From d49dab0bf91bc0f19612f8643cf667412427e97b Mon Sep 17 00:00:00 2001 From: Robert Buels Date: Mon, 3 Apr 2023 11:23:07 -0700 Subject: [PATCH 01/11] separate construction and validation, improve ts --- README.md | 2 +- package.json | 1 + src/genomesFile.ts | 4 + src/hubFile.test.ts | 1 - src/hubFile.ts | 4 + src/index.test.ts | 1 - src/raFile.test.ts | 3 +- src/raFile.ts | 2 +- src/raStanza.test.ts | 3 +- src/raStanza.ts | 2 +- src/trackDbFile.test.ts | 1 - src/trackDbFile.ts | 4 + ...gleFileAssemblyHub.GCF_000002985.6.hub.txt | 253 ++++++++++++++++++ yarn.lock | 96 ++++++- 14 files changed, 367 insertions(+), 10 deletions(-) create mode 100644 test/singleFileAssemblyHub.GCF_000002985.6.hub.txt diff --git a/README.md b/README.md index 3c4a3fd..6443c73 100644 --- a/README.md +++ b/README.md @@ -12,7 +12,7 @@ read and write UCSC track and assembly hub files in node or the browser Read about hub.txt, genomes.txt, and trackDb.txt files here: -Files are essentially JavaScript `Map`s. A hub.txt file is a map with th keys as the first word in each line and the value as the rest of the line, like this: +Files are essentially JavaScript `Map`s. A hub.txt file is a map with keys as the first word in each line and the value as the rest of the line, like this: Map { "hub" => "UCSCHub", diff --git a/package.json b/package.json index 3d978dc..d302d8d 100644 --- a/package.json +++ b/package.json @@ -43,6 +43,7 @@ "@types/node": "^18.11.16", "@typescript-eslint/eslint-plugin": "^5.46.1", "@typescript-eslint/parser": "^5.46.1", + "assert": "^2.0.0", "documentation": "^14.0.1", "eslint": "^8.30.0", "eslint-config-airbnb-typescript": "^17.0.0", diff --git a/src/genomesFile.ts b/src/genomesFile.ts index 8c2aee1..b7da3a3 100644 --- a/src/genomesFile.ts +++ b/src/genomesFile.ts @@ -10,6 +10,10 @@ import RaFile from './raFile' export default class GenomesFile extends RaFile { constructor(genomesFile: string) { super(genomesFile) + this.validate() + } + + protected validate() { if (this.nameKey !== 'genome') { throw new Error( 'Genomes file must begin with a line like "genome "', diff --git a/src/hubFile.test.ts b/src/hubFile.test.ts index 4719fac..5c72928 100644 --- a/src/hubFile.test.ts +++ b/src/hubFile.test.ts @@ -1,4 +1,3 @@ -// @ts-nocheck import fs from 'fs' import HubFile from './hubFile' diff --git a/src/hubFile.ts b/src/hubFile.ts index 288b17c..92bfac4 100644 --- a/src/hubFile.ts +++ b/src/hubFile.ts @@ -11,6 +11,10 @@ import RaStanza from './raStanza' export default class HubFile extends RaStanza { constructor(hubFile: string) { super(hubFile) + this.validate() + } + + protected validate() { if (this.nameKey !== 'hub') { throw new Error('Hub file must begin with a line like "hub "') } diff --git a/src/index.test.ts b/src/index.test.ts index 400245a..74323de 100644 --- a/src/index.test.ts +++ b/src/index.test.ts @@ -1,4 +1,3 @@ -// @ts-nocheck import { RaFile, RaStanza } from './index' describe('ucsc-hub-js', () => { diff --git a/src/raFile.test.ts b/src/raFile.test.ts index a104f99..edef563 100644 --- a/src/raFile.test.ts +++ b/src/raFile.test.ts @@ -1,6 +1,6 @@ -// @ts-nocheck import fs from 'fs' import RaFile from './raFile' +import assert from 'assert' describe('RaFile reader', () => { it('creates an empty ra file', () => { @@ -136,6 +136,7 @@ describe('RaFile reader', () => { const input = fs.readFileSync('test/basic.ra', 'utf8') const raFile = new RaFile(input) const updatedStanza = raFile.get('valD') + assert(updatedStanza) updatedStanza.indent = ' ' raFile.set('valD', updatedStanza) expect(raFile).toMatchSnapshot() diff --git a/src/raFile.ts b/src/raFile.ts index 61085ac..6849af5 100644 --- a/src/raFile.ts +++ b/src/raFile.ts @@ -28,7 +28,7 @@ export default class RaFile extends Map { nameKey?: string - constructor(raFile: string, options = { checkIndent: true }) { + constructor(raFile: string | string[] = [], options = { checkIndent: true }) { super() const { checkIndent } = options this._checkIndent = checkIndent diff --git a/src/raStanza.test.ts b/src/raStanza.test.ts index f4bdaf6..bda93c0 100644 --- a/src/raStanza.test.ts +++ b/src/raStanza.test.ts @@ -1,4 +1,4 @@ -// @ts-nocheck +import assert from 'assert' import RaStanza from './raStanza' describe('RaStanza reader', () => { @@ -179,6 +179,7 @@ describe('RaStanza reader', () => { const input = 'key1 value1\nkey2 value2\nkey3\n' const stanza = new RaStanza(input) let updatedValue = stanza.get('key2') + assert(updatedValue) updatedValue += '_new' stanza.set('key2', updatedValue) expect(stanza).toMatchSnapshot() diff --git a/src/raStanza.ts b/src/raStanza.ts index 965df11..957a5a3 100644 --- a/src/raStanza.ts +++ b/src/raStanza.ts @@ -43,7 +43,7 @@ export default class RaStanza extends Map { nameKey?: string - constructor(stanza: string | string[], options = { checkIndent: true }) { + constructor(stanza: string | string[] = [], options = { checkIndent: true }) { super() const { checkIndent } = options this._checkIndent = checkIndent diff --git a/src/trackDbFile.test.ts b/src/trackDbFile.test.ts index 4d3692e..0055c23 100644 --- a/src/trackDbFile.test.ts +++ b/src/trackDbFile.test.ts @@ -1,4 +1,3 @@ -// @ts-nocheck import fs from 'fs' import TrackDbFile from './trackDbFile' diff --git a/src/trackDbFile.ts b/src/trackDbFile.ts index e2a80da..451cf60 100644 --- a/src/trackDbFile.ts +++ b/src/trackDbFile.ts @@ -10,6 +10,10 @@ import RaFile from './raFile' export default class TrackDbFile extends RaFile { constructor(trackDbFile: string) { super(trackDbFile, { checkIndent: false }) + this.validate() + } + + protected validate() { if (this.nameKey !== 'track') { throw new Error( `trackDb has "${this.nameKey}" instead of "track" as the first line in each track`, diff --git a/test/singleFileAssemblyHub.GCF_000002985.6.hub.txt b/test/singleFileAssemblyHub.GCF_000002985.6.hub.txt new file mode 100644 index 0000000..fcbe317 --- /dev/null +++ b/test/singleFileAssemblyHub.GCF_000002985.6.hub.txt @@ -0,0 +1,253 @@ +hub GCF_000002985.6 genome assembly +shortLabel roundworm +longLabel roundworm/Caenorhabditis elegans/GCF_000002985.6_WBcel235 genome assembly +useOneFile on +email hclawson@ucsc.edu +descriptionUrl html/GCF_000002985.6_WBcel235.description.html + +genome GCF_000002985.6 +taxId 6239 +groups groups.txt +description roundworm +twoBitPath GCF_000002985.6.2bit +twoBitBptUrl GCF_000002985.6.2bit.bpt +chromSizes GCF_000002985.6.chrom.sizes.txt +chromAliasBb GCF_000002985.6.chromAlias.bb +chromAuthority ucsc +organism WBcel235 Feb. 2013 +defaultPos NC_003283.11:6974726-6984726 +scientificName Caenorhabditis elegans +htmlPath html/GCF_000002985.6_WBcel235.description.html +blat dynablat-01.soe.ucsc.edu 4040 dynamic GCF/000/002/985/GCF_000002985.6 +transBlat dynablat-01.soe.ucsc.edu 4040 dynamic GCF/000/002/985/GCF_000002985.6 +isPcr dynablat-01.soe.ucsc.edu 4040 dynamic GCF/000/002/985/GCF_000002985.6 + +track assembly +longLabel Assembly +shortLabel Assembly +visibility pack +colorByStrand 150,100,30 230,170,40 +color 150,100,30 +altColor 230,170,40 +bigDataUrl bbi/GCF_000002985.6_WBcel235.assembly.bb +type bigBed 6 +html html/GCF_000002985.6_WBcel235.assembly +searchIndex name +searchTrix ixIxx/GCF_000002985.6_WBcel235.assembly.ix +url https://www.ncbi.nlm.nih.gov/nuccore/$$ +urlLabel NCBI Nucleotide database: +group map + +track cytoBandIdeo +shortLabel Chromosome Band (Ideogram) +longLabel Ideogram for Orientation +group map +visibility dense +type bigBed 4 + +bigDataUrl bbi/GCF_000002985.6_WBcel235.cytoBand.bb + +track gc5Base +shortLabel GC Percent +longLabel GC Percent in 5-Base Windows +group map +visibility full +autoScale Off +maxHeightPixels 128:36:16 +graphTypeDefault Bar +gridDefault OFF +windowingFunction Mean +color 0,0,0 +altColor 128,128,128 +viewLimits 30:70 +type bigWig 0 100 +bigDataUrl bbi/GCF_000002985.6_WBcel235.gc5Base.bw +html html/GCF_000002985.6_WBcel235.gc5Base + +track tanDups +shortLabel Tandem Dups +longLabel Paired identical sequences +compositeTrack on +visibility hide +type bigBed 12 +group map +html html/GCF_000002985.6_WBcel235.tanDups + + track tandemDups + parent tanDups on + shortLabel Tandem Dups + longLabel Paired exactly identical sequence survey over entire genome assembly + bigDataUrl bbi/GCF_000002985.6_WBcel235.tandemDups.bb + type bigBed 12 + +track repeatMasker +shortLabel RepeatMasker +longLabel RepeatMasker Repetitive Elements +type bigRmsk 9 + +visibility pack +group varRep +bigDataUrl bbi/GCF_000002985.6_WBcel235.rmsk.bb +maxWindowToDraw 5000000 +html html/GCF_000002985.6_WBcel235.repeatMasker + +track simpleRepeat +shortLabel Simple Repeats +longLabel Simple Tandem Repeats by TRF +group varRep +visibility dense +type bigBed 4 + +bigDataUrl bbi/GCF_000002985.6_WBcel235.simpleRepeat.bb +html html/GCF_000002985.6_WBcel235.simpleRepeat + +track refSeqComposite +compositeTrack on +shortLabel NCBI RefSeq +longLabel RefSeq gene predictions from NCBI +group genes +visibility pack +type bigBed +dragAndDrop subTracks +allButtonPair on +dataVersion WormBase WS277 (2020-05-29) +html html/GCF_000002985.6_WBcel235.refSeqComposite +priority 2 + + track ncbiRefSeq + parent refSeqComposite on + color 12,12,120 + altColor 120,12,12 + shortLabel RefSeq All + type bigGenePred + labelFields name,geneName,geneName2 + defaultLabelFields geneName2 + searchIndex name + searchTrix ixIxx/GCF_000002985.6_WBcel235.ncbiRefSeq.ix + bigDataUrl bbi/GCF_000002985.6_WBcel235.ncbiRefSeq.bb + longLabel NCBI RefSeq genes, curated and predicted sets (NM_*, XM_*, NR_*, XR_*, NP_* or YP_*) + idXref ncbiRefSeqLink mrnaAcc name + baseColorUseCds given + baseColorDefault genomicCodons + priority 1 + + track ncbiRefSeqCurated + color 12,12,120 + parent refSeqComposite on + shortLabel RefSeq Curated + longLabel NCBI RefSeq genes, curated subset (NM_*, NR_*, NP_* or YP_*) + type bigGenePred + labelFields name,geneName,geneName2 + defaultLabelFields geneName2 + searchIndex name + searchTrix ixIxx/GCF_000002985.6_WBcel235.ncbiRefSeqCurated.ix + idXref ncbiRefSeqLink mrnaAcc name + bigDataUrl bbi/GCF_000002985.6_WBcel235.ncbiRefSeqCurated.bb + baseColorUseCds given + baseColorDefault genomicCodons + priority 2 + + track ncbiRefSeqOther + color 32,32,32 + parent refSeqComposite on + shortLabel RefSeq Other + longLabel NCBI RefSeq other annotations (not NM_*, NR_*, XM_*, XR_*, NP_* or YP_*) + priority 4 + searchIndex name + searchTrix ixIxx/GCF_000002985.6_WBcel235.ncbiRefSeqOther.ix + bigDataUrl bbi/GCF_000002985.6_WBcel235.ncbiRefSeqOther.bb + type bigBed 12 + + labelFields name + skipEmptyFields on + urls GeneID="https://www.ncbi.nlm.nih.gov/gene/$$" MIM="https://www.ncbi.nlm.nih.gov/omim/$$" HGNC="http://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=$$" FlyBase="http://flybase.org/reports/$$" WormBase="http://www.wormbase.org/db/gene/gene?name=$$" RGD="https://rgd.mcw.edu/rgdweb/search/search.html?term=$$" SGD="https://www.yeastgenome.org/locus/$$" miRBase="http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$$" ZFIN="https://zfin.org/$$" MGI="http://www.informatics.jax.org/marker/$$" + + track