@weng-lab/ui-components 1.3.3 → 2.0.1

package/dist/ui-components.es84.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"ui-components.es84.js","sources":["../../../node_modules/.pnpm/@mui+material@7.2.0_@emotion+react@11.14.0_@types+react@19.1.8_react@19.1.0__@emotion+s_56c3cb211b767c0a0b4c5f346237ccd0/node_modules/@mui/material/esm/styles/cssUtils.js"],"sourcesContent":["export function isUnitless(value) {\n  return String(parseFloat(value)).length === String(value).length;\n}\n\n// Ported from Compass\n// https://github.com/Compass/compass/blob/master/core/stylesheets/compass/typography/_units.scss\n// Emulate the sass function \"unit\"\nexport function getUnit(input) {\n  return String(input).match(/[\\d.\\-+]*\\s*(.*)/)[1] || '';\n}\n\n// Emulate the sass function \"unitless\"\nexport function toUnitless(length) {\n  return parseFloat(length);\n}\n\n// Convert any CSS <length> or <percentage> value to any another.\n// From https://github.com/KyleAMathews/convert-css-length\nexport function convertLength(baseFontSize) {\n  return (length, toUnit) => {\n    const fromUnit = getUnit(length);\n\n    // Optimize for cases where `from` and `to` units are accidentally the same.\n    if (fromUnit === toUnit) {\n      return length;\n    }\n\n    // Convert input length to pixels.\n    let pxLength = toUnitless(length);\n    if (fromUnit !== 'px') {\n      if (fromUnit === 'em') {\n        pxLength = toUnitless(length) * toUnitless(baseFontSize);\n      } else if (fromUnit === 'rem') {\n        pxLength = toUnitless(length) * toUnitless(baseFontSize);\n      }\n    }\n\n    // Convert length in pixels to the output unit\n    let outputLength = pxLength;\n    if (toUnit !== 'px') {\n      if (toUnit === 'em') {\n        outputLength = pxLength / toUnitless(baseFontSize);\n      } else if (toUnit === 'rem') {\n        outputLength = pxLength / toUnitless(baseFontSize);\n      } else {\n        return length;\n      }\n    }\n    return parseFloat(outputLength.toFixed(5)) + toUnit;\n  };\n}\nexport function alignProperty({\n  size,\n  grid\n}) {\n  const sizeBelow = size - size % grid;\n  const sizeAbove = sizeBelow + grid;\n  return size - sizeBelow < sizeAbove - size ? sizeBelow : sizeAbove;\n}\n\n// fontGrid finds a minimal grid (in rem) for the fontSize values so that the\n// lineHeight falls under a x pixels grid, 4px in the case of Material Design,\n// without changing the relative line height\nexport function fontGrid({\n  lineHeight,\n  pixels,\n  htmlFontSize\n}) {\n  return pixels / (lineHeight * htmlFontSize);\n}\n\n/**\n * generate a responsive version of a given CSS property\n * @example\n * responsiveProperty({\n *   cssProperty: 'fontSize',\n *   min: 15,\n *   max: 20,\n *   unit: 'px',\n *   breakpoints: [300, 600],\n * })\n *\n * // this returns\n *\n * {\n *   fontSize: '15px',\n *   '@media (min-width:300px)': {\n *     fontSize: '17.5px',\n *   },\n *   '@media (min-width:600px)': {\n *     fontSize: '20px',\n *   },\n * }\n * @param {Object} params\n * @param {string} params.cssProperty - The CSS property to be made responsive\n * @param {number} params.min - The smallest value of the CSS property\n * @param {number} params.max - The largest value of the CSS property\n * @param {string} [params.unit] - The unit to be used for the CSS property\n * @param {Array.number} [params.breakpoints]  - An array of breakpoints\n * @param {number} [params.alignStep] - Round scaled value to fall under this grid\n * @returns {Object} responsive styles for {params.cssProperty}\n */\nexport function responsiveProperty({\n  cssProperty,\n  min,\n  max,\n  unit = 'rem',\n  breakpoints = [600, 900, 1200],\n  transform = null\n}) {\n  const output = {\n    [cssProperty]: `${min}${unit}`\n  };\n  const factor = (max - min) / breakpoints[breakpoints.length - 1];\n  breakpoints.forEach(breakpoint => {\n    let value = min + factor * breakpoint;\n    if (transform !== null) {\n      value = transform(value);\n    }\n    output[`@media (min-width:${breakpoint}px)`] = {\n      [cssProperty]: `${Math.round(value * 10000) / 10000}${unit}`\n    };\n  });\n  return output;\n}"],"names":["getUnit","input","toUnitless","length"],"mappings":"AAOO,SAASA,EAAQC,GAAO;AAC7B,SAAO,OAAOA,CAAK,EAAE,MAAM,kBAAkB,EAAE,CAAC,KAAK;AACvD;AAGO,SAASC,EAAWC,GAAQ;AACjC,SAAO,WAAWA,CAAM;AAC1B;","x_google_ignoreList":[0]}

package/dist/ui-components.es85.js

@@ -0,0 +1,12 @@
+import "react";
+import o from "./ui-components.es81.js";
+import "./ui-components.es12.js";
+import { useDefaultProps as r } from "./ui-components.es255.js";
+process.env.NODE_ENV !== "production" && (o.node, o.object.isRequired);
+function i(e) {
+  return r(e);
+}
+export {
+  i as useDefaultProps
+};
+//# sourceMappingURL=ui-components.es85.js.map

package/dist/ui-components.es85.js.map

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+{"version":3,"file":"ui-components.es85.js","sources":["../../../node_modules/.pnpm/@mui+material@7.2.0_@emotion+react@11.14.0_@types+react@19.1.8_react@19.1.0__@emotion+s_56c3cb211b767c0a0b4c5f346237ccd0/node_modules/@mui/material/esm/DefaultPropsProvider/DefaultPropsProvider.js"],"sourcesContent":["'use client';\n\nimport * as React from 'react';\nimport PropTypes from 'prop-types';\nimport SystemDefaultPropsProvider, { useDefaultProps as useSystemDefaultProps } from '@mui/system/DefaultPropsProvider';\nimport { jsx as _jsx } from \"react/jsx-runtime\";\nfunction DefaultPropsProvider(props) {\n  return /*#__PURE__*/_jsx(SystemDefaultPropsProvider, {\n    ...props\n  });\n}\nprocess.env.NODE_ENV !== \"production\" ? DefaultPropsProvider.propTypes /* remove-proptypes */ = {\n  // ┌────────────────────────────── Warning ──────────────────────────────┐\n  // │ These PropTypes are generated from the TypeScript type definitions. │\n  // │ To update them, edit the TypeScript types and run `pnpm proptypes`. │\n  // └─────────────────────────────────────────────────────────────────────┘\n  /**\n   * @ignore\n   */\n  children: PropTypes.node,\n  /**\n   * @ignore\n   */\n  value: PropTypes.object.isRequired\n} : void 0;\nexport default DefaultPropsProvider;\nexport function useDefaultProps(params) {\n  return useSystemDefaultProps(params);\n}"],"names":["PropTypes","useDefaultProps","params","useSystemDefaultProps"],"mappings":";;;;AAWA,QAAQ,IAAI,aAAa,iBAQbA,EAAU,MAIbA,EAAU,OAAO;AAGnB,SAASC,EAAgBC,GAAQ;AACtC,SAAOC,EAAsBD,CAAM;AACrC;","x_google_ignoreList":[0]}

package/dist/ui-components.es86.js

@@ -0,0 +1,17 @@
+function s(f, a, e = void 0) {
+  const u = {};
+  for (const r in f) {
+    const l = f[r];
+    let o = "", i = !0;
+    for (let n = 0; n < l.length; n += 1) {
+      const t = l[n];
+      t && (o += (i === !0 ? "" : " ") + a(t), i = !1, e && e[t] && (o += " " + e[t]));
+    }
+    u[r] = o;
+  }
+  return u;
+}
+export {
+  s as default
+};
+//# sourceMappingURL=ui-components.es86.js.map

