@sjcrh/proteinpaint-client 2.198.0 → 2.200.0

package/dist/databrowser.ui-6H2KMSTJ.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../src/databrowser/dictionary.parse.js", "../src/databrowser/databrowser.ui.js"],
-  "sourcesContent": ["/*\n------ EXPORTED ------ \nparseDictionary()\n\t- div\n\t- input: STR\n\n------ Internal ------ \nTraditional data dictionary parsing: \n\t1. parseDataDictionary\n\nPhenotree parsing:\n\t1. parseConfig()\n\t2. trackMissingTerms\n*/\n\nexport function parseDictionary(input) {\n\t// Returns terms array for appInit({state.vocab.terms})\n\tconst terms = {}\n\n\tconst lines = input.trim().split(/\\r?\\n/)\n\t// process the header line\n\t// could have used lines.shift() here, but will want to track actual line numbers later for errors\n\tconst header = lines[0].split('\\t')\n\n\tconst term_idIndex = header.findIndex(l => l.toLowerCase().includes('term_id'))\n\tconst variableIndex = header.findIndex(l => l.toLowerCase().includes('variable')) // term_id col in phenotree\n\tif (term_idIndex != -1) parseDataDictionary(lines, header)\n\tif (variableIndex != -1) parsePhenotree(lines, header)\n\tif (variableIndex == -1 && term_idIndex == -1) {\n\t\tthrow `Unrecognized file format. Please check the header names.`\n\t}\n\t// if (varNameIndex != -1 && term_idIndex != -1) throw 'Unrecognized file format'\n\n\tfunction parseDataDictionary(lines, header) {\n\t\t/*\n\t\tParses data dictionary in a term_id to parent_id format\n\t\t\t- Parses tab delim data arranged in required cols: term_id, parent_id, name, type, values\n\t\t\t- Assumptions:\n\t\t\t\t1. Headers required\n\t\t\t\t2. No blank or '-' values in the term_id, parent_id, name, or type columns. Top grandparents must include 'root' for the parent_id\n\t\t\t\t3. No identical term ids \n\t\t*/\n\t\tconst parIdIndex = header.findIndex(l => l.toLowerCase().includes('parent_id'))\n\t\tif (parIdIndex == -1) {\n\t\t\tthrow `Missing required 'parent_id' header`\n\t\t}\n\t\tconst nameIndex = header.findIndex(l => l.toLowerCase().includes('name'))\n\t\tif (nameIndex == -1) {\n\t\t\tthrow `Missing required 'Name' header`\n\t\t}\n\t\tconst typeIndex = header.findIndex(l => {\n\t\t\tconst v = l.trim().toLowerCase()\n\t\t\treturn v === 'type'\n\t\t})\n\t\tif (typeIndex == -1) {\n\t\t\tthrow `Missing required 'Type' header`\n\t\t}\n\t\tconst valuesIndex = header.findIndex(l => l.toLowerCase().includes('values'))\n\t\tif (valuesIndex == -1) {\n\t\t\tthrow `Missing required 'Values' header`\n\t\t}\n\t\tif (parIdIndex == -1 || nameIndex == -1 || typeIndex == -1 || valuesIndex == -1) {\n\t\t\tthrow `Missing required header(s)`\n\t\t}\n\n\t\tconst parentIds = new Set()\n\n\t\tfor (const [i, line] of lines.entries()) {\n\t\t\tif (i === 0) continue\n\t\t\tconst lineNum = i + 1 //Use for error messages\n\n\t\t\ttry {\n\t\t\t\tconst cols = line.split('\\t')\n\n\t\t\t\t//validate column entries, no blank or '-' values\n\t\t\t\tfor (const [i, c] of cols.entries()) {\n\t\t\t\t\tconst colNum = i + 1\n\t\t\t\t\tlet foundProblem\n\t\t\t\t\tif (i == valuesIndex) continue //values can be blank\n\t\t\t\t\tif (c == '' || c == '-') {\n\t\t\t\t\t\tfoundProblem = true\n\t\t\t\t\t\tthrow `Blank or '-' entered for line ${lineNum}, column ${colNum}`\n\t\t\t\t\t}\n\t\t\t\t\tif (foundProblem == true) throw `Invalid entry for line ${lineNum}, column ${colNum}`\n\t\t\t\t}\n\n\t\t\t\tconst termId = cols[term_idIndex]\n\t\t\t\tconst type = cols[typeIndex]\n\n\t\t\t\tterms[termId] = {\n\t\t\t\t\tid: termId,\n\t\t\t\t\tname: cols[nameIndex].trim().replace(/\"/g, ''),\n\t\t\t\t\tparent_id: cols[parIdIndex] != 'root' ? cols[parIdIndex] : null,\n\t\t\t\t\ttype: cols[typeIndex] != 'non graphable' ? cols[typeIndex] : null\n\t\t\t\t}\n\n\t\t\t\tparentIds.add(terms[termId].parent_id)\n\n\t\t\t\tif (type == 'categorical') {\n\t\t\t\t\tterms[termId].values = {}\n\t\t\t\t}\n\t\t\t\tconst values = cols[valuesIndex].trim().replace(/\"/g, '').split(';')\n\n\t\t\t\tfor (const x of values) {\n\t\t\t\t\tconst v = x.trim()\n\t\t\t\t\tif (v == '') continue\n\t\t\t\t\tconst segments = v.split('=')\n\t\t\t\t\tconst key = segments.shift()\n\t\t\t\t\tconst label = segments.join('=')\n\t\t\t\t\tif (!label) throw `Values=\"${v}\" in line ${lineNum} not in a key = value format.`\n\t\t\t\t\tif (!terms[termId].values) terms[termId].values = {}\n\t\t\t\t\tterms[termId].values[key] = { label: label }\n\t\t\t\t}\n\n\t\t\t\tconst numValues = Object.keys(terms[termId].values).length\n\t\t\t\tterms[termId].groupsetting = { disabled: numValues < 3 }\n\n\t\t\t\tvalidateNumericTermCategories(terms[termId])\n\t\t\t} catch (e) {\n\t\t\t\tthrow `Line ${lineNum} error: ${e}`\n\t\t\t}\n\t\t}\n\t\tfor (const t in terms) terms[t].isleaf = !parentIds.has(terms[t].id)\n\t}\n\n\tfunction parsePhenotree(lines, header) {\n\t\t/* \n\t\tParses phenotree:\n\t\t\t- Parses tab delim data arranged in cols: levels(n), variable (i.e. term_id), type, and categories \n\t\t\t(i.e. previous configuration) as well as unit.\n\t\t\t- Only the variable and type cols are required\n\t\t\t- Blank and '-' values for levels converted to null.\n\t\t\t- Assumptions:\n\t\t\t\t1. Headers required. `Variable', 'Type', 'Categories', and 'Unit' may appear anywhere. \n\t\t\t\t'Level_[XX]' for optional hierarchy/level columns. 'Unit' is optional for numeric terms.\n\t\t\t\t2. Levels are defined left to right, highest to lowest, and in order, no gaps.