@weng-lab/ui-components 2.0.0 → 2.0.1

package/dist/ui-components.es54.js.map

@@ -1 +1 @@
-{"version":3,"file":"ui-components.es54.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/Modal/Modal.js"],"sourcesContent":["'use client';\n\nimport * as React from 'react';\nimport PropTypes from 'prop-types';\nimport clsx from 'clsx';\nimport HTMLElementType from '@mui/utils/HTMLElementType';\nimport elementAcceptingRef from '@mui/utils/elementAcceptingRef';\nimport composeClasses from '@mui/utils/composeClasses';\nimport FocusTrap from \"../Unstable_TrapFocus/index.js\";\nimport Portal from \"../Portal/index.js\";\nimport { styled } from \"../zero-styled/index.js\";\nimport memoTheme from \"../utils/memoTheme.js\";\nimport { useDefaultProps } from \"../DefaultPropsProvider/index.js\";\nimport Backdrop from \"../Backdrop/index.js\";\nimport useModal from \"./useModal.js\";\nimport { getModalUtilityClass } from \"./modalClasses.js\";\nimport useSlot from \"../utils/useSlot.js\";\nimport { jsx as _jsx, jsxs as _jsxs } from \"react/jsx-runtime\";\nconst useUtilityClasses = ownerState => {\n  const {\n    open,\n    exited,\n    classes\n  } = ownerState;\n  const slots = {\n    root: ['root', !open && exited && 'hidden'],\n    backdrop: ['backdrop']\n  };\n  return composeClasses(slots, getModalUtilityClass, classes);\n};\nconst ModalRoot = styled('div', {\n  name: 'MuiModal',\n  slot: 'Root',\n  overridesResolver: (props, styles) => {\n    const {\n      ownerState\n    } = props;\n    return [styles.root, !ownerState.open && ownerState.exited && styles.hidden];\n  }\n})(memoTheme(({\n  theme\n}) => ({\n  position: 'fixed',\n  zIndex: (theme.vars || theme).zIndex.modal,\n  right: 0,\n  bottom: 0,\n  top: 0,\n  left: 0,\n  variants: [{\n    props: ({\n      ownerState\n    }) => !ownerState.open && ownerState.exited,\n    style: {\n      visibility: 'hidden'\n    }\n  }]\n})));\nconst ModalBackdrop = styled(Backdrop, {\n  name: 'MuiModal',\n  slot: 'Backdrop'\n})({\n  zIndex: -1\n});\n\n/**\n * Modal is a lower-level construct that is leveraged by the following components:\n *\n * - [Dialog](/material-ui/api/dialog/)\n * - [Drawer](/material-ui/api/drawer/)\n * - [Menu](/material-ui/api/menu/)\n * - [Popover](/material-ui/api/popover/)\n *\n * If you are creating a modal dialog, you probably want to use the [Dialog](/material-ui/api/dialog/) component\n * rather than directly using Modal.\n *\n * This component shares many concepts with [react-overlays](https://react-bootstrap.github.io/react-overlays/#modals).\n */\nconst Modal = /*#__PURE__*/React.forwardRef(function Modal(inProps, ref) {\n  const props = useDefaultProps({\n    name: 'MuiModal',\n    props: inProps\n  });\n  const {\n    BackdropComponent = ModalBackdrop,\n    BackdropProps,\n    classes: classesProp,\n    className,\n    closeAfterTransition = false,\n    children,\n    container,\n    component,\n    components = {},\n    componentsProps = {},\n    disableAutoFocus = false,\n    disableEnforceFocus = false,\n    disableEscapeKeyDown = false,\n    disablePortal = false,\n    disableRestoreFocus = false,\n    disableScrollLock = false,\n    hideBackdrop = false,\n    keepMounted = false,\n    onClose,\n    onTransitionEnter,\n    onTransitionExited,\n    open,\n    slotProps = {},\n    slots = {},\n    // eslint-disable-next-line react/prop-types\n    theme,\n    ...other\n  } = props;\n  const propsWithDefaults = {\n    ...props,\n    closeAfterTransition,\n    disableAutoFocus,\n    disableEnforceFocus,\n    disableEscapeKeyDown,\n    disablePortal,\n    disableRestoreFocus,\n    disableScrollLock,\n    hideBackdrop,\n    keepMounted\n  };\n  const {\n    getRootProps,\n    getBackdropProps,\n    getTransitionProps,\n    portalRef,\n    isTopModal,\n    exited,\n    hasTransition\n  } = useModal({\n    ...propsWithDefaults,\n    rootRef: ref\n  });\n  const ownerState = {\n    ...propsWithDefaults,\n    exited\n  };\n  const classes = useUtilityClasses(ownerState);\n  const childProps = {};\n  if (children.props.tabIndex === undefined) {\n    childProps.tabIndex = '-1';\n  }\n\n  // It's a Transition like component\n  if (hasTransition) {\n    const {\n      onEnter,\n      onExited\n    } = getTransitionProps();\n    childProps.onEnter = onEnter;\n    childProps.onExited = onExited;\n  }\n  const externalForwardedProps = {\n    slots: {\n      root: components.Root,\n      backdrop: components.Backdrop,\n      ...slots\n    },\n    slotProps: {\n      ...componentsProps,\n      ...slotProps\n    }\n  };\n  const [RootSlot, rootProps] = useSlot('root', {\n    ref,\n    elementType: ModalRoot,\n    externalForwardedProps: {\n      ...externalForwardedProps,\n      ...other,\n      component\n    },\n    getSlotProps: getRootProps,\n    ownerState,\n    className: clsx(className, classes?.root, !ownerState.open && ownerState.exited && classes?.hidden)\n  });\n  const [BackdropSlot, backdropProps] = useSlot('backdrop', {\n    ref: BackdropProps?.ref,\n    elementType: BackdropComponent,\n    externalForwardedProps,\n    shouldForwardComponentProp: true,\n    additionalProps: BackdropProps,\n    getSlotProps: otherHandlers => {\n      return getBackdropProps({\n        ...otherHandlers,\n        onClick: event => {\n          if (otherHandlers?.onClick) {\n            otherHandlers.onClick(event);\n          }\n        }\n      });\n    },\n    className: clsx(BackdropProps?.className, classes?.backdrop),\n    ownerState\n  });\n  if (!keepMounted && !open && (!hasTransition || exited)) {\n    return null;\n  }\n  return /*#__PURE__*/_jsx(Portal, {\n    ref: portalRef,\n    container: container,\n    disablePortal: disablePortal,\n    children: /*#__PURE__*/_jsxs(RootSlot, {\n      ...rootProps,\n      children: [!hideBackdrop && BackdropComponent ? /*#__PURE__*/_jsx(BackdropSlot, {\n        ...backdropProps\n      }) : null, /*#__PURE__*/_jsx(FocusTrap, {\n        disableEnforceFocus: disableEnforceFocus,\n        disableAutoFocus: disableAutoFocus,\n        disableRestoreFocus: disableRestoreFocus,\n        isEnabled: isTopModal,\n        open: open,\n        children: /*#__PURE__*/React.cloneElement(children, childProps)\n      })]\n    })\n  });\n});\nprocess.env.NODE_ENV !== \"production\" ? Modal.propTypes /* remove-proptypes */ = {\n  // ┌────────────────────────────── Warning ──────────────────────────────┐\n  // │ These PropTypes are generated from the TypeScript type definitions. │\n  // │    To update them, edit the d.ts file and run `pnpm proptypes`.     │\n  // └─────────────────────────────────────────────────────────────────────┘\n  /**\n   * A backdrop component. This prop enables custom backdrop rendering.\n   * @deprecated Use `slots.backdrop` instead. While this prop currently works, it will be removed in the next major version.\n   * Use the `slots.backdrop` prop to make your application ready for the next version of Material UI.\n   * @default styled(Backdrop, {\n   *   name: 'MuiModal',\n   *   slot: 'Backdrop',\n   * })({\n   *   zIndex: -1,\n   * })\n   */\n  BackdropComponent: PropTypes.elementType,\n  /**\n   * Props applied to the [`Backdrop`](https://mui.com/material-ui/api/backdrop/) element.\n   * @deprecated Use `slotProps.backdrop` instead.\n   */\n  BackdropProps: PropTypes.object,\n  /**\n   * A single child content element.\n   */\n  children: elementAcceptingRef.isRequired,\n  /**\n   * Override or extend the styles applied to the component.\n   */\n  classes: PropTypes.object,\n  /**\n   * @ignore\n   */\n  className: PropTypes.string,\n  /**\n   * When set to true the Modal waits until a nested Transition is completed before closing.\n   * @default false\n   */\n  closeAfterTransition: PropTypes.bool,\n  /**\n   * The component used for the root node.\n   * Either a string to use a HTML element or a component.\n   */\n  component: PropTypes.elementType,\n  /**\n   * The components used for each slot inside.\n   *\n   * @deprecated Use the `slots` prop instead. This prop will be removed in a future major release. See [Migrating from deprecated APIs](https://mui.com/material-ui/migration/migrating-from-deprecated-apis/) for more details.