package/dist/ui-components.es86.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"ui-components.es86.js","sources":["../../../node_modules/.pnpm/@mui+utils@7.2.0_@types+react@19.1.8_react@19.1.0/node_modules/@mui/utils/esm/composeClasses/composeClasses.js"],"sourcesContent":["/* eslint no-restricted-syntax: 0, prefer-template: 0, guard-for-in: 0\n   ---\n   These rules are preventing the performance optimizations below.\n */\n\n/**\n * Compose classes from multiple sources.\n *\n * @example\n * ```tsx\n * const slots = {\n *  root: ['root', 'primary'],\n *  label: ['label'],\n * };\n *\n * const getUtilityClass = (slot) => `MuiButton-${slot}`;\n *\n * const classes = {\n *   root: 'my-root-class',\n * };\n *\n * const output = composeClasses(slots, getUtilityClass, classes);\n * // {\n * //   root: 'MuiButton-root MuiButton-primary my-root-class',\n * //   label: 'MuiButton-label',\n * // }\n * ```\n *\n * @param slots a list of classes for each possible slot\n * @param getUtilityClass a function to resolve the class based on the slot name\n * @param classes the input classes from props\n * @returns the resolved classes for all slots\n */\nexport default function composeClasses(slots, getUtilityClass, classes = undefined) {\n  const output = {};\n  for (const slotName in slots) {\n    const slot = slots[slotName];\n    let buffer = '';\n    let start = true;\n    for (let i = 0; i < slot.length; i += 1) {\n      const value = slot[i];\n      if (value) {\n        buffer += (start === true ? '' : ' ') + getUtilityClass(value);\n        start = false;\n        if (classes && classes[value]) {\n          buffer += ' ' + classes[value];\n        }\n      }\n    }\n    output[slotName] = buffer;\n  }\n  return output;\n}"],"names":["composeClasses","slots","getUtilityClass","classes","output","slotName","slot","buffer","start","i","value"],"mappings":"AAiCe,SAASA,EAAeC,GAAOC,GAAiBC,IAAU,QAAW;AAClF,QAAMC,IAAS,CAAA;AACf,aAAWC,KAAYJ,GAAO;AAC5B,UAAMK,IAAOL,EAAMI,CAAQ;AAC3B,QAAIE,IAAS,IACTC,IAAQ;AACZ,aAASC,IAAI,GAAGA,IAAIH,EAAK,QAAQG,KAAK,GAAG;AACvC,YAAMC,IAAQJ,EAAKG,CAAC;AACpB,MAAIC,MACFH,MAAWC,MAAU,KAAO,KAAK,OAAON,EAAgBQ,CAAK,GAC7DF,IAAQ,IACJL,KAAWA,EAAQO,CAAK,MAC1BH,KAAU,MAAMJ,EAAQO,CAAK;AAAA,IAGnC;AACA,IAAAN,EAAOC,CAAQ,IAAIE;AAAA,EACrB;AACA,SAAOH;AACT;","x_google_ignoreList":[0]}

package/dist/ui-components.es87.js

@@ -0,0 +1,24 @@
+import s from "./ui-components.es108.js";
+const t = {
+  active: "active",
+  checked: "checked",
+  completed: "completed",
+  disabled: "disabled",
+  error: "error",
+  expanded: "expanded",
+  focused: "focused",
+  focusVisible: "focusVisible",
+  open: "open",
+  readOnly: "readOnly",
+  required: "required",
+  selected: "selected"
+};
+function o(d, e, r = "Mui") {
+  const a = t[e];
+  return a ? `${r}-${a}` : `${s.generate(d)}-${e}`;
+}
+export {
+  o as default,
+  t as globalStateClasses
+};
+//# sourceMappingURL=ui-components.es87.js.map

package/dist/ui-components.es87.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"ui-components.es87.js","sources":["../../../node_modules/.pnpm/@mui+utils@7.2.0_@types+react@19.1.8_react@19.1.0/node_modules/@mui/utils/esm/generateUtilityClass/generateUtilityClass.js"],"sourcesContent":["import ClassNameGenerator from \"../ClassNameGenerator/index.js\";\nexport const globalStateClasses = {\n  active: 'active',\n  checked: 'checked',\n  completed: 'completed',\n  disabled: 'disabled',\n  error: 'error',\n  expanded: 'expanded',\n  focused: 'focused',\n  focusVisible: 'focusVisible',\n  open: 'open',\n  readOnly: 'readOnly',\n  required: 'required',\n  selected: 'selected'\n};\nexport default function generateUtilityClass(componentName, slot, globalStatePrefix = 'Mui') {\n  const globalStateClass = globalStateClasses[slot];\n  return globalStateClass ? `${globalStatePrefix}-${globalStateClass}` : `${ClassNameGenerator.generate(componentName)}-${slot}`;\n}\nexport function isGlobalState(slot) {\n  return globalStateClasses[slot] !== undefined;\n}"],"names":["globalStateClasses","generateUtilityClass","componentName","slot","globalStatePrefix","globalStateClass","ClassNameGenerator"],"mappings":";AACY,MAACA,IAAqB;AAAA,EAChC,QAAQ;AAAA,EACR,SAAS;AAAA,EACT,WAAW;AAAA,EACX,UAAU;AAAA,EACV,OAAO;AAAA,EACP,UAAU;AAAA,EACV,SAAS;AAAA,EACT,cAAc;AAAA,EACd,MAAM;AAAA,EACN,UAAU;AAAA,EACV,UAAU;AAAA,EACV,UAAU;AACZ;AACe,SAASC,EAAqBC,GAAeC,GAAMC,IAAoB,OAAO;AAC3F,QAAMC,IAAmBL,EAAmBG,CAAI;AAChD,SAAOE,IAAmB,GAAGD,CAAiB,IAAIC,CAAgB,KAAK,GAAGC,EAAmB,SAASJ,CAAa,CAAC,IAAIC,CAAI;AAC9H;","x_google_ignoreList":[0]}

package/dist/ui-components.es88.js

@@ -0,0 +1,11 @@
+import s from "./ui-components.es87.js";
+function l(r, a, i = "Mui") {
+  const t = {};
+  return a.forEach((e) => {
+    t[e] = s(r, e, i);
+  }), t;
+}
+export {
+  l as default
+};
+//# sourceMappingURL=ui-components.es88.js.map

package/dist/ui-components.es88.js.map

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+{"version":3,"file":"ui-components.es88.js","sources":["../../../node_modules/.pnpm/@mui+utils@7.2.0_@types+react@19.1.8_react@19.1.0/node_modules/@mui/utils/esm/generateUtilityClasses/generateUtilityClasses.js"],"sourcesContent":["import generateUtilityClass from \"../generateUtilityClass/index.js\";\nexport default function generateUtilityClasses(componentName, slots, globalStatePrefix = 'Mui') {\n  const result = {};\n  slots.forEach(slot => {\n    result[slot] = generateUtilityClass(componentName, slot, globalStatePrefix);\n  });\n  return result;\n}"],"names":["generateUtilityClasses","componentName","slots","globalStatePrefix","result","slot","generateUtilityClass"],"mappings":";AACe,SAASA,EAAuBC,GAAeC,GAAOC,IAAoB,OAAO;AAC9F,QAAMC,IAAS,CAAA;AACf,SAAAF,EAAM,QAAQ,CAAAG,MAAQ;AACpB,IAAAD,EAAOC,CAAI,IAAIC,EAAqBL,GAAeI,GAAMF,CAAiB;AAAA,EAC5E,CAAC,GACMC;AACT;","x_google_ignoreList":[0]}

