@weng-lab/ui-components 2.2.0 → 2.2.1

package/dist/ui-components.es57.js.map

@@ -1 +1 @@
-{"version":3,"file":"ui-components.es57.js","sources":["../src/components/BiosampleTable/AggregateDownload.tsx"],"sourcesContent":["import {\n  Button,\n  Tooltip,\n  Box,\n  Checkbox,\n  Dialog,\n  DialogActions,\n  DialogContent,\n  DialogTitle,\n  FormControlLabel,\n  Stack,\n  Typography,\n  Divider,\n  IconButton,\n} from \"@mui/material\";\nimport { useCallback, useMemo, useState } from \"react\";\nimport { Download } from \"@mui/icons-material\";\nimport { ontologyDownloadMap } from \"./ontologyDownloads\";\nimport { fetchFileSize, formatFileSize } from \"./helpers\";\nimport { useDownloadContext } from \"./DownloadContext\";\n\nexport type AggregateDownloadProps = {\n  ontology: string;\n};\n\n/**\n *\n * @param ontology\n * Finds available aggregate file urls for the given ontology in the form `[noccl, ccl]`\n */\n\nexport const getAvailableFiles = (ontology: string) => {\n  const key = ontology.toLowerCase().replace(/\\s+/g, \"_\");\n  return ontologyDownloadMap[key] ?? [];\n};\n\nexport const AggregateDownloadButton = ({ ontology }: AggregateDownloadProps) => {\n  const [isDialogOpen, setIsDialogOpen] = useState(false);\n  const [noccl, setNoccl] = useState(false);\n  const [all, setAll] = useState(false);\n  const [nocclFileSize, setNocclFileSize] = useState<number | null>(null);\n  const [allFileSize, setAllFileSize] = useState<number | null>(null);\n  const { onDownload } = useDownloadContext();\n\n  const availibleDownloads = getAvailableFiles(ontology);\n\n  const ncFile = availibleDownloads.find((d) => d.label === \"Excluding Cancer Cell Lines\")?.filename ?? undefined;\n  const allFile = availibleDownloads.find((d) => d.label === \"All Biosamples\")?.filename ?? undefined;\n\n  const handleOpenDialog = () => {\n    if (ncFile && !nocclFileSize) fetchFileSize(`https://downloads.wenglab.org/${ncFile}`, setNocclFileSize);\n    if (allFile && !allFileSize) fetchFileSize(`https://downloads.wenglab.org/${allFile}`, setAllFileSize);\n    setIsDialogOpen(true);\n  };\n\n  const handleDownload = useCallback(() => {\n    if (!availibleDownloads || availibleDownloads.length === 0) return;\n\n    const filesToDownload: { filename: string; label: string }[] = [];\n    if (noccl && ncFile) filesToDownload.push({ filename: ncFile, label: \"excluding_cancer_cell_lines\" });\n    if (all && allFile) filesToDownload.push({ filename: allFile, label: \"all_biosamples\" });\n\n    filesToDownload.forEach(({ filename, label }, index) => {\n      const url = `https://downloads.wenglab.org/${filename}`;\n\n      setTimeout(() => {\n        if (onDownload) {\n          // Use descriptive name: ontology_aggregate_ccres_label\n          const name = `${ontology}_aggregate_ccres_${label}`;\n          onDownload(url, name);\n        }\n\n        const link = document.createElement(\"a\");\n        link.href = url;\n        link.download = filename;\n\n        document.body.appendChild(link);\n        link.click();\n        document.body.removeChild(link);\n      }, index * 500); // 500ms delay between downloads (some browsers prevent against mutliple downloads at once)\n    });\n  }, [all, allFile, availibleDownloads, ncFile, noccl, onDownload, ontology]);\n\n  return (\n    <>\n      <Tooltip\n        title={\n          availibleDownloads.length === 0 ? (\n            \"No Aggregate cCRE Download Options\"\n          ) : (\n            <Box>\n              Download cCREs in {ontology.charAt(0).toUpperCase() + ontology.slice(1)}:\n              <ul style={{ margin: 0, paddingLeft: 16 }}>\n                {availibleDownloads.map((d) => (\n                  <li key={d.filename}>{d.label}</li>\n                ))}\n              </ul>\n              (Opens Download