\n   *\n   * @default {}\n   */\n  components: PropTypes.shape({\n    Backdrop: PropTypes.elementType,\n    Root: PropTypes.elementType\n  }),\n  /**\n   * The extra props for the slot components.\n   * You can override the existing props or add new ones.\n   *\n   * @deprecated Use the `slotProps` prop instead. This prop will be removed in a future major release. See [Migrating from deprecated APIs](https://mui.com/material-ui/migration/migrating-from-deprecated-apis/) for more details.\n   *\n   * @default {}\n   */\n  componentsProps: PropTypes.shape({\n    backdrop: PropTypes.oneOfType([PropTypes.func, PropTypes.object]),\n    root: PropTypes.oneOfType([PropTypes.func, PropTypes.object])\n  }),\n  /**\n   * An HTML element or function that returns one.\n   * The `container` will have the portal children appended to it.\n   *\n   * You can also provide a callback, which is called in a React layout effect.\n   * This lets you set the container from a ref, and also makes server-side rendering possible.\n   *\n   * By default, it uses the body of the top-level document object,\n   * so it's simply `document.body` most of the time.\n   */\n  container: PropTypes /* @typescript-to-proptypes-ignore */.oneOfType([HTMLElementType, PropTypes.func]),\n  /**\n   * If `true`, the modal will not automatically shift focus to itself when it opens, and\n   * replace it to the last focused element when it closes.\n   * This also works correctly with any modal children that have the `disableAutoFocus` prop.\n   *\n   * Generally this should never be set to `true` as it makes the modal less\n   * accessible to assistive technologies, like screen readers.\n   * @default false\n   */\n  disableAutoFocus: PropTypes.bool,\n  /**\n   * If `true`, the modal will not prevent focus from leaving the modal while open.\n   *\n   * Generally this should never be set to `true` as it makes the modal less\n   * accessible to assistive technologies, like screen readers.\n   * @default false\n   */\n  disableEnforceFocus: PropTypes.bool,\n  /**\n   * If `true`, hitting escape will not fire the `onClose` callback.\n   * @default false\n   */\n  disableEscapeKeyDown: PropTypes.bool,\n  /**\n   * The `children` will be under the DOM hierarchy of the parent component.\n   * @default false\n   */\n  disablePortal: PropTypes.bool,\n  /**\n   * If `true`, the modal will not restore focus to previously focused element once\n   * modal is hidden or unmounted.\n   * @default false\n   */\n  disableRestoreFocus: PropTypes.bool,\n  /**\n   * Disable the scroll lock behavior.\n   * @default false\n   */\n  disableScrollLock: PropTypes.bool,\n  /**\n   * If `true`, the backdrop is not rendered.\n   * @default false\n   */\n  hideBackdrop: PropTypes.bool,\n  /**\n   * Always keep the children in the DOM.\n   * This prop can be useful in SEO situation or\n   * when you want to maximize the responsiveness of the Modal.\n   * @default false\n   */\n  keepMounted: PropTypes.bool,\n  /**\n   * Callback fired when the component requests to be closed.\n   * The `reason` parameter can optionally be used to control the response to `onClose`.\n   *\n   * @param {object} event The event source of the callback.\n   * @param {string} reason Can be: `\"escapeKeyDown\"`, `\"backdropClick\"`.\n   */\n  onClose: PropTypes.func,\n  /**\n   * A function called when a 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setIsDialogOpen(false);\n        }}\n        aria-labelledby=\"export-dialog-title\"\n        disableScrollLock\n        slotProps={{\n          backdrop: {\n            sx: {\n              backgroundColor: \"rgba(255, 255, 255, 0.1)\",\n              backdropFilter: \"blur(2px)\",\n            },\n          },\n        }}\n        onClick={(e) => e.stopPropagation()}\n      >\n        <DialogTitle id=\"export-dialog-title\">\n          Download cCREs in {ontology.charAt(0).toUpperCase() + ontology.slice(1)}:\n        </DialogTitle>\n        <DialogContent>\n          <Stack>\n            <FormControlLabel\n              control={<Checkbox checked={all} onChange={(e) => setAll(e.target.checked)} disabled={!allFile} />}\n              label={`Aggregate cCREs (all biosamples)${allFileSize ? \" - \" + formatFileSize(allFileSize) : \"\"}`}\n            />\n            <FormControlLabel\n              control={<Checkbox checked={noccl} onChange={(e) => setNoccl(e.target.checked)} 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package/dist/ui-components.es55.js

