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Fran McDadeFran McDade
Fran McDade
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Fran McDade
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feat: request access via duos in addition to dbgap (#4127)
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‎app/apis/azul/anvil-cmg/common/entities.ts‎

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@@ -47,6 +47,7 @@ export interface DatasetEntity {
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consent_group: (string | null)[];
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dataset_id: string;
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description?: string;
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duos_id: string | null;
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registered_identifier: (string | null)[];
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title: string;
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}

‎app/components/Detail/components/AnVILCMG/components/RequestAccess/constants.ts‎

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import {
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ButtonProps,
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ListItemTextProps,
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MenuProps,
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SvgIconProps,
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} from "@mui/material";
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import {
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TEXT_BODY_500,
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TEXT_BODY_SMALL_400_2_LINES,
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} from "@databiosphere/findable-ui/lib/theme/common/typography";
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export const BUTTON_PROPS: ButtonProps = {
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color: "primary",
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variant: "contained",
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};
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export const LIST_ITEM_TEXT_PROPS: ListItemTextProps = {
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primaryTypographyProps: { variant: TEXT_BODY_500 },
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secondaryTypographyProps: { variant: TEXT_BODY_SMALL_400_2_LINES },
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};
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export const MENU_PROPS: Partial<MenuProps> = {
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variant: "menu",
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};
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export const SVG_ICON_PROPS: SvgIconProps = {
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fontSize: "small",
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};

‎app/components/Detail/components/AnVILCMG/components/RequestAccess/requestAccess.styles.ts‎

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import { Button } from "@mui/material";
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import styled from "@emotion/styled";
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import { css } from "@emotion/react";
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import { primaryDark } from "@databiosphere/findable-ui/lib/styles/common/mixins/colors";
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import { DropdownMenu } from "@databiosphere/findable-ui/lib/components/common/DropdownMenu/dropdownMenu";
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interface Props {
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open?: boolean;
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}
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export const StyledDropdownMenu = styled(DropdownMenu)`
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.MuiPaper-menu {
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max-width: 324px;
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.MuiListItemText-root {
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display: grid;
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gap: 4px;
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white-space: normal;
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}
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}
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`;
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export const StyledButton = styled(Button, {
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shouldForwardProp: (prop) => prop !== "open",
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})<Props>`
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padding-right: 8px;
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.MuiButton-endIcon {
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margin-left: -6px;
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}
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${(props) =>
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props.open &&
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css`
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background-color: ${primaryDark(props)};
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`}
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`;

‎app/components/Detail/components/AnVILCMG/components/RequestAccess/requestAccess.tsx‎

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import { Props } from "./types";
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import { ListItemText, MenuItem } from "@mui/material";
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import { Actions } from "@databiosphere/findable-ui/lib/components/Layout/components/BackPage/components/BackPageHero/components/Actions/actions";
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import { CallToActionButton } from "@databiosphere/findable-ui/lib/components/common/Button/components/CallToActionButton/callToActionButton";
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import ArrowDropDownRoundedIcon from "@mui/icons-material/ArrowDropDownRounded";
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import { StyledButton, StyledDropdownMenu } from "./requestAccess.styles";
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import {
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ANCHOR_TARGET,
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REL_ATTRIBUTE,
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} from "@databiosphere/findable-ui/lib/components/Links/common/entities";
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import {
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BUTTON_PROPS,
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LIST_ITEM_TEXT_PROPS,
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MENU_PROPS,
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SVG_ICON_PROPS,
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} from "./constants";
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import { getRequestAccessOptions } from "./utils";
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export const RequestAccess = ({
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datasetsResponse,
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}: Props): JSX.Element | null => {
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const options = getRequestAccessOptions(datasetsResponse);
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// If there are no request access options, return null.
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if (options.length === 0) return null;
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// If there is only one request access option, render a CallToActionButton.
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if (options.length === 1)
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return (
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<Actions>
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<CallToActionButton
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callToAction={{ label: "Request Access", url: options[0].href }}
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/>
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</Actions>
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);
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// Otherwise, render a dropdown menu for multiple request access options.
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return (
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<Actions>
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<StyledDropdownMenu
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{...MENU_PROPS}
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button={(props) => (
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<StyledButton
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{...BUTTON_PROPS}
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endIcon={<ArrowDropDownRoundedIcon {...SVG_ICON_PROPS} />}
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{...props}
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>
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Request Access
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</StyledButton>
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)}
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>
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{({ closeMenu }): JSX.Element[] => [
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...options.map(({ href, primary, secondary }, i) => (
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<MenuItem
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key={i}
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component="a"
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href={href}
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rel={REL_ATTRIBUTE.NO_OPENER_NO_REFERRER}
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target={ANCHOR_TARGET.BLANK}
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onClick={closeMenu}
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>
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<ListItemText
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{...LIST_ITEM_TEXT_PROPS}
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primary={primary}
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secondary={secondary}
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/>
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</MenuItem>
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)),
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]}
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</StyledDropdownMenu>
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</Actions>
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);
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};

‎app/components/Detail/components/AnVILCMG/components/RequestAccess/types.ts‎

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import { DatasetsResponse } from "../../../../../../apis/azul/anvil-cmg/common/responses";
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export interface Props {
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datasetsResponse: DatasetsResponse;
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}