\n\t\t\t\t3. No blanks or '-' between levels as well as no duplicate values in the same line.\n\t\t\t\t4. No identical term ids\n\t\t\t\t5. All non-leaf names/ids must be unique. \n\t\t*/\n\t\tif (variableIndex == -1) {\n\t\t\tthrow `Missing required 'Variable' header`\n\t\t}\n\n\t\tconst typeIndex = header.findIndex(l => {\n\t\t\tconst v = l.trim().toLowerCase()\n\t\t\treturn v === 'type'\n\t\t})\n\t\tif (typeIndex == -1) {\n\t\t\tthrow `Missing required 'Type' header`\n\t\t}\n\n\t\tconst categoriesIndex = header.findIndex(l => l.toLowerCase().includes('categories'))\n\n\t\tconst levelColIndexes = header.map((c, i) => (c.toLowerCase().includes('level_') ? i : -1)).filter(i => i != -1)\n\t\t//If no level cols provided, use key/Variable col as single level. Will print the id as name\n\t\tif (!levelColIndexes.length) levelColIndexes.push(variableIndex)\n\n\t\tconst unitIndex = header.findIndex(l => l.toLowerCase().includes('unit'))\n\n\t\tconst sampleTypeIndex = header.findIndex(l => {\n\t\t\tconst v = l.trim().toLowerCase()\n\t\t\treturn v === 'sample_type'\n\t\t})\n\n\t\t// see below\n\t\tconst additionalAttrIndexes = header.findIndex(l => l.toLowerCase().includes('additional attributes'))\n\n\t\t// caching and/or tracking variables\n\t\tconst termNameToId = {}\n\t\tconst parentTermNames = new Set()\n\t\tconst parent2ChildOrder = new Map()\n\t\tparent2ChildOrder.set(null, [])\n\n\t\tfor (const [i, line] of lines.entries()) {\n\t\t\tif (i === 0) continue\n\t\t\tconst lineNum = i + 1\n\n\t\t\ttry {\n\t\t\t\tconst cols = line.split('\\t')\n\t\t\t\tconst levelNames = levelColIndexes.map(i => cols[i].trim().replace(/\"/g, '')).filter(c => c != '-')\n\t\t\t\tif (levelNames.length != new Set(levelNames).size) {\n\t\t\t\t\tthrow `Non-unique levels in line ${lineNum}: ${JSON.stringify(levelNames)}`\n\t\t\t\t}\n\n\t\t\t\t// Create map of immediate parents to children, in order of appearance\n\t\t\t\tfor (const [i, lvlName] of levelNames.entries()) {\n\t\t\t\t\t// Messy?? Is there an more elegant way?\n\t\t\t\t\tif (i == 0) {\n\t\t\t\t\t\tif (parent2ChildOrder.get(null).indexOf(lvlName) == -1) parent2ChildOrder.get(null).push(lvlName)\n\t\t\t\t\t}\n\t\t\t\t\tif (i != levelNames.length - 1) {\n\t\t\t\t\t\tif (!parent2ChildOrder.has(lvlName)) parent2ChildOrder.set(lvlName, [])\n\t\t\t\t\t}\n\t\t\t\t\tfor (const n of levelNames) {\n\t\t\t\t\t\tif (i == levelNames.indexOf(n) - 1) {\n\t\t\t\t\t\t\tif (parent2ChildOrder.get(lvlName).indexOf(n) == -1) parent2ChildOrder.get(lvlName).push(n)\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t}\n\n\t\t\t\tconst name = levelNames.pop()\n\n\t\t\t\tconst firstDashIndex = cols.indexOf('-')\n\t\t\t\tif (firstDashIndex != -1 && firstDashIndex < cols.indexOf(name)) {\n\t\t\t\t\tthrow `Blank or '-' value detected between levels in line ${lineNum}`\n\t\t\t\t}\n\t\t\t\tconst term = parseCategories(cols[typeIndex], cols[categoriesIndex], lineNum, name)\n\n\t\t\t\tconst id = cols[variableIndex] || name\n\t\t\t\tif (id in terms) {\n\t\t\t\t\tconst orig = terms[id]\n\t\t\t\t\tthrow `Error: Multiple config rows for term.id='${id}': lines# ${orig.lineNum} and ${lineNum}`\n\t\t\t\t}\n\n\t\t\t\t//Create term object\n\t\t\t\tterms[id] = {\n\t\t\t\t\tid,\n\t\t\t\t\tname,\n\t\t\t\t\ttype: term.type,\n\t\t\t\t\tvalues: term.values,\n\t\t\t\t\tgroupsetting: term.groupsetting,\n\n\t\t\t\t\t// *** temporary attributes to be deleted later ***\n\t\t\t\t\tancestry: levelNames.slice(), // to be deleted later, used to fill in missing terms\n\t\t\t\t\tparent_name: levelNames.pop() || null, // will change this later to parent_id\n\t\t\t\t\tlineNum // to be deleted later\n\t\t\t\t}\n\n\t\t\t\t// pass additional properties to term obj\n\t\t\t\tif (cols[unitIndex] != null) terms[id].unit = cols[unitIndex]\n\t\t\t\tif (cols[sampleTypeIndex] != null) terms[id].sample_type = cols[sampleTypeIndex]\n\t\t\t\tif (cols[additionalAttrIndexes]) {\n\t\t\t\t\t/* file has additional attribute JSON column, and this line has value for it;\n\t\t\t\t\tdirectly assign json properties to the term object, no need to nest in \"term.attributes{}\"\n\t\t\t\t\te.g. default color scale for continuous mode for drug sensitivity terms\n\t\t\t\t\t*/\n\t\t\t\t\tObject.assign(terms[id], JSON.parse(cols[additionalAttrIndexes]))\n\t\t\t\t}\n\n\t\t\t\ttermNameToId[name] = id\n\t\t\t\tparentTermNames.add(terms[id].parent_name)\n\t\t\t} catch (e) {\n\t\t\t\tthrow `Line ${lineNum} error: ${e}`\n\t\t\t}\n\t\t}\n\t\t// some parent term levels may not have entries\n\t\ttrackMissingTerms(termNameToId, terms, parentTermNames, parent2ChildOrder)\n\n\t\tfor (const id in terms) {\n\t\t\tconst term = terms[id]\n\t\t\tterm.child_order = parent2ChildOrder.get(term.parent_name).indexOf(term.name) + 1\n\t\t\tterm.isleaf = !parentTermNames.has(term.name)\n\t\t\tterm.parent_id = termNameToId[term.parent_name] || null\n\t\t\tdelete term.parent_name\n\t\t\tdelete term.lineNum\n\t\t\t//term.ancestry = term.ancestry.map(name => termNameToId[name]).filter(d=>!!d)\n\t\t\tdelete term.ancestry\n\t\t}\n\t}\n\treturn { terms: Object.values(terms) }\n}\n\n/*\n **** Parsing Functions for Phenotree ****\n */\n\nfunction parseCategories(type, catJSON, lineNum, varName) {\n\tif (!type) throw `No type provided for variable: ${varName} on line ${lineNum}`\n\n\tconst term = {\n\t\ttype,\n\t\tvalues: catJSON == '' || catJSON == undefined ? {} : JSON.parse(catJSON)\n\t}\n\n\tvalidateNumericTermCategories(term)\n\n\tif (term.type == 'categorical') {\n\t\tconst numValues = Object.keys(term.values).length\n\t\tterm.groupsetting = { disabled: numValues < 3 }\n\t}\n\n\treturn term\n}\n\nfunction trackMissingTerms(termNameToId, terms, parentTermNames, parent2ChildOrder) {\n\tfor (const id in terms) {\n\t\tconst term = terms[id]\n\t\tfor (const [i, name] of term.ancestry.entries()) {\n\t\t\tif (name in termNameToId) {\n\t\t\t\t// a tsv line was already processed for this term\n\t\t\t\tconst id = termNameToId[name]\n\t\t\t\tconst ancestor = terms[id]\n\t\t\t\t/* if this term's ancestor has no level above it, previous processing of this ancestor\n\t\t\t\tshould also not have a term parent,\n\t\t\t\tOR if this ancestor another level above it,\n\t\t\t\tcheck that it is the same parent_term as previousy processed */\n\t\t\t\tif ((i - 1 < 0 && ancestor.parent_name) || ancestor.parent_name != term.ancestry[i - 1]) {\n\t\t\t\t\tthrow `Different parents for term=${name}, '${term.ancestry[i - 1]}' and '${ancestor.parent_name}'`\n\t\t\t\t}\n\t\t\t\tcontinue\n\t\t\t}\n\n\t\t\tterms[name] = {\n\t\t\t\tid: name,\n\t\t\t\tname,\n\t\t\t\tisleaf: false,\n\t\t\t\tancestry: term.ancestry.slice(0, i)\n\t\t\t}\n\n\t\t\tterms[name].parent_name = terms[name].ancestry.slice(-1)[0] || null\n\t\t\ttermNameToId[name] = name\n\t\t\tparentTermNames.add(name)\n\t\t}\n\t}\n}\n\nfunction validateNumericTermCategories(term) {\n\tif (term.type != 'integer' && term.type != 'float') return\n\t// term is numeric\n\tif (!term.values) return // .values{} is optional\n\tif (typeof term.values != 'object') throw 'numeric .values{} is not object'\n\t// values{} keys should be uncomputable categories, auto-assign the flag here\n\t// also make sure keys can be cast into numbers\n\tfor (const key in term.values) {\n\t\tif (key == '') throw 'Cannot use empty string as an uncomputable category'\n\t\t// key is not empty string\n\t\tconst tmp = Number(key)\n\t\tif (Number.isNaN(tmp)) {\n\t\t\t// this is by design so that all values in the db to match the column type for that value, otherwise the generated SQL statements would always have to include\n\t\t\tthrow `Uncomputable category of a numeric term is required to be a number (here uses non-numeric value of ${key}).`\n\t\t}\n\t\t// key is a valid category because it can be casted into a number\n\t\tterm.values[key].uncomputable = true\n\t}\n}\n", "import * as uiutils from '#dom/uiUtils'\nimport { appear } from '#dom/animation'\nimport { Tabs } from '../../dom/toggleButtons'\nimport { appInit } from '#mass/app'\nimport { parseDictionary } from './dictionary.parse'\nimport { sayerror } from '../client'\n\n/* \nLaunches MASS UI by uploading a custom data dictionary\n\n------ EXPORTED ------ \ninit_dictionaryUI()\n    - holder\n\n------ Internal ------ \nUI elements:\n\t- infoSection()\n\t- makeDataDictionaryTabs()\n\t\ta. makeTextEntryFilePathInput()\n\t\tb. makeFileUpload()\n\t\tc. makeCopyPasteInput()\n\t- submitButton()\n\nobj:{ data:[ {terms} ] }\n*/\n\nexport function init_databrowserUI(holder, debugmode) {\n\tconst wrapper = holder\n\t\t.append('div')\n\t\t.style('margin', '20px 20px 20px 40px')\n\t\t.style(\n\t\t\t'font-family',\n\t\t\t\"'Lucida Sans', 'Lucida Sans Regular', 'Lucida Grande', 'Lucida Sans Unicode', Geneva, Verdana, sans-serif\"\n\t\t)\n\t\t.style('place-items', 'center left')\n\t\t.style('overflow', 'hidden')\n\t\t.classed('sjpp-app-ui', true)\n\n\tconst obj = {}\n\n\t//Information section for user with documentation and example\n\tinfoSection(wrapper)\n\n\t//Data dictionary section\n\tmakeSectionHeader(wrapper, 'Data Dictionary')\n\tconst tabs_div = wrapper.append('div').style('margin-left', '2vw')\n\tmakeDataDictionaryTabs(tabs_div, obj)\n\n\t//Submit and reset button at the bottom.\n\tconst controlBtns_div = wrapper\n\t\t.append('div')\n\t\t.style('display', 'flex')\n\t\t.style('align-items', 'center')\n\t\t.style('margin', '40px 0px 40px 130px')\n\n\tsubmitButton(controlBtns_div, obj, wrapper, holder)\n\tuiutils.makeResetBtn(controlBtns_div, obj, '.databrowser_input')\n\n\t//Remove after testing\n\tif (debugmode) window.doms = obj\n\treturn obj\n}\n\nfunction infoSection(div) {\n\tdiv.append('div').style('margin', '10px').style('opacity', '0.65').html(`\n\t\t\t<ul>\n                <li>\n                    Please see the <a href=\"https://github.com/stjude/proteinpaint/wiki/Data-Browser\" target=\"_blank\">documentation</a> for more information.\n                </li>\n\t\t\t\t<li>\n\t\t\t\t\tDownload an example data dictionary <a href=\"https://proteinpaint.stjude.org/ppdemo/databrowser/dictionaryDemoData.tar.gz\" target=\"_self\" \"download>here</a>.\n\t\t\t\t</li>\n            </ul>`)\n}\n//Use function more as UI exapands\nfunction makeSectionHeader(div, text) {\n\tconst header = uiutils.makePrompt(div, text)\n\theader\n\t\t.style('font-size', '1.5em')\n\t\t.style('color', '#003366')\n\t\t.style('margin', '20px 10px 40px 10px')\n\t\t.classed('sjpp-databrowser-section-header', true)\n\tconst hr = div.append('hr')\n\thr.style('color', 'ligthgrey').style('margin', '-30px 0px 15px 0px').style('width', '50vw').style('opacity', '0.4')\n}\n\nfunction makeDataDictionaryTabs(tabs_div, obj) {\n\t// Creates the horizontal top tabs and callbacks for the data dictionary section\n\t// Rendering code and callback to the same parseDictionary().