@sjcrh/proteinpaint-client 2.187.0 → 2.188.0

package/dist/chunk-ZYY54HBU.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../../shared/utils/src/termdb.bins.js"],
-  "sourcesContent": ["import { format } from \"d3-format\"\nimport { getColors } from \"./common.js\"\nimport { isNumeric, isStrictNumeric, convertUnits } from \"./helpers.js\"\n\nexport default function validate_bins(binconfig) {\n\t// Number.isFinite('1') returns false, which is desired\n\n\tconst bc = binconfig\n\tif (!bc || typeof bc !== \"object\") throw \"bin schema must be an object\"\n\t// assign default type\n\tif (!(\"type\" in bc)) bc.type = \"regular-bin\"\n\n\tif (bc.type == \"custom-bin\") {\n\t\tif (!Array.isArray(bc.lst)) throw \"binconfig.lst must be an array\"\n\t\tif (!bc.lst.length) throw \"binconfig.lst must have entries\"\n\t\tconst first_bin = bc.lst[0]\n\t\tconst last_bin = bc.lst[bc.lst.length - 1]\n\n\t\tfor (const bin of bc.lst) {\n\t\t\tif (!(\"startinclusive\" in bin) && !(\"stopinclusive\" in bin)) {\n\t\t\t\tthrow \"custom bin.startinclusive and/or bin.stopinclusive must be defined\"\n\t\t\t}\n\n\t\t\tif (bin == first_bin) {\n\t\t\t\tif (\"startunbounded\" in bin && !bin.startunbounded) {\n\t\t\t\t\tthrow `a custom first bin must not set bin.startunbounded to false`\n\t\t\t\t}\n\t\t\t\tbin.startunbounded = true\n\t\t\t\tif (\"start\" in bin) {\n\t\t\t\t\tthrow \"a custom first bin must not set a bin.start value\"\n\t\t\t\t}\n\t\t\t\tif (\"start_percentile\" in bin) {\n\t\t\t\t\tthrow \"the first bin must not set a bin.start_percentile value\"\n\t\t\t\t}\n\t\t\t\tif (!(\"stop\" in bin)) {\n\t\t\t\t\tthrow `a custom first bin must define a bin.stop value`\n\t\t\t\t}\n\t\t\t\tif (!isStrictNumeric(bin.stop)) {\n\t\t\t\t\tthrow `a custom first bin.stop value should be numeric`\n\t\t\t\t}\n\t\t\t} else if (bin == last_bin) {\n\t\t\t\tif (!(\"start\" in bin)) {\n\t\t\t\t\tthrow `a custom last bin must define a bin.start value`\n\t\t\t\t}\n\t\t\t\tif (!isStrictNumeric(bin.start)) {\n\t\t\t\t\tthrow `a custom last bin.start must be numeric`\n\t\t\t\t}\n\t\t\t\tif (\"stopunbounded\" in bin && !bin.stopunbounded) {\n\t\t\t\t\tthrow \"a custom last bin must not set bin.stopunbounded to false\"\n\t\t\t\t}\n\t\t\t\tbin.stopunbounded = true\n\t\t\t\tif (\"stop\" in bin) {\n\t\t\t\t\tthrow \"a custom last bin must not set a bin.stop value\"\n\t\t\t\t}\n\t\t\t} else {\n\t\t\t\tif (bin.startunbounded || bin.stopunbounded) {\n\t\t\t\t\tthrow \"bin.startunbounded and bin.stopunbounded must not be set for non-first/non-last bins\"\n\t\t\t\t}\n\t\t\t\tif (!isStrictNumeric(bin.start))\n\t\t\t\t\tthrow \"bin.start must be numeric for a non-first bin\"\n\t\t\t\tif (!isStrictNumeric(bin.stop))\n\t\t\t\t\tthrow \"bin.stop must be numeric for a non-last bin\"\n\t\t\t}\n\t\t}\n\t} else if (bc.type == \"regular-bin\") {\n\t\t// required custom_bin parameter\n\t\tif (!Number.isFinite(bc.bin_size)) throw \"non-numeric bin_size\"\n\t\tif (bc.bin_size <= 0) throw \"bin_size must be greater than 0\"\n\n\t\tif (!bc.startinclusive && !bc.stopinclusive) {\n\t\t\tbc.startinclusive = 1\n\t\t\tbc.stopinclusive = 0\n\t\t}\n\n\t\tif (!bc.first_bin) throw \"first_bin{} missing\"\n\t\tif (typeof bc.first_bin != \"object\") throw \"first_bin{} is not an object\"\n\t\tif (!Object.keys(bc.first_bin).length) throw \"first_bin is an empty object\"\n\n\t\t{\n\t\t\tconst b = bc.first_bin\n\t\t\tb.startunbounded = true\n\t\t\t// requires stop_percentile, or stop\n\t\t\tif (b.stop_percentile) {\n\t\t\t\tif (!Number.isInteger(b.stop_percentile))\n\t\t\t\t\tthrow \"first_bin.stop_percentile should be integer\"\n\t\t\t\tif (b.stop_percentile <= 0 || b.stop_percentile >= 100)\n\t\t\t\t\tthrow \"first_bin.stop_percentile out of bound (0-100)\"\n\t\t\t} else if (!Number.isFinite(b.stop)) {\n\t\t\t\tthrow \"first_bin.stop not a number when stop_percentile is not set\"\n\t\t\t}\n\t\t}\n\n\t\tif (bc.last_bin) {\n\t\t\tconst b = bc.last_bin\n\t\t\t// requires start_percentile or start\n\t\t\tif (b.start_percentile) {\n\t\t\t\tif (!Number.isInteger(b.start_percentile))\n\t\t\t\t\tthrow \"last_bin.start_percentile should be integer\"\n\t\t\t\tif (b.start_percentile <= 0 || b.start_percentile >= 100)\n\t\t\t\t\tthrow \"last_bin.start_percentile out of bound (0-100)\"\n\t\t\t} else if (!Number.isFinite(b.start)) {\n\t\t\t\tthrow \"last_bin.start not a number when start_percentile is not set\"\n\t\t\t}\n\n\t\t\tb.stopunbounded = true\n\t\t\tif (\"stop\" in b) {\n\t\t\t\tthrow \"a regular last bin must not set a bin.stop value\"\n\t\t\t}\n\t\t}\n\t} else {\n\t\tthrow `invalid binconfig.type=\"${bc.type}\"`\n\t}\n}\n\nexport function compute_bins(binconfig, summaryfxn, valueConversion) {\n\t/*\n  Bins generator\n  \nbinconfig   \n  configuration of bins per the Numerical Binning Scheme\n\nsummaryfxn (percentiles)=> return {min, max, pX, pY, ...