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1 change: 1 addition & 0 deletions .eslintignore
Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
**/node_modules/*
**/out/*
**/.next/*
next-env.d.ts

build

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46 changes: 23 additions & 23 deletions __tests__/project-matrix-mapper.test.ts
Original file line number Diff line number Diff line change
Expand Up @@ -23,14 +23,14 @@ const COUNT_MATRIX = "Count Matrix";
const LARGE_INTESTINE = "large intestine";
const LYMPH_NODE = "lymph node";
const MOCK_PROJECT_MATRIX_FILE_0 = {
azul_url: "https://path/to/file0?version=0&catalog=dcp2ebi",
name: "123.loom",
size: 254147853,
url: "https://path/to/file0?version=0&catalog=dcp2ebi",
};
const MOCK_PROJECT_MATRIX_FILE_1 = {
azul_url: "https://path/to/file1?version=0&catalog=dcp2ebi",
name: "456.loom",
size: 254147854,
url: "https://path/to/file1?version=0&catalog=dcp2ebi",
};
const CONTRIBUTED_ANALYSES = {
genusSpecies: {
Expand All @@ -42,16 +42,16 @@ const CONTRIBUTED_ANALYSES = {
libraryConstructionApproach: {
[LibraryConstructionApproach.TENX_V2]: [
{
azul_url: MOCK_PROJECT_MATRIX_FILE_0.azul_url,
name: MOCK_PROJECT_MATRIX_FILE_0.name,
size: MOCK_PROJECT_MATRIX_FILE_0.size,
url: MOCK_PROJECT_MATRIX_FILE_0.url,
},
],
[LibraryConstructionApproach.SMART_SEQ2]: [
{
azul_url: MOCK_PROJECT_MATRIX_FILE_1.azul_url,
name: MOCK_PROJECT_MATRIX_FILE_1.name,
size: MOCK_PROJECT_MATRIX_FILE_1.size,
url: MOCK_PROJECT_MATRIX_FILE_1.url,
},
],
},
Expand All @@ -60,14 +60,14 @@ const CONTRIBUTED_ANALYSES = {
libraryConstructionApproach: {
[LibraryConstructionApproach.TENX_V2]: [
{
azul_url: MOCK_PROJECT_MATRIX_FILE_0.azul_url,
name: MOCK_PROJECT_MATRIX_FILE_0.name,
size: MOCK_PROJECT_MATRIX_FILE_0.size,
url: MOCK_PROJECT_MATRIX_FILE_0.url,
},
{
azul_url: MOCK_PROJECT_MATRIX_FILE_1.azul_url,
name: MOCK_PROJECT_MATRIX_FILE_1.name,
size: MOCK_PROJECT_MATRIX_FILE_1.size,
url: MOCK_PROJECT_MATRIX_FILE_1.url,
},
],
},
Expand Down Expand Up @@ -99,7 +99,7 @@ describe("MatrixMapper", () => {
expect(matrixView0.stage[0]).toEqual("adult");
expect(matrixView0.fileName).toEqual(MOCK_PROJECT_MATRIX_FILE_0.name);
expect(matrixView0.size).toEqual(MOCK_PROJECT_MATRIX_FILE_0.size);
expect(matrixView0.url).toEqual(MOCK_PROJECT_MATRIX_FILE_0.url);
expect(matrixView0.url).toEqual(MOCK_PROJECT_MATRIX_FILE_0.azul_url);

const matrixView1 = matrixViews[1];
expect(matrixView0.libraryConstructionApproach.length).toEqual(1);
Expand All @@ -112,7 +112,7 @@ describe("MatrixMapper", () => {
expect(matrixView1.stage[0]).toEqual("adult");
expect(matrixView1.fileName).toEqual(MOCK_PROJECT_MATRIX_FILE_1.name);
expect(matrixView1.size).toEqual(MOCK_PROJECT_MATRIX_FILE_1.size);
expect(matrixView1.url).toEqual(MOCK_PROJECT_MATRIX_FILE_1.url);
expect(matrixView1.url).toEqual(MOCK_PROJECT_MATRIX_FILE_1.azul_url);

const matrixView2 = matrixViews[2];
expect(matrixView0.libraryConstructionApproach.length).toEqual(1);
Expand All @@ -125,7 +125,7 @@ describe("MatrixMapper", () => {
expect(matrixView2.stage[0]).toEqual("adult");
expect(matrixView2.fileName).toEqual(MOCK_PROJECT_MATRIX_FILE_0.name);
expect(matrixView2.size).toEqual(MOCK_PROJECT_MATRIX_FILE_0.size);
expect(matrixView2.url).toEqual(MOCK_PROJECT_MATRIX_FILE_0.url);
expect(matrixView2.url).toEqual(MOCK_PROJECT_MATRIX_FILE_0.azul_url);

