - "./parser-typescript": "./plugins/typescript.js", - "./parser-typescript.js": "./plugins/typescript.js", - "./esm/parser-typescript.mjs": "./plugins/typescript.mjs", - "./parser-espree": "./plugins/acorn.js", - "./parser-espree.js": "./plugins/acorn.js", - "./esm/parser-espree.mjs": "./plugins/acorn.mjs", - "./parser-meriyah": "./plugins/meriyah.js", - "./parser-meriyah.js": "./plugins/meriyah.js", - "./esm/parser-meriyah.mjs": "./plugins/meriyah.mjs", - "./parser-angular": "./plugins/angular.js", - "./parser-angular.js": "./plugins/angular.js", - "./esm/parser-angular.mjs": "./plugins/angular.mjs", - "./parser-postcss": "./plugins/postcss.js", - "./parser-postcss.js": "./plugins/postcss.js", - "./esm/parser-postcss.mjs": "./plugins/postcss.mjs", - "./parser-graphql": "./plugins/graphql.js", - "./parser-graphql.js": "./plugins/graphql.js", - "./esm/parser-graphql.mjs": "./plugins/graphql.mjs", - "./parser-markdown": "./plugins/markdown.js", - "./parser-markdown.js": "./plugins/markdown.js", - "./esm/parser-markdown.mjs": "./plugins/markdown.mjs", - "./parser-glimmer": "./plugins/glimmer.js", - "./parser-glimmer.js": "./plugins/glimmer.js", - "./esm/parser-glimmer.mjs": "./plugins/glimmer.mjs", - "./parser-html": "./plugins/html.js", - "./parser-html.js": "./plugins/html.js", - "./esm/parser-html.mjs": "./plugins/html.mjs", - "./parser-yaml": "./plugins/yaml.js", - "./parser-yaml.js": "./plugins/yaml.js", - "./esm/parser-yaml.mjs": "./plugins/yaml.mjs" - }, - "engines": { - "node": ">=14" - }, - "files": [ - "LICENSE", - "README.md", - "bin/prettier.cjs", - "doc.d.ts", - "doc.js", - "doc.mjs", - "index.cjs", - "index.d.ts", - "index.d.ts", - "index.mjs", - "internal/cli.mjs", - "package.json", - "plugins/acorn.d.ts", - "plugins/acorn.js", - "plugins/acorn.mjs", - "plugins/angular.d.ts", - "plugins/angular.js", - "plugins/angular.mjs", - "plugins/babel.d.ts", - "plugins/babel.js", - "plugins/babel.mjs", - "plugins/estree.d.ts", - "plugins/estree.js", - "plugins/estree.mjs", - "plugins/flow.d.ts", - "plugins/flow.js", - "plugins/flow.mjs", - "plugins/glimmer.d.ts", - "plugins/glimmer.js", - "plugins/glimmer.mjs", - "plugins/graphql.d.ts", - "plugins/graphql.js", - "plugins/graphql.mjs", - "plugins/html.d.ts", - "plugins/html.js", - "plugins/html.mjs", - "plugins/markdown.d.ts", - "plugins/markdown.js", - "plugins/markdown.mjs", - "plugins/meriyah.d.ts", - "plugins/meriyah.js", - "plugins/meriyah.mjs", - "plugins/postcss.d.ts", - "plugins/postcss.js", - "plugins/postcss.mjs", - "plugins/typescript.d.ts", - "plugins/typescript.js", - "plugins/typescript.mjs", - "plugins/yaml.d.ts", - "plugins/yaml.js", - "plugins/yaml.mjs", - "standalone.d.ts", - "standalone.js", - "standalone.mjs" - ], - "preferUnplugged": true -} \ No newline at end of file diff --git a/.yarn/unplugged/term-size-npm-2.2.1-77ce7141d0/node_modules/term-size/package.json b/.yarn/unplugged/term-size-npm-2.2.1-77ce7141d0/node_modules/term-size/package.json deleted file mode 100644 index a070eb93f..000000000 --- a/.yarn/unplugged/term-size-npm-2.2.1-77ce7141d0/node_modules/term-size/package.json +++ /dev/null @@ -1,43 +0,0 @@ -{ - "name": "term-size", - "version": "2.2.1", - "description": "Reliably get the terminal window size (columns & rows)", - "license": "MIT", - "repository": "sindresorhus/term-size", - "funding": "https://github.com/sponsors/sindresorhus", - "author": { - "name": "Sindre Sorhus", - "email": "sindresorhus@gmail.com", - "url": "https://sindresorhus.com" - }, - "engines": { - "node": ">=8" - }, - "scripts": { - "test": "xo && ava && tsd" - }, - "files": [ - "index.js", - "index.d.ts", - "vendor" - ], - "keywords": [ - "terminal", - "size", - "console", - "window", - "width", - "height", - "columns", - "rows", - "lines", - "tty", - "redirected" - ], - "devDependencies": { - "ava": "^2.4.0", - "execa": "^3.4.0", - "tsd": "^0.11.0", - "xo": "^0.25.3" - } -} From be5650f22e8155bb54526312d371ad6d84f26a00 Mon Sep 17 00:00:00 2001 From: Garrett Stevens Date: Tue, 27 Aug 2024 17:39:43 +0000 Subject: [PATCH 04/12] Format CLI README when packing --- packages/apollo-cli/package.json | 3 ++- yarn.lock | 1 + 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/packages/apollo-cli/package.json b/packages/apollo-cli/package.json index 8a9526601..90c9418e8 100644 --- a/packages/apollo-cli/package.json +++ b/packages/apollo-cli/package.json @@ -28,7 +28,7 @@ "dev": "tsx bin/dev.js", "postpack": "shx rm -f oclif.manifest.json", "posttest": "yarn lint", - "prepack": "yarn build && oclif manifest && oclif readme", + "prepack": "yarn build && oclif manifest && oclif readme && prettier --write README.md", "prepare": "yarn build", "test": "mocha --require src/test/fixtures.ts 'src/**/*.test.ts'", "test:ci": "nyc mocha 'src/**/*.test.ts'", @@ -64,6 +64,7 @@ "mocha": "^10.2.0", "nyc": "^15.1.0", "oclif": "^4.4.2", + "prettier": "^3.3.2", "react-dom": "^18.2.0", "rxjs": "^7.4.0", "shx": "^0.3.3", diff --git a/yarn.lock b/yarn.lock index 15ea07300..e8995e00f 100644 --- a/yarn.lock +++ b/yarn.lock @@ -143,6 +143,7 @@ __metadata: nyc: "npm:^15.1.0" oclif: "npm:^4.4.2" open: "npm:^10.1.0" + prettier: "npm:^3.3.2" react-dom: "npm:^18.2.0" rxjs: "npm:^7.4.0" shx: "npm:^0.3.3" From 13c1c025fb99069b338081402907fcbc943d22c4 Mon Sep 17 00:00:00 2001 From: Garrett Stevens Date: Tue, 27 Aug 2024 17:50:56 +0000 Subject: [PATCH 05/12] Build shared before publishing --- .github/workflows/publish.yml | 18 +++++++++++++----- 1 file changed, 13 insertions(+), 5 deletions(-) diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml index 1d21d9658..cdf63d4da 100644 --- a/.github/workflows/publish.yml +++ b/.github/workflows/publish.yml @@ -6,18 +6,26 @@ on: jobs: publish-npm: - name: Publish to npm + name: Publish to NPM runs-on: ubuntu-latest steps: - - uses: actions/checkout@v4 + - name: Check out + uses: actions/checkout@v4 # Setup .npmrc file to publish to npm - - uses: actions/setup-node@v4 + - name: Use Node.js 18.x + uses: actions/setup-node@v4 with: node-version: 18 registry-url: https://registry.npmjs.org scope: '@apollo-annotation' - - run: yarn --immutable - - run: | + cache: yarn + - name: Install + run: yarn --immutable + - name: Build shared + run: yarn build + working-directory: packages/apollo-shared + - name: Publish + run: | yarn config set npmAuthToken ${{ secrets.NPM_TOKEN }} yarn workspaces foreach --no-private --all npm publish --tolerate-republish env: From 3f6870bf6e48ecc8971d5880331f4c2399c15b06 Mon Sep 17 00:00:00 2001 From: Garrett Stevens Date: Tue, 27 Aug 2024 20:50:43 +0000 Subject: [PATCH 06/12] Copy plugin to correct location when deploying --- .github/workflows/deploy/Dockerfile | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/deploy/Dockerfile b/.github/workflows/deploy/Dockerfile index b22aa1620..a2081dcb7 100644 --- a/.github/workflows/deploy/Dockerfile +++ b/.github/workflows/deploy/Dockerfile @@ -3,6 +3,7 @@ ARG JBROWSE_VERSION COPY ./httpd.conf /usr/local/apache2/conf/httpd.conf COPY ./jbrowse-plugin-apollo.umd.development.js /usr/local/apache2/htdocs/ COPY ./jbrowse-plugin-apollo.umd.production.min.js /usr/local/apache2/htdocs/ +COPY ./jbrowse-plugin-apollo.umd.production.min.js /usr/local/apache2/htdocs/apollo.js WORKDIR /usr/local/apache2/htdocs/ RUN < Date: Tue, 27 Aug 2024 21:46:36 +0000 Subject: [PATCH 07/12] Fix error when adding a new user with no role --- packages/apollo-schemas/src/user.schema.ts | 2 +- .../src/components/ManageUsers.tsx | 21 ++++++++++++++++++- 2 files changed, 21 insertions(+), 2 deletions(-) diff --git a/packages/apollo-schemas/src/user.schema.ts b/packages/apollo-schemas/src/user.schema.ts index c3be2f69f..f3c02a781 100644 --- a/packages/apollo-schemas/src/user.schema.ts +++ b/packages/apollo-schemas/src/user.schema.ts @@ -13,7 +13,7 @@ export class User { @Prop({ required: true, unique: true }) email: string - @Prop({ type: String, enum: ['readOnly', 'admin', 'user'] }) + @Prop({ type: String, enum: ['readOnly', 'admin', 'user', 'none'] }) role: Role } diff --git a/packages/jbrowse-plugin-apollo/src/components/ManageUsers.tsx b/packages/jbrowse-plugin-apollo/src/components/ManageUsers.tsx index c003004f4..0b6e87579 100644 --- a/packages/jbrowse-plugin-apollo/src/components/ManageUsers.tsx +++ b/packages/jbrowse-plugin-apollo/src/components/ManageUsers.tsx @@ -124,7 +124,26 @@ export function ManageUsers({ headerName: 'Role', width: 140, type: 'singleSelect', - valueOptions: ['', 'readOnly', 'user', 'admin'], + valueOptions: ['readOnly', 'user', 'admin', 'none'], + getOptionLabel(value) { + switch (value) { + case 'readOnly': { + return 'Read-only' + } + case 'user': { + return 'User' + } + case 'admin': { + return 'Admin' + } + case 'none': { + return 'None' + } + default: { + return 'unknown' + } + } + }, editable: true, }, { From 