@sjcrh/proteinpaint-client 2.181.0 → 2.183.0

package/dist/bam-BDWTA4O3.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../gdc/bam.js"],
+  "sourcesContent": ["import { dofetch3 } from '#common/dofetch'\nimport { sayerror, addGeneSearchbox, string2variant, Menu, Tabs, renderTable, table2col, make_one_checkbox } from '#dom'\nimport { first_genetrack_tolist } from '#common/1stGenetk'\nimport { contigNameNoChr2, mclass } from '#shared/common.js'\nimport urlmap from '#common/urlmap'\nimport { fileSize } from '#shared/fileSize.js'\nimport { keyupEnter } from '../src/client'\n\n/*\n\nSV_EXPAND: to be expanded to support SV review using subpanel\n\n*********** gdc_args{}\ngdc_args {}\n\trunFlags{}\n\tgdc_token: <string>,\n\tbam_files: [ {} ]\n\t\tfile_id: file uuid from gdc <string>,\n\t\ttrack_name: used for naming of track <string> //optional\n\t\tabout:[] // with keys corresponding to baminfo_cols[]\n\tcase_id: <string>\n\tssmInput:{}\n\t\tchr, pos, ref, alt\n\tcoordInput:{}\n\t\toutput obj from genesearch\n\tuseSsmOrGene: string, one of ssm/gene/unmapped\n\t\tto identify where to slice on that bam\n\t\twhen there are multiple options available, Tabs will be created on ui to toggle from\n\t\t- ssm:\n\t\t\tlist ssms cataloged by gdc, allow user to select one and slice bam on it (uses ssmInput)\n\t\t\tit's possible there's no ssm from gdc. if so this option will not be available\n\t\t- gene:\n\t\t\talways show. let user enter any locus/snp (uses coordInput)\n\t\t- unmapped:\n\t\t\tavailable if stream2download=true\n# after validation, create position or variant used for launching tk\n\tposition: {chr,start,stop}\n\tvariant: {chr,pos,ref,alt}\n\nchanges to UI <input> are stored on this object\nand is validated in validateInputs{}\n\n************ functions\nmakeTokenInput\nmakeGdcIDinput\n\tqueryCaseFileList\n\tsearchByGdcInputString\n\t\tmakeSsmGeneSearch\n\t\t\ttemp_renderGeneSearch\n\t\t\ttemp_renderSsmList\n\tupdate_singlefile_table\n\tupdate_multifile_table\n\tmakeArg_geneSearchbox\n\tgeneSearchInstruction\nmakeSubmitAndNoPermissionDiv\n\tvalidateInputs\n\tsliceBamAndRender\n\n**************** url parameters\ngdc_id=TCGA-06-0211\ngdc_ssm=E17K\ngdc_var=chr14:g.104780214C>T\ngdc_pos=chr7:55153818-55156225\n\n*/\n\nconst tip = new Menu({ padding: '' })\nconst gdc_genome = 'hg38'\nconst gdcDslabel = 'GDC' // hardcoded in multiple places\nconst variantFlankingSize = 60 // bp\nconst baminfo_cols = [\n\t{ title: 'Entity ID', key: 'entity_id' },\n\t{ title: 'Experimental Strategy', key: 'experimental_strategy' },\n\t{ title: 'Tissue Type', key: 'tissue_type' },\n\t{ title: 'Tumor Descriptor', key: 'tumor_descriptor' },\n\t{ title: 'Size', key: 'file_size', width: '10vw' }\n]\nconst ssmTableColumns = [\n\t{ label: 'Gene', width: '10vw', sortable: true },\n\t{ label: 'Mutation' },\n\t{ label: 'Consequence', sortable: true },\n\t{ label: 'Position' }\n]\nconst noPermissionMessage =\n\t'You are attempting to access a Sequence Read file that you are not authorized to access. <a href=https://gdc.cancer.gov/access-data/obtaining-access-controlled-data target=_blank>Please request dbGaP Access to the project</a>.'\n\n/*\nArguments:\n\ngenomes{}\nholder\ndebugmode=boolean\nhideTokenInput=true/false\n\tset to true in pp react wrapper that's integrated into gdc portal\n\twill be using cookie session id instead of token\nfilter0=str\n\toptional, stringified json obj as the cohort filter from gdc ATF\n\tsimply pass to backend to include in api queries\ncallbacks={}\n\tstandard optional callbacks\n\t.postRender\n\t\tcalled when all ui components finish updating, for testing\n\t\tsee helper runCallbackAfterUIupdate()\nstream2download=boolean\n\tif true, run the app in \"bam slice download\" mode..\ninputValue=str\n\toptional search str to launch a default view, for tape test\n\n\n** all above arguments are accessible to all helper functions **\n\n\nReturns:\n\ta public API object with callback\n*/\nexport async function bamsliceui(\n\t{ filter0, hideTokenInput = false, callbacks = {}, stream2download = false, inputValue, debugmode = false },\n\tholder,\n\tgenomes\n) {\n\tif (callbacks.postRender && typeof callbacks.postRender != 'function') throw 'callbacks.postRender is not function'\n\n\t// public api obj to be returned\n\tconst publicApi = {\n\t\tdom: {\n\t\t\ttip\n\t\t}\n\t}\n\n\tconst genome = genomes[gdc_genome]\n\tif (!genome) throw 'missing genome for ' + gdc_genome\n\n\t// central obj, see comments on top\n\tconst gdc_args = {\n\t\tbam_files: [],\n\t\trunFlags: {\n\t\t\t// presence of a flag indicates the corresponding ui component is not finished loading yet\n\t\t\trunflag_caseFileList: 1,\n\t\t\trunflag_gdcInput: 1\n\t\t}\n\t}\n\n\t// fill from url for quick testing: ?gdc_id=TCGA-44-6147&gdc_pos=chr9:5064699-5065299\n\t// unable to autoload toke file this way\n\tconst urlp = urlmap()\n\n\t/////////////////////////////////////////////////////\n\t// there are 2 ui holders: formdiv and blockHolder\n\t// formdiv collects multiple rows\n\t// each row is for a ui input\n\t// formdiv will be cleared upon submission\n\n\tconst backBtnDiv = holder.append('div').style('margin-left', '30px').style('display', 'none')\n\tbackBtnDiv\n\t\t.append('button')\n\t\t.html('&#171; Back To Input Form')\n\t\t.on('click', () => {\n\t\t\tbackBtnDiv.style('display', 'none')\n\t\t\tblockHolder.style('display', 'none').selectAll('*').remove()\n\t\t\tformdiv.style('display', 'block')\n\t\t})\n\n\tconst formdiv = holder.append('div').style('margin-left', '30px')\n\n\tconst formDiv = formdiv.append('div')\n\t// table with two columns\n\t// has two rows for inputting token and input string\n\n\t// show block & bam tk\n\tconst blockHolder = holder.append('div').style('display', 'none')\n\n\t/////////////////////////////////////////////////////\n\t// create UI components in formdiv\n\n\t// upload toke file\n\tif (!hideTokenInput) makeTokenInput()\n\n\t// <input> to enter gdc id, and doms for display case/file info\n\tconst gdcid_input = await makeGdcIDinput()\n\n\t// hold toggle ui for ssm list and gene search\n\t// contents are only rendered here after a case/file is found via searchByGdcInputString()\n\tconst ssmGeneDiv = formdiv.append('div').style('padding', '3px 10px').style('display', 'none')\n\n\t// submit button, \"no permission\" alert\n\tconst [submitButton, saydiv, noPermissionDiv] = makeSubmitAndNoPermissionDiv()\n\n\tconst defaultSearchString = inputValue || urlp.get('gdc_id')\n\tif (defaultSearchString) {\n\t\t// default search string is supplied either from runpp() or url. this is for testing only\n\t\tgdcid_input.property('value', defaultSearchString).node().dispatchEvent(new Event('search'))\n\t} else {\n\t\tdelete gdc_args.runFlags.runflag_gdcInput\n\t\trunCallbackAfterUIupdate()\n\t}\n\n\t//////////////////////// helper functions\n\n\tfunction runCallbackAfterUIupdate() {\n\t\tif (!callbacks.postRender) return\n\t\t/* this ensures postRender is only called when all ui parts are loaded\n\t\tat the end of rendering an ui part, and removal of its flag in runFlags{}, call this run() helper \n\t\t*/\n\t\tif (Object.keys(gdc_args.runFlags).length == 0) {\n\t\t\t// no flags. all ui components are updated;\n\t\t\tcallbacks.postRender(publicApi)\n\t\t} else {\n\t\t\t// some other ui is in midst of updating, do not run; this type of checking is agnostic to actual inserted flags\n\t\t}\n\t}\n\n\tfunction makeTokenInput() {\n\t\t// make one <tr> with two cells\n\t\tconst tr = formDiv.insert('div').attr('class', 'sja-gdcbam-tokendiv')\n\n\t\t// cell 1\n\t\ttr.insert('div').style('display', 'inline-block').style('width', '15vw').text('GDC Token File')\n\n\t\t// cell 2\n\t\tconst td = tr.insert('div').style('display', 'inline-block')\n\t\tconst input = td.append('input').attr('type', 'file').attr('aria-label', 'GDC token file')\n\n\t\tconst file_error_div = td.append('span').style('margin-left', '20px').style('display', 'none')\n\t\tinput.on('change', event => {\n\t\t\tconst file = event.target.files[0]\n\t\t\tif (!file) {\n\t\t\t\tinput.property('value', '')\n\t\t\t\treturn\n\t\t\t}\n\t\t\tif (!file.size) {\n\t\t\t\tinput.property('value', '')\n\t\t\t\tshow_input_check(file_error_div, 'Blank file ' + file.name)\n\t\t\t\treturn\n\t\t\t}\n\t\t\tconst reader = new FileReader()\n\t\t\treader.onload = event => {\n\t\t\t\tconst text = event.target.result.trim()\n\t\t\t\tif (text.length < 100) {\n\t\t\t\t\tinput.property('value', '')\n\t\t\t\t\tshow_input_check(file_error_div, 'Does not look like a toke file (content too short)')\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\tif (text.length > 1000) {\n\t\t\t\t\tinput.property('value', '')\n\t\t\t\t\tshow_input_check(file_error_div, 'Does not look like a toke file (content too long)')\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\tgdc_args.gdc_token = text\n\t\t\t}\n\t\t\treader.onerror = function () {\n\t\t\t\tinput.property('value', '')\n\t\t\t\tshow_input_check(file_error_div, 'Error reading file ' + file.name)\n\t\t\t\treturn\n\t\t\t}\n\t\t\tshow_input_check(file_error_div)\n\t\t\treader.readAsText(file, 'utf8')\n\t\t})\n\n\t\tsetTimeout(() => input.node().focus(), 1100)\n\t}\n\n\tasync function makeGdcIDinput() {\n\t\t// make one <tr> with two cells\n\t\tconst tr = formDiv.insert('div')\n\n\t\t// cell 1\n\t\ttr.append('div')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.style('width', '15vw')\n\t\t\t.style('padding-top', '5px')\n\t\t\t.text('Enter Search String')\n\t\t\t.style('vertical-align', 'top')\n\n\t\t// cell 2\n\t\tconst td = tr.append('div').style('display', 'inline-block')\n\n\t\tconst gdcid_input = td\n\t\t\t.append('input')\n\t\t\t.attr('type', 'search')\n\t\t\t.attr('size', 45)\n\t\t\t.attr('aria-label', 'Specify File Name / File UUID / Case ID / Case UUID')\n\t\t\t.style('padding', '3px 10px')\n\t\t\t.property('placeholder', 'File Name / File UUID / Case ID / Case UUID')\n\t\t\t.attr('class', 'sja-gdcbam-input') // for testing\n\t\t\t.attr('data-testid', 'sjpp-gdcbam-fileSearchInput')\n\t\t\t// clicking X in <input> fires \"search\" event. must listen to it and call callback without delay in order to clear the UI\n\t\t\t.on('search', searchByGdcInputString)\n\t\t\t.on('keyup', event => {\n\t\t\t\tif (keyupEnter(event)) {\n\t\t\t\t\t// press Enter to trigger search; this is needed as when embedded in GFF, \"search\" event above is not triggered by hitting Enter\n\t\t\t\t\tsearchByGdcInputString()\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\t// not pressed Enter, and do not debounce search. this avoid an err when hitting Enter too fast after entering string, that will trigger both \"search\" and \"keyup\" listeners and cause it to search twice (and show ssm table twice). also by not listening to keyup it allows users to manually type in search string without being interrupted, thus should be okay..\n\t\t\t\tgdc_loading.style('display', '').text('Press ENTER to search') // prompt\n\t\t\t\tgdcid_error_div.style('display', 'none')\n\t\t\t})\n\n\t\tconst gdc_loading = td.append('span').style('padding-left', '10px').style('display', 'none')\n\n\t\tconst gdcid_error_div = td\n\t\t\t.append('span')\n\t\t\t.attr('class', 'sja-gdcbam-gdcid_error_div') // for testing\n\t\t\t.style('display', 'none')\n\t\t\t.style('padding', '2px 5px')\n\n\t\ttd.append('br') // add line break from input box\n\n\t\tconst listCaseFileHandle = td\n\t\t\t.append('div')\n\t\t\t.attr('class', 'sja-gdcbam-listCaseFileHandle') // for testing\n\t\t\t.style('margin', '5px')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.text('Looking for BAM files from current cohort...')