const matrixView3 = matrixViews[3];
expect(matrixView0.libraryConstructionApproach.length).toEqual(1);
Expand All @@ -138,7 +138,7 @@ describe("MatrixMapper", () => {
expect(matrixView3.stage[0]).toEqual("adult");
expect(matrixView3.fileName).toEqual(MOCK_PROJECT_MATRIX_FILE_1.name);
expect(matrixView3.size).toEqual(MOCK_PROJECT_MATRIX_FILE_1.size);
expect(matrixView3.url).toEqual(MOCK_PROJECT_MATRIX_FILE_1.url);
expect(matrixView3.url).toEqual(MOCK_PROJECT_MATRIX_FILE_1.azul_url);
});

/**
Expand All @@ -153,7 +153,7 @@ describe("MatrixMapper", () => {
const matrixView0 = matrixViews[0];
expect(matrixView0.fileName).toEqual(MOCK_PROJECT_MATRIX_FILE_0.name);
expect(matrixView0.size).toEqual(MOCK_PROJECT_MATRIX_FILE_0.size);
expect(matrixView0.url).toEqual(MOCK_PROJECT_MATRIX_FILE_0.url);
expect(matrixView0.url).toEqual(MOCK_PROJECT_MATRIX_FILE_0.azul_url);
expect(matrixView0.organ.length).toEqual(2);
expect(matrixView0.organ.indexOf(LARGE_INTESTINE)).not.toEqual(-1);
expect(matrixView0.organ.indexOf(LYMPH_NODE)).not.toEqual(-1);
Expand All @@ -166,7 +166,7 @@ describe("MatrixMapper", () => {
const matrixView1 = matrixViews[1];
expect(matrixView1.fileName).toEqual(MOCK_PROJECT_MATRIX_FILE_1.name);
expect(matrixView1.size).toEqual(MOCK_PROJECT_MATRIX_FILE_1.size);
expect(matrixView1.url).toEqual(MOCK_PROJECT_MATRIX_FILE_1.url);
expect(matrixView1.url).toEqual(MOCK_PROJECT_MATRIX_FILE_1.azul_url);
expect(matrixView1.organ.length).toEqual(2);
expect(matrixView1.organ.indexOf(LARGE_INTESTINE)).not.toEqual(-1);
expect(matrixView1.organ.indexOf(LYMPH_NODE)).not.toEqual(-1);
Expand Down Expand Up @@ -200,7 +200,7 @@ describe("MatrixMapper", () => {
],
organ: [LYMPH_NODE, LARGE_INTESTINE],
size: MOCK_PROJECT_MATRIX_FILE_0.size,
url: MOCK_PROJECT_MATRIX_FILE_0.url,
url: MOCK_PROJECT_MATRIX_FILE_0.azul_url,
version: "1",
},
];
Expand All @@ -223,8 +223,8 @@ describe("MatrixMapper", () => {
genusSpecies: {
"Homo sapiens,Mus musculus": [
{
azul_url: MOCK_PROJECT_MATRIX_FILE_0.azul_url,
name: MOCK_PROJECT_MATRIX_FILE_0.name,
url: MOCK_PROJECT_MATRIX_FILE_0.url,
},
],
},
Expand All @@ -246,8 +246,8 @@ describe("MatrixMapper", () => {
genusSpecies: {
"Mus musculus,Homo sapiens": [
{
azul_url: MOCK_PROJECT_MATRIX_FILE_0.azul_url,
name: MOCK_PROJECT_MATRIX_FILE_0.name,
url: MOCK_PROJECT_MATRIX_FILE_0.url,
},
],
},
Expand All @@ -273,7 +273,7 @@ describe("MatrixMapper", () => {
libraryConstructionApproach: [LibraryConstructionApproach.TENX_V2],