9fca05ab738d12f0da486ece589340e8dff62368 Mon Sep 17 00:00:00 2001 From: Garrett Stevens Date: Tue, 27 Aug 2024 18:41:59 -0600 Subject: [PATCH 08/12] Sort package.json files --- .prettierrc.js | 13 - .prettierrc.mjs | 19 + package.json | 5 +- packages/apollo-cli/README.md | 908 +----------------- packages/apollo-cli/package.json | 78 +- .../apollo-collaboration-server/package.json | 54 +- packages/apollo-common/package.json | 16 +- packages/apollo-shared/package.json | 2 +- packages/jbrowse-plugin-apollo/package.json | 52 +- yarn.lock | 140 +++ 10 files changed, 264 insertions(+), 1023 deletions(-) delete mode 100644 .prettierrc.js create mode 100644 .prettierrc.mjs diff --git a/.prettierrc.js b/.prettierrc.js deleted file mode 100644 index b60d8e597..000000000 --- a/.prettierrc.js +++ /dev/null @@ -1,13 +0,0 @@ -/** @type {import("prettier").Options} */ - -module.exports = { - semi: false, - singleQuote: true, - proseWrap: 'always', - overrides: [ - { - files: ['.devcontainer/**/*.json', '.vscode/*.json', '**/tsconfig*.json'], - options: { parser: 'jsonc' }, - }, - ], -} diff --git a/.prettierrc.mjs b/.prettierrc.mjs new file mode 100644 index 000000000..ec3e4318e --- /dev/null +++ b/.prettierrc.mjs @@ -0,0 +1,19 @@ +import packagejson from 'prettier-plugin-packagejson' +/** + * @see https://prettier.io/docs/en/configuration.html + * @type {import("prettier").Config} + */ +const config = { + semi: false, + singleQuote: true, + proseWrap: 'always', + overrides: [ + { + files: ['.devcontainer/**/*.json', '.vscode/*.json', '**/tsconfig*.json'], + options: { parser: 'jsonc' }, + }, + ], + plugins: [packagejson], +} + +export default config diff --git a/package.json b/package.json index a22124eb2..7e11663a9 100644 --- a/package.json +++ b/package.json @@ -1,7 +1,7 @@ { "name": "apollo3", + "private": true, "description": "Monorepo containing Apollo front and back end code", - "packageManager": "yarn@4.3.1", "workspaces": [ "packages/*" ], @@ -42,10 +42,11 @@ "lint-staged": "^15.2.2", "npm-run-all": "^4.1.5", "prettier": "^3.3.2", + "prettier-plugin-packagejson": "^2.5.2", "react": "^18.2.0", "tsx": "^4.6.2", "typescript": "^5.5.3", "yargs": "^17.7.2" }, - "private": true + "packageManager": "yarn@4.3.1" } diff --git a/packages/apollo-cli/README.md b/packages/apollo-cli/README.md index 79aea0e6e..8707ab4d9 100644 --- a/packages/apollo-cli/README.md +++ b/packages/apollo-cli/README.md @@ -16,7 +16,7 @@ $ npm install -g @apollo-annotation/cli $ apollo COMMAND running command... $ apollo (--version) -@apollo-annotation/cli/0.1.19 linux-x64 node-v20.14.0 +@apollo-annotation/cli/0.1.19 linux-x64 node-v18.20.3 $ apollo --help [COMMAND] USAGE $ apollo COMMAND @@ -29,720 +29,7 @@ USAGE -- [`apollo assembly add-fasta`](#apollo-assembly-add-fasta) -- [`apollo assembly add-gff`](#apollo-assembly-add-gff) -- [`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 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 import`](#apollo-feature-import) -- [`apollo feature search`](#apollo-feature-search) - [`apollo help [COMMANDS]`](#apollo-help-commands) -- [`apollo login`](#apollo-login) -- [`apollo logout`](#apollo-logout) -- [`apollo refseq add-alias`](#apollo-refseq-add-alias) -- [`apollo refseq get`](#apollo-refseq-get) -- [`apollo status`](#apollo-status) -- [`apollo user get`](#apollo-user-get) - -## `apollo assembly add-fasta` - -Add new assembly from local or external fasta file - -``` -USAGE - $ apollo assembly add-fasta -i [--profile ] [--config-file ] [-a ] [-x ] [-f] - -FLAGS - -a, --assembly= Name for this assembly. Use the file name if omitted - -f, --force Delete existing assembly, if it exists - -i, --input-file= (required) Input fasta file - -x, --index= URL of the index. Required if input is an external source and ignored if input is a local - file - --config-file= Use this config file (mostly for testing) - --profile= Use credentials from this profile - -DESCRIPTION - Add new assembly from local or external fasta file - -EXAMPLES - From local file: - - $ apollo assembly add-fasta -i genome.fa -a myAssembly - - From external source we also need the URL of the index: - - $ apollo assembly add-fasta -i https://.../genome.fa -x https://.../genome.fa.fai -a myAssembly -``` - -_See code: -[src/commands/assembly/add-fasta.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/assembly/add-fasta.ts)_ - -## `apollo assembly add-gff` - -Add new assembly from gff or gft file - -``` -USAGE - $ apollo assembly add-gff -i [--profile ] [--config-file ] [-a ] [-o] [-f] - -FLAGS - -a, --assembly= Name for this assembly. Use the file name if omitted - -f, --force Delete existing assembly, if it exists - -i, --input-file= (required) Input gff or gtf file - -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-gff -i genome.gff -a myAssembly - - Import sequences only: - - $ apollo assembly add-gff -i genome.gff -a myAssembly -o -``` - -_See code: -[src/commands/assembly/add-gff.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/assembly/add-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/v0.1.19/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/v0.1.19/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/v0.1.19/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/v0.1.19/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/v0.1.19/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` - - - rootCredentials.username: - Username of root account. Only set this for "root" access type - - - rootCredentials.password: - 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/v0.1.19/packages/apollo-cli/src/commands/config.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 6605826fbd0eee691f83e73f -t exon -s 10 -e 20 -``` - -_See code: -[src/commands/feature/add-child.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/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/v0.1.19/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. he 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/v0.1.19/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/v0.1.19/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/v0.1.19/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/v0.1.19/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/v0.1.19/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/v0.1.19/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/v0.1.19/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/v0.1.19/packages/apollo-cli/src/commands/feature/get-id.ts)_ - -## `apollo feature import` - -Import features from local gff file - -``` -USAGE - $ apollo feature import -i -a [--profile ] [--config-file ] [-d] - -FLAGS - -a, --assembly= (required) Import into this assembly name or assembly ID - -d, --delete-existing Delete existing features before importing - -i, --input-file= (required) Input gff or gtf file - --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 -d -i features.gff3 -a myAssembly -``` - -_See code: -[src/commands/feature/import.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/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/v0.1.19/packages/apollo-cli/src/commands/feature/search.ts)_ ## `apollo help [COMMANDS]` @@ -765,197 +52,4 @@ DESCRIPTION _See code: [@oclif/plugin-help](https://github.com/oclif/plugin-help/blob/v6.0.8/src/commands/help.ts)_ -## `apollo login` - -Login to Apollo - -``` -USAGE - $ apollo login [--profile ] [--config-file ] [-a ] [-u ] [-p ] [-f] - [--port ] - -FLAGS - -a, --address= Address of Apollo server - -f, --force Force re-authentication even if user is already logged in - -p, --password= Password for - -u, --username= Username for root login - --config-file= Use this config file (mostly for testing) - --port= [default: 3000] Get token by listening to this port number (usually this is >= 1024 and < - 65536) - --profile= Use credentials from this profile - -DESCRIPTION - Login to Apollo - - Use the provided credentials to obtain and save the token to access Apollo. Once - the token for the given profile has been saved in the configuration file, users - do not normally need to execute this command again unless the token has expired. - To setup a new profile use "apollo config" - -EXAMPLES - The most basic and probably most typical usage is to login using the default - profile in configuration file: - - $ apollo login - - Login with a different profile: - - $ apollo login --profile my-profile -``` - -_See code: -[src/commands/login.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/login.ts)_ - -## `apollo logout` - -Logout of Apollo - -``` -USAGE - $ apollo logout [--profile ] [--config-file ] - -FLAGS - --config-file= Use this config file (mostly for testing) - --profile= Use credentials from this profile - -DESCRIPTION - Logout of Apollo - - Logout by removing the access token from the selected profile - -EXAMPLES - Logout default profile: - - $ apollo logout - - Logout selected profile - - $ apollo logout --profile my-profile -``` - -_See code: -[src/commands/logout.