\n\t\tqueryCaseFileList(listCaseFileHandle)\n\n\t\tconst userHasNoAccessDiv = td\n\t\t\t.append('div')\n\t\t\t.style('display', 'none')\n\t\t\t.style('width', '500px')\n\t\t\t.style('margin', '20px 3px')\n\t\t\t.html(noPermissionMessage)\n\n\t\t//////////////////////////\n\t\t// row 2, to display details of case/file\n\t\tconst baminfo_div = formdiv.append('div').style('display', 'none').style('margin', '20px 20px 20px 40px')\n\t\t// either baminfo_table or bamselection_table is displayed\n\t\t// baminfo_table is a static table showing details about one bam file\n\t\t// bamselection_table lists multiple bam files available from a sample, allowing user to select some forslicing\n\t\tconst baminfo_table = baminfo_div.append('div').attr('class', 'sja-gdcbam-onefiletable').style('display', 'none')\n\t\tconst bamselection_table = baminfo_div\n\t\t\t.append('div')\n\t\t\t.attr('class', 'sja-gdcbam-multifiletable')\n\t\t\t.style('display', 'none')\n\n\t\t// the update() will be called in pp react wrapper, when user changes cohort from gdc portal\n\t\tpublicApi.update = _arg => {\n\t\t\tsearchByGdcInputString(null, _arg?.filter0 || filter0)\n\t\t\tqueryCaseFileList(listCaseFileHandle, _arg?.filter0 || filter0)\n\t\t}\n\n\t\t/* arguments\n\t\teventNotUsed: d3v7 passes \"event\" as first argument which is unused, as searchByGdcInputString() is used as event listener\n\t\tfilter0override: new updated gdc filter object, to replace existing filter0\n\t\t*/\n\t\tasync function searchByGdcInputString(eventNotUsed, filter0override) {\n\t\t\tsaydiv.selectAll('*').remove()\n\t\t\tnoPermissionDiv.style('display', 'none')\n\t\t\tsubmitButton.style('display', 'inline-block')\n\n\t\t\t// disable submit button when a new case/file loaded, and delete previou ssmInput/coordInput\n\t\t\tsubmitButton.property('disabled', true)\n\t\t\tdelete gdc_args.coordInput\n\t\t\tdelete gdc_args.ssmInput\n\n\t\t\tgdcid_error_div.style('display', 'none')\n\t\t\tgdc_loading.style('display', 'none')\n\n\t\t\t/* as _actual() is highly variable in how it can end\n\t\t\t- in the middle\n\t\t\t- done input search and not found\n\t\t\t- found case and trigger ssm search\n\t\t\tthus no need to worry about triggering callback everywhere\n\t\t\t*/\n\t\t\ttry {\n\t\t\t\tawait searchByGdcInputString_actual(\n\t\t\t\t\tObject.keys(filter0override || {}).length ? filter0override : filter0 || null\n\t\t\t\t)\n\t\t\t} catch (e) {\n\t\t\t\tshow_input_check(gdcid_error_div, e.message || e)\n\t\t\t\tbaminfo_div.style('display', 'none')\n\t\t\t\tssmGeneDiv.style('display', 'none')\n\t\t\t}\n\t\t\trunCallbackAfterUIupdate()\n\t\t}\n\n\t\tasync function searchByGdcInputString_actual(_filter0) {\n\t\t\tconst gdc_id = gdcid_input.property('value').trim()\n\t\t\tif (!gdc_id.length) {\n\t\t\t\tbaminfo_div.style('display', 'none')\n\t\t\t\tsaydiv.selectAll('*').remove()\n\t\t\t\tssmGeneDiv.style('display', 'none')\n\t\t\t\treturn\n\t\t\t}\n\n\t\t\t// disable input field and show 'loading...' until response returned from gdc api\n\t\t\tgdcid_input.attr('disabled', 1)\n\t\t\tgdc_loading.style('display', '').text('Loading...')\n\n\t\t\tgdc_args.runFlags.runflag_gdcInput = 1\n\n\t\t\tconst body = { gdc_id }\n\t\t\tif (_filter0) body.filter0 = _filter0\n\t\t\tlet data\n\t\t\ttry {\n\t\t\t\tdata = await dofetch3('gdcbam', { body })\n\t\t\t} catch (e) {\n\t\t\t\tthrow e\n\t\t\t} finally {\n\t\t\t\tdelete gdc_args.runFlags.runflag_gdcInput // TEST if deleted when dofetch() throws\n\t\t\t}\n\t\t\t/* data = {\n\t\t\t\tfile_metadata:[]\n\t\t\t\tis_case_id:true\n\t\t\t\tis_case_uuid:true\n\t\t\t\tis_file_uuid:true\n\t\t\t\tis_file_id:true\n\t\t\t\tnumFilesSkippedByWorkflow:int\n\t\t\t}\n\t\t\t*/\n\n\t\t\tgdcid_input.attr('disabled', null) // enable input field\n\t\t\tgdc_loading.style('display', 'none') // hide loading\n\t\t\tgdc_args.bam_files = [] //empty bam_files array after each gdc api call\n\n\t\t\t/////////////////////////////////\n\t\t\t// possible exists before rendering ssm and gene ui\n\n\t\t\tif (data.error) throw 'Error: ' + data.error\n\t\t\tif (!Array.isArray(data.file_metadata)) throw 'Error: .file_metadata[] missing'\n\t\t\tif (data.file_metadata.length == 0) {\n\t\t\t\t// no viewable bam files\n\t\t\t\tif (data.numFilesSkippedByWorkflow) {\n\t\t\t\t\t// there are files skipped due to this reason. the value tells number of files rejected due to this reason\n\t\t\t\t\tthrow `File${data.numFilesSkippedByWorkflow > 1 ? 's' : ''} not viewable due to workflow type.`\n\t\t\t\t}\n\t\t\t\tthrow 'No viewable BAM files found'\n\t\t\t}\n\n\t\t\t// in react wrapper of gdc, session id is available from cookie, if so backend checks user's access to this bam\n\t\t\t// and if no access sets this flag\n\t\t\t// will show the prompt here but will still allow rest of ui to show, just to showcase app's capability\n\t\t\tuserHasNoAccessDiv.style('display', data.userHasNoAccess ? 'block' : 'none')\n\n\t\t\t/*\n\t\t\tin file_metadata[], each element is a bam file:\n\t\t\t{\n\t\t\t\tcase_id: \"9a2a226e-9605-4214-9320-469305e664e6\"\n\t\t\t\tentity_id: \"TCGA-49-AARQ-11A-21D-A413-08\"\n\t\t\t\texperimental_strategy: \"WXS\"\n\t\t\t\tfile_size: \"10.43 GB\"\n\t\t\t\tfile_uuid: \"f383b776-b162-4c61-909b-3b92d1853511\"\n\t\t\t\ttissue_type: str\n\t\t\t\ttumor_descriptor: str\n\t\t\t}\n\n\t\t\trecord case_id for the found file\n\t\t\tif the array has multiple files, all are from the same case\n\t\t\tso the case_id should be the same for all files\n\t\t\t*/\n\t\t\tgdc_args.case_id = data.file_metadata[0].case_id\n\n\t\t\tif (data.file_metadata.length == 1) {\n\t\t\t\t// has only 1 file\n\t\t\t\tupdate_singlefile_table(data, gdc_id)\n\t\t\t} else {\n\t\t\t\t// 2 or more files\n\t\t\t\tupdate_multifile_table(data.file_metadata)\n\t\t\t}\n\t\t\tshow_input_check(gdcid_error_div)\n\n\t\t\tgdc_args.runFlags.ssmSearch = 1\n\t\t\ttry {\n\t\t\t\tawait makeSsmGeneSearch()\n\t\t\t} catch (e) {\n\t\t\t\tthrow e\n\t\t\t} finally {\n\t\t\t\tdelete gdc_args.runFlags.ssmSearch\n\t\t\t}\n\t\t}\n\t\tfunction update_singlefile_table(data, gdc_id) {\n\t\t\t// will update table display, and also insert element into gdc_args.bam_files[]\n\t\t\tbaminfo_div.style('display', 'block')\n\t\t\tbaminfo_table.style('display', 'block').selectAll('*').remove()\n\t\t\tbamselection_table.style('display', 'none')\n\n\t\t\tconst onebam = data.file_metadata[0]\n\t\t\tconst file = {\n\t\t\t\tfile_id: onebam.file_uuid,\n\t\t\t\ttrack_name: onebam.entity_id, // assign track name as entity_id\n\t\t\t\tabout: []\n\t\t\t}\n\t\t\tgdc_args.bam_files.push(file)\n\n\t\t\tconst table = table2col({ holder: baminfo_table })\n\t\t\tfor (const col of baminfo_cols) {\n\t\t\t\tconst [td1, td2] = table.addRow()\n\t\t\t\ttd1.text(col.title)\n\t\t\t\ttd2.html(\n\t\t\t\t\tcol.url ? `<a href=${col.url}${onebam.file_uuid} target=_blank>${onebam[col.key]}</a>` : onebam[col.key]\n\t\t\t\t)\n\t\t\t\tconst id = file.about.push({ k: col.title, v: onebam[col.key] })\n\t\t\t}\n\t\t\tbaminfo_table.select('input').node()?.focus()\n\t\t}\n\n\t\tfunction