organ: [LYMPH_NODE, LARGE_INTESTINE],
size: MOCK_PROJECT_MATRIX_FILE_0.size,
url: MOCK_PROJECT_MATRIX_FILE_0.url,
url: MOCK_PROJECT_MATRIX_FILE_0.azul_url,
version: "1",
},
{
Expand All @@ -284,7 +284,7 @@ describe("MatrixMapper", () => {
libraryConstructionApproach: [LibraryConstructionApproach.TENX_V2],
organ: [LYMPH_NODE, LARGE_INTESTINE],
size: MOCK_PROJECT_MATRIX_FILE_1.size,
url: MOCK_PROJECT_MATRIX_FILE_1.url,
url: MOCK_PROJECT_MATRIX_FILE_1.azul_url,
version: "1",
},
];
Expand All @@ -308,7 +308,7 @@ describe("MatrixMapper", () => {
libraryConstructionApproach: [LibraryConstructionApproach.TENX_V2],
organ: [LYMPH_NODE],
size: MOCK_PROJECT_MATRIX_FILE_0.size,
url: MOCK_PROJECT_MATRIX_FILE_0.url,
url: MOCK_PROJECT_MATRIX_FILE_0.azul_url,
version: "1",
},
{
Expand All @@ -319,7 +319,7 @@ describe("MatrixMapper", () => {
libraryConstructionApproach: [LibraryConstructionApproach.TENX_V2],
organ: [LARGE_INTESTINE],
size: MOCK_PROJECT_MATRIX_FILE_1.size,
url: MOCK_PROJECT_MATRIX_FILE_1.url,
url: MOCK_PROJECT_MATRIX_FILE_1.azul_url,
version: "1",
},
];
Expand All @@ -343,7 +343,7 @@ describe("MatrixMapper", () => {
libraryConstructionApproach: [LibraryConstructionApproach.SMART_SEQ2],
organ: [LYMPH_NODE],
size: MOCK_PROJECT_MATRIX_FILE_0.size,
url: MOCK_PROJECT_MATRIX_FILE_0.url,
url: MOCK_PROJECT_MATRIX_FILE_0.azul_url,
version: "1",
},
{
Expand All @@ -354,7 +354,7 @@ describe("MatrixMapper", () => {
libraryConstructionApproach: [LibraryConstructionApproach.TENX_V2], // "10x .."
organ: [LYMPH_NODE],
size: MOCK_PROJECT_MATRIX_FILE_1.size,
url: MOCK_PROJECT_MATRIX_FILE_1.url,
url: MOCK_PROJECT_MATRIX_FILE_1.azul_url,
version: "1",
},
];
Expand Down Expand Up @@ -391,14 +391,14 @@ describe("MatrixMapper", () => {
genusSpecies: {
"Homo sapiens": [
{
azul_url: MOCK_PROJECT_MATRIX_FILE_0.azul_url,
name: MOCK_PROJECT_MATRIX_FILE_0.name,
size: MOCK_PROJECT_MATRIX_FILE_0.size,
url: MOCK_PROJECT_MATRIX_FILE_0.url,
},
{
azul_url: MOCK_PROJECT_MATRIX_FILE_1.azul_url,
name: MOCK_PROJECT_MATRIX_FILE_1.name,
size: MOCK_PROJECT_MATRIX_FILE_1.size,
url: MOCK_PROJECT_MATRIX_FILE_1.url,
},
],
},
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@@ -1,3 +1,4 @@
import { JSX } from "react";
import { AccessibilityBadgeProps } from "@databiosphere/findable-ui/lib/components/Detail/components/AccessibilityBadge/accessibilityBadge";
import { AccessibilityBadge as Badge } from "./accessibilityBadge.styles";