‎app/components/Detail/components/AnVILCMG/components/RequestAccess/utils.ts‎

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import { DatasetsResponse } from "../../../../../../apis/azul/anvil-cmg/common/responses";
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import { takeArrayValueAt } from "../../../../../../viewModelBuilders/azul/anvil-cmg/common/viewModelBuilders";
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import {
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processEntityArrayValue,
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processEntityValue,
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} from "../../../../../../apis/azul/common/utils";
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import { LABEL } from "@databiosphere/findable-ui/lib/apis/azul/common/entities";
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import { ListItemTextProps } from "@mui/material";
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/**
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* Generates a list of request access menu options based on the provided dataset response.
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* This function extracts identifiers (DUOS ID and dbGaP ID) from the datasets response and returns an array of menu option objects.
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* Each menu option contains a link `href` and title `primary` and description text `secondary`, to be used in Material UI's `MenuItem` and `ListItemText` component.
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* @param datasetsResponse - Response model return from datasets API.
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* @returns menu option objects with `href`, `primary`, and `secondary` properties.
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*/
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export function getRequestAccessOptions(
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datasetsResponse: DatasetsResponse
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): (Pick<ListItemTextProps, "primary" | "secondary"> & { href: string })[] {
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// Get the dbGaP ID and DUOS ID from the datasets response.
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const dbGapId = takeArrayValueAt(
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processEntityArrayValue(
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datasetsResponse.datasets,
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"registered_identifier",
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LABEL.EMPTY
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),
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0
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);
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const duosId = processEntityValue(
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datasetsResponse.datasets,
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"duos_id",
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LABEL.EMPTY
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);
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const options = [];
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if (duosId) {
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// If a DUOS ID is present, add a menu option for DUOS.
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options.push({
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href: `https://duos.org/dataset/${duosId}`,
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primary: "DUOS",
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secondary:
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"Request access via DUOS, which streamlines data access for NHGRI-sponsored studies, both registered and unregistered in dbGaP.",
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});
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}
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if (dbGapId) {
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// If a dbGaP ID is present, add a menu option for dbGaP.
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options.push({
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href: `https://dbgap.ncbi.nlm.nih.gov/aa/wga.cgi?adddataset=${dbGapId}`,
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primary: "dbGaP",
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secondary:
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"Request access via the dbGaP Authorized Access portal for studies registered in dbGaP, following the standard data access process.",
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});
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}
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return options;
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}

‎app/viewModelBuilders/azul/anvil-cmg/common/viewModelBuilders.ts‎

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@@ -39,7 +39,7 @@ import {
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ChipProps as MChipProps,
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FadeProps as MFadeProps,
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} from "@mui/material";
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import React from "react";
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import React, { ReactNode } from "react";
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import {
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ANVIL_CMG_CATEGORY_KEY,
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ANVIL_CMG_CATEGORY_LABEL,
@@ -112,6 +112,7 @@ import { Unused, Void } from "../../../common/entities";
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import { SUMMARY_DISPLAY_TEXT } from "./summaryMapper/constants";
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import { mapExportSummary } from "./summaryMapper/summaryMapper";
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import { ExportEntity } from "app/components/Export/components/AnVILExplorer/components/ExportEntity/exportEntity";
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import { RequestAccess } from "../../../../components/Detail/components/AnVILCMG/components/RequestAccess/requestAccess";
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/**
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* Build props for activity type BasicCell component from the given activities response.
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datasetsResponse: DatasetsResponse
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): React.ComponentProps<typeof C.BackPageHero> => {
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return {
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actions: getDatasetRequestAccess(datasetsResponse),
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breadcrumbs: getDatasetBreadcrumbs(datasetsResponse),
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callToAction: getDatasetCallToAction(datasetsResponse),
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title: getDatasetTitle(datasetsResponse),
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): CallToAction | undefined {
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const isReady = isResponseReady(datasetsResponse);
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const isAccessGranted = isDatasetAccessible(datasetsResponse);
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const registeredIdentifier = getDatasetRegisteredIdentifier(datasetsResponse);
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if (!isReady) {
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return;
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}
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if (!isReady) return;
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// Display export button if user is authorized to access the dataset.
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if (isAccessGranted) {
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return {
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url: `/datasets/${getDatasetEntryId(datasetsResponse)}/export`,
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};
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}
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// Display request access button if user is not authorized to access the dataset.
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if (registeredIdentifier === LABEL.UNSPECIFIED) {
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return {
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label: "Request Access",
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target: ANCHOR_TARGET.BLANK,
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url: `https://dbgap.ncbi.nlm.nih.gov/aa/wga.cgi?adddataset=${registeredIdentifier}`,
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};
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}
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// Otherwise, display nothing.
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}
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);
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}
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/**
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* Returns the `actions` prop for the Hero component from the given datasets response.
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* @param datasetsResponse - Response model return from datasets API.
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* @returns react node to be used as the `actions` props for the Hero component.
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*/
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function getDatasetRequestAccess(
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datasetsResponse: DatasetsResponse
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): ReactNode {
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const isReady = isResponseReady(datasetsResponse);
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const isAccessGranted = isDatasetAccessible(datasetsResponse);
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if (!isReady) return null;
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// Display nothing if user is authorized to access the dataset.
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if (isAccessGranted) return null;
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// Display request access button if user is not authorized to access the dataset.
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return RequestAccess({ datasetsResponse });
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}
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/**
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* Returns StatusBadge component props from the given datasets response.
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* @param datasetsResponse - Response model return from datasets API.

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