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/logout.ts)_ - -## `apollo refseq add-alias` - -Add reference name aliases from a file - -``` -USAGE - $ apollo refseq add-alias -i -a [--profile ] [--config-file ] - -FLAGS - -a, --assembly= (required) Name for this assembly. - -i, --input-file= (required) Input refname alias file - --config-file= Use this config file (mostly for testing) - --profile= Use credentials from this profile - -DESCRIPTION - Add reference name aliases from a file - - Reference name aliasing is a process to make chromosomes that are named slightly - differently but which refer to the same thing render properly. This command - reads a file with reference name aliases and adds them to the database. - -EXAMPLES - Add reference name aliases: - - $ apollo refseq add-alias -i alias.txt -a myAssembly -``` - -_See code: -[src/commands/refseq/add-alias.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/refseq/add-alias.ts)_ - -## `apollo refseq get` - -Get reference sequences - -``` -USAGE - $ apollo refseq get [--profile ] [--config-file ] [-a ] - -FLAGS - -a, --assembly=... Get reference sequences for these assembly names or IDs; use - to read it from stdin - --config-file= Use this config file (mostly for testing) - --profile= Use credentials from this profile - -DESCRIPTION - Get reference sequences - - Output the reference sequences in one or more assemblies in json format. This - command returns the sequence characteristics (e.g., name, ID, etc), not the DNA - sequences. Use `assembly sequence` for that. - -EXAMPLES - All sequences in the database: - - $ apollo refseq get - - Only sequences for these assemblies: - - $ apollo refseq get -a mm9 mm10 -``` - -_See code: -[src/commands/refseq/get.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/refseq/get.ts)_ - -## `apollo status` - -View authentication status - -``` -USAGE - $ apollo status [--profile ] [--config-file ] - -FLAGS - --config-file= Use this config file (mostly for testing) - --profile= Use credentials from this profile - -DESCRIPTION - View authentication status - - This command returns ": Logged in" if the selected profile has an - access token and ": Logged out" otherwise. Note that this command does - not check the validity of the access token. -``` - -_See code: -[src/commands/status.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/status.ts)_ - -## `apollo user get` - -Get list of users - -``` -USAGE - $ apollo user get [--profile ] [--config-file ] [-u ] [-r ] - -FLAGS - -r, --role= Get users with this role - -u, --username= Find this username - --config-file= Use this config file (mostly for testing) - --profile= Use credentials from this profile - -DESCRIPTION - Get list of users - - If set, filters username and role must be both satisfied to return an entry - -EXAMPLES - By username: - - $ apollo user get -u Guest - - By role: - - $ apollo user get -r admin - - Use jq for more control: - - $ apollo user get | jq '.[] | select(.createdAt > "2024-03-18")' -``` - -_See code: -[src/commands/user/get.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/user/get.ts)_ - diff --git a/packages/apollo-cli/package.json b/packages/apollo-cli/package.json index 90c9418e8..5fc1f1cde 100644 --- a/packages/apollo-cli/package.json +++ b/packages/apollo-cli/package.json @@ -1,22 +1,19 @@ { "name": "@apollo-annotation/cli", - "description": "Command line interface for the Apollo annotation server", "version": "0.1.19", - "author": "Apollo Team", + "description": "Command line interface for the Apollo annotation server", "repository": { "type": "git", "url": "https://github.com/GMOD/Apollo3.git", "directory": "packages/apollo-cli" }, - "bin": { - "apollo": "./bin/run.js" - }, + "author": "Apollo Team", "type": "module", + "exports": "./dist/index.js", "main": "", "types": "dist/index.d.ts", - "exports": "./dist/index.js", - "engines": { - "node": ">=18.0.0" + "bin": { + "apollo": "./bin/run.js" }, "files": [ "/bin", @@ -26,14 +23,44 @@ "scripts": { "build": "shx rm -rf dist && tsc -b", "dev": "tsx bin/dev.js", - "postpack": "shx rm -f oclif.manifest.json", - "posttest": "yarn lint", "prepack": "yarn build && oclif manifest && oclif readme && prettier --write README.md", + "postpack": "shx rm -f oclif.manifest.json", "prepare": "yarn build", "test": "mocha --require src/test/fixtures.ts 'src/**/*.test.ts'", + "posttest": "yarn lint", "test:ci": "nyc mocha 'src/**/*.test.ts'", "version": "oclif readme && git add README.md" }, + "oclif": { + "bin": "apollo", + "commands": "./dist/commands", + "dirname": "apollo-cli", + "helpOptions": { + "flagSortOrder": "none" + }, + "plugins": [ + "@oclif/plugin-help" + ], + "repositoryPrefix": "<%- repo %>/blob/v<%- version %>/packages/apollo-cli/<%- commandPath %>", + "topicSeparator": " ", + "topics": { + "assembly": { + "description": "Commands to handle assemblies" + }, + "change": { + "description": "Commands to handle the log of changes made to the database" + }, + "feature": { + "description": "Commands to handle features" + }, + "refseq": { + "description": "Commands to handle reference sequences" + }, + "user": { + "description": "Commands to handle users" + } + } + }, "dependencies": { "@inquirer/input": "^1.2.14", "@inquirer/password": "^1.1.14", @@ -72,35 +99,8 @@ "tsx": "^4.6.2", "typescript": "^5.5.3" }, - "oclif": { - "helpOptions": { - "flagSortOrder": "none" - }, - "bin": "apollo", - "dirname": "apollo-cli", - "commands": "./dist/commands", - "plugins": [ - "@oclif/plugin-help" - ], - "repositoryPrefix": "<%- repo %>/blob/v<%- version %>/packages/apollo-cli/<%- commandPath %>", - "topicSeparator": " ", - "topics": { - "assembly": { - "description": "Commands to handle assemblies" - }, - "change": { - "description": "Commands to handle the log of changes made to the database" - }, - "feature": { - "description": "Commands to handle features" - }, - "refseq": { - "description": "Commands to handle reference sequences" - }, - "user": { - "description": "Commands to handle users" - } - } + "engines": { + "node": ">=18.0.0" }, "publishConfig": { "access": "public" diff --git a/packages/apollo-collaboration-server/package.json b/packages/apollo-collaboration-server/package.json index 0fb68dd7a..fd7bc225d 100644 --- a/packages/apollo-collaboration-server/package.json +++ b/packages/apollo-collaboration-server/package.json @@ -1,27 +1,42 @@ { "name": "@apollo-annotation/collaboration-server", "version": "0.1.19", + "private": true, "description": "", - "author": "", "license": "Apache-2.0", - "engines": { - "node": ">=14" - }, + "author": "", "scripts": { "build": "yarn build:shared && rimraf dist && nest build", + "cypress:start": "GUEST_USER_ROLE=admin MONGODB_URI=\"mongodb://localhost:27017/apolloTestDb?directConnection=true\" LOG_LEVELS=error,warn yarn start", + "deb": "ts-node-dev src/main.ts", "start": "yarn build:shared && yarn start:nest --watch", + "start:debug": "yarn build:shared && yarn start:nest --debug --watch", "start:nest": "NODE_ENV=development nest start", "start:no-watch": "yarn build:shared && yarn start:nest", - "start:debug": "yarn build:shared && yarn start:nest --debug --watch", - "deb": "ts-node-dev src/main.ts", "start:prod": "NODE_ENV=production node dist/main.js", "test": "jest", - "test:watch": "jest --watch", + "test:cli:start": "ALLOW_ROOT_USER=true ROOT_USER_NAME=admin ROOT_USER_PASSWORD=pass MONGODB_URI=\"mongodb://localhost:27017/apolloTestCliDb?directConnection=true\" LOG_LEVELS=error,warn yarn start", "test:cov": "jest --coverage", "test:debug": "node --inspect-brk -r tsconfig-paths/register -r ts-node/register node_modules/.bin/jest --runInBand", "test:e2e": "jest --config ./test/jest-e2e.json", - "cypress:start": "GUEST_USER_ROLE=admin MONGODB_URI=\"mongodb://localhost:27017/apolloTestDb?directConnection=true\" LOG_LEVELS=error,warn yarn start", - "test:cli:start": "ALLOW_ROOT_USER=true ROOT_USER_NAME=admin ROOT_USER_PASSWORD=pass MONGODB_URI=\"mongodb://localhost:27017/apolloTestCliDb?directConnection=true\" LOG_LEVELS=error,warn yarn start" + "test:watch": "jest --watch" + }, + "jest": { + "collectCoverageFrom": [ + "**/*.(t|j)s" + ], + "coverageDirectory": "../coverage", + "moduleFileExtensions": [ + "js", + "json", + "ts" + ], + "rootDir": "src", + "testEnvironment": "node", + "testRegex": ".*\\.spec\\.ts$", + "transform": { + "^.+\\.(t|j)s$": "ts-jest" + } }, "dependencies": { "@apollo-annotation/common": "workspace:^", @@ -104,22 +119,7 @@ "tsconfig-paths": "^3.11.0", "typescript": "^5.5.3" }, - "jest": { - "moduleFileExtensions": [ - "js", - "json", - "ts" - ], - "rootDir": "src", - "testRegex": ".