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@@ -1,5 +1,5 @@
import { Stack as MStack } from "@mui/material";
import { ReactNode } from "react";
import { JSX, ReactNode } from "react";

interface StackProps {
children: ReactNode | ReactNode[];
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@@ -1,3 +1,4 @@
import { JSX } from "react";
import { Props } from "./types";
import { ListItemText, MenuItem } from "@mui/material";
import { Actions } from "@databiosphere/findable-ui/lib/components/Layout/components/BackPage/components/BackPageHero/components/Actions/actions";
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@@ -1,3 +1,4 @@
import { JSX } from "react";
import { ConsentTooltip } from "../ConsentTooltip/consentTooltip";

interface ConsentCodeListProps {
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@@ -1,3 +1,4 @@
import { JSX } from "react";
import { Tooltip } from "@mui/material";

interface ConsentTooltipProps {
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@@ -1,3 +1,4 @@
import { JSX } from "react";
import {
MdxMarkdown,
MDXSerializeResult,
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@@ -1,3 +1,4 @@
import { JSX } from "react";
import { ButtonPrimary } from "@databiosphere/findable-ui/lib/components/common/Button/components/ButtonPrimary/buttonPrimary";
import { AlertIcon } from "@databiosphere/findable-ui/lib/components/common/CustomIcon/components/AlertIcon/alertIcon";
import { SectionActions } from "@databiosphere/findable-ui/lib/components/common/Section/section.styles";
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@@ -1,3 +1,4 @@
import { JSX } from "react";
import { ButtonPrimary } from "@databiosphere/findable-ui/lib/components/common/Button/components/ButtonPrimary/buttonPrimary";
import { AlertIcon } from "@databiosphere/findable-ui/lib/components/common/CustomIcon/components/AlertIcon/alertIcon";
import { SectionActions } from "@databiosphere/findable-ui/lib/components/common/Section/section.styles";
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@@ -1,6 +1,6 @@
import { Override } from "@databiosphere/findable-ui/lib/config/entities";
import Router from "next/router";
import { Fragment, useEffect } from "react";
import { Fragment, JSX, useEffect } from "react";
import { ENTITY_STATUS } from "./common/entities";
import { EntityDeprecated } from "./components/EntityDeprecated/entityDeprecated";
import { EntityWithdrawn } from "./components/EntityWithdrawn/entityWithdrawn";
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@@ -1,3 +1,4 @@
import { JSX } from "react";
import { ButtonGroup } from "@databiosphere/findable-ui/lib/components/common/ButtonGroup/buttonGroup";
import { DialogTitle } from "@databiosphere/findable-ui/lib/components/common/Dialog/components/DialogTitle/dialogTitle";
import { ProjectMatrixView } from "../../../../../../viewModelBuilders/azul/hca-dcp/common/projectMatrixMapper/entities";
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@@ -1,7 +1,7 @@
import { GridPaper } from "@databiosphere/findable-ui/lib/components/common/Paper/paper.styles";
import { Table } from "@databiosphere/findable-ui/lib/components/Detail/components/Table/table";
import { ColumnDef, RowData } from "@tanstack/react-table";
import { Dispatch, SetStateAction, useEffect } from "react";
import { Dispatch, JSX, SetStateAction, useEffect } from "react";
import {
HCA_DCP_CATEGORY_KEY,
HCA_DCP_CATEGORY_LABEL,
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
import { useState } from "react";
import { JSX, useState } from "react";
import { ProjectMatrixView } from "../../../../../../viewModelBuilders/azul/hca-dcp/common/projectMatrixMapper/entities";
import { ArchivePreviewDialog } from "../ArchivePreviewDialog/archivePreviewDialog";
import { FileLocationArchivePreviewButton as Button } from "./fileLocationArchivePreview.styles";
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@@ -1,3 +1,4 @@
import { JSX } from "react";
import { ButtonGroupButton } from "@databiosphere/findable-ui/lib/components/common/ButtonGroup/components/ButtonGroupButton/buttonGroupButton";
import { ContentCopyIconSmall } from "@databiosphere/findable-ui/lib/components/common/CustomIcon/common/constants";
import { useFileLocation } from "@databiosphere/findable-ui/lib/hooks/useFileLocation";
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@@ -1,3 +1,4 @@
import { JSX } from "react";
import { FileDownloadButton } from "@databiosphere/findable-ui/lib/components/common/Button/components/FileDownloadButton/fileDownloadButton";
import { ButtonGroupButton } from "@databiosphere/findable-ui/lib/components/common/ButtonGroup/components/ButtonGroupButton/buttonGroupButton";
import { DownloadIconSmall } from "@databiosphere/findable-ui/lib/components/common/CustomIcon/common/constants";
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@@ -1,4 +1,4 @@
import { ReactNode } from "react";
import { JSX, ReactNode } from "react";
import { FileNameCell as Cell } from "./fileNameCell.styles";

export interface FileNameCellProps {
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@@ -1,3 +1,4 @@
import { JSX } from "react";
import { ALERT_PROPS } from "@databiosphere/findable-ui/lib/components/common/Alert/constants";
import { GridPaper } from "@databiosphere/findable-ui/lib/components/common/Paper/paper.styles";
import { Table } from "@databiosphere/findable-ui/lib/components/Detail/components/Table/table";
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@@ -1,3 +1,4 @@
import { JSX } from "react";
import { CollapsableSection } from "@databiosphere/findable-ui/lib/components/common/Section/components/CollapsableSection/collapsableSection";
import { MarkdownRenderer } from "@databiosphere/findable-ui/lib/components/MarkdownRenderer/markdownRenderer";
import { DescriptionProps } from "./types";
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@@ -1,3 +1,4 @@
import { JSX } from "react";
import { Table as MTable } from "@mui/material";
import { TableContainer } from "./table.styles";