}\n  - required function\n\n  - must accept an array of desired percentile values\n  and returns an object of computed properties\n  {\n    min: minimum value\n    max: maximum value\n    pX: percentile at X value, so p10 will be 10th percentile value\n    pY: .. corresponding to the desired percentile values \n  }\n*/\n\tconst bc = binconfig\n\n\tvalidate_bins(bc)\n\tif (bc.lst) {\n\t\tconst k2c = getColors(bc.lst.length) //to color bins\n\t\tfor (const bin of bc.lst) bin.color = k2c(bin.label)\n\t}\n\tif (bc.type == \"custom-bin\") return JSON.parse(JSON.stringify(bc.lst))\n\tif (typeof summaryfxn != \"function\")\n\t\tthrow \"summaryfxn required for modules/termdb.bins.js compute_bins()\"\n\tconst percentiles = target_percentiles(bc)\n\tconst summary = summaryfxn(percentiles)\n\tif (!summary || typeof summary !== \"object\")\n\t\tthrow \"invalid returned value by summaryfxn\"\n\tbc.results = { summary }\n\tif (!bc.binLabelFormatter) bc.binLabelFormatter = getNumDecimalsFormatter(bc)\n\n\t// round the min and max values for use as bin start and stop\n\t// in the first and last bins, respectively\n\tconst minFloor = Math.floor(summary.min * 100) / 100\n\tconst maxCeil = Math.ceil(summary.max * 100) / 100\n\tconst min = bc.first_bin.startunbounded\n\t\t? minFloor\n\t\t: bc.first_bin.start_percentile\n\t\t? summary[\"p\" + bc.first_bin.start_percentile]\n\t\t: bc.first_bin.start\n\tlet max = maxCeil, // in order to include the max value in the last bin\n\t\tlast_start,\n\t\tlast_stop\n\n\tif (bc.last_bin) {\n\t\tmax = bc.last_bin.stopunbounded\n\t\t\t? maxCeil // in order to include the max value in the last bin\n\t\t\t: bc.last_bin.stop_percentile\n\t\t\t? summary[\"p\" + bc.last_bin.stop_percentile]\n\t\t\t: isNumeric(bc.last_bin.stop) && bc.last_bin.stop <= summary.max // '0.0088' < 0.0088\n\t\t\t? bc.last_bin.stop\n\t\t\t: maxCeil // in order to include the max value in the last bin\n\t\tlast_start = isStrictNumeric(bc.last_bin.start_percentile)\n\t\t\t? summary[\"p\" + bc.last_bin.start_percentile]\n\t\t\t: isStrictNumeric(bc.last_bin.start)\n\t\t\t? bc.last_bin.start\n\t\t\t: undefined\n\t\tlast_stop = bc.last_bin.stopunbounded\n\t\t\t? null\n\t\t\t: bc.last_bin.stop_percentile\n\t\t\t? summary[\"p\" + bc.last_bin.stop_percentile]\n\t\t\t: isStrictNumeric(bc.last_bin.stop)\n\t\t\t? bc.last_bin.stop\n\t\t\t: null\n\t} else if (bc.lst) {\n\t\tconst last_bin = bc.lst[bc.lst.length - 1]\n\t\tlast_start = last_bin.start\n\t\tlast_stop =\n\t\t\t\"stop\" in last_bin && !last_bin.stopunbounded ? last_bin.stop : maxCeil\n\t\tmax = last_stop\n\t} else {\n\t\tlast_start = maxCeil\n\t\tlast_stop = maxCeil\n\t}\n\n\tconst numericMax = isStrictNumeric(max)\n\tconst numericLastStart = isStrictNumeric(last_start)\n\tconst numericLastStop = isStrictNumeric(last_stop)\n\n\tif (!numericMax && !numericLastStart) return [] //throw 'unable to compute the last bin start or stop'\n\n\tconst bins = []\n\tlet currBin = {\n\t\tstartunbounded: bc.first_bin.startunbounded,\n\t\tstart: bc.first_bin.startunbounded ? undefined : min,\n\t\tstop: isStrictNumeric(bc.first_bin.stop_percentile)\n\t\t\t? +summary[\"p\" + bc.first_bin.stop_percentile]\n\t\t\t: isStrictNumeric(bc.first_bin.stop)\n\t\t\t? +bc.first_bin.stop\n\t\t\t: min + bc.bin_size,\n\t\tstartinclusive: bc.startinclusive,\n\t\tstopinclusive: bc.stopinclusive,\n\t}\n\n\tif (!isStrictNumeric(currBin.stop))\n\t\tthrow \"the computed first_bin.stop is non-numeric\" + currBin.stop\n\tconst maxNumBins = 100 // harcoded limit for now to not stress sqlite\n\n\twhile (\n\t\t(numericMax && currBin.stop <= max) ||\n\t\t(currBin.startunbounded && !bins.length) ||\n\t\tcurrBin.stopunbounded\n\t) {\n\t\tbins.push(currBin)\n\t\t// force a computed last bin to have stopunbounded true\n\t\tif (currBin.stop >= max) {\n\t\t\tcurrBin.stopunbounded = true\n\t\t\tif (bins.length > 1) {\n\t\t\t\tdelete