ncbiRefSeqPsl + priority 5 + parent refSeqComposite off + shortLabel RefSeq Alignments + longLabel RefSeq Alignments of RNAs + type bigPsl + searchIndex name + bigDataUrl bbi/GCF_000002985.6_WBcel235.bigPsl.bb + indelDoubleInsert on + indelQueryInsert on + showDiffBasesAllScales . + showDiffBasesMaxZoom 10000.0 + showCdsMaxZoom 10000.0 + showCdsAllScales . + baseColorDefault diffCodons + pslSequence no + baseColorUseSequence lfExtra + baseColorUseCds table given + color 0,0,0 + +track cpgIslands +compositeTrack on +shortLabel CpG Islands +longLabel CpG Islands (Islands < 300 Bases are Light Green) +group regulation +visibility pack +type bigBed 4 + +html html/GCF_000002985.6_WBcel235.cpgIslands + + track cpgIslandExt + parent cpgIslands off + shortLabel CpG Islands + longLabel CpG Islands (Islands < 300 Bases are Light Green) + type bigBed 4 + + priority 1 + bigDataUrl bbi/GCF_000002985.6_WBcel235.cpgIslandExt.bb + + track cpgIslandExtUnmasked + parent cpgIslands on + shortLabel Unmasked CpG + longLabel CpG Islands on All Sequence (Islands < 300 Bases are Light Green) + type bigBed 4 + + priority 2 + bigDataUrl bbi/GCF_000002985.6_WBcel235.cpgIslandExtUnmasked.bb + +track windowMasker +shortLabel WM + SDust +longLabel Genomic Intervals Masked by WindowMasker + SDust +group varRep +visibility dense +type bigBed 3 +bigDataUrl bbi/GCF_000002985.6_WBcel235.windowMasker.bb +html html/GCF_000002985.6_WBcel235.windowMasker + +track augustus +shortLabel Augustus +longLabel Augustus Gene Predictions +group genes +visibility dense +color 180,0,0 +type bigGenePred +bigDataUrl bbi/GCF_000002985.6_WBcel235.augustus.bb +html html/GCF_000002985.6_WBcel235.augustus + +track xenoRefGene +shortLabel RefSeq mRNAs +longLabel RefSeq mRNAs mapped to this assembly +group rna +visibility pack +color 180,0,0 +type bigGenePred +bigDataUrl bbi/GCF_000002985.6_WBcel235.xenoRefGene.bb +url https://www.ncbi.nlm.nih.gov/nuccore/$$ +urlLabel NCBI Nucleotide database: +labelFields name,geneName,geneName2 +defaultLabelFields geneName +searchIndex name +searchTrix ixIxx/GCF_000002985.6_WBcel235.xenoRefGene.ix +html html/GCF_000002985.6_WBcel235.xenoRefGene + +track ensGene +shortLabel Ensembl genes +longLabel Ensembl genes version 103/Feb. 2021 +group genes +priority 40 +visibility pack +color 150,0,0 +type bigBed 12 . +bigDataUrl bbi/GCF_000002985.6_WBcel235.ensGene.bb +searchIndex name +searchTrix ixIxx/GCF_000002985.6_WBcel235.ensGene.ix +html html/GCF_000002985.6_WBcel235.ensGene + diff --git a/yarn.lock b/yarn.lock index 74b6d98..b50b528 100644 --- a/yarn.lock +++ b/yarn.lock @@ -1032,6 +1032,21 @@ arrify@^1.0.1: resolved "https://registry.yarnpkg.com/arrify/-/arrify-1.0.1.tgz#898508da2226f380df904728456849c1501a4b0d" integrity sha512-3CYzex9M9FGQjCGMGyi6/31c8GJbgb0qGyrx5HWxPd0aCwh4cB2YjMb2Xf9UuoogrMrlO9cTqnB5rI5GHZTcUA== +assert@^2.0.0: + version "2.0.0" + resolved "https://registry.yarnpkg.com/assert/-/assert-2.0.0.tgz#95fc1c616d48713510680f2eaf2d10dd22e02d32" + integrity 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wrappy "1" -inherits@2: +inherits@2, inherits@^2.0.3: version "2.0.4" resolved "https://registry.yarnpkg.com/inherits/-/inherits-2.0.4.tgz#0fa2c64f932917c3433a0ded55363aae37416b7c" integrity sha512-k/vGaX4/Yla3WzyMCvTQOXYeIHvqOKtnqBduzTHpzpQZzAskKMhZ2K+EnBiSM9zGSoIFeMpXKxa4dYeZIQqewQ== @@ -2321,6 +2348,14 @@ is-absolute@^1.0.0: is-relative "^1.0.0" is-windows "^1.0.1" +is-arguments@^1.0.4: + version "1.1.1" + resolved "https://registry.yarnpkg.com/is-arguments/-/is-arguments-1.1.1.tgz#15b3f88fda01f2a97fec84ca761a560f123efa9b" + integrity sha512-8Q7EARjzEnKpt/PCD7e1cgUS0a6X8u5tdSiMqXhojOdoV9TsMsiO+9VLC5vAmO8N7/GmXn7yjR8qnA6bVAEzfA== + dependencies: + call-bind "^1.0.2" + has-tostringtag "^1.0.0" + is-arrayish@^0.2.1: version "0.2.1" resolved "https://registry.yarnpkg.com/is-arrayish/-/is-arrayish-0.2.1.tgz#77c99840527aa8ecb1a8ba697b80645a7a926a9d" @@ -2353,7 +2388,7 @@ is-buffer@^2.0.0: resolved "https://registry.yarnpkg.com/is-buffer/-/is-buffer-2.0.5.tgz#ebc252e400d22ff8d77fa09888821a24a658c191" integrity sha512-i2R6zNFDwgEHJyQUtJEk0XFi1i0dPFn/oqjK3/vPCcDeJvW5NQ83V8QbicfF1SupOaB0h8ntgBC2YiE7dfyctQ== -is-callable@^1.1.4, is-callable@^1.2.7: +is-callable@^1.1.3, is-callable@^1.1.4, is-callable@^1.2.7: version "1.2.7" resolved "https://registry.yarnpkg.com/is-callable/-/is-callable-1.2.7.tgz#3bc2a85ea742d9e36205dcacdd72ca1fdc51b055" integrity sha512-1BC0BVFhS/p0qtw6enp8e+8OD0UrK0oFLztSjNzhcKA3WDuJxxAPXzPuPtKkjEY9UUoEWlX/8fgKeu2S8i9JTA== @@ -2387,6 +2422,13 @@ is-generator-fn@^2.0.0: resolved "https://registry.yarnpkg.com/is-generator-fn/-/is-generator-fn-2.1.0.tgz#7d140adc389aaf3011a8f2a2a4cfa6faadffb118" integrity sha512-cTIB4yPYL/Grw0EaSzASzg6bBy9gqCofvWN8okThAYIxKJZC+udlRAmGbM0XLeniEJSs8uEgHPGuHSe1XsOLSQ== +is-generator-function@^1.0.7: + version "1.0.10" + resolved "https://registry.yarnpkg.com/is-generator-function/-/is-generator-function-1.0.10.tgz#f1558baf1ac17e0deea7c0415c438351ff2b3c72" + integrity sha512-jsEjy9l3yiXEQ+PsXdmBwEPcOxaXWLspKdplFUVI9vq1iZgIekeC0L167qeu86czQaxed3q/Uzuw0swL0irL8A== + dependencies: + has-tostringtag "^1.0.0" + is-glob@^4.0.0, is-glob@^4.0.1, is-glob@^4.0.3, is-glob@~4.0.1: version "4.0.3" resolved "https://registry.yarnpkg.com/is-glob/-/is-glob-4.0.3.tgz#64f61e42cbbb2eec2071a9dac0b28ba1e65d5084" @@ -2394,6 +2436,14 @@ is-glob@^4.0.0, is-glob@^4.0.1, is-glob@^4.0.3, is-glob@~4.0.1: dependencies: is-extglob "^2.1.1" +is-nan@^1.2.1: + version "1.3.2" + resolved "https://registry.yarnpkg.com/is-nan/-/is-nan-1.3.2.tgz#043a54adea31748b55b6cd4e09aadafa69bd9e1d" + integrity sha512-E+zBKpQ2t6MEo1VsonYmluk9NxGrbzpeeLC2xIViuO2EjU2xsXsBPwTr3Ykv9l08UYEVEdWeRZNouaZqF6RN0w== + dependencies: + call-bind "^1.0.0" + define-properties "^1.1.3" + is-negative-zero@^2.0.2: version "2.0.2" resolved "https://registry.yarnpkg.com/is-negative-zero/-/is-negative-zero-2.0.2.tgz#7bf6f03a28003b8b3965de3ac26f664d765f3150" @@ -2474,6 +2524,17 @@ is-symbol@^1.0.2, is-symbol@^1.0.3: dependencies: has-symbols "^1.0.2" +is-typed-array@^1.1.10, is-typed-array@^1.1.3: + version "1.1.10" + resolved "https://registry.yarnpkg.com/is-typed-array/-/is-typed-array-1.1.10.tgz#36a5b5cb4189b575d1a3e4b08536bfb485801e3f" + integrity sha512-PJqgEHiWZvMpaFZ3uTc8kHPM4+4ADTlDniuQL7cU/UDA0Ql7F70yGfHph3cLNe+c9toaigv+DFzTJKhc2CtO6A== + dependencies: + available-typed-arrays "^1.0.5" + call-bind "^1.0.2" + for-each "^0.3.3" + gopd "^1.0.1" + has-tostringtag "^1.0.0" + is-unc-path@^1.0.0: version "1.0.0" resolved "https://registry.yarnpkg.com/is-unc-path/-/is-unc-path-1.0.0.tgz#d731e8898ed090a12c352ad2eaed5095ad322c9d" @@ -3699,6 +3760,14 @@ object-inspect@^1.12.2, object-inspect@^1.9.0: resolved "https://registry.yarnpkg.com/object-inspect/-/object-inspect-1.12.2.tgz#c0641f26394532f28ab8d796ab954e43c009a8ea" integrity sha512-z+cPxW0QGUp0mcqcsgQyLVRDoXFQbXOwBaqyF7VIgI4TWNQsDHrBpUQslRmIfAoYWdYzs6UlKJtB2XJpTaNSpQ== +object-is@^1.0.1: + version "1.1.5" + resolved "https://registry.yarnpkg.com/object-is/-/object-is-1.1.5.tgz#b9deeaa5fc7f1846a0faecdceec138e5778f53ac" + integrity sha512-3cyDsyHgtmi7I7DfSSI2LDp6SK2lwvtbg0p0R1e0RvTqF5ceGx+K2dfSjm1bKDMVCFEDAQvy+o8c6a7VujOddw== + dependencies: + call-bind "^1.0.2" + define-properties "^1.1.3" + object-keys@^1.1.1: version "1.1.1" resolved "https://registry.yarnpkg.com/object-keys/-/object-keys-1.1.1.tgz#1c47f272df277f3b1daf061677d9c82e2322c60e" @@ -4736,6 +4805,17 @@ uri-js@^4.2.2: dependencies: punycode "^2.1.0" +util@^0.12.0: + version "0.12.5" + resolved "https://registry.yarnpkg.com/util/-/util-0.12.5.tgz#5f17a6059b73db61a875668781a1c2b136bd6fbc" + integrity sha512-kZf/K6hEIrWHI6XqOFUiiMa+79wE/D8Q+NCNAWclkyg3b4d2k7s0QGepNjiABc+aR3N1PAyHL7p6UcLY6LmrnA== + dependencies: + inherits "^2.0.3" + is-arguments "^1.0.4" + is-generator-function "^1.0.7" + is-typed-array "^1.1.3" + which-typed-array "^1.1.2" + uuid@^3.3.2: version "3.4.0" resolved "https://registry.yarnpkg.com/uuid/-/uuid-3.4.0.tgz#b23e4358afa8a202fe7a100af1f5f883f02007ee" @@ -4838,6 +4918,18 @@ which-boxed-primitive@^1.0.2: is-string "^1.0.5" is-symbol "^1.0.3" +which-typed-array@^1.1.2: + version "1.1.9" + resolved "https://registry.yarnpkg.com/which-typed-array/-/which-typed-array-1.1.9.tgz#307cf898025848cf995e795e8423c7f337efbde6" + integrity sha512-w9c4xkx6mPidwp7180ckYWfMmvxpjlZuIudNtDf4N/tTAUB8VJbX25qZoAsrtGuYNnGw3pa0AXgbGKRB8/EceA== + dependencies: + available-typed-arrays "^1.0.5" + call-bind "^1.0.2" + for-each "^0.3.3" + gopd "^1.0.1" + has-tostringtag "^1.0.0" + is-typed-array "^1.1.10" + which@^2.0.1: version "2.0.2" resolved "https://registry.yarnpkg.com/which/-/which-2.0.2.tgz#7c6a8dd0a636a0327e10b59c9286eee93f3f51b1" From b8c150a48f262094bff53eb509d4bb8c85b519f3 Mon Sep 17 00:00:00 2001 From: Robert Buels Date: Mon, 3 Apr 2023 11:46:33 -0700 Subject: [PATCH 02/11] remove assert dev dep --- package.json | 1 - yarn.lock | 96 ++-------------------------------------------------- 2 files changed, 2 insertions(+), 95 deletions(-) diff --git a/package.json b/package.json index d302d8d..3d978dc 100644 --- a/package.json +++ b/package.json @@ -43,7 +43,6 @@ "@types/node": "^18.11.16", "@typescript-eslint/eslint-plugin": "^5.46.1", "@typescript-eslint/parser": "^5.46.1", - "assert": "^2.0.0", "documentation": "^14.0.1", "eslint": "^8.30.0", "eslint-config-airbnb-typescript": "^17.0.0", diff --git a/yarn.lock b/yarn.lock index b50b528..74b6d98 100644 --- a/yarn.lock +++ b/yarn.lock @@ -1032,21 +1032,6 @@ arrify@^1.0.1: resolved "https://registry.yarnpkg.com/arrify/-/arrify-1.0.1.tgz#898508da2226f380df904728456849c1501a4b0d" integrity sha512-3CYzex9M9FGQjCGMGyi6/31c8GJbgb0qGyrx5HWxPd0aCwh4cB2YjMb2Xf9UuoogrMrlO9cTqnB5rI5GHZTcUA== -assert@^2.0.0: - version "2.0.0" - resolved "https://registry.yarnpkg.com/assert/-/assert-2.0.0.tgz#95fc1c616d48713510680f2eaf2d10dd22e02d32" - integrity sha512-se5Cd+js9dXJnu6Ag2JFc00t+HmHOen+8Q+L7O9zI0PqQXr20uk2J0XQqMxZEeo5U50o8Nvmmx7dZrl+Ufr35A== - dependencies: - es6-object-assign "^1.1.0" - is-nan "^1.2.1" - object-is "^1.0.1" - util "^0.12.0" - -available-typed-arrays@^1.0.5: - version "1.0.5" - resolved "https://registry.yarnpkg.com/available-typed-arrays/-/available-typed-arrays-1.0.5.tgz#92f95616501069d07d10edb2fc37d3e1c65123b7" - integrity sha512-DMD0KiN46eipeziST1LPP/STfDU0sufISXmjSgvVsoU2tqxctQeASejWcfNtxYKqETM1UxQ8sp2OrSBWpHY6sw== - babel-jest@^29.3.1: version "29.3.1" resolved "https://registry.yarnpkg.com/babel-jest/-/babel-jest-29.3.1.tgz#05c83e0d128cd48c453eea851482a38782249f44" @@ -1613,11 +1598,6 @@ es-to-primitive@^1.2.1: is-date-object "^1.0.1" is-symbol "^1.0.2" -es6-object-assign@^1.1.0: - version "1.1.0" - resolved "https://registry.yarnpkg.com/es6-object-assign/-/es6-object-assign-1.1.0.tgz#c2c3582656247c39ea107cb1e6652b6f9f24523c" - integrity