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@@ -1,3 +1,4 @@
import { JSX } from "react";
import { SectionTitle } from "@databiosphere/findable-ui/lib/components/common/Section/components/SectionTitle/sectionTitle";
import { Grid, Typography } from "@mui/material";
import { NetworkIcon } from "../../../../../common/NetworkIcon/networkIcon";
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@@ -1,3 +1,4 @@
import { JSX } from "react";
import { Filters } from "@databiosphere/findable-ui/lib/common/entities";
import { useFileManifest } from "@databiosphere/findable-ui/lib/hooks/useFileManifest/useFileManifest";

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@@ -1,3 +1,4 @@
import { JSX } from "react";
import { FileManifestDownload } from "@databiosphere/findable-ui/lib/components/Export/components/ManifestDownload/components/ManifestDownloadEntity/components/FileManifestDownload/fileManifestDownload";
import { ManifestDownloadEntityProps } from "@databiosphere/findable-ui/lib/components/Export/components/ManifestDownload/components/ManifestDownloadEntity/manifestDownloadEntity";
import { useFileManifest } from "@databiosphere/findable-ui/lib/hooks/useFileManifest/useFileManifest";
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@@ -1,3 +1,4 @@
import { JSX } from "react";
import { LABEL } from "@databiosphere/findable-ui/lib/apis/azul/common/entities";
import { TypographyProps } from "@databiosphere/findable-ui/lib/components/common/Typography/common/entities";
import { NTagCell } from "../../../../components/index";
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@@ -1,3 +1,4 @@
import { JSX } from "react";
import { ConsentTooltip, NTagCell } from "app/components";

interface ConsentCodesCellProps {
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1 change: 1 addition & 0 deletions app/components/Index/components/CopyCell/copyCell.tsx
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@@ -1,3 +1,4 @@
import { JSX } from "react";
import { Cell, CellText, CopyToClipboard } from "./copyCell.styles";

interface CopyCellProps {
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@@ -1,3 +1,4 @@
import { JSX } from "react";
import {
CallToActionButton,
CallToActionButtonProps,
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@@ -1,3 +1,4 @@
import { JSX } from "react";
import {
HelpIconButton as DXHelpIconButton,
HelpIconButtonProps as DXHelpIconButtonProps,
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@@ -1,3 +1,4 @@
import { JSX } from "react";
import { TypographyWordBreak } from "@databiosphere/findable-ui/lib/components/common/Typography/TypographyWordBreak/TypographyWordBreak";
import { Link as DXLink } from "@databiosphere/findable-ui/lib/components/Links/components/Link/link";
import { useConfig } from "@databiosphere/findable-ui/lib/hooks/useConfig";
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2 changes: 1 addition & 1 deletion app/components/Layout/components/Content/content.tsx
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@@ -1,4 +1,4 @@
import { ReactNode } from "react";
import { JSX, ReactNode } from "react";
import { Content as MDXContent } from "./content.styles";

export interface ContentProps {
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@@ -1,3 +1,4 @@
import { JSX } from "react";
import { ANCHOR_TARGET } from "@databiosphere/findable-ui/lib/components/Links/common/entities";
import {
Brands,
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@@ -1,3 +1,4 @@
import { JSX } from "react";
import { Logo } from "@databiosphere/findable-ui/lib/components/Layout/components/Header/components/Content/components/Logo/logo";
import { ANCHOR_TARGET } from "@databiosphere/findable-ui/lib/components/Links/common/entities";
import { Brands } from "./hcaBranding.styles";
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@@ -1,3 +1,4 @@
import { JSX } from "react";
import { LogoExplorer } from "../../logoExplorer";

const anvilExplorer = "/images/anvilExplorer.png";
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@@ -1,3 +1,4 @@
import { JSX } from "react";
import { ImageSrc } from "@databiosphere/findable-ui/lib/components/common/StaticImage/staticImage";
import { Logo } from "@databiosphere/findable-ui/lib/components/Layout/components/Header/components/Content/components/Logo/logo";
import {
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@@ -1,5 +1,5 @@
import { OpenInNewIcon } from "@databiosphere/findable-ui/lib/components/common/CustomIcon/components/OpenInNewIcon/openInNewIcon";
import { ElementType } from "react";
import { ElementType, JSX } from "react";
import { Label, Text } from "./labelIconMenuItem.styles";

export interface LabelIconMenuItemProps {
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