\n\t// All data parsed in client and returned to obj.data\n\tconst tabs = [\n\t\t{\n\t\t\tlabel: 'Select File',\n\t\t\tactive: true,\n\t\t\twidth: 95,\n\t\t\tcallback: async (event, tab) => {\n\t\t\t\ttab.contentHolder.style('border', 'none').style('display', 'block')\n\t\t\t\tappear(tab.contentHolder)\n\n\t\t\t\ttab.contentHolder\n\t\t\t\t\t.append('div')\n\t\t\t\t\t.html(`<p style=\"margin-left: 10px; opacity: 0.65;\">Select a file from your computer.</p>`)\n\t\t\t\tmakeFileUpload(tab.contentHolder, obj)\n\n\t\t\t\tdelete tab.callback\n\t\t\t}\n\t\t},\n\t\t{\n\t\t\tlabel: 'Paste Data',\n\t\t\tactive: false,\n\t\t\twidth: 95,\n\t\t\tcallback: async (event, tab) => {\n\t\t\t\ttab.contentHolder.style('border', 'none').style('display', 'block')\n\t\t\t\tappear(tab.contentHolder)\n\n\t\t\t\ttab.contentHolder\n\t\t\t\t\t.append('div')\n\t\t\t\t\t.html(\n\t\t\t\t\t\t`<p style=\"margin-left: 10px; opacity: 0.65;\">Paste data dictionary or phenotree in a tab delimited format.</p>`\n\t\t\t\t\t)\n\t\t\t\tmakeCopyPasteInput(tab.contentHolder, obj)\n\t\t\t\tdelete tab.callback\n\t\t\t}\n\t\t},\n\t\t{\n\t\t\tlabel: 'File Path',\n\t\t\tactive: false,\n\t\t\twidth: 95,\n\t\t\tcallback: async (event, tab) => {\n\t\t\t\ttab.contentHolder.style('border', 'none').style('display', 'block')\n\t\t\t\tappear(tab.contentHolder)\n\n\t\t\t\ttab.contentHolder\n\t\t\t\t\t.append('div')\n\t\t\t\t\t.html(`<p style=\"margin-left: 10px; opacity: 0.65;\">Provide a URL file path.</p>`)\n\t\t\t\tuiutils.makePrompt(tab.contentHolder, 'URL')\n\t\t\t\tmakeTextEntryFilePathInput(tab.contentHolder, obj)\n\n\t\t\t\tdelete tab.callback\n\t\t\t}\n\t\t}\n\t]\n\tnew Tabs({ holder: tabs_div, tabs }).main()\n}\n\nfunction makeTextEntryFilePathInput(div, obj) {\n\t// Renders the file path input div and callback.\n\tconst filepath_div = div.append('div').style('display', 'inline-block')\n\tconst filepath = uiutils\n\t\t.makeTextInput(filepath_div)\n\t\t.style('border', '1px solid rgb(138, 177, 212)')\n\t\t.classed('databrowser_input', true)\n\t\t.on('keyup', async () => {\n\t\t\tconst data = filepath.property('value').trim()\n\t\t\tif (uiutils.isURL(data)) {\n\t\t\t\tconst txt = await fetch(data)\n\t\t\t\t\t.then(req => req.text())\n\t\t\t\t\t.then(txt => {\n\t\t\t\t\t\tobj.data = parseDictionary(txt)\n\t\t\t\t\t})\n\t\t\t} else {\n\t\t\t\t//TODO: implement serverside filepaths(?)\n\t\t\t}\n\t\t})\n}\n\nfunction makeFileUpload(div, obj) {\n\t// Renders the select file div and callback.\n\tconst upload_div = div.append('div').style('display', 'inline-block')\n\tconst upload = uiutils.makeFileUpload(upload_div).classed('databrowser_input', true)\n\tupload.on('change', event => {\n\t\tconst file = event.target.files[0]\n\t\tconst reader = new FileReader()\n\t\treader.onload = event => {\n\t\t\tobj.data = parseDictionary(event.target.result)\n\t\t}\n\t\treader.readAsText(file, 'utf8')\n\t})\n}\n\nfunction makeCopyPasteInput(div, obj) {\n\t// Renders the copy/paste div and callback.\n\tconst paste_div = div.append('div').style('display', 'block')\n\tconst paste = uiutils\n\t\t.makeTextAreaInput({ div: paste_div, rows: 10 })\n\t\t.style('border', '1px solid rgb(138, 177, 212)')\n\t\t.style('margin', '0px 0px 0px 20px')\n\t\t.classed('databrowser_input', true)\n\t\t.on('keyup', async () => {\n\t\t\tobj.data = parseDictionary(paste.property('value').trim())\n\t\t})\n}\n\n/*\n **** Submission Functions ****\n */\n\nfunction submitButton(div, obj, wrapper, holder) {\n\tconst submit = uiutils.makeBtn({\n\t\tdiv,\n\t\ttext: 'Create Data Browser',\n\t\tcolor: 'white',\n\t\tbackgroundColor: '#001aff',\n\t\tborder: '2px solid #001aff'\n\t})\n\tconst errorMessage_div = div.append('div')\n\tsubmit\n\t\t.style('margin-right', '10px')\n\t\t.style('font-size', '16px')\n\t\t.classed('sjpp-ui-submitBtn', true)\n\t\t.attr('type', 'submit')\n\t\t.on('click', () => {\n\t\t\tif (!obj.data || obj.data == undefined) {\n\t\t\t\tconst sayerrorDiv = errorMessage_div.append('div').style('display', 'inline-block').style('max-width', '20vw')\n\t\t\t\tsayerror(sayerrorDiv, 'Please provide data')\n\t\t\t\tsetTimeout(() => sayerrorDiv.remove(), 3000)\n\t\t\t} else {\n\t\t\t\twrapper.remove()\n\t\t\t\tappInit({\n\t\t\t\t\tholder: holder,\n\t\t\t\t\tstate: {\n\t\t\t\t\t\tvocab: {\n\t\t\t\t\t\t\tterms: obj.data.terms\n\t\t\t\t\t\t},\n\t\t\t\t\t\tplots: [\n\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\tchartType: 'dictionary'\n\t\t\t\t\t\t\t}\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}\n"],
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-  "names": ["lines", "header", "i", "id", "makeFileUpload", "txt", "event"]
-}

package/dist/dictionary-V37LXFIP.js

@@ -1,118 +0,0 @@
-import {
-  appInit
-} from "./chunk-5VOPABBA.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-Z5U6HOE4.js";
-import "./chunk-HYOEWQ5P.js";
-import "./chunk-HBW42TDT.js";
-import "./chunk-FN5XPUPH.js";
-import "./chunk-5ABGFJSP.js";
-import "./chunk-IIT367QZ.js";
-import "./chunk-RZGEKL77.js";
-import "./chunk-XPY6AWXO.js";
-import "./chunk-NELOT3NJ.js";
-import "./chunk-M6EF3WVV.js";
-import "./chunk-7IYJZZQI.js";
-import {
-  copyMerge,
-  getCompInit
-} from "./chunk-M3J4MINX.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-LFCYMSVA.js";
-import "./chunk-I6WR4CG7.js";
-import "./chunk-2X6W4E3W.js";
-import "./chunk-NYRZNRG5.js";
-import "./chunk-JNITUVXP.js";