package/dist/ui-components.es89.js

@@ -0,0 +1,10 @@
+import * as e from "react";
+import o from "./ui-components.es81.js";
+import "./ui-components.es12.js";
+const t = /* @__PURE__ */ e.createContext();
+process.env.NODE_ENV !== "production" && (o.node, o.bool);
+const c = () => e.useContext(t) ?? !1;
+export {
+  c as useRtl
+};
+//# sourceMappingURL=ui-components.es89.js.map

package/dist/ui-components.es89.js.map

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+{"version":3,"file":"ui-components.es89.js","sources":["../../../node_modules/.pnpm/@mui+system@7.2.0_@emotion+react@11.14.0_@types+react@19.1.8_react@19.1.0__@emotion+sty_7f3319f308133a2adcfe5767030e6962/node_modules/@mui/system/esm/RtlProvider/index.js"],"sourcesContent":["'use client';\n\nimport * as React from 'react';\nimport PropTypes from 'prop-types';\nimport { jsx as _jsx } from \"react/jsx-runtime\";\nconst RtlContext = /*#__PURE__*/React.createContext();\nfunction RtlProvider({\n  value,\n  ...props\n}) {\n  return /*#__PURE__*/_jsx(RtlContext.Provider, {\n    value: value ?? true,\n    ...props\n  });\n}\nprocess.env.NODE_ENV !== \"production\" ? RtlProvider.propTypes = {\n  children: PropTypes.node,\n  value: PropTypes.bool\n} : void 0;\nexport const useRtl = () => {\n  const value = React.useContext(RtlContext);\n  return value ?? false;\n};\nexport default RtlProvider;"],"names":["RtlContext","React","PropTypes","useRtl"],"mappings":";;;AAKA,MAAMA,IAA0B,gBAAAC,EAAM,cAAa;AAUnD,QAAQ,IAAI,aAAa,iBACbC,EAAU,MACbA,EAAU;AAEP,MAACC,IAAS,MACNF,EAAM,WAAWD,CAAU,KACzB;","x_google_ignoreList":[0]}