update_multifile_table(files) {\n\t\t\tconst columns = baminfo_cols.map(i => {\n\t\t\t\treturn { label: i.title, width: i.width }\n\t\t\t})\n\t\t\tconst rows = []\n\t\t\tfor (const [i, onebam] of files.entries()) {\n\t\t\t\tconst row = []\n\t\t\t\t// address section 508 requirement to have explicit or implicit labels for input elements\n\t\t\t\tconst elemId = onebam.entity_id\n\t\t\t\trow.ariaLabelledBy = elemId\n\t\t\t\tfor (const column of baminfo_cols) {\n\t\t\t\t\tconst value = onebam[column.key]\n\t\t\t\t\tif (column.url) {\n\t\t\t\t\t\trow.push({ html: `<a href=${row.url}${onebam.file_uuid} target=_blank>${value}</a>` })\n\t\t\t\t\t} else if (column.key == 'entity_id') {\n\t\t\t\t\t\trow.push({ value, elemId })\n\t\t\t\t\t} else {\n\t\t\t\t\t\trow.push({ value })\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\trows.push(row)\n\t\t\t}\n\n\t\t\tbaminfo_div.style('display', 'block')\n\t\t\tbamselection_table.style('display', 'block').selectAll('*').remove()\n\t\t\tbaminfo_table.style('display', 'none')\n\t\t\trenderTable({\n\t\t\t\trows,\n\t\t\t\tcolumns,\n\t\t\t\tdiv: bamselection_table,\n\t\t\t\tsingleMode: stream2download ? true : false, // if true, display radio to only select 1 for download; otherwise allow to selec >1 for viz\n\t\t\t\tdataTestId: 'sjpp-gdcbam-multiFileTable',\n\t\t\t\tnoButtonCallback: (i, node) => {\n\t\t\t\t\tconst onebam = files[i]\n\n\t\t\t\t\tif (stream2download) {\n\t\t\t\t\t\tgdc_args.bam_files = [\n\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\tfile_id: onebam.file_uuid,\n\t\t\t\t\t\t\t\ttrack_name: `${onebam.tissue_type}, ${onebam.tumor_descriptor}, ${onebam.experimental_strategy}, ${onebam.entity_id}`,\n\t\t\t\t\t\t\t\tabout: baminfo_cols.map(i => {\n\t\t\t\t\t\t\t\t\treturn { k: i.title, v: onebam[i.key] }\n\t\t\t\t\t\t\t\t})\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t]\n\t\t\t\t\t} else {\n\t\t\t\t\t\tif (node.checked) {\n\t\t\t\t\t\t\tgdc_args.bam_files.push({\n\t\t\t\t\t\t\t\tfile_id: onebam.file_uuid,\n\t\t\t\t\t\t\t\ttrack_name: `${onebam.tissue_type}, ${onebam.tumor_descriptor}, ${onebam.experimental_strategy}, ${onebam.entity_id}`,\n\t\t\t\t\t\t\t\tabout: baminfo_cols.map(i => {\n\t\t\t\t\t\t\t\t\treturn { k: i.title, v: onebam[i.key] }\n\t\t\t\t\t\t\t\t})\n\t\t\t\t\t\t\t})\n\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t// remove from array if checkbox unchecked\n\t\t\t\t\t\t\tgdc_args.bam_files = gdc_args.bam_files.filter(f => f.file_id != onebam.file_uuid)\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 gdcid_input\n\t}\n\n\tasync function queryCaseFileList(handle, filter0override) {\n\t\tgdc_args.runFlags.runflag_caseFileList = 1\n\t\ttry {\n\t\t\tawait queryCaseFileList_actual(handle, filter0override)\n\t\t} catch (e) {\n\t\t\thandle.text(e.message || e)\n\t\t} finally {\n\t\t\tdelete gdc_args.runFlags.runflag_caseFileList\n\t\t}\n\t\trunCallbackAfterUIupdate()\n\t}\n\n\tasync function queryCaseFileList_actual(handle, filter0override) {\n\t\tconst _filter0 = Object.keys(filter0override || {}).length ? filter0override : filter0 || null\n\t\tconst body = {}\n\t\tif (_filter0) body.filter0 = _filter0\n\t\tconst data = await dofetch3('gdcbam', { body }) // query same route without case_id\n\t\tif (data.error) throw data.error\n\t\t// data = { case2files={}, total=int, loaded=int }\n\t\tif (typeof data.case2files != 'object') throw 'wrong return'\n\n\t\t// \"bam slicing download\" app calls gdc api directly from client here and doesn't go through pp backend. thus it need the rest api host name which is determined by pp backend and diffs based on environments\n\t\tif (!data.restapihost) throw 'data.restapihost is missing'\n\t\tgdc_args.restapihost = data.restapihost\n\n\t\t/*\n\t\tif (data.total < data.loaded) handle.text(`Or, browse ${data.total} BAM files`)\n\t\telse handle.text(`Or, browse first ${data.loaded} BAM files out of ${data.total} total`)\n\t\t*/\n\t\thandle\n\t\t\t.text(`Or, Browse ${data.total} Available BAM Files`)\n\t\t\t.attr('data-testid', 'sjpp-gdcbam-availableBamFileHandleIsReady')\n\n\t\t// count number of bams per assay, allow checkbox to alter true/false for each assay here\n\t\tconst assays = new Map() // k: assay, v: {count:int, checked:bool}\n\t\tfor (const c in data.case2files) {\n\t\t\tfor (const f of data.case2files[c]) {\n\t\t\t\tconst e = f.experimental_strategy\n\t\t\t\tif (!assays.has(e)) {\n\t\t\t\t\tassays.set(e, { count: 1, checked: true })\n\t\t\t\t} else {\n\t\t\t\t\tassays.get(e).count += 1\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\n\t\tlet lastTabbedTime = Date.now()\n\n\t\thandle\n\t\t\t.classed('sja_clbtext', true) // not to override the class name used for testing\n\t\t\t.attr('tabindex', 0)\n\t\t\t.on('keyup', event => {\n\t\t\t\tif (event.key == 'Enter') {\n\t\t\t\t\tevent.target.click()\n\t\t\t\t}\n\t\t\t})\n\t\t\t.on('click', event => {\n\t\t\t\ttip.clear().showunder(event.target)\n\t\t\t\t{\n\t\t\t\t\t// show checkboxes for assays\n\t\t\t\t\tconst row = tip.d.append('div').style('margin', '10px')\n\t\t\t\t\tfor (const [k, o] of assays) {\n\t\t\t\t\t\tmake_one_checkbox({\n\t\t\t\t\t\t\tholder: row,\n\t\t\t\t\t\t\tlabeltext: `${k}, ${o.count}`,\n\t\t\t\t\t\t\tdivstyle: { display: 'inline', 'margin-right': '15px' },\n\t\t\t\t\t\t\tchecked: o.checked,\n\t\t\t\t\t\t\tcallback: () => {\n\t\t\t\t\t\t\t\to.checked = !o.checked\n\t\t\t\t\t\t\t\tmakeTable(tableDiv)\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t})\n\t\t\t\t\t}\n\n\t\t\t\t\trow\n\t\t\t\t\t\t.select('input')\n\t\t\t\t\t\t.on('keydown', event => {\n\t\t\t\t\t\t\tif (event.key == 'Tab' && event.shiftKey) lastTabbedTime = Date.now()\n\t\t\t\t\t\t})\n\t\t\t\t\t\t.on('blur', () => {\n\t\t\t\t\t\t\tif (Date.now() - lastTabbedTime > 500) return\n\t\t\t\t\t\t\thandle.node().focus()\n\t\t\t\t\t\t\ttip.hide()\n\t\t\t\t\t\t})\n\t\t\t\t\t\t.node()\n\t\t\t\t\t\t.focus()\n\t\t\t\t}\n\t\t\t\tconst tableDiv = tip.d.append('div')\n\t\t\t\tmakeTable(tableDiv)\n\t\t\t})\n\n\t\t// create new table to show list of available cases and bams, based on scoped things (data, assays), allow to click a bam and feed into main ui; skip bams with assay types that are unchecked\n\t\tfunction makeTable(tableDiv) {\n\t\t\ttableDiv.selectAll('*').remove()\n\t\t\tconst