@sjcrh/proteinpaint-client 2.191.4 → 2.193.0

package/dist/chunk-IW57W7EQ.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../src/app.mdsjson.js", "../gdc/launch.ts", "../src/app.parseurl.js"],
-  "sourcesContent": ["import * as client from './client'\n\n/*\n********************** EXPORTED\ninit_mdsjson\nvalidate_mdsjson\nget_json_tk\nget_scatterplot_data\n*/\n\nexport async function init_mdsjson(file_str, url_str) {\n\tlet json_files = [],\n\t\tjson_urls = []\n\n\tif (file_str && file_str.includes(',')) json_files = file_str.split(',')\n\telse if (file_str) json_files.push(file_str)\n\telse if (url_str && url_str.includes(',')) json_urls = url_str.split(',')\n\telse if (url_str) json_urls.push(url_str)\n\n\tconst tklst = []\n\tif (json_files.length) {\n\t\tconst json_url = undefined\n\t\tfor (const json_file of json_files) {\n\t\t\ttklst.push(await tklst_pipeline(json_file, json_url))\n\t\t}\n\t} else if (json_urls.length) {\n\t\tconst json_file = undefined\n\t\tfor (const json_url of json_urls) {\n\t\t\ttklst.push(await tklst_pipeline(json_file, json_url))\n\t\t}\n\t}\n\n\treturn tklst\n}\n\nasync function tklst_pipeline(json_file, json_url) {\n\tconst obj = await mdsjson_parse(json_file, json_url)\n\tvalidate_mdsjson(obj)\n\tconst tk = get_json_tk(obj)\n\treturn tk\n}\n\nasync function mdsjson_parse(json_file, json_url) {\n\tif (json_file !== undefined && json_file == '') throw '.jsonfile missing'\n\tif (json_url !== undefined && json_url == '') throw '.jsonurl missing'\n\n\tlet tmp\n\tif (json_file !== undefined) tmp = await client.dofetch('textfile', { file: json_file })\n\telse if (json_url !== undefined) tmp = await client.dofetch('urltextfile', { url: json_url })\n\tif (tmp.error) {\n\t\tthrow tmp.error\n\t}\n\treturn JSON.parse(tmp.text)\n}\n\nexport function validate_mdsjson(obj) {\n\tif (!obj) throw 'file is missing'\n\tif (!obj.type) throw 'dataset type is missing'\n\tconst svcnvfile = obj.svcnvfile || obj.svcnvurl\n\tconst vcffile = obj.vcffile || obj.vcfurl\n\tif (!svcnvfile && !vcffile) throw 'vcf or cnv file/url is required'\n\tif (Object.keys(obj).filter(x => x.includes('expression')).length) {\n\t\tif (!obj.expressionfile && !obj.expressionurl) throw 'expression file/url is missing'\n\t}\n\tif (Object.keys(obj).filter(x => x.includes('rnabam')).length) {\n\t\tif (!obj.rnabamfile && !obj.rnabamurl) throw 'rnabam file/url is missing'\n\t}\n\tif (obj.sampleset) {\n\t\tfor (const sample of obj.sampleset) {\n\t\t\tif (obj.sampleset.length != 1 && !sample.name) throw 'sampleset name is missing'\n\t\t\tif (!sample.samples) throw 'sampleset samples[] is missing'\n\t\t}\n\t}\n\tif (obj.sample2assaytrack) {\n\t\tfor (const [sample, assaylst] of Object.entries(obj.sample2assaytrack)) {\n\t\t\tif (!assaylst.length) throw 'assay[] missing for ' + sample\n\t\t\tfor (const assay of assaylst) {\n\t\t\t\tif (!assay.name) throw 'assay name is missing for ' + sample\n\t\t\t\tif (!assay.type) throw 'assay type is missing for ' + sample\n\t\t\t}\n\t\t}\n\t}\n\n\tif (obj.groupsamplebyattr) {\n\t\tif (!obj.groupsamplebyattr.attrlst) return '.attrlst[] missing from groupsamplebyattr'\n\t\tif (obj.groupsamplebyattr.attrlst.length == 0) return 'groupsamplebyattr.attrlst[] empty array'\n\n\t\tfor (const attr of obj.groupsamplebyattr.attrlst) {\n\t\t\tif (!attr.k) return 'k missing from one of groupsamplebyattr.attrlst[]'\n\t\t}\n\n\t\tif (obj.groupsamplebyattr.sortgroupby) {\n\t\t\tif (!obj.groupsamplebyattr.sortgroupby.key) return '.key missing from .sortgroupby'\n\t\t\tif (!obj.groupsamplebyattr.sortgroupby.order) return '.order[] missing from .sortgroupby'\n\t\t\tif (!Array.isArray(obj.groupsamplebyattr.sortgroupby.order)) return '.order must be an array'\n\t\t\t// values of order[] is not validated\n\t\t}\n\t\tif (!obj.groupsamplebyattr.attrnamespacer) obj.groupsamplebyattr.attrnamespacer = ', '\n\t}\n\n\tif (obj.fixedgeneexpression) {\n\t\tfor (const gene of obj.fixedgeneexpression) {\n\t\t\tif (!gene.gene) throw 'gene missing in fixedgeneexpression array'\n\t\t}\n\t}\n\n\t// hidden classes for vcf file\n\tif (obj.vcf) {\n\t\tif (!obj.vcf.hiddenclass) throw 'hiddenclasses[] missing from .vcf'\n\t}\n}\n\nexport function get_json_tk(tkobj) {\n\tconst track = {\n\t\ttype: tkobj.type,\n\t\tname: tkobj.name\n\t}\n\n\t// dense or full\n\tif (tkobj.isdense == 'true' || tkobj.isdense == true || tkobj.isfull === false) track.isdense = true\n\telse if (tkobj.isfull) track.isfull = true\n\n\t// svcnv file\n\tif (tkobj.svcnvfile) track.file = tkobj.svcnvfile\n\telse if (tkobj.svcnvurl) track.url = tkobj.svcnvurl\n\n\t// expressionrank\n\tif (Object.keys(tkobj).filter(x => x.includes('expression')).length) {\n\t\ttrack.checkexpressionrank = {\n\t\t\tfile: tkobj.expressionfile,\n\t\t\turl: tkobj.expressionurl\n\t\t}\n\t}\n\n\t// vcf\n\tif (Object.keys(tkobj).filter(x => x.includes('vcf')).length) {\n\t\ttrack.checkvcf = {\n\t\t\tfile: tkobj.vcffile,\n\t\t\turl: tkobj.vcfurl\n\t\t}\n\t}\n\n\t// hidden mutation classes\n\tif (tkobj.vcf) {\n\t\tif (tkobj.vcf.hiddenclass) {\n\t\t\ttrack.vcf = []\n\t\t\ttrack.vcf.hiddenclass = tkobj.vcf.hiddenclass\n\t\t}\n\t}\n\n\t// rna bam\n\tif (Object.keys(tkobj).filter(x => x.includes('rnabam')).length) {\n\t\ttrack.checkrnabam = {\n\t\t\tfile: tkobj.rnabamfile,\n\t\t\turl: tkobj.rnabamurl\n\t\t}\n\t}\n\n\t// sampleset\n\tif (tkobj.sampleset) {\n\t\ttrack.sampleset = tkobj.sampleset\n\t}\n\n\t// SampleAssayTrack\n\tif (tkobj.sample2assaytrack) {\n\t\ttrack.sample2assaytrack = tkobj.sample2assaytrack\n\t}\n\n\tif (tkobj.groupsamplebyattr) {\n\t\ttrack.groupsamplebyattr = tkobj.groupsamplebyattr\n\t}\n\n\t// fixed panel of gene expression\n\ttrack.fixedgeneexpression = tkobj.fixedgeneexpression\n\t// show all samples\n\ttrack.getallsamples = tkobj.getallsamples\n\n\t// cnv cutoff settings\n\ttrack.valueCutoff = tkobj.cnvValueCutoff !== undefined ? tkobj.cnvValueCutoff : undefined\n\ttrack.bplengthUpperLimit = tkobj.cnvLengthUpperLimit !== undefined ? tkobj.cnvLengthUpperLimit : undefined\n\n\t// loh cutoff settings\n\ttrack.segmeanValueCutoff = tkobj.segmeanValueCutoff !== undefined ? tkobj.segmeanValueCutoff : undefined\n\ttrack.lohLengthUpperLimit = tkobj.lohLengthUpperLimit !== undefined ? tkobj.lohLengthUpperLimit : undefined\n\n\t// multihide labels\n\ttrack.multihidelabel_vcf = tkobj.multihidelabel_vcf !== undefined ? tkobj.multihidelabel_vcf : undefined\n\ttrack.multihidelabel_fusion = tkobj.multihidelabel_fusion !== undefined ? tkobj.multihidelabel_fusion : undefined\n\ttrack.multihidelabel_sv = tkobj.multihidelabel_sv !