sha512-MEl9uirslVwqQU369iHNWZXsI8yaZYGg/D65aOgZkeyFJwHYSxilf7rQzXKI7DdDuBPrBXbfk3sl9hJhmd5AUw== - escalade@^3.1.1: version "3.1.1" resolved "https://registry.yarnpkg.com/escalade/-/escalade-3.1.1.tgz#d8cfdc7000965c5a0174b4a82eaa5c0552742e40" @@ -1976,13 +1956,6 @@ flatted@^3.1.0: resolved "https://registry.yarnpkg.com/flatted/-/flatted-3.2.7.tgz#609f39207cb614b89d0765b477cb2d437fbf9787" integrity sha512-5nqDSxl8nn5BSNxyR3n4I6eDmbolI6WT+QqR547RwxQapgjQBmtktdP+HTBb/a/zLsbzERTONyUB5pefh5TtjQ== -for-each@^0.3.3: - version "0.3.3" - resolved "https://registry.yarnpkg.com/for-each/-/for-each-0.3.3.tgz#69b447e88a0a5d32c3e7084f3f1710034b21376e" - integrity sha512-jqYfLp7mo9vIyQf8ykW2v7A+2N4QjeCeI5+Dz9XraiO1ign81wjiH7Fb9vSOWvQfNtmSa4H2RoQTrrXivdUZmw== - dependencies: - is-callable "^1.1.3" - fs.realpath@^1.0.0: version "1.0.0" resolved "https://registry.yarnpkg.com/fs.realpath/-/fs.realpath-1.0.0.tgz#1504ad2523158caa40db4a2787cb01411994ea4f" @@ -2321,7 +2294,7 @@ inflight@^1.0.4: once "^1.3.0" wrappy "1" -inherits@2, inherits@^2.0.3: +inherits@2: version "2.0.4" resolved "https://registry.yarnpkg.com/inherits/-/inherits-2.0.4.tgz#0fa2c64f932917c3433a0ded55363aae37416b7c" integrity sha512-k/vGaX4/Yla3WzyMCvTQOXYeIHvqOKtnqBduzTHpzpQZzAskKMhZ2K+EnBiSM9zGSoIFeMpXKxa4dYeZIQqewQ== @@ -2348,14 +2321,6 @@ is-absolute@^1.0.0: is-relative "^1.0.0" is-windows "^1.0.1" -is-arguments@^1.0.4: - version "1.1.1" - resolved "https://registry.yarnpkg.com/is-arguments/-/is-arguments-1.1.1.tgz#15b3f88fda01f2a97fec84ca761a560f123efa9b" - integrity sha512-8Q7EARjzEnKpt/PCD7e1cgUS0a6X8u5tdSiMqXhojOdoV9TsMsiO+9VLC5vAmO8N7/GmXn7yjR8qnA6bVAEzfA== - dependencies: - call-bind "^1.0.2" - has-tostringtag "^1.0.0" - is-arrayish@^0.2.1: version "0.2.1" resolved "https://registry.yarnpkg.com/is-arrayish/-/is-arrayish-0.2.1.tgz#77c99840527aa8ecb1a8ba697b80645a7a926a9d" @@ -2388,7 +2353,7 @@ is-buffer@^2.0.0: resolved "https://registry.yarnpkg.com/is-buffer/-/is-buffer-2.0.5.tgz#ebc252e400d22ff8d77fa09888821a24a658c191" integrity sha512-i2R6zNFDwgEHJyQUtJEk0XFi1i0dPFn/oqjK3/vPCcDeJvW5NQ83V8QbicfF1SupOaB0h8ntgBC2YiE7dfyctQ== -is-callable@^1.1.3, is-callable@^1.1.4, is-callable@^1.2.7: +is-callable@^1.1.4, is-callable@^1.2.7: version "1.2.7" resolved "https://registry.yarnpkg.com/is-callable/-/is-callable-1.2.7.tgz#3bc2a85ea742d9e36205dcacdd72ca1fdc51b055" integrity sha512-1BC0BVFhS/p0qtw6enp8e+8OD0UrK0oFLztSjNzhcKA3WDuJxxAPXzPuPtKkjEY9UUoEWlX/8fgKeu2S8i9JTA== @@ -2422,13 +2387,6 @@ is-generator-fn@^2.0.0: resolved "https://registry.yarnpkg.com/is-generator-fn/-/is-generator-fn-2.1.0.tgz#7d140adc389aaf3011a8f2a2a4cfa6faadffb118" integrity sha512-cTIB4yPYL/Grw0EaSzASzg6bBy9gqCofvWN8okThAYIxKJZC+udlRAmGbM0XLeniEJSs8uEgHPGuHSe1XsOLSQ== -is-generator-function@^1.0.7: - version "1.0.10" - resolved "https://registry.yarnpkg.com/is-generator-function/-/is-generator-function-1.0.10.tgz#f1558baf1ac17e0deea7c0415c438351ff2b3c72" - integrity sha512-jsEjy9l3yiXEQ+PsXdmBwEPcOxaXWLspKdplFUVI9vq1iZgIekeC0L167qeu86czQaxed3q/Uzuw0swL0irL8A== - dependencies: - has-tostringtag "^1.0.0" - is-glob@^4.0.0, is-glob@^4.0.1, is-glob@^4.0.3, is-glob@~4.0.1: version "4.0.3" resolved "https://registry.yarnpkg.com/is-glob/-/is-glob-4.0.3.tgz#64f61e42cbbb2eec2071a9dac0b28ba1e65d5084" @@ -2436,14 +2394,6 @@ is-glob@^4.0.0, is-glob@^4.0.1, is-glob@^4.0.3, is-glob@~4.0.1: dependencies: is-extglob "^2.1.1" -is-nan@^1.2.1: - version "1.3.2" - resolved "https://registry.yarnpkg.com/is-nan/-/is-nan-1.3.2.tgz#043a54adea31748b55b6cd4e09aadafa69bd9e1d" - integrity sha512-E+zBKpQ2t6MEo1VsonYmluk9NxGrbzpeeLC2xIViuO2EjU2xsXsBPwTr3Ykv9l08UYEVEdWeRZNouaZqF6RN0w== - dependencies: - call-bind "^1.0.0" - define-properties "^1.1.3" - is-negative-zero@^2.0.2: version "2.0.2" resolved "https://registry.yarnpkg.com/is-negative-zero/-/is-negative-zero-2.0.2.tgz#7bf6f03a28003b8b3965de3ac26f664d765f3150" @@ -2524,17 +2474,6 @@ is-symbol@^1.0.2, is-symbol@^1.0.3: dependencies: has-symbols "^1.0.2" -is-typed-array@^1.1.10, is-typed-array@^1.1.3: - version "1.1.10" - resolved "https://registry.yarnpkg.com/is-typed-array/-/is-typed-array-1.1.10.tgz#36a5b5cb4189b575d1a3e4b08536bfb485801e3f" - integrity sha512-PJqgEHiWZvMpaFZ3uTc8kHPM4+4ADTlDniuQL7cU/UDA0Ql7F70yGfHph3cLNe+c9toaigv+DFzTJKhc2CtO6A== - dependencies: - available-typed-arrays "^1.0.5" - call-bind "^1.0.2" - for-each "^0.3.3" - gopd "^1.0.1" - has-tostringtag "^1.0.0" - is-unc-path@^1.0.0: version "1.0.0" resolved "https://registry.yarnpkg.com/is-unc-path/-/is-unc-path-1.0.0.tgz#d731e8898ed090a12c352ad2eaed5095ad322c9d" @@ -3760,14 +3699,6 @@ object-inspect@^1.12.2, object-inspect@^1.9.0: resolved "https://registry.yarnpkg.com/object-inspect/-/object-inspect-1.12.2.tgz#c0641f26394532f28ab8d796ab954e43c009a8ea" integrity sha512-z+cPxW0QGUp0mcqcsgQyLVRDoXFQbXOwBaqyF7VIgI4TWNQsDHrBpUQslRmIfAoYWdYzs6UlKJtB2XJpTaNSpQ== -object-is@^1.0.1: - version "1.1.5" - resolved "https://registry.yarnpkg.com/object-is/-/object-is-1.1.5.tgz#b9deeaa5fc7f1846a0faecdceec138e5778f53ac" - integrity sha512-3cyDsyHgtmi7I7DfSSI2LDp6SK2lwvtbg0p0R1e0RvTqF5ceGx+K2dfSjm1bKDMVCFEDAQvy+o8c6a7VujOddw== - dependencies: - call-bind "^1.0.2" - define-properties "^1.1.3" - object-keys@^1.1.1: version "1.1.1" resolved "https://registry.yarnpkg.com/object-keys/-/object-keys-1.1.1.tgz#1c47f272df277f3b1daf061677d9c82e2322c60e" @@ -4805,17 +4736,6 @@ uri-js@^4.2.2: dependencies: punycode "^2.1.0" -util@^0.12.0: - version "0.12.5" - resolved "https://registry.yarnpkg.com/util/-/util-0.12.5.tgz#5f17a6059b73db61a875668781a1c2b136bd6fbc" - integrity sha512-kZf/K6hEIrWHI6XqOFUiiMa+79wE/D8Q+NCNAWclkyg3b4d2k7s0QGepNjiABc+aR3N1PAyHL7p6UcLY6LmrnA== - dependencies: - inherits "^2.0.3" - is-arguments "^1.0.4" - is-generator-function "^1.0.7" - is-typed-array "^1.1.3" - which-typed-array "^1.1.2" - uuid@^3.3.2: version "3.4.0" resolved "https://registry.yarnpkg.com/uuid/-/uuid-3.4.0.tgz#b23e4358afa8a202fe7a100af1f5f883f02007ee" @@ -4918,18 +4838,6 @@ which-boxed-primitive@^1.0.2: is-string "^1.0.5" is-symbol "^1.0.3" -which-typed-array@^1.1.2: - version "1.1.9" - resolved "https://registry.yarnpkg.com/which-typed-array/-/which-typed-array-1.1.9.tgz#307cf898025848cf995e795e8423c7f337efbde6" - integrity sha512-w9c4xkx6mPidwp7180ckYWfMmvxpjlZuIudNtDf4N/tTAUB8VJbX25qZoAsrtGuYNnGw3pa0AXgbGKRB8/EceA== - dependencies: - available-typed-arrays "^1.0.5" - call-bind "^1.0.2" - for-each "^0.3.3" - gopd "^1.0.1" - has-tostringtag "^1.0.0" - is-typed-array "^1.1.10" - which@^2.0.1: version "2.0.2" resolved "https://registry.yarnpkg.com/which/-/which-2.0.2.tgz#7c6a8dd0a636a0327e10b59c9286eee93f3f51b1" From 84b6d8ee5ffa2aba30ae9ae19a4a62183aea81e7 Mon Sep 17 00:00:00 2001 From: Robert Buels Date: Mon, 3 Apr 2023 12:09:37 -0700 Subject: [PATCH 03/11] missed a nocheck --- src/genomesFile.test.ts | 1 - 1 file changed, 1 deletion(-) diff --git a/src/genomesFile.test.ts b/src/genomesFile.test.ts index 5c4213e..7ef65df 100644 --- a/src/genomesFile.test.ts +++ b/src/genomesFile.test.ts @@ -1,4 +1,3 @@ -// @ts-nocheck import fs from 'fs' import GenomesFile from './genomesFile' From 49ac1fb18b939343cbc4603d032a25fdeaa3733b Mon Sep 17 00:00:00 2001 From: Robert Buels Date: Mon, 3 Apr 2023 12:54:41 -0700 Subject: [PATCH 04/11] start on a singleFileHub class --- src/__snapshots__/singleFileHub.test.ts.snap | 12 ++++++++ src/genomesFile.ts | 7 +---- src/hubFile.test.ts | 7 +---- src/hubFile.ts | 30 ++++---------------- src/raFile.ts | 16 +++++++++-- src/raStanza.ts | 16 +++++++++-- src/singleFileHub.test.ts | 14 +++++++++ src/singleFileHub.ts | 9 ++++++ src/trackDbFile.ts | 1 - 9 files changed, 70 insertions(+), 42 deletions(-) create mode 100644 src/__snapshots__/singleFileHub.test.ts.snap create mode 100644 src/singleFileHub.test.ts create mode 100644 src/singleFileHub.ts diff --git a/src/__snapshots__/singleFileHub.test.ts.snap b/src/__snapshots__/singleFileHub.test.ts.snap new file mode 100644 index 0000000..2470940 --- /dev/null +++ b/src/__snapshots__/singleFileHub.test.ts.snap @@ -0,0 +1,12 @@ +// Jest Snapshot v1, https://goo.gl/fbAQLP + +exports[`singleFileHub reads a basic singleFileAssemblyHub.txt file 1`] = ` +Map { + "hub" => "GCF_000002985.6 genome assembly", + "shortLabel" => "roundworm", + "longLabel" => "roundworm/Caenorhabditis elegans/GCF_000002985.6_WBcel235 genome assembly", + "useOneFile" => "on", + "email" => "hclawson@ucsc.edu", + "descriptionUrl" => "html/GCF_000002985.6_WBcel235.description.html", +} +`; diff --git a/src/genomesFile.ts b/src/genomesFile.ts index b7da3a3..3bb2fe1 100644 --- a/src/genomesFile.ts +++ b/src/genomesFile.ts @@ -8,12 +8,7 @@ import RaFile from './raFile' * with "genome " or if it has invalid entries */ export default class GenomesFile extends RaFile { - constructor(genomesFile: string) { - super(genomesFile) - this.validate() - } - - protected validate() { + public validate() { if (this.nameKey !== 'genome') { throw new Error( 'Genomes file must begin with a line like "genome "', diff --git a/src/hubFile.test.ts b/src/hubFile.test.ts index 5c72928..13c574f 100644 --- a/src/hubFile.test.ts +++ b/src/hubFile.test.ts @@ -12,15 +12,10 @@ describe('HubFile', () => { it("throws if the file doesn't start with a hub entry", () => expect( () => new HubFile('trackHub UCSCHub\nshortLabel UCSC Hub\n'), - ).toThrow(/file must begin with a line like/)) + ).toThrow(/missing required/)) it('throws if a hub is missing a required field', () => expect(() => new HubFile('hub UCSCHub\nshortLabel UCSC Hub\n')).toThrow( /file is missing required entr(y|ies):/, )) - - it('throws if a hub has an invalid field', () => - expect(() => new HubFile('hub UCSCHub\ninvalid invalid Label\n')).toThrow( - /file has invalid entr(y|ies):/, - )) }) diff --git a/src/hubFile.ts b/src/hubFile.ts index 92bfac4..b3e2443 100644 --- a/src/hubFile.ts +++ b/src/hubFile.ts @@ -9,16 +9,9 @@ import RaStanza from './raStanza' * entries */ export default class HubFile extends RaStanza { - constructor(hubFile: string) { - super(hubFile) - this.validate() - } - protected validate() { - if (this.nameKey !== 'hub') { - throw new Error('Hub file must begin with a line like "hub "') - } - const hubTxtFields = [ + const missingFields = [] as string[] + const requiredFields = [ 'hub', 'shortLabel', 'longLabel', @@ -26,22 +19,9 @@ export default class HubFile extends RaStanza { 'email', 'descriptionUrl', ] - const extraFields = [] as string[] - this.forEach((_value, key) => { - if (!hubTxtFields.includes(key)) { - extraFields.push(key) - } - }) - if (extraFields.length > 0) { - throw new Error( - `Hub file has invalid entr${ - extraFields.length === 1 ? 'y' : 'ies' - }: ${extraFields.join(', ')}`, - ) - } - const missingFields = [] as string[] - hubTxtFields.forEach(field => { - if (field !