-import "./chunk-3XVVN66M.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-VQZ2Z5YU.js";
-import "./chunk-NSTL4MY2.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-KYBIQBXE.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-OMR2DT66.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-HFNDKYVF.js";
-
-// plots/dictionary.js
-var MassDict = class _MassDict {
-  static type = "tree";
-  constructor(opts) {
-    this.type = _MassDict.type;
-    this.dom = {
-      holder: opts.holder.style("padding", "20px"),
-      header: opts.header
-    };
-  }
-  async init(appState) {
-    const config = appState.plots.find((p) => p.id === this.id) || {};
-    const opts = {
-      vocabApi: this.app.vocabApi,
-      holder: this.dom.holder,
-      state: this.getState(appState),
-      tree: {
-        click_term: (_term) => {
-          const term = _term.term || _term;
-          const _config = Object.assign({}, config?.spawnConfig, {
-            chartType: term.type == "survival" ? "survival" : "summary",
-            term: _term.term ? _term : { term }
-          });
-          this.app.dispatch({
-            type: "plot_create",
-            config: _config
-          });
-          this.app.dispatch({
-            type: "plot_delete",
-            id: this.id
-          });
-        }
-      }
-    };
-    if (config?.tree?.usecase) {
-      opts.tree.usecase = config.tree.usecase;
-    }
-    this.dom.holder.style("position", "relative");
-    const loadingDiv = this.dom.holder.append("div").attr("class", "sjpp-loading-overlay").style("display", "");
-    loadingDiv.append("div").attr("class", "sjpp-spinner");
-    try {
-      this.tree = await appInit(opts);
-    } finally {
-      loadingDiv.remove();
-    }
-  }
-  getState(appState) {
-    const config = appState.plots.find((p) => p.id === this.id) || {};
-    const tree = { usecase: { target: "dictionary" } };
-    if (config?.tree?.usecase?.specialCase) {
-      tree.usecase.specialCase = config.tree.usecase.specialCase;
-    }
-    return {
-      tree,
-      vocab: appState.vocab,
-      activeCohort: appState.activeCohort,
-      termfilter: appState.termfilter,
-      selectdTerms: appState.selectedTerms,
-      customTerms: appState.customTerms
-    };
-  }
-  main() {
-    if (this.dom.header) this.dom.header.text("Data Variables");
-    this.tree.dispatch({
-      type: "app_refresh",
-      state: this.state
-    });
-  }
-};
-var dictInit = getCompInit(MassDict);
-var componentInit = dictInit;
-function getPlotConfig(opts, app) {
-  const config = { hidePlotFilter: true };
-  return copyMerge(config, opts);
-}
-export {
-  componentInit,
-  dictInit,
-  getPlotConfig
-};
-//# sourceMappingURL=dictionary-V37LXFIP.js.map

package/dist/dnaMethylation-OIZMHMLK.js

@@ -1,38 +0,0 @@
-import {
-  SearchHandler
-} from "./chunk-M4TTGGT4.js";
-import "./chunk-5VOPABBA.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-Z5U6HOE4.js";
-import "./chunk-HYOEWQ5P.js";
-import "./chunk-HBW42TDT.js";
-import "./chunk-FN5XPUPH.js";
-import "./chunk-5ABGFJSP.js";
-import "./chunk-IIT367QZ.js";
-import "./chunk-RZGEKL77.js";
-import "./chunk-XPY6AWXO.js";
-import "./chunk-NELOT3NJ.js";
-import "./chunk-M6EF3WVV.js";
-import "./chunk-7IYJZZQI.js";
-import "./chunk-M3J4MINX.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-LFCYMSVA.js";
-import "./chunk-I6WR4CG7.js";
-import "./chunk-2X6W4E3W.js";
-import "./chunk-NYRZNRG5.js";
-import "./chunk-JNITUVXP.js";
-import "./chunk-3XVVN66M.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-VQZ2Z5YU.js";
-import "./chunk-NSTL4MY2.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-KYBIQBXE.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-OMR2DT66.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-HFNDKYVF.js";
-export {
-  SearchHandler
-};
-//# sourceMappingURL=dnaMethylation-OIZMHMLK.js.map

package/dist/dnaMethylation.integration.spec-CWPTJ74H.js

@@ -1,203 +0,0 @@
-import {
-  hg38
-} from "./chunk-7VB2BKXW.js";
-import {
-  SearchHandler
-} from "./chunk-M4TTGGT4.js";
-import {
-  sleep
-} from "./chunk-ECIBJXFT.js";
-import {
-  require_tape
-} from "./chunk-TUMA63WX.js";
-import {
-  vocabInit
-} from "./chunk-5VOPABBA.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-Z5U6HOE4.js";
-import "./chunk-HYOEWQ5P.js";
-import "./chunk-HBW42TDT.js";
-import "./chunk-FN5XPUPH.js";
-import "./chunk-5ABGFJSP.js";
-import "./chunk-IIT367QZ.js";
-import "./chunk-RZGEKL77.js";
-import "./chunk-XPY6AWXO.js";
-import "./chunk-NELOT3NJ.js";
-import "./chunk-M6EF3WVV.js";
-import "./chunk-7IYJZZQI.js";
-import "./chunk-M3J4MINX.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-LFCYMSVA.js";
-import {
-  TermTypes
-} from "./chunk-I6WR4CG7.js";
-import "./chunk-2X6W4E3W.js";
-import "./chunk-NYRZNRG5.js";
-import "./chunk-JNITUVXP.js";
-import "./chunk-3XVVN66M.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-VQZ2Z5YU.js";
-import "./chunk-NSTL4MY2.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-KYBIQBXE.js";
-import {
-  select_default
-} from "./chunk-I6Y4O3RR.js";
-import "./chunk-OMR2DT66.js";
-import "./chunk-DQC5FFGV.js";
-import {
-  __toESM
-} from "./chunk-HFNDKYVF.js";
-
-// termdb/handlers/test/dnaMethylation.integration.spec.ts
-var import_tape = __toESM(require_tape(), 1);
-var vocabApi = await getVocabApi();
-var handler = new SearchHandler();
-(0, import_tape.default)("\n", function(test) {