== undefined ? tkobj.multihidelabel_sv : undefined\n\n\ttrack.legend_vorigin = tkobj.legend_vorigin\n\n\treturn track\n}\n\nexport async function get_scatterplot_data(json_file, json_url) {\n\tlet data = {}\n\tconst obj = await mdsjson_parse(json_file, json_url)\n\tdata.mdssamplescatterplot = obj\n\treturn data\n}\n", "/* launch from runpp() call. GDC react wrappers in the GFF repo use this method, to launch apps in gdc portal\non matching with a flag, imports corresponding plot script, and returns api object to runpp()\nwhen no flags are matched, returns undefined\n*/\nexport async function mayLaunchGdcPlotFromRunpp(arg, app) {\n\tif (arg.geneSearch4GDCmds3) {\n\t\tconst _ = await import('./lollipop.js')\n\t\treturn await _.init(arg, app.holder0, app.genomes)\n\t}\n\tif (arg.launchGdcGb) {\n\t\tconst _ = await import('./gb.ts')\n\t\treturn await _.init(arg, app.holder0, app.genomes)\n\t}\n\tif (arg.launchGdcMatrix) {\n\t\tconst _ = await import('./oncomatrix.js')\n\t\treturn await _.init(arg, app.holder0, app.genomes)\n\t}\n\tif (arg.launchGdcHierCluster) {\n\t\tconst _ = await import('./geneExpClustering.js')\n\t\treturn await _.init(arg, app.holder0, app.genomes)\n\t}\n\tif (arg.launchGdcMaf) {\n\t\tconst _ = await import('./maf.js')\n\t\treturn await _.gdcMAFui(arg, app.holder0)\n\t}\n\tif (arg.launchGdcGrin2) {\n\t\tconst _ = await import('./grin2.ts')\n\t\treturn await _.gdcGRIN2ui(arg, app.holder0)\n\t}\n\tif (arg.launchGdcScRNAseq) {\n\t\tconst _ = await import('./singlecell.ts')\n\t\treturn await _.init(arg, app.holder0, app.genomes)\n\t}\n\tif (arg.launchGdcScApp) {\n\t\tconst _ = await import('./sc.ts')\n\t\treturn await _.init(arg, app.holder0, app.genomes)\n\t}\n\tif (arg.launchGdcCorrelation) {\n\t\tconst _ = await import('./correlation.ts')\n\t\treturn await _.init(arg, app.holder0, app.genomes)\n\t}\n\tif (arg.launchGdcDE) {\n\t\tconst _ = await import('./DE.ts')\n\t\treturn await _.init(arg, app.holder0, app.genomes)\n\t}\n\tif (arg.gdcbamslice) {\n\t\tconst _ = await import('./bam.js')\n\t\targ.gdcbamslice.filter0 = arg.filter0\n\t\treturn await _.bamsliceui(arg.gdcbamslice, app.holder0, app.genomes)\n\t}\n}\n\n/* launch from url param; this is for local testing and not used in gdc portal\nreturns true for a match\n*/\nexport async function mayLaunchGdcPlotFromUrlparam(urlp, arg) {\n\tif (urlp.has('gdcbamslice')) {\n\t\t// for local testing, not used in gdc portal\n\t\tconst _ = await import('./bam.js')\n\t\t_.bamsliceui(\n\t\t\t{\n\t\t\t\tdebugmode: arg.debugmode,\n\t\t\t\tstream2download: urlp.has('stream2download') // for testing only, launch the app in \"download mode\", will not visualize\n\t\t\t} as any,\n\t\t\targ.holder,\n\t\t\targ.genomes\n\t\t)\n\t\treturn true\n\t}\n\tif (urlp.has('gdcmaf')) {\n\t\t// for local testing, not used in gdc portal\n\t\tconst _ = await import('./maf.js')\n\t\tconst p: any = {\n\t\t\tdebugmode: arg.debugmode\n\t\t}\n\t\tif (urlp.has('filter0')) p.filter0 = urlp.get('filter0')\n\t\t_.gdcMAFui(p, arg.holder)\n\t\treturn true\n\t}\n\tif (urlp.has('gdcgrin2')) {\n\t\t// for local testing, not used in gdc portal\n\t\tconst _ = await import('./grin2.ts')\n\t\tconst p: any = {\n\t\t\tdebugmode: arg.debugmode\n\t\t}\n\t\tif (urlp.has('filter0')) p.filter0 = urlp.get('filter0')\n\t\t_.gdcGRIN2ui(p, arg.holder)\n\t\treturn true\n\t}\n\tif (urlp.has('gdccorrelation')) {\n\t\t// for local testing, not used in gdc portal\n\t\tconst _ = await import('./correlation.ts')\n\t\tconst p: any = {\n\t\t\tdebugmode: arg.debugmode\n\t\t}\n\t\tif (urlp.has('filter0')) p.filter0 = urlp.get('filter0')\n\t\t_.init(p, arg.holder, arg.genomes)\n\t\treturn true\n\t}\n}\n", "import blockinit from './block.init'\nimport * as client from './client'\nimport { loadstudycohort } from './tp.init'\nimport { string2pos } from './coord'\nimport * as mdsjson from './app.mdsjson'\nimport { getSavedToken } from '#common/dofetch'\nimport urlmap from '#common/urlmap'\nimport { first_genetrack_tolist } from '#common/1stGenetk'\nimport { parentCorsMessage, childCorsMessage } from '#common/embedder-helpers'\nimport { sayerror } from '#dom'\nimport { copyMerge } from '#rx'\nimport { mayLaunchGdcPlotFromUrlparam } from '../gdc/launch.ts'\n/*\n********************** EXPORTED\nparse()\nget_tklst()\n*/\n\nexport async function parse(arg) {\n\t/*\narg\n\t.jwt\n\t.genomes{}\n\t.hostURL\n\t.variantPageCall_snv\n\t.samplecart\n\t.holder\n\t.debugmode\n\nupon error, throw err message as a string\n*/\n\tconst urlp = urlmap()\n\tconst features = JSON.parse(sessionStorage.getItem('optionalFeatures'))\n\n\tif (urlp.has('appcard')) {\n\t\tconst ad = await import('../appdrawer/adSandbox')\n\t\tconst cardJsonFile = urlp.get('appcard')\n\t\tconst example = urlp.get('example')\n\t\tconst re = await client.dofetch2('/cards/index.json')\n\t\targ.app.drawer.opts.genomes = arg.genomes\n\t\targ.app.drawer.opts.fromApp = true\n\t\t//Quick fix to launch the sandbox within the current openSandbox code\n\t\targ.app.drawer.opts.app = {\n\t\t\tcardsPath: 'cards'\n\t\t}\n\t\tconst element = re.elements.findIndex(\n\t\t\tt =>\n\t\t\t\tt.sandboxJson == cardJsonFile ||\n\t\t\t\tt.sandboxHtml == cardJsonFile ||\n\t\t\t\tt.name.toUpperCase().includes(cardJsonFile.toUpperCase())\n\t\t)\n\n\t\t//Check if track/app can be shown on this server\n\t\t//If not show error message\n\t\tif (re.elements[element]?.configFeature) {\n\t\t\tif (!features[re.elements[element].configFeature]) {\n\t\t\t\tsayerror(arg.holder, `This track or app is not enabled on this site.`)\n\t\t\t\treturn\n\t\t\t}\n\t\t}\n\n\t\tif (example) {\n\t\t\targ.app.drawer.opts.example = example\n\t\t}\n\n\t\tif (element <= 0) {\n\t\t\tconst nestedCards = [...re.elements.filter(e => e.type == 'nestedCard')]\n\t\t\tlet element, c\n\t\t\tnestedCards.findIndex(t => {\n\t\t\t\tfor (const [i, child] of t.children.entries()) {\n\t\t\t\t\tif (\n\t\t\t\t\t\tchild.sandboxJson == cardJsonFile ||\n\t\t\t\t\t\tchild.sandboxHtml == cardJsonFile ||\n\t\t\t\t\t\tchild.name.toUpperCase().includes(cardJsonFile.toUpperCase())\n\t\t\t\t\t) {\n\t\t\t\t\t\telement = t\n\t\t\t\t\t\tc = i\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t})\n\t\t\tif (!element) {\n\t\t\t\tsayerror(arg.holder, `Invalid app card.