rows = []\n\t\t\tfor (const caseName in data.case2files) {\n\t\t\t\t// get the list of visible bam files passed assay filter\n\t\t\t\tconst files = data.case2files[caseName].filter(f => assays.get(f.experimental_strategy).checked)\n\t\t\t\tif (files.length == 0) continue // no files for this case due to assay filtering. do not show row\n\t\t\t\tfor (const f of files) {\n\t\t\t\t\t// f { tissue_type, tumor_descriptor, experimental_strategy, file_size, file_uuid }\n\t\t\t\t\trows.push([\n\t\t\t\t\t\t{ value: caseName, data: f },\n\t\t\t\t\t\t{ value: f.tissue_type },\n\t\t\t\t\t\t{ value: f.tumor_descriptor },\n\t\t\t\t\t\t{ value: f.experimental_strategy },\n\t\t\t\t\t\t{ value: f.file_size }\n\t\t\t\t\t])\n\t\t\t\t}\n\t\t\t}\n\t\t\trenderTable({\n\t\t\t\trows,\n\t\t\t\tcolumns: [\n\t\t\t\t\t{ label: 'Case', sortable: true },\n\t\t\t\t\t{ label: 'Tissue Type', sortable: true },\n\t\t\t\t\t{ label: 'Tumor Descriptor', sortable: true },\n\t\t\t\t\t{ label: 'Assay', sortable: true },\n\t\t\t\t\t{ label: 'File Size' } // barplot doesn't handle well size data range from mb to gb\n\t\t\t\t],\n\t\t\t\theader: { allowSort: true },\n\t\t\t\tdiv: tableDiv,\n\t\t\t\tnoButtonCallback: (i, node) => {\n\t\t\t\t\ttip.hide()\n\t\t\t\t\tgdcid_input.property('value', rows[i][0].data.file_uuid).node().dispatchEvent(new Event('search'))\n\t\t\t\t},\n\t\t\t\tsingleMode: true,\n\t\t\t\tdataTestId: 'sjpp-gdcbam-orBrowseFileTable'\n\t\t\t})\n\t\t\t//table.select('.sja_clbtext')?.node()?.focus() // auto focus on the first bam file\n\t\t}\n\t}\n\n\t// this is called after a file/case is found\n\t// case id is at gdc_args.case_id\n\t// query ssm associated with the case, show ssm/gene toggle ui\n\tasync function makeSsmGeneSearch() {\n\t\tdelete gdc_args.ssmInput // delete previous search result\n\t\tssmGeneDiv\n\t\t\t.style('display', 'block') // turn holder visible\n\t\t\t.selectAll('*')\n\t\t\t.remove() // clear holder, including ssm from previous case\n\n\t\tconst mutationMsgDiv = ssmGeneDiv.append('p').text('Searching for mutations...')\n\n\t\tconst data = await dofetch3('termdb/singleSampleMutation', {\n\t\t\tbody: {\n\t\t\t\t/* knowing that the query id is already case uuid, this prefix signals this to backend gdc code and thus no need for backend to sniff out if is case or sample id, which requires complete cache\n\t\t\t\tuse non-alphabetic characters so no need to worry about lower/upper case\n\t\t\t\tthis helps when backend caseid caching is incomplete, or truncated on dev machines\n\t\t\t\tthis is harmless and do not impact non-gdc code\n\t\t\t\t*/\n\t\t\t\tsample: '___' + gdc_args.case_id,\n\t\t\t\tgenome: gdc_genome,\n\t\t\t\tdslabel: gdcDslabel\n\t\t\t}\n\t\t})\n\t\tif (data.error) throw data.error\n\n\t\t// future: show this data with block or disco\n\n\t\tconst ssmLst = data.mlst.filter(m => m.dt == 1) // for now filter to only ssm, exclude cnv\n\n\t\tif (ssmLst.length == 0) {\n\t\t\tmutationMsgDiv.text('No mutations from this case.')\n\n\t\t\tif (stream2download) {\n\t\t\t\t// still show tab with 2 options\n\t\t\t\tconst tabs = [\n\t\t\t\t\t{\n\t\t\t\t\t\tlabel: 'Gene or position',\n\t\t\t\t\t\ttestid: 'sjpp-gdcbam-afterfindingcasetab-geneorpos',\n\t\t\t\t\t\tcallback: () => {\n\t\t\t\t\t\t\tgdc_args.useSsmOrGene = 'gene'\n\t\t\t\t\t\t\t// under Gene or position tab, only enable submit button when coordInput provided\n\t\t\t\t\t\t\tsubmitButton.property('disabled', !gdc_args.coordInput?.chr)\n\t\t\t\t\t\t}\n\t\t\t\t\t},\n\t\t\t\t\t{\n\t\t\t\t\t\tlabel: 'Unmapped reads',\n\t\t\t\t\t\ttestid: 'sjpp-gdcbam-afterfindingcasetab-unmapped',\n\t\t\t\t\t\tcallback: () => {\n\t\t\t\t\t\t\tgdc_args.useSsmOrGene = 'unmapped'\n\t\t\t\t\t\t\t// under Unmapped reads tab, should always eanble submit button\n\t\t\t\t\t\t\tsubmitButton.property('disabled', false)\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t]\n\t\t\t\tnew Tabs({ holder: ssmGeneDiv, tabs }).main()\n\t\t\t\tawait temp_renderGeneSearch(tabs[0].contentHolder)\n\t\t\t\ttabs[1].contentHolder.append('p').text('Only download unmapped reads from this BAM file.')\n\t\t\t} else {\n\t\t\t\t// no tab. just gene search\n\t\t\t\tawait temp_renderGeneSearch(ssmGeneDiv.append('div'))\n\t\t\t}\n\t\t\treturn\n\t\t}\n\n\t\t// found ssms\n\t\tmutationMsgDiv.remove()\n\t\t// display toggle between ssm list and gene search\n\t\tconst tabs = [\n\t\t\t{\n\t\t\t\tlabel: `${ssmLst.length} mutations${data.dt2total?.[0] ? ' (' + data.dt2total[0].total + ' total)' : ''}`,\n\t\t\t\ttestid: 'sjpp-gdcbam-afterfindingcasetab-ssm',\n\t\t\t\tcallback: () => {\n\t\t\t\t\tgdc_args.useSsmOrGene = 'ssm'\n\t\t\t\t\t// Under variants tab, only enable submit button when ssmInput provided\n\t\t\t\t\tsubmitButton.property('disabled', !gdc_args.ssmInput?.chr)\n\t\t\t\t}\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Gene or position',\n\t\t\t\ttestid: 'sjpp-gdcbam-afterfindingcasetab-geneorpos',\n\t\t\t\tcallback: () => {\n\t\t\t\t\tgdc_args.useSsmOrGene = 'gene'\n\t\t\t\t\t// Under Gene or position tab, only enable submit button when coordInput provided\n\t\t\t\t\tsubmitButton.property('disabled', !gdc_args.coordInput?.chr)\n\t\t\t\t}\n\t\t\t}\n\t\t]\n\n\t\tif (stream2download) {\n\t\t\ttabs.push({\n\t\t\t\tlabel: 'Unmapped reads',\n\t\t\t\ttestid: 'sjpp-gdcbam-afterfindingcasetab-unmapped',\n\t\t\t\tcallback: () => {\n\t\t\t\t\tgdc_args.useSsmOrGene = 'unmapped'\n\t\t\t\t\t// under Unmapped reads tab, should always eanble submit button\n\t\t\t\t\tsubmitButton.property('disabled', false)\n\t\t\t\t}\n\t\t\t})\n\t\t}\n\n\t\tnew Tabs({ holder: ssmGeneDiv, tabs }).main()\n\n\t\ttemp_renderSsmList(tabs[0].contentHolder, ssmLst)\n\t\tawait temp_renderGeneSearch(tabs[1].contentHolder)\n\t\tif (tabs[2]) tabs[2].contentHolder.append('p').text('Only download unmapped reads from this BAM file.')