Dialog)\n            </Box>\n          )\n        }\n        placement=\"left\"\n        arrow\n      >\n        <span>\n          <IconButton\n            onClick={(e) => {\n              e.stopPropagation();\n              handleOpenDialog();\n            }}\n            disabled={availibleDownloads.length === 0}\n          >\n            <Download />\n          </IconButton>\n        </span>\n      </Tooltip>\n      <Dialog\n        open={isDialogOpen}\n        onClose={(event) => {\n          (event as React.MouseEvent).stopPropagation();\n          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)} disabled={!ncFile} />}\n              label={`Aggregate cCREs (excluding cancer cell lines)${nocclFileSize ? \" - \" + formatFileSize(nocclFileSize) : \"\"}`}\n            />\n            {availibleDownloads.length <= 1 && (\n              <>\n                <Divider sx={{ marginTop: 1 }} />\n                <Typography marginTop={1}>\n                  <strong>No cancerous cell lines available in this tissue</strong>\n                </Typography>\n              </>\n            )}\n          </Stack>\n        </DialogContent>\n        <DialogActions>\n          <Button\n            onClick={() => {\n              setIsDialogOpen(false);\n            }}\n          >\n            Cancel\n          </Button>\n          <Button\n            variant=\"contained\"\n            onClick={() => {\n              handleDownload();\n              setIsDialogOpen(false);\n            }}\n          >\n            Download\n          </Button>\n        </DialogActions>\n      </Dialog>\n    </>\n  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+{"version":3,"file":"ui-components.es57.js","sources":["../../../node_modules/.pnpm/@mui+material@7.3.9_@emotion+react@11.14.0_@types+react@19.2.14_react@19.2.4__@emotion+_5efc65b7a21bb615fd4ee8d4bf58b896/node_modules/@mui/material/esm/TextField/TextField.js"],"sourcesContent":["'use client';\n\nimport * as React from 'react';\nimport PropTypes from 'prop-types';\nimport clsx from 'clsx';\nimport composeClasses from '@mui/utils/composeClasses';\nimport useId from '@mui/utils/useId';\nimport refType from '@mui/utils/refType';\nimport { styled } from \"../zero-styled/index.js\";\nimport { useDefaultProps } from \"../DefaultPropsProvider/index.js\";\nimport Input from \"../Input/index.js\";\nimport FilledInput from \"../FilledInput/index.js\";\nimport OutlinedInput from \"../OutlinedInput/index.js\";\nimport InputLabel from \"../InputLabel/index.js\";\nimport FormControl from \"../FormControl/index.js\";\nimport FormHelperText from \"../FormHelperText/index.js\";\nimport Select from \"../Select/index.js\";\nimport { getTextFieldUtilityClass } from \"./textFieldClasses.js\";\nimport useSlot from \"../utils/useSlot.js\";\nimport { jsx as _jsx, jsxs as _jsxs } from \"react/jsx-runtime\";\nconst variantComponent = {\n  standard: Input,\n  filled: FilledInput,\n  outlined: OutlinedInput\n};\nconst useUtilityClasses = ownerState => {\n  const {\n    classes\n  } = ownerState;\n  const slots = {\n    root: ['root']\n  };\n  return composeClasses(slots, getTextFieldUtilityClass, classes);\n};\nconst TextFieldRoot = styled(FormControl, {\n  name: 'MuiTextField',\n  slot: 'Root'\n})({});\n\n/**\n * The `TextField` is a convenience wrapper for the most common cases (80%).\n * It cannot be all things to all people, otherwise the API would grow out of control.