@@ -1,158 +1,215 @@
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-import e from "./ui-components.es81.js";
-import { clsx as h } from "./ui-components.es80.js";
-import P from "./ui-components.es118.js";
-import { j as b } from "./ui-components.es12.js";
-import w from "./ui-components.es40.js";
-import g from "./ui-components.es82.js";
-import c from "./ui-components.es145.js";
-import { getPaperUtilityClass as T } from "./ui-components.es181.js";
-import { useDefaultProps as x } from "./ui-components.es85.js";
-import $ from "./ui-components.es86.js";
-import j from "./ui-components.es111.js";
-import O from "./ui-components.es182.js";
-import { alpha as f } from "./ui-components.es56.js";
-const R = (o) => {
-  const {
-    square: r,
-    elevation: a,
-    variant: n,
-    classes: t
-  } = o, i = {
-    root: ["root", n, !r && "rounded", n === "elevation" && `elevation${a}`]
-  };
-  return $(i, T, t);
-}, E = w("div", {
-  name: "MuiPaper",
-  slot: "Root",
-  overridesResolver: (o, r) => {
-    const {
-      ownerState: a
-    } = o;
-    return [r.root, r[a.variant], !a.square && r.rounded, a.variant === "elevation" && r[`elevation${a.elevation}`]];
-  }
-})(g(({
-  theme: o
-}) => ({
-  backgroundColor: (o.vars || o).palette.background.paper,
-  color: (o.vars || o).palette.text.primary,
-  transition: o.transitions.create("box-shadow"),
-  variants: [{
-    props: ({
-      ownerState: r
-    }) => !r.square,
-    style: {
-      borderRadius: o.shape.borderRadius
-    }
-  }, {
-    props: {
-      variant: "outlined"
+function p(t, i) {
+  const e = [];
+  t = t.replace(/,/g, "");
+  let c, o, r;
+  if (t.includes(":") && t.includes("-"))
+    c = t.split(":")[0], o = parseInt(t.split(":")[1].split("-")[0]) || 0, r = parseInt(t.split(":")[1].split("-")[1]) || o + 1e3;
+  else if (t.includes("	")) {
+    const [h, l, d] = t.split("	");
+    c = h, o = parseInt(l), r = parseInt(d);
+  } else
+    return e;
+  const s = c.replace(/chrx$/, "chrX").replace(/chry$/, "chrY"), a = m[i][c];
+  return r > o && a && r <= a && e.push({
+    title: `${s}:${o.toLocaleString()}-${r.toLocaleString()}`,
+    domain: {
+      chromosome: s,
+      start: o,
+      end: r
+    },
+    description: `${s}:${o.toLocaleString()}-${r.toLocaleString()}`,
+    type: "Coordinate"
+  }), e;
+}
+function n(t, i, e) {
+  return t ? t.slice(0, i).map((c) => ({
+    title: e.getTitle(c),
+    description: e.getDescription(c),
+    domain: {
+      chromosome: c.coordinates.chromosome,
+      start: c.coordinates.start,
+      end: c.coordinates.end
     },
-    style: {
-      border: `1px solid ${(o.vars || o).palette.divider}`
-    }
-  }, {
-    props: {
-      variant: "elevation"
+    type: e.type
+  })) : [];
+}
+function g(t, i) {
+  return n(t, i, {
+    getTitle: (e) => e.id,
+    getDescription: (e) => `${e.coordinates.chromosome}:${e.coordinates.start}-${e.coordinates.end}`,
+    type: "SNP"
+  });
+}
+function $(t, i, e) {
+  return n(t, i, {
+    getTitle: (c) => c.name,
+    getDescription: (c) => {
+      let o = "";
+      return c.versions.forEach((r, s) => o += "V" + r.version + " " + r.id + (s === c.versions.length - 1 ? "" : `
+`)), `${c.description}
+${o}
+${c.coordinates.chromosome}:${c.coordinates.start}-${c.coordinates.end}`;
     },
-    style: {
-      boxShadow: "var(--Paper-shadow)",
-      backgroundImage: "var(--Paper-overlay)"
-    }
-  }]
-}))), N = /* @__PURE__ */ y.forwardRef(function(r, a) {
-  const n = x({
-    props: r,
-    name: "MuiPaper"
-  }), t = P(), {
-    className: i,
-    component: p = "div",
-    elevation: s = 1,
-    square: m = !1,
-    variant: l = "elevation",
-    ...v
-  } = n, d = {
-    ...n,