`)\n\t\t\t\treturn\n\t\t\t}\n\t\t\tad.openSandbox(element.children[c], arg.app.drawer.opts)\n\t\t} else {\n\t\t\tad.openSandbox(re.elements[element], arg.app.drawer.opts)\n\t\t}\n\t\treturn\n\t}\n\n\tif (await mayLaunchGdcPlotFromUrlparam(urlp, arg)) return // gdc plot launched\n\n\tif (urlp.has('termdb')) {\n\t\tconst value = urlp.get('termdb')\n\t\tconst state = typeof value === 'string' ? JSON.parse(value) : value\n\t\tconst opts = {\n\t\t\tholder: arg.holder,\n\t\t\tstate: copyMerge(state, arg.state || {})\n\t\t}\n\t\tconst _ = await import('../termdb/app')\n\t\tconst subapp = _.appInit(opts)\n\t\treturn subapp\n\t}\n\n\tif (urlp.has('massnative')) {\n\t\t/* ?massnative=hg38-test,TermdbTest\n\t\talternative url for mass={\"genome\":\"hg38-test\",\"dslabel\":\"TermdbTest\"}\n\t\ttidier to include in manuscript\n\t\tno customization supported, though later additional fields may be appended to customize something\n\t\tit is intended that the dataset should carry essential customizations so the link opens mass ui with expected customizations\n\t\t*/\n\t\tconst value = urlp.get('massnative')\n\t\tconst [genomename, dslabel] = value.split(',')\n\t\tif (!genomename || !dslabel) throw 'value is not \"genome,dslabel\"'\n\t\tconst opts = {\n\t\t\tholder: arg.holder,\n\t\t\tgenome: arg.genomes[genomename],\n\t\t\tstate: copyMerge(\n\t\t\t\t{\n\t\t\t\t\tgenome: genomename,\n\t\t\t\t\tdslabel\n\t\t\t\t},\n\t\t\t\targ.state || {}\n\t\t\t),\n\t\t\tpkgver: arg.app.pkgver,\n\t\t\tlaunchDate: arg.app.launchDate\n\t\t}\n\t\tif (!opts.genome) throw 'invalid genome'\n\t\tchildCorsMessage(opts)\n\n\t\tconst _ = await import('../mass/app')\n\t\tconst subapp = await _.appInit(opts)\n\t\treturn subapp\n\t}\n\n\tif (urlp.has('mass')) {\n\t\tconst value = urlp.get('mass')\n\t\tconst state = typeof value === 'string' ? JSON.parse(value) : value\n\t\tconst opts = {\n\t\t\tdebug: arg.app.debugmode,\n\t\t\tholder: arg.holder,\n\t\t\tstate: copyMerge(state, arg.state || {}),\n\t\t\tpkgver: arg.app.pkgver,\n\t\t\tlaunchDate: arg.app.launchDate\n\t\t}\n\t\tif (state.genome) {\n\t\t\topts.genome = arg.genomes[state.genome]\n\t\t} else if (state?.vocab?.genome) {\n\t\t\topts.genome = arg.genomes[state.vocab.genome]\n\t\t}\n\t\tchildCorsMessage(opts)\n\n\t\tconst _ = await import('../mass/app')\n\t\tconst subapp = await _.appInit(opts)\n\t\treturn subapp\n\t}\n\n\tif (urlp.has('mass-session-file') || urlp.has('mass-session-url')) {\n\t\tlet opts\n\t\tif (urlp.has('mass-session-file')) {\n\t\t\tconst file = urlp.get('mass-session-file')\n\t\t\tconst d = await client.dofetch3(`/textfile`, {\n\t\t\t\tmethod: 'POST',\n\t\t\t\tbody: JSON.stringify({ file })\n\t\t\t})\n\t\t\tif (typeof d != 'object') throw 'data not object'\n\t\t\tif (d.error) throw d.error\n\t\t\tif (!d.text) throw 'data.text missing'\n\t\t\tconst state = JSON.parse(d.text)\n\n\t\t\tif (features.overrideEmbedderHostInMassSession) {\n\t\t\t\t// on local dev, set this to override \"embedder{}\" setting in session file\n\t\t\t\t// to prevent redirecting to portal site and test the session with local pp\n\t\t\t\tstate.embedder.host = features.overrideEmbedderHostInMassSession\n\t\t\t\tstate.embedder.origin = 'http://' + features.overrideEmbedderHostInMassSession\n\t\t\t\tstate.embedder.href = `http://${features.overrideEmbedderHostInMassSession}/`\n\t\t\t}\n\n\t\t\tif (state.embedder?.origin && state.embedder.origin != window.location.origin) {\n\t\t\t\tparentCorsMessage({ state })\n\t\t\t\treturn\n\t\t\t}\n\n\t\t\topts = {\n\t\t\t\tdebug: arg.app.debugmode,\n\t\t\t\tholder: arg.holder,\n\t\t\t\tstate,\n\t\t\t\tgenome: arg.genomes[state.vocab.genome],\n\t\t\t\tpkgver: arg.app.pkgver,\n\t\t\t\tlaunchDate: arg.app.launchDate\n\t\t\t}\n\t\t} else if (urlp.has('mass-session-url')) {\n\t\t\tconst url = urlp.get('mass-session-url')\n\t\t\tconst d = await client.dofetch3('/urltextfile', {\n\t\t\t\tmethod: 'POST',\n\t\t\t\tbody: JSON.stringify({ url })\n\t\t\t})\n\t\t\tif (typeof d != 'object') throw 'data not object'\n\t\t\tif (d.error) throw d.error\n\t\t\tif (!d.text) throw 'data.text missing'\n\t\t\tconst state = JSON.parse(d.text)\n\n\t\t\tif (state.embedder?.origin && state.embedder.origin != window.location.origin) {\n\t\t\t\tparentCorsMessage({ state })\n\t\t\t\treturn\n\t\t\t}\n\n\t\t\topts = {\n\t\t\t\tdebug: arg.app.debugmode,\n\t\t\t\tholder: arg.holder,\n\t\t\t\tstate: copyMerge(state, arg.state || {}),\n\t\t\t\tgenome: arg.genomes[state.vocab.genome],\n\t\t\t\tpkgver: arg.app.pkgver,\n\t\t\t\tlaunchDate: arg.app.launchDate\n\t\t\t}\n\t\t}\n\t\tconst _ = await import('../mass/app')\n\t\tconst subapp = _.appInit(opts)\n\t\treturn subapp\n\t}\n\n\tif (urlp.has('mass-session-id')) {\n\t\tconst id = urlp.get('mass-session-id')\n\t\tconst src = urlp.get('src')\n\t\tlet res\n\t\tif (src == 'browser') {\n\t\t\tconst json = localStorage.getItem('savedMassSessions')\n\t\t\tconst savedSessions = JSON.parse(json)\n\t\t\tres = { state: savedSessions[id] }\n\t\t} else {\n\t\t\tconst fetchOpts = { headers: {}, body: { id } }\n\t\t\tif (src == 'cred') {\n\t\t\t\tconst dslabel = urlp.get('dslabel')\n\t\t\t\tconst route = urlp.get('route')\n\t\t\t\tfetchOpts.body.dslabel = dslabel\n\t\t\t\tfetchOpts.body.route = route\n\t\t\t\tfetchOpts.body.route = route\n\t\t\t\tconst jwt = getSavedToken(dslabel, route)\n\t\t\t\tif (jwt) fetchOpts.headers.authorization = `Bearer ${btoa(jwt)}`\n\t\t\t}\n\t\t\tres = await client.dofetch3(`/massSession`, fetchOpts)\n\t\t\tif (res.error) throw res.error\n\t\t}\n\t\tconst embedder = res.state?.embedder\n\t\tif (embedder?.origin && embedder.origin != window.location.origin) {\n\t\t\tparentCorsMessage(res)\n\t\t\treturn\n\t\t}\n\t\tconst opts = {\n\t\t\tdebug: arg.app.debugmode,\n\t\t\tholder: arg.holder,\n\t\t\tstate: copyMerge(res.state, arg.state || {}),\n\t\t\tgenome: arg.genomes[res.state.vocab.genome],\n\t\t\tsessionDaysLeft: res.sessionDaysLeft,\n\t\t\tsessionId: id,\n\t\t\tpkgver: arg.app.pkgver,\n\t\t\tlaunchDate: arg.app.launchDate\n\t\t}\n\t\tconst _ = await import('../mass/app')\n\t\tconst subapp = _.appInit(opts)\n\t\treturn subapp\n\t}\n\n\tif (urlp.has('genome') && arg.selectgenome) {\n\t\tconst n = urlp.get('genome')\n\t\tconst genome_options = [...arg.selectgenome.node().childNodes]\n\t\tconst selectedIndex = genome_options.findIndex(d => d.value == n)\n\t\tif (selectedIndex == -1) {\n\t\t\tsayerror(\n\t\t\t\targ.holder,\n\t\t\t\t`Invalid genome: ${n}. Please provide an available genome from this list: ${genome_options\n\t\t\t\t\t.map(d => d.value)\n\t\t\t\t\t.join(', ')\n\t\t\t\t\t.replace(/,(?