currBin.stop\n\t\t\t}\n\t\t}\n\t\tcurrBin.label = get_bin_label(currBin, bc, valueConversion)\n\t\tif (currBin.stopunbounded) break\n\n\t\tconst upper = currBin.stop + bc.bin_size\n\t\tconst previousStop = currBin.stop\n\t\tcurrBin = {\n\t\t\tstartinclusive: bc.startinclusive,\n\t\t\tstopinclusive: bc.stopinclusive,\n\t\t\tstart: previousStop,\n\t\t\tstop:\n\t\t\t\tnumericLastStop && (previousStop == last_start || upper > last_stop)\n\t\t\t\t\t? last_stop\n\t\t\t\t\t: numericLastStart && upper > last_start && previousStop != last_start\n\t\t\t\t\t? last_start\n\t\t\t\t\t: upper,\n\t\t}\n\n\t\tif (currBin.stop >= max) {\n\t\t\tcurrBin.stop = max\n\t\t\tif (bc.last_bin && bc.last_bin.stopunbounded) currBin.stopunbounded = 1\n\t\t\tif (bc.last_bin && bc.last_bin.stopinclusive) currBin.stopinclusive = 1\n\t\t}\n\t\tif (numericLastStart && currBin.start == last_start) {\n\t\t\tif (bc.last_bin && bc.last_bin.stopunbounded) currBin.stopunbounded = 1\n\t\t}\n\t\tif (currBin.start > currBin.stop) {\n\t\t\tif (\n\t\t\t\tnumericLastStart &&\n\t\t\t\tcurrBin.stop == last_start &&\n\t\t\t\tbc.last_bin &&\n\t\t\t\tbc.last_bin.stopunbounded\n\t\t\t)\n\t\t\t\tcurrBin.stopunbounded = true\n\t\t\telse break\n\t\t}\n\t\tif (bins.length + 1 >= maxNumBins) {\n\t\t\tbc.error = \"max_num_bins_reached\"\n\t\t\tbreak\n\t\t}\n\t}\n\tdelete bc.binLabelFormatter\n\tif (bins.length > 1) {\n\t\tdelete bins[bins.length - 1].stop\n\t}\n\tconst k2c = getColors(bins.length) //to color bins\n\tfor (const bin of bins) bin.color = k2c(bin.label)\n\treturn bins\n}\n\nfunction getNumDecimalsFormatter(bc) {\n\t//return format('rounding' in bc ? bc.rounding : '')\n\treturn \"rounding\" in bc ? format(bc.rounding) : (d) => d // default to labeling using the start/stop value as-is\n}\n\nexport function get_bin_label(bin, binconfig, valueConversion) {\n\t/*\n  Generate a numeric bin label given a bin configuration and an optional term valueConversion object\n*/\n\tif (!bin) return \"missing bin.label\"\n\tif (bin.label) return bin.label\n\n\tconst bc = binconfig\n\tif (!bc.binLabelFormatter) bc.binLabelFormatter = getNumDecimalsFormatter(bc)\n\tif (\n\t\t!bin.startunbounded &&\n\t\t!bin.stopunbounded &&\n\t\t!(\"startinclusive\" in bin) &&\n\t\t!(\"stopinclusive\" in bin)\n\t) {\n\t\tif (bc.startinclusive) bin.startinclusive = true\n\t\telse if (bc.stopinclusive) bin.stopinclusive = true\n\t}\n\n\tconst start = bc.use_as == \"bins\" || bin.start\n\tconst stop = bc.use_as == \"bins\" || bin.stop\n\n\tlet label_offset = 0\n\tif (\"label_offset\" in bc) {\n\t\tbc.label_offset_ignored = \"bin_size\" in bc && bc.bin_size < bc.label_offset\n\t\tif (!bc.label_offset_ignored) label_offset = bc.label_offset\n\t} else if (bc.bin_size === 1 && bc.termtype == \"integer\") {\n\t\tlabel_offset = 1\n\t}\n\n\t// one side-unbounded bins\n\t// label will be \">v\" or \"<v\"\n\tif (bin.startunbounded) {\n\t\tconst oper = bin.stopinclusive ? \"\u2264\" : \"<\" // \\u2264\n\t\tconst v1 = valueConversion\n\t\t\t? convertUnits(\n\t\t\t\t\tstop,\n\t\t\t\t\tvalueConversion.fromUnit,\n\t\t\t\t\tvalueConversion.toUnit,\n\t\t\t\t\tvalueConversion.scaleFactor,\n\t\t\t\t\ttrue\n\t\t\t  )\n\t\t\t: bc.binLabelFormatter(stop) //bin.startinclusive && label_offset ? stop - label_offset : stop)\n\t\treturn oper + v1\n\t}\n\t// a data value may coincide with the last bin's start\n\tif (bin.stopunbounded || start === stop) {\n\t\tconst oper = bin.startinclusive /*|| label_offset*/ ? \"\u2265\" : \">\" // \\u2265\n\t\tconst v0 = valueConversion\n\t\t\t? convertUnits(\n\t\t\t\t\tstart,\n\t\t\t\t\tvalueConversion.fromUnit,\n\t\t\t\t\tvalueConversion.toUnit,\n\t\t\t\t\tvalueConversion.scaleFactor,\n\t\t\t\t\ttrue\n\t\t\t  )\n\t\t\t: bc.binLabelFormatter(start) //bin.startinclusive || start == min ? start : start + label_offset)\n\t\treturn oper + v0\n\t}\n\n\t// two-sided bins\n\tif (label_offset && bin.startinclusive && !bin.stopinclusive) {\n\t\tif (\n\t\t\tNumber.isInteger(bc.bin_size) &&\n\t\t\tMath.abs(start - stop) === label_offset\n\t\t) {\n\t\t\t// make a simpler label when the range simply spans the bin_size\n\t\t\treturn (\n\t\t\t\t\"\" +\n\t\t\t\t(valueConversion\n\t\t\t\t\t? convertUnits(\n\t\t\t\t\t\t\tstart,\n\t\t\t\t\t\t\tvalueConversion.fromUnit,\n\t\t\t\t\t\t\tvalueConversion.toUnit,\n\t\t\t\t\t\t\tvalueConversion.scaleFactor,\n\t\t\t\t\t\t\ttrue\n\t\t\t\t\t  )\n\t\t\t\t\t: bc.binLabelFormatter(start))\n\t\t\t)\n\t\t} else {\n\t\t\tconst v0 = valueConversion\n\t\t\t\t? convertUnits(\n\t\t\t\t\t\tstart,\n\t\t\t\t\t\tvalueConversion.fromUnit,\n\t\t\t\t\t\tvalueConversion.toUnit,\n\t\t\t\t\t\tvalueConversion.scaleFactor,\n\t\t\t\t\t\ttrue\n\t\t\t\t  )\n\t\t\t\t: bc.binLabelFormatter(start)\n\t\t\tconst v1 = valueConversion\n\t\t\t\t? convertUnits(\n\t\t\t\t\t\tstop - label_offset,\n\t\t\t\t\t\tvalueConversion.fromUnit,\n\t\t\t\t\t\tvalueConversion.toUnit,\n\t\t\t\t\t\tvalueConversion.scaleFactor,\n\t\t\t\t\t\ttrue\n\t\t\t\t  )\n\t\t\t\t: bc.binLabelFormatter(stop - label_offset)\n\t\t\t// ensure that last two bin labels make sense (the last is stopunbounded)\n\t\t\treturn +v0 >= +v1 ? v0.toString() : v0 + \" to \" + v1\n\t\t}\n\t} else {\n\t\t// stop_inclusive || label_offset == 0\n\t\tconst oper0 = bin.startinclusive ? \"\" : \">\"\n\t\tconst oper1 = bin.stopinclusive ? \"\" : \"<\"\n\t\tconst v0 = valueConversion\n\t\t\t? convertUnits(\n\t\t\t\t\tstart,\n\t\t\t\t\tvalueConversion.fromUnit,\n\t\t\t\t\tvalueConversion.toUnit,\n\t\t\t\t\tvalueConversion.scaleFactor,\n\t\t\t\t\ttrue\n\t\t\t  )\n\t\t\t: Number.isInteger(start)\n\t\t\t? start\n\t\t\t: bc.binLabelFormatter(start)\n\t\tconst v1 = valueConversion\n\t\t\t? convertUnits(\n\t\t\t\t\tstop,\n\t\t\t\t\tvalueConversion.fromUnit,\n\t\t\t\t\tvalueConversion.toUnit,\n\t\t\t\t\tvalueConversion.scaleFactor,\n\t\t\t\t\ttrue\n\t\t\t  )\n\t\t\t: Number.isInteger(stop)\n\t\t\t? stop\n\t\t\t: bc.binLabelFormatter(stop)\n\t\t// after rounding the bin labels, the bin start may equal the last bin stop as derived from actual data\n\t\tif (+v0 >= +v1) {\n\t\t\tconst oper = bin.startinclusive ? \"\u2265\" : \">\" // \\u2265\n\t\t\treturn oper + v0\n\t\t} else {\n\t\t\treturn oper0 + v0 + \" to \" + oper1 + v1\n\t\t}\n\t}\n}\n\n// get bin range equation from bin label and bin properties\nexport function get_bin_range_equation(bin, binconfig) {\n\tconst x = '<span style=\"font-family:Times;font-style:italic;\">x</span>'\n\tlet range_eq\n\t// should always use computed (not user-customized) bin label to determine bin range text\n\tconst copy = structuredClone(bin)\n\tcopy.label = \"\" // mutate only the copy, and not the original bin argument\n\tconst bin_label = get_bin_label(copy, binconfig)\n\tif (bin.startunbounded || bin.stopunbounded) {\n\t\t// first or last bins, e.g. x \u2264 14 and x > 16\n\t\trange_eq = x + \" \" + bin_label\n\t} else if (bin.startinclusive) {\n\t\t// bins with startinclusive, e.g. 14 \u2264 x < 16\n\t\trange_eq = bin_label.replace(\"to <\", \"\u2264 \" + x + \" <\")\n\t} else if (bin.stopinclusive) {\n\t\t// bins with stopinclusive, e.g. 14 < x \u2264 16\n\t\trange_eq = bin_label.replace(\">\", \"\").replace(\"to\", \"< \" + x + \" \u2264\")\n\t}\n\treturn range_eq\n}\n\nexport function target_percentiles(binconfig) {\n\tconst percentiles = []\n\tconst f = binconfig.first_bin\n\tif (f && isStrictNumeric(f.start_percentile))\n\t\tpercentiles.push(f.start_percentile)\n\tif (f && isStrictNumeric(f.stop_percentile))\n\t\tpercentiles.push(f.stop_percentile)\n\tconst l = binconfig.last_bin\n\tif (l && isStrictNumeric(l.start_percentile))\n\t\tpercentiles.push(l.start_percentile)\n\tif (l && isStrictNumeric(l.stop_percentile))\n\t\tpercentiles.push(l.stop_percentile)\n\treturn percentiles\n}\n"],
-  "mappings": 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-  "names": ["k2c"]
-}

package/dist/condition-ARCN26MF.js

@@ -1,331 +0,0 @@
-import {
-  getPillNameDefault,
-  make_radios,
-  sayerror,
-  set_hiddenvalues,
-  throwMsgWithFilePathAndFnName
-} from "./chunk-LN3QYBGI.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-BTJFVY3R.js";
-import "./chunk-HYOEWQ5P.js";
-import "./chunk-HBW42TDT.js";
-import "./chunk-G6O3URDN.js";
-import "./chunk-FN5XPUPH.js";
-import "./chunk-KWM6B3NL.js";
-import "./chunk-UCLS2SVB.js";
-import "./chunk-UWYCEYML.js";
-import "./chunk-7UHUOC6F.js";
-import "./chunk-YC6ZJ7RP.js";
-import {
-  copyMerge
-} from "./chunk-MVTCBVSX.js";
-import "./chunk-2K5DSRBJ.js";
-import "./chunk-ZYY54HBU.js";
-import "./chunk-EGWVYY7K.js";
-import "./chunk-AMYSEKPF.js";
-import "./chunk-AQVOYTLS.js";
-import "./chunk-TV74I3Y5.js";
-import "./chunk-KSGA62R2.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-TOU7EVFQ.js";
-import "./chunk-OAWQ6LOO.js";
-import "./chunk-L4QG7XZE.js";