\n *\n * ## Advanced Configuration\n *\n * It's important to understand that the text field is a simple abstraction\n * on top of the following components:\n *\n * - [FormControl](/material-ui/api/form-control/)\n * - [InputLabel](/material-ui/api/input-label/)\n * - [FilledInput](/material-ui/api/filled-input/)\n * - [OutlinedInput](/material-ui/api/outlined-input/)\n * - [Input](/material-ui/api/input/)\n * - [FormHelperText](/material-ui/api/form-helper-text/)\n *\n * If you wish to alter the props applied to the `input` element, you can do so as follows:\n *\n * ```jsx\n * const inputProps = {\n *   step: 300,\n * };\n *\n * return <TextField id=\"time\" type=\"time\" inputProps={inputProps} />;\n * ```\n *\n * For advanced cases, please look at the source of TextField by clicking on the\n * \"Edit this page\" button above. Consider either:\n *\n * - using the upper case props for passing values directly to the components\n * - using the underlying components directly as shown in the demos\n */\nconst TextField = /*#__PURE__*/React.forwardRef(function TextField(inProps, ref) {\n  const props = useDefaultProps({\n    props: inProps,\n    name: 'MuiTextField'\n  });\n  const {\n    autoComplete,\n    autoFocus = false,\n    children,\n    className,\n    color = 'primary',\n    defaultValue,\n    disabled = false,\n    error = false,\n    FormHelperTextProps: FormHelperTextPropsProp,\n    fullWidth = false,\n    helperText,\n    id: idOverride,\n    InputLabelProps: InputLabelPropsProp,\n    inputProps: inputPropsProp,\n    InputProps: InputPropsProp,\n    inputRef,\n    label,\n    maxRows,\n    minRows,\n    multiline = false,\n    name,\n    onBlur,\n    onChange,\n    onFocus,\n    placeholder,\n    required = false,\n    rows,\n    select = false,\n    SelectProps: SelectPropsProp,\n    slots = {},\n    slotProps = {},\n    type,\n    value,\n    variant = 'outlined',\n    ...other\n  } = props;\n  const ownerState = {\n    ...props,\n    autoFocus,\n    color,\n    disabled,\n    error,\n    fullWidth,\n    multiline,\n    required,\n    select,\n    variant\n  };\n  const classes = useUtilityClasses(ownerState);\n  if (process.env.NODE_ENV !== 'production') {\n    if (select && !children) {\n      console.error('MUI: `children` must be passed when using the `TextField` component with `select`.');\n    }\n  }\n  const id = useId(idOverride);\n  const helperTextId = helperText && id ? `${id}-helper-text` : undefined;\n  const inputLabelId = label && id ? `${id}-label` : undefined;\n  const InputComponent = variantComponent[variant];\n  const externalForwardedProps = {\n    slots,\n    slotProps: {\n      input: InputPropsProp,\n      inputLabel: InputLabelPropsProp,\n      htmlInput: inputPropsProp,\n      formHelperText: FormHelperTextPropsProp,\n      select: SelectPropsProp,\n      ...slotProps\n    }\n  };\n  const inputAdditionalProps = {};\n  const inputLabelSlotProps = externalForwardedProps.slotProps.inputLabel;\n  if (variant === 'outlined') {\n    if (inputLabelSlotProps && typeof inputLabelSlotProps.shrink !== 'undefined') {\n      inputAdditionalProps.notched = inputLabelSlotProps.shrink;\n    }\n    inputAdditionalProps.label = label;\n  }\n  if (select) {\n    // unset defaults from textbox inputs\n    if (!SelectPropsProp || !SelectPropsProp.native) {\n      inputAdditionalProps.id = undefined;\n    }\n    inputAdditionalProps['aria-describedby'] = undefined;\n  }\n  const [RootSlot, rootProps] = useSlot('root', {\n    elementType: TextFieldRoot,\n    shouldForwardComponentProp: true,\n    externalForwardedProps: {\n      ...externalForwardedProps,\n      ...other\n    },\n    ownerState,\n    className: clsx(classes.root, className),\n    ref,\n    additionalProps: {\n      disabled,\n      error,\n      fullWidth,\n      required,\n      color,\n      variant\n    }\n  });\n  const [InputSlot, inputProps] = useSlot('input', {\n    elementType: InputComponent,\n    externalForwardedProps,\n    additionalProps: inputAdditionalProps,\n    ownerState\n  });\n  const [InputLabelSlot, inputLabelProps] = useSlot('inputLabel', {\n    elementType: InputLabel,\n    externalForwardedProps,\n    