=[^,]*$)/, ', or')}`\n\t\t\t)\n\t\t\treturn\n\t\t}\n\t\targ.selectgenome.node().selectedIndex = selectedIndex\n\t\targ.selectgenome.node().dispatchEvent(new Event('change'))\n\t}\n\n\tif (urlp.has('hicfile') || urlp.has('hicurl')) {\n\t\t// whole-genome view\n\t\tlet file, url, name\n\t\tif (urlp.has('hicfile')) {\n\t\t\tfile = urlp.get('hicfile')\n\t\t\tname = file.split('/').pop()\n\t\t} else {\n\t\t\turl = urlp.get('hicurl')\n\t\t\tname = url.split('/').pop()\n\t\t}\n\t\tconst gn = urlp.get('genome')\n\t\tif (!gn) throw 'genome is required for hic'\n\t\tconst genome = arg.genomes[gn]\n\t\tif (!genome) throw 'invalid genome'\n\t\tconst hic = {\n\t\t\tgenome,\n\t\t\tfile,\n\t\t\turl,\n\t\t\tname, //.basename(file || url),\n\t\t\thostURL: arg.hostURL,\n\t\t\tenzyme: urlp.get('enzyme'),\n\t\t\tholder: arg.holder\n\t\t}\n\t\tconst _ = await import('../tracks/hic/HicApp')\n\t\tawait _.hicInit(hic)\n\t\treturn\n\t}\n\n\t//////////// legacy, may be replaced by sampleScatter, kept for existing views on vizcom\n\tif (urlp.has('singlecell')) {\n\t\tif (!urlp.has('genome')) throw '\"genome\" is required for \"singlecell\"'\n\t\tconst genomename = urlp.get('genome')\n\t\tconst genomeobj = arg.genomes[genomename]\n\t\tif (!genomeobj) throw 'invalid genome: ' + genomename\n\n\t\tconst _ = await import('./singlecell')\n\t\t_.init(\n\t\t\t{\n\t\t\t\tgenome: genomeobj,\n\t\t\t\tjsonfile: urlp.get('singlecell')\n\t\t\t},\n\t\t\targ.holder\n\t\t)\n\t\treturn\n\t}\n\n\tif (urlp.has('mavbfile')) {\n\t\tif (!urlp.has('genome')) throw '\"genome\" is required for \"mavb\"'\n\t\tconst genomename = urlp.get('genome')\n\t\tconst genome = arg.genomes[genomename]\n\t\tif (!genome) throw 'invalid genome: ' + genomename\n\t\tconst _ = await import('./mavb')\n\t\t_.mavbparseinput(\n\t\t\t{\n\t\t\t\tgenome,\n\t\t\t\thostURL: arg.hostURL,\n\t\t\t\tfile: urlp.get('mavbfile')\n\t\t\t},\n\t\t\t() => {},\n\t\t\targ.holder,\n\t\t\targ.jwt\n\t\t)\n\t\treturn\n\t}\n\n\tif (urlp.has('mavburl')) {\n\t\tif (!urlp.has('genome')) throw '\"genome\" is required for \"mavb\"'\n\t\tconst genomename = urlp.get('genome')\n\t\tconst genome = arg.genomes[genomename]\n\t\tif (!genome) throw 'invalid genome: ' + genomename\n\t\tconst _ = await import('./mavb')\n\t\t_.mavbparseinput(\n\t\t\t{\n\t\t\t\tgenome,\n\t\t\t\thostURL: arg.hostURL,\n\t\t\t\turl: urlp.get('mavburl')\n\t\t\t},\n\t\t\t() => {},\n\t\t\targ.holder,\n\t\t\targ.jwt\n\t\t)\n\t\treturn\n\t}\n\n\t//////////// legacy, replaced by sampleScatter (just need to support adhoc data), kept for existing views on vizcom\n\tif (urlp.has('scatterplot')) {\n\t\tif (!urlp.has('genome')) throw '\"genome\" is required for \"scatterplot\"'\n\t\tconst genomename = urlp.get('genome')\n\t\tconst genome = arg.genomes[genomename]\n\t\tif (!genome) throw 'invalid genome: ' + genomename\n\n\t\tlet plot_data\n\t\tif (urlp.has('mdsjson') || urlp.has('mdsjsonurl')) {\n\t\t\tconst url_str = urlp.get('mdsjsonurl')\n\t\t\tconst file_str = urlp.get('mdsjson')\n\t\t\tplot_data = await mdsjson.get_scatterplot_data(file_str, url_str)\n\t\t}\n\t\tif (urlp.has('tsnejson')) {\n\t\t\tconst file_str = urlp.get('tsnejson')\n\t\t\tconst data = await client.dofetch('textfile', { file: file_str })\n\t\t\tif (data.error) throw data.error\n\t\t\telse if (data.text) {\n\t\t\t\tplot_data = {\n\t\t\t\t\tmdssamplescatterplot: {\n\t\t\t\t\t\tanalysisdata: JSON.parse(data.text)\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\n\t\t// if genome is defined in url, pass it to samplescatterplot\n\t\tplot_data.mdssamplescatterplot.genome = genome\n\t\tconst _ = await import('./mds.samplescatterplot')\n\t\t_.init(plot_data.mdssamplescatterplot, arg.holder, false)\n\t\treturn\n\t}\n\n\tif (urlp.has('block')) {\n\t\tif (!urlp.has('genome')) throw 'missing genome for block'\n\t\tconst genomename = urlp.get('genome')\n\t\tconst genomeobj = arg.genomes[genomename]\n\t\tif (!genomeobj) throw 'invalid genome: ' + genomename\n\n\t\tconst par = {\n\t\t\tnobox: 1,\n\t\t\thostURL: arg.hostURL,\n\t\t\tjwt: arg.jwt,\n\t\t\tholder: arg.holder,\n\t\t\tgenome: genomeobj,\n\t\t\tdogtag: genomename,\n\t\t\tdebugmode: arg.debugmode\n\t\t}\n\n\t\tlet position = null\n\t\tlet rglst = null\n\n\t\tif (urlp.has('position')) {\n\t\t\t// can be multiple regions joined by ;\n\t\t\t// first region is main panel, rest of regions are subpanels\n\n\t\t\tconst lst = urlp.get('position').split(';')\n\t\t\tif (lst[0]) {\n\t\t\t\t// if first region is blank, do not parse; it will be assigned with defaultcoord\n\t\t\t\tconst tmp = lst[0].split(/[:-]/)\n\t\t\t\tconst chr = tmp[0]\n\t\t\t\tconst start = Number.parseInt(tmp[1])\n\t\t\t\tconst stop = Number.parseInt(tmp[2])\n\t\t\t\tif (!chr) throw 'chr missing'\n\t\t\t\tif (Number.isNaN(start) || Number.isNaN(stop)) throw 'Invalid start/stop value in position'\n\t\t\t\t// valid position\n\t\t\t\tposition = { chr, start, stop }\n\t\t\t}\n\n\t\t\tconst subpanels = [] // collect rest of regions into this array\n\t\t\tfor (let i = 1; i < lst.length; i++) {\n\t\t\t\tif (!lst[i]) continue // skip blank string\n\t\t\t\tconst tmp = lst[i].split(/[:-]/)\n\t\t\t\tconst chr = tmp[0]\n\t\t\t\tconst start = Number.parseInt(tmp[1])\n\t\t\t\tconst stop = Number.parseInt(tmp[2])\n\t\t\t\tif (!chr) throw 'subpanel chr missing'\n\t\t\t\tif (Number.isNaN(start) || Number.isNaN(stop)) throw 'Invalid start/stop value in subpanel position'\n\t\t\t\t// valid pos\n\t\t\t\tsubpanels.push({\n\t\t\t\t\tchr,\n\t\t\t\t\tstart,\n\t\t\t\t\tstop,\n\t\t\t\t\twidth: 600,\n\t\t\t\t\tleftborder: 'rgba(200,0,0,.1)',\n\t\t\t\t\tleftpad: 5\n\t\t\t\t})\n\t\t\t}\n\t\t\tif (subpanels.length) {\n\t\t\t\t// has valid subpanels\n\t\t\t\tpar.subpanels = subpanels\n\t\t\t}\n\t\t}\n\n\t\tif (urlp.has('regions')) {\n\t\t\t// for a different purpose than \"position=\"\n\t\t\t// all regions here are shown in one view and scroll together, as in gmmode. it does not introduce subpanels\n\t\t\trglst = []\n\t\t\tfor (const s of urlp.get('regions').split(',')) {\n\t\t\t\tconst l = s.split(/[:-]/)\n\t\t\t\tconst chr = l[0]\n\t\t\t\tconst start = Number.parseInt(l[1])\n\t\t\t\tconst stop = Number.parseInt(l[2])\n\t\t\t\tif (Number.isNaN(start) || Number.isNaN(stop)) throw 'Invalid start/stop value in regions'\n\t\t\t\trglst.push({ chr: l[0], start: start, stop: stop })\n\t\t\t}\n\t\t}\n\n\t\tif (!position && !rglst) {\n\t\t\t// no position given, use default\n\t\t\tif (genomeobj.defaultcoord) {\n\t\t\t\tposition = {\n\t\t\t\t\tchr: genomeobj.defaultcoord.chr,\n\t\t\t\t\tstart: genomeobj.defaultcoord.start,\n\t\t\t\t\tstop: genomeobj.defaultcoord.stop\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\n\t\tif (position) {\n\t\t\tpar.chr = position.chr\n\t\t\tpar.start = position.start\n\t\t\tpar.stop = position.stop\n\t\t} else if (rglst) {\n\t\t\tpar.rglst = rglst\n\t\t}\n\n\t\tif (urlp.has('hlregion')) {\n\t\t\tconst lst = []\n\t\t\tfor (const t of urlp.get('hlregion').split(',')) {\n\t\t\t\tconst pos = string2pos(t, genomeobj, true)\n\t\t\t\tif (pos) lst.push(pos)\n\t\t\t}\n\t\t\tif (lst.length) par.hlregions = lst\n\t\t}\n\n\t\tpar.datasetqueries = may_get_officialmds(urlp)\n\n\t\tpar.tklst = await get_tklst(urlp, genomeobj)\n\n\t\tfirst_genetrack_tolist(arg.genomes[genomename], par.tklst)\n\n\t\tmayAddBedjfilterbyname(urlp, par.tklst)\n\t\tconst b = await import('./block')\n\t\tnew b.Block(par)\n\t\treturn\n\t}\n\n\tif (urlp.has('gene')) {\n\t\tconst str = urlp.get('gene')\n\t\tif (str.length == 0) throw 'zero length query string'\n\t\tconst par = {\n\t\t\thostURL: arg.hostURL,\n\t\t\tquery: str,\n\t\t\tholder: arg.holder,\n\t\t\tvariantPageCall_snv: arg.variantPageCall_snv,\n\t\t\tsamplecart: arg.samplecart,\n\t\t\tdebugmode: arg.debugmode\n\t\t}\n\t\t{\n\t\t\tlet genomename\n\t\t\tfor (let n in arg.genomes) {\n\t\t\t\tif (arg.genomes[n].isdefault) {\n\t\t\t\t\tgenomename = n\n\t\t\t\t\tbreak\n\t\t\t\t}\n\t\t\t}\n\t\t\tif (urlp.has('genome')) {\n\t\t\t\tgenomename = urlp.get('genome')\n\t\t\t}\n\t\t\tif (!genomename) throw 'No genome, and none set as default'\n\t\t\tpar.genome = arg.genomes[genomename]\n\t\t\tif (!par.genome) throw 'invalid genome: ' + genomename\n\t\t}\n\t\tlet ds = null\n\t\tif (urlp.has('dataset')) {\n\t\t\tpar.dataset = urlp.get('dataset').split(',')\n\t\t}\n\t\tif (urlp.has('hlaachange')) {\n\t\t\tpar.hlaachange = new Map()\n\t\t\tfor (const s of urlp.get('hlaachange').split(',')) {\n\t\t\t\tpar.hlaachange.set(s, false)\n\t\t\t}\n\t\t}\n\t\tif (urlp.has('hlregion')) {\n\t\t\tconst lst = []\n\t\t\tfor (const t of urlp.get('hlregion').split(',')) {\n\t\t\t\tconst pos = string2pos(t, par.genome, true)\n\t\t\t\tif (pos) lst.push(pos)\n\t\t\t}\n\t\t\tif (lst.length) par.hlregions = lst\n\t\t}\n\n\t\tpar.tklst = await get_tklst(urlp, par.genome)\n\n\t\tmayAddBedjfilterbyname(urlp, par.tklst)\n\n\t\tpar.datasetqueries = may_get_officialmds(urlp)\n\t\tawait blockinit(par)\n\t\treturn\n\t}\n\n\tif (urlp.has('disco')) {\n\t\t// a direct link to make manual testing easy\n\t\tconst genomeName = urlp.get('genome')\n\t\tconst genome = arg.genomes[genomeName]\n\t\tif (!genome) throw 'genome missing'\n\t\tconst dslabel = urlp.get('dslabel')\n\t\tif (!dslabel) throw 'dslabel missing'\n\t\tconst sample_id = urlp.get('sample')\n\t\tif (!sample_id) throw 'sample_id missing'\n\t\tconst vocabApi = (await import('#termdb/vocabulary')).vocabInit({ state: { genome: genomeName, dslabel } })\n\t\tconst termdbConfig = await vocabApi.getTermdbConfig()\n\t\tawait (await import('#plots/plot.disco.js')).default(termdbConfig, dslabel, { sample_id }, arg.holder, genome)\n\t\treturn\n\t}\n\n\t///////////// legacy, totally replaced by mass. kept for some views on vizcom\n\tif (urlp.has('study')) {\n\t\tconst v = urlp.get('study')\n\t\tif (v != '') {\n\t\t\tloadstudycohort(\n\t\t\t\targ.genomes,\n\t\t\t\tv,\n\t\t\t\targ.holder,\n\t\t\t\targ.hostURL,\n\t\t\t\tundefined, // jwt\n\t\t\t\tfalse, // no show\n\t\t\t\targ.app || {\n\t\t\t\t\tdebugmode: arg.debugmode,\n\t\t\t\t\tinstanceTracker: arg.instanceTracker || {},\n\t\t\t\t\tcallbacks: arg.callbacks || {}\n\t\t\t\t}\n\t\t\t)\n\t\t}\n\t}\n}\n\nfunction may_get_officialmds(urlp) {\n\tif (!urlp.has('mds')) return\n\tconst tmp = urlp.get('mds').split(',')\n\tif (tmp[0] && tmp[1]) {\n\t\tconst dataset = { dataset: tmp[0], querykey: tmp[1] }\n\t\tif (urlp.has('sample')) {\n\t\t\tdataset.singlesample = { name: urlp.get('sample') }\n\t\t\t// quick fix!!\n\t\t\t// tell  mds_load_query_bykey to load assay tracks in this context, but will not do so if launching sample view from main tk\n\t\t\tdataset.getsampletrackquickfix = true\n\t\t}\n\t\treturn [dataset]\n\t}\n\treturn\n}\n\nexport async function get_tklst(urlp, genomeobj) {\n\tconst tklst = []\n\n\tfor (const [key, value] of urlp) {\n\t\tconst tks = await mayGetTkobj(key, value, urlp, genomeobj)\n\t\tif (!tks) continue // no tkobj derived, parameter doesn't match with anything\n\t\tif (Array.isArray(tks)) tklst.push(...tks)\n\t\telse tklst.push(tks)\n\t}\n\n\tfor (const t of tklst) {\n\t\t// uncertain reason why all tk are labeled as custom\n\t\t// the mds3 tk has \"dslabel\" and should be official, do not label as custom, so in block.tk.menu won't show the delete button\n\t\tif (t.type == 'mds3' && t.dslabel) continue\n\t\tt.iscustom = true\n\t}\n\n\t// quick fix to modify behaviors of mds tracks collected through parameters\n\t// if isdense=1, turn to dense\n\t// if sample=..., change to a single sample track\n\tif (urlp.has('isdense')) {\n\t\ttklst\n\t\t\t.filter(t => t.type == client.tkt.mdssvcnv)\n\t\t\t.forEach(t => {\n\t\t\t\tt.isdense = true\n\t\t\t\tt.isfull = false\n\t\t\t})\n\t}\n\tif (urlp.has('sample')) {\n\t\ttklst\n\t\t\t.filter(t => t.type == client.tkt.mdssvcnv)\n\t\t\t.forEach(t => {\n\t\t\t\tt.singlesample = { name: urlp.get('sample') }\n\t\t\t\tt.getsampletrackquickfix = true\n\t\t\t\t// XXX this doesn't work to load assay tracks for a custom mds, can only load for official mds\n\t\t\t\t// for both custom and official, the expression rank track is not loaded.\n\t\t\t})\n\t}\n\treturn tklst\n}\n\n/*\nreturns:\n- object for one successfully parsed track\n- array for multiple track objects, could be empty!\n- null for no tracks\n*/\nexport async function mayGetTkobj(key, value, urlp, genomeobj) {\n\tif (key == 'mds3') {\n\t\t// official mds3 dataset; value is comma-joined dslabels\n\t\tconst lst = value.split(',')\n\t\tconst tks = []\n\t\tfor (const n of lst) {\n\t\t\tconst tk = {\n\t\t\t\ttype: client.tkt.mds3,\n\t\t\t\tdslabel: n\n\t\t\t}\n\t\t\tif (urlp.has('token')) tk.token = urlp.get('token') // temporary\n\t\t\tif (urlp.has('filterobj')) tk.filterObj = urlp.get('filterobj')\n\t\t\tif (urlp.has('cnvonly')) tk.hardcodeCnvOnly = true // for testing cnv-only mode via url param; in actual use this flag should be set in runpp()\n\t\t\tif (urlp.has('snvindelonly')) tk.snvIndelOnly = true // for testing snvindel-only mode\n\t\t\ttks.push(tk)\n\t\t}\n\t\treturn tks\n\t}\n\n\tif (key == 'mds3bcffile') {\n\t\t// \"name,path\" pairs to server-side vcf files\n\t\tconst [tkname, bcffile] = value.split(',')\n\t\tlet tk\n\t\tif (tkname && bcffile) {\n\t\t\ttk = {\n\t\t\t\ttype: client.tkt.mds3,\n\t\t\t\tname: tkname,\n\t\t\t\tbcf: { file: bcffile }\n\t\t\t}\n\t\t}\n\t\treturn tk\n\t}\n\tif (key == 'mds3bcfurl') {\n\t\t// \"name,url,indexURL\" to remote file. indexURL is optional when the index file is not co-locating with the bcf file\n\t\tconst [tkname, url, indexURL] = value.split(',')\n\t\tlet tk\n\t\tif (tkname && url) {\n\t\t\ttk = {\n\t\t\t\ttype: client.tkt.mds3,\n\t\t\t\tname: tkname,\n\t\t\t\tbcf: { url, indexURL }\n\t\t\t}\n\t\t}\n\t\treturn tk\n\t}\n\n\tif (key == 'arcfile') {\n\t\tconst lst = value.split(',')\n\t\tconst tks = []\n\t\tfor (let i = 0; i < lst.length; i += 2) {\n\t\t\tif (lst[i] && lst[i + 1]) {\n\t\t\t\ttks.push({\n\t\t\t\t\ttype: client.tkt.hicstraw,\n\t\t\t\t\tname: lst[i],\n\t\t\t\t\tbedfile: lst[i + 1],\n\t\t\t\t\tmode_hm: false,\n\t\t\t\t\tmode_arc: true\n\t\t\t\t})\n\t\t\t}\n\t\t}\n\t\treturn tks\n\t}\n\n\tif (key == 'mdsjson' || key == 'mdsjsonurl') {\n\t\tlet url_str, file_str\n\t\tif (key == 'mdsjson') file_str = value\n\t\telse url_str = value\n\t\treturn await mdsjson.init_mdsjson(file_str, url_str)\n\t}\n\n\tif (key == 'tkjsonfile') {\n\t\tconst re = await client.dofetch('textfile', { file: value })\n\t\tif (re.error) throw re.error\n\t\tif (!re.text) throw '.text missing'\n\t\tconst lst = JSON.parse(re.text)\n\t\tconst tks = []\n\t\tfor (const i of lst) {\n\t\t\tif (i.isfacet) {\n\t\t\t\tif (!genomeobj.tkset) genomeobj.tkset = []\n\t\t\t\tif (!i.tracks) throw '.tracks[] missing from