== 'descriptionUrl' && !this.get(field)) { + + requiredFields.forEach(field => { + if (!this.get(field)) { missingFields.push(field) } }) diff --git a/src/raFile.ts b/src/raFile.ts index 6849af5..092f8e9 100644 --- a/src/raFile.ts +++ b/src/raFile.ts @@ -28,10 +28,16 @@ export default class RaFile extends Map { nameKey?: string - constructor(raFile: string | string[] = [], options = { checkIndent: true }) { + constructor( + raFile: string | string[] = [], + options: { checkIndent?: boolean; skipValidation?: boolean } = { + checkIndent: true, + skipValidation: false, + }, + ) { super() const { checkIndent } = options - this._checkIndent = checkIndent + this._checkIndent = !!checkIndent let stanzas: string[] if (typeof raFile === 'string') { stanzas = raFile.trimEnd().split(/(?:[\t ]*\r?\n){2,}/) @@ -44,8 +50,14 @@ export default class RaFile extends Map { stanzas.forEach(stanza => { this.add(stanza) }) + + if (!options.skipValidation) { + this.validate() + } } + protected validate() {} + /** * Add a single stanza to the file * @param {string} stanza A single stanza diff --git a/src/raStanza.ts b/src/raStanza.ts index 957a5a3..2f480ac 100644 --- a/src/raStanza.ts +++ b/src/raStanza.ts @@ -43,10 +43,16 @@ export default class RaStanza extends Map { nameKey?: string - constructor(stanza: string | string[] = [], options = { checkIndent: true }) { + constructor( + stanza: string | string[] = [], + options: { checkIndent?: boolean; skipValidation?: boolean } = { + checkIndent: true, + skipValidation: false, + }, + ) { super() const { checkIndent } = options - this._checkIndent = checkIndent + this._checkIndent = !!checkIndent let stanzaLines: string[] if (typeof stanza === 'string') { stanzaLines = stanza.trimEnd().split(/\r?\n/) @@ -59,8 +65,14 @@ export default class RaStanza extends Map { stanzaLines.forEach(line => { this.add(line) }) + + if (!options.skipValidation) { + this.validate() + } } + protected validate() {} + /** * Add a single line to the stanza. If the exact line already exists, does * nothing. diff --git a/src/singleFileHub.test.ts b/src/singleFileHub.test.ts new file mode 100644 index 0000000..b98d0d9 --- /dev/null +++ b/src/singleFileHub.test.ts @@ -0,0 +1,14 @@ +import fs from 'fs' +import SingleFileHub from './singleFileHub' + +// test that singleFileHub can parse singleFileAssemblyHub.txt +describe('singleFileHub', () => { + it('reads a basic singleFileAssemblyHub.txt file', () => { + const input = fs.readFileSync( + 'test/singleFileAssemblyHub.GCF_000002985.6.hub.txt', + 'utf8', + ) + const singleFileHub = new SingleFileHub(input) + expect(singleFileHub).toMatchSnapshot() + }) +}) diff --git a/src/singleFileHub.ts b/src/singleFileHub.ts new file mode 100644 index 0000000..6c6c127 --- /dev/null +++ b/src/singleFileHub.ts @@ -0,0 +1,9 @@ +import HubFile from './hubFile' + +export default class SingleFileHub extends HubFile { + constructor(singleFileHub: string) { + const stanzas = singleFileHub.trimEnd().split(/(?:[\t ]*\r?\n){2,}/) + const hubSection = stanzas[0] + super(hubSection, { skipValidation: true }) + } +} diff --git a/src/trackDbFile.ts b/src/trackDbFile.ts index 451cf60..91c5046 100644 --- a/src/trackDbFile.ts +++ b/src/trackDbFile.ts @@ -10,7 +10,6 @@ import RaFile from './raFile' export default class TrackDbFile extends RaFile { constructor(trackDbFile: string) { super(trackDbFile, { checkIndent: false }) - this.validate() } protected validate() { From 8ca1a6830966b0b44e80e0d9d383a639dad9c136 Mon Sep 17 00:00:00 2001 From: Robert Buels Date: Mon, 3 Apr 2023 14:20:00 -0700 Subject: [PATCH 05/11] basic single file hub parsing --- src/__snapshots__/singleFileHub.test.ts.snap | 314 +++++++++++++++++++ src/genomesFile.test.ts | 2 +- src/genomesFile.ts | 30 +- src/singleFileHub.test.ts | 2 + src/singleFileHub.ts | 42 ++- src/trackDbFile.ts | 7 +- src/util.ts | 22 ++ 7 files changed, 393 insertions(+), 26 deletions(-) create mode 100644 src/util.ts diff --git a/src/__snapshots__/singleFileHub.test.ts.snap b/src/__snapshots__/singleFileHub.test.ts.snap index 2470940..9bed79c 100644 --- a/src/__snapshots__/singleFileHub.test.ts.snap +++ b/src/__snapshots__/singleFileHub.test.ts.snap @@ -10,3 +10,317 @@ Map { "descriptionUrl" => "html/GCF_000002985.6_WBcel235.description.html", } `; + +exports[`singleFileHub reads a basic singleFileAssemblyHub.txt file 2`] = ` +Map { + "GCF_000002985.6" => Map { + "genome" => "GCF_000002985.6", + "taxId" => "6239", + "groups" => "groups.txt", + "description" => "roundworm", + "twoBitPath" => "GCF_000002985.6.2bit", + "twoBitBptUrl" => "GCF_000002985.6.2bit.bpt", + "chromSizes" => "GCF_000002985.6.chrom.sizes.txt", + "chromAliasBb" => "GCF_000002985.6.chromAlias.bb", + "chromAuthority" => "ucsc", + "organism" => "WBcel235 Feb. 2013", + "defaultPos" => "NC_003283.11:6974726-6984726", + "scientificName" => "Caenorhabditis elegans", + "htmlPath" => "html/GCF_000002985.6_WBcel235.description.html", + "blat" => "dynablat-01.soe.ucsc.edu 4040 dynamic GCF/000/002/985/GCF_000002985.6", + "transBlat" => "dynablat-01.soe.ucsc.edu 4040 dynamic GCF/000/002/985/GCF_000002985.6", + "isPcr" => "dynablat-01.soe.ucsc.edu 4040 dynamic GCF/000/002/985/GCF_000002985.6", + }, +} +`; + +exports[`singleFileHub reads a basic singleFileAssemblyHub.txt file 3`] = ` +[ + Map { + "assembly" => Map { + "track" => "assembly", + "longLabel" => "Assembly", + "shortLabel" => "Assembly", + "visibility" => "pack", + "colorByStrand" => "150,100,30 230,170,40", + "color" => "150,100,30", + "altColor" => "230,170,40", + "bigDataUrl" => "bbi/GCF_000002985.6_WBcel235.assembly.bb", + "type" => "bigBed 6", + "html" => "html/GCF_000002985.6_WBcel235.assembly", + "searchIndex" => "name", + "searchTrix" => "ixIxx/GCF_000002985.6_WBcel235.assembly.ix", + "url" => "https://www.ncbi.nlm.nih.gov/nuccore/$$", + "urlLabel" => "NCBI Nucleotide database:", + "group" => "map", + }, + }, + Map { + "cytoBandIdeo" => Map { + "track" => "cytoBandIdeo", + "shortLabel" => "Chromosome Band (Ideogram)", + "longLabel" => "Ideogram for Orientation", + "group" => "map", + "visibility" => "dense", + "type" => "bigBed 4 +", + "bigDataUrl" => "bbi/GCF_000002985.6_WBcel235.cytoBand.bb", + }, + }, + Map { + "gc5Base" => Map { + "track" => "gc5Base", + "shortLabel" => "GC Percent", + "longLabel" => "GC Percent in 5-Base Windows", + "group" => "map", + "visibility" => "full", + "autoScale" => "Off", + "maxHeightPixels" => "128:36:16", + "graphTypeDefault" => "Bar", + "gridDefault" => "OFF", + "windowingFunction" => "Mean", + "color" => "0,0,0", + "altColor" => "128,128,128", + "viewLimits" => "30:70", + "type" => "bigWig 0 100", + "bigDataUrl" => "bbi/GCF_000002985.6_WBcel235.gc5Base.bw", + "html" => "html/GCF_000002985.6_WBcel235.gc5Base", + }, + }, + Map { + "tanDups" => Map { + "track" => "tanDups", + "shortLabel" => "Tandem Dups", + "longLabel" => "Paired identical sequences", + "compositeTrack" => "on", + "visibility" => "hide", + "type" => "bigBed 12", + "group" => "map", + "html" => "html/GCF_000002985.6_WBcel235.tanDups", + }, + }, + Map { + "tandemDups" => Map { + "track" => "tandemDups", + "parent" => "tanDups on", + "shortLabel" => "Tandem Dups", + "longLabel" => "Paired exactly identical sequence survey over entire genome assembly", + "bigDataUrl" => "bbi/GCF_000002985.6_WBcel235.tandemDups.bb", + "type" => "bigBed 12", + }, + }, + Map { + "repeatMasker" => Map { + "track" => "repeatMasker", + "shortLabel" => "RepeatMasker", + "longLabel" => "RepeatMasker Repetitive Elements", + "type" => "bigRmsk 9 +", + "visibility" => "pack", + "group" => "varRep", + "bigDataUrl" => "bbi/GCF_000002985.6_WBcel235.rmsk.bb", + "maxWindowToDraw" => "5000000", + "html" => "html/GCF_000002985.6_WBcel235.repeatMasker", + }, + }, + Map { + "simpleRepeat" => Map { + "track" => "simpleRepeat", + "shortLabel" => "Simple Repeats", + "longLabel" => "Simple Tandem Repeats by TRF", + "group" => "varRep", + "visibility" => "dense", + "type" => "bigBed 4 +", + "bigDataUrl" => "bbi/GCF_000002985.6_WBcel235.simpleRepeat.bb", + "html" => "html/GCF_000002985.6_WBcel235.simpleRepeat", + }, + }, + Map { + "refSeqComposite" => Map { + "track" => "refSeqComposite", + "compositeTrack" => "on", + "shortLabel" => "NCBI RefSeq", + "longLabel" => "RefSeq gene predictions from NCBI", + "group" => "genes", + "visibility" => "pack", + "type" => "bigBed", + "dragAndDrop" => "subTracks", + "allButtonPair" => "on", + "dataVersion" => "WormBase WS277 (2020-05-29)", + "html" => "html/GCF_000002985.6_WBcel235.refSeqComposite", + "priority" => "2", + }, + }, + Map { + "ncbiRefSeq" => Map { + "track" => "ncbiRefSeq", + "parent" => "refSeqComposite on", + "color" => "12,12,120", + "altColor" => "120,12,12", + "shortLabel" => "RefSeq All", + "type" => "bigGenePred", + "labelFields" => "name,geneName,geneName2", + "defaultLabelFields" => "geneName2", + "searchIndex" => "name", + "searchTrix" => "ixIxx/GCF_000002985.6_WBcel235.ncbiRefSeq.ix", + "bigDataUrl" => "bbi/GCF_000002985.6_WBcel235.ncbiRefSeq.bb", + "longLabel" => "NCBI RefSeq genes, curated and predicted sets (NM_*, XM_*, NR_*, XR_*, NP_* or YP_*)", + "idXref" => "ncbiRefSeqLink mrnaAcc name", + "baseColorUseCds" => "given", + "baseColorDefault" => "genomicCodons", + "priority" => "1", + }, + }, + Map { + "ncbiRefSeqCurated" => Map { + "track" => "ncbiRefSeqCurated", + "color" => "12,12,120", + "parent" => "refSeqComposite on", + "shortLabel" => "RefSeq Curated", + "longLabel" => "NCBI RefSeq genes, curated subset (NM_*, NR_*, NP_* or YP_*)", + "type" => "bigGenePred", + "labelFields" => "name,geneName,geneName2", + "defaultLabelFields" => "geneName2", + "searchIndex" => "name", + "searchTrix" => "ixIxx/GCF_000002985.6_WBcel235.ncbiRefSeqCurated.ix", + "idXref" => "ncbiRefSeqLink mrnaAcc name", + "bigDataUrl" => "bbi/GCF_000002985.6_WBcel235.ncbiRefSeqCurated.bb", + "baseColorUseCds" => "given", + "baseColorDefault" => "genomicCodons", + "priority" => "2", + }, + }, + Map { + "ncbiRefSeqOther" => Map { + "track" => "ncbiRefSeqOther", + "color" => "32,32,32", + "parent" => "refSeqComposite on", + "shortLabel" => "RefSeq Other", + "longLabel" => "NCBI RefSeq other annotations (not NM_*, NR_*, XM_*, XR_*, NP_* or YP_*)", + "priority" => "4", + "searchIndex" => "name", + "searchTrix" => "ixIxx/GCF_000002985.6_WBcel235.ncbiRefSeqOther.ix", + "bigDataUrl" => "bbi/GCF_000002985.6_WBcel235.ncbiRefSeqOther.bb", + "type" => "bigBed 12 +", + "labelFields" => "name", + "skipEmptyFields" => "on", + "urls" => "GeneID="https://www.ncbi.nlm.nih.gov/gene/$$" MIM="https://www.ncbi.nlm.nih.gov/omim/$$" HGNC="http://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=$$" FlyBase="http://flybase.org/reports/$$" WormBase="http://www.wormbase.org/db/gene/gene?name=$$" RGD="https://rgd.mcw.edu/rgdweb/search/search.html?term=$$" SGD="https://www.yeastgenome.org/locus/$$" miRBase="http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$$" ZFIN="https://zfin.org/$$" MGI="http://www.informatics.jax.org/marker/$$"", + }, + }, + Map { + "ncbiRefSeqPsl" => Map { + "track" => "ncbiRefSeqPsl", + "priority" => "5", + "parent" => "refSeqComposite off", + "shortLabel" => "RefSeq Alignments", + "longLabel" => "RefSeq Alignments of RNAs", + "type" => "bigPsl", + "searchIndex" => "name", + "bigDataUrl" => "bbi/GCF_000002985.6_WBcel235.bigPsl.bb", + "indelDoubleInsert" => "on", + "indelQueryInsert" => "on", + "showDiffBasesAllScales" => ".", + "showDiffBasesMaxZoom" => "10000.0", + "showCdsMaxZoom" => "10000.0", + "showCdsAllScales" => ".", + "baseColorDefault" => "diffCodons", + "pslSequence" => "no", + "baseColorUseSequence" => "lfExtra", + "baseColorUseCds" => "table given", + "color" => "0,0,0", + }, + }, + Map { + "cpgIslands" => Map { + "track" => "cpgIslands", + "compositeTrack" => "on", + "shortLabel" => "CpG Islands", + "longLabel" => "CpG Islands (Islands < 300 Bases are Light Green)", + "group" => "regulation", + "visibility" => "pack", + "type" => "bigBed 4 +", + "html" => "html/GCF_000002985.6_WBcel235.cpgIslands", + }, + }, + Map { + "cpgIslandExt" => Map { + "track" => "cpgIslandExt", + "parent" => "cpgIslands off", + "shortLabel" => "CpG Islands", + "longLabel" => "CpG Islands (Islands < 300 Bases are Light Green)", + "type" => "bigBed 4 +", + "priority" => "1", + "bigDataUrl" => "bbi/GCF_000002985.6_WBcel235.cpgIslandExt.bb", + }, + }, + Map { + "cpgIslandExtUnmasked" => Map { + "track" => "cpgIslandExtUnmasked", + "parent" => "cpgIslands on", + "shortLabel" => "Unmasked CpG", + "longLabel" => "CpG Islands on All Sequence (Islands < 300 Bases are Light Green)", + "type" => "bigBed 4 +", + "priority" => "2", + "bigDataUrl" => "bbi/GCF_000002985.6_WBcel235.cpgIslandExtUnmasked.bb", + }, + }, + Map { + "windowMasker" => Map { + "track" => "windowMasker", + "shortLabel" => "WM + SDust", + "longLabel" => "Genomic Intervals Masked by WindowMasker + SDust", + "group" => "varRep", + "visibility" => "dense", + "type" => "bigBed 3", + "bigDataUrl" => "bbi/GCF_000002985.6_WBcel235.windowMasker.bb", + "html" => "html/GCF_000002985.6_WBcel235.windowMasker", + }, + }, + Map { + "augustus" => Map { + "track" => "augustus", + "shortLabel" => "Augustus", + "longLabel" => "Augustus Gene Predictions", + "group" => "genes", + "visibility" => "dense", + "color" => "180,0,0", + "type" => "bigGenePred", + "bigDataUrl" => "bbi/GCF_000002985.6_WBcel235.augustus.bb", + "html" => "html/GCF_000002985.6_WBcel235.augustus", + }, + }, + Map { + "xenoRefGene" => Map { + "track" => "xenoRefGene", + "shortLabel" => "RefSeq mRNAs", + "longLabel" => "RefSeq mRNAs mapped to this assembly", + "group" => "rna", + "visibility" => "pack", + "color" => "180,0,0", + "type" => "bigGenePred", + "bigDataUrl" => "bbi/GCF_000002985.6_WBcel235.xenoRefGene.bb", + "url" => "https://www.ncbi.nlm.nih.gov/nuccore/$$", + "urlLabel" => "NCBI Nucleotide database:", + "labelFields" => "name,geneName,geneName2", + "defaultLabelFields" => "geneName", + "searchIndex" => "name", + "searchTrix" => "ixIxx/GCF_000002985.6_WBcel235.xenoRefGene.ix", + "html" => "html/GCF_000002985.6_WBcel235.xenoRefGene", + }, + }, + Map { + "ensGene" => Map { + "track" => "ensGene", + "shortLabel" => "Ensembl genes", + "longLabel" => "Ensembl genes version 103/Feb. 2021", + "group" => "genes", + "priority" => "40", + "visibility" => "pack", + "color" => "150,0,0", + "type" => "bigBed 12 .", + "bigDataUrl" => "bbi/GCF_000002985.6_WBcel235.ensGene.bb", + "searchIndex" => "name", + "searchTrix" => "ixIxx/GCF_000002985.6_WBcel235.ensGene.ix", + "html" => "html/GCF_000002985.6_WBcel235.ensGene", + }, + }, +] +`; diff --git a/src/genomesFile.test.ts b/src/genomesFile.test.ts index 7ef65df..db89072 100644 --- a/src/genomesFile.test.ts +++ b/src/genomesFile.test.ts @@ -20,5 +20,5 @@ describe('GenomesFile', () => { new GenomesFile( 'genome hg19\ntrackDb hg19/trackDb.txt\n\ngenome hg38\norganism Homo sapiens', ), - ).toThrow(/file entry .* is missing required entry:/)) + ).toThrow(/is missing required entry:/)) }) diff --git a/src/genomesFile.ts b/src/genomesFile.ts index 3bb2fe1..96c16b8 100644 --- a/src/genomesFile.ts +++ b/src/genomesFile.ts @@ -1,4 +1,5 @@ import RaFile from './raFile' +import { validateRequiredFieldsArePresent } from './util' /** * Class representing a genomes.txt file. @@ -8,34 +9,21 @@ import RaFile from './raFile' * with "genome " or if it has invalid entries */ export default class GenomesFile extends RaFile { - public validate() { + public validate(requiredFields = ['genome', 'trackDb']) { + // TODO: check if genome is hosted by UCSC and if not, require twoBitPath and groups + if (this.nameKey !== 'genome') { throw new Error( 'Genomes file must begin with a line like "genome "', ) } - // TODO: check if genome is hosted by UCSC and if not, require twoBitPath and groups - const requiredFields = [ - 'genome', - 'trackDb', - // 'twoBitPath', - // 'groups', - ] this.forEach((genome, genomeName) => { - const missingFields = [] as string[] - requiredFields.forEach(field => { - if (!genome.get(field)) { - missingFields.push(field) - } - }) - if (missingFields.length > 0) { - throw new Error( - `Genomes file entry ${genomeName} is missing required entr${ - missingFields.length === 1 ? 'y' : 'ies' - }: ${missingFields.join(', ')}`, - ) - } + validateRequiredFieldsArePresent( + genome, + requiredFields, + `genome ${genomeName}`, + ) }) } } diff --git a/src/singleFileHub.test.ts b/src/singleFileHub.test.ts index b98d0d9..577ae6d 100644 --- a/src/singleFileHub.test.ts +++ b/src/singleFileHub.test.ts @@ -10,5 +10,7 @@ describe('singleFileHub', () => { ) const singleFileHub = new SingleFileHub(input) expect(singleFileHub).toMatchSnapshot() + expect(singleFileHub.genome).toMatchSnapshot() + expect(singleFileHub.tracks).toMatchSnapshot() }) }) diff --git a/src/singleFileHub.ts b/src/singleFileHub.ts index 6c6c127..eb64211 100644 --- a/src/singleFileHub.ts +++ b/src/singleFileHub.ts @@ -1,9 +1,47 @@ +import GenomesFile from './genomesFile' import HubFile from './hubFile' +import TrackDbFile from './trackDbFile' +import { validateRequiredFieldsArePresent } from './util' export default class SingleFileHub extends HubFile { + public genome: GenomesFile + + public tracks: TrackDbFile[] + constructor(singleFileHub: string) { - const stanzas = singleFileHub.trimEnd().split(/(?:[\t ]*\r?\n){2,}/) - const hubSection = stanzas[0] + const [hubSection, genomeSection, ...trackSections] = singleFileHub + .trimEnd() + .split(/(?:[\t ]*\r?\n){2,}/) super(hubSection, { skipValidation: true }) + this.validateHub() + + this.genome = new GenomesFile(genomeSection, { skipValidation: true }) + this.validateGenomeSection() + + this.tracks = trackSections.map( + trackSection => new TrackDbFile(trackSection, { skipValidation: false }), + ) + } + + protected validateHub() { + if (this.nameKey !== 'hub') { + throw new Error('Hub file must begin with a line like "hub "') + } + + validateRequiredFieldsArePresent(this, [ + 'hub', + 'shortLabel', + 'longLabel', + 'email', + 'descriptionUrl', + ]) + } + + protected validateGenomeSection() { + if (this.genome.nameKey !== 'genome') { + throw new Error( + 'Genomes file must begin with a line like "genome "', + ) + } } } diff --git a/src/trackDbFile.ts b/src/trackDbFile.ts index 91c5046..f789aab 100644 --- a/src/trackDbFile.ts +++ b/src/trackDbFile.ts @@ -8,8 +8,11 @@ import RaFile from './raFile' * track is missing required keys */ export default class TrackDbFile extends RaFile { - constructor(trackDbFile: string) { - super(trackDbFile, { checkIndent: false }) + constructor( + trackDbFile: string, + options?: ConstructorParameters[1], + ) { + super(trackDbFile, { ...options, checkIndent: false }) } protected validate() { diff --git a/src/util.ts b/src/util.ts new file mode 100644 index 0000000..573892c --- /dev/null +++ b/src/util.ts @@ -0,0 +1,22 @@ +import RaStanza from './raStanza' + +// validate that all required fields are present in the map +export function validateRequiredFieldsArePresent( + map: RaStanza, + requiredFields: string[], + description = '', +) { + const missingFields: string[] = [] + requiredFields.forEach(field => { + if (!map.get(field)) { + missingFields.push(field) + } + }) + if (missingFields.length > 0) { + throw new Error( + `${description} is missing required entr${ + missingFields.length === 1 ? 'y' : 'ies' + }: ${missingFields.join(', ')}`, + ) + } +} From 5165aa4cb4fcaf765a63102c0ce811ac9b44adf6 Mon Sep 17 00:00:00 2001 From: Robert Buels Date: Tue, 4 Apr 2023 09:21:20 -0700 Subject: [PATCH 06/11] single file hub round tripping works --- src/__snapshots__/raFile.test.ts.snap | 5 + src/__snapshots__/singleFileHub.test.ts.snap | 6 +- src/index.ts | 3 +- src/raFile.test.ts | 7 +- src/singleFileHub.test.ts | 6 +- src/singleFileHub.ts | 8 ++ test/indented.ra | 4 + ...gleFileAssemblyHub.GCF_000002985.6.hub.txt | 133 +++++++++--------- 8 files changed, 99 insertions(+), 73 deletions(-) diff --git a/src/__snapshots__/raFile.test.ts.snap b/src/__snapshots__/raFile.test.ts.snap index 6c2ee64..c296273 100644 --- a/src/__snapshots__/raFile.test.ts.snap +++ b/src/__snapshots__/raFile.test.ts.snap @@ -72,6 +72,11 @@ Map { "key2" => "valH", "key3" => "valI", }, + "Foot" => Map { + "key1" => "Foot", + "key2" => "Ankle", + "key3" => "Knee", + }, } `; diff --git a/src/__snapshots__/singleFileHub.test.ts.snap b/src/__snapshots__/singleFileHub.test.ts.snap index 9bed79c..f6ad692 100644 --- a/src/__snapshots__/singleFileHub.test.ts.snap +++ b/src/__snapshots__/singleFileHub.test.ts.snap @@ -1,6 +1,6 @@ // Jest Snapshot v1, https://goo.gl/fbAQLP -exports[`singleFileHub reads a basic singleFileAssemblyHub.txt file 1`] = ` +exports[`singleFileHub losslessly roundtrips a full single-file hub 1`] = ` Map { "hub" => "GCF_000002985.6 genome assembly", "shortLabel" => "roundworm", @@ -11,7 +11,7 @@ Map { } `; -exports[`singleFileHub reads a basic singleFileAssemblyHub.txt file 2`] = ` +exports[`singleFileHub losslessly roundtrips a full single-file hub 2`] = ` Map { "GCF_000002985.6" => Map { "genome" => "GCF_000002985.6", @@ -34,7 +34,7 @@ Map { } `; -exports[`singleFileHub reads a basic singleFileAssemblyHub.txt file 3`] = ` +exports[`singleFileHub losslessly roundtrips a full single-file hub 3`] = ` [ Map { "assembly" => Map { diff --git a/src/index.ts b/src/index.ts index be73791..126fca9 100644 --- a/src/index.ts +++ b/src/index.ts @@ -3,5 +3,6 @@ import RaStanza from './raStanza' import TrackDbFile from './trackDbFile' import HubFile from './hubFile' import GenomesFile from './genomesFile' +import SingleFileHub from './singleFileHub' -export { RaFile, RaStanza, TrackDbFile, HubFile, GenomesFile } +export { RaFile, RaStanza, TrackDbFile, HubFile, GenomesFile, SingleFileHub } diff --git a/src/raFile.test.ts b/src/raFile.test.ts index edef563..839d749 100644 --- a/src/raFile.test.ts +++ b/src/raFile.test.ts @@ -90,7 +90,12 @@ describe('RaFile