ownerState\n  });\n  const [HtmlInputSlot, htmlInputProps] = useSlot('htmlInput', {\n    elementType: 'input',\n    externalForwardedProps,\n    ownerState\n  });\n  const [FormHelperTextSlot, formHelperTextProps] = useSlot('formHelperText', {\n    elementType: FormHelperText,\n    externalForwardedProps,\n    ownerState\n  });\n  const [SelectSlot, selectProps] = useSlot('select', {\n    elementType: Select,\n    externalForwardedProps,\n    ownerState\n  });\n  const InputElement = /*#__PURE__*/_jsx(InputSlot, {\n    \"aria-describedby\": helperTextId,\n    autoComplete: autoComplete,\n    autoFocus: autoFocus,\n    defaultValue: defaultValue,\n    fullWidth: fullWidth,\n    multiline: multiline,\n    name: name,\n    rows: rows,\n    maxRows: maxRows,\n    minRows: minRows,\n    type: type,\n    value: value,\n    id: id,\n    inputRef: inputRef,\n    onBlur: onBlur,\n    onChange: onChange,\n    onFocus: onFocus,\n    placeholder: placeholder,\n    inputProps: htmlInputProps,\n    slots: {\n      input: slots.htmlInput ? HtmlInputSlot : undefined\n    },\n    ...inputProps\n  });\n  return /*#__PURE__*/_jsxs(RootSlot, {\n    ...rootProps,\n    children: [label != null && label !== '' && /*#__PURE__*/_jsx(InputLabelSlot, {\n      htmlFor: id,\n      id: inputLabelId,\n      ...inputLabelProps,\n      children: label\n    }), select ? /*#__PURE__*/_jsx(SelectSlot, {\n      \"aria-describedby\": helperTextId,\n      id: id,\n      labelId: inputLabelId,\n      value: value,\n      input: InputElement,\n      ...selectProps,\n      children: children\n    }) : InputElement, helperText && /*#__PURE__*/_jsx(FormHelperTextSlot, {\n      id: helperTextId,\n      ...formHelperTextProps,\n      children: helperText\n    })]\n  });\n});\nprocess.env.NODE_ENV !== \"production\" ? TextField.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   * This prop helps users to fill forms faster, especially on mobile devices.\n   * The name can be confusing, as it's more like an autofill.\n   * You can learn more about it [following the specification](https://html.spec.whatwg.org/multipage/form-control-infrastructure.html#autofill).\n   */\n  autoComplete: PropTypes.string,\n  /**\n   * If `true`, the `input` element is focused during the first mount.\n   * @default false\n   */\n  autoFocus: PropTypes.bool,\n  /**\n   * @ignore\n   */\n  children: PropTypes.node,\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   * The color of the component.\n   * It supports both default and custom theme colors, which can be added as shown in the\n   * [palette customization guide](https://mui.com/material-ui/customization/palette/#custom-colors).\n   * @default 'primary'\n   */\n  color: PropTypes /* @typescript-to-proptypes-ignore */.oneOfType([PropTypes.oneOf(['primary', 'secondary', 'error', 'info', 'success', 'warning']), PropTypes.string]),\n  /**\n   * The default value. Use when the component is not controlled.\n   */\n  defaultValue: PropTypes.any,\n  /**\n   * If `true`, the component is disabled.\n   * @default false\n   */\n  disabled: PropTypes.bool,\n  /**\n   * If `true`, the label is displayed in an error state.\n   * @default false\n   */\n  error: PropTypes.bool,\n  /**\n   * Props applied to the [`FormHelperText`](https://mui.com/material-ui/api/form-helper-text/) element.\n   * @deprecated Use `slotProps.formHelperText` 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  FormHelperTextProps: PropTypes.object,\n  /**\n   * If `true`, the input will take up the full width of its container.\n   * @default false\n   */\n  fullWidth: PropTypes.bool,\n  /**\n   * The helper text content.\n   */\n  helperText: PropTypes.node,\n  /**\n   * The id of the `input` element.\n   * Use this prop to make `label` and `helperText` accessible for screen readers.