-    component: p,
-    elevation: s,
-    square: m,
-    variant: l
-  }, u = R(d);
-  return process.env.NODE_ENV !== "production" && t.shadows[s] === void 0 && console.error([`MUI: The elevation provided <Paper elevation={${s}}> is not available in the theme.`, `Please make sure that \`theme.shadows[${s}]\` is defined.`].join(`
-`)), /* @__PURE__ */ b.jsx(E, {
-    as: p,
-    ownerState: d,
-    className: h(u.root, i),
-    ref: a,
-    ...v,
-    style: {
-      ...l === "elevation" && {
-        "--Paper-shadow": (t.vars || t).shadows[s],
-        ...t.vars && {
-          "--Paper-overlay": t.vars.overlays?.[s]
-        },
-        ...!t.vars && t.palette.mode === "dark" && {
-          "--Paper-overlay": `linear-gradient(${f("#fff", c(s))}, ${f("#fff", c(s))})`
-        }
+    type: "Gene"
+  });
+}
+function u(t, i) {
+  return t.slice(0, i).map((e) => ({
+    title: e.disease_trait,
+    description: `${e.author.replace("_", " ")} (${e.studyid.split("-")[1]})
+${e.parent_terms.join(",")}
+ ${e.has_enrichment_info ? "Biosample Enrichment" : ""}`,
+    domain: void 0,
+    id: e.studyid,
+    type: "Study"
+  }));
+}
+function y(t) {
+  return t.map((i) => ({
+    title: i.label,
+    description: i.description ?? "",
+    domain: void 0,
+    id: i.value,
+    type: "Ome"
+  }));
+}
+function v(t, i) {
+  return n(t, i, {
+    getTitle: (e) => e.accession,
+    getDescription: (e) => `${e.coordinates.chromosome}:${e.coordinates.start}-${e.coordinates.end}`,
+    type: "iCRE"
+  });
+}
+function f(t, i) {
+  return n(t, i, {
+    getTitle: (e) => e.accession,
+    getDescription: (e) => `${e.coordinates.chromosome}:${e.coordinates.start}-${e.coordinates.end}${e.isiCRE ? ", iCRE" : ""}`,
+    type: "cCRE"
+  });
+}
+function R(t, i) {
+  return t.filter((e) => e.input !== e.v4_match_or_intersecting).slice(0, i).map((e) => {
+    const c = e.input_region, o = e.v4_match_or_intersecting;
+    return {
+      title: e.input,
+      // !!! Do not change this format without also modifying SCREEN's /search page. This specific formatting is relied upon
+      description: `(Registry ${e.input_latest_previous_version})
+${e.input_region}
+${o ? `Intersects v4 cCRE${o.includes(",") ? "s" : ""}: ${o.replace(",", ", ")}` : "No intersecting v4 cCREs"}`,
+      domain: {
+        chromosome: c.split(":")[0],
+        start: parseInt(c.split(":")[1].split("-")[0]),
+        end: parseInt(c.split(":")[1].split("-")[1])
       },
-      ...v.style
-    }
+      type: "Legacy cCRE"
+    };
   });
-});
-process.env.NODE_ENV !== "production" && (N.propTypes = {
-  // ┌────────────────────────────── Warning ──────────────────────────────┐
-  // │ These PropTypes are generated from the TypeScript type definitions. │
-  // │    To update them, edit the d.ts file and run `pnpm proptypes`.     │
-  // └─────────────────────────────────────────────────────────────────────┘
-  /**
-   * The content of the component.
-   */
-  children: e.node,
-  /**
-   * Override or extend the styles applied to the component.
-   */
-  classes: e.object,
-  /**
-   * @ignore
-   */
-  className: e.string,
-  /**
-   * The component used for the root node.
-   * Either a string to use a HTML element or a component.
-   */
-  component: e.elementType,
-  /**
-   * Shadow depth, corresponds to `dp` in the spec.
-   * It accepts values between 0 and 24 inclusive.
-   * @default 1
-   */
-  elevation: j(O, (o) => {
-    const {
-      elevation: r,
-      variant: a
-    } = o;
-    return r > 0 && a === "outlined" ? new Error(`MUI: Combining \`elevation={${r}}\` with \`variant="${a}"\` has no effect. Either use \`elevation={0}\` or use a different \`variant\`.`) : null;
-  }),
-  /**
-   * If `true`, rounded corners are disabled.
-   * @default false
-   */
-  square: e.bool,
-  /**
-   * @ignore
-   */
-  style: e.object,
-  /**
-   * The system prop that allows defining system overrides as well as additional CSS styles.
-   */
-  sx: e.oneOfType([e.arrayOf(e.oneOfType([e.func, e.object, e.bool])), e.func, e.object]),
-  /**
-   * The variant to use.