package/dist/ui-components.es9.js

@@ -0,0 +1,332 @@
+import { j as a } from "./ui-components.es12.js";
+import { isAutogeneratedRow as u, gridRowIdSelector as y, gridRowNodeSelector as p } from "@mui/x-data-grid-premium";
+import { AssayWheel as h } from "./ui-components.es7.js";
+import { DownloadButton as o } from "./ui-components.es8.js";
+import { AggregateDownloadButton as C, getAvailableFiles as b } from "./ui-components.es54.js";
+import { capitalize as d, Tooltip as N, Stack as x } from "@mui/material";
+import { InfoOutline as v, Check as w } from "@mui/icons-material";
+const k = {
+  field: "ontology",
+  headerName: "Organ/Tissue",
+  type: "singleSelect",
+  valueOptions: ["adipose", "adrenal gland", "blood", "blood vessel", "bone", "bone marrow", "brain", "breast", "connective tissue", "embryo", "epithelium", "esophagus", "eye", "fallopian tube", "gallbladder", "heart", "kidney", "large intestine", "limb", "liver", "lung", "lymphoid tissue", "mouth", "muscle", "nerve", "nose", "ovary", "pancreas", "paraythroid gland", "penis", "placenta", "prostate", "skin", "small intestine", "spinal cord", "spleen", "stomach", "testis", "thymus", "thyroid", "urinary bladder", "uterus", "vagina"],
+  valueFormatter: (e) => e && d(e)
+}, E = {
+  field: "displayname",
+  headerName: "Biosample",
+  valueFormatter: (e) => e && d(e),
+  maxWidth: 300
+}, A = {
+  field: "sampleType",
+  headerName: "Sample Type",
+  type: "singleSelect",
+  valueOptions: ["tissue", "primary cell", "cell line", "in vitro differentiated cells", "organoid"],
+  valueFormatter: (e) => e && d(e)
+}, D = {
+  field: "lifeStage",
+  headerName: "Life Stage",
+  type: "singleSelect",
+  valueOptions: ["adult", "embryonic"],
+  valueFormatter: (e) => e && d(e)
+}, S = {
+  field: "assays",
+  headerName: "Assays",
+  valueGetter: (e, l) => {
+    const s = [];
+    return l.dnase_experiment_accession && s.push("DNase"), l.atac_experiment_accession && s.push("ATAC"), l.h3k4me3_experiment_accession && s.push("H3K4me3"), l.h3k27ac_experiment_accession && s.push("H3K27ac"), l.ctcf_experiment_accession && s.push("CTCF"), s.join(",");
+  },
+  sortComparator: (e, l) => {
+    const s = e.split(",").filter((i) => i.length > 0).length, r = l.split(",").filter((i) => i.length > 0).length;
+    return s - r;
+  },
+  renderCell: (e) => {
+    if (e.rowNode.type === "group") return null;
+    const l = e.row;
+    return /* @__PURE__ */ a.jsx("div", { onClick: (s) => s.stopPropagation(), children: /* @__PURE__ */ a.jsx(h, { row: {
+      dnase: l.dnase_experiment_accession,
+      atac: l.atac_experiment_accession,
+      h3k4me3: l.h3k4me3_experiment_accession,
+      h3k27ac: l.h3k27ac_experiment_accession,
+      ctcf: l.ctcf_experiment_accession
+    } }) });
+  },
+  groupable: !1
+}, _ = ["Core", "Partial", "Ancillary"], n = (e) => !!e && e !== "NA", f = (e) => {
+  const l = {
+    dnase: n(e.dnase_file_accession),
+    h3k4me3: n(e.h3k4me3_file_accession),
+    h3k27ac: n(e.h3k27ac_file_accession),
+    ctcf: n(e.ctcf_file_accession),
+    atac: n(e.atac_file_accession)
+  };
+  if (!Object.values(l).includes(!0)) return null;
+  let s = "Ancillary";
+  return l.dnase && (s = "Partial", l.ctcf && l.h3k4me3 && l.h3k27ac && (s = "Core")), s;
+}, g = [..._, null], H = {
+  field: "collection",
+  headerName: "Collection",
+  type: "singleSelect",
+  valueOptions: [..._],
+  valueGetter: (e, l) => f(l),
+  renderCell: (e) => {
+    const l = e.row;
+    return l.dnase_experiment_accession && !n(l.dnase_file_accession) || l.h3k4me3_experiment_accession && !n(l.h3k4me3_file_accession) || l.h3k27ac_experiment_accession && !n(l.h3k27ac_file_accession) || l.ctcf_experiment_accession && !n(l.ctcf_file_accession) ? /* @__PURE__ */ a.jsx(N, { title: "This sample's H3K4me3 experiment data was not run through the ENCODE pipeline. This assay is ignored when placing this sample in its given collection", children: /* @__PURE__ */ a.jsxs(x, { direction: "row", alignItems: "center", children: [
+      l.name === "GM12866_ENCDO000ABQ" ? "NA" : f(l),
+      /* @__PURE__ */ a.jsx(v, { fontSize: "small" })
+    ] }) }) : f(l);
+  },
+  sortComparator: (e, l) => g.indexOf(e) - g.indexOf(l)
+}, F = {
+  field: "dnase_experiment_accession",
+  headerName: "DNase Exp. ID",
+  sortable: !1,
+  groupable: !1
+}, T = {
+  field: "h3k4me3_experiment_accession",
+  headerName: "H3K4me3 Exp. ID",
+  sortable: !1,
+  groupable: !1
+}, j = {
+  field: "h3k27ac_experiment_accession",
+  headerName: "H3K27ac Exp. ID",
+  sortable: !1,
+  groupable: !1
+}, K = {
+  field: "ctcf_experiment_accession",
+  headerName: "CTCF Exp. ID",
+  sortable: !1,
+  groupable: !1
+}, R = {
+  field: "atac_experiment_accession",
+  headerName: "ATAC Exp. ID",
+  sortable: !1,
+  groupable: !1
+}, $ = {
+  field: "dnase_file_accession",
+  headerName: "DNase File ID",
+  sortable: !1,
+  groupable: !1
+}, O = {
+  field: "h3k4me3_file_accession",
+  headerName: "H3K4me3 File ID",
+  sortable: !1,
+  groupable: !1
+}, Z = {
+  field: "h3k27ac_file_accession",
+  headerName: "H3K27ac File ID",
+  sortable: !1,
+  groupable: !1
+}, I = {
+  field: "ctcf_file_accession",
+  headerName: "CTCF File ID",
+  sortable: !1,
+  groupable: !1
+}, G = {
+  field: "atac_file_accession",
+  headerName: "ATAC File ID",
+  sortable: !1,
+  groupable: !1
+}, B = {
+  field: "dnaseZ",
+  headerName: "DNase Z-scores",
+  valueGetter: (e, l) => l.dnase_experiment_accession && l.dnase_file_accession ? `https://downloads.wenglab.org/Registry-V4/SCREEN/Signal-Files/${l.dnase_experiment_accession}-${l.dnase_file_accession}.tsv` : null,
+  renderCell: (e) => e.rowNode.type !== "group" && e.value && /* @__PURE__ */ a.jsx(o, { message: (l) => `Download DNase z-score by cCRE (.tsv) - ${l}`, url: e.value, displayName: e.row.displayname, assay: "DNase", ontology: e.row.ontology }),
+  groupable: !1,
+  sortable: !1
+}, U = {
+  field: "h3k4me3Z",
+  headerName: "H3K4me3 Z-scores",
+  valueGetter: (e, l) => (
+    //check if file exists to handle the two samples with unprocessed h3k4me3 experiments: GM12866_ENCDO000ABQ & neural_crest_cell_ENCDO222AAA
+    l.h3k4me3_experiment_accession && n(l.h3k4me3_file_accession) ? `https://downloads.wenglab.org/Registry-V4/SCREEN/Signal-Files/${l.h3k4me3_experiment_accession}-${l.h3k4me3_file_accession}.tsv` : null
+  ),
+  renderCell: (e) => {
+    if (["GM12866_ENCDO000ABQ", "neural_crest_cell_ENCDO222AAA"].includes(e.row.name)) return /* @__PURE__ */ a.jsx(o, { disabled: !0, message: () => "This sample's H3K4me3 experiment was not run through the ENCODE Pipeline and thus z-scores are not available", url: e.value, displayName: e.row.displayname, assay: "H3K4me3", ontology: e.row.ontology });
+    if (e.rowNode.type !== "group" && e.value) return /* @__PURE__ */ a.jsx(o, { message: (l) => `Download H3K4me3 z-score by cCRE (.tsv) - ${l}`, url: e.value, displayName: e.row.displayname, assay: "H3K4me3", ontology: e.row.ontology });
+  },
+  groupable: !1,
+  sortable: !1
+}, M = {
+  field: "h3k27acZ",
+  headerName: "H3K27ac Z-scores",
+  valueGetter: (e, l) => l.h3k27ac_experiment_accession && l.h3k27ac_file_accession ? `https://downloads.wenglab.org/Registry-V4/SCREEN/Signal-Files/${l.h3k27ac_experiment_accession}-${l.h3k27ac_file_accession}.tsv` : null,
+  renderCell: (e) => e.rowNode.type !== "group" && e.value && /* @__PURE__ */ a.jsx(o, { message: (l) => `Download H3K27ac z-score by cCRE (.tsv) - ${l}`, url: e.value, displayName: e.row.displayname, assay: "H3K27ac", ontology: e.row.ontology }),