\n   */\n  id: PropTypes.string,\n  /**\n   * Props applied to the [`InputLabel`](https://mui.com/material-ui/api/input-label/) element.\n   * Pointer events like `onClick` are enabled if and only if `shrink` is `true`.\n   * @deprecated Use `slotProps.inputLabel` 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  InputLabelProps: PropTypes.object,\n  /**\n   * [Attributes](https://developer.mozilla.org/en-US/docs/Web/HTML/Reference/Elements/input#attributes) applied to the `input` element.\n   * @deprecated Use `slotProps.htmlInput` 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  inputProps: PropTypes.object,\n  /**\n   * Props applied to the Input element.\n   * It will be a [`FilledInput`](https://mui.com/material-ui/api/filled-input/),\n   * [`OutlinedInput`](https://mui.com/material-ui/api/outlined-input/) or [`Input`](https://mui.com/material-ui/api/input/)\n   * component depending on the `variant` prop value.\n   * @deprecated Use `slotProps.input` 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  InputProps: PropTypes.object,\n  /**\n   * Pass a ref to the `input` element.\n   */\n  inputRef: refType,\n  /**\n   * The label content.\n   */\n  label: PropTypes.node,\n  /**\n   * If `dense` or `normal`, will adjust vertical spacing of this and contained components.\n   * @default 'none'\n   */\n  margin: PropTypes.oneOf(['dense', 'none', 'normal']),\n  /**\n   * Maximum number of rows to display when multiline option is set to true.\n   */\n  maxRows: PropTypes.oneOfType([PropTypes.number, PropTypes.string]),\n  /**\n   * Minimum number of rows to display when multiline option is set to true.\n   */\n  minRows: PropTypes.oneOfType([PropTypes.number, PropTypes.string]),\n  /**\n   * If `true`, a `textarea` element is rendered instead of an input.\n   * @default false\n   */\n  multiline: PropTypes.bool,\n  /**\n   * Name attribute of the `input` element.\n   */\n  name: PropTypes.string,\n  /**\n   * @ignore\n   */\n  onBlur: PropTypes.func,\n  /**\n   * Callback fired when the value is changed.\n   *\n   * @param {object} event The event source of the callback.\n   * You can pull out the new value by accessing `event.target.value` (string).\n   */\n  onChange: PropTypes.func,\n  /**\n   * @ignore\n   */\n  onFocus: PropTypes.func,\n  /**\n   * The short hint displayed in the `input` before the user enters a value.\n   */\n  placeholder: PropTypes.string,\n  /**\n   * If `true`, the label is displayed as required and the `input` element is required.\n   * @default false\n   */\n  required: PropTypes.bool,\n  /**\n   * Number of rows to display when multiline option is set to true.\n   */\n  rows: PropTypes.oneOfType([PropTypes.number, PropTypes.string]),\n  /**\n   * Render a [`Select`](https://mui.com/material-ui/api/select/) element while passing the Input element to `Select` as `input` parameter.\n   * If this option is set you must pass the options of the select as children.\n   * @default false\n   */\n  select: PropTypes.bool,\n  /**\n   * Props applied to the [`Select`](https://mui.com/material-ui/api/select/) element.\n   * @deprecated Use `slotProps.select` 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  SelectProps: PropTypes.object,\n  /**\n   * The size of the component.\n   * @default 'medium'\n   */\n  size: PropTypes /* @typescript-to-proptypes-ignore */.oneOfType([PropTypes.oneOf(['medium', 'small']), PropTypes.string]),\n  /**\n   * The props used for each slot inside.\n   * @default {}\n   */\n  slotProps: PropTypes /* @typescript-to-proptypes-ignore */.shape({\n    formHelperText: PropTypes.oneOfType([PropTypes.func, PropTypes.object]),\n    htmlInput: PropTypes.oneOfType([PropTypes.func, PropTypes.object]),\n    input: PropTypes.oneOfType([PropTypes.func, PropTypes.object]),\n    inputLabel: PropTypes.oneOfType([PropTypes.func, PropTypes.object]),\n    select: PropTypes.oneOfType([PropTypes.func, PropTypes.object])\n  }),\n  /**\n   * The components used for each slot inside.