@sjcrh/proteinpaint-client 2.185.0 → 2.186.0

package/dist/databrowser.ui-B2TNECC4.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 => l.toLowerCase().includes('type'))\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 => l.toLowerCase().includes('type'))\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\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[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 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-  "names": ["lines", "header", "i", "id", "makeFileUpload", "txt", "event"]
-}

package/dist/dictionary-YOTUFVES.js

@@ -1,109 +0,0 @@
-import {
-  appInit
-} from "./chunk-YWUVCXFS.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-3QBZ2Y77.js";
-import "./chunk-HYOEWQ5P.js";
-import "./chunk-FN5XPUPH.js";
-import "./chunk-G6O3URDN.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-KWM6B3NL.js";
-import "./chunk-UCLS2SVB.js";
-import "./chunk-6ZCHECOT.js";
-import {
-  copyMerge,
-  getCompInit
-} from "./chunk-MVTCBVSX.js";
-import "./chunk-2K5DSRBJ.js";
-import "./chunk-X4NI4JLQ.js";
-import "./chunk-L4QG7XZE.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-UWYCEYML.js";
-import "./chunk-7UHUOC6F.js";
-import "./chunk-ZYY54HBU.js";
-import "./chunk-EGWVYY7K.js";
-import "./chunk-AMYSEKPF.js";
-import "./chunk-TV74I3Y5.js";
-import "./chunk-KSGA62R2.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-TOU7EVFQ.js";
-import "./chunk-OAWQ6LOO.js";
-import "./chunk-KYBIQBXE.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-OMR2DT66.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.tree = await appInit(opts);
-  }
-  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-YOTUFVES.js.map

package/dist/dnaMethylation-TRFAZWRJ.js

@@ -1,36 +0,0 @@
-import {
-  SearchHandler
-} from "./chunk-KSN3EVKI.js";
-import "./chunk-YWUVCXFS.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-3QBZ2Y77.js";
-import "./chunk-HYOEWQ5P.js";
-import "./chunk-FN5XPUPH.js";
-import "./chunk-G6O3URDN.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-KWM6B3NL.js";
-import "./chunk-UCLS2SVB.js";
-import "./chunk-6ZCHECOT.js";
-import "./chunk-MVTCBVSX.js";
-import "./chunk-2K5DSRBJ.js";
-import "./chunk-X4NI4JLQ.js";
-import "./chunk-L4QG7XZE.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-UWYCEYML.js";
-import "./chunk-7UHUOC6F.js";
-import "./chunk-ZYY54HBU.js";
-import "./chunk-EGWVYY7K.js";
-import "./chunk-AMYSEKPF.js";
-import "./chunk-TV74I3Y5.js";
-import "./chunk-KSGA62R2.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-TOU7EVFQ.js";
-import "./chunk-OAWQ6LOO.js";
-import "./chunk-KYBIQBXE.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-OMR2DT66.js";
-import "./chunk-HFNDKYVF.js";
-export {
-  SearchHandler
-};
-//# sourceMappingURL=dnaMethylation-TRFAZWRJ.js.map

package/dist/dnaMethylation.integration.spec-SPFZO76D.js

@@ -1,201 +0,0 @@
-import {
-  hg38
-} from "./chunk-7VB2BKXW.js";
-import {
-  SearchHandler
-} from "./chunk-KSN3EVKI.js";
-import {
-  sleep
-} from "./chunk-SSPDNHDW.js";
-import {
-  require_tape
-} from "./chunk-QWOE5YTB.js";
-import {
-  vocabInit
-} from "./chunk-YWUVCXFS.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-3QBZ2Y77.js";
-import "./chunk-HYOEWQ5P.js";
-import "./chunk-FN5XPUPH.js";
-import "./chunk-G6O3URDN.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-KWM6B3NL.js";
-import "./chunk-UCLS2SVB.js";
-import "./chunk-6ZCHECOT.js";
-import "./chunk-MVTCBVSX.js";
-import "./chunk-2K5DSRBJ.js";
-import "./chunk-X4NI4JLQ.js";
-import "./chunk-L4QG7XZE.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-UWYCEYML.js";
-import "./chunk-7UHUOC6F.js";
-import "./chunk-ZYY54HBU.js";
-import {
-  TermTypes
-} from "./chunk-EGWVYY7K.js";
-import "./chunk-AMYSEKPF.js";
-import "./chunk-TV74I3Y5.js";
-import "./chunk-KSGA62R2.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-TOU7EVFQ.js";
-import "./chunk-OAWQ6LOO.js";
-import "./chunk-KYBIQBXE.js";
-import {
-  select_default
-} from "./chunk-I6Y4O3RR.js";
-import "./chunk-OMR2DT66.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-SPFZO76D.js.map

package/dist/dofetch-MH4MRMGY.js

@@ -1,50 +0,0 @@
-import {
-  clearServerDataCache,
-  dofetch,
-  dofetch2,
-  dofetch3,
-  getRequiredAuth,
-  getSavedToken,
-  includeEmbedder,
-  isInSession,
-  mayAddJwtToRequest,
-  mayShowAuthUi,
-  namedFetch,
-  processFormData,
-  setAuth,
-  setDsAuthOk,
-  setTokenByDsRoute
-} from "./chunk-6ZCHECOT.js";
-import "./chunk-MVTCBVSX.js";
-import "./chunk-2K5DSRBJ.js";
-import "./chunk-L4QG7XZE.js";
-import "./chunk-ZYY54HBU.js";
-import "./chunk-EGWVYY7K.js";
-import "./chunk-AMYSEKPF.js";
-import "./chunk-TV74I3Y5.js";
-import "./chunk-KSGA62R2.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-TOU7EVFQ.js";
-import "./chunk-OAWQ6LOO.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-MH4MRMGY.js.map