+  groupable: !1,
+  sortable: !1
+}, z = {
+  field: "ctcfZ",
+  headerName: "CTCF Z-scores",
+  valueGetter: (e, l) => l.ctcf_experiment_accession && l.ctcf_file_accession ? `https://downloads.wenglab.org/Registry-V4/SCREEN/Signal-Files/${l.ctcf_experiment_accession}-${l.ctcf_file_accession}.tsv` : null,
+  renderCell: (e) => e.rowNode.type !== "group" && e.value && /* @__PURE__ */ a.jsx(o, { message: (l) => `Download CTCF z-score by cCRE (.tsv) - ${l}`, url: e.value, displayName: e.row.displayname, assay: "CTCF", ontology: e.row.ontology }),
+  groupable: !1,
+  sortable: !1
+}, W = {
+  field: "atacZ",
+  headerName: "ATAC Z-scores",
+  valueGetter: (e, l) => l.atac_experiment_accession && l.atac_file_accession ? `https://downloads.wenglab.org/Registry-V4/SCREEN/Signal-Files/${l.atac_experiment_accession}-${l.atac_file_accession}.tsv` : null,
+  renderCell: (e) => e.rowNode.type !== "group" && e.value && /* @__PURE__ */ a.jsx(o, { message: (l) => `Download ATAC z-score by cCRE (.tsv) - ${l}`, url: e.value, displayName: e.row.displayname, assay: "ATAC", ontology: e.row.ontology }),
+  groupable: !1,
+  sortable: !1
+}, V = {
+  field: "dnase_signal_url",
+  headerName: "DNase Signal",
+  renderCell: (e) => e.rowNode.type !== "group" && e.value && /* @__PURE__ */ a.jsx(o, { message: (l) => `Download DNase Signal (.bigWig) - ${l}`, url: e.value, displayName: e.row.displayname, assay: "DNase", ontology: e.row.ontology }),
+  groupable: !1,
+  sortable: !1
+}, q = {
+  field: "h3k4me3_signal_url",
+  headerName: "H3K4me3 Signal",
+  valueGetter: (e, l) => l.h3k4me3_file_accession === "NA" ? null : e,
+  renderCell: (e) => {
+    if (["GM12866_ENCDO000ABQ", "neural_crest_cell_ENCDO222AAA"].includes(e.row.name)) return /* @__PURE__ */ a.jsx(o, { disabled: !0, message: () => "This sample's H3K4me3 experiment was not run through the ENCODE Pipeline and thus the signal file is not available", url: e.value, displayName: e.row.displayname, assay: "H3K4me3", ontology: e.row.ontology });
+    if (e.rowNode.type !== "group" && e.value) return /* @__PURE__ */ a.jsx(o, { message: (l) => `Download H3K4me3 Signal (.bigWig) - ${l}`, url: e.value, displayName: e.row.displayname, assay: "H3K4me3", ontology: e.row.ontology });
+  },
+  groupable: !1,
+  sortable: !1
+}, P = {
+  field: "h3k27ac_signal_url",
+  headerName: "H3K27ac Signal",
+  renderCell: (e) => e.rowNode.type !== "group" && e.value && /* @__PURE__ */ a.jsx(o, { message: (l) => `Download H3K27ac Signal (.bigWig) - ${l}`, url: e.value, displayName: e.row.displayname, assay: "H3K27ac", ontology: e.row.ontology }),
+  groupable: !1,
+  sortable: !1
+}, Q = {
+  field: "ctcf_signal_url",
+  headerName: "CTCF Signal",
+  renderCell: (e) => e.rowNode.type !== "group" && e.value && /* @__PURE__ */ a.jsx(o, { message: (l) => `Download CTCF Signal (.bigWig) - ${l}`, url: e.value, displayName: e.row.displayname, assay: "CTCF", ontology: e.row.ontology }),
+  groupable: !1,
+  sortable: !1
+}, L = {
+  field: "atac_signal_url",
+  headerName: "ATAC Signal",
+  renderCell: (e) => e.rowNode.type !== "group" && e.value && /* @__PURE__ */ a.jsx(o, { message: (l) => `Download ATAC Signal (.bigWig) - ${l}`, url: e.value, displayName: e.row.displayname, assay: "ATAC", ontology: e.row.ontology }),
+  groupable: !1,
+  sortable: !1
+}, J = {
+  field: "chromhmm_url",
+  headerName: "ChromHMM States",
+  renderCell: (e) => e.rowNode.type !== "group" && e.value && /* @__PURE__ */ a.jsx(o, { message: (l) => `Download ChromHMM States (.bigBed) - ${l}`, url: e.value, displayName: e.row.displayname, assay: "ChromHMM", ontology: e.row.ontology }),
+  groupable: !1,
+  sortable: !1
+}, X = {
+  field: "bedurl",
+  headerName: "cCREs (.bed)",
+  align: "center",
+  valueGetter: (e, l, s, r) => {
+    if (u(l)) {
+      const t = y(r, l), c = p(r, t);
+      return c.type === "group" && c.groupingField === "ontology" && typeof c.groupingKey == "string" ? b(c.groupingKey).map((m) => `https://downloads.wenglab.org/${m.filename}`).join(",") : null;
+    }
+    const i = [l.dnase_file_accession, l.h3k4me3_file_accession, l.h3k27ac_file_accession, l.ctcf_file_accession].filter((t) => t != null && t !== "NA");
+    return i.length ? `https://downloads.wenglab.org/Registry-V4/${i.join("_")}.bed` : null;
+  },
+  renderCell: (e) => {
+    if (e.rowNode.type === "group")
+      if (e.rowNode.groupingField === "ontology") {
+        const l = e.rowNode.groupingKey ?? "";
+        return /* @__PURE__ */ a.jsx(C, { ontology: l });
+      } else return null;
+    return /* @__PURE__ */ a.jsx(
+      o,
+      {
+        message: (l) => e.value ? `Download cCREs (.bed) - ${l}` : "cCREs only available for samples with DNase, H3K4me3, H3H27ac, and/or CTCF data",
+        url: e.value,
+        disabled: !e.value,
+        displayName: e.row.displayname,
+        assay: "cCREs",
+        ontology: e.row.ontology
+      }
+    );
+  },
+  groupable: !1,
+  sortable: !1
+}, Y = {
+  field: "bigbedurl",
+  headerName: "cCREs (.bigBed)",
+  align: "center",
+  valueGetter: (e, l) => l.name === "GM12866_ENCDO000ABQ" ? null : l.name === "neural_crest_cell_ENCDO222AAA" ? e.replaceAll("_NA_", "_") : e,
+  renderCell: (e) => e.rowNode.type !== "group" && /* @__PURE__ */ a.jsx(
+    o,
+    {
+      message: (l) => e.value ? `Download cCREs (.bigBed) - ${l}` : "cCREs only available for samples with DNase, H3K4me3, H3H27ac, and/or CTCF data",
+      url: e.value,
+      disabled: !e.value,
+      displayName: e.row.displayname,
+      assay: "cCREs",
+      ontology: e.row.ontology
+    }
+  ),
+  groupable: !1,
+  sortable: !1
+}, ee = {
+  field: "rnaSeq",
+  headerName: "Has RNA Seq",
+  type: "boolean",
+  valueGetter: (e, l) => u(l) ? null : !!l?.rna_seq_tracks?.length,
+  renderCell: (e) => e.value ? /* @__PURE__ */ a.jsx(w, {}) : null
+}, ce = [E, S, k, A, D, H, X, Y, F, $, B, V, R, G, W, L, T, O, U, q, j, Z, M, P, K, I, z, Q, J, ee], de = {
+  displayname: !1,
+  assays: !1,
+  ontology: !1,
+  sampleType: !1,
+  lifeStage: !1,
+  collection: !1,
+  bedurl: !1,
+  bigbedurl: !1,
+  dnase_experiment_accession: !1,
+  dnase_file_accession: !1,
+  dnaseZ: !1,
+  dnase_signal_url: !1,
+  atac_experiment_accession: !1,
+  atac_file_accession: !1,
+  atacZ: !1,
+  atac_signal_url: !1,
+  h3k4me3_experiment_accession: !1,
+  h3k4me3_file_accession: !1,
+  h3k4me3Z: !1,
+  h3k4me3_signal_url: !1,
+  h3k27ac_experiment_accession: !1,
+  h3k27ac_file_accession: !1,
+  h3k27acZ: !1,
+  h3k27ac_signal_url: !1,
+  ctcf_experiment_accession: !1,
+  ctcf_file_accession: !1,
+  ctcfZ: !1,
+  ctcf_signal_url: !1,
+  chromhmm_url: !1,
+  rnaSeq: !1
+};
+export {
+  de as allColsHidden,
+  S as assaysCol,
+  R as atacExpCol,
+  G as atacFileIdCol,
+  L as atacSignalUrlCol,
+  W as atacZscoreUrlCol,
+  X as ccreBedUrlCol,
+  Y as ccreBigBedUrlCol,
+  J as chromHmmUrlCol,
+  H as collectionCol,
+  ce as columns,
+  K as ctcfExpCol,
+  I as ctcfFileIdCol,
+  Q as ctcfSignalUrlCol,
+  z as ctcfZscoreUrlCol,
+  E as displayNameCol,
+  F as dnaseExpCol,
+  $ as dnaseFileIdCol,
+  V as dnaseSignalUrlCol,
+  B as dnaseZscoreUrlCol,
+  j as h3k27acExpCol,
+  Z as h3k27acFileIdCol,
+  P as h3k27acSignalUrlCol,
+  M as h3k27acZscoreUrlCol,
+  T as h3k4me3ExpCol,
+  O as h3k4me3FileIdCol,
+  q as h3k4me3SignalUrlCol,
+  U as h3k4me3ZscoreUrlCol,
+  D as lifeStageCol,
+  k as ontologyCol,
+  ee as rnaSeqCheckCol,
+  A as sampleTypeCol
+};
+//# sourceMappingURL=ui-components.es9.js.map