-  test.comment("-***- dnaMethylation search handler -***-");
-  test.end();
-});
-(0, import_tape.default)("Search handler layout", async (test) => {
-  const holder = getHolder();
-  await initializeSearchHandler({ holder });
-  const geneSearchInput = holder.select(".sja_genesearchinput").node();
-  test.ok(geneSearchInput, "should display gene search input");
-  if (test["_ok"]) holder.remove();
-  test.end();
-});
-(0, import_tape.default)("Coordinate search", async (test) => {
-  let term;
-  const callback = (_term) => {
-    term = _term;
-  };
-  const holder = getHolder();
-  await initializeSearchHandler({ holder, callback });
-  const geneSearchInput = holder.select(".sja_genesearchinput").node();
-  const chr = "chr17";
-  const start = 7661778;
-  const stop = 7687537;
-  const coord = `${chr}:${start}-${stop}`;
-  geneSearchInput.value = coord;
-  geneSearchInput.dispatchEvent(new KeyboardEvent("keyup", { key: "Enter", code: "Enter", bubbles: true }));
-  await sleep(100);
-  test.equal(term.chr, chr, "term.chr should equal input chr");
-  test.equal(term.start, start, "term.start should equal input start");
-  test.equal(term.stop, stop, "term.stop should equal input stop");
-  test.equal(term.type, TermTypes.DNA_METHYLATION, "term.type should be dnaMethylation");
-  if (test["_ok"]) holder.remove();
-  test.end();
-});
-(0, import_tape.default)("Single position search (chr:pos format)", async (test) => {
-  let term;
-  const callback = (_term) => {
-    term = _term;
-  };
-  const holder = getHolder();
-  await initializeSearchHandler({ holder, callback });
-  const geneSearchInput = holder.select(".sja_genesearchinput").node();
-  geneSearchInput.value = "chr17:7669073";
-  geneSearchInput.dispatchEvent(new KeyboardEvent("keyup", { key: "Enter", code: "Enter", bubbles: true }));
-  await sleep(100);
-  test.equal(term.chr, "chr17", "term.chr should equal input chr");
-  test.equal(term.start, 7669073, "term.start should be exact position, not 400bp-expanded");
-  test.equal(term.stop, 7669074, "term.stop should be start+1 for a single CpG site");
-  test.equal(term.type, TermTypes.DNA_METHYLATION, "term.type should be dnaMethylation");
-  if (test["_ok"]) holder.remove();
-  test.end();
-});
-(0, import_tape.default)("Single position search (chr:pos-pos format)", async (test) => {
-  let term;
-  const callback = (_term) => {
-    term = _term;
-  };
-  const holder = getHolder();
-  await initializeSearchHandler({ holder, callback });
-  const geneSearchInput = holder.select(".sja_genesearchinput").node();
-  geneSearchInput.value = "chr17:7669073-7669073";
-  geneSearchInput.dispatchEvent(new KeyboardEvent("keyup", { key: "Enter", code: "Enter", bubbles: true }));
-  await sleep(100);
-  test.equal(term.chr, "chr17", "term.chr should equal input chr");
-  test.equal(term.start, 7669073, "term.start should be exact position, not 400bp-expanded");
-  test.equal(term.stop, 7669074, "term.stop should be start+1 for a single CpG site");
-  test.equal(term.type, TermTypes.DNA_METHYLATION, "term.type should be dnaMethylation");
-  if (test["_ok"]) holder.remove();
-  test.end();
-});
-(0, import_tape.default)("Gene search", async (test) => {
-  let term;
-  const callback = (_term) => {
-    term = _term;
-  };
-  const holder = getHolder();
-  await initializeSearchHandler({ holder, callback });
-  const geneSearchInput = holder.select(".sja_genesearchinput").node();
-  const geneSymbol = "TP53";
-  geneSearchInput.value = geneSymbol;
-  geneSearchInput.dispatchEvent(new KeyboardEvent("keyup", { key: "Enter", code: "Enter", bubbles: true }));
-  await sleep(100);
-  const blockSvg = holder.select('[data-testid="sjpp_block_svg"]').node();
-  test.ok(blockSvg, "should render block svg");
-  const submitBtn = holder.select('[data-testid="sjpp-dnaMethylation-submitDiv"]').select("button").node();
-  submitBtn.click();
-  await sleep(100);
-  test.equal(term.chr, "chr17", "term.chr should be TP53 chr");
-  test.equal(term.start, 7661778, "term.start should be TP53 start");
-  test.equal(term.stop, 7687537, "term.stop should be TP53 stop");
-  test.equal(term.type, TermTypes.DNA_METHYLATION, "term.type should be dnaMethylation");
-  if (test["_ok"]) holder.remove();
-  test.end();
-});
-(0, import_tape.default)("Gene search with navigation", async (test) => {
-  let term;
-  const callback = (_term) => {
-    term = _term;
-  };
-  const holder = getHolder();
-  await initializeSearchHandler({ holder, callback });
-  const geneSearchInput = holder.select(".sja_genesearchinput").node();
-  const geneSymbol = "TP53";
-  geneSearchInput.value = geneSymbol;
-  geneSearchInput.dispatchEvent(new KeyboardEvent("keyup", { key: "Enter", code: "Enter", bubbles: true }));
-  await sleep(1e3);
-  const blockCoordInput = holder.select(".sja_Block_div").select("input").node();
-  const chr = "chr17";
-  const start = 7682350;
-  const stop = 7684350;
-  const coord = `${chr}:${start}-${stop}`;
-  blockCoordInput.value = coord;
-  blockCoordInput.dispatchEvent(new KeyboardEvent("keyup", { key: "Enter", code: "Enter", bubbles: true }));
-  await sleep(1e3);
-  const submitBtn = holder.select('[data-testid="sjpp-dnaMethylation-submitDiv"]').select("button").node();
-  submitBtn.click();
-  await sleep(100);
-  test.equal(term.chr, chr, "term.chr should equal input chr");