reader', () => { const input = fs.readFileSync('test/indented.ra', 'utf8') const raFile = new RaFile(input) expect(raFile).toMatchSnapshot() - expect(raFile._stanzaAndCommentOrder).toEqual(['valA', 'valD', 'valG']) + expect(raFile._stanzaAndCommentOrder).toEqual([ + 'valA', + 'valD', + 'valG', + 'Foot', + ]) expect(raFile.nameKey).toEqual('key1') expect(raFile.toString()).toEqual(input) }) diff --git a/src/singleFileHub.test.ts b/src/singleFileHub.test.ts index 577ae6d..d448426 100644 --- a/src/singleFileHub.test.ts +++ b/src/singleFileHub.test.ts @@ -3,7 +3,9 @@ import SingleFileHub from './singleFileHub' // test that singleFileHub can parse singleFileAssemblyHub.txt describe('singleFileHub', () => { - it('reads a basic singleFileAssemblyHub.txt file', () => { + it('roundtrips a full single-file hub', () => { + // NOTE: this file was slightly modified from the + // original to fix inconsistent indentation const input = fs.readFileSync( 'test/singleFileAssemblyHub.GCF_000002985.6.hub.txt', 'utf8', @@ -12,5 +14,7 @@ describe('singleFileHub', () => { expect(singleFileHub).toMatchSnapshot() expect(singleFileHub.genome).toMatchSnapshot() expect(singleFileHub.tracks).toMatchSnapshot() + + expect(singleFileHub.toString()).toEqual(input) }) }) diff --git a/src/singleFileHub.ts b/src/singleFileHub.ts index eb64211..396395f 100644 --- a/src/singleFileHub.ts +++ b/src/singleFileHub.ts @@ -44,4 +44,12 @@ export default class SingleFileHub extends HubFile { ) } } + + public toString() { + return [ + super.toString(), + this.genome.toString(), + ...this.tracks.map(track => track.toString()), + ].join('\n') + } } diff --git a/test/indented.ra b/test/indented.ra index 11db48c..5da24b4 100644 --- a/test/indented.ra +++ b/test/indented.ra @@ -10,3 +10,7 @@ key3 valC key1 valG key2 valH key3 valI + + key1 Foot + key2 Ankle + key3 Knee diff --git a/test/singleFileAssemblyHub.GCF_000002985.6.hub.txt b/test/singleFileAssemblyHub.GCF_000002985.6.hub.txt index fcbe317..bc359e5 100644 --- a/test/singleFileAssemblyHub.GCF_000002985.6.hub.txt +++ b/test/singleFileAssemblyHub.GCF_000002985.6.hub.txt @@ -111,72 +111,72 @@ dataVersion WormBase WS277 (2020-05-29) html html/GCF_000002985.6_WBcel235.refSeqComposite priority 2 - track ncbiRefSeq - parent refSeqComposite on - color 12,12,120 - altColor 120,12,12 - shortLabel RefSeq All - type bigGenePred - labelFields name,geneName,geneName2 - defaultLabelFields geneName2 - searchIndex name - searchTrix ixIxx/GCF_000002985.6_WBcel235.ncbiRefSeq.ix - bigDataUrl bbi/GCF_000002985.6_WBcel235.ncbiRefSeq.bb - longLabel NCBI RefSeq genes, curated and predicted sets (NM_*, XM_*, NR_*, XR_*, NP_* or YP_*) - idXref ncbiRefSeqLink mrnaAcc name - baseColorUseCds given - baseColorDefault genomicCodons - priority 1 - - track ncbiRefSeqCurated - color 12,12,120 - parent refSeqComposite on - shortLabel RefSeq Curated - longLabel NCBI RefSeq genes, curated subset (NM_*, NR_*, NP_* or YP_*) - type bigGenePred - labelFields name,geneName,geneName2 - defaultLabelFields geneName2 - searchIndex name - searchTrix ixIxx/GCF_000002985.6_WBcel235.ncbiRefSeqCurated.ix - idXref ncbiRefSeqLink mrnaAcc name - bigDataUrl bbi/GCF_000002985.6_WBcel235.ncbiRefSeqCurated.bb - baseColorUseCds given - baseColorDefault genomicCodons - priority 2 - - track ncbiRefSeqOther - color 32,32,32 - parent refSeqComposite on - shortLabel RefSeq Other - longLabel NCBI RefSeq other annotations (not NM_*, NR_*, XM_*, XR_*, NP_* or YP_*) - priority 4 - searchIndex name - searchTrix ixIxx/GCF_000002985.6_WBcel235.ncbiRefSeqOther.ix - bigDataUrl bbi/GCF_000002985.6_WBcel235.ncbiRefSeqOther.bb - type bigBed 12 + - labelFields name - skipEmptyFields on - urls GeneID="https://www.ncbi.nlm.nih.gov/gene/$$" MIM="https://www.ncbi.nlm.nih.gov/omim/$$" HGNC="http://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=$$" FlyBase="http://flybase.org/reports/$$" WormBase="http://www.wormbase.org/db/gene/gene?name=$$" RGD="https://rgd.mcw.edu/rgdweb/search/search.html?term=$$" SGD="https://www.yeastgenome.org/locus/$$" miRBase="http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$$" ZFIN="https://zfin.org/$$" MGI="http://www.informatics.jax.org/marker/$$" - - track ncbiRefSeqPsl - priority 5 - parent refSeqComposite off - shortLabel RefSeq Alignments - longLabel RefSeq Alignments of RNAs - type bigPsl - searchIndex name - bigDataUrl bbi/GCF_000002985.6_WBcel235.bigPsl.bb - indelDoubleInsert on - indelQueryInsert on - showDiffBasesAllScales . - showDiffBasesMaxZoom 10000.0 - showCdsMaxZoom 10000.0 - showCdsAllScales . - baseColorDefault diffCodons - pslSequence no - baseColorUseSequence lfExtra - baseColorUseCds table given - color 0,0,0 + track ncbiRefSeq + parent refSeqComposite on + color 12,12,120 + altColor 120,12,12 + shortLabel RefSeq All + type bigGenePred + labelFields name,geneName,geneName2 + defaultLabelFields geneName2 + searchIndex name + searchTrix ixIxx/GCF_000002985.6_WBcel235.ncbiRefSeq.ix + bigDataUrl bbi/GCF_000002985.6_WBcel235.ncbiRefSeq.bb + longLabel NCBI RefSeq genes, curated and predicted sets (NM_*, XM_*, NR_*, XR_*, NP_* or YP_*) + idXref ncbiRefSeqLink mrnaAcc name + baseColorUseCds given + baseColorDefault genomicCodons + priority 1 + + track ncbiRefSeqCurated + color 12,12,120 + parent refSeqComposite on + shortLabel RefSeq Curated + longLabel NCBI RefSeq genes, curated subset (NM_*, NR_*, NP_* or YP_*) + type bigGenePred + labelFields name,geneName,geneName2 + defaultLabelFields geneName2 + searchIndex name + searchTrix ixIxx/GCF_000002985.6_WBcel235.ncbiRefSeqCurated.ix + idXref ncbiRefSeqLink mrnaAcc name + bigDataUrl bbi/GCF_000002985.6_WBcel235.ncbiRefSeqCurated.bb + baseColorUseCds given + baseColorDefault genomicCodons + priority 2 + + track ncbiRefSeqOther + color 32,32,32 + parent refSeqComposite on + shortLabel RefSeq Other + longLabel NCBI RefSeq other annotations (not NM_*, NR_*, XM_*, XR_*, NP_* or YP_*) + priority 4 + searchIndex name + searchTrix ixIxx/GCF_000002985.6_WBcel235.ncbiRefSeqOther.ix + bigDataUrl bbi/GCF_000002985.6_WBcel235.ncbiRefSeqOther.bb + type bigBed 12 + + labelFields name + skipEmptyFields on + urls GeneID="https://www.ncbi.nlm.nih.gov/gene/$$" MIM="https://www.ncbi.nlm.nih.gov/omim/$$" HGNC="http://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=$$" FlyBase="http://flybase.org/reports/$$" WormBase="http://www.wormbase.org/db/gene/gene?name=$$" RGD="https://rgd.mcw.edu/rgdweb/search/search.html?term=$$" SGD="https://www.yeastgenome.org/locus/$$" miRBase="http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$$" ZFIN="https://zfin.org/$$" MGI="http://www.informatics.jax.org/marker/$$" + + track ncbiRefSeqPsl + priority 5 + parent refSeqComposite off + shortLabel RefSeq Alignments + longLabel RefSeq Alignments of RNAs + type bigPsl + searchIndex name + bigDataUrl bbi/GCF_000002985.6_WBcel235.bigPsl.bb + indelDoubleInsert on + indelQueryInsert on + showDiffBasesAllScales . + showDiffBasesMaxZoom 10000.0 + showCdsMaxZoom 10000.0 + showCdsAllScales . + baseColorDefault diffCodons + pslSequence no + baseColorUseSequence lfExtra + baseColorUseCds table given + color 0,0,0 track cpgIslands compositeTrack on @@ -250,4 +250,3 @@ bigDataUrl bbi/GCF_000002985.6_WBcel235.ensGene.bb searchIndex name searchTrix ixIxx/GCF_000002985.6_WBcel235.ensGene.ix html html/GCF_000002985.6_WBcel235.ensGene - From 49f7233e5da69649d75c0662603bd01cd4bb7beb Mon Sep 17 00:00:00 2001 From: Robert Buels Date: Tue, 4 Apr 2023 09:21:57 -0700 Subject: [PATCH 07/11] bump minor version --- package.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/package.json b/package.json index 3d978dc..3539201 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "@gmod/ucsc-hub", - "version": "0.1.7", + "version": "0.2.0", "description": "Read and write UCSC track and assembly hub files in node or the browser", "license": "MIT", "repository": "github:GMOD/ucsc-hub-js", From f68e4a52b59281b6098664e1b0d134a89344dc9e Mon Sep 17 00:00:00 2001 From: Robert Buels Date: Tue, 4 Apr 2023 09:26:11 -0700 Subject: [PATCH 08/11] rename SingleFileHub tracks -> trackDbs --- src/__snapshots__/singleFileHub.test.ts.snap | 6 +++--- src/singleFileHub.test.ts | 2 +- src/singleFileHub.ts | 6 +++--- 3 files changed, 7 insertions(+), 7 deletions(-) diff --git a/src/__snapshots__/singleFileHub.test.ts.snap b/src/__snapshots__/singleFileHub.test.ts.snap index f6ad692..6f18bfe 100644 --- a/src/__snapshots__/singleFileHub.test.ts.snap +++ b/src/__snapshots__/singleFileHub.test.ts.snap @@ -1,6 +1,6 @@ // Jest Snapshot v1, https://goo.gl/fbAQLP -exports[`singleFileHub losslessly roundtrips a full single-file hub 1`] = ` +exports[`singleFileHub roundtrips a full single-file hub 1`] = ` Map { "hub" => "GCF_000002985.6 genome assembly", "shortLabel" => "roundworm", @@ -11,7 +11,7 @@ Map { } `; -exports[`singleFileHub losslessly roundtrips a full single-file hub 2`] = ` +exports[`singleFileHub roundtrips a full single-file hub 2`] = ` Map { "GCF_000002985.6" => Map { "genome" => "GCF_000002985.6", @@ -34,7 +34,7 @@ Map { } `; -exports[`singleFileHub losslessly roundtrips a full single-file hub 3`] = ` +exports[`singleFileHub roundtrips a full single-file hub 3`] = ` [ Map { "assembly" => Map { diff --git a/src/singleFileHub.test.ts b/src/singleFileHub.test.ts index d448426..b93d0f1 100644 --- a/src/singleFileHub.test.ts +++ b/src/singleFileHub.test.ts @@ -13,7 +13,7 @@ describe('singleFileHub', () => { const singleFileHub = new SingleFileHub(input) expect(singleFileHub).toMatchSnapshot() expect(singleFileHub.genome).toMatchSnapshot() - expect(singleFileHub.tracks).toMatchSnapshot() + expect(singleFileHub.trackDbs).toMatchSnapshot() expect(singleFileHub.toString()).toEqual(input) }) diff --git a/src/singleFileHub.ts b/src/singleFileHub.ts index 396395f..52ea44f 100644 --- a/src/singleFileHub.ts +++ b/src/singleFileHub.ts @@ -6,7 +6,7 @@ import { validateRequiredFieldsArePresent } from './util' export default class SingleFileHub extends HubFile { public genome: GenomesFile - public tracks: TrackDbFile[] + public trackDbs: TrackDbFile[] constructor(singleFileHub: string) { const [hubSection, genomeSection, ...trackSections] = singleFileHub @@ -18,7 +18,7 @@ export default class SingleFileHub extends HubFile { this.genome = new GenomesFile(genomeSection, { skipValidation: true }) this.validateGenomeSection() - this.tracks = trackSections.map( + this.trackDbs = trackSections.map( trackSection => new TrackDbFile(trackSection, { skipValidation: false }), ) } @@ -49,7 +49,7 @@ export default class SingleFileHub extends HubFile { return [ super.toString(), this.genome.toString(), - ...this.tracks.map(track => track.toString()), + ...this.trackDbs.map(track => track.toString()), ].join('\n') } } From 02bf1e3a81f8b9d7230d2a9ac8e0180ef8985af7 Mon Sep 17 00:00:00 2001 From: Robert Buels Date: Tue, 4 Apr 2023 09:44:06 -0700 Subject: [PATCH 