package/dist/ui-components.es9.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"ui-components.es9.js","sources":["../src/components/BiosampleTable/columns.tsx"],"sourcesContent":["import {\n  GridColDef,\n  GridComparatorFn,\n  gridRowIdSelector,\n  gridRowNodeSelector,\n  gridRowSelector,\n  isAutogeneratedRow,\n} from \"@mui/x-data-grid-premium\";\nimport { AssayWheel } from \"./AssayWheel\";\nimport { CcreAssay, EncodeBiosample } from \"./types\";\nimport { DownloadButton } from \"./DownloadButton\";\nimport { AggregateDownloadButton, getAvailableFiles } from \"./AggregateDownload\";\nimport { capitalize, Stack, Tooltip } from \"@mui/material\";\nimport { Check, InfoOutline } from \"@mui/icons-material\";\n\n/**\n * @todo at some point, instead of checking for is rowNode.type === \"group\", can use isAutogeneratedRow instead\n */\n\nexport const ontologyCol: GridColDef<EncodeBiosample> = {\n  field: \"ontology\",\n  headerName: \"Organ/Tissue\",\n  type: \"singleSelect\",\n  valueOptions: [\n    \"adipose\",\n    \"adrenal gland\",\n    \"blood\",\n    \"blood vessel\",\n    \"bone\",\n    \"bone marrow\",\n    \"brain\",\n    \"breast\",\n    \"connective tissue\",\n    \"embryo\",\n    \"epithelium\",\n    \"esophagus\",\n    \"eye\",\n    \"fallopian tube\",\n    \"gallbladder\",\n    \"heart\",\n    \"kidney\",\n    \"large intestine\",\n    \"limb\",\n    \"liver\",\n    \"lung\",\n    \"lymphoid tissue\",\n    \"mouth\",\n    \"muscle\",\n    \"nerve\",\n    \"nose\",\n    \"ovary\",\n    \"pancreas\",\n    \"paraythroid gland\",\n    \"penis\",\n    \"placenta\",\n    \"prostate\",\n    \"skin\",\n    \"small intestine\",\n    \"spinal cord\",\n    \"spleen\",\n    \"stomach\",\n    \"testis\",\n    \"thymus\",\n    \"thyroid\",\n    \"urinary bladder\",\n    \"uterus\",\n    \"vagina\",\n  ],\n  valueFormatter: (value) => value && capitalize(value),\n};\n\nexport const displayNameCol: GridColDef<EncodeBiosample> = {\n  field: \"displayname\",\n  headerName: \"Biosample\",\n  valueFormatter: (value) => value && capitalize(value),\n  maxWidth: 300,\n};\n\nexport const sampleTypeCol: GridColDef<EncodeBiosample> = {\n  field: \"sampleType\",\n  headerName: \"Sample Type\",\n  type: \"singleSelect\",\n  valueOptions: [\"tissue\", \"primary cell\", \"cell line\", \"in vitro differentiated cells\", \"organoid\"],\n  valueFormatter: (value) => value && capitalize(value),\n};\n\nexport const lifeStageCol: GridColDef<EncodeBiosample> = {\n  field: \"lifeStage\",\n  headerName: \"Life Stage\",\n  type: \"singleSelect\",\n  valueOptions: [\"adult\", \"embryonic\"],\n  valueFormatter: (value) => value && capitalize(value),\n};\n\nexport const assaysCol: GridColDef<EncodeBiosample> = {\n  field: \"assays\",\n  headerName: \"Assays\",\n  valueGetter: (_, row) => {\n    const availableAssays = [];\n    if (row.dnase_experiment_accession) availableAssays.push(\"DNase\");\n    if (row.atac_experiment_accession) availableAssays.push(\"ATAC\");\n    if (row.h3k4me3_experiment_accession) availableAssays.push(\"H3K4me3\");\n    if (row.h3k27ac_experiment_accession) availableAssays.push(\"H3K27ac\");\n    if (row.ctcf_experiment_accession) availableAssays.push(\"CTCF\");\n    return availableAssays.join(\",\");\n  },\n  sortComparator: (v1, v2) => {\n    const count1 = v1.split(\",\").filter((s: string) => s.length > 0).length;\n    const count2 = v2.split(\",\").filter((s: string) => s.length > 0).length;\n    return count1 - count2;\n  },\n  renderCell: (params) => {\n    if (params.rowNode.type === \"group\") return null;\n    const row = params.row;\n    return (\n      <div onClick={(e) => e.stopPropagation()}>\n        <AssayWheel\n          row={{\n            dnase: row.dnase_experiment_accession,\n            atac: row.atac_experiment_accession,\n            h3k4me3: row.h3k4me3_experiment_accession,\n            h3k27ac: row.h3k27ac_experiment_accession,\n            ctcf: row.ctcf_experiment_accession,\n          }}\n        />\n      </div>\n    );\n  },\n  groupable: false,\n};\n\n// -- Collection Column Helpers --\n\nconst collections = [\"Core\", \"Partial\", \"Ancillary\"] as const;\n\n//Handles the two experiments that have unprocessed H3K4me3 samples which have \"NA\" values in file\n//GM12866_ENCDO000ABQ & neural_crest_cell_ENCDO222AAA\nconst fileExists = (fileID: string | null): Boolean => {\n  return !!fileID && fileID !== \"NA\"\n}\n\nconst getCollectionForSample = (sample: EncodeBiosample): (typeof collections)[number] | null => {\n  const filesAvailable: Record<CcreAssay, Boolean> = {\n    dnase: fileExists(sample.dnase_file_accession),\n    h3k4me3: fileExists(sample.h3k4me3_file_accession),\n    h3k27ac: fileExists(sample.h3k27ac_file_accession),\n    ctcf: fileExists(sample.ctcf_file_accession),\n    atac: fileExists(sample.atac_file_accession),\n  };\n  if (!Object.values(filesAvailable).includes(true)) return null; // True for grouping rows and GM12866_ENCDO000ABQ\n  let collection: (typeof collections)[number] = \"Ancillary\";\n  if (filesAvailable.dnase) {\n    collection = \"Partial\";\n    if (filesAvailable.ctcf && filesAvailable.h3k4me3 && filesAvailable.h3k27ac) {\n      collection = \"Core\";\n    }\n  }\n  return collection;\n};\n\n// define this to properly sort grouping rows and GM12866_ENCDO000ABQ\nconst sortOrder = [...collections, null]\n\nexport const collectionCol: GridColDef<EncodeBiosample> = {\n  field: \"collection\",\n  headerName: \"Collection\",\n  type: \"singleSelect\",\n  valueOptions: [...collections],\n  valueGetter: (_, row) => getCollectionForSample(row),\n  renderCell: (params) => {\n    const row = params.row\n    if (\n      (row.dnase_experiment_accession && !fileExists(row.dnase_file_accession)) ||\n      (row.h3k4me3_experiment_accession && !fileExists(row.h3k4me3_file_accession)) ||\n      (row.h3k27ac_experiment_accession && !fileExists(row.h3k27ac_file_accession)) ||\n      (row.ctcf_experiment_accession && !fileExists(row.ctcf_file_accession))\n    )\n      return (\n        <Tooltip title=\"This sample's H3K4me3 experiment data was not run through the ENCODE pipeline. This assay is ignored when placing this sample in its given collection\">\n          <Stack direction={\"row\"} alignItems={\"center\"}>\n            {row.name === \"GM12866_ENCDO000ABQ\" ? \"NA\" : getCollectionForSample(row)}\n            <InfoOutline fontSize=\"small\" />\n          </Stack>\n        </Tooltip>\n      );\n    else return getCollectionForSample(row);\n  },\n  sortComparator: (v1, v2) => sortOrder.indexOf(v1) - sortOrder.indexOf(v2),\n};\n\n//ENCODE Experiment Accession (plain text)\nexport const dnaseExpCol: GridColDef<EncodeBiosample> = {\n  field: \"dnase_experiment_accession\",\n  headerName: \"DNase Exp. ID\",\n  sortable: false,\n  groupable: false,\n};\nexport const h3k4me3ExpCol: GridColDef<EncodeBiosample> = {\n  field: \"h3k4me3_experiment_accession\",\n  headerName: \"H3K4me3 Exp. ID\",\n  sortable: false,\n  groupable: false,\n};\nexport const h3k27acExpCol: GridColDef<EncodeBiosample> = {\n  field: \"h3k27ac_experiment_accession\",\n  headerName: \"H3K27ac Exp. ID\",\n  