-import "./chunk-KYBIQBXE.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-OMR2DT66.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-HFNDKYVF.js";
-
-// termsetting/handlers/condition.ts
-var cutoffGrades = [1, 2, 3, 4, 5];
-function getHandler(self) {
-  return {
-    getPillName(d) {
-      return getPillNameDefault(self, d);
-    },
-    getPillStatus() {
-      return getPillStatus(self);
-    },
-    showEditMenu(div) {
-      if (self.q.mode == "discrete") {
-        return showMenu_discrete(self, div);
-      }
-      if (self.q.mode == "binary" || self.q.mode == "cuminc" || self.q.mode == "cox") {
-        return showMenu_cutoff(self, div);
-      }
-      console.error("invalid q.mode:", self.q.mode);
-      throw "invalid q.mode";
-    }
-    // async postMain() {
-    // 	const body = self.opts.getBodyParams?.() || {} //make sure term1_q is added
-    // 	const data = await self.vocabApi.getCategories(self.term, self.filter!, body)
-    // 	//not really sure this is necessary but it's consistent across other handlers
-    // 	self.category2samplecount = []
-    // 	for (const d of data.lst) {
-    // 		self.category2samplecount.push({
-    // 			key: d.key,
-    // 			label: d.label,
-    // 			count: d.samplecount
-    // 		})
-    // 		// }
-    // 	}
-    // }
-  };
-}
-function getPillStatus(self) {
-  const text = self.q?.name || self.q?.reuseId;
-  if (text) return { text };
-  if (self.q.mode == "discrete") {
-    if (self.q.breaks?.length) {
-      return { text: self.q.breaks.length + 1 + " groups" };
-    } else {
-      if (self.q.bar_by_grade) {
-        if (self.q.value_by_max_grade) return { text: "Max. Grade" };
-        if (self.q.value_by_most_recent) return { text: "Most Recent Grade" };
-        if (self.q.value_by_computable_grade) return { text: "Any Grade" };
-        return { text: "Error: unknown grade setting", bgcolor: "red" };
-      }
-      if (self.q.bar_by_children) return { text: "Sub-condition" };
-    }
-  }
-  if (self.q.mode == "binary") {
-    return {
-      text: self.usecase?.target == "regression" ? self.data.q.groups.find((x) => x.name != self.data.refGrp).name : "binary"
-    };
-  }
-  if (self.q.mode == "cuminc" || self.q.mode == "cox") {
-    if (!self.q.breaks || self.q.breaks.length == 0) throwMsgWithFilePathAndFnName("Missing q.breaks");
-    return { text: `Grades ${self.q.breaks[0]}-5` };
-  }
-  return {};
-}
-async function showMenu_discrete(self, div) {
-  const value_type_div = div.append("div").style("margin", "10px 0px 10px 5px").style("border-left", "solid 1px #ededed");
-  value_type_div.append("div").style("display", "inline-block").style("margin", "0px 0px 5px 5px").style("color", "rgb(136, 136, 136)").text("Grade type:");
-  const value_type_select = value_type_div.append("select").style("display", "inline").style("margin", "0px 10px").on("change", () => {
-    const i = value_type_select.property("selectedIndex");
-    self.q.bar_by_grade = i != 3;
-    self.q.bar_by_children = i == 3;
-    self.q.value_by_max_grade = i == 0;
-    self.q.value_by_most_recent = i == 1;
-    self.q.value_by_computable_grade = i == 2 || i == 3;
-    self.dom.tip.hide();
-    self.api.runCallback();
-  });
-  value_type_select.append("option").text("Max grade per patient");
-  value_type_select.append("option").text("Most recent grade per patient");
-  value_type_select.append("option").text("Any grade per patient");
-  if (self.term.subconditions) {
-    value_type_select.append("option").text("Sub-conditions");
-  }
-  value_type_select.property(
-    "selectedIndex",
-    self.q.bar_by_children ? 3 : self.q.value_by_computable_grade ? 2 : self.q.value_by_most_recent ? 1 : 0
-  );
-  if (self.q.bar_by_children) {
-    return;
-  }
-  const breaksSelectorDiv = div.append("div").style("margin", "20px 0px 10px 5px").style("border-left", "solid 1px #ededed");
-  breaksSelectorDiv.append("div").text("Divide grades into groups (optional):").style("margin", "0px 0px 10px 5px").style("color", "rgb(136, 136, 136)");
-  const holder = breaksSelectorDiv.append("div").style("display", "flex").style("align-items", "start").style("margin-left", "10px").style("width", "100%");
-  const gradeValuesDiv = holder.append("div").style("margin-right", "20px");
-  const rangeNameDiv = holder.append("div").style("display", "grid").style("grid-template-columns", "auto auto").style("column-gap", "20px").style("align-items", "center").style("margin-right", "5px");