09/11] update docs --- README.md | 61 ++++++++++++++++++++++++++++++++++++++++---- src/singleFileHub.ts | 18 ++++++++++--- 2 files changed, 70 insertions(+), 9 deletions(-) diff --git a/README.md b/README.md index 6443c73..8393cee 100644 --- a/README.md +++ b/README.md @@ -66,7 +66,7 @@ values of the first line of each section and the value is a `Map` of the lines i }, } -Example usage: +Example usage for a "standard" multi-file hub: ```javascript const fs = require('fs') @@ -85,6 +85,24 @@ console.log(trackDbFile.get('dnaseSignal').get('shortLabel')) // ↳ DNAse Signal ``` +Example usage for a single-file hub: + +```javascript +const fs = require('fs') +const { SingleFileHub } = require('@gmod/ucsc-hub') + +const hubFile = new HubFile(fs.readFileSync('hub.txt', 'utf8')) +console.log(hubFile.get('genomesFile')) +// ↳ genomes.txt + +const genomesFile = new GenomesFile(fs.readFileSync('genomes.txt', 'utf8')) +console.log(genomesFile.get('hg19').get('trackDb')) +// ↳ hg19/trackDb.txt + +const trackDbFile = new TrackDbFile(fs.readFileSync('hg19/trackDb.txt', 'utf8')) +console.log(trackDbFile.get('dnaseSignal').get('shortLabel')) +``` + ## API @@ -117,10 +135,14 @@ console.log(trackDbFile.get('dnaseSignal').get('shortLabel')) * [Parameters](#parameters-9) * [clear](#clear-1) * [toString](#tostring-1) -* [TrackDbFile](#trackdbfile) +* [SingleFileHub](#singlefilehub) * [Parameters](#parameters-10) + * [genome](#genome) + * [trackDbs](#trackdbs) +* [TrackDbFile](#trackdbfile) + * [Parameters](#parameters-11) * [settings](#settings) - * [Parameters](#parameters-11) + * [Parameters](#parameters-12) ### GenomesFile @@ -170,7 +192,7 @@ as it performs more validity checks than using `set()`. * `raFile` **([string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String) | [Array](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Array)<[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)>)** An ra file, either as a single string or an array of strings with one stanza per entry. Supports both LF and CRLF line terminators. (optional, default `[]`) -* `options` **[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)** (optional, default `{checkIndent:true}`) +* `options` **[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)** (optional, default `{checkIndent:true,skipValidation:false}`) * `options.checkIndent` **[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)** \[true] - Check if a the stanzas within the file are indented consistently and keep track of the indentation @@ -246,7 +268,7 @@ than using `set()`. * `stanza` **([string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String) | [Array](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Array)<[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)>)** An ra file stanza, either as a string or a array of strings with one line per entry. Supports both LF and CRLF line terminators. (optional, default `[]`) -* `options` **[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)** (optional, default `{checkIndent:true}`) +* `options` **[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)** (optional, default `{checkIndent:true,skipValidation:false}`) * `options.checkIndent` **[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)** \[true] - Check if a stanza is indented consistently and keep track of the indentation @@ -314,6 +336,34 @@ as a single line and all comments will have the same indentations as the rest of the stanza. Comments between joined lines will move before that line. +### SingleFileHub + +**Extends RaFile** + +Class representing a "single-file" hub.txt file that contains all the sections +of a hub in a single file. + +#### Parameters + +* `hubText` **([string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String) | [Array](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Array)<[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)>)** A hub.txt file as a string (optional, default `[]`) + + + +* Throws **[Error](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Error)** Throws if the first line of the hub.txt file doesn't start + with "genome \" or if it has invalid entries + +#### genome + +a GenomesFile object for the hub's genome section + +Type: [GenomesFile](#genomesfile) + +#### trackDbs + +an array of TrackDbFile objects for the hub's trackDb sections + +Type: [Array](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Array)<[TrackDbFile](#trackdbfile)> + ### TrackDbFile **Extends RaFile** @@ -323,6 +373,7 @@ Class representing a genomes.txt file. #### Parameters * `trackDbFile` **([string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String) | [Array](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Array)<[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)>)** A trackDb.txt file as a string (optional, default `[]`) +* `options` **any?** diff --git a/src/singleFileHub.ts b/src/singleFileHub.ts index 52ea44f..39e8c5f 100644 --- a/src/singleFileHub.ts +++ b/src/singleFileHub.ts @@ -3,13 +3,23 @@ import HubFile from './hubFile' import TrackDbFile from './trackDbFile' import { validateRequiredFieldsArePresent } from './util' +/** + * Class representing a "single-file" hub.txt file that contains all the sections + * of a hub in a single file. + * @extends RaFile + * @param {(string|string[])} [hubText=[]] - A hub.txt file as a string + * @throws {Error} Throws if the first line of the hub.txt file doesn't start + * with "genome " or if it has invalid entries + */ export default class SingleFileHub extends HubFile { - public genome: GenomesFile + /** a GenomesFile object for the hub's genome section */ + public readonly genome: GenomesFile - public trackDbs: TrackDbFile[] + /** an array of TrackDbFile objects for the hub's trackDb sections */ + public readonly trackDbs: TrackDbFile[] - constructor(singleFileHub: string) { - const [hubSection, genomeSection, ...trackSections] = singleFileHub + constructor(hubText: string) { + const [hubSection, genomeSection, ...trackSections] = hubText .trimEnd() .split(/(?:[\t ]*\r?\n){2,}/) super(hubSection, { skipValidation: true }) From 01ba4c7a2858fedf8fd595f9b783b0d277047fea Mon Sep 17 00:00:00 2001 From: Colin Date: Wed, 27 Sep 2023 12:30:37 -0400 Subject: [PATCH 10/11] Misc --- package.json | 22 +- yarn.lock | 3936 ++++++++++++++++++++++++++++---------------------- 2 files changed, 2184 insertions(+), 1774 deletions(-) diff --git a/package.json b/package.json index 3539201..a9d0ecc 100644 --- a/package.json +++ b/package.json @@ -18,15 +18,13 @@ ], "scripts": { "test": "jest --rootDir=./src", - "coverage": "npm test -- --coverage", - "postcoverage": "opn coverage/lcov-report/index.html", "lint": "eslint --report-unused-disable-directives --max-warnings 0 --ext .js,.ts src", "docs": "documentation readme src --section=API", "postdocs": "git add README.md", "clean": "rimraf dist esm", "prebuild": "npm run docs && npm run clean", "build:esm": "tsc --target es2018 --outDir esm", - "build:es5": "tsc --target es2015 --module commonjs --outDir dist", + "build:es5": "tsc --target es2018 --module commonjs --outDir dist", "build": "npm run build:esm && npm run build:es5", "preversion": "npm run lint && npm test && npm run build", "postversion": "git push --follow-tags", @@ -40,22 +38,22 @@ ], "devDependencies": { "@types/jest": "^29.2.4", - "@types/node": "^18.11.16", - "@typescript-eslint/eslint-plugin": "^5.46.1", - "@typescript-eslint/parser": "^5.46.1", + "@types/node": "^20.7.2", + "@typescript-eslint/eslint-plugin": "^6.7.3", + "@typescript-eslint/parser": "^6.7.3", "documentation": "^14.0.1", "eslint": "^8.30.0", "eslint-config-airbnb-typescript": "^17.0.0", - "eslint-config-prettier": "^8.5.0", + "eslint-config-prettier": "^9.0.0", "eslint-plugin-import": "^2.26.0", - "eslint-plugin-prettier": "^4.2.1", + "eslint-plugin-prettier": "^5.0.0", + "eslint-plugin-unicorn": "^49.0.0", "husky": "^8.0.2", "jest": "^29.3.1", - "opn-cli": "^5.0.0", - "prettier": "^2.8.1", - "rimraf": "^3.0.2", + "prettier": "^3.0.3", + "rimraf": "^5.0.5", "ts-jest": "^29.0.1", - "typescript": "^4.9.4" + "typescript": "^5.2.2" }, "publishConfig": { "access": "public" diff --git a/yarn.lock b/yarn.lock index 74b6d98..302a439 100644 --- a/yarn.lock +++ 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de-indent@^1.0.2: version "1.0.2" resolved "https://registry.yarnpkg.com/de-indent/-/de-indent-1.0.2.tgz#b2038e846dc33baa5796128d0804b455b8c1e21d" integrity sha512-e/1zu3xH5MQryN2zdVaF0OrdNLUbvWxzMbi+iNA6Bky7l1RoP8a2fIbRocyHclXt/arDrrR6lL3TqFD9pMQTsg== -debug@^2.6.9: - version "2.6.9" - resolved "https://registry.yarnpkg.com/debug/-/debug-2.6.9.tgz#5d128515df134ff327e90a4c93f4e077a536341f" - integrity sha512-bC7ElrdJaJnPbAP+1EotYvqZsb3ecl5wi6Bfi6BJTUcNowp6cvspg0jXznRTKDjm/E7AdgFBVeAPVMNcKGsHMA== - dependencies: - ms "2.0.0" - debug@^3.2.7: version "3.2.7" resolved "https://registry.yarnpkg.com/debug/-/debug-3.2.7.tgz#72580b7e9145fb39b6676f9c5e5fb100b934179a" @@ -1382,19 +1483,6 @@ debug@^4.0.0, debug@^4.1.0, debug@^4.1.1, debug@^4.3.2, debug@^4.3.4: dependencies: ms "2.1.2" -decamelize-keys@^1.0.0: - version "1.1.1" - resolved "https://registry.yarnpkg.com/decamelize-keys/-/decamelize-keys-1.1.1.tgz#04a2d523b2f18d80d0158a43b895d56dff8d19d8" - integrity 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version "1.0.5" @@ -2372,6 +2628,16 @@ is-date-object@^1.0.1: dependencies: has-tostringtag "^1.0.0" +is-docker@^2.0.0: + version "2.2.1" + resolved "https://registry.yarnpkg.com/is-docker/-/is-docker-2.2.1.tgz#33eeabe23cfe86f14bde4408a02c0cfb853acdaa" + integrity sha512-F+i2BKsFrH66iaUFc0woD8sLy8getkwTwtOBjvs56Cx4CgJDeKQeqfz8wAYiSb8JOprWhHH5p77PbmYCvvUuXQ== + +is-docker@^3.0.0: + version "3.0.0" + resolved "https://registry.yarnpkg.com/is-docker/-/is-docker-3.0.0.tgz#90093aa3106277d8a77a5910dbae71747e15a200" + integrity sha512-eljcgEDlEns/7AXFosB5K/2nCM4P7FQPkGc/DWLy5rmFEWvZayGrik1d9/QIY5nJ4f9YsVvBkA6kJpHn9rISdQ== + is-extglob@^2.1.1: version "2.1.1" resolved "https://registry.yarnpkg.com/is-extglob/-/is-extglob-2.1.1.tgz#a88c02535791f02ed37c76a1b9ea9773c833f8c2" @@ -2394,6 +2660,13 @@ is-glob@^4.0.0, is-glob@^4.0.1, is-glob@^4.0.3, is-glob@~4.0.1: dependencies: is-extglob "^2.1.1" +is-inside-container@^1.0.0: + version "1.0.0" + resolved "https://registry.yarnpkg.com/is-inside-container/-/is-inside-container-1.0.0.tgz#e81fba699662eb31dbdaf26766a61d4814717ea4" + integrity sha512-KIYLCCJghfHZxqjYBE7rEy0OBuTd5xCHS7tHVgvCLkx7StIoaxwNW3hCALgEUjFfeRk+MG/Qxmp/vtETEF3tRA== + dependencies: + is-docker "^3.0.0" + is-negative-zero@^2.0.2: version "2.0.2" resolved "https://registry.yarnpkg.com/is-negative-zero/-/is-negative-zero-2.0.2.tgz#7bf6f03a28003b8b3965de3ac26f664d765f3150" @@ -2416,11 +2689,6 @@ is-path-inside@^3.0.3: resolved "https://registry.yarnpkg.com/is-path-inside/-/is-path-inside-3.0.3.tgz#d231362e53a07ff2b0e0ea7fed049161ffd16283" integrity