-   * @default 'elevation'
-   */
-  variant: e.oneOfType([e.oneOf(["elevation", "outlined"]), e.string])
-});
+}
+const b = [{
+  label: "Proteomics",
+  value: "proteomics",
+  keywords: ["protein", "mass spec"]
+}, {
+  label: "WGS",
+  value: "WGS",
+  keywords: ["whole genome sequencing", "genome sequencing", "genomics"],
+  description: "Whole Genome Sequencing"
+}, {
+  label: "WGBS",
+  value: "WGBS",
+  keywords: ["whole genome bisulfite sequencing", "epigenomics", "methylation"],
+  description: "Whole Genome Bisulfite Sequencing"
+}, {
+  label: "ATAC",
+  value: "ATAC",
+  keywords: ["chromatin accessibility", "atac-seq"],
+  description: "ATAC-seq"
+}, {
+  label: "RNA",
+  value: "RNA",
+  keywords: ["rna-seq", "transcriptomics", "gene expression"],
+  description: "RNA-seq"
+}, {
+  label: "Metabolomics",
+  value: "metabolomics"
+}, {
+  label: "Lipidomics",
+  value: "lipidomics"
+}, {
+  label: "Metallomics",
+  value: "metallomics"
+}, {
+  label: "Exposomics",
+  value: "exposomics"
+}], m = {
+  GRCh38: {
+    chr1: 248956422,
+    chr2: 242193529,
+    chr3: 198295559,
+    chr4: 190214555,
+    chr5: 181538259,
+    chr6: 170805979,
+    chr7: 159345973,
+    chr8: 145138636,
+    chr9: 138394717,
+    chr10: 133797422,
+    chr11: 135086622,
+    chr12: 133275309,
+    chr13: 114364328,
+    chr14: 107043718,
+    chr15: 101991189,
+    chr16: 90338345,
+    chr17: 83257441,
+    chr18: 80373285,
+    chr19: 58617616,
+    chr20: 64444167,
+    chr21: 46709983,
+    chr22: 50818468,
+    chrX: 156040895,
+    chrx: 156040895,
+    chrY: 57227415,
+    chry: 57227415
+  },
+  mm10: {
+    chr1: 195471971,
+    chr2: 182113224,
+    chr3: 160039680,
+    chr4: 156508116,
+    chr5: 151834684,
+    chr6: 149736546,
+    chr7: 145441459,
+    chr8: 129401213,
+    chr9: 124595110,
+    chr10: 130694993,
+    chr11: 122082543,
+    chr12: 120129022,
+    chr13: 120421639,
+    chr14: 124902244,
+    chr15: 104043685,
+    chr16: 98207768,
+    chr17: 94987271,
+    chr18: 90702639,
+    chr19: 61431566,
+    chrX: 171031299,
+    chrx: 171031299,
+    chrY: 91744698,
+    chry: 91744698
+  }
+};
+function C(t) {
+  const i = t.includes("	"), e = t.includes("-"), c = t.length >= 4 && /^[0-9xyXY]$/.test(t[3]);
+  return (i || e) && t.startsWith("chr") && c;
+}
 export {
-  N as default
+  b as OmesList,
+  f as ccreResultList,
+  $ as geneResultList,
+  p as getCoordinates,
+  v as icreResultList,
+  C as isDomain,
+  R as legacyCcreResultList,
+  y as omeResultsList,
+  g as snpResultList,
+  u as studyResultList
 };
 //# sourceMappingURL=ui-components.es55.js.map

package/dist/ui-components.es55.js.map

@@ -1 +1 @@
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+{"version":3,"file":"ui-components.es55.js","sources":["../src/components/GenomeSearch/utils.ts"],"sourcesContent":["import { CCREResponse, GeneResponse, ICREResponse, LegacyCcreResponse, Result, ResultType, SnpResponse, StudyResponse } from \"./types\";\n\n/**\n * Get the coordinates from a string input.\n * @param input - The input string to search for coordinates\n * @param assembly - The assembly to search for coordinates\n * @returns An array of results with the coordinates\n */\nexport function getCoordinates(input: string, assembly: string): Result[] {\n  const results: Result[] = [];\n  input = input.replace(/,/g, \"\");\n\n  let chromosome: string, start: number, end: number;\n\n  if (input.includes(\":\") && input.includes(\"-\")) {\n    chromosome = input.split(\":\")[0];\n    start = parseInt(input.split(\":\")[1].split(\"-\")[0]) || 0;\n    end = parseInt(input.split(\":\")[1].split(\"-\")[1]) || start + 1000;\n  } else if (input.includes(\"\\t\")) {\n    const [chr, startStr, endStr] = input.split(\"\\t\");\n    chromosome = chr;\n    start = parseInt(startStr);\n    end = parseInt(endStr);\n  } else {\n    return results;\n  }\n\n  // Normalize