*\\.spec\\.ts$", - "transform": { - "^.+\\.(t|j)s$": "ts-jest" - }, - "collectCoverageFrom": [ - "**/*.(t|j)s" - ], - "coverageDirectory": "../coverage", - "testEnvironment": "node" - }, - "private": true + "engines": { + "node": ">=14" + } } diff --git a/packages/apollo-common/package.json b/packages/apollo-common/package.json index 6c1d5cc1c..cb1bf5287 100644 --- a/packages/apollo-common/package.json +++ b/packages/apollo-common/package.json @@ -17,6 +17,14 @@ "bson-objectid": "^2.0.4", "tslib": "^2.3.1" }, + "devDependencies": { + "@apollo-annotation/mst": "workspace:^", + "@nestjs/common": "^10.1.0", + "@nestjs/core": "^10.1.0", + "@types/node": "^18.14.2", + "mongoose": "^6.12.0", + "typescript": "^5.5.3" + }, "peerDependencies": { "@mui/material": "^5.11.14", "@mui/x-data-grid": "^7.0.0", @@ -29,14 +37,6 @@ "rxjs": "^7.4.0", "tss-react": "^4.6.1" }, - "devDependencies": { - "@apollo-annotation/mst": "workspace:^", - "@nestjs/common": "^10.1.0", - "@nestjs/core": "^10.1.0", - "@types/node": "^18.14.2", - "mongoose": "^6.12.0", - "typescript": "^5.5.3" - }, "publishConfig": { "access": "public" } diff --git a/packages/apollo-shared/package.json b/packages/apollo-shared/package.json index 76aab1fcd..22934e8f8 100644 --- a/packages/apollo-shared/package.json +++ b/packages/apollo-shared/package.json @@ -3,9 +3,9 @@ "version": "0.1.19", "main": "./dist/index.js", "scripts": { - "start": "tsc --build --watch", "build": "yarn clean && tsc --build", "clean": "rimraf dist", + "start": "tsc --build --watch", "test": "glob -c \"tsx --test --test-reporter spec \" \"**/*.test.ts\"", "test:ci": "NODE_V8_COVERAGE=./coverage glob -c \"tsx --test --test-reporter spec --experimental-test-coverage \" \"**/*.test.ts\"" }, diff --git a/packages/jbrowse-plugin-apollo/package.json b/packages/jbrowse-plugin-apollo/package.json index 3dd4ce879..9007996cb 100644 --- a/packages/jbrowse-plugin-apollo/package.json +++ b/packages/jbrowse-plugin-apollo/package.json @@ -2,17 +2,17 @@ "name": "@apollo-annotation/jbrowse-plugin-apollo", "version": "0.1.19", "description": "Apollo plugin for JBrowse 2", + "keywords": [ + "jbrowse", + "jbrowse2" + ], "repository": { "type": "git", "url": "https://github.com/GMOD/Apollo3.git", "directory": "packages/jbrowse-plugin-apollo" }, - "author": "JBrowse Team", "license": "Apache-2.0", - "keywords": [ - "jbrowse", - "jbrowse2" - ], + "author": "JBrowse Team", "main": "dist/index.js", "module": "dist/index.esm.js", "typings": "dist/index.d.ts", @@ -20,13 +20,6 @@ "dist", "src" ], - "config": { - "jbrowse": { - "plugin": { - "name": "Apollo" - } - } - }, "scripts": { "setup": "rimraf .jbrowse && jbrowse create .jbrowse", "clean": "rimraf dist", @@ -47,8 +40,12 @@ "prepack": "yarn build", "postversion": "git push --follow-tags" }, - "jbrowse-plugin": { - "name": "Apollo" + "config": { + "jbrowse": { + "plugin": { + "name": "Apollo" + } + } }, "dependencies": { "@apollo-annotation/common": "workspace:^", @@ -74,18 +71,6 @@ "socket.io-client": "^4.5.4", "tslib": "^2.3.1" }, - "peerDependencies": { - "@jbrowse/core": "^2.13.1", - "@mui/material": "^5.11.14", - "mobx": "^6.6.1", - "mobx-react": "^7.2.1", - "mobx-state-tree": "^5.1.7", - "prop-types": "^15.8.1", - "react": "^18.2.0", - "react-dom": "^18.2.0", - "rxjs": "^7.4.0", - "tss-react": "^4.6.1" - }, "devDependencies": { "@jbrowse/cli": "^2.6.2", "@jbrowse/core": "^2.13.1", @@ -123,7 +108,22 @@ "tss-react": "^4.6.1", "typescript": "^5.5.3" }, + "peerDependencies": { + "@jbrowse/core": "^2.13.1", + "@mui/material": "^5.11.14", + "mobx": "^6.6.1", + "mobx-react": "^7.2.1", + "mobx-state-tree": "^5.1.7", + "prop-types": "^15.8.1", + "react": "^18.2.0", + "react-dom": "^18.2.0", + "rxjs": "^7.4.0", + "tss-react": "^4.6.1" + }, "publishConfig": { "access": "public" + }, + "jbrowse-plugin": { + "name": "Apollo" } } diff --git a/yarn.lock b/yarn.lock index e8995e00f..a269b764f 100644 --- a/yarn.lock +++ b/yarn.lock @@ -5575,6 +5575,13 @@ __metadata: languageName: node linkType: hard +"@pkgr/core@npm:^0.1.0": + version: 0.1.1 + resolution: "@pkgr/core@npm:0.1.1" + checksum: 10c0/3f7536bc7f57320ab2cf96f8973664bef624710c403357429fbf680a5c3b4843c1dbd389bb43daa6b1f6f1f007bb082f5abcb76bb2b5dc9f421647743b71d3d8 + languageName: node + linkType: hard + "@popperjs/core@npm:^2.11.0, @popperjs/core@npm:^2.11.8": version: 2.11.8 resolution: "@popperjs/core@npm:2.11.8" @@ -8480,6 +8487,7 @@ __metadata: lint-staged: "npm:^15.2.2" npm-run-all: "npm:^4.1.5" prettier: "npm:^3.3.2" + prettier-plugin-packagejson: "npm:^2.5.2" react: "npm:^18.2.0" tsx: "npm:^4.6.2" typescript: "npm:^5.5.3" @@ -11273,6 +11281,13 @@ __metadata: languageName: node linkType: hard +"detect-indent@npm:^7.0.1": + version: 7.0.1 + resolution: "detect-indent@npm:7.0.1" + checksum: 10c0/47b6e3e3dda603c386e73b129f3e84844ae59bc2615f5072becf3cc02eab400bed5a4e6379c49d0b18cf630e80c2b07e87e0038b777addbc6ef793ad77dd05bc + languageName: node + linkType: hard + "detect-newline@npm:^3.0.0": version: 3.1.0 resolution: "detect-newline@npm:3.1.0" @@ -11280,6 +11295,13 @@ __metadata: languageName: node linkType: hard +"detect-newline@npm:^4.0.0": + version: 4.0.1 + resolution: "detect-newline@npm:4.0.1" + checksum: 10c0/1cc1082e88ad477f30703ae9f23bd3e33816ea2db6a35333057e087d72d466f5a777809b71f560118ecff935d2c712f5b59e1008a8b56a900909d8fd4621c603 + languageName: node + linkType: hard + "detect-node@npm:^2.1.0": version: 2.1.0 resolution: "detect-node@npm:2.1.0" @@ -12671,6 +12693,19 @@ __metadata: languageName: node linkType: hard +"fast-glob@npm:^3.3.0": + version: 3.3.2 + resolution: "fast-glob@npm:3.3.2" + dependencies: + "@nodelib/fs.stat": "npm:^2.0.2" + "@nodelib/fs.walk": "npm:^1.2.3" + glob-parent: "npm:^5.1.2" + merge2: "npm:^1.3.0" + micromatch: "npm:^4.0.4" + checksum: 10c0/42baad7b9cd40b63e42039132bde27ca2cb3a4950d0a0f9abe4639ea1aa9d3e3b40f98b1fe31cbc0cc17b664c9ea7447d911a152fa34ec5b72977b125a6fc845 + languageName: node + linkType: hard + "fast-json-stable-stringify@npm:2.x, fast-json-stable-stringify@npm:^2.0.0, fast-json-stable-stringify@npm:^2.1.0": version: 2.1.0 resolution: "fast-json-stable-stringify@npm:2.1.0" @@ -13295,6 +13330,13 @@ __metadata: languageName: node linkType: hard +"get-stdin@npm:^9.0.0": + version: 9.0.0 + resolution: "get-stdin@npm:9.0.0" + checksum: 10c0/7ef2edc0c81a0644ca9f051aad8a96ae9373d901485abafaabe59fd347a1c378689d8a3d8825fb3067415d1d09dfcaa43cb9b9516ecac6b74b3138b65a8ccc6b + languageName: node + linkType: hard + "get-stream@npm:^2.2.0": version: 2.3.1 resolution: "get-stream@npm:2.3.1" @@ -13377,6 +13419,13 @@ __metadata: languageName: node linkType: hard +"git-hooks-list@npm:^3.0.0": + version: 3.1.0 + resolution: "git-hooks-list@npm:3.1.0" + checksum: 10c0/f1b93dd11b80b2a687b99a8bb553c0d07f344532d475b3ac2a5ff044d40fa71567ddcfa5cb39fae0b4e43a670a33f02f71ec3b24b7263233f3a3df89deddfb5a + languageName: node + linkType: hard + "github-slugger@npm:^1.5.0": version: 1.5.0 resolution: "github-slugger@npm:1.5.0" @@ -13550,6 +13599,19 @@ __metadata: languageName: node linkType: hard +"globby@npm:^13.1.2": + version: 13.2.2 + resolution: "globby@npm:13.2.2" + dependencies: + dir-glob: "npm:^3.0.1" + fast-glob: "npm:^3.3.0" + ignore: "npm:^5.2.4" + merge2: "npm:^1.4.1" + slash: "npm:^4.0.0" + checksum: 10c0/a8d7cc7cbe5e1b2d0f81d467bbc5bc2eac35f74eaded3a6c85fc26d7acc8e6de22d396159db8a2fc340b8a342e74cac58de8f4aee74146d3d146921a76062664 + languageName: node + linkType: hard + "gopd@npm:^1.0.1": version: 1.0.1 resolution: "gopd@npm:1.0.1" @@ -14037,6 +14099,13 @@ __metadata: languageName: node linkType: hard +"ignore@npm:^5.2.4": + version: 5.3.2 + resolution: "ignore@npm:5.3.2" + checksum: 10c0/f9f652c957983634ded1e7f02da3b559a0d4cc210fca3792cb67f1b153623c9c42efdc1c4121af171e295444459fc4a9201101fb041b1104a3c000bccb188337 + languageName: node + linkType: hard + "ignore@npm:^5.3.1": version: 5.3.1 resolution: "ignore@npm:5.3.1" @@ -14538,6 +14607,13 @@ __metadata: languageName: node linkType: hard +"is-plain-obj@npm:^4.1.0": + version: 4.1.0 + resolution: "is-plain-obj@npm:4.1.0" + checksum: 10c0/32130d651d71d9564dc88ba7e6fda0e91a1010a3694648e9f4f47bb6080438140696d3e3e15c741411d712e47ac9edc1a8a9de1fe76f3487b0d90be06ac9975e + languageName: node + linkType: hard + "is-plain-object@npm:^5.0.0": version: 5.0.0 resolution: "is-plain-object@npm:5.0.0" @@ -18829,6 +18905,21 @@ __metadata: languageName: node linkType: hard +"prettier-plugin-packagejson@npm:^2.5.2": + version: 2.5.2 + resolution: "prettier-plugin-packagejson@npm:2.5.2" + dependencies: + sort-package-json: "npm:2.10.1" + synckit: "npm:0.9.1" + peerDependencies: + prettier: ">= 1.16.0" + peerDependenciesMeta: + prettier: + optional: true + checksum: 10c0/ddaf6a662f0156ad1a34d4e891b6ea05398de4fe56d6d14f4802f79b4824c71602e09661e665e0228232313a5cd27fe6d9d481080d6dd41620f9cf7fb285d240 + languageName: node + linkType: hard + "prettier@npm:^3.3.2": version: 3.3.2 resolution: "prettier@npm:3.3.2" @@ -20534,6 +20625,13 @@ __metadata: languageName: node linkType: hard +"slash@npm:^4.0.0": + version: 4.0.0 + resolution: "slash@npm:4.0.0" + checksum: 10c0/b522ca75d80d107fd30d29df0549a7b2537c83c4c4ecd12cd7d4ea6c8aaca2ab17ada002e7a1d78a9d736a0261509f26ea5b489082ee443a3a810586ef8eff18 + languageName: node + linkType: hard + "slice-ansi@npm:^3.0.0": version: 3.0.0 resolution: "slice-ansi@npm:3.0.0" @@ -20691,6 +20789,31 @@ __metadata: languageName: node linkType: hard +"sort-object-keys@npm:^1.1.3": + version: 1.1.3 + resolution: "sort-object-keys@npm:1.1.3" + checksum: 10c0/3bf62398658d3ff4bbca0db4ed8f42f98abc41433859f63d02fb0ab953fbe5526be240ec7e5d85aa50fcab6c937f3fa7015abf1ecdeb3045a2281c53953886bf + languageName: node + linkType: hard + +"sort-package-json@npm:2.10.1": + version: 2.10.1 + resolution: "sort-package-json@npm:2.10.1" + dependencies: + detect-indent: "npm:^7.0.1" + detect-newline: "npm:^4.0.0" + get-stdin: "npm:^9.0.0" + git-hooks-list: "npm:^3.0.0" + globby: "npm:^13.1.2" + is-plain-obj: "npm:^4.1.0" + semver: "npm:^7.6.0" + sort-object-keys: "npm:^1.1.3" + bin: + sort-package-json: cli.js + checksum: 10c0/7511c57e4661be222bce68522fb90f72e77a2a4694d05df0e55e70e72736944371a4be82a7cb1be4402455bbfd23857b0fabae3bbe9a1ae1351ff7caac64a468 + languageName: node + linkType: hard + "source-map-js@npm:^1.0.2": version: 1.2.0 resolution: "source-map-js@npm:1.2.0" @@ -21318,6 +21441,16 @@ __metadata: languageName: node linkType: hard +"synckit@npm:0.9.1": + version: 0.9.1 + resolution: "synckit@npm:0.9.1" + dependencies: + "@pkgr/core": "npm:^0.1.0" + tslib: "npm:^2.6.2" + checksum: 10c0/d8b89e1bf30ba3ffb469d8418c836ad9c0c062bf47028406b4d06548bc66af97155ea2303b96c93bf5c7c0f0d66153a6fbd6924c76521b434e6a9898982abc2e + languageName: node + linkType: hard + "tapable@npm:^2.1.1, tapable@npm:^2.2.0, tapable@npm:^2.2.1": version: 2.2.1 resolution: "tapable@npm:2.2.1" @@ -21832,6 +21965,13 @@ __metadata: languageName: node linkType: hard +"tslib@npm:^2.6.2": + version: 2.7.0 + resolution: "tslib@npm:2.7.0" + checksum: 10c0/469e1d5bf1af585742128827000711efa61010b699cb040ab1800bcd3ccdd37f63ec30642c9e07c4439c1db6e46345582614275daca3e0f4abae29b0083f04a6 + languageName: node + linkType: hard + "tss-react@npm:^4.6.1": version: 4.9.2 resolution: "tss-react@npm:4.9.2" From 4a1117e2732ff5a66755aecad59cc782de0533c6 Mon Sep 17 00:00:00 2001 From: Garrett Stevens Date: Tue, 27 Aug 2024 18:42:33 -0600 Subject: [PATCH 09/12] Update yarn SDK files --- .yarn/sdks/eslint/bin/eslint.js | 7 ++++++- .yarn/sdks/eslint/lib/api.js | 7 ++++++- .yarn/sdks/eslint/lib/unsupported-api.js | 7 ++++++- .yarn/sdks/eslint/package.json | 2 +- .yarn/sdks/prettier/bin/prettier.cjs | 7 ++++++- .yarn/sdks/prettier/index.cjs | 7 ++++++- .yarn/sdks/prettier/package.json | 2 +- .yarn/sdks/typescript/bin/tsc | 7 ++++++- .yarn/sdks/typescript/bin/tsserver | 7 ++++++- .yarn/sdks/typescript/lib/tsc.js | 7 ++++++- .yarn/sdks/typescript/lib/tsserver.js | 11 ++++++++++- .yarn/sdks/typescript/lib/tsserverlibrary.js | 11 ++++++++++- .yarn/sdks/typescript/lib/typescript.js | 7 ++++++- .yarn/sdks/typescript/package.json | 2 +- 14 files changed, 77 insertions(+), 14 deletions(-) diff --git a/.yarn/sdks/eslint/bin/eslint.js b/.yarn/sdks/eslint/bin/eslint.js index 42eab9933..e6604ff59 100755 --- a/.yarn/sdks/eslint/bin/eslint.js +++ b/.yarn/sdks/eslint/bin/eslint.js @@ -8,6 +8,7 @@ const {pathToFileURL} = require(`url`); const relPnpApiPath = "../../../../.pnp.cjs"; const absPnpApiPath = resolve(__dirname, relPnpApiPath); +const absUserWrapperPath = resolve(__dirname, `./sdk.user.cjs`); const absRequire = createRequire(absPnpApiPath); const absPnpLoaderPath = resolve(absPnpApiPath, `../.pnp.loader.mjs`); @@ -23,5 +24,9 @@ if (existsSync(absPnpApiPath)) { } } +const wrapWithUserWrapper = existsSync(absUserWrapperPath) + ? exports => absRequire(absUserWrapperPath)(exports) + : exports => exports; + // Defer to the real eslint/bin/eslint.js your application uses -module.exports = absRequire(`eslint/bin/eslint.js`); +module.exports = wrapWithUserWrapper(absRequire(`eslint/bin/eslint.js`)); diff --git a/.yarn/sdks/eslint/lib/api.js b/.yarn/sdks/eslint/lib/api.js index ea2b46a70..8addf97fb 100644 --- a/.yarn/sdks/eslint/lib/api.js +++ b/.yarn/sdks/eslint/lib/api.js @@ -8,6 +8,7 @@ const {pathToFileURL} = require(`url`); const relPnpApiPath = "../../../../.pnp.cjs"; const absPnpApiPath = resolve(__dirname, relPnpApiPath); +const absUserWrapperPath = resolve(__dirname, `./sdk.user.cjs`); const absRequire = createRequire(absPnpApiPath); const absPnpLoaderPath = resolve(absPnpApiPath, `../.pnp.loader.mjs`); @@ -23,5 +24,9 @@ if (existsSync(absPnpApiPath)) { } } +const wrapWithUserWrapper = existsSync(absUserWrapperPath) + ? exports => absRequire(absUserWrapperPath)(exports) + : exports => exports; + // Defer to the real eslint your application uses -module.exports = absRequire(`eslint`); +module.exports = wrapWithUserWrapper(absRequire(`eslint`)); diff --git a/.yarn/sdks/eslint/lib/unsupported-api.js b/.yarn/sdks/eslint/lib/unsupported-api.js index f5f8e24d0..c2b464ce6 100644 --- a/.yarn/sdks/eslint/lib/unsupported-api.js +++ b/.yarn/sdks/eslint/lib/unsupported-api.js @@ -8,6 +8,7 @@ const {pathToFileURL} = require(`url`); const relPnpApiPath = "../../../../.pnp.cjs"; const absPnpApiPath = resolve(__dirname, relPnpApiPath); +const absUserWrapperPath = resolve(__dirname, `./sdk.user.cjs`); const absRequire = createRequire(absPnpApiPath); const absPnpLoaderPath = resolve(absPnpApiPath, `../.pnp.loader.mjs`); @@ -23,5 +24,9 @@ if (existsSync(absPnpApiPath)) { } } +const wrapWithUserWrapper = existsSync(absUserWrapperPath) + ? exports => absRequire(absUserWrapperPath)(exports) + : exports => exports; + // Defer to the real eslint/use-at-your-own-risk your application uses -module.exports = absRequire(`eslint/use-at-your-own-risk`); +module.exports = wrapWithUserWrapper(absRequire(`eslint/use-at-your-own-risk`)); diff --git a/.yarn/sdks/eslint/package.json b/.yarn/sdks/eslint/package.json index 7468a956b..263cd3d50 100644 --- a/.yarn/sdks/eslint/package.json +++ b/.yarn/sdks/eslint/package.json @@ -1,6 +1,6 @@ { "name": "eslint", - "version": "8.51.0-sdk", + "version": "8.57.0-sdk", "main": "./lib/api.js", "type": "commonjs", "bin": { diff --git a/.yarn/sdks/prettier/bin/prettier.cjs b/.yarn/sdks/prettier/bin/prettier.cjs index 00f1f7f74..9a4098f7d 100755 --- a/.yarn/sdks/prettier/bin/prettier.cjs +++ b/.yarn/sdks/prettier/bin/prettier.cjs @@ -8,6 +8,7 @@ const {pathToFileURL} = require(`url`); const relPnpApiPath = "../../../../.pnp.cjs"; const absPnpApiPath = resolve(__dirname, relPnpApiPath); +const absUserWrapperPath = resolve(__dirname, `./sdk.user.cjs`); const absRequire = createRequire(absPnpApiPath); const absPnpLoaderPath = resolve(absPnpApiPath, `../.pnp.loader.mjs`); @@ -23,5 +24,9 @@ if (existsSync(absPnpApiPath)) { } } +const wrapWithUserWrapper = existsSync(absUserWrapperPath) + ? exports => absRequire(absUserWrapperPath)(exports) + : exports => exports; + // Defer to the real prettier/bin/prettier.cjs your application uses -module.exports = absRequire(`prettier/bin/prettier.cjs`); +module.exports = wrapWithUserWrapper(absRequire(`prettier/bin/prettier.cjs`)); diff --git a/.yarn/sdks/prettier/index.cjs b/.yarn/sdks/prettier/index.cjs index d546c6a75..57cb2ab17 100644 --- a/.yarn/sdks/prettier/index.cjs +++ b/.yarn/sdks/prettier/index.cjs @@ -8,6 +8,7 @@ const {pathToFileURL} = require(`url`); const relPnpApiPath = "../../../.pnp.cjs"; const absPnpApiPath = resolve(__dirname, relPnpApiPath); +const absUserWrapperPath = resolve(__dirname, `./sdk.user.cjs`); const absRequire = createRequire(absPnpApiPath); const absPnpLoaderPath = resolve(absPnpApiPath, `../.pnp.loader.mjs`); @@ -23,5 +24,9 @@ if (existsSync(absPnpApiPath)) { } } +const wrapWithUserWrapper = existsSync(absUserWrapperPath) + ? exports => absRequire(absUserWrapperPath)(exports) + : exports => exports; + // Defer to the real prettier your application uses -module.exports = absRequire(`prettier`); +module.exports = wrapWithUserWrapper(absRequire(`prettier`)); diff --git a/.yarn/sdks/prettier/package.json b/.yarn/sdks/prettier/package.json index 6e68f38b6..b26338148 100644 --- a/.yarn/sdks/prettier/package.json +++ b/.yarn/sdks/prettier/package.json @@ -1,6 +1,6 @@ { "name": "prettier", - "version": "3.2.5-sdk", + "version": "3.3.2-sdk", "main": "./index.cjs", "type": "commonjs", "bin": "./bin/prettier.cjs" diff --git a/.yarn/sdks/typescript/bin/tsc b/.yarn/sdks/typescript/bin/tsc index a6bb0e2c1..867a7bdfe 100755 --- a/.yarn/sdks/typescript/bin/tsc +++ b/.yarn/sdks/typescript/bin/tsc @@ -8,6 +8,7 @@ const {pathToFileURL} = require(`url`); const relPnpApiPath = "../../../../.pnp.cjs"; const absPnpApiPath = resolve(__dirname, relPnpApiPath); +const absUserWrapperPath = resolve(__dirname, `./sdk.user.cjs`); const absRequire = createRequire(absPnpApiPath); const absPnpLoaderPath = resolve(absPnpApiPath, `../.pnp.loader.mjs`); @@ -23,5 +24,9 @@ if (existsSync(absPnpApiPath)) { } } +const wrapWithUserWrapper = existsSync(absUserWrapperPath) + ? exports => absRequire(absUserWrapperPath)(exports) + : exports => exports; + // Defer to the real typescript/bin/tsc your application uses -module.exports = absRequire(`typescript/bin/tsc`); +module.exports = wrapWithUserWrapper(absRequire(`typescript/bin/tsc`)); diff --git a/.yarn/sdks/typescript/bin/tsserver b/.yarn/sdks/typescript/bin/tsserver index 957bed200..3fc5aa31c 100755 --- a/.yarn/sdks/typescript/bin/tsserver +++ b/.yarn/sdks/typescript/bin/tsserver @@ -8,6 +8,7 @@ const {pathToFileURL} = require(`url`); const relPnpApiPath = "../../../../.pnp.cjs"; const absPnpApiPath = resolve(__dirname, relPnpApiPath); +const absUserWrapperPath = resolve(__dirname, `./sdk.user.cjs`); const absRequire = createRequire(absPnpApiPath); const absPnpLoaderPath = resolve(absPnpApiPath, `../.pnp.loader.mjs`); @@ -23,5 +24,9 @@ if (existsSync(absPnpApiPath)) { } } +const wrapWithUserWrapper = existsSync(absUserWrapperPath) + ? exports => absRequire(absUserWrapperPath)(exports) + : exports => exports; + // Defer to the real typescript/bin/tsserver your application uses -module.exports = absRequire(`typescript/bin/tsserver`); +module.exports = wrapWithUserWrapper(absRequire(`typescript/bin/tsserver`)); diff --git a/.yarn/sdks/typescript/lib/tsc.js b/.yarn/sdks/typescript/lib/tsc.js index a262a77d0..da411bdba 100644 --- a/.yarn/sdks/typescript/lib/tsc.js +++ b/.yarn/sdks/typescript/lib/tsc.js @@ -8,6 +8,7 @@ const {pathToFileURL} = require(`url`); const relPnpApiPath = "../../../../.pnp.cjs"; const absPnpApiPath = resolve(__dirname, relPnpApiPath); +const absUserWrapperPath = resolve(__dirname, `./sdk.user.cjs`); const absRequire = createRequire(absPnpApiPath); const absPnpLoaderPath = resolve(absPnpApiPath, `../.pnp.loader.mjs`); @@ -23,5 +24,9 @@ if (existsSync(absPnpApiPath)) { } } +const wrapWithUserWrapper = existsSync(absUserWrapperPath) + ? exports => absRequire(absUserWrapperPath)(exports) + : exports => exports; + // Defer to the real typescript/lib/tsc.js your application uses -module.exports = absRequire(`typescript/lib/tsc.js`); +module.exports = wrapWithUserWrapper(absRequire(`typescript/lib/tsc.js`)); diff --git a/.yarn/sdks/typescript/lib/tsserver.js b/.yarn/sdks/typescript/lib/tsserver.js index 1dae54c1a..6249c4675 100644 --- a/.yarn/sdks/typescript/lib/tsserver.js +++ b/.yarn/sdks/typescript/lib/tsserver.js @@ -8,6 +8,7 @@ const {pathToFileURL} = require(`url`); const relPnpApiPath = "../../../../.pnp.cjs"; const absPnpApiPath = resolve(__dirname, relPnpApiPath); +const absUserWrapperPath = resolve(__dirname, `./sdk.user.cjs`); const absRequire = createRequire(absPnpApiPath); const absPnpLoaderPath = resolve(absPnpApiPath, `../.pnp.loader.mjs`); @@ -23,7 +24,15 @@ if (existsSync(absPnpApiPath)) { } } -const moduleWrapper = tsserver => { +const wrapWithUserWrapper = existsSync(absUserWrapperPath) + ? exports => absRequire(absUserWrapperPath)(exports) + : exports => exports; + +const moduleWrapper = exports => { + return wrapWithUserWrapper(moduleWrapperFn(exports)); +}; + +const moduleWrapperFn = tsserver => { if (!process.versions.pnp) { return tsserver; } diff --git a/.yarn/sdks/typescript/lib/tsserverlibrary.js b/.yarn/sdks/typescript/lib/tsserverlibrary.js index 7f9d7f964..0e50e0a2b 100644 --- a/.yarn/sdks/typescript/lib/tsserverlibrary.js +++ b/.yarn/sdks/typescript/lib/tsserverlibrary.js @@ -8,6 +8,7 @@ const {pathToFileURL} = require(`url`); const relPnpApiPath = "../../../../.pnp.cjs"; const absPnpApiPath = resolve(__dirname, relPnpApiPath); +const absUserWrapperPath = resolve(__dirname, `./sdk.user.cjs`); const absRequire = createRequire(absPnpApiPath); const absPnpLoaderPath = resolve(absPnpApiPath, `../.pnp.loader.mjs`); @@ -23,7 +24,15 @@ if (existsSync(absPnpApiPath)) { } } -const moduleWrapper = tsserver => { +const wrapWithUserWrapper = existsSync(absUserWrapperPath) + ? exports => absRequire(absUserWrapperPath)(exports) + : exports => exports; + +const moduleWrapper = exports => { + return wrapWithUserWrapper(moduleWrapperFn(exports)); +}; + +const moduleWrapperFn = tsserver => { if (!process.versions.pnp) { return tsserver; } diff --git a/.yarn/sdks/typescript/lib/typescript.js b/.yarn/sdks/typescript/lib/typescript.js index 317b60b4c..7b6cc2207 100644 --- a/.yarn/sdks/typescript/lib/typescript.js +++ b/.yarn/sdks/typescript/lib/typescript.js @@ -8,6 +8,7 @@ const {pathToFileURL} = require(`url`); const relPnpApiPath = "../../../../.pnp.cjs"; const absPnpApiPath = resolve(__dirname, relPnpApiPath); +const absUserWrapperPath = resolve(__dirname, `./sdk.user.cjs`); const absRequire = createRequire(absPnpApiPath); const absPnpLoaderPath = resolve(absPnpApiPath, `../.pnp.loader.mjs`); @@ -23,5 +24,9 @@ if (existsSync(absPnpApiPath)) { } } +const wrapWithUserWrapper = existsSync(absUserWrapperPath) + ? exports => absRequire(absUserWrapperPath)(exports) + : exports => exports; + // Defer to the real typescript your application uses -module.exports = absRequire(`typescript`); +module.exports = wrapWithUserWrapper(absRequire(`typescript`)); diff --git a/.yarn/sdks/typescript/package.json b/.yarn/sdks/typescript/package.json index d32f3913d..0c65a6950 100644 --- a/.yarn/sdks/typescript/package.json +++ b/.yarn/sdks/typescript/package.json @@ -1,6 +1,6 @@ { "name": "typescript", - "version": "5.2.2-sdk", + "version": "5.5.3-sdk", "main": "./lib/typescript.js", "type": "commonjs", "bin": { From eb689cdcb55b2ea755f238836e5a2c89a14dbc00 Mon Sep 17 00:00:00 2001 From: Garrett Stevens Date: Tue, 27 Aug 2024 20:54:49 -0600 Subject: [PATCH 10/12] Give new demo users the "user" role --- .github/workflows/deploy/compose.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/deploy/compose.yml b/.github/workflows/deploy/compose.yml index a3943cfdc..a1bcef471 100644 --- a/.github/workflows/deploy/compose.yml +++ b/.github/workflows/deploy/compose.yml @@ -12,6 +12,7 @@ services: FILE_UPLOAD_FOLDER: /data/uploads LOG_LEVELS: error,warn,log,debug ALLOW_GUEST_USER: true + DEFAULT_NEW_USER_ROLE: user URL: ${URL} JWT_SECRET: ${JWT_SECRET} SESSION_SECRET: ${SESSION_SECRET} From 7e2698a0695fa60e8391ca1e95dcb2d5c8f402b6 Mon Sep 17 00:00:00 2001 From: Garrett Stevens Date: Wed, 28 Aug 2024 16:29:46 -0600 Subject: [PATCH 11/12] Restore missing commands to README --- packages/apollo-cli/README.md | 906 ++++++++++++++++++++++++++++++++++ 1 file changed, 906 insertions(+) diff --git a/packages/apollo-cli/README.md b/packages/apollo-cli/README.md index 8707ab4d9..7768c3b24 100644 --- a/packages/apollo-cli/README.md +++ b/packages/apollo-cli/README.md @@ -29,7 +29,720 @@ USAGE +- [`apollo assembly add-fasta`](#apollo-assembly-add-fasta) +- [`apollo assembly add-gff`](#apollo-assembly-add-gff) +- [`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 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 import`](#apollo-feature-import) +- [`apollo feature search`](#apollo-feature-search) - [`apollo help [COMMANDS]`](#apollo-help-commands) +- [`apollo login`](#apollo-login) +- [`apollo logout`](#apollo-logout) +- [`apollo refseq add-alias`](#apollo-refseq-add-alias) +- [`apollo refseq get`](#apollo-refseq-get) +- [`apollo status`](#apollo-status) +- [`apollo user get`](#apollo-user-get) + +## `apollo assembly add-fasta` + +Add new assembly from local or external fasta file + +``` +USAGE + $ apollo assembly add-fasta -i [--profile ] [--config-file ] [-a ] [-x ] [-f] + +FLAGS + -a, --assembly= Name for this assembly. Use the file name if omitted + -f, --force Delete existing assembly, if it exists + -i, --input-file= (required) Input fasta file + -x, --index= URL of the index. Required if input is an external source and ignored if input is a local + file + --config-file= Use this config file (mostly for testing) + --profile= Use credentials from this profile + +DESCRIPTION + Add new assembly from local or external fasta file + +EXAMPLES + From local file: + + $ apollo assembly add-fasta -i genome.fa -a myAssembly + + From external source we also need the URL of the index: + + $ apollo assembly add-fasta -i https://.../genome.fa -x https://.../genome.fa.fai -a myAssembly +``` + +_See code: +[src/commands/assembly/add-fasta.