-  test.equal(term.start, 7682349, "term.start should equal input start");
-  test.equal(term.stop, 7684349, "term.stop should equal input stop");
-  test.equal(term.type, TermTypes.DNA_METHYLATION, "term.type should be dnaMethylation");
-  if (test["_ok"]) holder.remove();
-  test.end();
-});
-async function getVocabApi() {
-  const vocabApi2 = vocabInit({ state: { vocab: { genome: "hg38-test", dslabel: "TermdbTest" } } });
-  if (!vocabApi2) throw "vocabApi is missing";
-  await vocabApi2.getTermdbConfig();
-  return vocabApi2;
-}
-function getHolder() {
-  const holder = select_default("body").append("div");
-  return holder;
-}
-async function initializeSearchHandler(opts) {
-  const callback = opts.callback || (() => {
-  });
-  const hg38_copy = structuredClone(hg38);
-  hg38_copy.hasSNP = false;
-  await handler.init({
-    holder: opts.holder,
-    app: { vocabApi },
-    genomeObj: hg38_copy,
-    callback
-  });
-}
-//# sourceMappingURL=dnaMethylation.integration.spec-CWPTJ74H.js.map

package/dist/dnaMethylation.integration.spec-CWPTJ74H.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../termdb/handlers/test/dnaMethylation.integration.spec.ts"],
-  "sourcesContent": ["import tape from 'tape'\nimport * as d3s from 'd3-selection'\nimport { SearchHandler } from '../dnaMethylation.ts'\nimport { hg38 } from '../../../test/testdata/genomes'\nimport { sleep } from '../../../test/test.helpers.js'\nimport { vocabInit } from '../../vocabulary'\nimport { TermTypes } from '#shared/terms.js'\n\n/*\nTests:\n\tSearch handler layout\n\tCoordinate search\n\tGene search\n\tGene search with navigation\n*/\n\n/**************\n test sections\n***************/\n\nconst vocabApi: any = await getVocabApi()\nconst handler = new SearchHandler()\n\ntape('\\n', function (test) {\n\ttest.comment('-***- dnaMethylation search handler -***-')\n\ttest.end()\n})\n\ntape('Search handler layout', async test => {\n\tconst holder = getHolder()\n\tawait initializeSearchHandler({ holder })\n\tconst geneSearchInput = holder.select('.sja_genesearchinput').node()\n\ttest.ok(geneSearchInput, 'should display gene search input')\n\tif (test['_ok']) holder.remove()\n\ttest.end()\n})\n\ntape('Coordinate search', async test => {\n\tlet term\n\tconst callback = _term => {\n\t\tterm = _term\n\t}\n\tconst holder = getHolder()\n\tawait initializeSearchHandler({ holder, callback })\n\tconst geneSearchInput: any = holder.select('.sja_genesearchinput').node()\n\tconst chr = 'chr17'\n\tconst start = 7661778\n\tconst stop = 7687537\n\tconst coord = `${chr}:${start}-${stop}`\n\tgeneSearchInput.value = coord\n\tgeneSearchInput.dispatchEvent(new KeyboardEvent('keyup', { key: 'Enter', code: 'Enter', bubbles: true }))\n\tawait sleep(100)\n\ttest.equal(term.chr, chr, 'term.chr should equal input chr')\n\ttest.equal(term.start, start, 'term.start should equal input start')\n\ttest.equal(term.stop, stop, 'term.stop should equal input stop')\n\t/** No longer necessary to pass the unit or name in the search handler.\n\t * Commenting out for now. Search handler may become more sophisticated and\n\t * require handling these properties in the future. */\n\t// test.equal(term.id, coord, 'term.id should equal input coord')\n\t// const unit = vocabApi.termdbConfig.queries.dnaMethylation.unit\n\t// const name = `${coord} ${unit}`\n\t// test.equal(term.name, name, 'term.name should be <coord> <unit>')\n\ttest.equal(term.type, TermTypes.DNA_METHYLATION, 'term.type should be dnaMethylation')\n\tif (test['_ok']) holder.remove()\n\ttest.end()\n})\n\ntape('Single position search (chr:pos format)', async test => {\n\tlet term\n\tconst callback = _term => {\n\t\tterm = _term\n\t}\n\tconst holder = getHolder()\n\tawait initializeSearchHandler({ holder, callback })\n\tconst geneSearchInput: any = holder.select('.sja_genesearchinput').node()\n\tgeneSearchInput.value = 'chr17:7669073'\n\tgeneSearchInput.dispatchEvent(new KeyboardEvent('keyup', { key: 'Enter', code: 'Enter', bubbles: true }))\n\tawait sleep(100)\n\ttest.equal(term.chr, 'chr17', 'term.chr should equal input chr')\n\ttest.equal(term.start, 7669073, 'term.start should be exact position, not 400bp-expanded')\n\ttest.equal(term.stop, 7669074, 'term.stop should be start+1 for a single CpG site')\n\ttest.equal(term.type, TermTypes.DNA_METHYLATION, 'term.type should be dnaMethylation')\n\tif (test['_ok']) holder.remove()\n\ttest.end()\n})\n\ntape('Single position search (chr:pos-pos format)', async test => {\n\tlet term\n\tconst callback = _term => {\n\t\tterm = _term\n\t}\n\tconst holder = getHolder()\n\tawait initializeSearchHandler({ holder, callback })\n\tconst geneSearchInput: any = holder.select('.sja_genesearchinput').node()\n\tgeneSearchInput.value = 'chr17:7669073-7669073'\n\tgeneSearchInput.dispatchEvent(new KeyboardEvent('keyup', { key: 'Enter', code: 'Enter', bubbles: true }))\n\tawait sleep(100)\n\ttest.equal(term.chr, 'chr17', 'term.chr should equal input chr')\n\ttest.equal(term.start, 7669073, 'term.start should be exact position, not 400bp-expanded')\n\ttest.equal(term.stop, 7669074, 'term.stop should be start+1 for a single CpG site')\n\ttest.equal(term.type, TermTypes.DNA_METHYLATION, 'term.type should be dnaMethylation')\n\tif (test['_ok']) holder.remove()\n\ttest.end()\n})\n\ntape('Gene search', async test => {\n\tlet term\n\tconst callback = _term => {\n\t\tterm = _term\n\t}\n\tconst holder = getHolder()\n\tawait