From 0a9a954a715443a35389087febdfd3bd04892ffc Mon Sep 17 00:00:00 2001 From: Patrick Kalita Date: Fri, 31 Mar 2023 16:08:16 -0700 Subject: [PATCH 1/2] Use cross-platform temp file and file opening utilities --- .gitignore | 1 + bin/og2dot.js | 31 ++- package-lock.json | 645 ++++++++++++++++++++++++++++++++++++++-------- package.json | 4 +- 4 files changed, 561 insertions(+), 120 deletions(-) diff --git a/.gitignore b/.gitignore index d584d24..4663e4a 100644 --- a/.gitignore +++ b/.gitignore @@ -4,3 +4,4 @@ examples/*.dot *.log dist/ docs/ +.vscode diff --git a/bin/og2dot.js b/bin/og2dot.js index c3815ec..34ee5b9 100755 --- a/bin/og2dot.js +++ b/bin/og2dot.js @@ -4,6 +4,11 @@ import { readFileSync, existsSync, writeFileSync } from 'fs'; import { Command } from 'commander'; import { OboGraphViz } from '../dist/index.js'; import { execSync } from 'child_process' +import tmp from 'tmp'; +import open from 'open'; + +// remove all controlled temporary objects on process exit +tmp.setGracefulCleanup(); function multiple(value, previous) { return previous.concat([value]); @@ -39,8 +44,6 @@ if (options['stylemap']) { styleMap = Object.assign({}, styleMap, JSON.parse(options['stylemap'])); } -var useDatabaseID = options['database-id'] - var compoundRelations = options['compoundRelations'] || [] if (options['compoundRelationsInverse']) { for (let x of options['compoundRelationsInverse']) { @@ -48,10 +51,10 @@ if (options['compoundRelationsInverse']) { } } -var text = "" program.args.forEach (function (filename) { - if (!existsSync (filename)) + if (!existsSync (filename)) { inputError ("File does not exist: " + filename) + } var data = readFileSync (filename) //var og = require(filename); var og = JSON.parse(data) @@ -62,21 +65,17 @@ program.args.forEach (function (filename) { var outfile = options['outfile'] var outfmt = options['to'] if (outfmt && outfmt == 'png') { - var fn = '/tmp/foo.dot' - writeFileSync(fn, dot) - const pngfile = outfile + let dotFile = tmp.fileSync({ postfix: '.dot' }).name; + writeFileSync(dotFile, dot) + var pngfile = outfile if (!pngfile) { - pngfile = '/tmp/foo.png' + pngfile = tmp.fileSync({ postfix: '.png', keep: true }).name; } - var cmd = 'dot '+fn+' -Grankdir=BT -Tpng -o ' + pngfile + var cmd = `dot ${dotFile} -Grankdir=BT -Tpng -o ${pngfile}`; execSync(cmd); - if (outfile) { - //console.log("File is here: "+outfile) - // do nothing - already output - } - else { - console.log("Opening "+pngfile); - execSync('open '+pngfile); + if (!outfile) { + console.log("Opening " + pngfile); + open(pngfile); } } else { diff --git a/package-lock.json b/package-lock.json index 0596c86..aa36b40 100644 --- a/package-lock.json +++ b/package-lock.json @@ -12,7 +12,9 @@ "bbop-graph": "^0.0.19", "commander": "^9.2.0", "graphlib": "^2.1.8", - "graphlib-dot": "^0.6.4" + "graphlib-dot": "^0.6.4", + "open": "^9.1.0", + "tmp": "^0.2.1" }, "bin": { "og2dot": "bin/og2dot.js" @@ -177,8 +179,7 @@ "node_modules/balanced-match": { "version": "1.0.0", "resolved": "https://registry.npmjs.org/balanced-match/-/balanced-match-1.0.0.tgz", - "integrity": "sha1-ibTRmasr7kneFk6gK4nORi1xt2c=", - "dev": true + "integrity": "sha1-ibTRmasr7kneFk6gK4nORi1xt2c=" }, "node_modules/bbop-core": { "version": "0.0.5", @@ -205,6 +206,14 @@ "npm": ">= 2.7.4" } }, + "node_modules/big-integer": { + "version": "1.6.51", + "resolved": "https://registry.npmjs.org/big-integer/-/big-integer-1.6.51.tgz", + "integrity": "sha512-GPEid2Y9QU1Exl1rpO9B2IPJGHPSupF5GnVIP0blYvNOMer2bTvSWs1jGOUg04hTmu67nmLsQ9TBo1puaotBHg==", + "engines": { + "node": ">=0.6" + } + }, "node_modules/binary-extensions": { "version": "2.2.0", "resolved": "https://registry.npmjs.org/binary-extensions/-/binary-extensions-2.2.0.tgz", @@ -242,11 +251,21 @@ "url": "https://github.com/sponsors/sindresorhus" } }, + "node_modules/bplist-parser": { + "version": "0.2.0", + "resolved": "https://registry.npmjs.org/bplist-parser/-/bplist-parser-0.2.0.tgz", + "integrity": "sha512-z0M+byMThzQmD9NILRniCUXYsYpjwnlO8N5uCFaCqIOpqRsJCrQL9NK3JsD67CN5a08nF5oIL2bD6loTdHOuKw==", + "dependencies": { + "big-integer": "^1.6.44" + }, + "engines": { + "node": ">= 5.10.0" + } + }, "node_modules/brace-expansion": { "version": "1.1.11", "resolved": "https://registry.npmjs.org/brace-expansion/-/brace-expansion-1.1.11.tgz", "integrity": "sha512-iCuPHDFgrHX7H2vEI/5xpz07zSHB00TpugqhmYtVmMO6518mCuRMoOYFldEBl0g187ufozdaHgWKcYFb61qGiA==", - "dev": true, "dependencies": { "balanced-match": "^1.0.0", "concat-map": "0.0.1" @@ -258,6 +277,20 @@ "integrity": "sha512-qhAVI1+Av2X7qelOfAIYwXONood6XlZE/fXaBSmW/T5SzLAmCgzi+eiWE7fUvbHaeNBQH13UftjpXxsfLkMpgw==", "dev": true }, + "node_modules/bundle-name": { + "version": "3.0.0", + "resolved": "https://registry.npmjs.org/bundle-name/-/bundle-name-3.0.0.tgz", + "integrity": "sha512-PKA4BeSvBpQKQ8iPOGCSiell+N8P+Tf1DlwqmYhpe2gAhKPHn8EYOxVT+ShuGmhg8lN8XiSlS80yiExKXrURlw==", + "dependencies": { + "run-applescript": "^5.0.0" + }, + "engines": { + "node": ">=12" + }, + "funding": { + "url": "https://github.com/sponsors/sindresorhus" + } + }, "node_modules/cacheable-request": { "version": "6.1.0", "resolved": "https://registry.npmjs.org/cacheable-request/-/cacheable-request-6.1.0.tgz", @@ -530,8 +563,7 @@ "node_modules/concat-map": { "version": "0.0.1", "resolved": "https://registry.npmjs.org/concat-map/-/concat-map-0.0.1.tgz", - "integrity": "sha1-2Klr13/Wjfd5OnMDajug1UBdR3s=", - "dev": true + "integrity": "sha1-2Klr13/Wjfd5OnMDajug1UBdR3s=" }, "node_modules/configstore": { "version": "5.0.1", @@ -560,7 +592,6 @@ "version": "7.0.3", "resolved": "https://registry.npmjs.org/cross-spawn/-/cross-spawn-7.0.3.tgz", "integrity": "sha512-iRDPJKUPVEND7dHPO8rkbOnPpyDygcDFtWjpeWNCgy8WP2rXcxXL8TskReQl6OrB2G7+UJrags1q15Fudc7G6w==", - "dev": true, "dependencies": { "path-key": "^3.1.0", "shebang-command": "^2.0.0", @@ -574,7 +605,6 @@ "version": "2.0.2", "resolved": "https://registry.npmjs.org/which/-/which-2.0.2.tgz", "integrity": "sha512-BLI3Tl1TW3Pvl70l3yq3Y64i+awpwXqsGBYWkkqMtnbXgrMD+yj7rhW0kuEDxzJaYXGjEW5ogapKNMEKNMjibA==", - "dev": true, "dependencies": { "isexe": "^2.0.0" }, @@ -662,12 +692,85 @@ "node": ">=4.0.0" } }, + "node_modules/default-browser": { + "version": "4.0.0", + "resolved": "https://registry.npmjs.org/default-browser/-/default-browser-4.0.0.tgz", + "integrity": "sha512-wX5pXO1+BrhMkSbROFsyxUm0i/cJEScyNhA4PPxc41ICuv05ZZB/MX28s8aZx6xjmatvebIapF6hLEKEcpneUA==", + "dependencies": { + "bundle-name": "^3.0.0", + "default-browser-id": "^3.0.0", + "execa": "^7.1.1", + "titleize": "^3.0.0" + }, + "engines": { + "node": ">=14.16" + }, + "funding": { + "url": "https://github.com/sponsors/sindresorhus" + } + }, + "node_modules/default-browser-id": { + "version": "3.0.0", + "resolved": "https://registry.npmjs.org/default-browser-id/-/default-browser-id-3.0.0.tgz", + "integrity": "sha512-OZ1y3y0SqSICtE8DE4S8YOE9UZOJ8wO16fKWVP5J1Qz42kV9jcnMVFrEE/noXb/ss3Q4pZIH79kxofzyNNtUNA==", + "dependencies": { + "bplist-parser": "^0.2.0", + "untildify": "^4.0.0" + }, + "engines": { + "node": ">=12" + }, + "funding": { + "url": "https://github.com/sponsors/sindresorhus" + } + }, + "node_modules/default-browser/node_modules/execa": { + "version": "7.1.1", + "resolved": "https://registry.npmjs.org/execa/-/execa-7.1.1.tgz", + "integrity": "sha512-wH0eMf/UXckdUYnO21+HDztteVv05rq2GXksxT4fCGeHkBhw1DROXh40wcjMcRqDOWE7iPJ4n3M7e2+YFP+76Q==", + "dependencies": { + "cross-spawn": "^7.0.3", + "get-stream": "^6.0.1", + "human-signals": "^4.3.0", + "is-stream": "^3.0.0", + "merge-stream": "^2.0.0", + "npm-run-path": "^5.1.0", + "onetime": "^6.0.0", + "signal-exit": "^3.0.7", + "strip-final-newline": "^3.0.0" + }, + "engines": { + "node": "^14.18.0 || ^16.14.0 || >=18.0.0" + }, + "funding": { + "url": "https://github.com/sindresorhus/execa?sponsor=1" + } + }, + "node_modules/default-browser/node_modules/human-signals": { + "version": "4.3.1", + "resolved": "https://registry.npmjs.org/human-signals/-/human-signals-4.3.1.tgz", + "integrity": "sha512-nZXjEF2nbo7lIw3mgYjItAfgQXog3OjJogSbKa2CQIIvSGWcKgeJnQlNXip6NglNzYH45nSRiEVimMvYL8DDqQ==", + "engines": { + "node": ">=14.18.0" + } + }, "node_modules/defer-to-connect": { "version": "1.1.3", "resolved": "https://registry.npmjs.org/defer-to-connect/-/defer-to-connect-1.1.3.tgz", "integrity": "sha512-0ISdNousHvZT2EiFlZeZAHBUvSxmKswVCEf8hW7KWgG4a8MVEu/3Vb6uWYozkjylyCxe0JBIiRB1jV45S70WVQ==", "dev": true }, + "node_modules/define-lazy-prop": { + "version": "3.0.0", + "resolved": "https://registry.npmjs.org/define-lazy-prop/-/define-lazy-prop-3.0.0.tgz", + "integrity": "sha512-N+MeXYoqr3pOgn8xfyRPREN7gHakLYjhsHhWGT3fWAiL4IkAt0iDw14QiiEm2bE30c5XX5q0FtAA3CK5f9/BUg==", + "engines": { + "node": ">=12" + }, + "funding": { + "url": "https://github.com/sponsors/sindresorhus" + } + }, "node_modules/diff": { "version": "5.0.0", "resolved": "https://registry.npmjs.org/diff/-/diff-5.0.0.tgz", @@ -763,21 +866,6 @@ "url": "https://github.com/sindresorhus/execa?sponsor=1" } }, - "node_modules/execa/node_modules/onetime": { - "version": "6.0.0", - "resolved": "https://registry.npmjs.org/onetime/-/onetime-6.0.0.tgz", - "integrity": "sha512-1FlR+gjXK7X+AsAHso35MnyN5KqGwJRi/31ft6x0M194ht7S+rWAvd7PHss9xSKMzE0asv1pyIHaJYq+BbacAQ==", - "dev": true, - "dependencies": { - "mimic-fn": "^4.0.0" - }, - "engines": { - "node": ">=12" - }, - "funding": { - "url": "https://github.com/sponsors/sindresorhus" - } - }, "node_modules/find-up": { "version": "5.0.0", "resolved": "https://registry.npmjs.org/find-up/-/find-up-5.0.0.tgz", @@ -806,8 +894,7 @@ "node_modules/fs.realpath": { "version": "1.0.0", "resolved": "https://registry.npmjs.org/fs.realpath/-/fs.realpath-1.0.0.tgz", - "integrity": "sha1-FQStJSMVjKpA20onh8sBQRmU6k8=", - "dev": true + "integrity": "sha1-FQStJSMVjKpA20onh8sBQRmU6k8=" }, "node_modules/fsevents": { "version": "2.3.2", @@ -845,7 +932,6 @@ "version": "6.0.1", "resolved": "https://registry.npmjs.org/get-stream/-/get-stream-6.0.1.tgz", "integrity": "sha512-ts6Wi+2j3jQjqi70w5AlN8DFnkSwC+MqmxEzdEALB2qXZYV3X/b1CTfgPLGJNMeAWxdPfU8FO1ms3NUfaHCPYg==", - "dev": true, "engines": { "node": ">=10" }, @@ -1022,7 +1108,6 @@ "version": "1.0.6", "resolved": "https://registry.npmjs.org/inflight/-/inflight-1.0.6.tgz", "integrity": "sha1-Sb1jMdfQLQwJvJEKEHW6gWW1bfk=", - "dev": true, "dependencies": { "once": "^1.3.0", "wrappy": "1" @@ -1031,8 +1116,7 @@ "node_modules/inherits": { "version": "2.0.3", "resolved": "https://registry.npmjs.org/inherits/-/inherits-2.0.3.tgz", - "integrity": "sha1-Yzwsg+PaQqUC9SRmAiSA9CCCYd4=", - "dev": true + "integrity": "sha1-Yzwsg+PaQqUC9SRmAiSA9CCCYd4=" }, "node_modules/ini": { "version": "1.3.8", @@ -1064,6 +1148,20 @@ "is-ci": "bin.js" } }, + "node_modules/is-docker": { + "version": "3.0.0", + "resolved": "https://registry.npmjs.org/is-docker/-/is-docker-3.0.0.tgz", + "integrity": "sha512-eljcgEDlEns/7AXFosB5K/2nCM4P7FQPkGc/DWLy5rmFEWvZayGrik1d9/QIY5nJ4f9YsVvBkA6kJpHn9rISdQ==", + "bin": { + "is-docker": "cli.js" + }, + "engines": { + "node": "^12.20.0 || ^14.13.1 || >=16.0.0" + }, + "funding": { + "url": "https://github.com/sponsors/sindresorhus" + } + }, "node_modules/is-extglob": { "version": "2.1.1", "resolved": "https://registry.npmjs.org/is-extglob/-/is-extglob-2.1.1.tgz", @@ -1082,6 +1180,23 @@ "node": ">=8" } }, + "node_modules/is-inside-container": { + "version": "1.0.0", + "resolved": "https://registry.npmjs.org/is-inside-container/-/is-inside-container-1.0.0.tgz", + "integrity": "sha512-KIYLCCJghfHZxqjYBE7rEy0OBuTd5xCHS7tHVgvCLkx7StIoaxwNW3hCALgEUjFfeRk+MG/Qxmp/vtETEF3tRA==", + "dependencies": { + "is-docker": "^3.0.0" + }, + "bin": { + "is-inside-container": "cli.js" + }, + "engines": { + "node": ">=14.16" + }, + "funding": { + "url": "https://github.com/sponsors/sindresorhus" + } + }, "node_modules/is-installed-globally": { "version": "0.4.0", "resolved": "https://registry.npmjs.org/is-installed-globally/-/is-installed-globally-0.4.0.tgz", @@ -1141,7 +1256,6 @@ "version": "3.0.0", "resolved": "https://registry.npmjs.org/is-stream/-/is-stream-3.0.0.tgz", "integrity": "sha512-LnQR4bZ9IADDRSkvpqMGvt/tEJWclzklNgSw48V5EAaAeDd6qGvN8ei6k5p0tvxSR171VmGyHuTiAOfxAbr8kA==", - 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"integrity": "sha1-tSQ9jz7BqjXxNkYFvA0QNuMKtp8=", - "dev": true + "integrity": "sha1-tSQ9jz7BqjXxNkYFvA0QNuMKtp8=" }, "write-file-atomic": { "version": "3.0.3", diff --git a/package.json b/package.json index 74bd6fe..af4afc0 100644 --- a/package.json +++ b/package.json @@ -22,7 +22,9 @@ "bbop-graph": "^0.0.19", "commander": "^9.2.0", "graphlib": "^2.1.8", - "graphlib-dot": "^0.6.4" + "graphlib-dot": "^0.6.4", + "open": "^9.1.0", + "tmp": "^0.2.1" }, "devDependencies": { "@types/node": "^17.0.31", From 86916271ec3df91fc75061a77abc35ddab771c4e Mon Sep 17 00:00:00 2001 From: Patrick Kalita Date: Fri, 31 Mar 2023 16:45:38 -0700 Subject: [PATCH 2/2] Raise minimum Node version to 14.x --- .github/workflows/main.yaml | 2 +- README.md | 2 +- package.json | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml index 0b6b025..87a7792 100644 --- a/.github/workflows/main.yaml +++ b/.github/workflows/main.yaml @@ -13,7 +13,7 @@ jobs: strategy: matrix: - node-version: [12.x, 14.x, 16.x] + node-version: [14.x, 16.x, 18.x] steps: - uses: actions/checkout@v3 diff --git a/README.md b/README.md index acbcf83..c1c0d67 100644 --- a/README.md +++ b/README.md @@ -8,7 +8,7 @@ ## Requirements -* Node.js ≥ 12.20 +* Node.js ≥ 14.16 ## Installation diff --git a/package.json b/package.json index af4afc0..4436376 100644 --- a/package.json +++ b/package.json @@ -15,7 +15,7 @@ "url": "git+https://github.com/INCATools/obographviz.git" }, "engines": { - "node": ">=12" + "node": ">=14.16" }, "type": "module", "dependencies": {