sortable: false,\n  groupable: false,\n};\nexport const ctcfExpCol: GridColDef<EncodeBiosample> = {\n  field: \"ctcf_experiment_accession\",\n  headerName: \"CTCF Exp. ID\",\n  sortable: false,\n  groupable: false,\n};\nexport const atacExpCol: GridColDef<EncodeBiosample> = {\n  field: \"atac_experiment_accession\",\n  headerName: \"ATAC Exp. ID\",\n  sortable: false,\n  groupable: false,\n};\n\n//ENCODE File ID (plain text)\nexport const dnaseFileIdCol: GridColDef<EncodeBiosample> = {\n  field: \"dnase_file_accession\",\n  headerName: \"DNase File ID\",\n  sortable: false,\n  groupable: false,\n};\nexport const h3k4me3FileIdCol: GridColDef<EncodeBiosample> = {\n  field: \"h3k4me3_file_accession\",\n  headerName: \"H3K4me3 File ID\",\n  sortable: false,\n  groupable: false,\n};\nexport const h3k27acFileIdCol: GridColDef<EncodeBiosample> = {\n  field: \"h3k27ac_file_accession\",\n  headerName: \"H3K27ac File ID\",\n  sortable: false,\n  groupable: false,\n};\nexport const ctcfFileIdCol: GridColDef<EncodeBiosample> = {\n  field: \"ctcf_file_accession\",\n  headerName: \"CTCF File ID\",\n  sortable: false,\n  groupable: false,\n};\nexport const atacFileIdCol: GridColDef<EncodeBiosample> = {\n  field: \"atac_file_accession\",\n  headerName: \"ATAC File ID\",\n  sortable: false,\n  groupable: false,\n};\n\nexport const dnaseZscoreUrlCol: GridColDef<EncodeBiosample> = {\n  field: \"dnaseZ\",\n  headerName: \"DNase Z-scores\",\n  valueGetter: (_, row) =>\n    row.dnase_experiment_accession && row.dnase_file_accession\n      ? `https://downloads.wenglab.org/Registry-V4/SCREEN/Signal-Files/${row.dnase_experiment_accession}-${row.dnase_file_accession}.tsv`\n      : null,\n  renderCell: (params) =>\n    params.rowNode.type !== \"group\" &&\n    params.value && (\n      <DownloadButton\n        message={(fileSize) => `Download DNase z-score by cCRE (.tsv) - ${fileSize}`}\n        url={params.value}\n        displayName={params.row.displayname}\n        assay=\"DNase\"\n        ontology={params.row.ontology}\n      />\n    ),\n  groupable: false,\n  sortable: false,\n};\n\nexport const h3k4me3ZscoreUrlCol: GridColDef<EncodeBiosample> = {\n  field: \"h3k4me3Z\",\n  headerName: \"H3K4me3 Z-scores\",\n  valueGetter: (_, row) =>\n    //check if file exists to handle the two samples with unprocessed h3k4me3 experiments: GM12866_ENCDO000ABQ & neural_crest_cell_ENCDO222AAA\n    row.h3k4me3_experiment_accession && fileExists(row.h3k4me3_file_accession)\n      ? `https://downloads.wenglab.org/Registry-V4/SCREEN/Signal-Files/${row.h3k4me3_experiment_accession}-${row.h3k4me3_file_accession}.tsv`\n      : null,\n  renderCell: (params) => {\n    if ([\"GM12866_ENCDO000ABQ\", \"neural_crest_cell_ENCDO222AAA\"].includes(params.row.name))\n      return (\n        <DownloadButton\n          disabled\n          message={() =>\n            \"This sample's H3K4me3 experiment was not run through the ENCODE Pipeline and thus z-scores are not available\"\n          }\n          url={params.value}\n          displayName={params.row.displayname}\n          assay=\"H3K4me3\"\n          ontology={params.row.ontology}\n        />\n      );\n    else if (!(params.rowNode.type === \"group\") && params.value)\n      return (\n        <DownloadButton\n          message={(fileSize) => `Download H3K4me3 z-score by cCRE (.tsv) - ${fileSize}`}\n          url={params.value}\n          displayName={params.row.displayname}\n          assay=\"H3K4me3\"\n          ontology={params.row.ontology}\n        />\n      );\n  },\n  groupable: false,\n  sortable: false,\n};\n\nexport const h3k27acZscoreUrlCol: GridColDef<EncodeBiosample> = {\n  field: \"h3k27acZ\",\n  headerName: \"H3K27ac Z-scores\",\n  valueGetter: (_, row) =>\n    row.h3k27ac_experiment_accession && row.h3k27ac_file_accession\n      ? `https://downloads.wenglab.org/Registry-V4/SCREEN/Signal-Files/${row.h3k27ac_experiment_accession}-${row.h3k27ac_file_accession}.tsv`\n      : null,\n  renderCell: (params) =>\n    params.rowNode.type !== \"group\" &&\n    params.value && (\n      <DownloadButton\n        message={(fileSize) => `Download H3K27ac z-score by cCRE (.tsv) - ${fileSize}`}\n        url={params.value}\n        displayName={params.row.displayname}\n        assay=\"H3K27ac\"\n        ontology={params.row.ontology}\n      />\n    ),\n  groupable: false,\n  sortable: false,\n};\n\nexport const ctcfZscoreUrlCol: GridColDef<EncodeBiosample> = {\n  field: \"ctcfZ\",\n  headerName: \"CTCF Z-scores\",\n  valueGetter: (_, row) =>\n    row.ctcf_experiment_accession && row.ctcf_file_accession\n      ? `https://downloads.wenglab.org/Registry-V4/SCREEN/Signal-Files/${row.ctcf_experiment_accession}-${row.ctcf_file_accession}.tsv`\n      : null,\n  renderCell: (params) =>\n    params.rowNode.type !== \"group\" &&\n    params.value && (\n      <DownloadButton\n        message={(fileSize) => `Download CTCF z-score by cCRE (.tsv) - ${fileSize}`}\n        url={params.value}\n        displayName={params.row.displayname}\n        assay=\"CTCF\"\n        ontology={params.row.ontology}\n      />\n    ),\n  groupable: false,\n  sortable: false,\n};\n\nexport const atacZscoreUrlCol: GridColDef<EncodeBiosample> = {\n  field: \"atacZ\",\n  headerName: \"ATAC Z-scores\",\n  valueGetter: (_, row) =>\n    row.atac_experiment_accession && row.atac_file_accession\n      ? `https://downloads.wenglab.org/Registry-V4/SCREEN/Signal-Files/${row.atac_experiment_accession}-${row.atac_file_accession}.tsv`\n      : null,\n  renderCell: (params) =>\n    params.rowNode.type !== \"group\" &&\n    params.value && (\n      <DownloadButton\n        message={(fileSize) => `Download ATAC z-score by cCRE (.tsv) - ${fileSize}`}\n        url={params.value}\n        displayName={params.row.displayname}\n        assay=\"ATAC\"\n        ontology={params.row.ontology}\n      />\n    ),\n  groupable: false,\n  sortable: false,\n};\n\nexport const dnaseSignalUrlCol: GridColDef<EncodeBiosample> = {\n  field: \"dnase_signal_url\",\n  headerName: \"DNase Signal\",\n  renderCell: (params) =>\n    params.rowNode.type !== \"group\" &&\n    params.value && (\n      <DownloadButton\n        message={(fileSize) => `Download DNase Signal (.bigWig) - ${fileSize}`}\n        url={params.value}\n        displayName={params.row.displayname}\n        assay=\"DNase\"\n        ontology={params.row.ontology}\n      />\n    ),\n  groupable: false,\n  sortable: false,\n};\n\nexport const h3k4me3SignalUrlCol: GridColDef<EncodeBiosample> = {\n  field: \"h3k4me3_signal_url\",\n  headerName: \"H3K4me3 Signal\",\n  valueGetter: (value, row) => (row.h3k4me3_file_accession === \"NA\" ? null : value),\n  renderCell: (params) => {\n    if ([\"GM12866_ENCDO000ABQ\", \"neural_crest_cell_ENCDO222AAA\"].includes(params.row.name))\n      return (\n        <DownloadButton\n          disabled\n          message={() =>\n            \"This sample's H3K4me3 experiment was not run through the ENCODE Pipeline and thus the signal file is not available\"\n          }\n          url={params.value}\n          displayName={params.row.displayname}\n          assay=\"H3K4me3\"\n          ontology={params.row.ontology}\n        />\n      );\n    else if (!