-  gradeValuesDiv.append("div").style("margin-bottom", "5px").style("color", "rgb(136, 136, 136)").text("Cutoff grades");
-  const textarea = gradeValuesDiv.append("textarea").style("width", "100px").style("height", "70px").on("keyup", textarea2gradeUI);
-  gradeValuesDiv.append("div").style("font-size", ".6em").style("margin-left", "1px").style("color", "#858585").html("Enter numeric values </br>seperated by ENTER");
-  if (self.q.breaks?.length) {
-    textarea.property("value", self.q.breaks.join("\n"));
-  }
-  textarea2gradeUI();
-  function textarea2gradeUI() {
-    rangeNameDiv.selectAll("*").remove();
-    const breaks = textarea2breaks();
-    if (!breaks.length) {
-      delete self.q.breaks;
-      delete self.q.groups;
-      return;
-    }
-    if (!self.term.values) throwMsgWithFilePathAndFnName(`Missing term values`);
-    const grades = Object.keys(self.term.values).filter((g) => !self.term.values?.[g].uncomputable).map(Number).sort((a, b) => a - b);
-    const groups = getGroups(grades, breaks);
-    rangeNameDiv.append("div").style("margin-bottom", "3px").style("color", "rgb(136, 136, 136)").text("Range");
-    rangeNameDiv.append("div").style("margin-bottom", "3px").style("color", "rgb(136, 136, 136)").text("Label");
-    for (const [i, g] of groups.entries()) {
-      rangeNameDiv.append("div").text(g.name.replace(/Grades* /, ""));
-      rangeNameDiv.append("div").append("input").attr("type", "text").property("value", g.name).style("margin", "2px 0px").on("change", function() {
-        groups[i].name = this.value;
-      });
-    }
-    self.q.breaks = breaks;
-    self.q.groups = groups;
-  }
-  function textarea2breaks() {
-    const str = textarea.property("value").trim();
-    if (!str) return [];
-    const lst = [...new Set(str.split("\n"))];
-    const breaks = [];
-    for (const x of lst) {
-      const b = Number(x);
-      if (!Number.isInteger(b)) {
-        sayerror(div, "cutoff grade must be an integer value");
-        return [];
-      }
-      if (b < 1 || b > 5) {
-        sayerror(div, `cutoff grade must be within grades 1-5`);
-        return [];
-      }
-      breaks.push(b);
-    }
-    if (!breaks.length) return [];
-    return breaks.sort((i, j) => i - j);
-  }
-  div.append("button").text("Apply").style("margin", "10px").on("click", (event) => {
-    event.target.disabled = true;
-    event.target.innerHTML = "Loading...";
-    self.api.runCallback();
-  });
-}
-function showMenu_cutoff(self, div) {
-  const holder = div.append("div").style("margin", "10px").style("display", "grid").style("grid-template-columns", "auto auto").style("gap", "20px");
-  holder.append("div").text("Grade cutoff").style("opacity", 0.4);
-  const sd = holder.append("div");
-  const gradeSelect = sd.append("select").on("change", changeGradeSelect);
-  for (const i of cutoffGrades) {
-    gradeSelect.append("option").text(self.term.values?.[i].label);
-  }
-  gradeSelect.property("selectedIndex", self.q.breaks[0] - 1);
-  holder.append("div").text(self.q.mode == "binary" ? "Group 1" : "Censored").style("opacity", 0.4);
-  const g1n = holder.append("div").style("opacity", 0.4);
-  holder.append("div").text(self.q.mode == "binary" ? "Group 2" : "Event").style("opacity", 0.4);
-  const g2n = holder.append("div").style("opacity", 0.4);
-  changeGradeSelect();
-  function changeGradeSelect() {
-    const grade = gradeSelect.property("selectedIndex") + 1;
-    g1n.selectAll("*").remove();
-    g2n.selectAll("*").remove();
-    const grades = Object.keys(self.term.values).map(Number).sort((a, b) => a - b);
-    for (const i of grades) {
-      if (i < grade) {
-        g1n.append("div").text(self.term.values?.[i].label);
-      } else {
-        g2n.append("div").text(self.term.values?.[i].label);
-      }
-    }
-  }
-  const timeUnit = self.vocabApi.termdbConfig.timeUnit;
-  let timeScaleChoice;
-  if (self.q.mode == "cox") {
-    timeScaleChoice = self.q.timeScale;
-    holder.append("div").text("Time axis").style("opacity", 0.4);
-    const options = [
-      {
-        label: timeUnit.charAt(0).toUpperCase() + timeUnit.slice(1),
-        value: "time"
-      },
-      { label: "Age", value: "age" }
-    ];
-    if (self.q.timeScale == "age") {
-      options[1].checked = true;
-    } else {