a facet table'\n\t\t\t\tif (!Array.isArray(i.tracks)) throw '.tracks[] not an array from a facet table'\n\t\t\t\ti.tklst = i.tracks\n\t\t\t\tdelete i.tracks\n\t\t\t\tfor (const t of i.tklst) {\n\t\t\t\t\tif (!t.assay) throw '.assay missing from a facet track'\n\t\t\t\t\tif (!t.sample) throw '.sample missing from a facet track'\n\t\t\t\t\t// must assign tkid otherwise the tk buttons from facet table won't work\n\t\t\t\t\tt.tkid = Math.random().toString()\n\t\t\t\t}\n\t\t\t\tgenomeobj.tkset.push(i)\n\t\t\t} else {\n\t\t\t\t// must be a track\n\t\t\t\ttks.push(i)\n\t\t\t}\n\t\t}\n\t\treturn tks\n\t}\n\n\tif (key == 'bamfile') {\n\t\tconst lst = value.split(',')\n\t\tconst tks = []\n\t\tfor (let i = 0; i < lst.length; i += 2) {\n\t\t\tif (lst[i] && lst[i + 1]) {\n\t\t\t\ttks.push({\n\t\t\t\t\ttype: client.tkt.bam,\n\t\t\t\t\tname: lst[i],\n\t\t\t\t\tfile: lst[i + 1]\n\t\t\t\t})\n\t\t\t}\n\t\t}\n\t\treturn tks\n\t}\n\tif (key == 'bamurl') {\n\t\tconst lst = value.split(',')\n\t\tconst tks = []\n\t\tfor (let i = 0; i < lst.length; i += 2) {\n\t\t\tif (lst[i] && lst[i + 1]) {\n\t\t\t\ttks.push({\n\t\t\t\t\ttype: client.tkt.bam,\n\t\t\t\t\tname: lst[i],\n\t\t\t\t\turl: lst[i + 1]\n\t\t\t\t})\n\t\t\t}\n\t\t}\n\t\treturn tks\n\t}\n\tif (key == 'bedjfile') {\n\t\tconst lst = value.split(',')\n\t\tconst tks = []\n\t\tfor (let i = 0; i < lst.length; i += 2) {\n\t\t\tif (lst[i] && lst[i + 1]) {\n\t\t\t\ttks.push({\n\t\t\t\t\ttype: client.tkt.bedj,\n\t\t\t\t\tname: lst[i],\n\t\t\t\t\tfile: lst[i + 1]\n\t\t\t\t})\n\t\t\t}\n\t\t}\n\t\treturn tks\n\t}\n\tif (key == 'bedjurl') {\n\t\tconst lst = value.split(',')\n\t\tconst tks = []\n\t\tfor (let i = 0; i < lst.length; i += 2) {\n\t\t\tif (lst[i] && lst[i + 1]) {\n\t\t\t\ttks.push({\n\t\t\t\t\ttype: client.tkt.bedj,\n\t\t\t\t\tname: lst[i],\n\t\t\t\t\turl: lst[i + 1]\n\t\t\t\t})\n\t\t\t}\n\t\t}\n\t\treturn tks\n\t}\n\tif (key == 'hictkfile' || key == 'hictkurl') {\n\t\t// name,enzyme,file/url\n\t\tconst isfile = key == 'hictkfile'\n\t\tconst lst = value.split(',')\n\t\tconst norm = urlp.has('hictknorm') ? urlp.get('hictknorm').split(',') : null\n\t\tconst tks = []\n\t\tfor (let i = 0; i < lst.length; i += 3) {\n\t\t\tif (lst[i] && lst[i + 1] && lst[i + 2]) {\n\t\t\t\tconst t = {\n\t\t\t\t\ttype: client.tkt.hicstraw,\n\t\t\t\t\tname: lst[i],\n\t\t\t\t\tenzyme: lst[i + 1],\n\t\t\t\t\tnormalizationmethod: norm ? norm[i / 3] : null\n\t\t\t\t}\n\t\t\t\tif (isfile) {\n\t\t\t\t\tt.file = lst[i + 2]\n\t\t\t\t} else {\n\t\t\t\t\tt.url = lst[i + 2]\n\t\t\t\t}\n\t\t\t\ttks.push(t)\n\t\t\t}\n\t\t}\n\t\treturn tks\n\t}\n\tif (key == 'ldfile') {\n\t\tconst lst = value.split(',')\n\t\tconst tks = []\n\t\tfor (let i = 0; i < lst.length; i += 2) {\n\t\t\tif (lst[i] && lst[i + 1]) {\n\t\t\t\ttks.push({\n\t\t\t\t\ttype: client.tkt.ld,\n\t\t\t\t\tname: lst[i],\n\t\t\t\t\tfile: lst[i + 1]\n\t\t\t\t})\n\t\t\t}\n\t\t}\n\t\treturn tks\n\t}\n\tif (key == 'bigwigfile') {\n\t\tconst lst = value.split(',')\n\t\tconst tks = []\n\t\tfor (let i = 0; i < lst.length; i += 2) {\n\t\t\tif (lst[i] && lst[i + 1]) {\n\t\t\t\ttks.push({\n\t\t\t\t\ttype: client.tkt.bigwig,\n\t\t\t\t\tname: lst[i],\n\t\t\t\t\tfile: lst[i + 1],\n\t\t\t\t\tscale: { auto: 1 }\n\t\t\t\t})\n\t\t\t}\n\t\t}\n\t\treturn tks\n\t}\n\tif (key == 'bigwigurl') {\n\t\tconst lst = value.split(',')\n\t\tconst tks = []\n\t\tfor (let i = 0; i < lst.length; i += 2) {\n\t\t\tif (lst[i] && lst[i + 1]) {\n\t\t\t\ttks.push({\n\t\t\t\t\ttype: client.tkt.bigwig,\n\t\t\t\t\tname: lst[i],\n\t\t\t\t\turl: lst[i + 1],\n\t\t\t\t\tscale: { auto: 1 }\n\t\t\t\t})\n\t\t\t}\n\t\t}\n\t\treturn tks\n\t}\n\tif (key == 'junctionfile') {\n\t\t// legacy\n\t\tconst lst = value.split(',')\n\t\tconst tks = []\n\t\tfor (let i = 0; i < lst.length; i += 2) {\n\t\t\tif (lst[i] && lst[i + 1]) {\n\t\t\t\ttks.push({\n\t\t\t\t\ttype: client.tkt.junction,\n\t\t\t\t\tname: lst[i],\n\t\t\t\t\ttracks: [\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\tfile: lst[i + 1]\n\t\t\t\t\t\t}\n\t\t\t\t\t]\n\t\t\t\t})\n\t\t\t}\n\t\t}\n\t\treturn tks\n\t}\n\tif (key == 'junctionurl') {\n\t\tconst lst = value.split(',')\n\t\tconst tks = []\n\t\tfor (let i = 0; i < lst.length; i += 2) {\n\t\t\tif (lst[i] && lst[i + 1]) {\n\t\t\t\ttks.push({\n\t\t\t\t\ttype: client.tkt.junction,\n\t\t\t\t\tname: lst[i],\n\t\t\t\t\ttracks: [\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\turl: lst[i + 1]\n\t\t\t\t\t\t}\n\t\t\t\t\t]\n\t\t\t\t})\n\t\t\t}\n\t\t}\n\t\treturn tks\n\t}\n\t/*\n\tif (urlp.has('vcffile')) {\n\t\tconst lst = urlp.get('vcffile').split(',')\n\t\tfor (let i = 0; i < lst.length; i += 2) {\n\t\t\tif (lst[i] && lst[i + 1]) {\n\t\t\t\ttklst.push({\n\t\t\t\t\ttype: 'vcf',\n\t\t\t\t\tname: lst[i],\n\t\t\t\t\tfile: lst[i + 1]\n\t\t\t\t})\n\t\t\t}\n\t\t}\n\t}\n\tif (urlp.has('vcfurl')) {\n\t\tconst lst = urlp.get('vcfurl').split(',')\n\t\tfor (let i = 0; i < lst.length; i += 2) {\n\t\t\tif (lst[i] && lst[i + 1]) {\n\t\t\t\ttklst.push({\n\t\t\t\t\ttype: 'vcf',\n\t\t\t\t\tname: lst[i],\n\t\t\t\t\turl: lst[i + 1]\n\t\t\t\t})\n\t\t\t}\n\t\t}\n\t}\n\t*/\n\tif (key == 'aicheckfile') {\n\t\tconst lst = value.split(',')\n\t\tconst tks = []\n\t\tfor (let i = 0; i < lst.length; i += 2) {\n\t\t\tif (lst[i] && lst[i + 1]) {\n\t\t\t\ttks.push({\n\t\t\t\t\ttype: 'aicheck',\n\t\t\t\t\tname: lst[i],\n\t\t\t\t\tfile: lst[i + 1]\n\t\t\t\t})\n\t\t\t}\n\t\t}\n\t\treturn tks\n\t}\n\tif (key == 'bampilefile') {\n\t\tconst lst = value.split(',')\n\t\tlet links = null\n\t\tif (urlp.has('bampilelink')) {\n\t\t\tlinks = urlp.get('bampilelink').split(',').map(decodeURIComponent)\n\t\t}\n\t\tconst tks = []\n\t\tfor (let i = 0; i < lst.length; i += 2) {\n\t\t\tif (lst[i] && lst[i + 1]) {\n\t\t\t\tconst tk = {\n\t\t\t\t\ttype: client.tkt.bampile,\n\t\t\t\t\tname: lst[i],\n\t\t\t\t\tfile: lst[i + 1]\n\t\t\t\t}\n\t\t\t\tif (links && links[i / 2]) {\n\t\t\t\t\ttk.link = links[i / 2]\n\t\t\t\t}\n\t\t\t\ttks.push(tk)\n\t\t\t}\n\t\t}\n\t\treturn tks\n\t}\n\tif (key == 'svcnvfpkmurl') {\n\t\tconst lst = value.split(',')\n\t\t// defines a single track, all members using url\n\t\tconst name = lst[0]\n\t\tconst type2url = {}\n\t\tfor (let i = 1; i < lst.length; i += 2) {\n\t\t\ttype2url[lst[i]] = lst[i + 1]\n\t\t}\n\t\tlet tk\n\t\tif (type2url.svcnv || type2url.vcf) {\n\t\t\ttk = {\n\t\t\t\ttype: client.tkt.mdssvcnv,\n\t\t\t\tname: name\n\t\t\t}\n\t\t\tif (type2url.svcnv) {\n\t\t\t\ttk.url = type2url.svcnv\n\t\t\t}\n\t\t\tif (type2url.vcf) {\n\t\t\t\ttk.checkvcf = {\n\t\t\t\t\turl: type2url.vcf,\n\t\t\t\t\tindexURL: type2url.vcfindex\n\t\t\t\t}\n\t\t\t}\n\t\t\tif (type2url.fpkm) {\n\t\t\t\ttk.checkexpressionrank = {\n\t\t\t\t\tdatatype: 'FPKM',\n\t\t\t\t\turl: type2url.fpkm,\n\t\t\t\t\tindexURL: type2url.fpkmindex\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\treturn tk\n\t}\n\tif (key == 