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/assembly/add-fasta.ts)_ + +## `apollo assembly add-gff` + +Add new assembly from gff or gft file + +``` +USAGE + $ apollo assembly add-gff -i [--profile ] [--config-file ] [-a ] [-o] [-f] + +FLAGS + -a, --assembly= Name for this assembly. Use the file name if omitted + -f, --force Delete existing assembly, if it exists + -i, --input-file= (required) Input gff or gtf file + -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-gff -i genome.gff -a myAssembly + + Import sequences only: + + $ apollo assembly add-gff -i genome.gff -a myAssembly -o +``` + +_See code: +[src/commands/assembly/add-gff.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/assembly/add-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/v0.1.19/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/v0.1.19/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/v0.1.19/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/v0.1.19/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/v0.1.19/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` + + - rootCredentials.username: + Username of root account. Only set this for "root" access type + + - rootCredentials.password: + 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/v0.1.19/packages/apollo-cli/src/commands/config.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 6605826fbd0eee691f83e73f -t exon -s 10 -e 20 +``` + +_See code: +[src/commands/feature/add-child.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/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/v0.1.19/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. he 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/v0.1.19/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/v0.1.19/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/v0.1.19/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/v0.1.19/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/v0.1.19/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/v0.1.19/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/v0.1.19/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/v0.1.19/packages/apollo-cli/src/commands/feature/get-id.ts)_ + +## `apollo feature import` + +Import features from local gff file + +``` +USAGE + $ apollo feature import -i -a [--profile ] [--config-file ] [-d] + +FLAGS + -a, --assembly= (required) Import into this assembly name or assembly ID + -d, --delete-existing Delete existing features before importing + -i, --input-file= (required) Input gff or gtf file + --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 -d -i features.gff3 -a myAssembly +``` + +_See code: +[src/commands/feature/import.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/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/v0.1.19/packages/apollo-cli/src/commands/feature/search.ts)_ ## `apollo help [COMMANDS]` @@ -52,4 +765,197 @@ DESCRIPTION _See code: [@oclif/plugin-help](https://github.com/oclif/plugin-help/blob/v6.0.8/src/commands/help.ts)_ +## `apollo login` + +Login to Apollo + +``` +USAGE + $ apollo login [--profile ] [--config-file ] [-a ] [-u ] [-p ] [-f] + [--port ] + +FLAGS + -a, --address= Address of Apollo server + -f, --force Force re-authentication even if user is already logged in + -p, --password= Password for + -u, --username= Username for root login + --config-file= Use this config file (mostly for testing) + --port= [default: 3000] Get token by listening to this port number (usually this is >= 1024 and < + 65536) + --profile= Use credentials from this profile + +DESCRIPTION + Login to Apollo + + Use the provided credentials to obtain and save the token to access Apollo. Once + the token for the given profile has been saved in the configuration file, users + do not normally need to execute this command again unless the token has expired. + To setup a new profile use "apollo config" + +EXAMPLES + The most basic and probably most typical usage is to login using the default + profile in configuration file: + + $ apollo login + + Login with a different profile: + + $ apollo login --profile my-profile +``` + +_See code: +[src/commands/login.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/login.ts)_ + +## `apollo logout` + +Logout of Apollo + +``` +USAGE + $ apollo logout [--profile ] [--config-file ] + +FLAGS + --config-file= Use this config file (mostly for testing) + --profile= Use credentials from this profile + +DESCRIPTION + Logout of Apollo + + Logout by removing the access token from the selected profile + +EXAMPLES + Logout default profile: + + $ apollo logout + + Logout selected profile + + $ apollo logout --profile my-profile +``` + +_See code: +[src/commands/logout.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/logout.ts)_ + +## `apollo refseq add-alias` + +Add reference name aliases from a file + +``` +USAGE + $ apollo refseq add-alias -i -a [--profile ] [--config-file ] + +FLAGS + -a, --assembly= (required) Name for this assembly. + -i, --input-file= (required) Input refname alias file + --config-file= Use this config file (mostly for testing) + --profile= Use credentials from this profile + +DESCRIPTION + Add reference name aliases from a file + + Reference name aliasing is a process to make chromosomes that are named slightly + differently but which refer to the same thing render properly. This command + reads a file with reference name aliases and adds them to the database. + +EXAMPLES + Add reference name aliases: + + $ apollo refseq add-alias -i alias.txt -a myAssembly +``` + +_See code: +[src/commands/refseq/add-alias.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/refseq/add-alias.ts)_ + +## `apollo refseq get` + +Get reference sequences + +``` +USAGE + $ apollo refseq get [--profile ] [--config-file ] [-a ] + +FLAGS + -a, --assembly=... Get reference sequences for these assembly names or IDs; use - to read it from stdin + --config-file= Use this config file (mostly for testing) + --profile= Use credentials from this profile + +DESCRIPTION + Get reference sequences + + Output the reference sequences in one or more assemblies in json format. This + command returns the sequence characteristics (e.g., name, ID, etc), not the DNA + sequences. Use `assembly sequence` for that. + +EXAMPLES + All sequences in the database: + + $ apollo refseq get + + Only sequences for these assemblies: + + $ apollo refseq get -a mm9 mm10 +``` + +_See code: +[src/commands/refseq/get.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/refseq/get.ts)_ + +## `apollo status` + +View authentication status + +``` +USAGE + $ apollo status [--profile ] [--config-file ] + +FLAGS + --config-file= Use this config file (mostly for testing) + --profile= Use credentials from this profile + +DESCRIPTION + View authentication status + + This command returns ": Logged in" if the selected profile has an + access token and ": Logged out" otherwise. Note that this command does + not check the validity of the access token. +``` + +_See code: +[src/commands/status.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/status.ts)_ + +## `apollo user get` + +Get list of users + +``` +USAGE + $ apollo user get [--profile ] [--config-file ] [-u ] [-r ] + +FLAGS + -r, --role= Get users with this role + -u, --username= Find this username + --config-file= Use this config file (mostly for testing) + --profile= Use credentials from this profile + +DESCRIPTION + Get list of users + + If set, filters username and role must be both satisfied to return an entry + +EXAMPLES + By username: + + $ apollo user get -u Guest + + By role: + + $ apollo user get -r admin + + Use jq for more control: + + $ apollo user get | jq '.[] | select(.createdAt > "2024-03-18")' +``` + +_See code: +[src/commands/user/get.