chromosome name to use capital X and Y\n  const normalizedChromosome = chromosome.replace(/chrx$/, \"chrX\").replace(/chry$/, \"chrY\");\n\n  const chrLength = chromosomeLengths[assembly][chromosome];\n  if (end > start && chrLength && end <= chrLength) {\n    results.push({\n      title: `${normalizedChromosome}:${start.toLocaleString()}-${end.toLocaleString()}`,\n      domain: {\n        chromosome: normalizedChromosome,\n        start: start,\n        end: end,\n      },\n      description: `${normalizedChromosome}:${start.toLocaleString()}-${end.toLocaleString()}`,\n      type: \"Coordinate\",\n    });\n  }\n\n  return results;\n}\n\n// Common interface for result formatting options\ninterface ResultFormatterOptions<T> {\n  getTitle: (result: T) => string;\n  getDescription: (result: T) => string;\n  type: string;\n}\n\n// Generic formatter function\nfunction formatResults<T extends { coordinates: { chromosome: string; start: number; end: number } }>(\n  results: T[] | null,\n  limit: number,\n  options: ResultFormatterOptions<T>\n): Result[] {\n  if (!results) {\n    return [];\n  }\n  return results.slice(0, limit).map((result) => ({\n    title: options.getTitle(result),\n    description: options.getDescription(result),\n    domain: {\n      chromosome: result.coordinates.chromosome,\n      start: result.coordinates.start,\n      end: result.coordinates.end,\n    },\n    type: options.type as ResultType,\n  }));\n}\n\n// Specific formatters using the generic function\nexport function snpResultList(results: SnpResponse[], limit: number): Result[] {\n  return formatResults(results, limit, {\n    getTitle: (result) => result.id,\n    getDescription: (result) =>\n      `${result.coordinates.chromosome}:${result.coordinates.start}-${result.coordinates.end}`,\n    type: \"SNP\",\n  });\n}\n\nexport function geneResultList(results: GeneResponse[], limit: number, showVersions: boolean): Result[] {\n  return formatResults(results, limit, {\n    getTitle: (result) => result.name,\n    getDescription: (result) => {\n      let idStr = \"\";\n      result.versions.forEach(\n        (x, i) => (idStr += \"V\" + x.version + \" \" + x.id + (i === result.versions.length - 1 ? \"\" : \"\\n\"))\n      );\n      return `${result.description}\\n${idStr}\\n${result.coordinates.chromosome}:${result.coordinates.start}-${result.coordinates.end}`;\n    },\n    type: \"Gene\",\n  });\n}\n\nexport function studyResultList(results: StudyResponse[], limit: number): Result[] {\n  return results.slice(0, limit).map((result) => ({\n    title: result.disease_trait,\n    description: `${result.author.replace(\"_\", \" \")} (${result.studyid.split(\"-\")[1]})\\n${result.parent_terms.join(\",\")}\\n ${result.has_enrichment_info ? \"Biosample Enrichment\" : \"\"}`,\n    domain: undefined,\n    id: result.studyid,\n    type: \"Study\",\n  }));\n}\n\nexport function omeResultsList(results: OmeOption[]): Result[] {\n  return results.map((ome) => ({\n    title: ome.label,\n    description: ome.description ?? \"\",\n    domain: undefined,\n    id: ome.value,\n    type: \"Ome\",\n  }));\n}\n\nexport function icreResultList(results: ICREResponse[], limit: number): Result[] {\n  return formatResults(results, limit, {\n    getTitle: (result) => result.accession,\n    getDescription: (result) =>\n      `${result.coordinates.chromosome}:${result.coordinates.start}-${result.coordinates.end}`,\n    type: \"iCRE\",\n  });\n}\n\nexport function ccreResultList(results: CCREResponse[], limit: number): Result[] {\n  return formatResults(results, limit, {\n    getTitle: (result) => result.accession,\n    getDescription: (result) =>\n      `${result.coordinates.chromosome}:${result.coordinates.start}-${\n        result.coordinates.end\n      }${result.isiCRE ? \", iCRE\" : \"\"}`,\n    type: \"cCRE\",\n  });\n}\n\nexport function legacyCcreResultList(results: LegacyCcreResponse[], limit: number): Result[] {\n  return results\n    .filter((result) => result.input !