'svcnvfpkmfile') {\n\t\tconst lst = value.split(',')\n\t\t// defines a single track, all members using file\n\t\tconst name = lst[0]\n\t\tconst type2file = {}\n\t\tfor (let i = 1; i < lst.length; i += 2) {\n\t\t\ttype2file[lst[i]] = lst[i + 1]\n\t\t}\n\t\tlet tk\n\t\tif (type2file.svcnv || type2file.vcf) {\n\t\t\ttk = {\n\t\t\t\ttype: client.tkt.mdssvcnv,\n\t\t\t\tname: name\n\t\t\t}\n\t\t\tif (type2file.svcnv) {\n\t\t\t\ttk.file = type2file.svcnv\n\t\t\t}\n\t\t\tif (type2file.vcf) {\n\t\t\t\ttk.checkvcf = {\n\t\t\t\t\tfile: type2file.vcf\n\t\t\t\t}\n\t\t\t}\n\t\t\tif (type2file.fpkm) {\n\t\t\t\ttk.checkexpressionrank = {\n\t\t\t\t\tdatatype: 'FPKM',\n\t\t\t\t\tfile: type2file.fpkm\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\treturn tk\n\t}\n\tif (key == 'mdsjunctionfile') {\n\t\tconst lst = value.split(',')\n\t\tconst tks = []\n\t\tfor (let i = 0; i < lst.length; i += 2) {\n\t\t\tif (lst[i] && lst[i + 1]) {\n\t\t\t\ttks.push({\n\t\t\t\t\ttype: 'mdsjunction',\n\t\t\t\t\tname: lst[i],\n\t\t\t\t\tfile: lst[i + 1]\n\t\t\t\t})\n\t\t\t}\n\t\t}\n\t\treturn tks\n\t}\n\tif (key == 'junctionmatrix') {\n\t\tconst lst = value.split(',')\n\t\tconst tks = []\n\t\tfor (let i = 0; i < lst.length; i += 2) {\n\t\t\tif (lst[i] && lst[i + 1]) {\n\t\t\t\ttks.push({\n\t\t\t\t\ttype: 'mdsjunction',\n\t\t\t\t\tname: lst[i],\n\t\t\t\t\tfile2: lst[i + 1] // quick fix to support new file type\n\t\t\t\t})\n\t\t\t}\n\t\t}\n\t\treturn tks\n\t}\n\n\tif (key == 'junctionrnapeg') {\n\t\tconst lst = value.split(',')\n\t\tconst tks = []\n\t\tfor (let i = 0; i < lst.length; i += 2) {\n\t\t\tif (lst[i] && lst[i + 1]) {\n\t\t\t\ttks.push({\n\t\t\t\t\ttype: client.tkt.junction,\n\t\t\t\t\tname: lst[i],\n\t\t\t\t\ttracks: [{ rnapegfile: lst[i + 1] }]\n\t\t\t\t})\n\t\t\t}\n\t\t}\n\t\treturn tks\n\t}\n}\n\nfunction mayAddBedjfilterbyname(urlp, tklst) {\n\t/* !! a quick fix !!\n\tthe filter string will be applied to all bedj tracks,\n\trather than specific for a track\n\tmay mess up with other bedj tracks shown at the same time\n\t*/\n\tif (urlp.has('bedjfilterbyname')) {\n\t\tfor (const t of tklst) {\n\t\t\tif (t.type == 'bedj') t.filterByName = urlp.get('bedjfilterbyname')\n\t\t}\n\t}\n}\n"],
-  "mappings": 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-  "names": ["element"]
-}

package/dist/chunk-J4SOF2ZH.js

@@ -1,263 +0,0 @@
-import {
-  hierCluster_renderers_exports
-} from "./chunk-SHWLROJG.js";
-import {
-  hierCluster_interactivity_exports
-} from "./chunk-NSXZPWRP.js";
-import {
-  Matrix
-} from "./chunk-6A3IPDE2.js";
-import {
-  filterJoin,
-  getNormalRoot
-} from "./chunk-SA7APTJR.js";
-import {
-  clusterMethodLst,
-  distanceMethodLst,
-  dofetch3
-} from "./chunk-7EMWHCVW.js";
-import {
-  deepEqual,
-  getCompInit
-} from "./chunk-M3J4MINX.js";
-import {
-  NUMERIC_DICTIONARY_TERM,
-  TermTypes2Dt
-} from "./chunk-NOEAT6CX.js";
-import {
-  colorScaleMap
-} from "./chunk-4UWS5Y3N.js";
-import {
-  extent,
-  linear
-} from "./chunk-OAWQ6LOO.js";
-
-// plots/matrix/hierCluster.js
-var HierCluster = class _HierCluster extends Matrix {
-  static type = "hierCluster";
-  constructor(opts) {
-    super(opts);
-    this.type = _HierCluster.type;
-    this.chartType = _HierCluster.type;
-  }
-  async init(appState) {
-    await super.init(appState);
-    this.maySetSandboxHeader(appState);
-    this.hcClipId = this.seriesClipId + "-hc";
-    this.dom.hcClipRect = this.dom.svg.select("defs").append("clipPath").attr("id", this.hcClipId).attr("clipPathUnits", "userSpaceOnUse").append("rect").attr("display", "block");
-    this.dom.topDendrogram = this.dom.svg.insert("g", "g").attr("clip-path", `url(#${this.hcClipId})`).append("g").attr("class", "sjpp-matrix-dendrogram").attr("data-testid", "hierCluster_top_dendrogram").on("click", (event) => {
-      const clickedClusterId = this.getClusterFromTopDendrogram(event);
-      if (clickedClusterId) {
-        this.clickedClusterIds = this.getAllChildrenClusterIds(clickedClusterId);
-        this.clickedClusterIds.push(clickedClusterId);
-        const clickedCluster = this.hierClusterData.clustering.col.mergedClusters.get(clickedClusterId);
-        const clickedClusterSampleNames = clickedCluster.children.map((c) => c.name);
-        this.addSelectedSamplesOptions(clickedClusterSampleNames, event);
-      } else {
-        delete this.clickedClusterIds;
-      }
-      if (this.clickedLeftClusterIds) {
-        delete this.clickedLeftClusterIds;
-        this.plotDendrogramHclust();
-      } else this.plotDendrogramHclust("top");
-    });
-    this.dom.leftDendrogram = this.dom.svg.insert("g", "g").attr("class", "sjpp-matrix-dendrogram").attr("data-testid", "hierCluster_left_dendrogram").on("click", (event) => {
-      const clickedLeftClusterId = this.getClusterFromLeftDendrogram(event);
-      if (clickedLeftClusterId) {
-        this.clickedLeftClusterIds = this.getAllChildrenClusterIds(clickedLeftClusterId, true);
-        this.clickedLeftClusterIds.push(clickedLeftClusterId);
-        const clickedLeftCluster = this.hierClusterData.clustering.row.mergedClusters.get(clickedLeftClusterId);
-        const clickedLeftClusterRowsNames = clickedLeftCluster.children.map((c) => c.name);
-        this.addSelectedRowsOptions(clickedLeftClusterRowsNames, event);
-      } else {
-        delete this.clickedLeftClusterIds;
-      }
-      if (this.clickedClusterIds) {
-        delete this.clickedClusterIds;
-        this.plotDendrogramHclust();
-      } else this.plotDendrogramHclust("left");
-    });
-  }
-  async setHierClusterData(_data = {}) {
-    this.prevServerData = this.currServerData;
-    const [d, twlst] = await this.requestData({});
-    if (d.error) throw d.error;
-    this.currServerData = structuredClone(d);
-    if (!deepEqual(this.prevServerData, this.currServerData)) {
-      delete this.clickedClusterIds;
-      delete this.clickedLeftClusterIds;
-    }
-    const s = this.settings.hierCluster;
-    if (!d.clustering) {
-      if (d.gene) {
-        throw `Cannot do clustering: data is only available for 1 gene (${d.gene}). Try again by adding more genes.`;
-      }
-    }
-    this.hierClusterData = d;
-    const c = this.hierClusterData.clustering;
-    this.setHierColorScale(c);
-    const samples = {};
-    for (const [i, column] of c.col.order.entries()) {
-      samples[column.name] = { sample: column.name };
-      for (const [j, row] of c.row.order.entries()) {
-        const tw = twlst.find((tw2) => tw2.$id === row.name || tw2.id === row.name);
-        const value = c.matrix[j][i];
-        samples[column.name][tw.$id] = {
-          key: tw.term.name,
-          values: [
-            {
-              sample: column.name,
-              dt: TermTypes2Dt[this.state.config.dataType],
-              label: s.termGroupName,