\n\t}\n\n\t// TODO new tabs ssm/cnv/fusion/disco, click an item from any tab to optionally launch block view of and narrow down region; also\n\tfunction temp_renderSsmList(div, mlst) {\n\t\tconst gene2mlst = new Map() // group by gene\n\t\tfor (const m of mlst) {\n\t\t\tif (!gene2mlst.has(m.gene)) gene2mlst.set(m.gene, [])\n\t\t\tgene2mlst.get(m.gene).push(m)\n\t\t}\n\t\tconst rows = []\n\t\tfor (const [gene, mlst] of gene2mlst) {\n\t\t\tfor (const m of mlst) {\n\t\t\t\tconst row = []\n\t\t\t\t// address section 508 requirement to have explicit or implicit labels for input elements\n\t\t\t\tconst elemId = `${gene}-${m.mname}`.replace(/\\W+/g, '_')\n\t\t\t\trow.ariaLabelledBy = elemId\n\t\t\t\trow.push({ value: gene, data: m })\n\t\t\t\trow.push({ value: m.mname, elemId })\n\t\t\t\trow.push({ value: mclass[m.class]?.label || 'Unknown' })\n\t\t\t\trow.push({ value: m.chr + ':' + m.pos + ' ' + m.ref + '>' + m.alt })\n\t\t\t\trows.push(row)\n\t\t\t}\n\t\t}\n\t\trenderTable({\n\t\t\trows,\n\t\t\tcolumns: ssmTableColumns,\n\t\t\theader: { allowSort: true },\n\t\t\tdiv,\n\t\t\tnoButtonCallback: (i, node) => {\n\t\t\t\tconst m = rows[i][0].data\n\t\t\t\tgdc_args.ssmInput = {\n\t\t\t\t\tchr: m.chr,\n\t\t\t\t\tpos: m.pos - 1, // convert 1-based to 0-based\n\t\t\t\t\tref: m.ref,\n\t\t\t\t\talt: m.alt\n\t\t\t\t}\n\t\t\t\tsubmitButton.property('disabled', false)\n\t\t\t},\n\t\t\tdataTestId: 'sjpp-gdcbam-ssmTable',\n\t\t\tsingleMode: true\n\t\t})\n\n\t\tif (urlp.has('gdc_ssm')) {\n\t\t\t// a quick fix. update later when table accepts array index of item selected by default\n\t\t\tfor (const [gene, mlst] of gene2mlst) {\n\t\t\t\tfor (const m of mlst) {\n\t\t\t\t\t// should send array index of selected item to renderTable() to auto check radio button\n\t\t\t\t\tif (m.mname == urlp.get('gdc_ssm')) {\n\t\t\t\t\t\tgdc_args.ssmInput = {\n\t\t\t\t\t\t\tchr: m.chr,\n\t\t\t\t\t\t\tpos: m.pos - 1, // convert 1-based to 0-based\n\t\t\t\t\t\t\tref: m.ref,\n\t\t\t\t\t\t\talt: m.alt\n\t\t\t\t\t\t}\n\t\t\t\t\t\tsubmitButton.property('disabled', false)\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\n\t\tdiv.select('input').node().focus()\n\t}\n\tasync function temp_renderGeneSearch(div) {\n\t\tconst geneSearchRow = div.append('div').style('display', 'grid').style('grid-template-columns', '300px auto')\n\t\tgeneSearchRow.append('div').text('Enter gene, position, SNP, or variant')\n\n\t\t// create gene search box\n\t\tgdc_args.coordInput = addGeneSearchbox(await makeArg_geneSearchbox(geneSearchRow))\n\n\t\tgeneSearchInstruction(div)\n\t}\n\n\tasync function makeArg_geneSearchbox(div) {\n\t\tconst opt = {\n\t\t\tgenome,\n\t\t\ttip,\n\t\t\trow: div.append('div'),\n\t\t\tallowVariant: true,\n\t\t\t// after getting valid result from geneSearchbox, enable submit button\n\t\t\tcallback: () => submitButton.property('disabled', false)\n\t\t}\n\t\tif (urlp.has('gdc_pos')) {\n\t\t\tconst t = urlp.get('gdc_pos').split(/[:\\-]/)\n\t\t\tif (t.length == 3) {\n\t\t\t\topt.defaultCoord = {\n\t\t\t\t\tchr: t[0],\n\t\t\t\t\tstart: Number(t[1]),\n\t\t\t\t\tstop: Number(t[2])\n\t\t\t\t}\n\t\t\t}\n\t\t} else if (urlp.has('gdc_var')) {\n\t\t\tconst variant = await string2variant(urlp.get('gdc_var'), genome)\n\t\t\tif (variant) {\n\t\t\t\topt.defaultCoord = variant\n\t\t\t}\n\t\t}\n\t\treturn opt\n\t}\n\n\tfunction makeSubmitAndNoPermissionDiv() {\n\t\tconst div = formdiv.append('div')\n\n\t\t// 1st <td> with submit button\n\t\tconst submitButton = div\n\t\t\t.insert('div')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.append('button')\n\t\t\t.attr('data-testid', 'sjpp-gdcbam-submitBtn')\n\t\t\t.style('margin', '20px 20px 20px 40px')\n\t\t\t.style('padding', '10px 25px')\n\t\t\t.style('border-radius', '35px')\n\t\t\t.text('Submit')\n\t\t\t//submit button should be disabled when first created, enabled after a case/file\n\t\t\t//selected and variant/postion/unmapped selected\n\t\t\t.attr('disabled', true)\n\t\t\t.on('click', async () => {\n\t\t\t\tif (JSON.parse(sessionStorage.getItem('optionalFeatures')).gdcBamDemoMode) {\n\t\t\t\t\tlaunchDemoMode() // in demo mode, do not validate arg and will run with non-gdc data\n\t\t\t\t\treturn\n\t\t\t\t}\n\n\t\t\t\ttry {\n\t\t\t\t\tsaydiv.selectAll('*').remove()\n\t\t\t\t\tvalidateInputs(gdc_args, genome, hideTokenInput)\n\t\t\t\t\tsubmitButton.text('Loading ...')\n\t\t\t\t\tsubmitButton.property('disabled', true)\n\t\t\t\t\tawait sliceBamAndRender()\n\t\t\t\t} catch (e) {\n\t\t\t\t\tif (e == 'Permission denied') {\n\t\t\t\t\t\t// backend throws {error:'Permission denied'} to signal the display of this alert\n\t\t\t\t\t\tnoPermissionDiv.style('display', 'inline-block')\n\t\t\t\t\t\tsubmitButton.style('display', 'none')\n\t\t\t\t\t} else {\n\t\t\t\t\t\tsaydiv.selectAll('*').remove()\n\t\t\t\t\t\tsayerror(saydiv, e)\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\t// turn submit button back to active so ui can be reused later\n\t\t\t\tsubmitButton.text('Submit')\n\t\t\t\tsubmitButton.property('disabled', false)\n\t\t\t})\n\n\t\t// 2nd <td> as notification holder\n\t\tconst saydiv = div.insert('div').style('display', 'inline-block')\n\t\tconst noPermissionDiv = div.insert('div').style('display', 'none').style('margin', '20px')\n\t\tnoPermissionDiv.append('div').text('Access Alert').style('font-size', '1.5em').style('opacity', 0.4)\n\t\tnoPermissionDiv\n\t\t\t.append('div')\n\t\t\t.style('border-top', 'solid 1px #eee')\n\t\t\t.style('border-bottom', 'solid 1px #eee')\n\t\t\t.style('padding', '20px 0px')\n\t\t\t.style('margin-top', '5px')\n\t\t\t.html(noPermissionMessage)\n\t\treturn [submitButton, saydiv, noPermissionDiv]\n\t}\n\n\tasync function sliceBamAndRender() {\n\t\tconst args = gdc_args\n\n\t\t// create arg for block init\n\t\tconst par = {\n\t\t\tnobox: 1,\n\t\t\tgenome,\n\t\t\tholder: blockHolder,\n\t\t\tdebugmode\n\t\t}\n\n\t\tif (args.useSsmOrGene == 'unmapped') {\n\t\t\t/* when this option is in use, app must be running in \"download mode\"\n\t\t\teven if par is block param, it's fine to skip chr/start/stop on it\n\t\t\tas later it will not reach visualization step and will not instantiate a block\n\t\t\t*/\n\t\t\tpar.unmapped = 1\n\t\t} else {\n\t\t\tif (args.position) {\n\t\t\t\tpar.chr = args.position.chr\n\t\t\t\tpar.start = args.position.start\n\t\t\t\tpar.stop = args.position.stop\n\t\t\t} else if (args.variant) {\n\t\t\t\tpar.chr = args.variant.chr\n\t\t\t\tpar.start = args.variant.pos - variantFlankingSize\n\t\t\t\tpar.stop = args.variant.pos + variantFlankingSize\n\t\t\t} else {\n\t\t\t\tthrow 'SV_EXPAND here'\n\t\t\t}\n\t\t}\n\n\t\tconst headers = { 'Content-Type': 'application/json', Accept: 'application/json' }\n\t\tif (args.gdc_token) {\n\t\t\theaders['X-Auth-Token'] = args.gdc_token\n\t\t}\n\n\t\t//////////////////////////////////////////////\n\t\t//\n\t\t// call backend to slice bam and write to cache file\n\t\t//\n\t\t//////////////////////////////////////////////\n\t\tfor (const [idx, file] of args.bam_files.entries()) {\n\t\t\t// file = {file_id,track_name,about[]}\n\n\t\t\tsubmitButton.text(`Slicing BAM File ${idx + 1} of ${args.bam_files.length}...