(params.rowNode.type === \"group\") && params.value)\n      return (\n        <DownloadButton\n          message={(fileSize) => `Download H3K4me3 Signal (.bigWig) - ${fileSize}`}\n          url={params.value}\n          displayName={params.row.displayname}\n          assay=\"H3K4me3\"\n          ontology={params.row.ontology}\n        />\n      );\n  },\n  groupable: false,\n  sortable: false,\n};\n\nexport const h3k27acSignalUrlCol: GridColDef<EncodeBiosample> = {\n  field: \"h3k27ac_signal_url\",\n  headerName: \"H3K27ac Signal\",\n  renderCell: (params) =>\n    params.rowNode.type !== \"group\" &&\n    params.value && (\n      <DownloadButton\n        message={(fileSize) => `Download H3K27ac Signal (.bigWig) - ${fileSize}`}\n        url={params.value}\n        displayName={params.row.displayname}\n        assay=\"H3K27ac\"\n        ontology={params.row.ontology}\n      />\n    ),\n  groupable: false,\n  sortable: false,\n};\n\nexport const ctcfSignalUrlCol: GridColDef<EncodeBiosample> = {\n  field: \"ctcf_signal_url\",\n  headerName: \"CTCF Signal\",\n  renderCell: (params) =>\n    params.rowNode.type !== \"group\" &&\n    params.value && (\n      <DownloadButton\n        message={(fileSize) => `Download CTCF Signal (.bigWig) - ${fileSize}`}\n        url={params.value}\n        displayName={params.row.displayname}\n        assay=\"CTCF\"\n        ontology={params.row.ontology}\n      />\n    ),\n  groupable: false,\n  sortable: false,\n};\n\nexport const atacSignalUrlCol: GridColDef<EncodeBiosample> = {\n  field: \"atac_signal_url\",\n  headerName: \"ATAC Signal\",\n  renderCell: (params) =>\n    params.rowNode.type !== \"group\" &&\n    params.value && (\n      <DownloadButton\n        message={(fileSize) => `Download ATAC Signal (.bigWig) - ${fileSize}`}\n        url={params.value}\n        displayName={params.row.displayname}\n        assay=\"ATAC\"\n        ontology={params.row.ontology}\n      />\n    ),\n  groupable: false,\n  sortable: false,\n};\n\nexport const chromHmmUrlCol: GridColDef<EncodeBiosample> = {\n  field: \"chromhmm_url\",\n  headerName: \"ChromHMM States\",\n  renderCell: (params) =>\n    params.rowNode.type !== \"group\" &&\n    params.value && (\n      <DownloadButton\n        message={(fileSize) => `Download ChromHMM States (.bigBed) - ${fileSize}`}\n        url={params.value}\n        displayName={params.row.displayname}\n        assay=\"ChromHMM\"\n        ontology={params.row.ontology}\n      />\n    ),\n  groupable: false,\n  sortable: false,\n};\n\nexport const ccreBedUrlCol: GridColDef<EncodeBiosample> = {\n  field: \"bedurl\",\n  headerName: \"cCREs (.bed)\",\n  align: \"center\",\n  valueGetter: (_, row, __, apiRef) => {\n    if (isAutogeneratedRow(row)) {\n      const id = gridRowIdSelector(apiRef, row);\n      const rowNode = gridRowNodeSelector(apiRef, id);\n      const isGroupingByOntology = rowNode.type === \"group\" && rowNode.groupingField === \"ontology\";\n      if (isGroupingByOntology && typeof rowNode.groupingKey === \"string\") {\n        return getAvailableFiles(rowNode.groupingKey)\n          .map((x) => `https://downloads.wenglab.org/${x.filename}`)\n          .join(\",\");\n      } else return null;\n    }\n    const signalIDs = [\n      row.dnase_file_accession,\n      row.h3k4me3_file_accession,\n      row.h3k27ac_file_accession,\n      row.ctcf_file_accession,\n    ].filter((id) => id !== null && id !== undefined && id !== \"NA\");\n    if (!signalIDs.length) return null // aka is ATAC-only\n    return `https://downloads.wenglab.org/Registry-V4/${signalIDs.join(\"_\")}.bed`;\n  },\n  renderCell: (params) => {\n    if (params.rowNode.type === \"group\") {\n      if (params.rowNode.groupingField === \"ontology\") {\n        const ontology = (params.rowNode.groupingKey as string) ?? \"\";\n        return <AggregateDownloadButton ontology={ontology} />;\n      } else return null;\n    }\n    return (\n      <DownloadButton\n        message={(fileSize) =>\n          params.value ? `Download cCREs (.bed) - ${fileSize}` : \"cCREs only available for samples with DNase, H3K4me3, H3H27ac, and/or CTCF data\"\n        }\n        url={params.value}\n        disabled={!params.value} //aka is ATAC-only\n        displayName={params.row.displayname}\n        assay=\"cCREs\"\n        ontology={params.row.ontology}\n      />\n    );\n  },\n  groupable: false,\n  sortable: false,\n};\n\nexport const ccreBigBedUrlCol: GridColDef<EncodeBiosample> = {\n  field: \"bigbedurl\",\n  headerName: \"cCREs (.bigBed)\",\n  align: 'center',\n  valueGetter: (value: string, row) => {\n    if (row.name === \"GM12866_ENCDO000ABQ\") return null //This sample has no cCREs file\n    if (row.name === \"neural_crest_cell_ENCDO222AAA\") return value.replaceAll('_NA_', '_') //The url in file includes \"NA\" H3K4me3 file ID\n    else return value\n  },\n  renderCell: (params) =>\n    params.rowNode.type !== \"group\" && (\n      <DownloadButton\n        message={(fileSize) =>\n          params.value ? `Download cCREs (.bigBed) - ${fileSize}` : \"cCREs only available for samples with DNase, H3K4me3, H3H27ac, and/or CTCF data\"\n        }\n        url={params.value}\n        disabled={!params.value} //aka is ATAC-only\n        displayName={params.row.displayname}\n        assay=\"cCREs\"\n        ontology={params.row.ontology}\n      />\n    ),\n  groupable: false,\n  sortable: false,\n};\n\nexport const rnaSeqCheckCol: GridColDef<EncodeBiosample> = {\n  field: \"rnaSeq\",\n  headerName: \"Has RNA Seq\",\n  type: \"boolean\",\n  valueGetter: (_, row) => (isAutogeneratedRow(row) ? null : !!row?.rna_seq_tracks?.length),\n  renderCell: (params) => {\n    if (params.value) {\n      return <Check />;\n    } else return null;\n  },\n};\n\nexport const columns: GridColDef<EncodeBiosample>[] = [\n  displayNameCol,\n  assaysCol,\n  ontologyCol,\n  sampleTypeCol,\n  lifeStageCol,\n  collectionCol,\n  ccreBedUrlCol,\n  ccreBigBedUrlCol,\n  dnaseExpCol,\n  dnaseFileIdCol,\n  dnaseZscoreUrlCol,\n  dnaseSignalUrlCol,\n  atacExpCol,\n  atacFileIdCol,\n  atacZscoreUrlCol,\n  atacSignalUrlCol,\n  h3k4me3ExpCol,\n  h3k4me3FileIdCol,\n  h3k4me3ZscoreUrlCol,\n  h3k4me3SignalUrlCol,\n  h3k27acExpCol,\n  h3k27acFileIdCol,\n  h3k27acZscoreUrlCol,\n  h3k27acSignalUrlCol,\n  ctcfExpCol,\n  ctcfFileIdCol,\n  ctcfZscoreUrlCol,\n  ctcfSignalUrlCol,\n  chromHmmUrlCol,\n  rnaSeqCheckCol,\n];\n\n/**\n * useful for resetting visible columns by spreading this then overriding with visible cols\n */\nexport const allColsHidden = {\n  displayname: false,\n  assays: false,\n  ontology: false,\n  sampleType: false,\n  lifeStage: false,\n  collection: false,\n  bedurl: false,\n  bigbedurl: false,\n  dnase_experiment_accession: false,\n  dnase_file_accession: false,\n  dnaseZ: false,\n  dnase_signal_url: false,\n  atac_experiment_accession: false,\n  atac_file_accession: false,\n  atacZ: false,\n  atac_signal_url: false,\n  h3k4me3_experiment_accession: false,\n  h3k4me3_file_accession: false,\n  h3k4me3Z: false,\n  h3k4me3_signal_url: false,\n  h3k27ac_experiment_accession: 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