initializeSearchHandler({ holder, callback })\n\tconst geneSearchInput: any = holder.select('.sja_genesearchinput').node()\n\tconst geneSymbol = 'TP53'\n\tgeneSearchInput.value = geneSymbol\n\tgeneSearchInput.dispatchEvent(new KeyboardEvent('keyup', { key: 'Enter', code: 'Enter', bubbles: true }))\n\tawait sleep(100)\n\tconst blockSvg = holder.select('[data-testid=\"sjpp_block_svg\"]').node()\n\ttest.ok(blockSvg, 'should render block svg')\n\tconst submitBtn: any = holder.select('[data-testid=\"sjpp-dnaMethylation-submitDiv\"]').select('button').node()\n\tsubmitBtn.click()\n\tawait sleep(100)\n\ttest.equal(term.chr, 'chr17', 'term.chr should be TP53 chr')\n\ttest.equal(term.start, 7661778, 'term.start should be TP53 start')\n\ttest.equal(term.stop, 7687537, 'term.stop should be TP53 stop')\n\t// See note above\n\t// const coord = 'chr17:7661778-7687537'\n\t// test.equal(term.id, coord, 'term.id should equal input coord')\n\t// const unit = vocabApi.termdbConfig.queries.dnaMethylation.unit\n\t// const name = `${coord} ${unit}`\n\t// test.equal(term.name, name, 'term.name should be <coord> <unit>')\n\ttest.equal(term.type, TermTypes.DNA_METHYLATION, 'term.type should be dnaMethylation')\n\tif (test['_ok']) holder.remove()\n\ttest.end()\n})\n\ntape('Gene search with navigation', async test => {\n\tlet term\n\tconst callback = _term => {\n\t\tterm = _term\n\t}\n\tconst holder = getHolder()\n\tawait initializeSearchHandler({ holder, callback })\n\t// search by gene symbol\n\tconst geneSearchInput: any = holder.select('.sja_genesearchinput').node()\n\tconst geneSymbol = 'TP53'\n\tgeneSearchInput.value = geneSymbol\n\tgeneSearchInput.dispatchEvent(new KeyboardEvent('keyup', { key: 'Enter', code: 'Enter', bubbles: true }))\n\tawait sleep(1000)\n\t// then navigate to 2kb region within gene\n\tconst blockCoordInput: any = holder.select('.sja_Block_div').select('input').node()\n\tconst chr = 'chr17'\n\tconst start = 7682350\n\tconst stop = 7684350\n\tconst coord = `${chr}:${start}-${stop}`\n\tblockCoordInput.value = coord\n\tblockCoordInput.dispatchEvent(new KeyboardEvent('keyup', { key: 'Enter', code: 'Enter', bubbles: true }))\n\tawait sleep(1000)\n\tconst submitBtn: any = holder.select('[data-testid=\"sjpp-dnaMethylation-submitDiv\"]').select('button').node()\n\tsubmitBtn.click()\n\tawait sleep(100)\n\t// term coordinate should equal coordinate of target region\n\t// TODO: term.start and term.stop are actually different by 1bp compared\n\t// to input start and input stop, respectively. This is different behavior\n\t// than when inputting a coordinate into the gene search box outside of block (see the \"Coordinate search\" test section above). Should resolve this discrepancy.\n\ttest.equal(term.chr, chr, 'term.chr should equal input chr')\n\ttest.equal(term.start, 7682349, 'term.start should equal input start')\n\ttest.equal(term.stop, 7684349, 'term.stop should equal input stop')\n\t// See note above\n\t// const new_coord = 'chr17:7682349-7684349'\n\t// test.equal(term.id, new_coord, 'term.id should equal input coord')\n\t// const unit = vocabApi.termdbConfig.queries.dnaMethylation.unit\n\t// const name = `${new_coord} ${unit}`\n\t// test.equal(term.name, name, 'term.name should be <coord> <unit>')\n\ttest.equal(term.type, TermTypes.DNA_METHYLATION, 'term.type should be dnaMethylation')\n\tif (test['_ok']) holder.remove()\n\ttest.end()\n})\n\n/*************************\n reusable helper functions\n**************************/\n\nasync function getVocabApi() {\n\tconst vocabApi = vocabInit({ state: { vocab: { genome: 'hg38-test', dslabel: 'TermdbTest' } } })\n\tif (!vocabApi) throw 'vocabApi is missing'\n\tawait vocabApi.getTermdbConfig()\n\treturn vocabApi\n}\n\nfunction getHolder() {\n\tconst holder = d3s.select('body').append('div')\n\treturn holder\n}\n\nasync function initializeSearchHandler(opts) {\n\tconst callback = opts.callback || (() => {})\n\tconst hg38_copy = structuredClone(hg38)\n\thg38_copy.hasSNP = false // to allow coordinate input\n\tawait handler.init({\n\t\tholder: opts.holder,\n\t\tapp: { vocabApi },\n\t\tgenomeObj: hg38_copy,\n\t\tcallback\n\t})\n}\n"],
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-  "names": ["tape", "vocabApi"]
-}

package/dist/dofetch-IWPZQB5N.js

@@ -1,51 +0,0 @@
-import {
-  clearServerDataCache,
-  dofetch,
-  dofetch2,
-  dofetch3,
-  getRequiredAuth,
-  getSavedToken,
-  includeEmbedder,
-  isInSession,
-  mayAddJwtToRequest,
-  mayShowAuthUi,
-  namedFetch,
-  processFormData,
-  setAuth,
-  setDsAuthOk,
-  setTokenByDsRoute
-} from "./chunk-M6EF3WVV.js";
-import "./chunk-7IYJZZQI.js";
-import "./chunk-M3J4MINX.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-LFCYMSVA.js";
-import "./chunk-I6WR4CG7.js";
-import "./chunk-2X6W4E3W.js";
-import "./chunk-JNITUVXP.js";
-import "./chunk-3XVVN66M.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-VQZ2Z5YU.js";
-import "./chunk-NSTL4MY2.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-KYBIQBXE.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-OMR2DT66.js";
-import "./chunk-HFNDKYVF.js";
-export {
-  clearServerDataCache,
-  dofetch,
-  dofetch2,
-  dofetch3,
-  getRequiredAuth,
-  getSavedToken,
-  includeEmbedder,
-  isInSession,
-  mayAddJwtToRequest,
-  mayShowAuthUi,
-  namedFetch,
-  processFormData,
-  setAuth,
-  setDsAuthOk,
-  setTokenByDsRoute
-};
-//# sourceMappingURL=dofetch-IWPZQB5N.js.map