-      options[0].checked = true;
-    }
-    make_radios({
-      holder: holder.append("div"),
-      options,
-      styles: { padding: "" },
-      callback: (v) => timeScaleChoice = v
-    });
-  }
-  div.append("button").text("Apply").style("margin", "10px").on("click", (event) => {
-    if (!self.q.breaks || self.q.breaks.length == 0) throwMsgWithFilePathAndFnName("Missing q.breaks");
-    const grade = gradeSelect.property("selectedIndex") + 1;
-    self.q.breaks[0] = grade;
-    if (self.q.mode == "binary") {
-      const grades = Object.keys(self.term.values).map(Number).sort((a, b) => a - b);
-      self.q.groups = getGroups(grades, self.q.breaks);
-      self.refGrp = self.q.groups[0].name;
-    }
-    if (self.q.mode == "cox") self.q.timeScale = timeScaleChoice;
-    event.target.disabled = true;
-    event.target.innerHTML = "Loading...";
-    self.api.runCallback();
-  });
-}
-function getGroups(grades, breaks) {
-  grades.sort((a, b2) => a - b2);
-  const groups = [];
-  let group = { values: [] };
-  let b;
-  for (const g of grades) {
-    if (breaks.includes(g)) {
-      b = g;
-      const max = Math.max(...group.values);
-      if (!groups.length) {
-        if (group.values.length == 1) {
-          if (group.values[0] !== 0) throw "unexpected group value";
-          group.name = "Grade 0";
-        } else {
-          if (group.values.length == 2 && group.values.includes(-1) && group.values.includes(0)) {
-            group.name = "Not tested/Grade 0";
-          } else {
-            group.name = group.values.includes(-1) ? `Not tested/Grade 0 - Grade ${max}` : `Grades 0-${max}`;
-          }
-        }
-      } else {
-        group.name = group.values.length == 1 ? `Grade ${group.values[0]}` : `${group.name}-${max}`;
-      }
-      groups.push(group);
-      group = {
-        name: `Grade ${b}`,
-        values: [g]
-      };
-    } else {
-      group.values.push(g);
-    }
-  }
-  group.name = `Grades ${b}-5`;
-  groups.push(group);
-  return groups;
-}
-function fillTW(tw, vocabApi, defaultQ) {
-  set_hiddenvalues(tw.q, tw.term);
-  if (defaultQ) {
-    copyMerge(tw.q, defaultQ);
-  }
-  if (!Object.keys(tw.q).includes("mode")) tw.q.mode = "discrete";
-  if (!tw.q.valueFor) {
-    const q = tw.q;
-    if (!q.bar_by_grade && !q.bar_by_children) q.bar_by_grade = true;
-    tw.q.valueFor = tw.q.bar_by_children ? "children" : "grade";
-  }
-  if (tw.q.valueFor == "grade") {
-    if (tw.q.value_by_max_grade || tw.q.value_by_most_recent || tw.q.value_by_computable_grade) {
-    } else {
-      tw.q.value_by_max_grade = true;
-    }
-  }
-  if (tw.q.mode == "binary" || tw.q.mode == "cox" || tw.q.mode == "cuminc") {
-    const defaultBreak = tw.q.mode == "binary" ? 1 : 3;
-    if (!tw.q.breaks?.length) tw.q.breaks = [defaultBreak];
-    if (tw.q.breaks.length != 1 || ![1, 2, 3, 4, 5].includes(tw.q.breaks[0])) throw "invalid tw.q.breaks";
-  }
-  if (tw.q.valueFor == "grade") {
-    if (tw.q.breaks?.length) {
-      if (!tw.term.values) throw "missing term.values";
-      if (tw.q.mode == "discrete" || tw.q.mode == "binary") {
-        const grades = Object.keys(tw.term.values).filter((g) => tw.q.mode == "discrete" ? !tw.term.values?.[g].uncomputable : g).map(Number).sort((a, b) => a - b);
-        tw.q.groups = getGroups(grades, tw.q.breaks);
-      }
-    }
-    if (tw.q.mode == "cox") {
-      if (!tw.q.timeScale) tw.q.timeScale = "time";
-      if (!["age", "time"].includes(tw.q.timeScale)) throw "invalid q.timeScale";
-    }
-  }
-}
-export {
-  fillTW,
-  getHandler
-};
-//# sourceMappingURL=condition-ARCN26MF.js.map

package/dist/controls-PKWN2JGN.js

@@ -1,40 +0,0 @@
-import {
-  controlsInit,
-  renderTerm1Label,
-  term0_term2_defaultQ
-} from "./chunk-LN3QYBGI.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-BTJFVY3R.js";
-import "./chunk-HYOEWQ5P.js";
-import "./chunk-HBW42TDT.js";
-import "./chunk-G6O3URDN.js";
-import "./chunk-FN5XPUPH.js";
-import "./chunk-KWM6B3NL.js";
-import "./chunk-UCLS2SVB.js";
-import "./chunk-UWYCEYML.js";
-import "./chunk-7UHUOC6F.js";
-import "./chunk-YC6ZJ7RP.js";
-import "./chunk-MVTCBVSX.js";
-import "./chunk-2K5DSRBJ.js";
-import "./chunk-ZYY54HBU.js";
-import "./chunk-EGWVYY7K.js";
-import "./chunk-AMYSEKPF.js";
-import "./chunk-AQVOYTLS.js";
-import "./chunk-TV74I3Y5.js";
-import "./chunk-KSGA62R2.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-TOU7EVFQ.js";