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/user/get.ts)_ + From 08590d4ae6effd0b5bf84071ff816df6ef89cff2 Mon Sep 17 00:00:00 2001 From: Garrett Stevens Date: Wed, 28 Aug 2024 16:22:03 -0600 Subject: [PATCH 12/12] Use chai to deeply compare annotation features --- packages/apollo-cli/package.json | 2 +- packages/apollo-shared/package.json | 3 + .../src/GFF3/gff3ToAnnotationFeature.test.ts | 79 +++++++++++++++++- .../src/GFF3/gff3ToAnnotationFeature.ts | 2 +- yarn.lock | 82 ++++++++++++++++++- 5 files changed, 160 insertions(+), 8 deletions(-) diff --git a/packages/apollo-cli/package.json b/packages/apollo-cli/package.json index 5fc1f1cde..b097e1220 100644 --- a/packages/apollo-cli/package.json +++ b/packages/apollo-cli/package.json @@ -82,7 +82,7 @@ "@istanbuljs/esm-loader-hook": "^0.2.0", "@istanbuljs/nyc-config-typescript": "^1.0.2", "@oclif/test": "^3.1.3", - "@types/chai": "^4", + "@types/chai": "^4.3.19", "@types/cli-progress": "^3", "@types/inquirer": "^9.0.7", "@types/mocha": "^10", diff --git a/packages/apollo-shared/package.json b/packages/apollo-shared/package.json index 22934e8f8..1b91a530f 100644 --- a/packages/apollo-shared/package.json +++ b/packages/apollo-shared/package.json @@ -26,8 +26,11 @@ "devDependencies": { "@nestjs/common": "^10.1.0", "@nestjs/core": "^10.1.0", + "@types/chai": "^4.3.19", "@types/node": "^18.14.2", "@types/rimraf": "^3", + "chai": "^5.1.1", + "chai-exclude": "^3.0.0", "glob": "^11.0.0", "mobx": "^6.6.1", "mobx-state-tree": "^5.1.7", diff --git a/packages/apollo-shared/src/GFF3/gff3ToAnnotationFeature.test.ts b/packages/apollo-shared/src/GFF3/gff3ToAnnotationFeature.test.ts index 6a412af5d..9dbfec41e 100644 --- a/packages/apollo-shared/src/GFF3/gff3ToAnnotationFeature.test.ts +++ b/packages/apollo-shared/src/GFF3/gff3ToAnnotationFeature.test.ts @@ -1,11 +1,14 @@ /* eslint-disable @typescript-eslint/no-floating-promises */ -import { strict as assert } from 'node:assert' import { describe, it } from 'node:test' import gff from '@gmod/gff' +import { assert, use } from 'chai' +import chaiExclude from 'chai-exclude' import { gff3ToAnnotationFeature } from './gff3ToAnnotationFeature' import { AnnotationFeatureSnapshot } from '@apollo-annotation/mst' +use(chaiExclude) + const testCases: [string, string, AnnotationFeatureSnapshot][] = [ [ 'a feature with no children', @@ -23,15 +26,83 @@ const testCases: [string, string, AnnotationFeatureSnapshot][] = [ }, }, ], + [ + 'a feature with two children', + `ctgA est EST_match 1050 3202 . + . ID=Match1;Name=agt830.5;Target=agt830.5 1 654 +ctgA est match_part 1050 1500 . + . Parent=Match1;Name=agt830.5;Target=agt830.5 1 451 +ctgA est match_part 3000 3202 . + . Parent=Match1;Name=agt830.5;Target=agt830.5 452 654 +`, + { + _id: '66cf9fbb4e947fa2c27d3d6a', + refSeq: 'ctgA', + type: 'EST_match', + min: 1049, + max: 3202, + strand: 1, + children: { + '66cf9fbb4e947fa2c27d3d68': { + _id: '66cf9fbb4e947fa2c27d3d68', + refSeq: 'ctgA', + type: 'match_part', + min: 1049, + max: 1500, + strand: 1, + attributes: { + gff_source: ['est'], + gff_name: ['agt830.5'], + gff_target: ['agt830.5 1 451'], + }, + }, + '66cf9fbb4e947fa2c27d3d69': { + _id: '66cf9fbb4e947fa2c27d3d69', + refSeq: 'ctgA', + type: 'match_part', + min: 2999, + max: 3202, + strand: 1, + attributes: { + gff_source: ['est'], + gff_name: ['agt830.5'], + gff_target: ['agt830.5 452 654'], + }, + }, + }, + attributes: { + gff_source: ['est'], + gff_id: ['Match1'], + gff_name: ['agt830.5'], + gff_target: ['agt830.5 1 654'], + }, + }, + ], ] +interface AnnotationFeatureSnapshotWithChildrenArray + extends Omit { + children?: AnnotationFeatureSnapshotWithChildrenArray[] +} + +function childrenToArray( + feature: AnnotationFeatureSnapshot, +): AnnotationFeatureSnapshotWithChildrenArray { + const { children } = feature + if (!children) { + return feature as AnnotationFeatureSnapshotWithChildrenArray + } + const childrenArray = Object.values(children).map((child) => + childrenToArray(child), + ) + return { ...feature, children: childrenArray } +} + function compareFeatures( feature1: AnnotationFeatureSnapshot, feature2: AnnotationFeatureSnapshot, ) { - assert.deepEqual( - { ...feature1, _id: undefined }, - { ...feature2, _id: undefined }, + assert.deepEqualExcludingEvery( + childrenToArray(feature1), + childrenToArray(feature2), + '_id', ) } diff --git a/packages/apollo-shared/src/GFF3/gff3ToAnnotationFeature.ts b/packages/apollo-shared/src/GFF3/gff3ToAnnotationFeature.ts index 34d9146b9..f632f448f 100644 --- a/packages/apollo-shared/src/GFF3/gff3ToAnnotationFeature.ts +++ b/packages/apollo-shared/src/GFF3/gff3ToAnnotationFeature.ts @@ -80,7 +80,7 @@ function getFeatureMinMax(gff3Feature: GFF3Feature): [number, number] { function convertFeatureAttributes( gff3Feature: GFF3Feature, -): Record | undefined { +): Record | undefined { const convertedAttributes: Record = {} const scores = gff3Feature .map((f) => f.score) diff --git a/yarn.lock b/yarn.lock index a269b764f..031baa538 100644 --- a/yarn.lock +++ b/yarn.lock @@ -129,7 +129,7 @@ __metadata: "@oclif/core": "npm:^3.18.2" "@oclif/plugin-help": "npm:^6.0.8" "@oclif/test": "npm:^3.1.3" - "@types/chai": "npm:^4" + "@types/chai": "npm:^4.3.19" "@types/cli-progress": "npm:^3" "@types/inquirer": "npm:^9.0.7" "@types/mocha": "npm:^10" @@ -390,9 +390,12 @@ __metadata: "@jbrowse/core": "npm:^2.13.1" "@nestjs/common": "npm:^10.1.0" "@nestjs/core": "npm:^10.1.0" + "@types/chai": "npm:^4.3.19" "@types/node": "npm:^18.14.2" "@types/rimraf": "npm:^3" bson-objectid: "npm:^2.0.4" + chai: "npm:^5.1.1" + chai-exclude: "npm:^3.0.0" generic-filehandle: "npm:^3.0.0" glob: "npm:^11.0.0" jwt-decode: "npm:^3.1.2" @@ -6951,13 +6954,20 @@ __metadata: languageName: node linkType: hard -"@types/chai@npm:*, @types/chai@npm:^4": +"@types/chai@npm:*": version: 4.3.11 resolution: "@types/chai@npm:4.3.11" checksum: 10c0/0c216ac4a19bfbf8318bb104d32e50704ee2ffc4b538b976c4326e6638fee121462402caa570662227a2a218810388aadb14bdbd3d3d474ec300b00695db448a languageName: node linkType: hard +"@types/chai@npm:^4.3.19": + version: 4.3.19 + resolution: "@types/chai@npm:4.3.19" + checksum: 10c0/8fd573192e486803c4d04185f2b0fab554660d9a1300dbed5bde9747ab8bef15f462a226f560ed5ca48827eecaf8d71eed64aa653ff9aec72fb2eae272e43a84 + languageName: node + linkType: hard + "@types/cli-progress@npm:^3, @types/cli-progress@npm:^3.11.5": version: 3.11.5 resolution: "@types/cli-progress@npm:3.11.5" @@ -8767,6 +8777,13 @@ __metadata: languageName: node linkType: hard +"assertion-error@npm:^2.0.1": + version: 2.0.1 + resolution: "assertion-error@npm:2.0.1" + checksum: 10c0/bbbcb117ac6480138f8c93cf7f535614282dea9dc828f540cdece85e3c665e8f78958b96afac52f29ff883c72638e6a87d469ecc9fe5bc902df03ed24a55dba8 + languageName: node + linkType: hard + "ast-types-flow@npm:^0.0.7": version: 0.0.7 resolution: "ast-types-flow@npm:0.0.7" @@ -9848,6 +9865,17 @@ __metadata: languageName: node linkType: hard +"chai-exclude@npm:^3.0.0": + version: 3.0.0 + resolution: "chai-exclude@npm:3.0.0" + dependencies: + fclone: "npm:^1.0.11" + peerDependencies: + chai: ">= 5" + checksum: 10c0/c0bbe2f29398e9a9338e0aa86835668b701bf220e49ec24cf80d58f3b322b4a9dd332e3052c757f97ea5ba2c0086c64c7014a3b07862fa370480f350ceac4066 + languageName: node + linkType: hard + "chai@npm:*, chai@npm:^4.3.10": version: 4.3.10 resolution: "chai@npm:4.3.10" @@ -9863,6 +9891,19 @@ __metadata: languageName: node linkType: hard +"chai@npm:^5.1.1": + version: 5.1.1 + resolution: "chai@npm:5.1.1" + dependencies: + assertion-error: "npm:^2.0.1" + check-error: "npm:^2.1.1" + deep-eql: "npm:^5.0.1" + loupe: "npm:^3.1.0" + pathval: "npm:^2.0.0" + checksum: 10c0/e7f00e5881e3d5224f08fe63966ed6566bd9fdde175863c7c16dd5240416de9b34c4a0dd925f4fd64ad56256ca6507d32cf6131c49e1db65c62578eb31d4566c + languageName: node + linkType: hard + "chalk-template@npm:0.4.0": version: 0.4.0 resolution: "chalk-template@npm:0.4.0" @@ -9967,6 +10008,13 @@ __metadata: languageName: node linkType: hard +"check-error@npm:^2.1.1": + version: 2.1.1 + resolution: "check-error@npm:2.1.1" + checksum: 10c0/979f13eccab306cf1785fa10941a590b4e7ea9916ea2a4f8c87f0316fc3eab07eabefb6e587424ef0f88cbcd3805791f172ea739863ca3d7ce2afc54641c7f0e + languageName: node + linkType: hard + "check-more-types@npm:2.24.0, check-more-types@npm:^2.24.0": version: 2.24.0 resolution: "check-more-types@npm:2.24.0" @@ -11117,6 +11165,13 @@ __metadata: languageName: node linkType: hard +"deep-eql@npm:^5.0.1": + version: 5.0.2 + resolution: "deep-eql@npm:5.0.2" + checksum: 10c0/7102cf3b7bb719c6b9c0db2e19bf0aa9318d141581befe8c7ce8ccd39af9eaa4346e5e05adef7f9bd7015da0f13a3a25dcfe306ef79dc8668aedbecb658dd247 + languageName: node + linkType: hard + "deep-extend@npm:^0.6.0": version: 0.6.0 resolution: "deep-extend@npm:0.6.0" @@ -12788,6 +12843,13 @@ __metadata: languageName: node linkType: hard +"fclone@npm:^1.0.11": + version: 1.0.11 + resolution: "fclone@npm:1.0.11" + checksum: 10c0/dbe3ebd0883edeec2998874bf951aa03198d727f1091351b22af250ff53e227ee94872487ae88ba7280b2469fb164a7d4dd4e5ece10afd4988ab4712f49bc43b + languageName: node + linkType: hard + "fd-slicer@npm:~1.1.0": version: 1.1.0 resolution: "fd-slicer@npm:1.1.0" @@ -16385,6 +16447,15 @@ __metadata: languageName: node linkType: hard +"loupe@npm:^3.1.0": + version: 3.1.1 + resolution: "loupe@npm:3.1.1" + dependencies: + get-func-name: "npm:^2.0.1" + checksum: 10c0/99f88badc47e894016df0c403de846fedfea61154aadabbf776c8428dd59e8d8378007135d385d737de32ae47980af07d22ba7bec5ef7beebd721de9baa0a0af + languageName: node + linkType: hard + "lower-case@npm:^2.0.2": version: 2.0.2 resolution: "lower-case@npm:2.0.2" @@ -18737,6 +18808,13 @@ __metadata: languageName: node linkType: hard +"pathval@npm:^2.0.0": + version: 2.0.0 + resolution: "pathval@npm:2.0.0" + checksum: 10c0/602e4ee347fba8a599115af2ccd8179836a63c925c23e04bd056d0674a64b39e3a081b643cc7bc0b84390517df2d800a46fcc5598d42c155fe4977095c2f77c5 + languageName: node + linkType: hard + "pause-stream@npm:0.0.11": version: 0.0.11 resolution: "pause-stream@npm:0.0.11"