`)\n\n\t\t\t// translate par{} into request body\n\t\t\tconst body = {\n\t\t\t\tdownloadgdc: 1,\n\t\t\t\tgdcFileUUID: file.file_id\n\t\t\t}\n\n\t\t\tif (par.unmapped) {\n\t\t\t\tbody.gdcFilePosition = 'unmapped'\n\t\t\t\tbody.unmapped = 1\n\t\t\t} else {\n\t\t\t\tbody.gdcFilePosition = par.chr + ':' + par.start + '-' + par.stop\n\t\t\t\t// SV_EXPAND\n\t\t\t\tbody.regions = [{ chr: par.chr, start: par.start, stop: par.stop }]\n\t\t\t}\n\n\t\t\tif (stream2download) {\n\t\t\t\t// detour\n\n\t\t\t\theaders.compression = false\n\t\t\t\t// cookie is domain based and will be automatically passed on all requests\n\n\t\t\t\tconst url = `${gdc_args.restapihost}/slicing/view/${file.file_id}?region=${body.gdcFilePosition}`\n\t\t\t\tconst response = await fetch(url, { method: 'GET', headers })\n\t\t\t\tconst data = await response.blob()\n\t\t\t\t// download the file to client\n\t\t\t\tconst a = document.createElement('a')\n\t\t\t\ta.href = URL.createObjectURL(data)\n\t\t\t\tif (par.unmapped) {\n\t\t\t\t\ta.download = file.track_name + '.unmapped.bam'\n\t\t\t\t} else {\n\t\t\t\t\ta.download = `${file.track_name}.${par.chr}.${par.start}.${par.stop}.bam`\n\t\t\t\t}\n\t\t\t\ta.style.display = 'none'\n\t\t\t\tdocument.body.appendChild(a)\n\t\t\t\ta.click()\n\t\t\t\tdocument.body.removeChild(a)\n\t\t\t\treturn\n\t\t\t}\n\n\t\t\tconst fileStat = await dofetch3('tkbam', { headers, body }) // stat about the cached gdc bam slice file\n\t\t\tif (fileStat.error) throw fileStat.error\n\n\t\t\t// when clicking \"Back To\" button and resubmit another region, the same file info will be reused and must avoid inserting duplicating entries here\n\t\t\t{\n\t\t\t\tconst i = file.about.find(i => i.k == 'Slice file size')\n\t\t\t\tif (i) i.v = fileStat.size\n\t\t\t\telse file.about.push({ k: 'Slice file size', v: fileStat.size })\n\t\t\t}\n\t\t\tif (fileStat.time) {\n\t\t\t\tconst i = file.about.find(i => i.k == 'Stream time')\n\t\t\t\tif (i) i.v = Math.round(fileStat.time) + ' seconds'\n\t\t\t\telse file.about.push({ k: 'Stream time', v: Math.round(fileStat.time) + ' seconds' })\n\t\t\t}\n\t\t\tif (fileStat.truncated) {\n\t\t\t\t// insert entry if not found\n\t\t\t\tif (!file.about.find(i => i.k == 'Truncated'))\n\t\t\t\t\tfile.about.push({ k: 'Truncated', v: 'BAM slice size exceeds limit and is truncated' })\n\t\t\t} else {\n\t\t\t\t// delete entry if found\n\t\t\t\tconst i = file.about.findIndex(i => i.k == 'Truncated')\n\t\t\t\tif (i > 0) file.about.splice(i, 1)\n\t\t\t}\n\t\t}\n\n\t\tformdiv.style('display', 'none')\n\t\tbackBtnDiv.style('display', 'block')\n\t\tblockHolder.style('display', 'block')\n\n\t\t//////////////////////////////////////////////\n\t\t//\n\t\t// file slices are cached. launch block\n\t\t//\n\t\t//////////////////////////////////////////////\n\t\tpar.tklst = []\n\t\tfor (const file of args.bam_files) {\n\t\t\tconst tk = {\n\t\t\t\ttype: 'bam',\n\t\t\t\tname: file.track_name || 'Sample BAM slice',\n\t\t\t\tgdcToken: args.gdc_token,\n\t\t\t\tgdcFile: {\n\t\t\t\t\tuuid: file.file_id,\n\t\t\t\t\t// SV_EXPAND\n\t\t\t\t\t// tk remembers position for which slice is requested. this position is sent to backend to make the hashed cache file name persistent; must compose string consistently as chr:start-stop; using different separator will result in different hash\n\t\t\t\t\tposition: par.chr + ':' + par.start + '-' + par.stop\n\t\t\t\t},\n\t\t\t\taboutThisFile: file.about\n\t\t\t}\n\t\t\tif (args.variant) {\n\t\t\t\ttk.variants = [args.variant]\n\t\t\t}\n\t\t\tpar.tklst.push(tk)\n\t\t}\n\t\tfirst_genetrack_tolist(genome, par.tklst)\n\t\tconst _ = await import('../src/block')\n\t\tnew _.Block(par)\n\t}\n\n\tasync function launchDemoMode() {\n\t\tformdiv.style('display', 'none')\n\t\tbackBtnDiv.style('display', 'block')\n\t\tblockHolder.style('display', 'block')\n\t\tblockHolder\n\t\t\t.append('div')\n\t\t\t.style('margin', '25px')\n\t\t\t.style('font-weight', 'bold')\n\t\t\t.text('Running in demo mode and showing non-GDC data.')\n\t\t// create arg for block init\n\t\tconst hg19 = genomes.hg19 // use hg19 since demo file is hg19-based. intentionally not using hg38 file since demo only works on local where hg19 file is present, also signifies it's not using gdc hg38-based data\n\t\tconst par = {\n\t\t\tnobox: 1,\n\t\t\tgenome: hg19,\n\t\t\tholder: blockHolder,\n\t\t\tdebugmode,\n\t\t\tchr: 'chr17',\n\t\t\tstart: 7578191,\n\t\t\tstop: 7578591,\n\t\t\ttklst: [\n\t\t\t\t{\n\t\t\t\t\ttype: 'bam',\n\t\t\t\t\tname: 'Demo BAM Track',\n\t\t\t\t\t// can switch to other examples\n\t\t\t\t\tfile: 'proteinpaint_demo/hg19/bam/TP53_del.bam',\n\t\t\t\t\tvariants: [{ chr: 'chr17', pos: 7578382, ref: 'AGCAGCGCTCATGGTGGGG', alt: 'A' }]\n\t\t\t\t}\n\t\t\t]\n\t\t}\n\t\tfirst_genetrack_tolist(hg19, par.tklst)\n\t\t// pretend the gene track is gencode (which gdc uses, and only show two p53 isoforms)\n\t\tpar.tklst[1].name = 'GENCODE'\n\t\tpar.tklst[1].filterByName = `NM_000546\n\t\tNM_001126115`\n\t\tconst _ = await import('../src/block')\n\t\tnew _.Block(par)\n\t}\n\n\treturn publicApi\n}\n\nfunction geneSearchInstruction(d) {\n\td.append('div').style('opacity', 0.7).html(`<ul>\n\t\t<li>Enter gene, position, SNP, or variant.\n\t\tThe BAM file will be sliced at the given position and visualized.</li>\n\t\t<li>\n\t\t\t<span>Position</span>\n\t\t\t<ul><li>Example: chr17:7676339-7676767</li>\n\t\t\t    <li>Coordinates are hg38 and 1-based.</li>\n\t\t\t</ul>\n\t\t</li>\n\t\t<li>SNP example: rs28934574</li>\n\t\t<li>\n\t\t\t<span>Variant:</span>\n\t\t\t<ul>\n\t\t\t  <li>Example: chr2.208248388.C.T</li>\n\t\t\t  <li>Fields are separated by periods. Coordinate is hg38 and 1-based. Reference and alternative alleles are on forward strand.