-import "./chunk-OAWQ6LOO.js";
-import "./chunk-L4QG7XZE.js";
-import "./chunk-KYBIQBXE.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-OMR2DT66.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-HFNDKYVF.js";
-export {
-  controlsInit,
-  renderTerm1Label,
-  term0_term2_defaultQ
-};
-//# sourceMappingURL=controls-PKWN2JGN.js.map

package/dist/controls.config-NFRPXFUJ.js

@@ -1,38 +0,0 @@
-import {
-  configUiInit,
-  initByInput
-} from "./chunk-LN3QYBGI.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-BTJFVY3R.js";
-import "./chunk-HYOEWQ5P.js";
-import "./chunk-HBW42TDT.js";
-import "./chunk-G6O3URDN.js";
-import "./chunk-FN5XPUPH.js";
-import "./chunk-KWM6B3NL.js";
-import "./chunk-UCLS2SVB.js";
-import "./chunk-UWYCEYML.js";
-import "./chunk-7UHUOC6F.js";
-import "./chunk-YC6ZJ7RP.js";
-import "./chunk-MVTCBVSX.js";
-import "./chunk-2K5DSRBJ.js";
-import "./chunk-ZYY54HBU.js";
-import "./chunk-EGWVYY7K.js";
-import "./chunk-AMYSEKPF.js";
-import "./chunk-AQVOYTLS.js";
-import "./chunk-TV74I3Y5.js";
-import "./chunk-KSGA62R2.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-TOU7EVFQ.js";
-import "./chunk-OAWQ6LOO.js";
-import "./chunk-L4QG7XZE.js";
-import "./chunk-KYBIQBXE.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-OMR2DT66.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-HFNDKYVF.js";
-export {
-  configUiInit,
-  initByInput
-};
-//# sourceMappingURL=controls.config-NFRPXFUJ.js.map

package/dist/correlation-DPT6XL2U.js

@@ -1,97 +0,0 @@
-import {
-  appInit
-} from "./chunk-C62CSWMV.js";
-import "./chunk-FA44G3GZ.js";
-import "./chunk-SKMFMGCD.js";
-import "./chunk-W6XQR5UL.js";
-import "./chunk-BRMASRRS.js";
-import "./chunk-7NOKTEHK.js";
-import "./chunk-XSA3VIEQ.js";
-import "./chunk-UVPAZM3G.js";
-import "./chunk-DMAHNBGN.js";
-import "./chunk-HZETQJGD.js";
-import "./chunk-MHCTLVGE.js";
-import "./chunk-PRZWSBMA.js";
-import "./chunk-LN3QYBGI.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-BTJFVY3R.js";
-import "./chunk-HYOEWQ5P.js";
-import "./chunk-HBW42TDT.js";
-import "./chunk-G6O3URDN.js";
-import "./chunk-FN5XPUPH.js";
-import "./chunk-KWM6B3NL.js";
-import "./chunk-UCLS2SVB.js";
-import "./chunk-UWYCEYML.js";
-import "./chunk-7UHUOC6F.js";
-import "./chunk-YC6ZJ7RP.js";
-import "./chunk-MVTCBVSX.js";
-import "./chunk-2K5DSRBJ.js";
-import "./chunk-ZYY54HBU.js";
-import "./chunk-EGWVYY7K.js";
-import "./chunk-AMYSEKPF.js";
-import "./chunk-AQVOYTLS.js";
-import "./chunk-TV74I3Y5.js";
-import "./chunk-KSGA62R2.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-TOU7EVFQ.js";
-import "./chunk-OAWQ6LOO.js";
-import "./chunk-L4QG7XZE.js";
-import "./chunk-KYBIQBXE.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-OMR2DT66.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-HFNDKYVF.js";
-
-// gdc/correlation.ts
-var gdcGenome = "hg38";
-var gdcDslabel = "GDC";
-async function init(arg, holder, genomes) {
-  const massApi = await appInit({
-    //debug: arg.debugmode, // is debug accepted?
-    genome: genomes[gdcGenome],
-    holder,
-    state: {
-      genome: gdcGenome,
-      dslabel: gdcDslabel,
-      termfilter: { filter0: arg.filter0 },
-      nav: { activeTab: 1, header_mode: "only_buttons" },
-      plots: arg.state?.plots || [
-        { chartType: "summaryInput" }
-        // default shows summaryInput ui, can change
-        //{ chartType: 'barchart', term: {id: 'case.demographic.gender'} }, // uncomment for quicker testing
-      ]
-    },
-    opts: Object.assign(
-      {
-        // todo additional customizations
-        // dictionary:{header:'Select a variable to build Correlation Plot'}
-        // some way to make gene exp violin/boxplot to use log scale by default, but numeric dict term should not
-      },
-      arg.opts || {}
-    ),
-    app: arg.opts?.app || {}
-  });
-  const api = {
-    update: async (updateArg) => {
-      if (!massApi) return;
-      if ("filter0" in updateArg) {
-        massApi.dispatch({
-          type: "app_refresh",
-          subactions: [
-            {
-              type: "filter_replace",
-              filter0: updateArg.filter0
-            }
-          ]
-        });
-      }
-    },
-    triggerAbort: (reason = "") => massApi.triggerAbort(reason)
-  };
-  return api;
-}
-export {
-  init
-};
-//# sourceMappingURL=correlation-DPT6XL2U.js.map