-              // gene: tw.term.name,
-              // chr: tw.term.chr,
-              // pos: `${tw.term.start}-${tw.term.stop}`,
-              value
-              // the color will be computed in matrix.cells, so that
-              // it can get updated even when there are no nonsetting state diff
-            }
-          ]
-        };
-      }
-    }
-    this.hcTermNameOrder = this.settings.hierCluster.sortClusterRows == "asListed" ? twlst.map((t) => t.term.name) : this.settings.hierCluster.sortClusterRows == "byName" ? twlst.map((t) => t.term.name).sort() : this.config.dataType === NUMERIC_DICTIONARY_TERM ? c.row.order.map((row) => twlst.find((t) => t.$id == row.name || t.term.id == row.name)?.term.name) : c.row.order.map((row) => twlst.find((t) => t.$id == row.name)?.term.name);
-    if (this.hcTermNameOrder.includes(void 0)) throw `unable to map row.name to term.name`;
-    this.hcTermSorter = (a, b) => {
-      const i = this.hcTermNameOrder.indexOf(a.tw.term.name);
-      const j = this.hcTermNameOrder.indexOf(b.tw.term.name);
-      if (i == -1 && j == -1) return 0;
-      if (i == -1) return 1;
-      if (j == -1) return -1;
-      return i - j;
-    };
-    this.hcSampleNameOrder = c.col.order.map((col) => col.name);
-    this.hcSampleSorter = (a, b) => {
-      const i = this.hcSampleNameOrder.indexOf(a.sample);
-      const j = this.hcSampleNameOrder.indexOf(b.sample);
-      if (i == -1 && j == -1) return 0;
-      if (i == -1) return 1;
-      if (j == -1) return -1;
-      return i - j;
-    };
-    const byTermId = {};
-    for (const tw of twlst) {
-      if (d.byTermId?.[tw.term.name]) byTermId[tw.$id] = d.byTermId[tw.term.name];
-    }
-    this.hierClusterSamples = {
-      refs: { byTermId, bySampleId: d.bySampleId },
-      lst: c.col.order.map((c2) => samples[c2.name]),
-      samples,
-      removedHierClusterTerms: d.removedHierClusterTerms
-    };
-  }
-  async requestData() {
-    const body = this.currRequestOpts?.hierCluster || this.getHCRequestBody(this.state);
-    const twlst = this.hcTermGroup.lst;
-    const data = await dofetch3("termdb/cluster", { body, signal: this.api.getAbortSignal?.() });
-    return [data, twlst];
-  }
-  getHCRequestBody(state) {
-    this.hcTermGroup = this.config.termgroups.find((grp) => grp.type == "hierCluster") || this.termOrder?.find((t) => t.grp.type == "hierCluster")?.grp;
-    const s = state.config.settings.hierCluster;
-    const dictionaryLegendFilter = {
-      type: "tvslst",
-      in: true,
-      join: "and",
-      lst: state.config.legendValueFilter.lst.filter((f) => !f.tvs.legendFilterType)
-    };
-    const terms = this.getClusterRowTermsAsParameter();
-    if (!terms.length) throw "no data";
-    if (!clusterMethodLst.find((i) => i.value == s.clusterMethod)) throw "Invalid cluster method";
-    if (!distanceMethodLst.find((i) => i.value == s.distanceMethod)) throw "Invalid distance method";
-    const body = {
-      genome: state.vocab.genome,
-      dslabel: state.vocab.dslabel,
-      dataType: state.config.dataType,
-      clusterMethod: s.clusterMethod,
-      distanceMethod: s.distanceMethod,
-      zScoreTransformation: s.zScoreTransformation,
-      terms,
-      filter: getNormalRoot(filterJoin([state.filter, dictionaryLegendFilter])),
-      filter0: state.filter0
-    };
-    if (state.config.dataType == "proteomeAbundance") {
-      body.proteomeDetails = {
-        organism: state.config.proteomeDetails?.organism,
-        assay: state.config.proteomeDetails?.assay,
-        cohort: state.config.proteomeDetails?.cohort
-      };
-    }
-    return body;
-  }
-  combineData() {
-    if (!this.hierClusterSamples) return;
-    const d = this.data;
-    const removedHierClusterTerms = this.hierClusterSamples.removedHierClusterTerms;
-    const samples = {};
-    const lst = [];
-    for (const sampleId in this.hierClusterSamples.samples) {
-      const s = this.hierClusterSamples.samples[sampleId];
-      samples[sampleId] = s;
-      lst.push(s);
-      if (sampleId in d.samples) Object.assign(s, d.samples[sampleId]);
-      const _ref_ = this.hierClusterSamples.refs.bySampleId[sampleId] || {};
-      if (!s._ref_) s._ref_ = _ref_;
-      else Object.assign(s._ref_, _ref_);
-    }
-    const t = this.hierClusterSamples.refs.byTermId;
-    for (const $id of Object.keys(t)) {
-      d.refs.byTermId[$id] = Object.assign({}, d.refs.byTermId[$id] || {}, t[$id]);
-    }
-    this.data = { samples, lst, refs: d.refs, removedHierClusterTerms };
-  }
-  setHierColorScale(c) {
-    const hc = this.settings.hierCluster;
-    const scale = linear(colorScaleMap[hc.colorScale].domain, colorScaleMap[hc.colorScale].range).clamp(true);
-    const globalMinMaxes = [];
-    for (const row of c.matrix) {
-      globalMinMaxes.push(...extent(row));
-    }
-    const absMax = Math.min(hc.zScoreCap, Math.max(...extent(globalMinMaxes).map(Math.abs)));
-    const [min, max] = hc.zScoreTransformation ? [-absMax, absMax] : [Math.min(...globalMinMaxes), Math.max(...globalMinMaxes)];
-    this.hierClusterValues = { scale, min, max };
-  }
-  getValueColor(value) {
-    const hc = this.settings.hierCluster;
-    if (hc.zScoreTransformation) {
-      const zScoreCap = this.settings.hierCluster.zScoreCap;
-      return this.hierClusterValues.scale((value - -zScoreCap) / (zScoreCap * 2));
-    } else {
-      return this.hierClusterValues.scale(value / this.hierClusterValues.max);
-    }
-  }
-  /* returns list of gene terms as request parameter, e.g. {gene,chr,start,stop}
-  	request parameter only need term but not tw, as it will simply fetch continuous sample values on terms without transform
-  
-  	use of this function is unfortunate because:
-  		the incomplete migration of {name} to {gene} for gene-based term
-  		geneset edit ui is hardcoded to return {name}
-  		existing plot states contain {name}
-  
-  	!!! migration instruction !!!
-  	- term.name is for display only, if a term is gene-based, it has term.gene=str
-  	- a geneVariant term can be based on a genomic range (and not a gene), in that case it won't have term.gene and cannot be used where gene is expected, e.g. gene-based clustering analysis
-  
-  	*/
-  getClusterRowTermsAsParameter() {
-    const lst = this.hcTermGroup.lst.map(this.opts.app.vocabApi.getTwMinCopy);
-    lst.sort((a, b) => a.term.name < b.term.name ? -1 : 1);
-    return lst;
-  }
-};
-for (const methods of [hierCluster_renderers_exports, hierCluster_interactivity_exports]) {
-  for (const methodName in methods) HierCluster.prototype[methodName] = methods[methodName];
-}
-var hierClusterInit = getCompInit(HierCluster);
-var componentInit = hierClusterInit;
-
-export {
-  HierCluster,
-  hierClusterInit,
-  componentInit
-};
-//# sourceMappingURL=chunk-J4SOF2ZH.js.map