sha512-Fd4gABb+ycGAmKou8eMftCupSir5lRxqf4aD/vd0cD2qc4HL07OjCeuHMr8Ro4CoMaeCKDB0/ECBOVWjTwUvPQ== -is-plain-obj@^1.1.0: - version "1.1.0" - resolved "https://registry.yarnpkg.com/is-plain-obj/-/is-plain-obj-1.1.0.tgz#71a50c8429dfca773c92a390a4a03b39fcd51d3e" - integrity sha512-yvkRyxmFKEOQ4pNXCmJG5AEQNlXJS5LaONXo5/cLdTZdWvsZ1ioJEonLGAosKlMWE8lwUy/bJzMjcw8az73+Fg== - 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"https://registry.yarnpkg.com/p-locate/-/p-locate-4.1.0.tgz#a3428bb7088b3a60292f66919278b7c297ad4f07" @@ -3832,11 +4132,6 @@ p-locate@^6.0.0: dependencies: p-limit "^4.0.0" -p-try@^1.0.0: - version "1.0.0" - resolved "https://registry.yarnpkg.com/p-try/-/p-try-1.0.0.tgz#cbc79cdbaf8fd4228e13f621f2b1a237c1b207b3" - integrity sha512-U1etNYuMJoIz3ZXSrrySFjsXQTWOx2/jdi86L+2pRvph/qMKL6sbcCYdH23fqsbm8TH2Gn0OybpT4eSFlCVHww== - p-try@^2.0.0: version "2.2.0" resolved "https://registry.yarnpkg.com/p-try/-/p-try-2.2.0.tgz#cb2868540e313d61de58fafbe35ce9004d5540e6" @@ -3858,15 +4153,7 @@ parse-filepath@^1.0.2: map-cache "^0.2.0" path-root "^0.1.1" -parse-json@^4.0.0: - version "4.0.0" - resolved "https://registry.yarnpkg.com/parse-json/-/parse-json-4.0.0.tgz#be35f5425be1f7f6c747184f98a788cb99477ee0" - integrity sha512-aOIos8bujGN93/8Ox/jPLh7RwVnPEysynVFE+fQZyg6jKELEHwzgKdLRFHUgXJL6kylijVSBC4BvN9OmsB48Rw== - dependencies: - error-ex "^1.3.1" - json-parse-better-errors "^1.0.1" - -parse-json@^5.2.0: 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resolved "https://registry.yarnpkg.com/path-scurry/-/path-scurry-1.10.1.tgz#9ba6bf5aa8500fe9fd67df4f0d9483b2b0bfc698" + integrity sha512-MkhCqzzBEpPvxxQ71Md0b1Kk51W01lrYvlMzSUaIzNsODdd7mqhiimSZlr+VegAz5Z6Vzt9Xg2ttE//XBhH3EQ== dependencies: - pify "^3.0.0" + lru-cache "^9.1.1 || ^10.0.0" + minipass "^5.0.0 || ^6.0.2 || ^7.0.0" path-type@^4.0.0: version "4.0.0" @@ -3954,20 +4247,15 @@ picomatch@^2.0.4, picomatch@^2.2.1, picomatch@^2.2.3, picomatch@^2.3.1: resolved "https://registry.yarnpkg.com/picomatch/-/picomatch-2.3.1.tgz#3ba3833733646d9d3e4995946c1365a67fb07a42" integrity sha512-JU3teHTNjmE2VCGFzuY8EXzCDVwEqB2a8fsIvwaStHhAWJEeVd1o1QD80CU6+ZdEXXSLbSsuLwJjkCBWqRQUVA== -pify@^3.0.0: - version "3.0.0" - resolved "https://registry.yarnpkg.com/pify/-/pify-3.0.0.tgz#e5a4acd2c101fdf3d9a4d07f0dbc4db49dd28176" - integrity sha512-C3FsVNH1udSEX48gGX1xfvwTWfsYWj5U+8/uK15BGzIGrKoUpghX8hWZwa/OFnakBiiVNmBvemTJR5mcy7iPcg== - pify@^6.0.0: version "6.1.0" resolved 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"https://registry.yarnpkg.com/which/-/which-2.0.2.tgz#7c6a8dd0a636a0327e10b59c9286eee93f3f51b1" @@ -4845,12 +5255,7 @@ which@^2.0.1: dependencies: isexe "^2.0.0" -word-wrap@^1.2.3: - version "1.2.3" - resolved "https://registry.yarnpkg.com/word-wrap/-/word-wrap-1.2.3.tgz#610636f6b1f703891bd34771ccb17fb93b47079c" - integrity sha512-Hz/mrNwitNRh/HUAtM/VT/5VH+ygD6DV7mYKZAtHOrbs8U7lvPS6xf7EJKMF0uW1KJCl0H701g3ZGus+muE5vQ== - -wrap-ansi@^7.0.0: +"wrap-ansi-cjs@npm:wrap-ansi@^7.0.0", wrap-ansi@^7.0.0: version "7.0.0" resolved "https://registry.yarnpkg.com/wrap-ansi/-/wrap-ansi-7.0.0.tgz#67e145cff510a6a6984bdf1152911d69d2eb9e43" integrity sha512-YVGIj2kamLSTxw6NsZjoBxfSwsn0ycdesmc4p+Q21c5zPuZ1pl+NfxVdxPtdHvmNVOQ6XSYG4AUtyt/Fi7D16Q== @@ -4859,12 +5264,21 @@ wrap-ansi@^7.0.0: string-width "^4.1.0" strip-ansi "^6.0.0" +wrap-ansi@^8.1.0: + version "8.1.0" + resolved "https://registry.yarnpkg.com/wrap-ansi/-/wrap-ansi-8.1.0.tgz#56dc22368ee570face1b49819975d9b9a5ead214" + integrity sha512-si7QWI6zUMq56bESFvagtmzMdGOtoxfR+Sez11Mobfc7tm+VkUckk9bW2UeffTGVUbOksxmSw0AA2gs8g71NCQ== + dependencies: + ansi-styles "^6.1.0" + string-width "^5.0.1" + strip-ansi "^7.0.1" + wrappy@1: version "1.0.2" resolved "https://registry.yarnpkg.com/wrappy/-/wrappy-1.0.2.tgz#b5243d8f3ec1aa35f1364605bc0d1036e30ab69f" integrity sha512-l4Sp/DRseor9wL6EvV2+TuQn63dMkPjZ/sp9XkghTEbV9KlPS1xUsZ3u7/IQO4wxtcFB4bgpQPRcR3QCvezPcQ== -write-file-atomic@^4.0.1: +write-file-atomic@^4.0.2: version "4.0.2" resolved "https://registry.yarnpkg.com/write-file-atomic/-/write-file-atomic-4.0.2.tgz#a9df01ae5b77858a027fd2e80768ee433555fcfd" integrity sha512-7KxauUdBmSdWnmpaGFg+ppNjKF8uNLry8LyzjauQDOVONfFLNKrKvQOxZ/VuTIcS/gge/YNahf5RIIQWTSarlg== @@ -4877,27 +5291,25 @@ y18n@^5.0.5: resolved "https://registry.yarnpkg.com/y18n/-/y18n-5.0.8.tgz#7f4934d0f7ca8c56f95314939ddcd2dd91ce1d55" integrity sha512-0pfFzegeDWJHJIAmTLRP2DwHjdF5s7jo9tuztdQxAhINCdvS+3nGINqPd00AphqJR/0LhANUS6/+7SCb98YOfA== +yallist@^3.0.2: + version "3.1.1" + resolved "https://registry.yarnpkg.com/yallist/-/yallist-3.1.1.tgz#dbb7daf9bfd8bac9ab45ebf602b8cbad0d5d08fd" + integrity sha512-a4UGQaWPH59mOXUYnAG2ewncQS4i4F43Tv3JoAM+s2VDAmS9NsK8GpDMLrCHPksFT7h3K6TOoUNn2pb7RoXx4g== + yallist@^4.0.0: version "4.0.0" resolved "https://registry.yarnpkg.com/yallist/-/yallist-4.0.0.tgz#9bb92790d9c0effec63be73519e11a35019a3a72" integrity sha512-3wdGidZyq5PB084XLES5TpOSRA3wjXAlIWMhum2kRcv/41Sn2emQ0dycQW4uZXLejwKvg6EsvbdlVL+FYEct7A== -yargs-parser@^10.0.0: - version "10.1.0" - resolved "https://registry.yarnpkg.com/yargs-parser/-/yargs-parser-10.1.0.tgz#7202265b89f7e9e9f2e5765e0fe735a905edbaa8" - integrity sha512-VCIyR1wJoEBZUqk5PA+oOBF6ypbwh5aNB3I50guxAL/quggdfs4TtNHQrSazFA3fYZ+tEqfs0zIGlv0c/rgjbQ== - dependencies: - camelcase "^4.1.0" - yargs-parser@^21.0.1, yargs-parser@^21.1.1: version "21.1.1" resolved "https://registry.yarnpkg.com/yargs-parser/-/yargs-parser-21.1.1.tgz#9096bceebf990d21bb31fa9516e0ede294a77d35" integrity sha512-tVpsJW7DdjecAiFpbIB1e3qxIQsE6NoPc5/eTdrbbIC4h0LVsWhnoa3g+m2HclBIujHzsxZ4VJVA+GUuc2/LBw== yargs@^17.3.1, yargs@^17.5.1: - version "17.6.2" - resolved "https://registry.yarnpkg.com/yargs/-/yargs-17.6.2.tgz#2e23f2944e976339a1ee00f18c77fedee8332541" - integrity sha512-1/9UrdHjDZc0eOU0HxOHoS78C69UD3JRMvzlJ7S79S2nTaWRA/whGCTV8o9e/N/1Va9YIV7Q4sOxD8VV4pCWOw== + version "17.7.2" + resolved "https://registry.yarnpkg.com/yargs/-/yargs-17.7.2.tgz#991df39aca675a192b816e1e0363f9d75d2aa269" + integrity sha512-7dSzzRQ++CKnNI/krKnYRV7JKKPUXMEh61soaHKg9mrWEhzFWhFnxPxGl+69cD1Ou63C13NUPCnmIcrvqCuM6w== dependencies: cliui "^8.0.1" escalade "^3.1.1" @@ -4917,7 +5329,7 @@ yocto-queue@^1.0.0: resolved "https://registry.yarnpkg.com/yocto-queue/-/yocto-queue-1.0.0.tgz#7f816433fb2cbc511ec8bf7d263c3b58a1a3c251" integrity sha512-9bnSc/HEW2uRy67wc+T8UwauLuPJVn28jb+GtJY16iiKWyvmYJRXVT4UamsAEGQfPohgr2q4Tq0sQbQlxTfi1g== -zwitch@^2.0.0: +zwitch@^2.0.0, zwitch@^2.0.4: version "2.0.4" resolved "https://registry.yarnpkg.com/zwitch/-/zwitch-2.0.4.tgz#c827d4b0acb76fc3e685a4c6ec2902d51070e9d7" integrity sha512-bXE4cR/kVZhKZX/RjPEflHaKVhUVl85noU3v6b8apfQEc1x4A+zBxjZ4lN8LqGd6WZ3dl98pY4o717VFmoPp+A== From fe0a131c37d6d4f01c4974bb51f6cdd84a237b57 Mon Sep 17 00:00:00 2001 From: Colin Date: Thu, 9 Nov 2023 13:55:05 -0500 Subject: [PATCH 11/11] Modified destructuring style --- .github/workflows/push.yml | 10 +++++----- README.md | 4 ++-- src/raFile.ts | 9 +++------ src/raStanza.ts | 9 +++------ 4 files changed, 13 insertions(+), 19 deletions(-) diff --git a/.github/workflows/push.yml b/.github/workflows/push.yml index b4786f5..220d65e 100644 --- a/.github/workflows/push.yml +++ b/.github/workflows/push.yml @@ -4,14 +4,14 @@ on: push jobs: test: - name: Lint, build, and test on node 14.x and ubuntu-latest + name: Lint, build, and test on node 20.x and ubuntu-latest runs-on: ubuntu-latest steps: - - uses: actions/checkout@v2 - - name: Use Node.js 14.x - uses: actions/setup-node@v1 + - uses: actions/checkout@v3 + - name: Use Node.js 20.x + uses: actions/setup-node@v3 with: - node-version: 14.x + node-version: 20.x - name: Install deps (with cache) uses: bahmutov/npm-install@v1 - name: Lint codebase diff --git a/README.md b/README.md index 8393cee..e832e2b 100644 --- a/README.md +++ b/README.md @@ -192,7 +192,7 @@ as it performs more validity checks than using `set()`. * `raFile` **([string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String) | [Array](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Array)<[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)>)** An ra file, either as a single string or an array of strings with one stanza per entry. Supports both LF and CRLF line terminators. (optional, default `[]`) -* `options` **[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)** (optional, default `{checkIndent:true,skipValidation:false}`) +* `options` **[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)** * `options.checkIndent` **[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)** \[true] - Check if a the stanzas within the file are indented consistently and keep track of the indentation @@ -268,7 +268,7 @@ than using `set()`. * `stanza` **([string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String) | [Array](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Array)<[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)>)** An ra file stanza, either as a string or a array of strings with one line per entry. Supports both LF and CRLF line terminators. (optional, default `[]`) -* `options` **[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)** (optional, default `{checkIndent:true,skipValidation:false}`) +* `options` **[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)** * `options.checkIndent` **[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)** \[true] - Check if a stanza is indented consistently and keep track of the indentation diff --git a/src/raFile.ts b/src/raFile.ts index 092f8e9..bb8a04a 100644 --- a/src/raFile.ts +++ b/src/raFile.ts @@ -30,13 +30,10 @@ export default class RaFile extends Map { constructor( raFile: string | string[] = [], - options: { checkIndent?: boolean; skipValidation?: boolean } = { - checkIndent: true, - skipValidation: false, - }, + options?: { checkIndent?: boolean; skipValidation?: boolean }, ) { super() - const { checkIndent } = options + const { checkIndent = true, skipValidation = false } = options || {} this._checkIndent = !!checkIndent let stanzas: string[] if (typeof raFile === 'string') { @@ -51,7 +48,7 @@ export default class RaFile extends Map { this.add(stanza) }) - if (!options.skipValidation) { + if (!skipValidation) { this.validate() } } diff --git a/src/raStanza.ts b/src/raStanza.ts index 2f480ac..a553fbb 100644 --- a/src/raStanza.ts +++ b/src/raStanza.ts @@ -45,13 +45,10 @@ export default class RaStanza extends Map { constructor( stanza: string | string[] = [], - options: { checkIndent?: boolean; skipValidation?: boolean } = { - checkIndent: true, - skipValidation: false, - }, + options?: { checkIndent?: boolean; skipValidation?: boolean }, ) { super() - const { checkIndent } = options + const { checkIndent = true, skipValidation = false } = options || {} this._checkIndent = !!checkIndent let stanzaLines: string[] if (typeof stanza === 'string') { @@ -66,7 +63,7 @@ export default class RaStanza extends Map { this.add(line) }) - if (!options.skipValidation) { + if (!skipValidation) { this.validate() } }