\n   * @default {}\n   */\n  slots: PropTypes.shape({\n    formHelperText: PropTypes.elementType,\n    htmlInput: PropTypes.elementType,\n    input: PropTypes.elementType,\n    inputLabel: PropTypes.elementType,\n    root: PropTypes.elementType,\n    select: PropTypes.elementType\n  }),\n  /**\n   * The system prop that allows defining system overrides as well as additional CSS styles.\n   */\n  sx: PropTypes.oneOfType([PropTypes.arrayOf(PropTypes.oneOfType([PropTypes.func, PropTypes.object, PropTypes.bool])), PropTypes.func, PropTypes.object]),\n  /**\n   * Type of the `input` element. It should be [a valid HTML5 input type](https://developer.mozilla.org/en-US/docs/Web/HTML/Reference/Elements/input#input_types).\n   */\n  type: PropTypes.string,\n  /**\n   * The value of the `input` element, required for a controlled component.\n   */\n  value: PropTypes.any,\n  /**\n   * The variant to use.\n   * @default 'outlined'\n   */\n  variant: PropTypes.oneOf(['filled', 'outlined', 'standard'])\n} : void 0;\nexport default 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package/dist/ui-components.es58.js

@@ -1,73 +1,215 @@
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-import G from "./ui-components.es18.js";
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-    onClose: l,
-    onDownloadSVG: b,
-    onDownloadPNG: u,
-    plotTitle: j
-  } = o;
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-    label: "PNG",
-    action: u
-  }, e[0] = u, e[1] = n) : n = e[1];
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-    label: "SVG",
-    action: b
-  }, e[2] = b, e[3] = r) : r = e[3];
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-    transform: "translate(-50%, -50%)",
-    bgcolor: "background.paper",
-    boxShadow: 24,
-    borderRadius: 2,
-    p: 3,
-    width: 360
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-  e[8] !== j ? (i = /* @__PURE__ */ t.jsxs(y, { variant: "h6", fontWeight: 600, mb: 1, children: [
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-    j
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-  return e[20] !== l || e[21] !== h || e[22] !== c ? (x = /* @__PURE__ */ t.jsx(k, { open: h, onClose: l, children: c }), e[20] = l, e[21] = h, e[22] = c, e[23] = x) : x = e[23], x;
-};
-function I(o) {
-  return o.action;
+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
+    },
+    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}`;
+    },
+    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 B(o) {
-  return /* @__PURE__ */ t.jsxs(D, { direction: "row", alignItems: "center", justifyContent: "space-between", children: [
-    /* @__PURE__ */ t.jsx(y, { variant: "body1", children: o.label }),
-    /* @__PURE__ */ t.jsx(C, { color: "primary", onClick: o.action, "aria-label": `Download ${o.label}`, children: /* @__PURE__ */ t.jsx(G, {}) })
-  ] }, o.label);
+function y(t) {
+  return t.map((i) => ({
+    title: i.label,
+    description: i.description ?? "",
+    domain: void 0,
+    id: i.value,
+    type: "Ome"
+  }));
+}
+function v(t, i) {
+  return n(t, i, {
+    getTitle: (e) => e.accession,
+    getDescription: (e) => `${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])
+      },
+      type: "Legacy cCRE"
+    };
+  });
+}
+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 {
-  P 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.es58.js.map

package/dist/ui-components.es58.js.map

@@ -1 +1 @@
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+{"version":3,"file":"ui-components.es58.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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