</li>\n\t\t\t</ul>\n\t\t</li>\n\t\t<li>\n\t\t\t<span>Supported HGVS formats for variants:</span>\n\t\t\t<ul>\n\t\t\t  <li>SNV: chr2:g.208248388C>T</li>\n\t\t\t  <li>MNV: chr2:g.119955155_119955159delinsTTTTT</li>\n\t\t\t  <li>Insertion: chr5:g.171410539_171410540insTCTG</li>\n\t\t\t  <li>Deletion: chr10:g.8073734delTTTAGA</li>\n\t\t\t</ul>\n\t\t</li>\n\t\t</ul>`)\n}\n\nfunction show_input_check(holder, error_msg) {\n\t// if error_msg was supplied it will appear as red next to input field\n\t// if error_msg is not supplied, check mark will appear next to field after entering value\n\tholder\n\t\t.style('display', 'inline-block')\n\t\t.style('color', error_msg ? 'red' : 'green')\n\t\t.html(error_msg ? '&#10060; ' + error_msg : '&#10003;')\n}\n\nfunction validateInputs(args, genome, hideTokenInput = false) {\n\tif (!hideTokenInput) {\n\t\tif (!args.gdc_token) throw 'GDC token missing'\n\t\tif (typeof args.gdc_token !== 'string') throw 'GDC token is not string'\n\t}\n\tif (!args.bam_files.length) throw 'No BAM file selected'\n\tfor (const file of args.bam_files) {\n\t\tif (!file.file_id) throw 'file uuid is missing'\n\t\tif (typeof file.file_id !== 'string') throw 'file uuid is not string'\n\t}\n\n\tif (args.useSsmOrGene == 'unmapped') {\n\t\t// do not supply a new attribute\n\t\treturn\n\t}\n\n\t/* if selecting one ssm from ssm table, args.variant{} is created\n\t   if searched variant string in <input>, args.variant{} is created\n\t   if searched position in <input>, args.position is created\n\t   at bam slicing request, it will use args.position or args.variant, whichever is present\n\t   thus must delete any previous setting\n\t*/\n\tdelete args.position\n\tdelete args.variant\n\n\tif (args.useSsmOrGene == 'ssm') {\n\t\tconst s = args.ssmInput\n\t\tif (!s) throw 'No variant selected'\n\t\tif (!s.chr) throw 'ssmInput.chr missing'\n\t\tif (!Number.isInteger(s.pos)) throw 'ssmInput.pos not integer'\n\t\tif (!s.ref) throw 'ssmInput.ref missing'\n\t\tif (!s.alt) throw 'ssmInput.alt missing'\n\t\targs.variant = s\n\t\treturn\n\t}\n\t// using coordInput\n\tconst ci = args.coordInput\n\tif (!ci.chr) throw 'No valid position or variant was entered'\n\tconst [nocount, hascount] = contigNameNoChr2(genome, [ci.chr])\n\tif (nocount + hascount == 0) throw 'Invalid chromosome name: ' + ci.chr\n\tconst chr = nocount ? 'chr' + ci.chr : ci.chr\n\tif (Number.isInteger(ci.pos)) {\n\t\t// is variant\n\t\tif (!ci.ref) throw 'Reference allele missing from variant string'\n\t\tif (!ci.alt) throw 'Alternative allele missing from variant string'\n\t\targs.variant = {\n\t\t\tchr,\n\t\t\tpos: ci.pos - 1, // convert 1-based to 0-based\n\t\t\tref: ci.ref,\n\t\t\talt: ci.alt\n\t\t}\n\t} else {\n\t\t// is range\n\t\tif (!Number.isInteger(ci.start) || !Number.isInteger(ci.stop)) throw 'non-integer start/stop'\n\t\targs.position = {\n\t\t\tchr,\n\t\t\tstart: ci.start,\n\t\t\tstop: ci.stop\n\t\t}\n\t}\n}\n"],
+  "mappings": 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+  "names": ["event", "gdcid_input", "i", "tabs", "mlst", "submitButton", "saydiv", "noPermissionDiv"]
+}

package/dist/barchart-4Q6LVJY4.js

@@ -0,0 +1,45 @@
+import {
+  Barchart,
+  barInit,
+  componentInit,
+  getDefaultBarSettings,
+  getPlotConfig,
+  negateTermLabel
+} from "./chunk-OXJ2TWDO.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-V6DLLX4N.js";
+import "./chunk-7RN3L2BX.js";
+import "./chunk-A6TQGNDQ.js";
+import "./chunk-HYZG6OPC.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-LSEFWW72.js";
+import "./chunk-5EF5U7MX.js";
+import "./chunk-2K5DSRBJ.js";
+import "./chunk-UCLS2SVB.js";
+import "./chunk-MVTCBVSX.js";
+import "./chunk-SEQLC4AD.js";
+import "./chunk-L4QG7XZE.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-KQMEJUWI.js";
+import "./chunk-UJU3Q7QJ.js";
+import "./chunk-WGL6FIUE.js";
+import "./chunk-6ITDJ5UR.js";
+import "./chunk-XYFDBYOY.js";
+import "./chunk-TV74I3Y5.js";
+import "./chunk-IH7ILDJS.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-TOU7EVFQ.js";
+import "./chunk-OAWQ6LOO.js";
+import "./chunk-SEEYV6P2.js";
+import "./chunk-NDWTN4U5.js";
+import "./chunk-OMR2DT66.js";
+import "./chunk-HFNDKYVF.js";
+export {
+  Barchart,
+  barInit,
+  componentInit,
+  getDefaultBarSettings,
+  getPlotConfig,
+  negateTermLabel
+};
+//# sourceMappingURL=barchart-4Q6LVJY4.js.map

package/dist/barchart.data-EXENRVMU.js

@@ -0,0 +1,22 @@
+import {
+  getBarchartData,
+  getCategoryData
+} from "./chunk-KQMEJUWI.js";
+import "./chunk-UJU3Q7QJ.js";
+import "./chunk-WGL6FIUE.js";
+import "./chunk-6ITDJ5UR.js";
+import "./chunk-XYFDBYOY.js";
+import "./chunk-TV74I3Y5.js";
+import "./chunk-IH7ILDJS.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-TOU7EVFQ.js";
+import "./chunk-OAWQ6LOO.js";
+import "./chunk-SEEYV6P2.js";
+import "./chunk-NDWTN4U5.js";
+import "./chunk-OMR2DT66.js";
+import "./chunk-HFNDKYVF.js";
+export {
+  getBarchartData,
+  getCategoryData
+};
+//# sourceMappingURL=barchart.data-EXENRVMU.js.map

package/dist/barchart.events-XRGND6I7.js

@@ -0,0 +1,45 @@
+import {
+  addAsGroup,
+  addGvCols,
+  addGvRowVals,
+  getHandlers,
+  hideCategory,
+  listSamples
+} from "./chunk-OXJ2TWDO.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-V6DLLX4N.js";
+import "./chunk-7RN3L2BX.js";
+import "./chunk-A6TQGNDQ.js";
+import "./chunk-HYZG6OPC.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-LSEFWW72.js";
+import "./chunk-5EF5U7MX.js";
+import "./chunk-2K5DSRBJ.js";
+import "./chunk-UCLS2SVB.js";
+import "./chunk-MVTCBVSX.js";
+import "./chunk-SEQLC4AD.js";
+import "./chunk-L4QG7XZE.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-KQMEJUWI.js";
+import "./chunk-UJU3Q7QJ.js";
+import "./chunk-WGL6FIUE.js";
+import "./chunk-6ITDJ5UR.js";
+import "./chunk-XYFDBYOY.js";
+import "./chunk-TV74I3Y5.js";
+import "./chunk-IH7ILDJS.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-TOU7EVFQ.js";
+import "./chunk-OAWQ6LOO.js";
+import "./chunk-SEEYV6P2.js";
+import "./chunk-NDWTN4U5.js";
+import "./chunk-OMR2DT66.js";
+import "./chunk-HFNDKYVF.js";
+export {
+  addAsGroup,
+  addGvCols,
+  addGvRowVals,
+  getHandlers as default,
+  hideCategory,
+  listSamples
+};
+//# sourceMappingURL=barchart.events-XRGND6I7.js.map