== result.v4_match_or_intersecting) //filter v4 cCREs\n    .slice(0, limit)\n    .map((result) => {\n      const region = result.input_region;\n      const overlapping = result.v4_match_or_intersecting\n      return {\n        title: result.input,\n        // !!! Do not change this format without also modifying SCREEN's /search page. This specific formatting is relied upon\n        description: `(Registry ${result.input_latest_previous_version})\\n${result.input_region}\\n${overlapping ? `Intersects v4 cCRE${overlapping.includes(\",\") ? \"s\" : \"\"}: ${overlapping.replace(\",\", \", \")}` : \"No intersecting v4 cCREs\"}`,\n        domain: {\n          chromosome: region.split(\":\")[0],\n          start: parseInt(region.split(\":\")[1].split(\"-\")[0]),\n          end: parseInt(region.split(\":\")[1].split(\"-\")[1]),\n        },\n        type: \"Legacy cCRE\",\n      };\n    });\n}\n\nexport interface OmeOption {\n  label: string;\n  value: string;\n  keywords?: string[];\n  description?: string;\n}\n//allows the user to search more freely and get the result they are looking for\n//will look at label as well as keywords\nexport const OmesList: OmeOption[] = [\n  {\n    label: \"Proteomics\",\n    value: \"proteomics\",\n    keywords: [\"protein\", \"mass spec\"],\n  },\n  {\n    label: \"WGS\",\n    value: \"WGS\",\n    keywords: [\"whole genome sequencing\", \"genome sequencing\", \"genomics\"],\n    description: \"Whole Genome Sequencing\"\n  },\n  {\n    label: \"WGBS\",\n    value: \"WGBS\",\n    keywords: [\"whole genome bisulfite sequencing\", \"epigenomics\", \"methylation\"],\n    description: \"Whole Genome Bisulfite Sequencing\"\n  },\n  {\n    label: \"ATAC\",\n    value: \"ATAC\",\n    keywords: [\"chromatin accessibility\", \"atac-seq\"],\n    description: \"ATAC-seq\"\n  },\n  {\n    label: \"RNA\",\n    value: \"RNA\",\n    keywords: [\"rna-seq\", \"transcriptomics\", \"gene expression\"],\n    description: \"RNA-seq\"\n  },\n  {\n    label: \"Metabolomics\",\n    value: \"metabolomics\",\n  },\n  {\n    label: \"Lipidomics\",\n    value: \"lipidomics\",\n  },\n  {\n    label: \"Metallomics\",\n    value: \"metallomics\",\n  },\n  {\n    label: \"Exposomics\",\n    value: \"exposomics\",\n  },\n];\n\n// Object to store chromosome lengths for GRCh38 and mm10\nconst chromosomeLengths: { [key: string]: { [key: string]: number } } = {\n  GRCh38: {\n    chr1: 248956422,\n    chr2: 242193529,\n    chr3: 198295559,\n    chr4: 190214555,\n    chr5: 181538259,\n    chr6: 170805979,\n    chr7: 159345973,\n    chr8: 145138636,\n    chr9: 138394717,\n    chr10: 133797422,\n    chr11: 135086622,\n    chr12: 133275309,\n    chr13: 114364328,\n    chr14: 107043718,\n    chr15: 101991189,\n    chr16: 90338345,\n    chr17: 83257441,\n    chr18: 80373285,\n    chr19: 58617616,\n    chr20: 64444167,\n    chr21: 46709983,\n    chr22: 50818468,\n    chrX: 156040895,\n    chrx: 156040895,\n    chrY: 57227415,\n    chry: 57227415,\n  },\n  mm10: {\n    chr1: 195471971,\n    chr2: 182113224,\n    chr3: 160039680,\n    chr4: 156508116,\n    chr5: 151834684,\n    chr6: 149736546,\n    chr7: 145441459,\n    chr8: 129401213,\n    chr9: 124595110,\n    chr10: 130694993,\n    chr11: 122082543,\n    chr12: 120129022,\n    chr13: 120421639,\n    chr14: 124902244,\n    chr15: 104043685,\n    chr16: 98207768,\n    chr17: 94987271,\n    chr18: 90702639,\n    chr19: 61431566,\n    chrX: 171031299,\n    chrx: 171031299,\n    chrY: 91744698,\n    chry: 91744698,\n  },\n};\n\nexport function isDomain(input: string) {\n  const hasTabs = input.includes(\"\\t\");\n  const hasHyphens = input.includes(\"-\");\n  const hasChromosomeNumber = input.length >= 4 && /^[0-9xyXY]$/.test(input[3]);\n  return (hasTabs || hasHyphens) && input.startsWith(\"chr\") && 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